RNA Virus Evolutionary Origins

TEM of an influenza virus particle. Credit: Cynthia Goldsmith

This is probably one of the coolest papers I’ve read in a while and I encourage everyone to read it. “Origins and Evolution of the Global RNA Virome” by Wolf et al., (Nov/Dec, 2018) attempts to reconstruct RNA virus evolution by taking advantage of the massive amount of new virus data science has gotten in the past few years thanks to metagenomics advances. 

The really major takeaways

  • dsRNA viruses evolved from +ssRNA viruses at least twice, and the prokaryotic dsRNA viruses actually are in the same grade as Reoviridae (i.e. rotaviruses) while another group of eukaryotic dsRNA viruses evolved separately
  • -ssRNA viruses evolved from dsRNA viruses
  • lots of extensive horizontal virus and gene transfer, coexpressed gene exchange across distantly related hosts. Even tips of the tree can have cross-kingdom host-range
Bacteria have mostly DNA viruses

We’ve found very few RNA viruses in bacteria (and archaea), which the paper suggests could have something to do with the bacteria cells not having many compartments or a nuclear envelope. The idea given was DNA viruses are at a disadvantage to RNA viruses in eukaryotes because they have to deal with more barriers. I’d imagine this could have a compounding effect as DNA viruses are usually not so great at host-switching and often tightly coevolve with their hosts, while RNA viruses often employ a strategy where they have many potential hosts. Infecting many hosts may facilitate horizontal gene transfer between very different viruses. This combined with rapid mutation rates in RNA viruses may further enhance diversity, while the prokaryotes keep getting infected by a clade of often strain-specific dsDNA phages. 

RNA viruses have still been found in bacteria (+ssRNA Leviviridae and dsRNA cystoviridae). But we have never discovered a -ssRNA prokyarotic virus. Bacteriophages do have the well-characterized cystoviruses which are dsRNA, and lump in with the Reo-like eukaryotic viruses (which is quite cool). If bacteria have dsRNA viruses, and -ssRNA viruses in eukaryotes came from dsRNA viruses, it doesn’t seem so unlikely that a similar event could occur twice. Here’s hoping my lab is able to isolate a -ssRNA phage.

United by a single gene

For background, RNA viruses have an RNA genome while their hosts have a DNA genome. This means hosts are aren’t making RNA from RNA, but only RNA from DNA. So hosts don’t need to encode an RNA-dependent-RNA polymerase (RdRp), meaning all RNA viruses are united by this single requirement that they make an RdRp. All other genes are basically impossible to use for creating really deep evolutionary trees, though some genes for capsid proteins, helicases, and capping enzymes, might be decent choices for a relatively deep analysis.

These authors looked at 4,617 RNA virus RNA-dependent-RNA polymerases (RdRps), did quite a bit of work, and ultimately created a phylogenetic tree consisting of 5 major branching events. 

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Figure 10 from the Wolf et al., 2018 paper. It is open-access! I thought this figure basically summed up the entire paper.  

Imagine we’re starting in RNA world, and the first branching event is the +ssRNA viruses from our outgroup(s), the Group II introns and the Non-LTR retrotransposons (which would be ancient, even older than retroviruses). Reverse transcriptase can bring us into the DNA world. The first major branch is leading to the bacteriophage +ssRNA viruses, the Leviviruses, which then split into these fungi and plant virus groups, notably “Mitoviruses” which infect fungi and mitochondria. It seems the base of the tree was an RNA replicon that was reproducing in the mitochondria (bacteria) which had no capsid, and later during eukaryotic evolution, (wherein endosymbiotic bacteria became mitochondria), they gained either a host-derived single-jelly roll capsid protein or one from a DNA virus to form the ancestral RNA virus. This protein is the most common capsid protein seen in +ssRNA viruses.

 

*As I’m reading in a 2018 paper, scientists have also found evidence (meaning they found the sequence just not an isolate) of mitoviruses in contemporary plant mitochondria by looking at plant transcriptomes. They add that “genuine plant mitoviruses were immediate ancestors to endogenized mitovirus elements now widespread in land plant genomes.” 

The second branch is referred to as the “Picornavirus supergroup” and contains a bunch of +ssRNA viruses, notably the nidoviruses which include the largest RNA viruses, as well as this branch of dsRNA viruses nested within the group! This is the largest/most diverse branch, with the authors suggesting diversification had already been occurring before the Cambrian explosion. I am assuming as they reference ctenophores, sponges and cnidarian viromes, they’re indicating substantial diversification had occurred during the Ediacaran. By the way, I love this casual mention of the Cambrian, to remind readers that Opabinia had viruses. The base of this branch also seems to be where the authors placed the origin of viral single jelly-roll capsid proteins, which they say were acquired from cells. As viral genomes get bigger they start acquiring helicases as well. 

The third branch contains a bunch more +ssRNA viruses like the flaviviruses and alpha viruses, with the capping enzyme CapE being ancestral to this group. Though the authors do point out there were likely three convergent evolution events where viruses acquired this capping enzyme. They suggest gene capture was an especially dominant strategy of these viruses. I wrote about an especially cool group in this branch– the Jingmenviruses which contain an animal multicomponent virus which packages its five segments into five separate virions. 

Then comes branch 4, which are the majority of the dsRNA viruses. The Cystoviruses (which are enveloped bacteriophages), the Reoviridae, and the Totivirus group. It looks like this branch has the broadest host range, infecting protists, bacteria, fungi, plants, animals. Branch 4 is a pretty puzzling one– I want to know how cystoviruses became exclusively bacterial viruses, and how exactly they came around. Based on the tree, the ancestor appears eukaryotic, however the authors suggested picobirnaviruses (branch 2 dsRNA) may be prokaryotic viruses, and that totiviruses (branch 4) may potentially include prokaryotic viruses, which could indicate a prokaryotic virus ancestral state. That being said they were pretty confident that the reovirus group is closer to cystoviruses, as they have these unique T=1 capsids, surrounded by T=13 outer shells. 

Branch 5 is all the -ssRNA viruses we’ve found which includes the Mononegavirales (rhabdoviruses like rabies and paramyxoviruses like measles), the Bunyavirales (like Hanta virus) and the orthomyxoviruses (like influenza). Their host range is pretty small, perhaps because they’ve diversified most recently.  One instance of a -ssRNA virus found in protists which was most definitely a HVT event via an arthropod host. No prokaryotic at all, though I wouldn’t be surprised if there was some undiscovered second branch of -ssRNA viruses that came from dsRNA prokaryotic viruses. Another thought that occurred to me was the -ssRNA viruses which have coated RNA and very rarely recombine, could be further limited if they have less horizontal gene transfer opportunity.

The authors humbly make the important point that we know very, very little in the grand scheme of things about virus evolution. RdRp evolutionary history does not equal RNA virus evolutionary history necessarily, but it provides a rough framework from which to build on I think. I didn’t really get into it much but the paper goes into a lot of detail on horizontal virus/gene transfer events and how there’s not very strong phylogenetic signal in relation to host.

RNA viruses in Archaea? 

I can’t find any RNA virus isolates that infect archaea, however metagenomics studies like this one have identified putative archaeal RNA viruses, most likely with Sulfolobus archaea as the host. These putative viral sequences were distinct from one another indicating there may be abundant diversity within archaea RNA viruses. 

 

***a note– A pet peeve of mine is using polyphyletic groups as group names. I don’t like that we call bacteria viruses “phages,” and eukaryotic viruses “viruses,” and archaea viruses we’re split. Cystoviruses (host is Pseudomonas)  for example, are closer to human rotaviruses than they are to any other bacteriophage we know of. I’ve even seen yeast viruses called “phages” because yeast are single-celled eukaryotes, and I’ve seen algae viruses called “phages,” but then giant viruses of algae and amoeba are so flashy that virologists of course call them “viruses.” It’s just so much easier to discuss things using monophyletic groups. 

Imagine if a zoologist said they only studied animals that fly. “I study butterflies, birds–but not flightless birds (cuz that’s a WHOLE DIFFERENT ANIMAL SO SLOW DOWN THERE!!), bats, pterosaurs, bees, and the occasional flying squirrel.” So why do virus people tend to talk like that? ~end rant

Evolution of amphibian genome size

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When I was a kid, one of my favorite things to tell people was that the organism with the biggest genome was an amoeba. This is probably not true. Scientists used to think it was an amoeba; Polychaos dubium, however because that estimate has been somewhat contested, the current largest genome found may actually belong to Paris japonica, a Japanese flower.

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Paris japonica: record sized genome

Which is probably still just as surprising to the average child. The largest animal genome almost certainly belongs to the marbled lungfish, with at least 130 billion bps (132.83 pg), followed by the salamander, Nexturus lewisi. So we have amoebas, some plants, and some fish and amphibians with giant genomes of over a hundred billion basepairs meanwhile humans have a baby genome in comparison of just 3 billion basepairs. Pathetic.

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The marbled lungfish has a giant transposon-filled genome

Amphibian genomes are more varied than you might expect

Amphibians present an especially interesting case as not only are they tetrapods (where polyploidy is considerably rare— it pops up in fish more frequently), but amphibians also have the largest range of genome size of any group of vertebrates.

One would expect genome size to correlate with number of genes and organismal complexity, and to an extent that’s true. In prokaryotes, more genes means a bigger genome– and certainly eukaryotes have bigger genomes than prokaryotes, and are more “complex.” However, the relationship ends there. Eukaryotic genomes are full of complex regulatory regions, introns, and mobile elements or “junk DNA” (possibly a misnomer, as we really don’t understand the genome well enough to really determine what is “junk”). Genomes can undergo polyploidization, dramatic increases in tandem repeats and transposable elements, insertions/deletions, gene duplications etc., but there is absolutely a potential fitness cost to having a larger genome.

Amphibian genome size in relation to climate change, life cycle: not very related actually

A very cool paper that came out in nature Ecology & Evolution, delved into this conundrum of how closely related organisms have evolved such a huge diversity of genome size. They focused on amphibian genome evolution, with the expectation being that there’d be a strong relationship between genome size, life cycle complexity, and climate. What they ended up finding was that that’s not really the case. Despite having a huge range of genome size, amphibians actually seem to display macroevolutionary homogeneity generally within Anura (frogs), Caudata (salamanders), and Gymnophiona (caecilians), with only a few instances of dramatic shifts in genome size. Screen Shot 2018-11-04 at 4.06.50 PM

The authors measured amphibian genome sizes (and I believe took from the, already vast record of, batrachian genome size data) and tested for rate heterogeneity, and whether amphibian genomes underwent a more Brownian motion pattern of evolution (random and gradual), or underwent dramatic changes (“saltation” as biologists say). They further wanted to construct an ancestral state of what the genome may have looked like for common ancestors of living taxa, and then they wanted to use their gigantic dataset to delve more deeply into the question of how life history, climate, and genome size relate to one another. If you’re into that kind of thing, I’d definitely read the paper, they made some very nice figures!

Salamander genomes are giant– but generally evolve gradually

Caudata have by far the largest genomes, with the smallest salamander genomes still exceeding Gymnophiona and Anurans. The authors were also able to perform an ancestral state reconstruction for genome size on a time scale (i.e. species 1 and species 2 diverged X amount of years ago and their common ancestor at that divergence point had a genome that was Y size). They estimated that the common ancestor of all salamanders had a genome of around 43 pg and then proceeded to evolve gradually as a function of time. This is a huge jump from the common ancestor of all amphibians which looks to be between 4.62 and 7.57 pg. The root of Anurans seems to be at about 200-225 million years ago, meaning they’ve been evolving gradually as a function of time for that long, and still have not even overlapped with the smallest salamander genomes. Gymnophiona (root at 50-275 mya) have also not reached the range of salamander genome size.

This dramatic genome size increase in salamanders is primarily the result of one a dramatic increase in Long Terminal Repeat transposable elements, as well as generally having more genes, longer introns, and a lower substitution and deletion rate. When measuring evolutionary Gymnophiona had the largest spread, with some species having rates around the lowest salamander rates and others having the highest across all amphibians by far. Salamanders had much lower rates than frogs.

Even though people tend to (wrongly) shove amphibians away in their minds as being “primitive” or “simple” tetrapods not worth our time, amphibians and their genomes are almost certainly worth our time (especially given they’ve been around since the Devonian)! They have the broadest range of genome size of any vertebrate group, they’re found all over the globe, and they have varying life cycles and climatic pressures.

Source:

Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate. Nature Ecology & Evolution. H. Christoph Liedtke, David J. Gower, Mark Wilkinson & Ivan Gomez-Mestre. 24 September 2018.

 

 

 

Microbe that could contaminate Mars

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Recently there was an exciting discovery of evidence for a lake underneath the ice caps of Mars. Despite the already abundant evidence of water on Mars, this is evidence for an actual large stable body of liquid water. The water’s freezing temperature can be lowered with the huge amounts of salts present, as well as the ice caps exerting pressure. About nothing would be more exciting than finding life anywhere else in our solar system (or beyond!), but the possibility of life evolving and then being seeded on other planets is also pretty cool to imagine. But, if you’ve seen that Star Trek TNG episode about the terraformers, you’ll already know seeding a planet with life if the planet already contains its own life, violates the prime directive. So this would be out of the question (but it is still amazing that we could send a microbe-filled package to another star system and let evolution take over).

Some life on Earth is tolerant of such extreme conditions, that people once actually thought it couldn’t possibly have come from this planet. Even though most people jump to archaea when they think of extremophiles, the example that comes to my mind (that I believe everyone should familiarize themselves with) is a bacterium called Deinococcus radiodurans. 

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Deinococcus radiodurans

This polyextremophile can survive conditions that don’t even exist on Earth. It can survive extreme cold, acidity, dessication, a vacuum, and as the name suggests, ridiculous levels of radiation. It was discovered in the 50s when, after subjecting meat to high doses of gamma radiation, one bacteria species survived to spoil the meat.

It’s not that the radiation doesn’t hurt the bacteria. It does. It shatters the genome, but Deinococcus is able to stitch its genome back together–with high fidelity–extremely quickly. But given that no place on Earth is subject to as much radiation as Deinococcus can withstand, it’s suspected this bacteria evolved the radiation resistance trait as a result of adapting to dehydration which also causes DNA damage. Despite being able to survive intense environmental stress, Deinococcus does not form endospores, nor does it have some particularly magical or exciting genetic code.

While most bacteria only carry around one copy of their genome, Deinococcus carries between 4 and 10 copies consisting of two chromosomes, a megaplasmid, and a small plasmid, stacked on top of one another. Deinococcus also grows in tetrads which further helps protect it from damage. If you’re looking to isolate this bacterium, it helpfully produces the carotenoid pigment deinoxanthin, which makes it distinctively pink. It also is unique in that it is neither completely Gram-negative or Gram-positive, containing elements of both, with thick cell walls (characteristic of Gram-positive), and a second membrane (characteristic of Gram-negative). Having five layers as well as this pink pigment probably also helps protect them from stress.

One thing I could not find was whether Deinococcus radiodurans had any known phages. I mean, of course it HAS phages, but has anyone actually isolated any? I personally, would love to study a virus that’s able to infect this incredibly tough bacterium.

Help protect mice from gamma radiation – Deinococcus Mn(2+)-Decapeptide complex

When studying Deinococcus, researchers suspected the manganese (Mn)(II)-based antioxidant complex that could potentially be used to protect humans and animals from radiation from a future terrorist attack. It was reported to be highly radioprotective of proteins and was screened on cultured cells and enzymes and shown to protect them from ionizing radiation. The researchers from this PLOS one article exposed mice to high doses of radiation (enough to kill) and all the mice that took the MDP survived. The MDP protected white blood cells, helped stop damage to bone marrow from radiation, and also protected hematopoietic stem cells (which are cells that can turn into any type of blood cell). The MDP also helped in radiation recovery so could be used as a helpful post-exposure therapy as well as a prophylactic.

A fungus that can do the job Deinococcus couldn’t

As incredible as Deinococcus radiodurans is, it has not been as useful as scientists had hoped for cleaning up radioactive waste. Even though scientists have been able to genetically engineer Deinococcus to break down heavy metals and toxins, it has huge trouble actually growing at a very low pH and it can’t form biofilms under the extreme conditions.

What they eventually found was Rhodotorula taiwanensis, a red yeast that actually tolerates acidic conditions and forms biofilms in extreme conditions. It also tolerates–even happily lives around– insanely dangerous metals such as mercury chloride that would kill people no problem.tumblr_inline_o5v80icdwS1sj66vg_540

While the yeast are happy in heavy metals and low pH, they are pretty unhappy in high heat conditions. That being said, the yeast don’t need to be at the pit of the nuclear waste to get the cleanup job done, they can be nearby in a comfortable temperature and capture leaking waste.

The Koala genome: retroviruses, chlamydia, survival, and a eucalyptus diet

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As reported in a recent 2018 Nature genetics article, some awesome scientists have just sequenced the complete koala genome and have been able to provide insight into how to hopefully conserve this vulnerable species. They have also provided the very important public service of reminding us all how cool koalas are.

Koalas seem to be unusually unlucky animals, constantly succumbing to lymphoma, leukemia, getting hit by cars, and chronic infections of chlamydia (if you didn’t know this already, then I’m very sorry to have ruined your day). Scientists suspected for a while that many koalas must have a suppressed immune system to allow for such a high rate of disease, and were reminded of HIV, hence the term KAIDS (Koala AIDS)

When scientists looked more closely at pieces of the koala genome and koala viral loads, they found something really terrifying: koalas are basically in the process of an evolutionary arms race between retroviruses that are endogenous and/or exogenous. So not only do they have transmittable retroviruses, they also have retroviruses in the process of integrating into the germline and being vertically transmittable. They found many similar koala retroviruses that are inherited in a Mendelian fashion (integrated into the germline) like your typical allele, so there is a spectrum in the population. BUT because they are both exogenous and endogenous, the koalas also transmit the retroviruses sexually.

I noticed while reading the new genome paper by Rebecca Johnson et al., that they mention Koala genomes are approximately 47.5% interspersed repeats and 44% of those are transposable elements. That is a lot, and as the paper mentions, they were able to study centromeres (the area in the center of the chromosome). Centromeres tend to have higher order satellite arrays, but when an animal has less, as in gibbons, transposable elements likely represent an important component of smaller centromeres instead. The reason I mention gibbons is because crazily enough, the gammaretrovirus, Gibbon ape leukemia virus (GaLV) is the closest relative of Koala retrovirus (KoRV). This is the result of a transspecies transmission, though scientists have not pinpointed the exact intermediate host (gibbons are placental mammals from Thailand, koalas are marsupials from Australia). Bats always come to mind as a possible candidate, but who knows.

Koala survival and conservation

During a wave of koala deaths about 100 or so years ago from disease, some were able to survive these exogenous retroviruses due to integrated ape leukemia virus in their genome. Because viral sequences were present at the same integration site in all koala cells, this clues us in that the virus had been endogenized and could now be inherited. New exogenous retroviruses do not have a preferential integration site in the genome for contrast. This endogenous process had to have been very recent, like as in, in the past century or so recent which is pretty amazing to think about given we generally think of endogenous retroviruses being ancient remnants of a once deadly disease. The endogenous viruses actually serve to protect the koalas from some exogenous retroviruses.

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Gammaretrovirus genome

Koalas populations have undergone two especially dramatic decreases unrelated to disease. One, about 30-40,000 years ago when most Australian species suffered (so probably a habitat disaster or climate change rather than koala-specific disease). Then, again during European settlement when people decided to kill them– because humans seem to have a bizarre need to destroy anything cute and harmless.

The key to Koala survival is genetic diversity. We have destroyed much of their natural habitat which can result in population isolation which results in inbreeding and a decrease in gene flow and diversity. By looking at the genome and doing some coalescent analyses, the group was able to look at the koala population history and genetic diversity. The did find some koalas were able to maintain their genetic diversity and some level of habitat connectivity– but this is a delicate situation and it is absolutely vital to their species that they maintain gene flow. Southern koalas seemed to have significant inbreeding depression and were suffering from a lack of genetic diversity. Many small populations are in big trouble as they may suffer more from genetic abnormalities.

Retroelements, for background

In case you are unfamiliar with retroelements and other viruses that integrate into genomes: A provirus (or prophage as it’s referred to in bacterial viruses) such as HIV or Lambda phage, is a virus which integrates its genetic material into the host genome, so it can be passed down through cell generation. However, because HIV does not infect germline cells, and because it has an RNA intermediate that must be converted to DNA to integrate (hence the “retro”), it is referred to as an exclusively exogenous retrovirus and cannot be passed down to the next generation.

The retroviral sequences in our genomes are remnants of many, MANY retrovirus infections throughout our evolution that were passed through our germline (‘virus fossils’ if you will). These are termed endogenous retroviruses and have almost all lost their ability to be transmissible or exist outside the host at all after millions of years of genetic drift and host defense. While they once may have provided a selective advantage by providing some host immunity, they also would have been a tricky thing to deal with for the genome. Too many active transposable elements are detrimental to the genome stability, and in mammals we even have something called fetal oocyte attrition– where most oocytes in the fetal female are destroyed if they have too many transposable elements.

Retrotransposable elements that lack an extracellular phase in our genomes include LINES and SINES (Long/Short interspersed nuclear elements). Most other RT-retroelements do not have an extracellular phase and are not transmissible to other hosts so are not called retroviruses. They may have evolved from RT-retroelements to become extracellular via horizontal gene transfer from other viruses.

Back to the Koalas… Koala Retroviruses and Chlamydia

Another paper had previously shown that koalas infected with the retrovirus KoRV-B, rather than KoRV-A, were also more likely to have chlamydial disease. Chlamydia is quite common bacteria found in koala populations, but some koalas seem to just be carriers and do not progress to chlamydial disease. Other koalas have no chlamydia at all and of course do not chlamydial disease. Some unfortunate ones have chlamydial disease and the researchers hypothesized these koalas with chlamydial disease are more likely to have exogenous retroviruses suppressing their immune system.

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Penny the Koala, getting treated for Chlamydia, from https://www.bbc.com/news/magazine-22207442

As I mentioned, koala retroviruses can be both endogenous and exogenous, so if the Koala only has endogenous retrovirus, it is immunocompetent and less likely to show disease or even be infected at all by Chlamydia. KoRV-B was a statistically significant predictor of chlamydial disease, as it seems to be only exogenous and cannot infect germ cells as it uses a different receptor.

This group’s data supported other researcher’s assumption that all northern Australian koalas carry endogenous KoRV-A strain, but they also found about 25% of koalas they tested carried the KoRV-B subgroup. Multiple studies have now shown that TOTAL KoRV gDNA load or KoRV viral RNA load was correlated with chlamydial disease, so it seems other KoRVs (which are present in all koalas) do not cause the immunosuppression that KoRV-B causes.

That being said, 46% of the koalas tested who actually had chlamydial disease were negative for KoRV-B and one koala did not have chlamydial disease despite being infected and being positive for KoRV-B.

New insights from the whole genome of koalas on diet, immune system, sex!

Koalas are now the fourth marsupial to have their genome sequenced (which makes me really want to sequence more marsupials in the hopes of getting my own nature paper—I love a good fishing expedition). The group was able to characterize novel lactation proteins that help protect the young while their still in the pouch. The proteins produced in koala milk have antimicrobial and antifungal effects, notably against Chlamydia, which would be important for the young who lack a developed immune system. They also found immune genes involved in the response to chlamydial genes (perhaps the koala retrovirus researchers should go back and look for links between these genes and their various retrovirus findings in relationship to chlamydial disease vs. carrier state vs. no chlamydia!).

But how koalas are able to handle their intense eucalyptus diet, may have to do with the expansion within a cytochrome P450 gene family. Bitter tastes help animals avoid potentially toxic plants. Koalas have more bitter taste receptor genes than most mammals, so they can detect toxic metabolites in eucalyptus, indicating they may be able to figure out which leaves to eat. While eucalyptus is toxic to most animals, the koalas tend to be selective in which leaves they eat and do manage to avoid as much of the toxic metabolite as possible and get the most nutrients as possible from the plant.eucalyptus-leaves-make-koala-bears-high_6816d9eceb8f5043

Back to the repeat elements in the genome: They were also able to fully characterize repeat-rich noncoding RNAs, including RSX. RSX in koalas mediates X inactivation in females which is what also occurs in placental mammals as a method of dosage compensation (so females do not get twice as many proteins from the X chromosome as males, one X is inactivated in cells). Sex determination and dosage compensation are really interesting to compare in birds, monotremes, marsupials and placental mammals, so I found that little tidbit pretty exciting. Beyond their sex determination, the researchers also found genes involved in induction of ovulation as koalas are induced ovulators.

Vaccine design and conservation

Annotating immune genes and studying diseased vs. healthy koalas has useful implications for designing vaccines against chlamydia. The research group found that differences in particular immune genes in koalas involved in a clinical trial for vaccines may have explained differences in their immune response to the vaccine. They were also able to look at the expression levels of different immune genes to see which were up-regulated or down-regulated in sick vs. healthy koalas. They were of course able to quantify and see where the retroviruses were integrating into the genomes, which will also help them hopefully produce vaccines and combat the resulting diseases from retroviruses.

Sources:

  1. Adaptation and conservation insights from the koala genome. RebeccaN. Johnson et al. 2018. https://doi.org/10.1038/s41588-018-0153-5
  2. Infection with koala retrovirus subgroup B (KoRV-B), but not KoRV-A, is associated with chlamydial disease in free-ranging koalas (Phascolarctos cinereus). https://doi.org/10.1038/s41598-017-00137-4

 

 

 

 

Banded Mongoose: mutualism, cooperative breeding, and vital adaptations

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 Banded mongooses in Kruger National Park, South Africa (Peet van Schalkwyk ©)

“It is the hardest thing in the world to frighten a mongoose, because he is eaten up from nose to tail with curiosity. The motto of all the mongoose family is ‘Run and find out'” —Rudyard Kipling, Rikki-Tikki-Tavi

Cultural inheritance in banded mongooses

The banded mongoose is a bit of an anomaly in the mammal world. Instead of the offspring being raised by their parents (and behaving similarly to their parents), they instead inherit their behaviors from other adult mongooses. The adults are random, rather than closely related to the offspring, but take on a parental role in the sense that they sort of “adopt” a baby/juvenile (about one month old) and show it how to forage, hunt, stay safe from predators, and otherwise be a mongoose properly. These role models or “escorts” will carry around the pups and teach them closely for about two months. The plasticity of mongoose behavior is sufficient to allow for pups to behave more similarly to their role models than to their parents.

This kind of transmittance of behavior is known as cultural inheritance, and is actually quite common in the animal world– but the unique setup in mongooses provides an opportunity to easily decouple the direct genetic inheritance from parents and the cultural inheritance resulting from behavioral plasticity (social learning).

Cultural evolution is becoming one of the most popular topics in biology as more and more scientists are beginning to notice how new behaviors can sweep through a population in less than a generation. The classic non-human example of this would be humpback whale songs changing year to year.

While cultural evolution occurs more quickly than genetic evolution in one sense, it also allows for genetic diversity to persist. Higher behavioral plasticity results in higher variety of trait and higher variety of preference for those traits. It can actually slow down evolution towards physiological adaptation for an environment by slowing the adaptation of physiological change. That being said, it can allow for more rapid adaption and by relying on social learning, only one or a few members of a population need to “discover” a new behavior for it to spread through the population.

It’s possible the mongooses have evolved this escort system as a way to maintain diverse foraging methods and reduce competition in their groups. Maintaining plasticity in foraging behaviors would be useful for social animals that have a wide variety of food sources, as the mongoose does.

Timon and Pumbaa: based on a true story

p02bk7tkSo admittedly Timon is a Meerkat not a banded mongoose, but it’s the same family so it’s close. In a cool example of mutualism, Warthogs (which, by the way, are awesome animals and don’t get nearly enough love) can rid themselves of ticks and bugs by getting groomed by mongooses.

Warthogs–which should look kind of scary to a small mongoose, actually get along quite well with them. Wild pigs tend to have quite a few ectoparasites and bugs inhabiting their skin/fur which can provide an easy snack for the banded mongoose. Warthogs have learned to lay down when mongooses are nearby, so they can pick off the parasites. Besides allowing mongooses to groom them, they also welcome vervet monkeys to snack on their ticks.

Mutualism between mammals is somewhat rare, but wild pigs and mongooses (and vervets for that matter) are highly intelligent and it shouldn’t come as much of a shock that they are able to enjoy the company of other species.

Mutualistic foraging between dwarf mongooses and hornbills

In another species of mongoose, the dwarf mongoose of the Taru desert often cooperatively forages with large birds, particularly hornbills, who share the same prey. The hornbills will wait to start foraging around termite mounds if the mongooses are sleeping and the mongooses will wait for the hornbills to be nearby to begin their foraging. This is true mutualism, as, while many animals have instances of exploiting each other’s coincidental presence for their benefit, the hornbills and dwarf mongoose actually plan their foraging activities around the other.

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The mongooses and the hornbills will warn each other of predators while they forage. The hornbills will even warn the mongooses when there are predators nearby that do NOT prey on the hornbills. The hornbills recognize predators specific to the mongoose as they will not warn against predators that do not prey on the mongoose. This is a pretty unique relationship as most cases of mutualism do not involve so much complex compensative behavior between species. The two species will communicate to one another with different vocalizations, and hornbills will sometimes wake up the sleepy mongooses when they’re impatiently waiting to start snapping up unfortunate insects.

Convergent evolution of neurotoxin resistance

Mongooses are mostly known for fighting cobras (partly because they’re exceptionally quick) but their resistance to the alpha-neurotoxin in cobra venom is what especially allows for this feat.

Acetylcholine is a very important neurotransmitter, so there are acetylcholine receptors all over your muscle cells that need to be free to bind (or not bind) acetylcholine, allowing your muscles to expand/contract. This neurotoxin, called alpha-bungarotoxin (alpha-BTX), works by binding to these acetylcholine receptors and blocking them up resulting in paralysis and eventually death. However the mongoose, the snakes themselves, and several other animals have independently evolved to alter the shape of their acetylcholine receptors so the neurotoxin, alpha-BTX, doesn’t bind.

Tweaks to the nicotinic acetylcholine receptor to prevent snake neurotoxin binding have been shown to have evolved at least four separate times in mammals (the honey badger, pigs, mongooses, and hedgehogs), but in the mongoose, the tweak involves a glycosylation site on the receptor matching the site present in snakes.

Syncing up birthdays

Despite being highly social and altruistic, meerkats are a more vicious member of the mongoose family and are especially well known to participate in infanticide. As meerkats live in a matriarchy with intense dominance hierarchies, many babies do not stand a chance from more dominant pregnant females. Banded mongooses however, have managed to evolve to sync up their birth so they’re all born on the same day. This prevents infanticide as all females are on essentially identical schedules (hormonally and in how they spend their time), so pups are never left alone with other females.

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Photo credit: Feargus Cooney

While most mammals have adapted to differentiate their own offspring very well, the banded mongoose benefits from having all pups be treated equally by the adult mongooses. Syncing up birth to the day or few days is a useful strategy, also seen in flamingos, where both male and female flamingos will even produce and feed crop milk to young who are not their own. However unlike flamingos, syncing up birthdays seems to be more about preventing infanticide and having a more lax dominance hierarchy.

This is a pretty unique strategy as usually species tend to fall on a continuum of high to minimal parental care. In this case, the banded mongoose receives a lot of “parental care” but not necessarily much from their parents. In almost all of nature, the level of paternal parental care is based on certainty of paternity, yet the mongoose has no idea who its close kin are. The behavior where a species mentors and takes care of young they know are not their own is, of course also seen in humans. Mongooses are exceptional in their array of cooperative behaviors– displaying reciprocity, altruism, cooperative breeding, and mutualism. But knowing humans, most will probably continue to believe we are special and entirely disconnected from these evolutionary adaptations.

Sources:

  1. Dwarf mongoose and hornbill mutualism in the Taru desert, Kenya. O. Anne-E. Rasa – Behavioral Ecology and Sociobiology – 1983
  2. How the mongoose can fight the snake: the binding site of the mongoose acetylcholine receptor. D. Barchan-S. Kachalsky-D. Neumann-Z. Vogel-M. Ovadia-E. Kochva-S. Fuchs – Proceedings of the National Academy of Sciences – 1992
  3. Decoupling of Genetic and Cultural Inheritance in a Wild Mammal. Catherine Sheppard-Harry Marshall-Richard Inger-Faye Thompson-Emma Vitikainen-Sam Barker-Hazel Nichols-David Wells-Robbie Mcdonald-Michael Cant – Current Biology – 2018
  4. Reproductive competition and the evolution of extreme birth synchrony in a cooperative mammal. S. Hodge-M. Bell-M. Cant – Biology Letters – 2010

New Rhabdoviruses in bat ectoparasites: as told by a rabid supporter of bat research

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vesicular stomatitis virus, taken by the CDC

Few things disturb me more than rabies. The thought of a small, bullet-shaped virus encoding only five genes, causing an incurable, creeping infection along the nervous system, into the brain, then spreading everywhere, all while causing the host to become violent and delirious– is a bit overwhelming to dwell on. Even for someone who reads about infectious disease everyday. But rabies, for all the attention it gets, belongs to a group that seems almost neglected otherwise.

Rabies, a member of the Lyssavirus genus, is unquestionably the most famous Rhabdovirus (which is fair– it’s the most deadly virus known to man), so it might be surprising to hear that most members of the rhabdovirus family don’t even seem to infect mammals.

Despite bats being well known reservoirs for some of the world’s most deadly viruses (Henipaviruses, Marburg, and Ebola to throw some names out there), bat ectoparasites have been pretty neglected by viral ecologists. This is especially surprising as arboviruses (viruses transmitted by an arthropod vector e.g., Dengue), have only been spreading further geographically as our climate heats up. Even more surprising, these bat parasite viruses are often close relatives of rabies, yet so far seem relatively harmless.

Most rhabdoviruses that actually infect bats (that we know of) have been lyssaviruses, but that could partly be because detection methods for rhabdoviruses in bats (and their ectoparasites) were often restricted to lyssaviruses. Now that we’re starting to look a bit harder, we’re realizing there’s probably a lot more viral diversity than we’d planned for.

Kanyawara virus: how much of a concern are rhabdoviruses, really?

The Kanyawara virus, a nycteribiid bat fly virus found in western Uganda, is raising some questions about rhabdovirus diversity and potential pathogenicity. A phylogenetic analysis placed the virus within a genus containing bat rhabdoviruses; Ledantevirus. If the most recent common ancestor of these viruses was bat-associated, this means is that it is likely this virus infects bats as well and is not an arthropod-specific virus, but rather and arthropod-vectored virus. Viruses that infect bats can result in bat-borne zoonoses, examples include basically all the worst things we usually think of when thinking about viruses.

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Nycteribiid: Why does this thing even exist though

The researchers tested nine bats for the Kanyawara virus but no virus was found in any of them. The researchers mentioned they suspect this is due to transient viremia rather than that the virus never infects bats, but they don’t really know.

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darling member of the same genus as the host of the parasite carrying Kanyawara virus

Rhabdoviruses infect a huge range of hosts, but it seems arthropods play the biggest role in rhabdovirus ecology. Plant rhabdoviruses are usually transmitted by arthropods, fish rhabdoviruses are often transmitted by aquatic arthropods, and many viruses have been found in both vertebrates and arthropods or are vectored by arthropods. That being said, many rhabdoviruses are insect-only viruses which would make them significantly less concerning. However bats are way overrepresented amongst non-arthropod hosts in terms of how many rhabdoviruses infect them as a preferred host.

Host-parasite coevolution

Previous phylogenetic analyses done by a group at Cambridge show rhabdoviruses as closely coevolving with their hosts. When a host phylogeny closely matches a virus phylogeny this is strong evidence for coevolution. The more detailed phylogeny in this study, shows a less mirrored picture. Basically there’s a positive correlation between genetic distance of the hosts and genetic distance of the viruses, but the viruses seem to switch easily between closely related species.

The group found only two major host switch types in the phylogeny (a host switch being more broad in this case, when a virus from one host cluster such as plants, arthropods, or vertebrates switches over). Three phylogenetic transitions were from an arthropod-vectored vertebrate virus to a vertebrate-specific virus. Two were arthropod-vectored to arthropod-specific. One arthropod-vectored, to arthropod-specific group, the sigma viruses, actually lost their vertebrate hosts and are now vertically transmitted.

This type of analysis is useful because it allows us to predict with some confidence whether a virus isolated from a host is a likely pathogenic threat based on where it might fit in a phylogeny. These types of large scale phylogenetic analyses are becoming even more useful now that we are discovering so many viruses but can’t necessarily keep up with understanding their biology.

If most rhabdoviruses are harmless, but rabies (a rhabdovirus) can infect basically anything, and is the most deadly pathogen known to man, you can imagine how confusing it is when a new rhabdovirus emerges. We really don’t know what’s out there, even when it comes to human rhabdoviruses. Recent studies have isolated new rhabdoviruses in apparently healthy people in West Africa, some of which were extremely similar genetically to Bas-Congo virus (a virus associated with a hemorrhagic fever outbreak in 2009)– yet we don’t know how they were transmitted, how common this is, and why even closely related rhabdoviruses of vertebrates can switch between asymptomatic and deadly.

Bats are exceptionally diverse, so their parasites are quite diverse with them. These parasites’ parasites (the viruses) are then unsurprisingly quite diverse as well. Bats are then an ideal reservoir for some truly horrific viruses to circulate and happily evolve in, as bats have a unique immune system allowing them to harbor zoonotic viruses and remain asymptomatic. As interactions between bats and humans increase there’s now further selective pressure and opportunity for viruses to expand their host range to hosts with less fine-tuned, dampened immune systems–like, us for example.

Sources:

  1. Kanyawara Virus: A Novel Rhabdovirus Infecting Newly Discovered Nycteribiid Bat Flies Infesting Previously Unknown Pteropodid Bats in Uganda. Tony Goldberg-Andrew Bennett-Robert Kityo-Jens Kuhn-Colin Chapman – Scientific Reports – 2017

2. The evolution, diversity, and host associations of rhabdoviruses. Ben Longdon-Gemma Murray-William Palmer-Jonathan Day-Darren Parker-John Welch-Darren Obbard-Francis Jiggins – Virus Evolution – 2015

Bioluminescence- the immense diversity of organisms that glow

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Bioluminescence is a beautiful evolutionary phenomenon which has aided organisms in defending against predators, attracting mates, attracting prey, communicating, and even coping with metabolic stress. A ton of groups contain bioluminescent members (fungi, echinoderms, cnidarians, the list goes on and on) including some real evolutionary stand-outs.

In most cases (but not all!), bioluminescence results from enzyme-catalyzed oxidation of luciferins—light-emitting compounds—by luciferases. There can be many different luciferase compounds used even in closely related species.

New luciferin found in glowworms

A newly identified luciferin was discovered in caves in New Zealand (because of course it would be in a cave in New Zealand) in glowworms. This luciferin uses Xanthurenic acid and tyrosine as the two precursors to the glow. This particular glowworm is Arachnocampa luminosa, a species of fungus gnat that, in its larval stage, produces sticky threads by building a long muscousy tube and moving along the tube sort of vomiting up little sticky threads to trap insect prey. How disgustingly beautiful nature can be!

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Waitomo caves 

Glowworms are not really worms, but rather, larvae of several families of beetle and fungus gnat–however the bioluminescence is not homologous among the groups (so it’s arisen independently many times over). While it’s not always just the larvae that glows, the larvae emits the brightest blue-green glow. The glow helps the glowworms attract insects, attract mates, and protects them from predation (it also inspired James Cameron to make the blockbuster hit, Pocahontas with Glowworms Avatar).

Deep sea Cephalopods like to flash each other

An especially cool evolutionary example is of a deep-sea octopus, whose “suckers,” which still retain a sucker appearance and sucker-like traits, have had many of their muscle cells replaced with light producing cells. Researchers suspect this may have occurred as the result of once being a shallow-water bottom dwelling octopus, and moving to a deep open-ocean environment where suckers were less necessary.

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Deep sea octopus

Now it appears, the octopi use these glowing suckers for communicating to one another via visual signaling. They may also be using them for attracting a favorite prey item of theirs—copepods (small crustaceans). This is an unusual prey item for an octopus, but the copepods are attracted to the bioluminescence.

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Toyama Bay, Japan where firefly squid gather to spawn. Credit: Brian J. Skerry/Getty Images

For a more flashy light show, I’d recommend the firefly squid. Their deep blue lights (produced by photophores) are used for communicating with mates and perhaps rival squid. The light can also be used to break up the body pattern to confuse predators and attract small fish to prey on (because deep sea fish just cannot seem to learn which glowing lights mean danger). The really cool thing about firefly squid though, is not so much the light they produce, but the evolution of their eye that seemed to come with it. They are thought to be one of the only cephalopods to have color vision (by the way, cephalopod eyes: a fascinating topic). They have three visual pigments while other cephalopods only have one, and this may be so they can better distinguish ambient light from bioluminescent light, and perhaps because their light color is pretty unique from other bioluminescence emitted in the deep sea.

Symbiotic bacteria- lux operon helps flashlight fish and bobtail squid

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In perhaps the most of obvious function of bioluminescence: The flashlight fish (Anomalous katoptron in this case, though there are several species), produces light using symbiotic bacteria. The fish’s light organs are located under it’s eyes so it can turn the light on and off by blinking. These organs are packed with bioluminescent bacteria to produce a greenish-blue light. Researchers found that the fish blink less (meaning their organs are open) in the presence of their planktonic prey indicating they use their bioluminescence for finding prey.

 

Quorum sensing and a beautiful tale of symbiosis

One of my favorite bioluminescent evolutionary excerpts is that of Vibrio fischeri and Euprymna scollops (the Hawaiian bobtail squid). V. fischeri is a symbiotic bacterium that produces bioluminescence through the lux operon (which involves another luciferase oxidizing a compound to produce blue-green light). The Vibrio interact with the squid (using type IV pili) which starts the maturation of light organs in the squid. These bacteria help the squid conceal its shadow while its foraging for food under the moonlight. This protects the squid from predators while providing the bacteria with a stable home. 980x

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simplified diagram of lux operon at low and high cell density

What makes this bacterium especially notable, is that it was one of the first bacteria to be discovered to use quorum sensing. Quorum sensing is a gene expression regulation tool (often called “bacteria communication” and totally going to be on your exam tomorrow) where the Vibrio’s gene expression responds to changes in bacteria cell density. A signal molecule- N-acylhomoserine lactone (AHL), is synthesized by LuxI (a protein produced by the lux operon I mentioned earlier) and leaves the bacteria cells. LuxR forms a complex with AHL and binds the lux box causing the activation of luminescence genes. The bacteria colonize the squid’s light organ at a very high density producing lots of this AHL molecule.

Millipedes: Glow first used for coping with climate, co-opted for warning signal

 

If you’re ever in California, be on the lookout for the Motyxia millipedes. They’re pretty easy to spot as they emit a teal glow from their entire body. They also produce poison cyanide which many other millipedes do as well. Instead of concentrating their glow to one light organ and instead of emitting light from a luciferase reaction, they glow all over their exoskeleton using a photoprotein whose homology is unknown.

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M. sequoiae (left), M. bistipita (right)

But what’s REALLY cool about the Mytoxia is that for a while it was thought that bioluminescence evolved in the millipedes as a way to warn predators. However, when researchers discovered that another species (previously Xystocheir bistipita, now reclassified as Mytoxia bistipita) glows, but much more faintly, they looked more into it.

They found that Mytoxia may have actually evolved to cope with hot, dry climates (this species is found in the Sierra Nevada Mountains). The glow of M. bistipita is much less intense and they also have fewer predators than other species. Millepedes have difficulty metabolizing oxygen in hot, dry climates which creates toxic byproducts (like peroxide). Their bioluminescent photoprotein actually helps to neutralize these toxic byproducts. The researchers concluded that the millipedes colonized higher elevations more recently than the bioluminescence evolved, and that with that colonization came more predation. Only then did they co-opt the trait for warning predators of their poison cyanide production. The brighter the millipede, the more cyanide it contained!

Sources:

  1. Paul E. Marek, Wendy Moore. Discovery of a glowing millipede in California and the gradual evolution of bioluminescence in Diplopoda. Proceedings of the National Academy of Sciences, 2015.
  2. Jens Hellinger, Peter Jägers, Marcel Donner, Franziska Sutt, Melanie D. Mark, Budiono Senen, Ralph Tollrian, Stefan Herlitze. The Flashlight Fish Anomalops katoptron Uses Bioluminescent Light to Detect Prey in the Dark. PLOS ONE, 2017.
  3. Quorum Sensing in the Squid-Vibrio Symbiosis. Subhash C. Verma and  Tim Miyashiro. Int J Mol Sci. 2013 Aug.

Botulinum toxin found in new, common bacteria

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Clostridium botulinum, Photo: Eye of Science

Evolutionarily, horizontal gene transfer between bacteria is generally not so groundbreaking. In this case however, it’s a little more newsworthy. A lot of bacteria carry plasmids, which are mobile little DNA structures that are not part of the bacterial chromosome and can be transferred to other bacteria. Often plasmids contain genes that may provide some selective advantage (otherwise why bother keeping them?), such as a toxin or an antibiotic resistance gene. Enterococcus happens to be a frequent plasmid-carrier, which makes it an especially good candidate for frequent horizontal gene transfer. But first, Clostridium. 

Clostridum is an especially fun group of bacteria including some really famous germs:

  • C. tetani (Tetanus),
  • C. difficile (the bacteria in your gut that gives you stomach issues after you take antibiotics as it swarms in on all the spaces other bacteria used to be, before they were killed by antibiotics),
  • C. perfrinigens (perhaps the nastiest of all, gas gangrene),
  • the less famous C. sordelli (which is a rare–but plenty horrific, pregnancy and abortion-associated infection almost always resulting in death by toxic shock syndrome)
  • And of course, C. botulinum, the primary culprit of botulism.
What is Botulinum toxin?

C. botulium is known for releasing botulinum toxin (BoNT), a toxin which interferes with the release of the neurotransmitter—acetylcholine, from axon terminals at the neuromuscular junction resulting in flaccid paralysis (you can’t breathe).

The toxin (a protein) works by binding to receptors at the neuromuscular junction. It is then taken into the cell by receptor-mediated endocytosis. A conformational change occurs inside the early endosome (due to a pH change). A piece of the protein (the light chain) is translocated to the cytosol when another piece of the protein (the heavy chain) forms a sort of channel. This light chain can then cleave these important complex-forming “SNARE” proteins, which are vital to normal vesicular transport and neurotransmitter (which in this case is acetylcholine) release. So without these SNARE proteins, the little acetylcholine vesicles don’t get to where they need to be. In normal neurotransmitter release, SNARE proteins would work to tether the vesicles to the membrane so the cell and vesicle membranes could fuse to allow the release of neurotransmitters.

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Visualized by me on Pymol- PDB file: 3BTA, BoNT, Serotype A. You too, can play around with it in pymol/swissPDB/Chimera/some other visualizer!

Botulinum toxin is the deadliest toxin known, requiring just two billionths of a gram to kill one person. It’s so dangerous that when type H (one serotype of the toxin) was discovered and failed to be controlled by typical botulinum antibodies, the type H toxin became the only example of a genetic sequence that was hidden from public databases due to security concerns. I say “may be” because how would we really know?

Not just in C. botulinum anymore

While we used to take comfort in knowing we could probably avoid Clostridium botulium by just avoiding puffed up canned food, rotten meat, and organic honey, that may no longer be the case. For the first time, the botulinum toxin has been found in a completely different (and very distantly related) bacteria: Enterococcus.

This new variant of the toxin called BoNT/En, was found in South Carolina, in an E. faecium strain isolated from cows. And it wasn’t just the toxin that was found. Several associated proteins that prevent the toxin from being degraded were also found. That being said, the BoNT/En variant didn’t give the cow it was found in, botulism, and it was not actually very harmful initially in mice. Researchers had to manipulate the toxin to better target mice before it was able to actually kill them (I know. Trying to give mice botulism is upsetting, and the reason why I stick to cells and microbes for my research). They are testing the toxin on human neurons to see how toxic it is to humans.

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Enterococcus

What makes this particular jump so terrifying is that Enterococcus is a highly abundant group of bacteria all over our bodies. It is ubiquitous in animals and actually a significant human pathogen. E. faecium is a very hardy bacterium easily evolving antibiotic-resistance and actually pretty difficult to get rid of in hospital surfaces. The thought of a dangerous neurotoxin being easily transferred to a ubiquitous and antibiotic-resistant bacteria is somewhat frightening. That being said, plasmids containing incredibly dangerous neurotoxins would likely need to provide a selective advantage to the host to stick around (and it’s possible in E. faecium’s case, it could even provide a slight disadvantage). BoNT can be carried in a bacteriophage, in a plasmid, or on a chromosome, but carrying a sizable gene cluster you don’t need in evolution has usually resulted in a “you don’t use it, you lose it” outcome. As plasmids by themselves are slightly disadvantageous to carry, what keeps them around is any selective advantage the genes they contain provide.

Where did these toxins come from?

Researchers found that the homolog of BoNT in Clostridium, seemed to be a flagellin gene. These flagellins contain collegenase which breaks down peptide bonds in collagen, so they are also a proteolytic toxin family like the Clostridia neurotoxins. They believe that the neurotoxin and adjacent genesevolved from an ancestral collagenase-like gene cluster.  This gene cluster was likely duplicated and evolved separately to become the BoNT we know today.

My case against Botox: amazing, but maybe take it easy?

Botox can be useful for treating cerebral palsy, urinary incontinence, wrinkles, sweating, spasms, headaches, and tinnitus. While no one’s reportedly died from cosmetic Botox use (presumably because people are probably extra careful with such a terrifying substance), there’s a risk of the toxin spreading beyond the injection site and causing respiratory paralysis. While ordinarily I’m totally accepting of people’s desire to do strange or expensive things in the name of beauty, my (probably illogical) fear is that all it takes is one new guy thinking a smudged decimal point is a comma and you’re dead of flaccid paralysis.

Consider that a muscle with a cut nerve will quickly result in atrophy which will definitely make you look worse, not better. Not using your face muscles isn’t going to prevent you from wrinkling because the issue is not the muscles, but the soft tissue decline that comes with age. Neuromodulators like Botox are very expensive, usually require a high enough dose to actually be effective and wear off in a few months, meaning you would have to get several injections a year to stay smooth and shiny, and the repeated injections are when people tend to see more negative side effects and require a higher dose.

Paralyzing muscles over and over again is not great for you long-term so maybe try sunscreen, a nice skincare routine, and drink plenty of water instead? Mistakes happen, people misplace decimal points, I’d rather not be near it personally. Just a friendly PSA to remind you to definitely do your research if you want to mess around with botulinum toxin!

Sources:

  1. Sicai Zhang et al. Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium. Cell Host and Microbe, 2018
  2. P.K. Nigam, Anjana Nigam. Botulinum Toxin. Indian Journal of Dermatology. 2010 Jan-Mar; 55(1): 8–14.
  3. Doxey AC, Lynch MD, Müller KM, Meiering EM, McConkey BJ. Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster. 2008.

Cryptococcus — (r)evolutionary genius

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If you’re in the market for a particularly fun fungus to tell your friends about, I’d suggest the pathogenic yeast, Cryptococcus.

Cryptococcus is primarily known for causing Cryptococcal meningitis—a leading cause of death in AIDS patients. This is Cryptococcus neoformans, which, while more common really only infects the immunocompromised. Its cousin, Cryptococcus gatti, frequently infects immunocompetent, healthy individuals and is an important emerging pathogen. Weirdly enough, C. gatti infections all seem to come from trees. The fungal pathogen has dispersed all over the world surprisingly, scientists believe, due to continental drift. In the past few years, there’s been large outbreaks of the less common Cryptococcus gatti in the Pacific Northwest/Canada and South Africa.

Sex has something to do with it

Cryptococcus needs a lot of sugar to reproduce, particularly inositol which is all over the human brain and spinal cord which is probably why Cryptococcus is known for causing meningitis. Cryptococcus (depending on the species) has between about 6 to 12 genes involved in inositol transport while most fungi have only about two. While inositol is needed for reproduction and results in higher virulence, which mating type the fungus is may also play a large role in pathogenicity.

In yeasts there are two mating types, MATa and MATα. MATα strains are able to produce an extensive hyphen phase in the haploid state called monokaryotic fruiting. All the clonal C. gattii VGII (or C. deuterogatti) that have been infecting people have notably been from the same mating type: Matα. MATα strains are capable of same-sex mating which could be the origin for the outbreak around Vancouver. In C. neoformans, MATα strains which have their own genes specific to that mating type, are associated with higher virulence (but there’s no evidence of this with C. gattii). 

From Springer 2010, isolations of C. gatti from human clinical, veterinary, environmental sources. Underestimation of actual prevalence.

Hypermutator

Researchers found that several isolated C. deuterogatti strains contained mutations in MSH2, one of the genes involved in mismatch repair (genes that fix DNA replication errors). The human homologous MSH2 gene has the same effect where humans with mutations in MSH2 can have Lynch Syndrome, where they’re prone to various cancers.

The mutations in MSH2 in fungi were tested and resulted in their genomes mutating at a faster pace but growing at the same rate as wildtype Cryptococcus strains. When exposed to stressful conditions however, such as antifungals like rapamycin and FK506, the mutant strains rapidly took over as they could quickly acquire resistance to drugs. In the process of acquiring drug resistance the strains actually decreased in virulence and were significantly weakened compared to the outbreak strains.

So the hypermutators are much more fit in stressful conditions and can rapidly outcompete the wildtype strains, however they make a less fit pathogen without significant selective pressures present. This brings up an interesting question in host-pathogen evolution—what kind of genome makes for an ideal pathogen? Fungi in general are lousy pathogens, especially in people. Certainly white-nose syndrome in bats and chytrid fungus in amphibians have devastated populations but there aren’t a whole lot of “in between” fungal pathogens. Having a lower mutation rate than bacteria or viruses contributes to their easiness to treat. While in bacteria a hypermutator strain rapidly evolving drug resistance usually sounds like a bad thing, in this case hypermutator strains taking over would at least lower the virulence and fitness of the fungus as a pathogen.

It’s even worse in men

As is the case with many pathogens, there is an increased incidence of the disease in men and when it does appear mortality rates are significantly higher in men. C. neoformans isolates from females had a slower growth rate and released more capsular glucoronoxylomannan (GXM), (a virulence factor and immunosuppressant). Testosterone was associated with higher levels of GXM release while 17-β estradiol was associated with lower levels and slower growth rate. Furthermore, macrophages from females were better at fighting off C. neoformans than macrophages from males which were more damaged from the infection. This may explain why infections are more common in men.

While Cryptococcus neoformans has been a common issue for a while, Cryptococcus gatti has only recently emerging as a prominent pathogen, which scientists believe could be the result of climate change. These Cryptococcus infections infect healthy people and are fatal if left untreated.

Sources:

  1. The second STE12 homologue of Cryptococcus neoformans is MATa-specific and plays an important role in virulence. Y. Chang-L. Penoyer-K. Kwon-Chung – Proceedings of the National Academy of Sciences – 2001
  2. The Role of Host Gender in the Pathogenesis of Cryptococcus neoformans Infections. Erin Mcclelland-Letizia Hobbs-Johanna Rivera-Arturo Casadevall-Wayne Potts-Jennifer Smith-Jeramia Ory – PLoS ONE – 2013
  3. Highly Recombinant VGII Cryptococcus gattii Population Develops Clonal Outbreak Clusters through both Sexual Macroevolution and Asexual Microevolution. R. Billmyre-D. Croll-W. Li-P. Mieczkowski-D. Carter-C. Cuomo-J. Kronstad-J. Heitman – mBio – 2014

 

Cretaceous pterosaur diversification and extinction

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Artist: Mark Witton

Few things are as disappointing as learning that no pterosaurs survived the K/Pg extinction. This has always been especially hard for me to emotionally accept due to their immense diversity. The typical explanation usually told is that they were wiped out with the non-avian dinosaurs after the chicxulub impact, and that they were barely alive by that time anyway because all the birds had filled up the flying niches. However recent evidence indicates that pterosaurs actually were doing very well up until 65 million years ago. Why they went extinct may have nothing to do with birds or a failure to diversify. Serial size reduction allowed for smaller pterosaurs to survive through other extinctions. Reaching sexual maturity before being fully grown allowed for smaller hatchlings maturing more quickly, allowing for more reduction in size by accelerating evolution somewhat. So if there were smaller pterosaurs at the end of the Cretaceous, AND pterosaurs have previously proven to be capable of relatively rapid phylogenetic size decreases, why did no pterosaurs survive?

The Cretaceous is more known for its giant, “small-plane sized” pterosaurs (Arambourgiania, Quetzalcoatlus, and one that’s been in the news more recently for “terrorizing” Transylvania: Hatzegopteryx). For background pterosaurs are split into two major suborders, with Rhamphorhynchoids being a paraphyletic group characterized by having teeth, long tails, and a cruropatagium that stretched between the feet (like how bats have it). Most were small and lacked bony head crests. They appeared in the Triassic and went extinct during the Cretaceous though there is no strong evidence to indicate they were outcompeted by pterodactyloids which is a common assumption.

Pterodactyloids, the other suborder, did not appear until the late Jurassic and were much more successful and diverse in the Cretaceous. While all pterosaurs are outstanding creatures, the pterosaurs this post is concerned with would all be pterodactlyoid members.

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Rhamphorhynchoid on left, Pterodactyloid on right

No fossils of pterosaurs have been found from after the K/Pg extinction (and I don’t believe there ever will be 😦 ). But while there are certainly no pterosaurs alive today, there is a lot of evidence indicating that pterosaurs were actually quite diverse even at the end of the Cretaceous, and that some were even very small. The discovery of small pterosaurs from the late Cretaceous does seem to indicate that the reason for their clade’s total extinction was not simply because they were just “too large.”

Small pterosaurs may have been more abundant in Cretaceous than previously thought

A small azhdarchoid (azhdarchoids being the most recent common ancestor of Quetzalcoatlus and Tapejara, and all its descendents) pterosaur was discovered from the Campanian Northumberland Formation of British Columbia. With an estimated 1.5m wingspan, the pterosaur specimen is described as being about the size of a large seagull. The specimen found might not actually be an azcharchoid, but it certainly was from a pterosaur. Researchers were able to analyze the bones to determine whether or not it was juvenile or adult and found that the specimen was either fully grown or very close to being fully grown. For more on that, read the paper here.

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Pterosaurs preserve terribly. They’re bones are hollow, their skeletons are fragile, they didn’t routinely die in nice, preserving environments. During the Cretaceous, pterosaurs shifted from marine to more non-marine habitats. This may account for the lack of data on small, difficult to preserve pterosaur fossils in the late Cretaceous. Terrestrial habitats do not preserve fragile fossils. Even much larger, denser bones do not often preserve well in terrestrial environments. The fossils that have been found from pterosaurs of this period are usually in very bad shape and are only fragments of the entire skeleton. Often times, fossils have to be looked at by many bird and pterosaur specialists before it can even be determined that the bone WAS from a pterosaur.  There is a lot of growing evidence suggesting that smaller pterosaurs in the late Cretaceous were not as rare as once believed.

Birds not the cause of pterosaur extinction

Pterosaurs were excellent fliers, almost definitely warm-blooded like birds (due to the energy expense of their lifestyle) and seemed able to adapt to a wide variety of niches. So it’s strange to imagine them going extinct due to their failure to diversify in the presence of birds. A study showed that pterosaurs actually diversified more after birds appeared. Pterosaurs had about a 160 million-year run on Earth and were relatively similar morphologically for the first 70 million years. They then began to experiment, trying out many modes of life. As birds became more successful, the pterosaurs actually responded by diversifying more. The emergence of birds (at least 50 million years after the first pterosaurs), encouraged the pterosaurs to try out new diets and feeding styles as seen by the rapid diversification of skull shapes in the fossil record. The general direction they went towards was much larger bodies. This was when the famous giant Quetzcoatlus types emerged.

sources:

  1. A small azhdarchoid pterosaur from the latest Cretaceous, the age of flying giants. Martin-Silverstone, Elizabeth, et al. Royal Society Open Science. 2016.
  2. Evolution of morphological disparity in pterosaurs. Katherine Prentice, Marcello Ruta, Michael Benton – Journal of Systematic Palaeontology – 2011

 

 

 

Hantavirus may pose bigger zoonotic threat than we thought

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The adorable host of a virus that causes your lungs to fill with fluid.

A small, innocuous looking virus with just three genome segments, causes one of the most deadly infections in the United States. Hantaviruses circulate worldwide causing either hemorrhagic fever with renal syndrome (HFRS) or, in the case of the North and South American strains, Hantavirus pulmonary syndrome (HPS). Famously recognized in 1993 in the Four Corners region of the U.S., Sin Nombre Virus, a strain of hantavirus, still infects at least a few people in the U.S. every year.

Hantaviruses are thought of as a virus people only get directly from rodents, which cannot be transmitted person-to-person. Infections result from exposure to contaminated excretions/secretions of rodents infected with the virus, though the rodents themselves show no signs of disease. These rodents also transmit the virus to each other.

Coevolution with hosts

While many species may be drivers for the evolution of another, the term coevolution is applied when two species influence each other so much that they are evolving together, where one undergoes genetic change the other responds with genetic change. They are undergoing speciation together. It was thought for a while that rodents were unharmed by the virus due to long, ongoing rodent-hantavirus coevolution. Significant phylogenetic congruities have been shown, for example, the phylogeny shown:

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Host species phylogeny on left, virus phylogeny on right, lines indicate which host virus infects.

New research might be indicating that’s not as true as we thought, phylogenetic analysis studies may be flawed, host range my be bigger, and rodent speciation doesn’t match up. While I’m not enough of a hantavirus or rodent expert to weigh in on this, certainly “whoa if true” to the coevolution theory.

Person-Person Transmission

In 1996, an outbreak of hantavirus in Argentina occurred, yet there was especially low rodent density and there was strong evidence for person-person transmission.

Then in 2011, a similarly unusually outbreak in Chile occurred. An Andes hantavirus, a close relative to the North American Sin Nombre virus (meaning “no name” as the native Americans), was shown to be transmitted person-to-person. In an outbreak of 5 human cases, symptoms developed in 2 household contacts and 2 healthcare workers after exposure to the first patient patient. Analysis of isolates from each patient supported person-person transmission for the all secondary-case patients.

Hantavirus found in human saliva

You might optimistically tell yourself that maybe this Andes hantavirus was a unique case. And maybe hantavirus was still really just a rodent disease that rarely spilled over to a person. But in Sweden in 2008, a Puumala hantavirus that causes hemorrhagic fever with renal syndrome (nephropathia epidemica) was found in human saliva of 10 patients. Whether or not this is actually a mode of transmission or not remains to be seen, but it does seem like hantaviruses are becoming more adept at infecting and transmitting between human hosts.

Climate change’s effect on hantavirus?

Hantaviruses frequently jump hosts and seem to circulate amongst bats, moles, shrews, and rodents, but climate change and human impact generally decreases rodent diversity. Intuitively you may assume hantaviruses would be less able to jump hosts as global warming/human impact goes on.

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Perhaps colder areas will actually see a decrease in hantavirus outbreaks as a result of global warming, due to the expected decrease in vole/northern rodent species populations. Yet that doesn’t seem to be what’s happening. Hantavirus surveillance has indicated an INCREASE, not only in outbreaks, but in genetic diversity and abundance in rodent populations.

If climate change does end up resulting in low rodent densities, this may also present another hantavirus risk– providing selective pressure for the virus to change transmittance route.

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deer mouse dusted with fluorescent powder to identify which mice got in most fights/matings thereby spreading more hantavirus. It was big, old mice.

Sources:

  1. University of Utah. “Big, Old Mice Spread Deadly Hantavirus.” ScienceDaily. ScienceDaily, 9 January 2009.

2. Phylogeny and Origins of Hantaviruses Harbored by Bats, Insectivores, and Rodents. Wen-Ping Guo-Xian-Dan Lin-Wen Wang-Jun-Hua Tian-Mei-Li Cong-Hai-Lin Zhang-Miao-Ruo Wang-Run-Hong Zhou-Jian-Bo Wang-Ming-Hui Li-Jianguo Xu-Edward Holmes-Yong-Zhen Zhang – PLoS Pathogens – 2013

3. An Unusual Hantavirus Outbreak in Southern Argentina: Person-to-Person Transmission? Rachel Wells – Emerging Infectious Diseases – 1997

4. Hantavirus RNA in Saliva from Patients with Hemorrhagic Fever with Renal Syndrome. Lisa Pettersson-Jonas Klingström-Jonas Hardestam-Åke Lundkvist-Clas Ahlm-Magnus Evander – Emerging Infectious Diseases – 2008

5. Person-to-Person Household and Nosocomial Transmission of Andes Hantavirus, Southern Chile, 2011. Constanza Martinez-Valdebenito-Mario Calvo-Cecilia Vial-Rita Mansilla-Claudia Marco-R. Palma-Pablo Vial-Francisca Valdivieso-Gregory Mertz-Marcela Ferrés – Emerging Infectious Diseases – 2014

 

Salty Antarctic Lake Provides Clue to Viral Evolution

In the Vestfold Hills region of Antarctica, a team of researchers have discovered a unique method of genetic exchange happening in a deep lake—so salty it remains unfrozen down to minus 20 degrees. In it, lives members of Haloarchaea, a class of Euryarchaeota that thrive in high salt conditions. These extremophiles are able to thrive by having extremely high rates of horizontal gene transfer, swapping genes with other genera even, to more rapidly evolve. Despite the shockingly high rate of gene sharing, the lake still maintains distinct species with no one dominant species winning out. The lake is incredibly cold, providing very little energy, so the archaea in this area only produce about six generations a year because they have to metabolize and reproduce so slowly.

While people have been aware of the archaeal extremophiles there for some time, it was only recently that anyone noticed their plasmids.

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Haloarchaea colonies

The team discovered plasmids in one strain that were not behaving like regular plasmids. Plasmids are pieces of DNA independent of the host genome which replicate independently and are kept around usually only if they have some beneficial gene to the organism (e.g. antibiotic resistance). What differentiates a plasmid from a virus is the method of transmitting genetic information.

For background, a plasmid typically relies cell-cell contact or “conjugation”–when a sex pilus of a bacterial cell containing the plasmid will combine with another bacterium to transfer the plasmid, or is picked up as naked DNA. Other horizontal gene transfer methods would be transduction (genetic transfer via a virus) or transformation (the collecting of naked DNA from the environment).

Viruses travel, encased in a protein coat, and rely on lysing or budding off their host cell and finding new cells to attach to and enter (or, in the case of retroviruses and lysogens, integrating in the host DNA and being activated later in any of that host’s progeny).

But these plasmids are acting like viruses. The pR1SE (plasmid) encodes proteins that go into the host membrane and allow the membrane to bud into vesicles containing plasmid DNA. These vesicles could then infect more of the archaeal species, plasmid-less members. The plasmids could then replicate themselves in their new host cell.

Besides this just being cool because it’s a way we’ve never seen before of transmitting DNA (and because anything involving archaea in extreme environments is cool), it also may be representative of some early stage of viral evolution.

Viral evolution is a hugely debated topic with no one really agreeing on how viruses came about, whether they evolved many times or once then diversified, which came first in the evolution of life etc., but this does seem to support the idea that at least some groups of viruses may have started as plasmids.

Some people think the obvious answer to viral evolution is gene reduction (a lot of giant virus fans), others think it’s gene addition (what this supports). I think the answer is gradually proving to be both—that viruses have evolved independently many times throughout history, and you could probably find at least a few examples to best support each major theory.

Source:

  1. Susanne Erdmann, Bernhard Tschitschko, Ling Zhong, Mark J. Raftery, Ricardo Cavicchioli. A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells. Nature Microbiology, 2017

2. High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Ricardo Cavicchioli et al. PNAS. 2013

Echinoderms’ deviation from the universal code

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The very strangeness of Echinodermata is partly responsible for the dedication that specialists in the group feel. We revel in their weirdness.
-Rich Mooi

Given that every biology student in the world has been introduced to the standard genetic code, and likely uses it frequently, it is kind of baffling that so few of us ever bother to think much about it. As a longtime lover of systematics/molecular evolution, the knowledge that the “universal genetic code” is not actually universal has always caused me some level of concern when imagining how scientists cope with such an issue or if they even cope with the issue at all.

Usually when you look this up you find a lot of “the code is essentially universal, only a few exceptions have been found” which would imply that maybe one or two extremely obscure microorganisms violated this rule slightly. But mammals mitochondria actually contains four out of 64 codons that do not match the universal code. Echinoderms, yeast, platyhelminth worms, all follow slightly different mitochondrial DNA codes and protozoan and some bacteria even follow different nuclear DNA codes (nuclear being the only DNA bacteria have).

While there are 64 codons, there are fewer than 64 tRNAs, which use an anticodon sequence to recognize a codon on mRNA and carry the appropriate amino acid at the other end. Different tRNAs with the various amino acids will sort of float in and out until the right one’s bound. The third position of the anticodon (the ‘wobble position’) however, binds very loosely to the DNA which is why the tRNA usually relies on recognizing the first two nucleotides. Some amino acids can have multiple tRNAs recognizing them but RNA modifications in the anticodon region of tRNAs can result in the evolution of a deviation to the universal genetic code. The echinoderm’s genetic code evolution is particularly intriguing which is hardly surprising given everything else about them.

A recent Nature paper shows an example of how this works in echinoderms. In echinoderm mitochondrial DNA, the codon AAA, which according to the “universal code” should code for a lysine, actually codes for an asparagine. Analyzing the tRNALys isolated from a sea urchin, they discovered a modified hydroxylated nucleoside; hydroxyl-N6-threonylcarbamoyladenosine. This modified nucleoside adjacent to the anticodon prevents the mt-tRNALys from misreading AAA as lysine, allowing AAA to code for an asparagine.

Mitochondria generally use a codon-anticodon pairing rule that allows unmodified uridine at the anticodon first position to pair with all four nucleotides at the third codon position. When an amino acid only has two codons corresponding to it, the G forms a base-pair with pyrimidine, and modified uridines (5-carboxymethylaminomethyl-uridine being a commonly heard modification to the wobble position base) can discriminate purines from pyrimidines. The presence of a pseudouridine in starfish mt-tRNAAsn in the middle of the anticodon allows the tRNA to decode the AAA codon more efficiently than the unmodified tRNA. Also interesting, the mt-tRNAs possessing anticodons similar to tRNAAsn, but which only decode two codons each (tRNAHis, tRNAAsp and tRNATyr) all possess unmodified U (position 35), further indicating pseudouridine (Ψ35) is important for decoding the three codons.

While certainly not all examples of a modified genetic code work quite this way, it’s intriguing to realize how something generally portrayed as being set in stone, is relatively labile and dynamic.

Given that systematics has favored mitochondrial DNA for many phylogenetic analyses, this could have an effect on the results if using an amino acid alignment or a distance matrix where each amino acid change is weighted a certain amount. You could imagine an alignment between mammals, echinoderms, and reptiles for example, where an AAA to an AAG would be a synonymous mutation (as in, not changing the protein) in mammals and reptiles, but a nonsynonymous mutation (changing the amino acid) in echinoderms, thus deserving a different score. AGA and AGG which both code Arginine in the ‘universal’ code, code for a stop codon in our mtDNA, while our nuclear DNA’s stop codon (UGA), codes a tryptophan. An AUA isoleucine in our nuclear DNA is read as a methionine in our mtDNA. There are likely many more “exceptions to the rule” that we have no idea exist.

Sources:

  1. Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria. Asuteka NagaoMitsuhiro OharaKenjyo MiyauchiShin-ichi YokoboriAkihiko YamagishiKimitsuna Watanabe Tsutomu Suzuki. Nature Structural & Molecular Biology (2017).

2. Tomita, K.Ueda, T. & Watanabe, K. The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondriaNucleic Acids Res.2716831689 (1999).

Inducing cannibalism, “listening” for caterpillars- Plant defense

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To protect themselves from hungry caterpillars, a tomato plant was shown to release chemicals that make it taste terrible to the caterpillars. The chemicals are so upsetting to the caterpillars that they decide to eat other caterpillars instead.

The research team who discovered this, sprayed the tomato plants with methyl jasmonate (which the plants produce in response to stress) to trigger defense mechanisms. The chemical acts as a signal, causing the plant to alter its chemistry, resulting in a plant that was much less appetizing to the caterpillars. The methyl jasmonate also can attract enemies of caterpillars like predators and parasitoids which will eat the herbivores.

So a tomato plant is being eaten by caterpillars and releases a chemical to warn the other plants and the other plants respond by releasing toxins that cause the caterpillars to become cannibalistic and eat each other instead of the plant. So the plants are communicating with one another and working together to alter the behavior of the caterpillar. The result is apparently larger stressed caterpillars nibbling on smaller caterpillars nearby causing some disgusting oozing.

What’s especially disturbing is the caterpillars seem to still revert to cannibalism even when other plant options are nearby. Why disperse farther when you could just eat a closer, unlucky smaller caterpillar I suppose.

Also congrats to that lucky undergrad who helped conduct this research and already got his name on a nature paper.

Listening for munching

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Recording device next to munching caterpillar

In more amazing ways plants are able to ward off caterpillars, some plants seem to even respond to the vibrations of herbivory. the cabbage butterfly caterpillar munching the leaves an Arabidopsis plant results in the leaf moving up and down a miniscule amount. These vibrations were able to be recorded and played back to the plants so the scientists could compare plants left in silence to plants exposed to munching sounds (but no actual physical damage). The plants that were in the presence of the recording of chewing vibrations created an increased amount of mustard oil. Mustard oil is used as a defense against herbivores.

So just listening to the munching even with no caterpillars present somehow makes the plants better able to ward off future attacks.

The plants were exposed to other vibratory sounds none of which triggered any response. They have absolutely no idea how this works but it definitely provides more evidence that plants are amazingly adept to responding to all kinds of stimuli and information in the environment despite having no brains and being underestimated by basically everyone in science who is not a botanist.

Sources:

  1. John Orrock, Brian Connolly, Anthony Kitchen. Induced defences in plants reduce herbivory by increasing cannibalism. Nature Ecology & Evolution, 2017
  2. Plants respond to leaf vibrations caused by insect herbivore chewing. M. Appel, R. B. Cocroft. July 2014

Phytoestrogens aid flightless parrot- Soy will still not give men breasts

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Phytoestrogens are simply plant-derived xenoestrogens (mimics of estrogen). They’re abundant in legumes (soy, notably), but also present in many other plants. Despite their presence in certain plants being touted as scary, I’d say they’re pretty misunderstood.

Phytoestrogens help breeding success of kākāpō, the flightless nocturnal parrot

The darling flightless parrot of New Zealand has a struggling population partly because it only breeds once every few years. They seem to only breed during mast years (when plants produce a ton of edible fruit/seeds) and seek out fruit from the native rimu tree, which suggested the birds breeding success may rely on the presence of phytoestrogens found in the native plants. The hypothesis is that kākāpō don’t produce enough estrogen to make a fertile egg but the phytoestrogens act as supplements.qjjo1oz4sopgxokvcjww.jpg

The scientist conducting this study tested the native plants for estrogenic content and found high levels of phytoestrogens. They looked at the ligand binding region of the progesterone receptor, the androgen receptor, the estrogen receptor 1, and estrogen receptor 2 in four native parrot species, and non-native parrots and compared them with chicken receptors. They found that in most receptors there was more then 90% homology except in the estrogen 1 receptor. Parrot estrogen receptors are actually genetically different, containing an extra 8 amino acids in the hormone binding region, which changes the binding strength to estrogen.

Soy probably pretty good for you

Screen Shot 2017-07-30 at 11.12.05 AM.pngActive compounds of soy include isoflavones- daidzein, genistein, and glycitein. They act as phytoestrogens, a word which seems to frighten some people. A popular belief amongst anti-soy people is that men who ingest too much soy are going to re-enter puberty and turn into estrogen-filled feminized men (heaven forbid).

But this is not really what’s going on.

Phytoestrogens are structurally similar to estradiol so they have the ability to cause either estrogenic or antiestrogenic effects by blocking estrogen receptors. Phytoestrogens have weak estrogen activity in your body, so they may also bind weakly to estrogen receptors. They don’t displace estrogen, they supplement it.

Plants like soy have evolved phytoestrogens to protect from harmful microbes and to help form nitrogen-fixing root nodules.

So the expectation is that they act like antiestrogens in high estrogen concentration environments, and act like estrogen in low estrogen environments.

There are actually a lot of different estrogen receptors in the human body so the same chemical could be and agonist on one estrogen receptor type and an antagonist on another. So the phytoestrogens in plants could trigger an increase or decrease in endogenous estrogen through feedback loops.

It is almost certainly a serious oversimplification to say phytoestrogens are estrogen mimetics. Lots of compounds have partial agonist activity, meaning that at one concentration they are agonists and at a different concentration they are antagonists. It is possible they could affect the different receptors differently.

Reasons to even get excited over Phytoestrogens

Certain hormonal cancer (uterine, prostate, breast etc.) risks could possibly be lowered with phytoestrogen consumption. If they do actually compete with and block estrogen (an antagonist) at estrogen receptors in the breasts, cervix, or uterus, or if they depress estrogen production, they could tend to inhibit estrogen dependent tumors.

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Phytoestrogens may even provide some sort of benefit to women undergoing menopause and experiencing hot flashes, and post-menopausal women at risk for developing osteoporosis and issues in cognitive function which can sometimes be experienced due to dramatic hormone changes.

If phytoestrogens are agonists at estrogen receptors on osteoblasts and osteoclasts they will help reduce osteoporosis. These estrogen receptors are quite different from the receptors on breast tissue.

From a meta analysis on the effects of isoflavones on bone mineral density in menopausal women: “Isoflavone intervention significantly attenuates bone loss of the spine in menopausal women. These favorable effects become more significant when more than 90 mg/day of isoflavones are consumed. And soy isoflavone consumption for 6 months can be enough to exert beneficial effects on bone in menopausal women.”

Soy phytoestrogens are associated with much less negative effects than synthetic endocrine disruptors. And while results of most of these soy studies are dubious—varying with age, level of consumption, and the composition of the individual’s intestinal microflora, soy studies are just as well supported as pretty much any other “eat/drink more of (vegetable, tea, “superfood” etc) and (some health benefit) happens” claims.

While most people tend to be skeptical of simply ingesting a plant and deriving benefits (especially when they are comparing the plant to the highly powerful and concentrated drugs we’ve developed), underestimating and understudying plants has brought about, and continues to bring about, death and illness to plenty of people. So maybe it provides small benefits, but at the very least research does seem to have debunked the myth that soy is dangerous for people.

Constituents of soy if you’re still worried

 

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  • Protein
  • Oil- large amounts of polyunsaturated fatty acids (i.e. linoleic acid (omega 3))
  • Carbohydrates
  • Vitamins and minerals- K, P, Ca, Mg, Fe, B-Vitamins, antioxidants
  • Isoflavones
  • Phytosterols– Disogenin –sterol- is converted to progesterone in body
  • Phospholipids
  • Saponins*- being looked at especially
  • Ferritins- Soybean is a good source of iron
  • Phytic acid
  • Glyceollins- antiestrogen activity
  • Lunasin- peptide

Sources:

  1. Unique oestrogen receptor ligand-binding domain sequence of native parrots: a possible link between phytoestrogens and breeding success. Catherine E. J. Davis A , Adrian H. Bibby A , Kevin M. Buckley A , Kenneth P. McNatty A and Janet L. Pitman. 11 July 2017.
  2. 2014 Jul 7. Do soy isoflavones improve cognitive function in postmenopausal women? A meta-analysis. Cheng PF1, Chen JJ, Zhou XY, Ren YF, Huang W, Zhou JJ, Xie P.
  3. 2003 Jan-Feb. Effects of soy and other natural products on LDL:HDL ratio and other lipid parameters: a literature review. Hermansen K1, Dinesen B, Hoie LH, Morgenstern E, Gruenwald J. .
  4. Soy intake and risk of endocrine-related gynaecological cancer: a meta-analysis. Myung SK, Ju W, Choi HJ, Kim SC; Korean Meta-Analysis (KORMA) Study Group.
  5. Soy intake and cancer risk: a review of the in vitro and in vivo data. Messina MJ1, Persky V, Setchell KD, Barnes S.
  6. 2014 May 28. Effects of isoflavones and amino acid therapies for hot flashes and co-occurring symptoms during the menopausal transition and early postmenopause: A systematic review. Thomas Ismail, Taylor-Swanson Cray, Schnall, Mitchell, Woods
  7. Clinical studies show no effects of soy protein or isoflavones on reproductive hormones in men: results of a meta-analysis. Hamilton-Reeves JM1, Vazquez G, Duval SJ, Phipps WR, Kurzer MS, Messina MJ.
  8. Soy isoflavone intake increases bone mineral density in the spine of menopausal women: meta-analysis of randomized controlled trials. Ma DF1, Qin LQ, Wang PY, Katoh R.
  9. Soy isoflavones for osteoporosis: an evidence-based approach. Taku K1, Melby MK, Nishi N, Omori T, Kurzer MS.

Platypus venom- weird and unique, as expected

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“Do you think God gets stoned? I think so — look at the platypus.”

-Robin Williams

Venom isn’t very special in the animal kingdom, but our anthropocentric mindsets tend to focus more on large mammals than anything else, so to us it seems pretty mystical. Only a dozen or so mammals deliver venom, almost all of which deliver it via a bite for defense or predation. The platypus is unique in that it is so far the only animal known to use venom for a purpose other than defense or predation.

Only the male platypus has venom. And the male platypus only seems to have potent venom seasonally. The season when they have a lot of venom is unsurprisingly mating season, as the males actually use their venom, injected via venomous spurs on their hind legs, for intraspecific competition with other platypus males to keep territories and mates. While technically the echidna has venom, it can’t erect it’s spurs, and simply excretes a milky secretion.

platypus-spur-png.pngTheir venom, though nonlethal, causes excruciating pain for hours or days and is essentially nonresponsive to morphine. Only nerve-blocking agents (or antivenom) can provide relief.

A 2010 study found 83 peptides in platypus venom, many of which resemble venom genes from snakes, sea stars, and spiders. The platypus and reptiles have independently co-opted the same genes for venom usage making the platypus venom a cool example of molecular convergent evolution.

And just so the monotremes can continue to follow their pattern of general nonconformity and being surprisingly different from each other, the echidna venom gland transcriptome looks very different from the platypus one. You can read this post on their weird sex chromosomes for more.

The venom induces Ca2+ influx in cells, which results in neurotransmitter release. Defensin-Like peptides (defensins being immune proteins that usually defend the host from microbes), C-type natriuretic peptides (OvCNPs), nerve growth factor (OvNGF), and hyaluronidase have also been found. These peptides cause muscle relaxation, inflammation by promoting histamine release, and form ion channels in the lipid membranes of cells. The venom also contains a D-amino acid (as opposed to just all L-amino acids, which is the isomer previously thought to be the only conformation manufactured by cells).

First venomous animals were mammals

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Artist interpretation of Euchambersia mirabilis

The platypus having venom and laying eggs isn’t even that weird, as it seems to be that that was the norm for the ancestors of mammals. Euchambersia mirabilis, a therocephalian therapsid from the end of the Permian (~255 mya), which were some of the “almost-mammals” (the term “mammal-like reptile” is horribly outdated and silly but for some reason people still use it), was determined to have venom glands. Venom glands which appeared way before snakes and lizards evolved them, and actually millions of years before any snakes even existed.

bk9781849736633-00001-f1_hi-resSo while venom in mammals is very rare now, it may actually be an ancestral characteristic. Venom relatively expensive to have as it requires some method of injection into another animal, a gland, and then the making of proteins. It’s also suspected to be expensive because the loss of venom in animals that are no longer under pressure to produce any, is very common. Venom has a weak phylogenetic signal—similar types of venom are not necessarily found near each other on a phylogenetic tree, so genetically it seems not very “difficult” for various venoms to arise.

Monotreme venom as diabetes treatment?

The hormone, glucagon-like peptide-1 (GLP-1), is secreted in the gut, stimulating the release of insulin to lower blood glucose. But GLP-1 typically degrades within minutes in humans.

People with type 2 diabetes can’t maintain a normal blood sugar balance, but maybe they could if they had a less rapidly degrading GLP-1.

However in the platypus, there’s conflicting functions of the GLP-1. Not only is it a regulator of blood glucose in the gut, it is also in their venom. This conflict between the two different functions has resulted in the evolution of a dramatically changed GLP-1 system. GLP-1 in monotremes is resistant to the rapid degradation that occurs in other animals, and degrades by a completely different mechanism.

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GLP-1 and diabetes relationship

The function of GLP-1 in the venom seems to have resulted in the evolution of a stable form of GLP-1 in monotremes. Stable GLP-1 molecules can potentially be used as a type 2 diabetes treatment.

Both platypus and echidnas have evolved the same long-lasting form of the hormone GLP-1 despite echidnas not having spurs.

 

Sources:

  1. Kita, Masaki, David Stc. Black, Osamu Ohno, Kaoru Yamada, Hideo Kigoshi, and Daisuke Uemura. “Duck-Billed Platypus Venom Peptides Induce Ca2 Influx in Neuroblastoma Cells.” Journal of the American Chemical Society50 (2009)
  2. Enkhjargal Tsend-Ayush, Chuan He, Mark A. Myers, Sof Andrikopoulos, Nicole Wong, Patrick M. Sexton, Denise Wootten, Briony E. Forbes, Frank Grutzner. Monotreme glucagon-like peptide-1 in venom and gut: one gene – two very different functions. Scientific Reports, 2016
  3. Julien Benoit, Luke A. Norton, Paul R. Manger, Bruce S. Rubidge. Reappraisal of the envenoming capacity of Euchambersia mirabilis (Therapsida, Therocephalia) using μCT-scanning techniques. PLOS ONE, 2017

Cholera- it’s all about the phage

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If, like me, you’ve been reading about the unusually horrific outbreak of cholera in Yemen, you may be wondering how it got so bad. While an understanding of ecology is central to fighting any disease, if feels especially important when discussing cholera, as the current Yemen outbreak is being almost entirely blamed on war resulting in collapsing infrastructure resulting in millions of people losing access to clean drinking water. On top of that, the malnutrition of many children in the area results in them being more susceptible to Vibrio infection.

To add to that, access to rehydration therapy (the common treatment for cholera when intravenous fluids and antibiotics aren’t an option) is low, and the vaccine campaign has been dropped with the justification being that the limited amounts of vaccine would not be as effective in Yemen as they would in areas where less people are infected.

The varieties of Vibrio

The most important vibrio species to human disease are Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae. Vibrio species have flagella and pili which are important virulence factors–notably the toxin co-regulated pilus. The cell walls of Vibrio contain lipopolysaccharides consisting of lipid A (endotoxin), core polysaccharide, and an O polysaccharide side chain. Vibrio can then be divided into serogroups based on this O polysaccharide (200 serogroups in V. cholerae’s case).

V. cholerae O1 and V. cholerae O139 both produce cholera toxin (which causes a rise in cAMP resulting in the cell losing nutrients, which is why you not only need tons of water, but also need to replenish lost electrolytes). These are the serogroups associated with cholera epidemics. Many strains of V. cholerae do not have this toxin and do not cause epidemics though they may still cause illness.

The O1 serogroup is further subdivided into three serotypes: Inaba, Ogawa, and Hikojima. There are then two “biotypes” of V. cholera O1: Classical and El Tor. These biotypes can be further subdivided but let’s just stop here.

The cholera that were famous for killing lots of people in the 1800s were all of the Classical type. The cholera that is responsible for today’s pandemic is of the El Tor biotype.

The CTXφ phage

V. cholerae secretes cholera toxin. This is the toxin that causes the “rice-water” stool (not diarrhea really, as it’s just mucus and water), resulting in dehydration of the host. Colonization of the small intestine required the toxin co-regulated pilus (coded by the vibrio pathogenicity island).PMC3282888_TOMICROJ-6-14_F2.png

The genes for cholera toxin are not in the Vibrio genome unless the bacteria has been infected by a CTXphi (CTXφ) filamentous phage, which inserts it’s genome into the V. cholerae genome. The CTXφ can transmit cholera toxin genes from one V. cholerae sstrain to another (via horizontal gene transfer).

Infectious CTXφ particles are produced when V. cholerae infects humans. Phages are then secreted from the infected bacteria without lysing the cell.

Seasonal epidemics inversely correlated with environmental cholera phage presence

Cholera seasons usually make sense as they tend to coincide with monsoon season. But perhaps less obvious (or totally obvious if you’re into viruses) cholera phages have a very dramatic influence on seasonality.

The presence of viruses infecting V. cholerae O1 or O139 inversely correlates with the occurrence of viable V. cholerae in the environment and the number of cholera cases. Both epidemic and nonepidemic serogroups have been shown to sometimes carry lysogenic phages which reproduce and kill epidemic strains. Lysogenic phages integrate into the genome so it replicates with every reproduction of the bacteria

One common O1 phage can use several V. cholerae non-O1/non-O139 strains as alternative hosts.

Having alternative hosts present combined with the lysogenic V. cholerae strains can result in a cholera phage “bloom,” thus lowering the transmission of phage-sensitive, more virulent cholerae strains.

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Concentration of lytic vibriophages in the aquatic environment of Dhaka, Bangladesh, and the estimated number of cholera cases. From Faruque et al 2004.

Phage and Vibrio waves controlling epidemics

 Cholera outbreaks occur in waves with different serogroups dominating at different times.

The absence of one phage specific for one cholerae type provides an opportunity for that serogroup to begin the seasonal epidemic. However, the phages for that serotype will eventually amplify in the environment and attack this serogroup, ending that epidemic.

A different cholerae serogroup would then be resistant to that first phage or carry it as a prophage in the genome—so it isn’t killing that bacteria. A second epidemic wave from the new dominating serogroup can now occur until phages specific to this new serotype bloom, thus ending the epidemic.

Some serotypes will be resistant to all the phages that were killing the virulent phages in the environment, and these serotypes will occupy the interepidemic periods. These strains usually lack typical virulence factors that would make them particularly good pathogens, but are instead more environmentally adapted than the other more virulent strains.

These resistant serotypes may ALSO harbor prophages—phages integrated in the genome—which kill virulent serogroups and may pick up virulence factors via horizontal gene transfer.
If this happens, new serotypes that were previously not very virulent may emerge as the new epidemic serotype.

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Vibriophage

Self-limiting seasonal epidemic also probably caused by phage

A naturally occurring lytic phage, JSF4 (lytic meaning it simply lyses the cell), infects and kills Vibrio that are sensitive to it.

In a study from 2005, it was shown that the peak of cholera season was preceded by a peak in V. cholerae presence which was then followed with a peak in JSF4 phage presence as the epidemic ended. JSF4 phages would then also be excreted in the diarrhea of sick cholera patients. So the patients at the end of the epidemic end up ingesting both a lot of V. cholerae as well as JSF4 phage which kills the bacteria. The increase of phage results in the decrease of V. cholerae and the epidemic ends.

This is likely why outbreaks are self-limiting.

V. cholerae O139 spread by turtles

Screen Shot 2017-07-14 at 12.56.28 AM.pngWhile O1 causes the majority of outbreaks, O139 is confined to Southeast Asia. Recently however, it’s been discovered that soft-shelled turtles in China are big carriers of O139. While a lot of aquatic animals spread cholera, the soft-shelled turtles have been definitively linked to human disease and make excellent hosts as they are unaffected by the bacteria which clings to many of their surfaces and intestines. These turtles are then consumed by people, to spread more cholera to new unsuspecting hosts. If turtles being cute wasn’t a good enough reason to stop eating them, maybe this is?

Sources:

Jiazheng Wang, Meiying Yan, He Gao, Xin Lu, Biao Kan. Colonization of Vibrio cholerae on the Soft-shelled Turtle. Applied and Environmental Microbiology, 2017

Faruque, S. M., I. B. Naser, M. J. Islam, A. S. G. Faruque, A. N. Ghosh, G. B. Nair, D. A. Sack, and J. J. Mekalanos. “Seasonal epidemics of cholera inversely correlate with the prevalence of environmental cholera phages.” Proceedings of the National Academy of Sciences 102.5 (2005)

Faruque, S. M., M. J. Islam, Q. S. Ahmad, A. S. G. Faruque, D. A. Sack, G. B. Nair, and J. J. Mekalanos. “Self-limiting nature of seasonal cholera epidemics: Role of host-mediated amplification of phage.” Proceedings of the National Academy of Sciences 102.17 (2005)

Murray, Patrick R., Ken S. Rosenthal, and Michael A. Pfaller. Medical microbiology. Philadelphia, PA: Mosby/Elsevier, 2016.

A microbe manipulating sex- and how it can fight Zika

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A fan favorite, and probably the most successful genus on the planet–at least on land—the bacteria, Wolbachia infects an estimate between 40 to 65% of all arthropod and nematode species. This microbe is constantly drifting across the line between mutualist and parasite to it’s host. Some hosts are unable to survive and reproduce without a Wolbachia infection whilst others are killed by it.

Wolbachia as a mutualist

Plenty of species have become reliant on this microbe. The caterpillar of the spotted tentiform leaf miner uses Wolbachia to create green islands on yellowing leaves which remain fresh for munching on.

It provides a benefit to certain nematode worms, such as Brugia malayi and Wuchereria bancrofti which cause elephantiasis, and which cannot survive without a Wolbachia infection. Image1.jpg

Some Wolbachia bacteria provide metabolic advantages to their hosts such as in bed bugs who use it to synthesize B-vitamins that are absent in their blood meals. Wolbachia can even mediate iron metabolism in Drosophila.

But most exciting given the recent explosion of flavivirus infections (Zika traveling farther and farther north every summer for example), Wolbachia provides flies with resistance to many RNA viruses.

Wolbachia as a sex-determinator

In leafhoppers, Zyginidia pullula, females have two X chromosomes while males have only one X chromosome, yet when infected with Wolbachia, the X0 genetic males appeared to be female.

Some females of the Japanese butterfly, Eurema mandarin have a sex chromosome system where the males are (ZZ) and the females are (ZWEurema_blanda_on_flower_by_kadavoor.JPG). This incongruence between chromosomal and phenotypic sex can be explained by feminization of genetic males induced by Wolbachia. Two strains of WolbachiawCI and wFem, have been found in E. mandarina and the females having male chromosomes (ZZ) are consistently infected with both wCI and wFem. However females with only wCI are true females (ZW). Despite having male chromosomes, ZZ females are physically female and fully fertile.

A similar thing happens in woodlice (pillbugs? Roly-polys?), where all the ZZ males infected with Wolbachia develop as female. The W chromosome is sometimes lost entirely in these populations and sex is entirely determined by presence or absence of Wolbachia.

Who needs males?

Wolbachia has evolved into an intracellular parasite, and while it can infect many different organs, it is most famous for infecting the testes and the ovaries. Wolbachia are too large for sperm, but fit nicely into mature eggs so the infection is inherited maternally through the eggs.

So now the evolutionary dilemma that keeps Wolbachia on the balance between parasite and mutualist is, if males are an evolutionary dead-end, how does this intracellular parasite that needs its host to survive and reproduce, and it’s host species to continue thriving, evolve to both spread throughout populations but not allow evolutionary cheater strains to ruin everything? Wolbachia has developed numerous ways of targeting males to help itself spread such as:

  • Male killing- infected male larvae die, so more infected females are born
  • Feminization- where infected males develop as females or infertile pseudofemales
  • Parthenogenesis- when females reproduce without males
  • Cytoplasmic incompatibility (CI)- when Wolbachia-infected males can’t successfully reproduce with uninfected females or females infected with another Wolbachia strain.CI-causing Wolbachia interferes with the chromosomes during mitosis so they no longer divide in sync.

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Warren et al, 2008, Nature Reviews, Microbiology.

Mosquitos carrying Wolbachia have a higher reproductive success when present in a population with mosquitoes not carrying Wolbachia. When a male mosquito carrying Wolbachia tries to mate with a female who is not carrying Wolbachia, the female’s eggs won’t hatch. However females with Wolbachia do not have this issue and produce perfectly healthy offspring which are all also carriers of Wolbachia. So you can imagine how the Wolbachia is able to sweep through a mosquito population. The female Wolbachia carriers have a much higher fitness than the non-carriers.

Scientists have taken advantage of this evolutionary strategy in fighting mosquito-transmitted viruses such as Dengue and Zika. The Aedes aegypti, a black-and-white striped species of mosquito infects people with Dengue virus which has no vaccine or real treatment and causes pains, fevers, rashes, and headaches. A plan (credited to evolution/ecology biologist, Scott O’Neill) to release Wolbachia infected mosquitos into the wild to lower dengue spread is becoming more and more popular. Wolbachia stops Aedes mosquitoes from carrying degue virus. Wolbachia carrying females have a selective advantage and should sweep through the population.

Wolbachia to rescue us from Dengue (and others?)- The original plan

An unusually virulent strain of Wolbachia the ‘popcorn’ strain, essentially halves the mosquito lifespand (it’s pretty gruesome, the bacteria essentially reproduce like crazy in the brains, eyes, and muscles filling up neurons). Dengue takes a long time to be able to reproduce and make it to the salivary glands so it can be transmitted, so only older mosquitos can transmit it.

Unfortunately Aedes (and Anopheles which transmist malaria) are not natural hosts of Wolbachia infections, so Scott O’Neill carefully developed a new symbiosis by injecting eggs. This took forever to work, until one lucky grad student was able to make it a success. Finally, an egg was stably infected and a line of Wolbachia-carrying Aedes was created. But after all that work, the strain was too virulent and the females did NOT have a selective advantage and actually had lower numbers of eggs with lower viabilities (honestly, they should have seen this coming really).

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But none of that even ended up mattering because some other scientists figured out that Wolbachia stops dengue virus from replicating. Simply the presence of a nonvirulent strain of Wolbachia in the population was enough to stop the spread of dengue. So the team switched to a less virulent strain, wMel, and successfully started a line of wMel carrying Aedes mosquitos.

wMelwAlbB update and some critiques of the data

As amazing as Wolbachia is, it will take at least a few years to get significant results and many years to eliminate any particular mosquito-transmitted pathogen with this method. Some papers say Wolbachia was able to make not only dengue, but also Plasmodium and other flaviviruses less able to replicate, but others said the opposite. It would be kind of important to figure out how the Wolbachia is inhibiting the virus because no one seems to agree if it’s general or specific. But now with significant selective pressures on all these diseases I’d suspect it’d be easy to switch host vectors because mosquitos bite hosts, geographically spreading infections very far (potentially) exposing the virus to a wide variety of new potential hosts vector species.

In a 2016 paper looking at the progress of the wMel strains, they collected Ae. Aegypti after one year and it continued to have low levels of dengue (which implies it was passed around through tons of mosquitos and not a whole lot of apparent evolution has taken place in terms of resistance) but what if the some of the dengue viruses switched species?

They could try passing the dengue through many mosquitos perhaps in a mixed host population. Or basically just try to provide the virus with as many opportunities as you can for it to evolve in the hopes that you may understand potential mechanisms the different diseases may have to get around this one Wolbachia infected species of vectors.

While the paper shows wMelwAlbB, the superinfection, that strain of Wolbachia actually doesn’t appear to inhibit DENV very much. But later in the paper, it’s very dramatically different so it’s difficult to say if the data is actually supporting that the superinfection sweep will work.

As far as how they ensure the right strain is dominating all the time given selective pressures towards different mosquito sex alteration methods, that remains unanswered. Combined male-killing CI strains readily become extinct following invasion so CI strains are more selected for but sex-ratio distortion decreases male infection and therefore reduces the occurrence of CI meaning that you might expect selective pressure for evolution from CI to CI/sex ratio distortion to sex ratio distortion only.

Wolbachia’s potential

Using Wolbachia’s ability to stop mosquitos from carrying Zika, Dengue, Chikungunya, Plasmodium—the parasite responsible for malaria, may mean the eventual elimination of these diseases in humans.

It may even be used to someday stop nematode worms from causing blindness, disability, elephantitis etc in many millions of people every year.

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Particularly inspiring about this story is how ecologists and evolutionary biologists ended up being the ones to figure out a way to eliminate viral infections. Yet more evidence that pre-med students or medical researcher hopefuls shouldn’t blow off biodiversity/ecology/evolution classes in college.

Sources

Kageyama, Daisuke, Satoko Narita, and Masaya Watanabe. “Insect Sex Determination Manipulated by Their Endosymbionts: Incidences, Mechanisms and Implications.” Insects 3.4 (2012): 161-99.

I contain multitudes: the microbes within us and a grander view of life. Ed Yong, 2016

Bacterium offers way to control dengue fever. Natasha Gilbert – Nature – 2011.

Establishment of a Wolbachia Superinfection in Aedes aegypti Mosquitoes as a Potential Approach for Future Resistance Management. D. Joubert-Thomas Walker-Lauren Carrington-Jyotika Bruyne-Duong Kien-Nhat Hoang-Nguyen Chau-Iñaki Iturbe-Ormaetxe-Cameron Simmons-Scott O’Neill – PLOS Pathogens – 2016

 

 

Homosexuality in animals

bottlenose_dolphin_1249780c.jpg Since it’s pride month, I thought the evolution of homosexuality warranted some attention. It turns out homosexuality is common throughout the animal kingdom, while homophobia is only seen in one species.

While sexuality is complex and seems to have a lot to do with epigenetics, as well as conditions in the uterus during fetal brain development, this variety is not limited to humans. Instead of thinking of humans as unique and separate from other animals, try to consider that brains, social structure, and cognitive ability exist on a spectrum with humans simply sometimes possessing a “higher degree” of whatever special unique thing we think we have. Such as love and sexuality. Homosexuality is especially common in primates and marine mammals (it’s correlated with intelligence in species). Same-sex relationships amongst animals strengthen social structures and can be particularly useful in systems with a lot of parental care, systems where the females outlive the males (humans?), and systems where not all males get an equal number of mates. Bottlenose dolphins for example are well-known for their bisexual behavior which strengthens social bonds.

When talking about homosexuality in nature, brief periods or episodes of homosexuality are actually pretty common. Male dominance mating (which is very common in giraffes), isn’t really “true homosexuality” because the males do not form any kind of bond, and the males will usually mate with females if they can. Cases of males or females rejecting the opposite sex and forming permanent pair bonds is more rare but absolutely happens.

Female-female couples

Young-albatross-female-couple-02.jpgA classic female-female coupling that actually makes a lot of evolutionary sense from a reproductive point of view, is the Laysan Albatross. The Laysan Albatross is monogamous and mates for life, and almost a third of the parent pairs are both female. This is useful as sometimes males will mate with more than the just their one female mate (basically he cheats on her in the hopes of making more offspring) and as the Albatross has evolved to require high parental care from both parents, female-female parents are actually a necessity in many cases where the father is absent.

Macaques are also rather known for their “lesbianism,” which in this case, has nothing to do with parenting and more to do with them just preferring sex with other female macaques. The males just can’t keep up.

Not all dominant mounting is males

While males mating with other males is very common, scientists have sometimes argued that a lot of that “mating” is simply the males exerting dominance over each other. Females do it to though, especially in the case of the female spotted hyenas who live in a matriarchy. The female hyena is even larger and more terrifying than the male hyena and leads the family.

Rams

gay-rams.jpgA study of gay sheep, was actually pretty historical as it really confirmed that there is a biological basis for sexual preference in animals. Sheep do seem to have a much higher rate of homosexuality than other animals where as many as 1 in 10 rams can be gay. Rams have undergone a lot of selective breeding which may provide some evidence that genes are involved in sexual preference. A region in the hypothalamus which is generally much bigger in rams than in ewes was found in gay rams to be the same size as the female’s. The hypothalamic region size variations affected levels of aromatase, an enzyme which converts androgens into estrogens. This supported the theory that hormones present during fetal development plays a role in determining sexual preference.

Bonobos

Bonobos are so closely related to us that it hardly seems worth it to mention them, but they are fascinating none the less. They exist in a peaceful (compared to chimps and humans) matriarchal society where sex occurs between basically every pairing you can imagine, excluding close family members (evolution doesn’t favor inbreeding). If you want to learn more about these super gay cousins of ours, I highly recommend primatologist, Frans de Waal’s books. He’s basically the top authority on bonobo sex. Really the best of the best.

Adoptive gay vulture dads
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In what may be one of the cutest stories I’ve read all year, two male griffon vultures from Amsterdam have recently been given the opportunity to raise a chick together. These two males are long-term mates who had been building nests together for months but were unable to produce an egg together (obviously). The zookeepers remarked that it was unfortunate as they were one of the most devoted culture couples observed.

Vultures are monogamous and have biparental care systems, so the males together could still make great parents. When a vulture egg was abandoned, and no heterosexual vultures would agree to incubate it, they gave the egg to the long-term male couple. The males ended up being very enthusiastic helicopter parents, proving that they could successfully hatch an egg even without a female helping. They carefully took turns incubating it, and when it hatched they proved to be protective, loving parents. The fathers have split their jobs equally, taking turns caring for their baby, looking for food, defending the nest, and feeding the baby.

Gay Penguins

Possibly the most famous gay couple in the animal kingdom is the penguin couple from the central park zoo, Roy and Silo. The two chinstrap penguins, where internationally celebrated for successfully hatching and caring for an egg they were given. Their caretakers noticed that they engaged in mating behaviors with one another and seemed to instinctually want an egg of their own, once seeming to try and hatch a rock that resembled an egg. Other gay penguin couples have been observed actually trying to steal eggs from other penguins, a behavior that’s not uncommon in heterosexual penguins either. Penguins typically engage in multiple long term relationships (kind of like humans do), and interestingly, many of them will switch around between male and female partners in their lifetime.

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sources

Oregon Health & Science University. “Biology Behind Homosexuality In Sheep, Study Confirms.” ScienceDaily. ScienceDaily, 9 March 2004.

Our Inner Ape, Frans de Waal

Polyploidy in tetrapods

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African Clawed Frog

Polyploidy is the condition where an organism possesses more than two sets of chromosomes. Most people probably only associate it with plants, as polyploidy in animals has been relatively understudied, and unisexuals—animals that are entirely female, are typically ignored because they use hybridization and parthenogenesis (though personally I think it may be male refusal to accept that they aren’t as permanent or resilient as they may have hoped—see the degenerate Y chromosome). The most famous female-only species are probably the New Mexico whiptails, Cnemidophorus neomexicanus, or “lesbian lizards,” a hybrid species of lizard that no longer involves males in their reproduction but still often perform courtship rituals to stimulate ovulation.

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Females perform courtship rituals to stimulate ovulation. Nature is amazing.

Both parthenogenesis (when eggs develop with no fertilization) and hybridogenesis (fertilization occurs but paternal DNA isn’t passed on) are pretty common in amphibians. A more intriguing example than the lizards, though one that’s gotten less press until now, is the unisexual Ambystoma hybrid salamanders. This salamander ranges from triploid to pentaploid with Ambystoma nothagenes using genes from males from three different salamander species– Ambystoma lateraleAmbystoma texanum, and Ambystoma tigrinum.

The Ambystoma females always require sperm from a related species to fertilize their eggs and initiate development and generally just discard the sperm genome. Sometimes the unisexual sexually reproduces instead and there is a genome addition or genome replacement event where the maternal genome is discarded or the female acquires the male’s genes and then keeps only some of the genes after mating.

What’s kind of intriguing about this case of “kleptogenesis”, or gene stealing, is that the females basically express genes from the different males at a relatively equal rate. How exactly they choose which genes to use and which to throw away is not known, nor is how these genes come together to make a good hybrid.

Why do it? 

How Ambystoma, a six-million-year-old lineage, and how other polyploids/unisexuals/hybrid species survive when in competition with “regular” diploids living in the same spatial niche, is also not understood. It’s generally considered that polyploidy is a short-term strategy evolved in environments that are less stable. Which is why Ambystoma being a polyploid for so long is especially surprising.

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Ambystoma, female polyploid

While polyploidy can be advantageous, it’s initially unstable before becoming a competitive strategy. The presence of duplicated genes can help fuel diversification and evolutionary success.

Heterosis, gene redundancy, and asexual reproduction can all be considered advantages of polyploidy. Heterosis is essentially the ability to make better use of heterozygosity. Gene redundancy allows you to better diversity and provides a protection from harmful mutations. And asexual reproduction enables you to reproduce without a sexual mate around.

Polyploidy in animals is a case of convergent evolution where many fish and amphibians have acquired it separately. All the polyploids have acquired their genomes differently and in different ways. The unisexuals and males in the salamander group have higher gene exchange than other polyploids which may explain the “balance” in the genome not seen in other polyploids. Instead of gene silencing or dominance evolving, it seems natural selection has favored a more balanced genome because that’s just what worked for these girls. If you lose some gene contribution it’s less dramatic this way than if you’d put almost everything into one male salamander only for him to do something inconvenient like die or not show up to mate.

Faster regenerators

There’s some serious selective pressures for salamanders to survive injuries. They have the ability to regenerate tissue, so if part of their tails snap off, they can grow back. A study published in the Journal of Zoology showed that these polyploid all-female salamanders regenerate lost tissue 36% faster than other salamander species.

Within 10 weeks, after having had 40% of their tails cut off, the all-female salamanders had full length tails. The diploid sexually-reproducing relatives needed another 5 weeks to finish growing their tails.

The explanation may have to do with more genes meaning more proteins meaning faster regeneration. And if you can’t regenerate you don’t do so well so this could have been an added pressure to explain how this lineage was able to stay polyploid for six million years.

Sources:

  1. J. Saccucci, R. D. Denton, M. L. Holding, H. L. Gibbs. Polyploid unisexual salamanders have higher tissue regeneration rates than diploid sexual relatives. Journal of Zoology, 2016;
  2. Comai, Luca. “The advantages and disadvantages of being polyploid.” Nature Reviews Genetics11 (2005)
  3. Kyle E. McElroy, Robert D. Denton, Joel Sharbrough, Laura Bankers, Maurine Neiman, H. Lisle Gibbs. Genome Expression Balance in a Triploid Trihybrid Vertebrate. Genome Biology and Evolution, 2017
  4. Evolutionary Significance of Whole-Genome Duplication. Mcgrath-M. Lynch – Polyploidy and Genome Evolution – 2012

The struggle against antibiotic resistance

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“Animals may be evolution’s icing, but bacteria are the cake.” –Andrew Knoll, Life on a Young Planet

Rapid evolution of multi-drug resistant bacteria due to overuse of antibiotics is one of the biggest threats facing humans today. Luckily scientists, motivated by terror of a superbug killing us all, have been working pretty hard recently on trying to solve this problem.

Teixobactin

A new class of antibiotics was discovered with the help of a new device, the iChip. Humans have been unable to figure out how to isolate and culture most (99%) of the Earth’s bacteria, but the iChip was successfully used to culture previously unculturable soil bacteria, notably Eleftheria terrae. This bacteria was found to produce Teixobactin, an antibiotic that micorbes have an exceptionally difficult time evolving resistance to (like, so difficult none have been able to do it yet). Because most antibiotics are usually discovered by accident via fungi or other microbes, being unable to culture most of what was in the soil has been a pretty big barrier in our search. Teixobactin is active against gram-positive bacteria and works by inhibiting cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). Peptidoglycan is what makes up the thick walls of Gram-positive bacteria. Gram-negative bacteria also have peptidoglycan but in much smaller amounts and are protected by a second outer membrane which Gram positive bacteria do not have.

Screen Shot 2017-06-06 at 8.38.59 PM.pngStaphylococcus aureus (MRSA/VRSA) and Mycobacterium tuberculosis (TB), two ofthe biggest names in the antibiotic resistance crisis, were both killed by and unable to develop resistance to, Teixobactin.

Teixobactin is probably more robust against mutations of pathogens, because of its antibiotic mechanism is so unusual. Most antibiotics involve binding to relatively mutatable proteins. Teixobactin however, binds to much less mutatable fatty molecules.

Vancomycin 3.0

Vancomycin has been in use since 1958 and was once considered a last-resort drug because it seemed bacteria were not very good at developing resistance to it but it’s a pretty serious drug. It has a higher toxicity level than most antibiotics you’d usually be prescribed so it is used only for the treatment of life-threatening Gram-positive infections. It kills bacteria by preventing cell wall synthesis by binding to peptides ending in two copies of D-alanine. Unfortunately bacteria were able to replace a D-alanine with a D-lactate (D-lac). Scientists decided to fix this by creating a new vancomycin that binds to peptides ending in D-ala and D-lalc. Other scientists came up with ways to manipulate vancomycin to kill cells by stopping cell wall synthesis in a new way or causing the outer wall membrane to leak.

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The new vancomycin, vancomycin 3.0, has three antimicrobial targets in one antibiotic. It was shown to be effective against vancomycin resistant Enterococcus (VRE) and vancomycin resistant Staphylococcus (VRS). A three-pronged approach presumably means that for a bacterium to be resistant, it would have to have three non-lethal mutations to get around this drug.

Phage-therapy

Bacteriophages, viruses that infect bacteria, are also being used as a method to treat bacterial infections. While this concept is not especially new, it’s been relatively neglected by the U.S.. Phage therapy would take a long time to get FDA approval and it still needs a lot more research. The coevolution of bacteria and bacteriophages, while certainly studied a lot in model organisms, is an important factor to consider when blindly expecting phage therapy to work. The nice thing about phages over antibiotics, is that antibiotics can sometimes have unpleasant side-effects, cause allergic reactions, or have high toxicity to the people/animals taking them. Phage are harmless and extremely specific to their targets, unlike broad-spectrum antibiotics. However phage are huge spreaders of antibiotic resistant genes as they are relatively important engagers in horizontal gene transfer (where genes, instead of being inherited, are picked up and incorporated into a genome via viral infection or collection of raw DNA).

Phage therapy saves man with multidrug-resistant infection

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credit:  Dr Graham Beards
 

In 2015, a four-phage cocktail was administered to target a man with a serious Acinetobacter baumannii infection which had been causing hallucinations and was killing his kidneys. This was the first instance of phages being used intravenously to treat someone almost dead due to an infection caused by a drug-resistant bacteria. Luckily he was married to a genius woman who happened to be an infectious-disease specialist and decided a phage-cocktail was his best bet. It was difficult trying to find the right bacteriophages but it worked in the end.

The Gram-negatives

One of the biggest struggles in finding new antibiotics is Gram-negative bacteria are often intrinsically resistant to antibiotics because their outer membrane is impermeable to large glycopeptide molecules, and so many antibiotics seem to target the cell wall.

Some Gram-negative bacteria that can cause pretty serious infections include Klebsiella (pneumonia, blood, wound), Acinetobacter (pneumonia, blood or wound infections), Pseudomonas aeruginosa (burns, wounds, respiratory), E. coli, Vibrio (Cholera), Yersinia pestis (“the plague”), and Neisseria gonorrhoeae (gonorrhea).

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Neisseria gonorrhoeae

Luckily, a lot of these don’t usually infect people (the first three basically never infect healthy people), however antibiotic resistant sexually transmitted diseases are actually on the rise in the United States and could become a very serious and difficult to control problem pretty rapidly. Gonorrhea’s not really a big deal if you catch it early and treat it, but it’s asymptomatic in many people (making them untreated, unknowing carriers) and left ignored, causes infertility and pelvic inflammatory disease.

So even though we might feel relief at these new discoveries, keep in mind that no antibiotic will work on all bacterial pathogens, and allergies to antibiotics are very common so we can’t just be left with a single last-resort. We kind of need a lot of options.

Sources:

  1. Okano, Akinori, Nicholas A. Isley, and Dale L. Boger. “Peripheral modifications of [Ψ[CH 2 NH]Tpg 4 ]vancomycin with added synergistic mechanisms of action provide durable and potent antibiotics.” Proceedings of the National Academy of Sciences (2017)
  2. “A new antibiotic kills pathogens without detectable resistance.” Ling et al (2015)

 

Coleoids exhibit unusual RNA editing

“It is widely known that the interestingness of an animal is proportional to how difficult it is to figure out where its butthole is. The octopus is therefore, very interesting.” -Zefrank1, True Facts About the Octopus

Coleoids, an evolutionary mystery

Squid, cuttlefish, and octopi are always intriguing to people because they represent the only branch other than vertebrates which have developed sophisticated behavior and intelligence. Them being much more closely related to oysters, and us being more closely related to sea cucumbers is pretty amazing. So seeing as understanding the cephalopod brain is the closest we could get to meeting an intelligent alien, it’s understandable these creatures are so popular even outside of career mollusk experts (the dream job).

The evolutionary journey to ridiculous intelligence might have involved exhibiting an unusual amount of RNA editing—about half their transcribed genes. The type of RNA editing the scientists are talking about is generally Adenosine to Inosine which behaves like a G nucleotide. This can have effects including altering the protein being translated, any secondary RNA structures, splicing, miRNA and siRNA, sequestration (localization), and heterochromatin formation.

RNA editing is a relatively undiscussed phenomenon because in almost every other animal, it doesn’t seem to amount to much that we can observe. Usually RNA editing does not result in codon changes, so observable protein changes. While RNA processing such as splicing and 5’ capping is common in eukaryotes, RNA editing to expand the proteome is not. Cephalopods however, use the edited RNA to make new proteins. So one octopus gene may produce many proteins as opposed to just one.

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Liscovitch-Brauer et al 2017

 

What makes people think it may be linked to their intelligence is that the RNA editing most often occurred in genes related to nervous system functions. Many of the RNA edits occurred in proteins controlling neural circuits and nerve cell excitability. And, especially cool, the Nautilus (a shelled cephalopod which has a smaller brain, less sophisticated nervous system and is not known for its intelligence), did not exhibit as high rates of RNA editing as the other cephalopods.

Why RNA editing?

It was previously shown that an octopus living in the Antarctic was able to adapt and survive the freezing temperatures via RNA editing to alter their potassium channels. Potassium channels which open and close during neuron firing, basically slow down in the cold so an RNA edit that resulting in a slightly different protein which performed better in the cold, was selected for. If RNA editing is so useful then why don’t more things do it all the time? The conservation of the flanking editing sites indicates a selective advantage, however this sophisticated RNA editing comes at an evolutionary cost of significantly slowing down mutation rate. Because so many sites are nonsynonymously edited the surrounding sequence conservation dramatically reduces the number of mutations and genomic polymorphisms in protein-coding regions. Essentially mutations occurring at an editing site, it can’t be edited anymore and so there’s more pressure to conserve sites.

We could think of it as strange that they evolved advanced RNA-editing, or maybe they just found a nice alternative to waiting around for mutations to fix in a population like we do, when they had those tentacles with minds of their own and those incredibly giant brains to fine-tune.

  1. RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses. Garrett-J. Rosenthal – Science – 2012
  2. Liscovitch-Brauer et al. Trade-off between transcriptome plasticity and genome evolution in cephalopods. Cell, 2017 DOI: 10.1016/j.cell.2017.03.025

by Irene Hoxie

Venezuelan equine encephalitis outbreaks- convergent evolution of a single amino acid substitution

Venezuelan equine encephalitis virus (VEEV) is a nasty virus in horses that causes CNS disorders, resulting in a high biphasic fever, decreased appetite, depression, lethargy, ataxia, stumbling, and in severe cases, nonsupperative meningoencephalitis. So basically, it’s a horse farmer’s nightmare. If it does manage to infect people it just causes some flu-like symptoms and then it’s over, but in horses it can spread through a herd and kill them all.

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Ecology of VEEV

VEEV continuously circulates by having an enzootic and epizootic strain where the enzootic strain passes through rodents and causes no viremia in horses. It is specific to the Culex mosquito and circles continuously in the rodent population relatively unnoticed by anyone.

Screen Shot 2017-06-01 at 5.38.25 PMBut every decade or so, epizootic strains emerge. These are not specific to a particular mosquito and cause viremia in horses, the amplifier for the epizootic strain. Subtypes of VEE and density of mosquito populations, as well as herd immunity determine how fast the disease will spread.

Serotypes IAB and IC are virulent in horses and produce high virus titers (epizootic).

A study that looked at the history of these outbreaks found there has been convergent evolution from the enzootic ID lineage.

Researchers identify key to epizootic VEEV

A study from 2006 (which in science time is forever ago, but which probably didn’t get the attention it deserved with the general public) wanted to identify mutations mediating emergence of epidemic serotype. They suspected that the origin of all epidemic strains involves enzootic strains and that these strains alter their serotype to induce high-titer viremia sufficient to be amplified in equines. Viruses usually have very small genomes which only contain a small number of proteins. Changing an amino acid can dramatically alter the way a protein may fold or interact with a receptor, so viruses that circulate in a reservoir, and then emerge as epidemics, could be the result of a small number of genetic changes.

2006 study

In this study, they performed phylogenetic analysis of alphaviruses in the VEE complex to determine genetic differences between the most recent ID strain before 1992-1993 outbreak, and the epidemic IC strain from the 1992-1993 outbreak. They then used reverse genetic approaches to recreate hypothetic emergence of a 1992-1993 outbreak and measured viremia titer and virulence.

They found that the key amino acid changes allowing for an epizootic outbreak were a glycine to an arginine at position 193 in the E2 envelope protein, and a threonine to an arginine at position 213 of the E2 envelope protein.

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E2 positive charge mutations have accompanied all epidemic emergences, so they tested these two mutations by making a clone of the “enzootic/epizootic border strain” ZPC738 and added either both mutations, or each one separately.

They found the Gly-193à Arg mutation had no effect on mAb reactivity; enzootic-specific Ab still reacted against strain ZPC738. The Thr-213àArg resulted in antigenicity change from enzootic (mAb 1A1B-9-reactive) to epidemic (1A3A-5-reactive). The Combination of both also resulted in IDàIC serotype change. Individual Arg substitutions had little effect on plaque size, but a combination of both resulted in plaques characteristic of epidemic strains

They ZPC738 clone had a low viremia as expected and the Arg-193 viruses did not produce detectable viremia with no disease seen. The Arg-213 virus however, increased virulence and viremia with the neurological disease and viremia titer consistent with epidemic phenotype.

The double mutant (Arg-213 and Arg-193) produced higher viremia 24hrs after infection but lower viremia 36-48hrs post infection.

The takeaway was that epidemic serotype IC VEEV can arise from a single mutation in enzootic serotype ID. Residue 213 responded to positive selection, and Arg substitution induced high-titer equine viremia. The high titer (104 to 106) and high mutation rate (on the order of 10-4 mutants/nucleotide) means RNA viruses likely have a mutation to be more virulent, broaden tropism, broaden host range, etc. at any given time. Which is terrifying to think about.

RNA virus evolution too often ignored in “vaccine wars”

This study shows the barriers for an outbreak are ecological conditions. Enzootic strains circulate continuously, so vaccines should continue to be used even when there’s no outbreak, which unfortunately often doesn’t happen because people don’t see the point in spending money on a vaccine if nobody’s horses are getting sick.

This paper or at least a summary should certainly be shown to more people as it provides direct evidence of just a single amino acid substitution causing an epidemic and is a great argument for continuing to vaccinate, even if a disease is not common anymore (because maybe it’s not common because the vaccine is stopping it from becoming an epidemic in humans). In the vaccine wars amongst humans, RNA virus evolution and ecology as well as RNA zoonosis is weirdly too often left out of the discussion.

Source: Venezuelan encephalitis emergence mediated by a phylogenetically predicted viral mutation. 2006. Michael Anishchenko, Richard A. Bowen, Slobodan Paessler, Laura Austgen, Ivorlyne P. Greene, and Scott C. Weaver

Multicomponent virus in mosquitoes

Animal viruses typically have a non-segmented genome all packaged together in one particle. Sometimes animal viruses, such as influenza, have a segmented genome—where the genome is cut up into separate pieces—but still, it is always packaged together in one viral particle. This means one particle is all that’s needed to infect a cell. In multicomponent viruses, the genome is split up into multiple pieces AND packaged separately. In this scenario, multiple viral particles must infect one cell.

This setup is not uncommon in plants, although usually there’s only two MAYBE three particles to one virus. But members of a newly described group of animal viruses can have five components.

Guaico Culex virus

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Guaico Culex virus (GCXV) was isolated from mosquitoes in Central and South America. So far no other animals have been shown to be infected with any multicomponent viruses (a source of apparent confusion on the internet). The close relative, Jingmen tick virus (JMTV) was isolated from a red colobus monkey but it is not actually a multicomponent virus. It is merely a segmented virus with all the segments in a single virion. Both are members of the recently discovered Jingmenvirus group.

GCXV has five particles to it, but the fifth one does not appear to be necessary for infection and actually seems to provide no apparent advantage to fitness or virulence. This is surprising as while producing different amounts of each segment does make sense, if the virus can infect without one of the segments, how would the segment not be lost?

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The evolutionary history of Jingmenviruses is an especially surprising part. Phylogenetic analysis has continuously placed them as being closely related to Flaviviruses, which include, among others, Zika, West Nile, and Dengue. Not only does this show multicomponent viruses evolving independently outside of any multicomponent plant viruses, it also may help provide insight into the evolution of RNA virus segmentation in general. There must be different evolutionary paths that allow for convergence on this phenotype, but it’s surprising this was able to ever evolve in an animal at all.

Vector transmission (which is more of a plant thing), seems to be the best/only way these viruses are able to be multicomponent, but animals have plenty of viruses they get from vectors too so why wouldn’t there be potential for a multicomponent virus to eventually spread from a mosquito to a mammal?

Plant viruses are more prone to coinfection and there’s a lot of examples of common helper and dependent virus relationships, which may explain why more multicomponent viruses evolve in plants. Why this is more common in plants and fungi probably has something to do with plants not moving much.

Very little is known about multicomponent viruses because they don’t cause human disease. But studying viral segmentation is pretty important if you consider that Influenza’s segmented genome has allowed it to go from a mild inconvenience one year, to a deadly pandemic in other years. And studying viral evolutionary strategies more commonly used in plants is pretty important considering plant viruses can wipe out an entire species in a season (plants don’t have fancy immune systems like we do). It would be interesting if they looked at how segment combinations work in these multicomponent viruses and what are the genetic limits of compatibility.

Source:

Jason T. Ladner, Michael R. Wiley, Brett Beitzel, …, Laura D. Kramer, Robert B. Tesh, Gustavo Palacios. 2016. “A Multicomponent Animal Virus Isolated from Mosquitoes” http://www.cell.com/cell-host-microbe/fulltext/S1931-3128(16)30310-9

Archaea viruses- very weird, as expected

Viruses found in more extreme environments seem to be more morphologically diverse than the viruses that infect mesophilic microbes. Furthermore, the diversity of viruses infecting different domains of life varies greatly. Bacteriophages are almost entirely from one order of dsDNA viruses, with about 96% of all of them being head-tail phages (think T4, lambda etc). Meanwhile animals get infected with ssRNA, dsRNA, ssDNA, dsDNA, and retroviruses. Almost no DNA viruses attack plants and fungi, possibly because they have cell walls (which may have even evolved to protect them from viruses?), but then RNA viruses found a way to swoop in and occupy these new niches.

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(Nasir et al. 2014) So far, no RNA viruses have been confirmed to infect archaea, and almost all their viruses are double-stranded DNA viruses. RNA is more labile than DNA at high temperatures (DNA is a much more stable molecule than RNA) so the lack of RNA archaeal viruses could indicate either the first archaea were extremophiles or archaea that were extremophiles benefitted by escaping RNA viral infections, causing an increase in extremophile archaea and decrease in mesophilic archaea.

Acidianus two-tailed virus

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So far the only virus that’s been discovered to grow outside of cells. Acidianus two-tailed virus was isolated from a 87-93 ºC, acidic hot spring in Italy. This is an enveloped lemon-shaped virus with 72 open reading frames and tails at both ends. When they infect Acidianus archaea at 85 ºC, they lysogenize. However in stressful conditions such as cold shocking them at 75°C (yeah this is chilly for them) the virus actually lyses the cells releasing virions four days later. This is actually very unique in archaeal viruses, the other ones tend to lysogenize.

Unique life cycle

The virions don’t finish growing though before lysis. They actually emerge as little lemon-shaped, tailess virions and then grow the tails outside the cell. The tail growth seems to be temperature dependent, with them growing tails at 75 ºC but taking over a week, and then growing tails very quickly if the temperature is closer to 85 degrees. While the two tails grow, with NO CONTACT TO THE CELL, the virions shrink. The weird viral morphology of having two long tails may help the virus find hosts.

Something very strange is that these viruses have a gene containing an AAA ATPase domain, something found in motor proteins like dynein and kinesin. But scientists don’t know what it’s for, and while it might make sense for a giant virus to have collect some strange genes it may not need, most viruses tend to want to limit their genome size.

We need to know more

Archaea viruses are understudied and so far, almost a total mystery. Almost all of their genomes have no homologs to anything else discovered. Questions regarding virus evolution, early life evolution, viral ability to cross domains, when did viruses diversify, and how did the first archaea and then eukaryotes come about are still unresolved, so studying archaea viruses would be far from useless.

Sources

Archaeal viruses and bacteriophages: comparisons and contrasts, Maija Pietilä-Tatiana Demina-Nina Atanasova-Hanna Oksanen-Dennis Bamford – Trends in Microbiology – 2014

Häring M, Vestergaard G, Rachel R, Chen L, Garrett RA, & Prangishvili D (2005). Virology: independent virus development outside a host. Nature, 436

The Wonderful World of Archaeal Viruses. David Prangishvili – Annual Review of Microbiology – 2013

R. Danovaro et al., “Virus-mediated archaeal hecatomb in the deep seafloor,” Science Advances, doi:10.1126/sciadv.1600492, 2016.

Figure: Consider something viral in your research. Forest Rohwer & Merry Youle, Nature Reviews Microbiology 9308-309 (May 2011). doi:10.1038/nrmicro2563

The distribution and impact of viral lineages in domains of life. Arshan Nasir-Patrick Forterre-Kyung Kim-Gustavo Caetano-Anollã©S – Frontiers in Microbiology – 2014

Sex determination in monotremes- way weirder than the whole laying eggs thing

baby-platypus

Sex determination and sex chromosome evolution is a lot less well-understood than most people would probably assume. One of the most puzzling cases is that of the platypus and echidna, the only members left of a group of mammals that diverged from theria about 210 million years ago.

Way more than just two

The platypus has 10 sex chromosomes, while the echidna has nine. Sex determination occurs by the sex chromosomes aligning during male meiosis as X1Y1X2Y2X3Y3X4Y4X5Y5, so five X chromosomes go into one sperm cell, and five Y chromosomes go into another. What happens if the chromosomes align “incorrectly” is entirely unknown, and considering how understudied monotremes are, unlikely that we’d get to see any examples (but I’d imagine one could learn a lot about their sex-determination from that).

No SRY or DMRT1

In placental mammals and marsupials, the SRY gene on the Y chromosome is what determines sex, as it controls the formation of testes.

Birds however, have a ZZ/ZW system where the females are actually the heterogamateic sex having a Z and a W sex chromosome. Sex determination in birds is controlled in a dosage-dependent manner where the females only have one copy of the DMRT1 gene, while the males, being ZZ have two copies.

What’s really interesting though, is that the SRY gene is absent in monotremes and very few genes have actually been identified on the Y. One gene suspected to play a role in sex determination is Y chromosome gene, anti-Müllerian hormone, Amhy, though the molecular bases actually determining sex in monotremes is still not known.

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Weird Homology

Platypus X1Y1X2Y2X3 are homologous to echidna X1Y1X2Y2X3, however the platypus X5 is homologous to echidna X4, platypus Y5 is homologous to echidna Y3, and platypus X4 and Y3 homologs are in echidna autosome 27 whereas echidna X5 and Y4 are in autosomal platypus chromosomes.

Genes found on the therian X chromosome are orthologous to platypus chromosome 6, the homolog of echidna autosome 16. SOX3, thought to be the sort of “X-version of SRY” is autosomal in monotremes, as well as other non-therian vertebrates. SRY is probably a derived trait that only evolved after the divergence of monotremes from other mammals.

That being said, no homology has been shown so far between any platypus X chromosomes and therian X. Monotremes XY chromosomes are unique but show some homology with bird chromosomes, which is especially interesting considering in birds sex-determination works very differently from mammals and females are the heterogametic sex.

Whether sex-determination works in monotremes as a dosage-dependent set up (like in birds), or in a Y-gene set up as seen in humans, is still unknown.

Monotremes are relatively ignored because there’s just not very many of them, but for an evolutionary biologist they can be very useful in trying to answer questions related to amniotic lineages and divergence. While still mammals, they are genetically very distant from other mammals, even though people tend to maybe think of marsupials and monotremes as being more similar (both Australian, both not placentals), monotremes are a real anomaly.

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sources:

  1. Diego Cortez, Ray Marin, Deborah Toledo-Flores, Laure Froidevaux, Angélica Liechti, Paul D. Waters, Frank Grützner, Henrik Kaessmann. Origins and functional evolution of Y chromosomes across mammalsNature, 2014
  2. Grützner F., et alNature,  doi:10.1038/nature03021 (2004).
  3. Sex determination in platypus and echidna: autosomal location of SOX3 confirms the absence of SRY from monotremes. M. Wallis-P. Waters-M. Delbridge-P. Kirby-A. Pask-F. Grützner-W. Rens-M. Ferguson-Smith-J. Graves – Chromosome Research – 2007

New Giant Virus Discovered

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Electron microscope image by Schulz et al

Encodes aminoacyl transfer RNA synthetases with specificities for all 20 amino acids. Evolutionarily, probably just a gene collector.

Published in April 7, 2017’s Science, researchers have discovered another group of giant viruses—the Klosneuviruses. They were discovered in Austria, at a Klosterneuburg waste water treatment plant biomass, and ranged from .86 Mb (Indivirues) to 1.57 Mb (Klosneuvirus).

Klosneuvirus has a 1.57 Mb genome coding 1272 genes, 335 or so of which are shared eukaryotes. Like other giant viruses, Klosneuviruses seem to infect protists–Cercozoans and the marine flagellate, Cafeteria specifically. Surprisingly they do not seem to infect Amoebas (which are thought of as the typical host for giant viruses and therefor often used as bait when hunting for new viruses).

Klosneuviruses have managed to evolve complex translation system components including “25 tRNAs with anticodons for at least 14 different amino acids, as well as more than 40 translation-related proteins, including 19 aminoacyl tRNA synthetases (aaRSs) with distinct amino acid specificities, 11 translation initiation and elongation factors, a peptide chain release factor, and several tRNA modifying enzymes.”

The researchers performed a maximum likelihood phylogeny from a concatenation of five conserved genes nucleocytoplasmic large DNA viruses (NCLDVs) and found that Klosneuvirus is evolutionarily most closely related to Mimiviruses but still very distinct due to it’s sophisticated translational system components.

The discovery of Klosneuviruses supports the hypothesis that giant viruses more likely evolved from smaller viruses and their large genome is largely the result of accumulation from host genes. There’s been a lot of different hypotheses floating around since the relatively recent discovery of giant viruses, notably that they may be a fourth domain of life. This discovery makes that seem less likely. Giant virus research will probably be huge in helping to tackle questions regarding viral evolution, the origin of life, and deep evolutionary relationships between bacteria, archaea, and eukaryotes.

 

Original paper:

Schulz, Frederik, Natalya Yutin, Natalia N. Ivanova, Davi R. Ortega, Tae Kwon Lee, Julia Vierheilig, Holger Daims, Matthias Horn, Michael Wagner, Grant J. Jensen, Nikos C. Kyrpides, Eugene V. Koonin, and Tanja Woyke. “Giant viruses with an expanded complement of translation system components.” Science 356.6333 (2017): 82-85.

 

The Last Rhyncocephalians

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You might think that’s just a lizard, but the two species of tuatara (Sphenodon punctatus and Sphenodon guntheri) are not even squamates. They are the only surviving members of Rhynchocephalia—a group of reptiles who were doing great during the Triassic through the Cretaceous, but then took a big hit during the K/Pg extinction.

 Tuataras—“the living fossil” evolves faster than any other animal.

At this rate, they may be as puzzling as turtles soon.

Tuataras are often referred to as “living fossils” because in about 200 million years, they have supposedly barely changed their morphology (to read more on that see http://onlinelibrary.wiley.com/doi/10.1111/pala.12284/full).

Researchers recovered DNA from 8,000 year-old tuatara bones and compared it to modern tuatara DNA samples. They found the tuatara had the fastest rate of molecular evolution of any animal studied. This was especially surprising given the thought that slow metabolism would imply slower evolution due to lower mutation rate from less DNA damage.

This is pretty cool evidence for showing that anatomical change can be strongly decoupled from genomic evolution, and it is an excellent example of proof that so-called “living fossils” (coelacanth being the classic example), do not evolve any slower than other animals.

The cause of the fast mutation rate is possibly explained partly by the mitochondiral genome in tuataras. Being single-stranded for a longer time may allow for more change. As for why tuataras haven’t changed much in 200 million years, it’s possible they just haven’t HAD to. Isolated in little islands in New Zealand with less pressure from predation, and able to cope with changes in climate by behavioral evolution, tuataras may not have been under the same selective pressures other amniotes faced.

 Tuataras still remain slowest at literally everything else.

And the irony of something famously dubbed “a living fossil” whilst winning title for “fastest evolving genome studied,” continues. Tuataras do pretty much everything–other than evolve–incredibly slowly. They take 10 to 20 years to sexually mature, 30 years to reach their full size, and often live to 100 years in the wild (even longer in captivity). It takes females one to three years to have egg yolk ready for breeding, seven months to form the shell, and then 12 to 15 MORE months for the little baby tuataras to hatch.

Slow Metabolism, Low Temperature

They also have an extremely slow metabolism–slower than other reptiles. This is probably partly to do with their lower body temperature. While most reptiles have body temperatures at around 20 °C, the tuatara prefers to keep it at a cool 5.2–11.2 °C (with it’s optimal temperature for running around being about 16 to 21°C). They can tolerate much colder weather than most reptiles and can even hibernate.

A slow, but no less exciting, love story

First time father of 11 babies at age 111! Henry the tuatara finally had sex for what was believed to be his first time, with a younger (typical man amirite?) female tuatara named Mildred. Mildred, who was only 80 at the time, had 11 hatchlings. It took him 40 years to muster up the courage (40 years, for those of you unfamiliar with courtships, is longer than most females prefer). To be fair to Henry, he apparently took an interest in Mildred after a cancerous growth was removed from his genital region.

In 2010, Henry and Mildred starred in the short film “Love in Cold Blood,” about the Sphenodon courtship. It won Best New Zealand Film and Best New New Zealand Emerging Talent. Congrats to Henry and Mildred.

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Henry at his big debut (Photo by JOHN HAWKINS/The Southland Times)

If I ever find myself in a scenario where I have to identify a tuatara, how will I manage it?

For starters, tuataras have a parietal eye at the top of their head. It’s not for vision, but is probably involved in hormone and circadian rhythm regulation, and UV ray absorption to produce vitamin D. The parietal eye is only visible in recently hatched tuataras and becomes covered with age. While parietal eyes are actually pretty common in non-mammalian vertebrates, the tuatara parietal eye does have a retina, cornea, lens and nerve endings. Being that parietal eyes are present in lampreys (the best living representation we have for the earliest vertebrates, and a clue that it’s an ancestral trait) tuatara third eyes probably do not seem as shocking now. But still, AMAZING.

Tuataras also have the ability to regenerate their tails (yet another reason to stop calling humans the “pinnacle of evolution”). We can’t regenerate our tails. We barely even have tails.

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Bones are all pretty different too

They have no eardrum and no ear hole. And their diapsid skull lacks modifications seen in other diapsid skulls. Essentially they look less like an amniote than any other amniote with amphiecoelus vertebrae (centra with both ends concave). They have retained their gastralia, a likely ancestral trait of diapsids, and when looking at their skulls, the tip looks like a beak.

Teeth but not teeth but still kind of teeth

Their teeth aren’t really teeth, but rather sharp jaw bone projections. They don’t get replaced if the tuatara loses one. So old tuataras have to switch up their diet when their teeth get worn down…seems like a kind of flawed design when you’re able to live for a century in the wild but who am I to judge? Luckily tuataras barely need to eat at all due to their very slow metabolism so perhaps it’s okay to not have fancy teeth. They have two rows on the top of their jaw and one on the bottom (which, for those of you unfamiliar with odontology, is not how teeth usually go).

 Is climate change going to harm this incredible organism?

While herpetologists and conservational biologists have been worrying about the effects climate change may have on sex-ratios in reptiles (reptiles commonly follow a temperature sex-determination system), this encouraging paper on female turtles compensating for colder temperatures by switching nesting areas to warmer areas, ensuring the sex-ratio stayed balanced, might give you hope!

These guys have survived ice ages and a mass extinction, so if anthropogenic global warming eliminates them, then we’ll really feel like shitheads. Tuataras already almost went extinct because rats were eating all their eggs which was probably unimaginably stressful for them, so please let’s not take any chances!

Sources

  1. The Allan Wilson Centre which has a tuatara genome project http://www.allanwilsoncentre.ac.nz/massey/learning/departments/centres-research/allan-wilson-centre/our-research/strategic-initiatives/the-tuatara-genome-project.cfm
  2. Rapid molecular evolution in a living fossil. Jennifer M. Hay, Sankar Subramanian, Craig D. Millar, , Elmira Mohandesan, David M. Lambert http://www.cell.com/trends/genetics/fulltext/S0168-9525(08)00003-6?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0168952508000036%3Fshowall%3Dtrue
  3. Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Joshua S. Rest et al. http://www.sciencedirect.com/science/article/pii/S1055790303001088
  4. Macroevolutionary patterns in Rhynchocephalia: is the tuatara (Sphenodon punctatus) a living fossil? Jorge A. Herrera-Flores, Thomas L. Stubbs, Michael J. Benton http://onlinelibrary.wiley.com/doi/10.1111/pala.12284/full
  5. pictures: https://www.flickr.com/photos/rocknvole/5396228887, https://a-z-animals.com/animals/tuatara/pictures/3192/, https://creativecommons.org/licenses/by-sa/3.0/deed.en
  6. https://tuatarafilm.wordpress.com/how-it-all-began/