Tag Archives: genes

A better potato: researchers sequence the tuber’s entire genome for the first time ever

Researchers at the Max Planck Institute for Plant Breeding Research have set the groundwork for supercharging the potato, by mapping out the tuber’s complete genome.

Image credits James Hills.

Fried, mashed, or thrown in a stew, the humble potato has a special place in our hearts and our plates that nothing else seems to be able to fill. Researchers seem to love this tasty tuber as well, and have put significant effort into decoding its genetic secrets. This impressive work will allow us to create better varieties of potato much faster than traditional breeding methods allow for, with implications for the quality of our meals, the enjoyment we derive from it, and global food security.

Super Tuber

“The potato is becoming more and more integral to diets worldwide including even Asian countries like China where rice is the traditional staple food. Building on this work, we can now implement genome-assisted breeding of new potato varieties that will be more productive and also resistant to climate change — this could have a huge impact on delivering food security in the decades to come.”

The potato has not changed very much in the last 100 years or so. The overwhelming majority of varieties that are available in shops today are the same ones that were put to market over the last century and before. While these traditional cultivars are very popular, they do underline that there is a lack of variety of potatoes being grown, cooked, and enjoyed around the world. Thus, it stands to reason that improvements can be made to the baseline potato in order to make it more palatable, more resilient, or more abundant.

That’s what the team at the Max Planck Institute for Plant Breeding Research hopes to achieve with the full sequencing of the plant’s genome. The work, led by geneticist Korbinian Schneeberger, represents the first full assembly of the potato genome in history, allowing for researchers to work with a much better view of the plant’s genetic intricacies, and thus much more accuracy when trying to breed new varieties of the plant.

Low genetic diversity within a species — and the potato is a good example of one such species — means that it can have difficulties thriving in certain contexts, and leaves it vulnerable to disease. The near-extinction of the Gros Michel banana due to the Panama disease is a great example of such a genetic vulnerability at work. In the case of the potato, the Irish famine of the 1840s stands testament to how completely potato crops can be wiped out by pathogens. During this tragic event, Europeans were growing a single variety of potatoes, which was vulnerable to blight; as such, potato crops failed across the continent.

The Green Revolution of the 1950s and 60s saw a great diversification of crop varieties in staples like rice or wheat, but not potatoes. Efforts to breed new varieties with higher yields or more disease resistance have, so far, remained largely unsuccessful.

Potatoes, the team explains, inherit two copies of each chromosome from every parent — unlike humans, who inherit one copy of every chromosome from their parents. This makes them a species with four copies of each chromosome, a ‘tetraploid’, making them exceedingly difficult and slow to be coaxed into generating new varieties with desirable combinations of traits.

The same tetraploid structure also makes it technically difficult to reconstruct the potato’s genome.

To work around this issue, the team sequenced the DNA of potatoes working not with mature plants, but with large numbers of individual pollen cells. These contain only two copies of each parent chromosome, which made it easier for the team to use established genetic methods to reconstruct the plant’s genome.

The results should give scientists and plant breeders a powerful new tool with which to identify desirable gene variants in the potato and work to establish new varieties that contain them. Essentially, it gives them a baseline against which they can reliably compare individual plants and establish exactly where their desirable properties originate — and then work to reproduce them.

The paper “Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar” has been published in the journal Nature Genetics.

Wild microorganisms are evolving to eat plastic pollution

Microorganisms around the world are likely evolving to be able to degrade and consume plastic materials.

Image via Pixabay.

A new global assessment of microorganism genomes, the largest study of its kind, found that wild bacteria and microbes are evolving to be able to consume plastics. Overall, the authors report that an average of one in four of the organisms analyzed in the study carried at least one enzyme that could degrade plastic. Furthermore, the number and types of enzymes matched the amount and type of plastic pollution at the location where samples of different organisms were collected — suggesting that this is a natural, ongoing process, caused by the presence of plastic in the environment.

These results are evidence that plastic pollution is producing “a measurable effect” on the world’s microbes, the authors conclude.

Plastic bacteria

“We found multiple lines of evidence supporting the fact that the global microbiome’s plastic-degrading potential correlates strongly with measurements of environmental plastic pollution — a significant demonstration of how the environment is responding to the pressures we are placing on it,” said Prof Aleksej Zelezniak, at Chalmers University of Technology in Sweden.

Millions of tons of plastic are dumped in the oceans and landfills every year, and plastic pollution has become endemic everywhere on Earth. Addressing this issue will be one of the defining challenges of future generations along with efforts to reduce our reliance on such materials and improve our ability to recycle and cleanly dispose of used plastic. However, plastics are hard to degrade — that hardiness is one of their selling points to begin with.

According to the findings, microbes in soils and oceans across the globe are also hard at work on the same project. The study analyzed over 200 million genes from DNA samples taken from environments all around the world and found 30,000 different enzymes that could degrade 10 different types of plastics. such compounds could serve us well in our efforts to recycle plastics, breaking them down into their building blocks. Having more efficient recycling methods on hand would go a long way towards cutting our need to produce more plastics.

“We did not expect to find such a large number of enzymes across so many different microbes and environmental habitats. This is a surprising discovery that really illustrates the scale of the issue,” says Jan Zrimec, also at Chalmers University, first author of the study.

The team started with a dataset of 95 microbial enzymes already known to degrade plastic; these compounds were identified in species of bacteria found in dumps and similar places rife with plastic.

They then looked at the genes that encode those enzymes and looked for similar genes in environmental DNA samples collected at 236 sites around the world. To rule out any false positives, they compared the enzymes with enzymes from the human gut — all of which are known to be unable to degrade plastic.

Roughly 12,000 new enzymes were identified from ocean samples. Higher levels of degrading enzymes were routinely found in samples taken at deeper points, which is consistent with how plastic pollution levels vary with depth. Some 18,000 suitable genes were identified in soil samples. Here, too, the researchers underscore the effect of environmental factors: soils tend to contain higher levels of plastics with phthalate additives than the ocean, and more enzymes that can attack these substances were identified in soil samples.

Overall, roughly 60% of the enzymes identified in this study did not fit into a previously-known class, suggesting that they act through chemical pathways that were previously unknown to science.

“The next step would be to test the most promising enzyme candidates in the lab to closely investigate their properties and the rate of plastic degradation they can achieve,” said Zelezniak. “From there you could engineer microbial communities with targeted degrading functions for specific polymer types.”

The paper “Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends” has been published in the journal Microbial Ecology.

Moral judgment condemning drug use and casual sex may be rooted in our genes

Prior research suggests that people who condemn drug use over moral grounds also tend to judge others harshly who engage in promiscuous, non-monogamous sex. A new study that involved more than 8,000 twins not only confirmed this link but also showed the association may be mediated by genes. Those who wrap their negative views regarding sexuality and drug use in a veneer of morality may, deep down, actually be looking out for their own reproductive strategy by shaming others in order to control the environment.

Public condemnation of casual sex and illicit drug use has never really gone away, despite massive cultural shifts during the 1960s counterculture movement. Although upbringing certainly has a part to play in shaping one’s views of the world and moral compass, psychologists have amassed increasing evidence that many of the instances when we righteously point our fingers may be selfish acts of self-interest.

It’s common for people who disapprove of illicit drug use to also frown upon casual sex. Each of these instances shouldn’t bother other people since it doesn’t affect them directly in any way unless they interact with people who engage in them. But past studies have shown that openness to engage in casual sex is partially explained by genes. And those who are inclined to engage in noncommittal sex are also more likely to use recreational drugs.

“People adopt behaviors and attitudes, including certain moral views, that are advantageous to their own interests. People tend to associate recreational drug use with noncommitted sex. As such, people who are heavily oriented toward high commitment in sexual relationships morally condemn recreational drugs, as they benefit from environments in which high sexual commitment is the norm,” said Annika Karinen, a researcher at Vrije Universiteit Amsterdam in the Netherlands and lead author of the new study.

Karinen and colleagues decided to investigate whether there is any genetic basis surrounding moral views on both sex and illicit drug use. They employed a dataset from a survey of 8,118 Finnish fraternal and identical twins. Identical twins share almost all their genes while fraternal twins share roughly half of their genes. As such, twin studies are the perfect natural laboratory that allows scientists to tease out genetic factors from environmental ones when assessing behaviors.

Each participant had to answer a set of questions that measured their moral views surrounding the use of drugs and openness to non-committed sex, as well as political affiliations, religiosity, and other facts.

When comparing the results of the questionnaires between fraternal and identical twin pairs, the Dutch psychologists found that moral views concerning both recreational drugs and casual sex are approximately 50% heritable, while the other 50% can be explained by the environment in which people grew up and the unique experiences not shared by the twins. Moreover, the relationship between openness to casual sex and views on drugs is about 75% attributable to genetic effects.

“These findings run counter to the idea that within-family similarities in views toward drugs and sex reflect social transmission from parents to offspring; instead, such similarities appear to reflect shared genes,” the researchers wrote in the journal Psychological Science.

Those who frown upon casual sex and drug use (which they associate with casual sex) may be looking out for a sexual strategy that revolves around committed sex into which they’ve invested a lot of resources. People who engage in casual sex are seen as a threat to the monogamous reproductive strategy because there’s the risk of losing one’s partner in an environment where casual sex is deemed acceptable. By judging other people’s sexuality and drug use from a moral high ground, people who prefer monogamous relationships have a weapon they can wield to control the sexuality of others to serve their own interests.

“Important parts of hot-button culture-war issues flow from differences in lifestyle preferences between people, and those differences in lifestyle preferences appear to partly have a genetic basis,” Karinen added.

Swiss researchers develop virus that makes cancer tumors destroy themselves

New research at the University of Zurich (UZH) points the way towards a new type of anti-tumor treatment. This, they hope, will help protect patients from the side effects of cancer therapy.

A piece of tumor that was scanned and modelled in 3D (red: blood vessels, turquoise: tumor cells, yellow: therapeutic antibody). Image credits: Plückthun Lab.

Tumors are notoriously tricky to eliminate. The new approach, therefore, involves using our own bodies to produce therapeutic compounds at the tumor’s exact location. This should dramatically limit the negative side effects of traditional interventions because, unlike chemotherapy or radiotherapy, this approach does no harm to normal healthy cells. In fact, this approach could, potentially, also be used for targeted delivery of medicine against COVID-19 directly to the lungs.

Viral aides

It all revolves around a genetically-modified respiratory virus (an adenovirus, to be exact) which delivers genes encoding anti-cancer and signaling compounds directly into tumor cells. Here, they cause the cells to produce the very substances that destroy them, as well as chemical signals such as cytokines, which tells our immune system that the tumor is a target.

“We trick the tumor into eliminating itself through the production of anti-cancer agents by its own cells,” says postdoctoral fellow Sheena Smith, who led the development of the delivery approach.

“The therapeutic agents, such as therapeutic antibodies or signaling substances, mostly stay at the place in the body where they’re needed instead of spreading throughout the bloodstream where they can damage healthy organs and tissues” adds Andreas Plückthun, who led the research effort.

The team christened their new approach SHREAD: SHielded, REtargetted ADenovirus. It draws on the previous work of the same team, including ways to guide the virus to particular areas of the body, as well as methods to hide them from our immune system.

In order to test their approach, the authors used SHREAD to induce a breast tumor in the mammaries of a lab mouse to produce trastuzumab, a clinically approved breast cancer antibody. In a few days, levels of the antibody inside the tumor itself were higher than they could have been if they were injected directly. At the same time, they were significantly lower in the bloodstream and other tissues compared to what’s seen with direct injections — this helps reduce side effects.

The team used high-resolution 3D imaging methods and tissues rendered totally transparent to see how the antibody creates pores in blood vessels of the tumor and destroys tumor cells from the inside out.

One of the best parts of this approach is that it’s not limited only to cancer. The authors explained that by insulating healthy tissues from significant levels of an active substance, it also opens the door for other therapies. For example, it makes it possible to more easily use ‘biologics’, a family of protein-based drugs. If administered using a traditional injection, such biologics would be too toxic for use, they explain.

The team is currently working on applying SHREAD to anti-COVID-19 therapies.

“By delivering the SHREAD treatment to patients via an inhaled aerosol, our approach could allow targeted production of COVID antibody therapies in lung cells, where they are needed most,” Smith explains. “This would reduce costs, increase accessibility of COVID therapies and also improve vaccine delivery with the inhalation approach.”

The paper “The SHREAD gene therapy platform for paracrine delivery improves tumor localization and intratumoral effects of a clinical antibody” has been published in the journal PNAS.

One gene can turn mosquitoes from females to males, which don’t bite

Researchers at Virginia Tech have found that they can turn female Aedes aegypti mosquitoes into males by tweaking a single gene in their DNA.

Image via Pixabay.

The findings could help us reduce the spread of mosquito-borne diseases. Female mosquitoes need to bite mammals in order to absorb their blood — which is converted into nutrients for their eggs. Males, on the other hand, don’t. They spend their days sipping on nectar.

Mosquito bites create an ideal opportunity for diseases such as malaria, Zika, or Dengue to spread, as they involve a small amount of the insect’s saliva entering the victim’s tissues. Shifting the ratio towards males can thus nip such diseases in the bud.

Changing demographics

“The presence of a male-determining locus (M locus) establishes the male sex in Aedes aegypti and the M locus is only inherited by the male offspring, much like the human Y chromosome,” said Zhijian Tu, a professor in the Department of Biochemistry in the College of Agriculture and Life Sciences, lead author of the study describing the process.

“By inserting Nix, a previously discovered male-determining gene in the M locus of Aedes aegypti, into a chromosomal region that can be inherited by females, we showed that Nix alone was sufficient to convert females to fertile males. This may have implications for developing future mosquito control techniques.”

The team produced several such gene-modified mosquitoes that express an extra copy of the Nix gene that is activated by its own promoter.

This sex conversion was found to be highly effective and “stable over many generations in the laboratory”, the team explains, suggesting that it would be useful in wild populations without constant reintroduction of modified mosquitoes.

However, these converted males can’t fly naturally. In order to remedy this, the team found that a second gene (myo-sex) needs to be added to the M locus as well. The team inactivated the myo-sex gene in wild-type males to confirm its function — and these insects lost their ability to fly.

Flight is important for these sex-changed insects as mosquitoes rely exclusively on flight for feeding, mating, and escaping predators. In other words a flightless mosquito, no matter how well-engineered, won’t do us much good. This being said, however, the authors report that sex-changed males were still able to father sex-converted offspring if they were presented with an anesthetized wild female.

All in all, the Nix gene has great potential as a tool to reduce the population of biting mosquitoes, and thus, the spread of disease. However, there’s still a lot of work to be done in the lab before such insects can be released into the wild.

The paper “Nix alone is sufficient to convert female Aedes aegypti into fertile males and myo-sex is needed for male flight” has been published in the journal Proceedings of the National Academy of Sciences.

Our genes could make us seek, or avoid, fatty foods

While most of us would agree that fat (when properly used) makes food taste amazing, new research shows this isn’t a steadfast law. Our enjoyment of fats lies, at least in part, on having the right genes for it.

Image credits Steve Buissinne.

New research from the Monell Chemical Senses Center in Philadelphia, Pennsylvania found that our genetic makeup plays an important role in our enjoyment (and even perception) of fatty foods.

Fat chance

“Person-to-person diversity in the positive perception of fattiness derives partially from an individual’s genetic make-up,” said senior author Danielle Reed, PhD, Monell Associate Director.

“How the taste, smell, and flavor of food and drink affect liking, and therefore the amount and type of food consumed, ultimately affects human health.”

The team worked with identical and fraternal twins who had reached adulthood and attended the annual Twins Days Festival in Twinsburg, OH, in 2018.

Participants were asked to rate how good low- and high-fat potato chips tasted, and estimate how much fat they contained. Participants also gave a saliva sample so the team could look at their DNA.

Genetically-identical twins had more similar preferences for the chips compared to fraternal twins (which are more genetically-distinct). The team also sequenced the genetic material of these participants, looking at hundreds of thousands of locations in their DNA strands where relevant genes were likely to lie.

The use of twins allowed the team to compare very similar genomes, and they identified two new specific gene variants that correlated with the enjoyment of fatty food.

The findings are important because our enjoyment of food drives our purchasing patterns, the authors explain.

“Most people assume more liking drives more intake, but decades of research tell us the reverse is true — we avoid what we don’t like,” said Hayes. “I may love bacon, but if I listen to my cardiologist, I’m still not going to eat it every morning.”

The results suggest that although fats are an important part of our food, some people are born with a genetic makeup that pushes them to like, or avoid, fat. In the future, the team plans to examine whether such factors are universal by testing people around the world with different types of fat in different food items.

The paper “Studies of Human Twins Reveal Genetic Variation That Affects Dietary Fat Perception” has been published in the journal Chemical Senses.

Fruit and nectar eaters are nature’s most resilient alcohol drinkers

New research at the University of Calgary in Canada has identified nature’s stoutest drinkers — unsurprisingly, they’re all fruit eaters.

Primates like humans, chimpanzees, gorillas, alongside other mammals whose diets contain lots of fruit such as bats are nature’s best drinkers, the paper reports. Such animals had an evolutionary incentive to develop the ability to metabolize alcohol, they explain, which created a selective pressure in favor of this ability. However, it’s not just mammals that partake — pound for pound, bees are known to be some of the heaviest drinkers out there.

It’s in my genes

“Being able to eat a lot of fruit or nectar without being subject to the effects of ethanol would certainly open up an important food resource,” explains lead author Mareike Janiak from the University of Calgary.

Fruits are very useful in one’s diet: they’re full of good nutrients and contain a lot of energy in the form of sugars. But bacteria also know this and are liable to start eating (fermenting) those compounds into alcohol. Alcohol concentrations in fruits past their prime can reach up to 8.1%, the study reports. Nectar, the sweet liquid flowers produce to attract pollinating insects, can still reach a respectable 3.1% alcohol concentration. For comparison, beers typically revolve around the 4.1% alcohol concentration mark.

It’s understandable, then, that fruit-eaters could be exposed to quite a generous helping of alcohol during breakfast, lunch, and dinner.

The ability to metabolize alcohol would, therefore, be quite desirable for fruit-eating species, the paper explains, as it would prevent them from getting completely smashed on a daily basis — which helps with things such as avoiding predators, impressing potential mates, or just maintaining basic motor coordination.

In order to understand how different species developed this ability, Janiak and her team studied genetic data for over 85 different mammal species looking for a gene called AHD7. This gene encodes the production of the enzyme alcohol dehydrogenase 7, which is part of a larger family of proteins that mediates chemical redox reactions. This particular one is specialized in alcohols and, in short, it allows bodies to either break it down into its constituent parts or recombine it from said parts. In short, AHD7 is what allows us to process alcohol (and its inebriating effects) out of our systems.

Mammal species who regularly consume fruit or nectar are more likely to have a variant of ADH7 that’s more efficient at processing alcohol, the team reports. Among the species that have this gene variant number bonobos, aya-ayes, chimpanzees, gorillas, as well as humans. They say it comes down to our shared genetic history, tied together by a common ancestor “at least 10 million years ago, long before we began fermenting beverages on purpose”.

However, “it is a fallacy to assume that other animals share our metabolic adaptations, rather than taking into consideration each species’ unique physiology,” the authors note.

Fruit- and nectar-eating bats are also very good at processing alcohol, the team found, likely because “being inebriated would be bad news for a flying mammal, so being able to better metabolize ethanol could be an important adaptation for them”.

In contrast, mammals who typically exclude fruits or nectar from their diet — including horses, cows, or elephants — are poor at metabolizing alcohol because they have lost their functioning version of ADH7.

The paper “Genetic evidence of widespread variation in ethanol metabolism among mammals: revisiting the ‘myth’ of natural intoxication” has been published in the journal Biology Letters.

New genetic research effort aims to make watermelons tastier, more resilient

If you like watermelons, this team has big news for you.

Image credits Aline Ponce.

A new research effort aims to pave the way towards new and improved watermelons. The study took a comprehensive look at the genomes of all seven watermelon species to create a database that plant breeders can use to produce tastier, plumper, and more resistant watermelons.

The Better Melon

“As humans domesticated watermelon over the past 4,000 years, they selected fruit that were red, sweet and less bitter,” said Zhangjun Fei, a faculty member at Boyce Thompson Institute and co-leader of the international effort.

“Unfortunately, as people made watermelons sweeter and redder, the fruit lost some abilities to resist diseases and other types of stresses.”

Back in 2013, Fei co-led the creation of the first watermelon reference genome. This database was built from an East Asian cultivated variety ‘97103’. That variety, and likely the watermelon you’re imagining right now belongs to the Citrullus lanatus species, i.e. the sweet fruit with a juicy red interior.

However, Fei explains that there are six other wild species of watermelon that have pale, hard, bitter fruits, but possess other desirable qualities — such as a higher resilience against man-made climate change. Introducing the genes that generate such qualities into cultivated watermelon varieties can help make the fruits tastier, better able to grow in diverse climates, as well as more resistant to pests, diseases, and other factors. But, in order for us to get there, we first need to know which genes these are.

In order to find out, the team started with the reference genome Fei worked on in 2013, and created an improved version. The previous work relied on short-read sequencing technologies, Fei explains, while the newer one uses long-read sequencing technologies, allowing for “a much higher quality genome that will be a much better reference for the watermelon community.”

Next, the group sequenced the genomes of 414 watermelons across all seven species. By comparing these genomes both to the new reference genome and to each other, they were able to determine the evolutionary relationship of the different watermelon species.

“One major discovery from our analysis is that one wild species that is widely used in current breeding programs, C. amarus, is a sister species and not an ancestor as was widely believed,” Fei said.

Modern watermelon cultivars were domesticated by breeding out the fruits’ bitterness while increasing their sweetness, size, and reddening their flesh. Over the past few hundred years, the fruits kept becoming sweeter, but also improved in regards to flavor and crispiness of texture. The team identified several regions of the watermelon genome that could be leveraged to continue improving these qualities in cultivars.

“The sweet watermelon has a very narrow genetic base,” says Amnon Levi, a research geneticist and watermelon breeder at that U.S. Department of Agriculture, one of the study’s co-authors. “But there is wide genetic diversity among the wild species, which gives them great potential to contain genes that provide them tolerance to pests and environmental stresses.”

The team also published an accompanying paper analyzing 1,175 melons, including cantaloupe and honeydew varieties. The researchers found 208 genomic regions that were associated with fruit mass, quality, and morphological characteristics, which could be useful for melon breeding.

The paper “Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits” has been published in the journal Nature Genetics.

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What is biodiversity

A shorthand of the terms ‘biological diversity’, biodiversity refers to the variety of life, in all its forms and all its levels, on Earth. But why do we need biodiversity? Can’t we just have a planet populated solely with humans and those few plants and animals that are tasty?

We probably could, for a few days — then everything would grind to a halt (i.e. everything dies). Let’s see why.

Levels of biodiversity

In general, biodiversity is considered at three (progressively-wider) levels: genetic diversity, species diversity, and ecosystem diversity.

Genetic diversity refers to the level of genetic variety within a single species. While individuals of the same species are very similar from a genetic point of view, there’s also surprising variation between them. Individuals can show genetic differences between one another, as well as whole groups or populations. For example, two sparrows in New York will be a little different, genetically speaking. The differences between a sparrow in London and one in New York, however, would be much more pronounced.

Not all groups have the same degree of genetic diversity. For example, kangaroos come from a relatively recent evolutionary line, and are thus pretty similar from a genetic standpoint. Dasyurids, a group of carnivorous marsupials that includes the Tasmanian Devil, the Numbat, and quolls, come from a more ancient lineage and are far more diverse (as they’ve had more time to develop).

Image via Pixabay.

Species diversity refers to the number of different species that live in a particular area or habitat. Some habitats harbor a lot of species diversity — mountain ranges or coral reefs come to mind. Others, such as salt flats or heavily polluted areas that aren’t very nice places to live in, have very poor diversity.

The world might seem to be bursting at the seams with life, but it’s actually not that diverse a place; unless you count invertebrates. Invertebrates are animals that lack a spine and make up about 99% of all animal species. The group includes crabs, snails, worms, corals, and sea stars, but is overwhelmingly represented by insects. The good news, however, is that insects are surprisingly adaptable and versatile and end up fulfilling many vital ecosystem roles (more on that later).

Ecosystem diversity represents the variety of different ecosystems in a given area. An easy way to think of ecosystems is to imagine them as natural, local ‘economies’ that are affected by factors pertaining to their physical environment (local climate, precipitation levels, soil composition, etc) and the make-up and interaction of the species that live in said environment. An ecosystem is the product of the organisms interacting with the environment.

What has biodiversity ever done for us?

Coral reefs are some of the most biodiverse ecosystems out there.
Image via Pixabay.

You’d literally be dead without it.

One of the things you start to notice when studying biology is that life has a very interesting way of enabling life (the “Gaia hypothesis“). To help you get an idea of what I mean, let’s take a look at early life on Earth.

The first things to ever live around here were simple, microscopic things — bacteria, basically. The first direct evidence of life on Earth hails from around 3.5 billion years ago (fossilized microorganisms found in Apex chert rocks in the Pilbara Craton, Australia), but life likely evolved a bit earlier. It probably wasn’t very easy to make a living on Earth back in the day, however; these organisms likely lived in colonies around hydrothermal vents. These vents put out heat and chemical compounds, which the bacteria could capture to eke out energy from. This type of metabolism, which is known as chemolithoautotrophic (which means “self-feeding on chemicals and rocks), generates very little energy compared to oxygen respiration.

Homey!
Image credits Schmidt Ocean Institute via USGS.

Humans can exist in the form we have today because, unlike those early bacteria, we have ample access to oxygen to breathe. That oxygen, however, wasn’t always there — bacteria and plants released it into the atmosphere over the course of geological time. In other words, we can exist as we do today because life, over millions and billions of years, worked to create the conditions we live in.

But… that’s just life doing its thing, right? How does biodiversity fit into this story? Well, the short of it is that biodiversity is what keeps life and ecosystems going — life as we know it today requires a baseline of biodiversity to work.

Why biodiversity is the spice of life

Image via Pixabay.

Diversity is life’s insurance policy. As a rule of thumb, the more genetically-diverse a species is, the better its chances of not going extinct; ecosystems with greater species diversity are more resilient to shocks such as invasive species, climate shifts, or meteorites. Areas with greater ecosystem diversity can take more ‘damage’ (lose more ecosystems) before things break down completely. Let’s expand on each of those points independently.

First, consider the banana. Chances are that every banana you’ve even gulped down is, on a genetic level, exactly the same as every other banana you’ve ever eaten. That’s because the banana cultivar you’re overwhelmingly likely to encounter is a Cavendish banana (95% of all commercially-available bananas). All Cavendish bananas are clones of one another. The plants are propagated through the use of suckers, lateral offshoots of a parent plant that are cut and planted in the soil.

The reason Cavendish is so prominent today is that the original (and better-tasting) banana cultivar, the Gros Michel, was virtually wiped clean away from South America by the Panama disease. Why did this fungus-driven disease have such an easy time destroying the Gros Michel? Well, just like the Cavendish, Gros Michel bananas were basically clones of one another — so a pathogen that could infect and kill one plant could infect and kill all its species. The only reason the Gros Michel variety isn’t extinct right now is that some cultures survived in other areas of the world where the Panama disease hasn’t (as of now) reached. This example illustrates why insufficient genetic diversity can spell doom for a species.

Koa e Kea variety of banana afflicted by Fusarium wilt (Panama disease).
Image credits Scot Nelson / Flickr.

To understand why species diversity matters, we have to talk about ecological niches. Just like you have a job (if not, good luck), your neighbor has a job, and so on, each species has a ‘job’ it performs for the ecosystem. We call these jobs ‘ecological niches’. If the job doesn’t get done, the whole thing starts to crack. If enough jobs don’t get done, the local economy (ecosystem) collapses completely.

Let’s take pollinators as an example. They zip this way and that carrying pollen, thus fertilizing plants and crops, and indirectly helping to grow things for everyone to eat. If a single species is performing this role, and it gets wiped out for some reason, a critical ecosystem ‘service’ or ‘function’ (pollination) won’t be performed. Some, like plants, act as suppliers of food; herbivores harvest and concentrate nutrients and energy from plants, and carnivores keep herbivore numbers in check so they don’t overwhelm the plants. Bacteria and fungi make sure all that food keeps being recirculated in the ecosystems through decomposition (rot).

In ecosystems with high species diversity, several species compete or complement each other over the same niche. So if one pollinator species can’t perform the task, another one is there to pick up the slack. This makes the ecosystem as a whole more stable and resilient.

Crop fieds are a type of artificial ecosystem, but they’re much less robust than natural ones.
Image via Pixabay.

The next level is ecosystem diversity. Just like different species intermingle in an ecosystem and have particular roles, ecosystems interact with one another. If you think of the Earth as a huge ecosystem, then the sum of each of these ‘local’ ecosystems needs to perform a certain threshold of jobs (ecosystem services) for the whole system to be viable. For example, if there aren’t enough net-oxygen-generating ecosystems to supply all the demand for the gas, animals will start dying left and right. If there aren’t enough ecosystems to filter water, recycle nutrients, suck up carbon dioxide or other pollutants, and everything else that life needs, then the Earth will be downsizing on said life.

Where climate warming comes in

Species go extinct all the time, that’s just how life rolls. Generally, however, this natural or baseline rate of extinction is easily absorbed by ecosystems at large. Existing species cover now-free niches, or new species altogether evolve to exploit the opportunity.

From a biodiversity point of view, the issue with climate change is how fast it’s driving species extinct. Species go extinct when they fail to adapt to their environment or their competition. While natural processes can drive pretty fast and dramatic changes (think of how a meteorite impact killed the dinos and made mammals reign), most of the time they’re pretty gradual, which gives species some time to adapt or evolve to suit the present conditions. Natural changes, in general, also tend to impact a relatively limited area.

Global mean temperature anomalies (with 1951-1980 mean temperatures as baseline) between 1850-2017 as reported by Berkeley Earth, a California-based non-profit research organization.
Image credits Berkeley Earth.

Man-made climate warming is very fast — blisteringly fast from a geological point of view. The root of the issue is that our emissions are changing environments (this is the thing life needs to adapt to) way, way, way faster than biological evolution works. It also impacts the Earth in its entirety, affecting all ecosystems at the same time — so there aren’t any ‘unburdened’ ones to pick up the slack for those that are struggling since they’re all struggling.

To push the metaphor full circle, we’re closing the jobs in manufacturing and opening up new ones only in programming in the equivalent of a few hours, but programming school takes a few years to complete and very few people already know how to do it. Our way of life is driving the global economy — all of it — into a deep recession. The risk is that, by the time we take action to stop it, all the species that know how to manufacture the things we need to survive will be dead.

Hopefully, this handy guide helps you get a better idea of what biodiversity is and why it’s important. The world is a beautiful place, but we need to understand that it’s built on very complex and often fragile relationships. We need to make room and opportunity for these relationships to unfold, or we risk the world adapting to us — and wake up in a world that we’re no longer adapted for.

And we all know what nature likes to do to the species that can’t adapt, don’t we?

There’s no single “gay gene” that determines sexual behavior, research shows

The idea that a single “gay gene” exists has been disproven by scientists, who found that homosexual behavior is instead influenced by a wide group of genetic variants, each of which has a small, cumulative effect.

Credit: Wikipedia Commons

The study, published in the journal Science, was carried out by an international team of researchers. They compared the situation to factors determining a person’s height, in which multiple genetic and environmental factors play roles.

 “This study highlights both the importance of genetics as well as the complexity of the genetics, but genetics is not the whole story,” said Dr. Benjamin Neale, co-author of the study from the Broad Institute in the US.

The team looked at data from about 500.000 individuals. About 4% of men and nearly 3% of women said they had ever had a same-sex sexual experience. They did not focus on identity or orientation and did not include transgender individuals.

Then, by looking at the sexual behavior and relatedness of individuals, they estimated that about a third of the variation in same-sex behavior is explained by genetics. That clashes with previous twin studies that put the figure at about 30% to 50%.

“I hope that the science can be used to educate people a little bit more about how natural and normal same-sex behavior is,” said Neale. “It’s written into our genes and it’s part of our environment. This is part of our species and it’s part of who we are.”

The team looked at which genetic variants might be behind the link. They found five genetic variants that showed a clear link to same-sex sexual behavior — two in both men and women, two found only in men and one found only in women. The team believes one of these, found only in men, might be involved in sex hormone regulation.

These five genetic variants explain less than 1% of the variation in same-sex behavior among participants – suggesting many other variants are involved, each playing a very small role. it is not possible to use genetic information to predict whether an individual will have same-sex partners, they concluded.

The authors said their findings call into question the idea that sexuality exists on a single scale.

 “There seem to be genes associated with opposite-sex attraction and other genes associated with same-sex attraction, and these are not related,” Dr. Brendan Zietsch, co-author of the research, said. “These results suggest we shouldn’t be measuring sexual preference on a single continuum from straight to gay, but rather two separate dimensions: attraction to the same sex and attraction to the opposite sex.”

Limitations and questioning

The study has limitations, including that it is based mainly on people of European ancestry, while the age range of participants does not fully reflect that of the wider population. It also relied on self-reported behavior.

The idea that genetics might play a role in same-sex attraction was propelled into the spotlight in 1993 when Dean Hamer, a scientist at the US National Cancer Institute, and his team found links between DNA markers on the X chromosome and male sexual orientation.

Subsequent research has thrown up mixed results, although recent studies have supported the theory that genetics plays a role in sexual orientation.

Qazi Rahman, a leading authority on sexual orientation research from King’s College London, welcomed the study but said that the databases involved only captured information from a small percentage of people who were invited to participate. That, he said, means that the genetic variants found in the latest research might reflect another trait particular to those who chose to respond.

The study has generated debate and concern, including within the renowned Broad Institute itself. Several scientists who are part of the L.G.B.T.Q. community there said they were worried the findings could give ammunition to people who seek to use science to bolster biases and discrimination against gay people.

“I deeply disagree about publishing this,” said Steven Reilly, a geneticist and postdoctoral researcher who is on the steering committee of the institute’s L.G.B.T.Q. affinity group, Out@Broad. “It seems like something that could easily be misconstrued,” he said

Pufferfish.

Pufferfish spines and the hair on your head are governed by the same set of genes

The same set of genes that gives mammals hair and birds feathers helps the pufferfish grow spines.

Pufferfish.

Image credits Kevin Yi.

While the spines that cover pufferfish are readily apparent, how they got to be there isn’t. New research, however, has identified the genes responsible for the evolution and development of these striking skin ornaments, finding that the process is similar to how other vertebrates get their hair or feathers.

Fish, puffed

“Pufferfish are some of the strangest fish in the ocean, particularly because they have a reduced skeleton, beak-like dentition and they form spines instead of scales — not everywhere, but just in certain patches around the body,” says corresponding author Gareth Fraser, an Assistant Professor at the University of Florida.

“It just blows me away that regardless of how evolutionarily-different skin structures in animals are, they still use the same collection of genes during development.”

Fraser and his team analyzed the development of the spines in pufferfish embryos. Initially, they expected to see them form from scales, in essence, that some of the scales themselves would morph into the spines. However, what they found was that the spines’ development is independent of that of the scales. In addition to this, they identified the genetic network that underpins the development of the scales, and it’s the same one that governs hair and feather formation in other vertebrates.

After identifying these genes, the team decided to block some (CRISPR-Cas9 and other genetic techniques) that are classic markers of skin appendage development to see what would happen. This approach allowed the researchers to reduce the number of spines that grew on pufferfish, and make them ‘sprout’ in more varied places around their body. Normally, the spines are localized to specific areas on the pufferfish where they can offer the most protection, Fraser explains.

“When pufferfish inflate by ingesting water or in some cases air, their skin becomes stretched, especially around the abdomen and is more susceptible to damage, such as being torn,” he says. “Spines reinforce the puffed-up abdomen. In extreme cases, some pufferfish have lost all other spines on their body and retain only the abdominal spines.”

The diversity seen in spine location among pufferfish is likely the result of different ecological pressures, he adds. Different morphological set-ups of spines may allow pufferfish to access new ecological niches. “As the climate changes and environments become different, pufferfish may use these evolving traits to tolerate and adapt to change,” Fraser says. Ultimately, him and his team hope to identify the genetic differences that create the wealth of diversity in spine layout and morphology.

“We can manipulate different things associated with pufferfish diversity, which gives us clues about the function of genes that are necessary for normal development and helps us understand the evolution and patterns of pufferfish spines.”

“Pufferfish are wildly-derived fish that are incredibly different from other groups, and ultimately, we want to see if there’s something specific to the genome of the pufferfish that can provide clues to suggest mechanisms that allow them to create these weird structures.”

The paper “Evolution and developmental diversity of skin spines in pufferfishes” has been published in the journal iScience.

Escherichia Coli.

Researchers film bacteria sharing antibiotic resistance in real time — and find a potential fix

New research into how antibiotic resistance spreads among bacterial populations points the way forward to fighting this growing threat.

Escherichia Coli.

Escherichia Coli.
Image credits Gerd Altmann.

Growing levels of antibiotic resistance, both in scope and sheer effectiveness, is a very real threat for us. It’s easy, in this day and age, to consider most bacteria and the diseases they cause as simple nuisances. But that safety is owed to the antibiotics and active compounds we’ve developed to protect us — should they turn ineffective, we’re as much at the mercy of these germs as any other organism on the planet.

However, new research shows it isn’t unstoppable. Robust, yes; backed-up with redundancy systems, yes — but not unstoppable.

The tiny pump that could

The research was carried out by a team of researchers from the Université Lyon and CNRS, the French National Center for Scientific Research. They successfully filmed the process of antibiotic resistance acquisition in real time, thus finding a new and central player that takes part in this process.

Antibiotic resistance primarily spreads among bacteria through a process known as (bacterial) conjugation, which is basically the sharing of genetic material. Systematic genetic sequencing of both pathogenic and environmental strains of bacteria suggests that a very wide range of genetic elements can be shared via conjugation which encodes resistance to most or all of the antibiotic classes currently in use.

So we know how it goes down, but we’re still in the dark in regards to how long it takes for conjugation to work its magic and how antibiotics interfere with the process. That’s what the present research aimed to find out.

The team worked with a strain of Escherichia Coli (E.coli) bacteria resistant to tetracycline, a commonly used antibiotic. Tetracycline works by attaching itself to the bacteria’s molecular mechanisms, rendering them unable to produce proteins. The team exposed the bacteria to tetracycline in the presence of another strain that was not resistant to the substance. Previous research told the team that, in such conditions, the spread of antibiotic resistance hinges on the first strain clearing the drug out using “efflux pumps” on their membrane before it can wreak havoc internally, thus conferring them some degree of resistance to the drug.

The team reports seeing DNA transmission being carried out between individuals of the two strains with one specific efflux pump, the TetA pump. Using fluorescent marking and live-cell microscopy, the researchers tracked the spread the DNA encoding this pump from resistant bacteria and how the recipient ones expressed the genes.

It only took 1 to 2 hours for the single-stranded DNA fragments put out by the efflux pumps to be turned into a double-stranded DNA molecule and, subsequently, into a functional protein, they report. In effect, that is the timeframe required for resistance to spread between different strains of bacteria. You can see the process in the video below; green bacteria are the donors (i.e. resistant E.coli strain) and the red ones are the recipients. In effect, everything you see turning green is learning tetracycline resistance from its peers.

 

Given the way tetracycline works — by blocking the production of proteins — you’d reasonably expect it to block the ‘red’ bacteria from synthesizing TetA efflux pumps (they’re made of proteins). However, the team is surprised to report that this isn’t the case. Paradoxically, the bacteria were able to survive and develop a resistance to tetracycline even in the presence of this drug — which suggested there’s another, unknown factor at work here.

It seems to be another efflux pump, they explain. Called AcrAB-TolC (scientists are good with naming stuff), this pump is present in virtually all bacteria, but serves a general role. As such, it’s less efficient than TetA at ejecting tetracycline, but it is still able to remove a small quantity from the cell, allowing the bacteria to carry out a minimal level of protein synthesis. This process allows bacteria to become durably resistant to antibiotics should they be provided with the right genes from the environment.

However, the findings also point the way to a potential fix for acquired antibiotic resistance.

“We could even consider a therapy combining an antibiotic and a molecule able to inhibit this generalist pump,” says Christian Lesterlin, a researcher at Lyon’s Molecular Microbiology and Structural Biochemistry laboratory and the paper’s corresponding author.

“While it is still too soon to envisage the therapeutic application of such an inhibitor, numerous studies are currently being performed in this area given the possibility of reducing antibiotic resistance and preventing its spread to the various bacterial species.”

The paper “Role of AcrAB-TolC multidrug efflux pump in drug-resistance acquisition by plasmid transfer” has been published in the journal Science.

The man who is ageing too fast

Credit: Moonassi for Mosaic.

Nobuaki Nagashima has Werner syndrome, which causes his body to age at super speed. This condition is teaching us more about what controls our genes, and could eventually help us find a way to slow ageing – or stop it altogether.

Nobuaki Nagashima was in his mid-20s when he began to feel like his body was breaking down. He was based in Hokkaido, the northernmost prefecture of Japan, where for 12 years he had been a member of the military, vigorously practising training drills out in the snow. It happened bit by bit – cataracts at the age of 25, pains in his hips at 28, skin problems on his leg at 30.

At 33, he was diagnosed with Werner syndrome, a disease that causes the body to age too fast. Among other things, it shows as wrinkles, weight loss, greying hair and balding. It’s also known to cause hardening of the arteries, heart failure, diabetes and cancer.Newsletter: 

I meet Nagashima under the white light of a Chiba University Hospital room, around 25 miles west of Tokyo. A grey newsboy cap covers his hairless head freckled with liver spots. His eyebrows are thinned to a few wisps. Black-rimmed glasses help with his failing eyesight, his hip joints – replaced with artificial ones after arthritis – ache as he stands to slowly walk across the room. These ailments you might expect to see in an 80-year-old. But Nagashima is just 43.

He tells me that he has been in and out of hospital ever since his diagnosis. That his deteriorating health forced him to leave the military. Nagashima has had five or six surgeries, from his toes to hips to eyes, to treat ageing-related ailments. He’s lost 15 kilograms since he was first diagnosed. He needs a walking stick to do a distance over a few metres, and has a temporary job at the City Hall, going to the office when his body will allow but working from home when it doesn’t.

He remembers driving home after his diagnosis, crying to himself. When he told his parents, his mother apologised for not giving birth to a stronger person. But his father told him that if he could endure this disease, he was indeed strong, and maybe scientists would learn from him, gaining knowledge that could help others.

Credit: Moonassi for Mosaic.

Apart from the X and Y sex chromosomes, we inherit two copies of every gene in our bodies – one from our mother and one from our father. Werner syndrome is what’s called an autosomal recessive disorder, meaning it only shows when a person inherits a mutated version of a gene called WRN from both parents.

Nagashima’s parents are ageing normally. They each have one functional copy of WRN, so their bodies don’t show any symptoms of the disease. But he was unfortunate to have received two mutated copies of WRN. His grandparents are still alive and as well as one might expect for a couple in their 90s, and the family are unaware of any other Werner cases in their family history.

WRN was discovered only in 1996, and since then there have been few examples of Werner. As of 2008, there were only 1,487 documented cases worldwide, with 1,128 of them in Japan.

Lest this seem like a uniquely Japanese condition, George Martin, co-director of the International Registry of Werner Syndrome at the University of Washington, thinks the number of actual cases globally is around seven times higher than the numbers recorded today. He says most cases around the world will not have come to the attention of any physicians or registries.

Credit: Moonassi for Mosaic.

The huge imbalance in Japanese cases he puts down to two factors. First, the mountains and islands of the Japanese landscape and the isolating effect that’s had on the population through history – people in more isolated regions in the past were more likely to end up having children with someone more similar to them genetically. A similar effect is seen in the Italian island of Sardinia, which also has a cluster of Werner cases. Second, the startling nature of the condition, and the higher frequency with which it appears in Japan (affecting an estimated one in a million people worldwide but one in 100,000 in Japan), means the Japanese medical system is more aware than most when Werner syndrome appears.

In Chiba University Hospital, they hold records of 269 clinically diagnosed patients in total, 116 of whom are still alive. One of them is Sachi Suga, who can only get around in a wheelchair. Her muscles are so weak she can no longer climb in and out of the bath, which makes it difficult to keep up the Japanese practice of ofuro, the ritual of relaxing each night in a deep tub of steaming hot water. She used to cook breakfast regularly for herself and her husband, but now she cannot stand at a stove for more than a minute or two at a time. She’s resorted to preparing quicker-to-make miso soup the night before, which he eats before leaving for work at 5.30am.

Waif-like in a short black wig, Suga has tiny wrists as delicate as glass, and she speaks to me in a hoarse, throaty whisper. She tells me of the home aid worker who visits three times a week to help wrap her ulcer-covered legs in bandages. She has terrible back and leg pain. “It hurt so much, I wanted my legs to be cut off.” Yet on the positive side, the 64-year-old has long surpassed the average life expectancy of around 55 for people with Werner syndrome.

Only a handful of people with Werner currently attend Chiba. Recently, they started a support group. “Once our conversation started, I forgot about the pain completely,” says Suga. Nagashima says the meetings often end with the same question: “Why do I have this disease?”

If you were to unravel the 23 pairs of chromosomes in one of your cells you would end up with about two metres of DNA. That DNA is folded up into a space about a 10,000th of that distance across – far more compacted than even the tightest origami design. This compacting happens with help from proteins called histones.

DNA, and the histones that package it up, can acquire chemical marks. These don’t change the underlying genes, but they do have the power to silence or to amplify a gene’s activity. Where the marks are put or what form they take seems to be influenced by our experiences and environment – in response to smoking or stress, for instance. Some seem to be down to random chance, or the result of a mutation, as in cancer. Scientists call this landscape of markings the epigenome. We do not know yet exactly why our cells add these epigenetic marks, but some of them seem to be connected to ageing.

Steve Horvath, professor of human genetics and biostatistics at the University of California, Los Angeles, has used one type of these, called methylation marks, to create an “epigenetic clock” that, he says, looks beyond the external signs of ageing like wrinkles or grey hair, to more accurately measure how biologically old you are. The marks can be read from blood, urine, organ or skin tissue samples.

Horvath’s team analysed blood cells from 18 people with Werner syndrome. It was as if the methylation marking was happening on fast-forward: the cells had an epigenetic age notably higher than those from a control group without Werner.

Nagashima’s and Suga’s genetic information is part of a database held by Chiba University. There is also a Japan-wide database of Werner syndrome and the International Registry at the University of Washington. These registries are providing researchers with insights into how our genes work, how they interact with the epigenome, and how that fits with ageing as a whole.

Scientists now understand that WRN is key to how the whole cell, how all our DNA works – in reading, copying, unfolding and repairing. Disruption to WRN leads to widespread instability throughout the genome. “The integrity of the DNA is altered, and you get more mutations… more deletions and aberrations. This is all over the cells,” says George Martin. “Big pieces are cut out and rearranged.” The abnormalities are not just in the DNA but in the epigenetic marks around it too.

The million-dollar question is whether these marks are imprints of diseases and ageing or whether the marks cause diseases and ageing – and ultimately death. And if the latter, could editing or removing epigenetic marks prevent or reverse any part of ageing or age-related disease?

Before we can even answer that, the fact is, we know relatively little about the processes through which epigenetic marks are actually added and why. Horvath sees methylation marks as like the face of a clock, not necessarily the underlying mechanism that makes it tick. The nuts and bolts may be indicated by clues like the WRN gene, and other researchers have been getting further glimpses beneath the surface.

In 2006 and 2007, Japanese researcher Shinya Yamanaka published two studies which found that putting four specific genes – now called Yamanaka factors – into any adult cell could rewind it to an earlier, embryonic state, a stem cell, from which it could then be turned into any other type of cell. This method, which earned Yamanaka the Nobel Prize, has become a mainspring for stem cell studies. But what made this all the more interesting was that it completely reset the epigenetic age of the cells to a prenatal stage, erasing the epigenetic marks.

Researchers replicated Yamanaka’s experiments in mice with a condition called Hutchinson–Gilford progeria syndrome, which has similar symptoms to Werner but only affects children (Werner is sometimes called adult progeria). Remarkably, the mice rejuvenated briefly, but they died within a couple of days. Totally reprogramming the cells had also led to cancer and loss of the cells’ ability to function.

Then in 2016, scientists at the Salk Institute in California engineered a way to partially rewind the cells of mice with progeria using a lower dose of the Yamanaka factors for a shorter period. The premature ageing slowed down in these mice. They not only looked healthier and livelier than progeria mice who hadn’t had the treatment, but their cells were also found to have fewer epigenetic marks. Moreover, they lived 30 per cent longer than the untreated mice. When the researchers applied this same treatment to normally ageing mice, their pancreases and muscles also rejuvenated.

Separately, the same scientists are also using gene editing technology on mice to add or subtract other epigenetic marks and see what happens. They’re also trying to modify the histone proteins to see if that can alter genes’ activity. Some of these techniques have already shown results in reversing diabetes, kidney disease and muscular dystrophy in mice. The team are now trying similar experiments on rodents to see if they can reduce the symptoms of arthritis and Parkinson’s disease.

The big question remains: is the disappearance of the epigenetic marks related to the reversal of cell development – and possibly the ageing of the cell – or an unrelated side-effect? Scientists are still trying to understand how changes in epigenetic marks relate to ageing, and how Yamanaka factors are able to reverse age-related conditions.

Horvath says that, from an epigenetic point of view, there are clear commonalities in ageing across many regions of the body. Epigenetic ageing in the brain is similar to that of the liver or the kidney, showing similar patterns of methylation marks. When you look at it in terms of these marks, he says, “ageing is actually rather straightforward, because it’s highly reproducible in different organs”.

There’s a feverishness around the idea of resetting or reprogramming the epigenetic clock, Horvath tells me. He sees huge potential in all of it, but says it has the feel of a gold rush. “Everybody has a shovel in their hand.”

Jamie Hackett, a molecular biologist at the European Molecular Biology Laboratory in Rome, says the excitement comes from the suggestion that you can have an influence over your genes. Previously there was a fatalistic sense of being stuck with what you are given, and nothing you can do about it.

Back in the Chiba hospital room, Nagashima removes one of his high-top sneakers, which he has cushioned with insoles to make walking more bearable.

He tells me about his former girlfriend. They had wanted to marry. She was understanding after his diagnosis and even took a genetic test so they could be sure they would not pass the condition on to their kids. But when her parents discovered his condition, they disapproved. The relationship ended.Newsletter: 

He has a new girlfriend now. He wants to make her his life partner, he tells me, but to do so he must get up the courage to ask for her parents’ permission.

Nagashima slips down a brown sock, revealing a white bandage wrapped around the sole of his swollen foot and ankles. Beneath, his skin is raw, revealing red ulcers caused by his disease. “Itai,” he says. It hurts. Then he smiles. “Gambatte,” he says – I will endure.

Nobuaki Nagashima was in his mid-20s when he began to feel like his body was breaking down. He was based in Hokkaido, the northernmost prefecture of Japan, where for 12 years he had been a member of the military, vigorously practising training drills out in the snow. It happened bit by bit – cataracts at the age of 25, pains in his hips at 28, skin problems on his leg at 30.

At 33, he was diagnosed with Werner syndrome, a disease that causes the body to age too fast. Among other things, it shows as wrinkles, weight loss, greying hair and balding. It’s also known to cause hardening of the arteries, heart failure, diabetes and cancer. Newsletter: 

I meet Nagashima under the white light of a Chiba University Hospital room, around 25 miles west of Tokyo. A grey newsboy cap covers his hairless head freckled with liver spots. His eyebrows are thinned to a few wisps. Black-rimmed glasses help with his failing eyesight, his hip joints – replaced with artificial ones after arthritis – ache as he stands to slowly walk across the room. These ailments you might expect to see in an 80-year-old. But Nagashima is just 43.

He tells me that he has been in and out of hospital ever since his diagnosis. That his deteriorating health forced him to leave the military. Nagashima has had five or six surgeries, from his toes to hips to eyes, to treat ageing-related ailments. He’s lost 15 kilograms since he was first diagnosed. He needs a walking stick to do a distance over a few metres, and has a temporary job at the City Hall, going to the office when his body will allow but working from home when it doesn’t.

He remembers driving home after his diagnosis, crying to himself. When he told his parents, his mother apologised for not giving birth to a stronger person. But his father told him that if he could endure this disease, he was indeed strong, and maybe scientists would learn from him, gaining knowledge that could help others.

Apart from the X and Y sex chromosomes, we inherit two copies of every gene in our bodies – one from our mother and one from our father. Werner syndrome is what’s called an autosomal recessive disorder, meaning it only shows when a person inherits a mutated version of a gene called WRN from both parents.

Nagashima’s parents are ageing normally. They each have one functional copy of WRN, so their bodies don’t show any symptoms of the disease. But he was unfortunate to have received two mutated copies of WRN. His grandparents are still alive and as well as one might expect for a couple in their 90s, and the family are unaware of any other Werner cases in their family history. WRN was discovered only in 1996, and since then there have been few examples of Werner. As of 2008, there were only 1,487 documented cases worldwide, with 1,128 of them in Japan.

Lest this seem like a uniquely Japanese condition, George Martin, co-director of the International Registry of Werner Syndrome at the University of Washington, thinks the number of actual cases globally is around seven times higher than the numbers recorded today. He says most cases around the world will not have come to the attention of any physicians or registries.

The huge imbalance in Japanese cases he puts down to two factors. First, the mountains and islands of the Japanese landscape and the isolating effect that’s had on the population through history – people in more isolated regions in the past were more likely to end up having children with someone more similar to them genetically. A similar effect is seen in the Italian island of Sardinia, which also has a cluster of Werner cases. Second, the startling nature of the condition, and the higher frequency with which it appears in Japan (affecting an estimated one in a million people worldwide but one in 100,000 in Japan), means the Japanese medical system is more aware than most when Werner syndrome appears.

In Chiba University Hospital, they hold records of 269 clinically diagnosed patients in total, 116 of whom are still alive. One of them is Sachi Suga, who can only get around in a wheelchair. Her muscles are so weak she can no longer climb in and out of the bath, which makes it difficult to keep up the Japanese practice of ofuro, the ritual of relaxing each night in a deep tub of steaming hot water. She used to cook breakfast regularly for herself and her husband, but now she cannot stand at a stove for more than a minute or two at a time. She’s resorted to preparing quicker-to-make miso soup the night before, which he eats before leaving for work at 5.30am.

Waif-like in a short black wig, Suga has tiny wrists as delicate as glass, and she speaks to me in a hoarse, throaty whisper. She tells me of the home aid worker who visits three times a week to help wrap her ulcer-covered legs in bandages. She has terrible back and leg pain. “It hurt so much, I wanted my legs to be cut off.” Yet on the positive side, the 64-year-old has long surpassed the average life expectancy of around 55 for people with Werner syndrome.

Only a handful of people with Werner currently attend Chiba. Recently, they started a support group. “Once our conversation started, I forgot about the pain completely,” says Suga. Nagashima says the meetings often end with the same question: “Why do I have this disease?”

His mother apologised for not giving birth to a stronger person. But his father told him that if he could endure this disease, he was indeed strong.

If you were to unravel the 23 pairs of chromosomes in one of your cells you would end up with about two metres of DNA. That DNA is folded up into a space about a 10,000th of that distance across – far more compacted than even the tightest origami design. This compacting happens with help from proteins called histones.

DNA, and the histones that package it up, can acquire chemical marks. These don’t change the underlying genes, but they do have the power to silence or to amplify a gene’s activity. Where the marks are put or what form they take seems to be influenced by our experiences and environment – in response to smoking or stress, for instance. Some seem to be down to random chance, or the result of a mutation, as in cancer. Scientists call this landscape of markings the epigenome. We do not know yet exactly why our cells add these epigenetic marks, but some of them seem to be connected to ageing.

Steve Horvath, professor of human genetics and biostatistics at the University of California, Los Angeles, has used one type of these, called methylation marks, to create an “epigenetic clock” that, he says, looks beyond the external signs of ageing like wrinkles or grey hair, to more accurately measure how biologically old you are. The marks can be read from blood, urine, organ or skin tissue samples.

Horvath’s team analysed blood cells from 18 people with Werner syndrome. It was as if the methylation marking was happening on fast-forward: the cells had an epigenetic age notably higher than those from a control group without Werner.

The million-dollar question is whether these marks are imprints of diseases and ageing or whether the marks cause diseases and ageing – and ultimately death.

Nagashima’s and Suga’s genetic information is part of a database held by Chiba University. There is also a Japan-wide database of Werner syndrome and the International Registry at the University of Washington. These registries are providing researchers with insights into how our genes work, how they interact with the epigenome, and how that fits with ageing as a whole.

Scientists now understand that WRN is key to how the whole cell, how all our DNA works – in reading, copying, unfolding and repairing. Disruption to WRN leads to widespread instability throughout the genome. “The integrity of the DNA is altered, and you get more mutations… more deletions and aberrations. This is all over the cells,” says George Martin. “Big pieces are cut out and rearranged.” The abnormalities are not just in the DNA but in the epigenetic marks around it too.

The million-dollar question is whether these marks are imprints of diseases and ageing or whether the marks cause diseases and ageing – and ultimately death. And if the latter, could editing or removing epigenetic marks prevent or reverse any part of ageing or age-related disease?

Before we can even answer that, the fact is, we know relatively little about the processes through which epigenetic marks are actually added and why. Horvath sees methylation marks as like the face of a clock, not necessarily the underlying mechanism that makes it tick. The nuts and bolts may be indicated by clues like the WRN gene, and other researchers have been getting further glimpses beneath the surface.

In 2006 and 2007, Japanese researcher Shinya Yamanaka published two studies which found that putting four specific genes – now called Yamanaka factors – into any adult cell could rewind it to an earlier, embryonic state, a stem cell, from which it could then be turned into any other type of cell. This method, which earned Yamanaka the Nobel Prize, has become a mainspring for stem cell studies. But what made this all the more interesting was that it completely reset the epigenetic age of the cells to a prenatal stage, erasing the epigenetic marks.

Researchers replicated Yamanaka’s experiments in mice with a condition called Hutchinson–Gilford progeria syndrome, which has similar symptoms to Werner but only affects children (Werner is sometimes called adult progeria). Remarkably, the mice rejuvenated briefly, but they died within a couple of days. Totally reprogramming the cells had also led to cancer and loss of the cells’ ability to function.

Then in 2016, scientists at the Salk Institute in California engineered a way to partially rewind the cells of mice with progeria using a lower dose of the Yamanaka factors for a shorter period. The premature ageing slowed down in these mice. They not only looked healthier and livelier than progeria mice who hadn’t had the treatment, but their cells were also found to have fewer epigenetic marks. Moreover, they lived 30 per cent longer than the untreated mice. When the researchers applied this same treatment to normally ageing mice, their pancreases and muscles also rejuvenated.

Separately, the same scientists are also using gene editing technology on mice to add or subtract other epigenetic marks and see what happens. They’re also trying to modify the histone proteins to see if that can alter genes’ activity. Some of these techniques have already shown results in reversing diabetes, kidney disease and muscular dystrophy in mice. The team are now trying similar experiments on rodents to see if they can reduce the symptoms of arthritis and Parkinson’s disease.

The big question remains: is the disappearance of the epigenetic marks related to the reversal of cell development – and possibly the ageing of the cell – or an unrelated side-effect? Scientists are still trying to understand how changes in epigenetic marks relate to ageing, and how Yamanaka factors are able to reverse age-related conditions.

Horvath says that, from an epigenetic point of view, there are clear commonalities in ageing across many regions of the body. Epigenetic ageing in the brain is similar to that of the liver or the kidney, showing similar patterns of methylation marks. When you look at it in terms of these marks, he says, “ageing is actually rather straightforward, because it’s highly reproducible in different organs”.

There’s a feverishness around the idea of resetting or reprogramming the epigenetic clock, Horvath tells me. He sees huge potential in all of it, but says it has the feel of a gold rush. “Everybody has a shovel in their hand.”

Jamie Hackett, a molecular biologist at the European Molecular Biology Laboratory in Rome, says the excitement comes from the suggestion that you can have an influence over your genes. Previously there was a fatalistic sense of being stuck with what you are given, and nothing you can do about it.

The excitement comes from the suggestion that you can have an influence over your genes.

Back in the Chiba hospital room, Nagashima removes one of his high-top sneakers, which he has cushioned with insoles to make walking more bearable.

He tells me about his former girlfriend. They had wanted to marry. She was understanding after his diagnosis and even took a genetic test so they could be sure they would not pass the condition on to their kids. But when her parents discovered his condition, they disapproved. The relationship ended.

He has a new girlfriend now. He wants to make her his life partner, he tells me, but to do so he must get up the courage to ask for her parents’ permission.

Nagashima slips down a brown sock, revealing a white bandage wrapped around the sole of his swollen foot and ankles. Beneath, his skin is raw, revealing red ulcers caused by his disease. “Itai,” he says. It hurts. Then he smiles. “Gambatte,” he says – I will endure.

This article first appeared on Mosaic and is republished here under a Creative Commons licence.

Tomato.

Team sequences the pan-genome of tomatoes in a bid to make them tasty again

Researchers at the Agricultural Research Service (ARS) and the Boyce Thompson Institute (BTI) want to bring back the tasty tomato of yore.

Tomato.

Image credits Mauro Borghesi.

Sadly, it seems that store-bought tomatoes just aren’t very tasty. An international research team thinks they have the way to fix this tasteless problem, though. They have finished constructing the pan-genome for the cultivated tomato and its wild relatives, mapping almost 5,000 previously undocumented genes. Armed with this knowledge, researchers might be able to bring the flavor back.

They don’t make them like they used to

“These novel genes discovered from the tomato pan-genome added substantial information to the tomato genome repertoire and provide additional opportunities for tomato improvement,” says co-author Zhangjun Fei, a bioinformatics scientist at the Boyce Thompson Institute.

“The presence and absence profiles of these genes in different tomato populations have shed important lights on how human selection of desired traits have reshaped the tomato genomes.”

A genome is the map of an organism’s genes and their functions. Genomes are, unsurprisingly, sequenced for individual organisms, and these are in turn used to create a kind of reference genome for the rest of the species. The team’s pan-genome, on the other hand, includes all of the genes from 725 different cultivated and closely related wild tomatoes, which revealed 4,873 genes that were absent from the original reference genome.

So what seems to be the problem with our tomatoes? Where’s the taste? The team reports that cultivated tomatoes show a wide range of physical and metabolic variation but, by and large, they’ve all been through several severe bottlenecks during their domestication and later breeding. In effect, this means that today’s tomatoes aren’t very genetically diverse.

Modern breeders, the team explains, have focused on traits such as yield, shelf life, disease resistance, and stress tolerance, which are economically important to growers. However, the pan-genome does point to a few genes we can use to improve the flavor, too.

“One of the most important discoveries from constructing this pan-genome is a rare form of a gene labeled TomLoxC, which mostly differs in the version of its DNA gene promoter,” explained James Giovannoni, a molecular biologist at the Agricultural Research Service (ARS) and paper co-author.

“The gene influences fruit flavor by catalyzing the biosynthesis of a number of lipid (fat)-involved volatiles–compounds that evaporate easily and contribute to aroma.”

TomLoxC also facilitates the production of apocarotenoids — a class of organic chemicals derived from carotenoids including vitamin A precursors — which function as signaling molecules for various responses in plants, including environmental stresses. The compounds also have a variety of floral and fruity odors that are important in tomato taste, the team notes.

The rarer version of TomLoxC was found in only 2% of older or heirloom varieties of large tomato. The common version was present in 91% of currant-sized wild tomatoes, primarily Solanum pimpinellifolium, the wild predecessor of the cultivated tomato. It is becoming more common in newer varieties.

“It appears that there may have been strong selection pressure against or at least no selection for the presence of this version of TomLoxC early in the domestication of tomatoes,” Giovannoni added. “The increase in prevalence of this form in modern tomatoes likely reflects breeders’ renewed interest in improved flavor.”

The team says that with the pan-genome in hand, breeders should be able to quickly increase the flavor of mass-produced tomatoes without sacrificing the traits that make them so economically-viable.

“These novel genes discovered from the tomato pan-genome added substantial information to the tomato genome repertoire and provide additional opportunities for tomato improvement. The presence and absence profiles of these genes in different tomato populations have shed important lights on how human selection of desired traits have reshaped the tomato genomes,” said Fei.

The team also expects that the nearly new tomato 5,000 genes they’ve identified in the pan-genome will help breeders improve it in further ways. Tomatoes, although they are fruits, botanically, are one of the most eaten vegetables worldwide, with a total annual production of 182 million tons (worth more than $60 billion). In the U.S., tomatoes are the second-most consumed vegetable after potatoes. Each American eats an average of 20.3 pounds of fresh tomatoes and an additional 73.3 pounds of processed tomatoes per year (estimated based on 2017 figures).

The paper “The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor” has been published in the journal Nature Genetics.

Python.

A new study explains how snakes lost their legs

Efforts to understand how changes in the genome lead to changes in phenotypes is showing us why snakes don’t have legs.

Python.

Image via Pixabay.

While snakes and lizards belong to the same order (Squamata), they differ in one obvious aspect: snakes do not have limbs. New research is looking into the genetic changes that led to this outward difference. The study, led by Juliana Gusson Roscito at the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden, Germany, also analyzed eye degradation in certain subterranean mammals.

Different within, different without

“The research consisted of an investigation of the genomes of several species of vertebrates, including the identification of genomic regions that changed only in snakes or subterranean mammals, while remaining unchanged in other species that have not lost their limbs or have normal eyes,” Roscito said.

Mammals with degraded visual systems seem to have shed certain genes from their genomes — mainly those associated with the formation of the crystalline lens and photoreceptor cells in the eyes. This process was very likely gradual, taking successive mutations during the evolutionary process but, eventually, these genes completely lost their ability to encode proteins. However, Roscito says, this isn’t what happened to snakes — they haven’t lost the genes associated with limb-formation.

“To be more precise, the study that sequenced the genome of a snake did detect the loss of one gene, but only one,” she adds. “Therefore, the approach we chose in our research consisted of investigating not the genes but the elements that regulate gene expression.”

Gene expression — whether a gene is ‘active’ or not — depends on regulatory elements that are outside of the gene itself. These basically allow or block the information inside the gene to be transcribed into RNA and then be carried off to generate a protein. This process is regulated by cis-regulatory elements (CREs), sequences of nucleotides in DNA placed near the genes they regulate. These CREs can significantly alter a genome’s functionality via the genes they block or enable.

“A regulatory element can activate or inhibit the expression of a gene in a certain part of the organism, such as the limbs, for example, while a different regulatory element can activate or inhibit the expression of the same gene in a different part, such as the head,” Roscito explains.

“If the gene is lost, it ceases to be expressed in both places and can often have a negative effect on the organism’s formation. However, if only one of the regulatory elements is lost, expression may disappear in one part while being conserved in the other.”

However, it’s pretty difficult to accurately identify CREs. Genes all follow a certain structural pattern, having base pairs at each end of the gene — so they’re easy to delineate. CREs have to be identified indirectly, usually by comparing DNA sequences from different species. That’s exactly what the team did for this study: they compared the genomes of snakes with those of various other reptile and vertebrates (that have limbs). As “genome sequences for reptiles with well-developed limbs are scarce”, the team writes, they sequenced and assembled the genome of Salvator merianae, the tegu lizard, themselves. This is “the first species of the teiid lineage ever sequenced,” the authors add.

Gold Tegu.

The gold tegu, Tupinambis teguixin.
Image credits Joel Santana.

Using this genome as a reference, the team looked at the genomes of several other species. These included two snakes (boa and python) three other limbed reptiles (green anole lizard, dragon lizard, and gecko) three birds, an alligator, three turtles, 14 mammals, a frog, and a coelacanth (a very rare type of fish). They ‘aligned’ these 29 genomes together and used that as a basis for their analysis.

Armed with 5,000 possible candidates for regulatory elements in the DNAs of these species, the team looked at the genomes of several species of snakes. They managed to narrow down the search to a set of CREs whose mutation may have led to the disappearance of limbs in snakes.

“There are several studies concerning a well-known regulatory element that regulates a gene that, when modified, causes various defects in limbs. Snakes have mutations in this CRE. In a study published in 2016, the mouse CRE was replaced with the snake version, resulting in practically limbless descendants,” Roscito says. “This was a functional demonstration of a mechanism that may have led to limb loss in snakes.”

“However, this CRE is only one of the regulatory elements for one of several genes that control limb formation. Our study extended the set of CREs. We showed that several other regulatory elements responsible for regulating many genes have mutated in snakes. The signature is far more comprehensive. An entire signaling cascade is affected.”

The paper “Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution” has been published in the journal Nature Communications.

Pocillopora damicornis.

Widespread coral species shows unique adaptations against environmental changes

One coral species is evolving to cope with climate change, a new paper reveals.

Pocillopora damicornis.

Pocillopora damicornis. Dampier Archipelago, western Australia.
Image credits coral.aims.gov.au

Researchers from the University of Miami (UM) found that the cauliflower coral (Pocillopora damicornis) evolved unique tricks against environmental change. Roughly one-third of its genome is unique among all reef-building corals — and many of these unique genes relate to immune functions, the team explains.

Unique adaptations

This wealth of genes, the team adds, may give P. damicornis a unique edge in survival amid today’s changing environments. As warmer temperatures and higher ocean acidity wreak havoc on reefs across the world, this coral — one of the most abundant and widespread reef-building corals in the world — may help us better understand how anthozoans deal with stress.

“This coral is traditionally thought of as a weed, and yet it may be one of the last corals to survive environmental changes such as climate change,” said Nikki Traylor-Knowles, an assistant professor of marine biology and ecology at the UM Rosenstiel School and senior author of the study.

For the study, the team analyzed the genetic sequences of two healthy fragments and two bleached fragments of P. damicornis. The genome was then compared to publicly available genomes of several coral and cnidarian (jellyfish) species. The results suggest that hard corals like P. damicornis rely heavily on their innate immune systems when adapting to changes in the environment.

Pocillopora damicornis purple.

Pocillopora damicornis. Photographed in a deep, very sheltered habitat on Houtman Abrolhos Islands, south-western Australia.
Image credits coral.aims.gov.au

That in itself isn’t very surprising. An animal’s immune system is a vital part of its survival strategy. Those with stronger immune systems are better equipped to deal with environmental changes, giving them an evolutionary edge. However, P. damicornis had way more genes related to immune functions than the team expected to find — suggesting it has a very robust immune system. As such, it would have a better shot at staying alive even under climate change scenarios, the team adds.

“The study shows that [P. damicornis] is an important coral with a very complex and unique immune system, which may explain why it is able to survive in so many different locations,” said the paper’s lead author Ross Cunning.

“This study helps us better understand how corals deal with stress,” said Traylor-Knowles. “Its complex immune system indicates that it may have the tools to deal with environmental change much more easily than other corals.”

The paper “Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution” has been published in the journal Scientific Reports.

Credit: Pixabay.

Scientists find more than 1,200 genes linked to educational attainment

Credit: Pixabay.

Credit: Pixabay.

As part of one of the largest human genetics studies to date, an international team of scientists has identified more than 1,200 genetic variants associated with the level of education a person completes. A ‘polygenic score’, which the researchers developed based on these variants, can explain more than 11% of the variance in educational attainment between the participants.

The study published in the journal Nature Genetics involved a staggering 1.1 million participants from 15 countries. The meta-analysis used information derived from 71 datasets, including some of the largest genetic datasets in the world, such as the UK Biobank and those belonging to personal genomics company 23andMe.

Researchers spent more than two years analyzing the genetic information on the participants, which they linked to questionnaires that gauged the number of school years they completed. The study participants were age 30 and older and were of European descent.

Previously, a much smaller study identified 74 gene variants — some known to be involved in brain development — that were moderately predictive of the number of completed school years. This time, the huge pool of data managed to surface a wealth of new gene variants that may influence the educational attainment — 1,271 gene variants, to be more precise. Some of these genes are involved in neuron-to-neuron communication and neurotransmitter secretion.

“[The study] moves us in a clearer direction in understanding the genetic architecture of complex behavior traits like educational attainment,” said co-first author Robbee Wedow, a graduate student in CU Boulder’s Department of Sociology and researcher with the Institute for Behavioral Genetics.

These 1,271 genes serve to explain about 4% of the variation in the number of completed school years across the individuals sampled in the meta-analysis. However, when the effects of all the variants were measured across the genome, the researchers were able to develop a polygenic score. The score was predictive of 11-13% of the variation in educational attainment.

However, the researchers stress that individual gene variants have little predictive value.

“It would be completely misleading to characterize our results as identifying genes for education,” said corresponding author Daniel Benjamin, an associate professor at the Center for Economic and Social Research at the University of Southern California.

Of course, having a low polygenic score doesn’t mean that a person won’t achieve a high level of education or is ‘handicapped’ in some way. Socioeconomic status, personality (i.e. ambition), family — these are all important factors that may be far more important than genes in predicting educational attainment. In other words, it’s a matter of both nature and nurture.

The study is still important, nevertheless, as it helps scientists zoom-in on the contribution of the “nature” part. In doing so, the study helps paint a clearer picture of the complex interplay between genetics and the environment in shaping a person’s level of education.

“The most exciting part of this study is the polygenic score. Its level of predictive power for a behavioral outcome is truly remarkable,” said Wedow.

Credit: Memorial Sloan Kettering Cancer Center.

How cross-species jumping genes might have driven our evolution

Credit: Memorial Sloan Kettering Cancer Center.

Credit: Memorial Sloan Kettering Cancer Center.

We inherit genes from our parents — but that doesn’t mean that all of the DNA in our genome is solely sourced from humans, or even mammals for that matter. In a new study, researchers have found that the transfer of genes between species is more widespread than previously thought, something which may have significantly altered the course of mammalian evolution, and, consequently, that of our lineage.

Some genes “jump”

Believe it or not, genes can jump from one species to another, even in such cases when they’re extremely different from one another — for instance, from plants to animals. Such genes are called cross-species ‘jumping genes’ or transposable elements. Much of our DNA and that of many other organisms is represented by jumping genes. For example, 25% of the genome of cows and sheep are derived from jumping genes.

“Jumping genes, properly called retrotransposons, copy and paste themselves around genomes, and in genomes of other species. How they do this is not yet known although insects like ticks or mosquitoes or possibly viruses may be involved – it’s still a big puzzle,” said Professor David Adelson, Director of the University of Adelaide’s Bioinformatics Hub, and lead author of the new study published in the journal Genome Biology.

“This process is called horizontal transfer, differing from the normal parent-offspring transfer, and it’s had an enormous impact on mammalian evolution.”

[panel style=”panel-success” title=”What are jumping genes” footer=””]
Transposable elements (TEs), also known as “jumping genes,” are DNA sequences that move from one location on the genome to another.

There are two different types of transposons: autosomal transposons and non-autosomal transposons. They are present in all forms of life from bacteria to plants to mammals.[/panel]

Adelson and colleagues combed through the genomes of 759 species of plants, animals, and fungi. They zoomed-in on two particular jumping genes — L1 and BovB.

The BovB jumping genes has appeared in many species that are wide apart on the evolutionary tree. Credit: University of Adelaide.

The BovB jumping gene has appeared in many species that are wide apart on the evolutionary tree. Credit: University of Adelaide.

The L1 element is important in humans, having been associated with cancer and neurological disorders, and previously it was thought to be inherited solely from parent to offspring. But after analyzing a myriad of species, scientists actually found that L1 is a jumping gene, an important discovery that might one day enable researchers to backtrack the evolution of various diseases.

According to Adelson, L1s are abundant in plants and animals, sometimes appearing sporadically in fungi. Most surprisingly, however, L1s are missing from the platypus and echidna, the two Australian monotremes. This suggests that the gene appeared in the mammalian evolutionary pathway after the divergence from monotremes.

The BovB element is much younger than L1, but that doesn’t make it any less interesting. It was first discovered in cows, however, it has since been shown to jump between many different animals, including reptiles, elephants, and marsupials. Adelson believes that ticks are most likely the vector of cross-species BovB transfer.

The new findings suggest that BovB as jumped from even more species than previously thought. It transferred at least twice between frogs and bats, for instance, perhaps with the help of vectors such as bedbugs, leeches, and locusts.

It’s interesting how genes from extremely different foreign creatures can become embedded into our genomes and shape our evolution. We’re only just beginning to understand how jumping genes work, though, which leaves a lot of room for surprises.

“Even though our recent work involved the analysis of genomes from over 750 species, we have only begun to scratch the surface of horizontal gene transfer,” says Professor Adelson. “There are many more species to investigate and other types of jumping genes.”

Wings

CRISPR was used to change a butterfly’s wing color

Butterflies have complex color and scale patterns that allow them to camouflage, attract mates, or warn predators. Researchers used CRISPR/Cas9 to study the genes of one butterfly species to see how they contribute to the wing color and scale structure. Surprisingly, they found that the scale and color of the wings are linked to the same genes.

Wings

The wings of each melanin gene mutant.
image credits

The squinting bush brown butterfly, Bicyclus anynana, comes from East Africa and is typically a dark brown color. A postdoctoral fellow at the National University of Singapore, Yuji Matsuoka, disabled five of the butterfly’s pigment genes with CRISPR/Cas9. CRISPR is a new gene editing system that is capable of adding and disabling genes to different organisms easily and cheaply. The mutations not only changed the color of the butterfly to a light brown/yellow, but also altered the wing scale structure.

“Our research indicates that the color and structure of wing scales are intimately related because pigment molecules also affect the structure of scales,” says senior author Antónia Monteiro, a biologist at the National University of Singapore’s Faculty of Science and Yale-NUS College in Singapore. “Some end products of the melanin pathway, which produces butterfly wing pigments, play a role in both scale pigmentation and scale morphology.”

One mutation prevented the manifestation of the pigment dopa-melanin and it also caused an extra sheet of chitin to form horizontally on the upper surface of the wing scale. However, when the different pigment dopamine-melanin was mutated, there were suddenly vertical blades of chitin. This work shows that butterfly color and scale structure are intimately linked and seem to work together. These fives genes could constrain the evolution of a butterfly’s color.

The wildtype butterfly (left) and with mutations (right).
Image credits: William H. Piel and Antónia Monteiro.

The morphology of wing scales is very different between butterfly species. Melanin seems to be an important molecule in this process and it is likely not the only one. These results also help us to know more about the development and evolution of butterfly wing scales.

“Some butterflies can have vivid hues just by having simple thin films of chitin on their scales that interfere with incoming light to create shades known as structural colors without producing corresponding pigments,” says Monteiro. “Light beams reflecting off the top and bottom surfaces of the chitin layer can interfere with each other and accentuate specific colors depending on the thickness of the film, so our results might be interesting in this context.”

One interesting application of this result could be to bioengineer bright colors based on butterfly scales in the future. Above all, this discovery helps us to better understand butterfly coloration and wing scale structure.

Journal reference: Matsuoka et al. 2018. Melanin Pathway Genes Regulate Color and Morphology of Butterfly Wing Scales. Cell Reports.

Credit: Pixabay.

Scientists found nearly 1,000 new genes linked to intelligence

Credit: Pixabay.

Credit: Pixabay.

Dutch researchers uncovered 1,016 genes that they associated with intelligence, 939 of which are completely new to science. The findings help to identify the biological underpinnings of cognitive functions, but also those of related neurological and psychiatric disorders.

The team, led by Danielle Posthuma, a statistical geneticist at the Vrije Universiteit Amsterdam in the Netherlands, performed a genome-wide association study (GWAS) of almost 270,000 individuals. In such studies, scientists analyzed a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. Generally, GWASs look for associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other organism.

Each person took neurocognitive tests that gauged their level of intelligence, whose scores were then paired with variations in DNA — the SNPs. This is a straightforward method for identifying which mutations are associated with high intelligence.

Of the over 9 million mutations that were detected in this huge sample, the researchers found 205 regions in DNA linked with intelligence, 190 of which were new to science, as well as 1,016 specific genes, of which only 77 had been previously discovered. The mutations that were linked with high intelligence seem to protect overall cognitive health, with people carrying these mutations being less likely to develop Alzheimer’s, ADHD, depressive symptoms, and schizophrenia. On the downside, high intelligence mutations were linked to a higher incidence of autism. People with high intelligence were also likely to live longer, the team reported in Nature. 

Previously, Posthuma and colleagues identified 40 new genes linked to intelligence in a cohort of about 80,000 people. This time, they certainly outdid themselves.

The study used a novel statistical method called MAGMA to pinpoint specific types of cells and tissue where the genes were expressed. Many of the genes were expressed in a region of the brain called the basal ganglia, a cluster of neurons known to be involved in learning, cognition, and emotion. This suggests parts of this brain region are worth targetting with new pharmaceutical drugs in order to prevent or treat some psychiatric disorders.

In a separate study, also published in the journal Naturethe researchers identified nearly 500 genes and 124 loci (regions in DNA) associated with neurotic traits by combing through databases of 449,400 individuals from the UK Biobank and 23andMe. Neurotic traits include anxiety and depression.

This study suggests that people who worry a lot inherited different genes than those who more likely to be depressed, which suggests there are different genetic pathways that underlie these behaviors.

Both studies are remarkable in that they provide new leads for unraveling the neurobiology of neuroticism but also serious psychiatric diseases.