How Pools of Genetic Diversity Affect a Species’ Fate

Samantha Mash for Quanta Magazine

A new, deeper understanding of how the breeding structure of species affects their genetic diversity is giving conservationists better tools for saving animals. In March 2018 at the Ol Pejeta Conservancy in Kenya, surrounded by his devoted keepers, Sudan the northern white rhino breathed his last. He wasn’t the only remaining northern white rhino because three females in protective captivity survived him.

But Sudan’s death ended any hope of those females breeding naturally and rendered the northern white rhino effectively extinct. The moment made headlines, and the world lamented the high-profile extinction. But it wasn’t a true species extinction event. Northern white rhinos are just a distinct subset, or subspecies, of white rhino. More than 10,000 white rhinos are still left in the southern subspecies. White rhinos as a species aren’t even endangered.

Nevertheless, ever since Sudan’s death, Cynthia Steiner, an associate director in conservation genetics for the San Diego Zoo Wildlife Alliance, and her colleagues have gone to great lengths to try to reboot the northern subspecies. They’re working to turn stem cells collected from the remaining females into embryos for in vitro fertilization. They want more northern white rhinos, and mixing in genes from southern white rhino males just won’t do.

“Before, people would say, we need to save the species,” Steiner explained. “But that’s not enough if you think about it. When you talk about species, you’re not considering the whole evolutionary potential of all the different groups that make up that species. That’s why the new notion is: We really want to save the genetic structure of the species, these different populations — subspecies — that have unique characteristics at the genomic level.”

In recent years, biologists have developed a deeper understanding of how the relationship between genetic diversity and population structure can influence the fate of a species. They’ve long understood how geography and ecological variations often partition species into subspecies or other small distinct populations of individuals who are more closely related to one another than to outsiders.

Now, with the help of better tools and techniques for studying the genomes of creatures in the wild, researchers are discovering the full extent of how much the genetic dynamics within and among those populations can affect how resiliently a species can evolve and adapt to changing conditions over time………..

Continue reading….

By : Anna Funk

Source: How Pools of Genetic Diversity Affect a Species’ Fate | Quanta Magazine

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Want To Improve Your Memory? Try These Unexpected Tips

Amanda Northrop/Vox

The brain is an extraordinary organ, with many wonderful qualities, including the ability to forget — which may actually be a good thing. “If we remembered everything that we experienced, our brains would be hoarders, clogged with all sorts of useless crap that gets in the way of what we really need,” says Charan Ranganath, a professor of psychology and the director of the Dynamic Memory Lab at the University of California Davis.

In today’s constantly plugged-in, always-on world, people are faced with a barrage of information — emails, news, pointless meetings, traffic updates, chitchat from family members — far more than anyone can process, Ranganath explains. “Instead, evolution favored quality over quantity,” he says. “We get good quality memories for the stuff that we are paying attention to, and that is often the important stuff.

But if we’re not paying attention to something, we will never really get a good memory of it to begin with.” These issues with remembering often rear their heads at the least convenient times: when you’re in a rush and can’t find your keys, when you enter a room and don’t know what you came for, when you’re talking with an acquaintance whose name escapes you, when a friend refers to a nice moment you shared and you have no recollection.

This kind of forgetting is completely normal, Ranganath says, but is frustrating nonetheless. (Other, more severe conditions can cause memory loss and interruptions to memory recall, such as trauma, Alzheimer’s, and ADHD. Strategies to address these disorders may include therapy and medication, more intensive than the tips outlined here.)

Generally, though, hope is not lost if your recall is a little rusty. Memory is an active process, not a passive one, says clinical neuropsychologist Michelle Braun. “Which kind of undermines a longstanding myth that brain health is just a product of genetics and there’s really nothing we can do about it,” she says. Paying a little more attention and savoring special events can help you remember life’s moments, big and small.

Start paying undivided attention to important events and interactions

The responsibilities of modern life mean there are more priorities than ever vying for your attention. How many times have you walked away from a conversation having no idea what was discussed because you were distracted by your phone? “You can get impoverished memories for past events because you were never really there in the first place,” Ranganath says

Absentmindedness is one of memory researcher Daniel Schacter’s “seven sins of memory,” common weaknesses in memory everyone experiences. This is when you don’t pay attention to where you put your keys or are so scatterbrained you miss an important doctor’s appointment. “If we’re, for example, engaging in multitasking, we may never really encode the information about where did I just leave my keys or glasses,” says Schacter, a professor of psychology at Harvard University. ….Continue reading

Source: Memory loss: Expert advice for improving memory and concentration – Vox

.

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What We Know About Why Some People Never Get Covid 19

Americans who haven’t had covid-19 are now officially in the minority. A study published this week from the US Centers for Disease Control and Prevention (CDC) found that 58% of randomly selected blood samples from adults contained antibodies indicating that they had previously been infected with the virus; among children, that rate was 75%.

What is different about that minority of people that hasn’t yet gotten infected? Stories abound of close calls, of situations where people are sure they could have (or should have) gotten sick, but somehow dodged infection. Not all the questions are answered yet, but the question of what distinguishes the never-covid cohort is a growing area of research even as the US moves “out of the full-blown” pandemic. Here are the possibilities that scientists are considering to explain why some people haven’t contracted the virus.

They behave differently

We’ve seen it play out time and time again—some people adhere more strictly to protocols known to reduce transmission of the virus, including wearing a mask and getting vaccinated. Some people avoid large public settings and may have even been doing so before the pandemic, says Nicholas Pullen, a biology professor at the University of Northern Colorado. Then again, that doesn’t tell the whole story; as Pullen himself notes: “Ironically, I happen to be one of those ‘never COVIDers’ and I teach in huge classrooms!”

They’ve trained their immune systems

The immune system, as any immunologist or allergist can tell you, is complicated. Though vaccination against covid-19 can make symptoms more mild for some people, it can prevent others from contracting the illness altogether.

Growing evidence suggests that there may be other ways that people are protected against the virus even without specific vaccines against it. Some could have previously been infected with other coronaviruses, which may allow their immune systems to remember and fight similarly shaped viruses. Another study suggests that strong defenses in the innate immune system, barriers and other processes that prevent pathogens from infecting a person’s body, may also prevent infection.

An innate immune system that’s already not functioning as well due to other medical conditions or lifestyle factors such as sleep or diet may put a person at higher risk of getting sick from a pathogen. There’s not single answer here yet, but initial studies are intriguing and may offer avenues for future treatments for covid-19 and other conditions.

They’re genetically different

In the past, studies have found interesting associations between certain genetic variants and people’s susceptibility to communicable diseases such as HIV, tuberculosis, and the flu. Naturally, researchers wondered if such a variant could exist for covid-19. One June 2021 study that was not peer reviewed found an association between a genetic variant and lower risk of contracting covid-19; another large-scale study, focused on couples in which one person got sick while the other didn’t, kicked off in Oct. 2021.

“My speculation is that something will be borne out there, because it has been well observed that resistance embedded in genetic variation is selected in pandemics,” Pullen says. But most experts suspect that even if they are able to identify such a variant with some certainty, it’s likely to be rare. For now, it’s best for those who haven’t gotten covid to assume they’re as susceptible as anyone else. Whatever the reasons some people haven’t yet gotten sick, the best defense remains staying up to date with vaccinations and avoiding contact with the virus.

Source: What we know about why some people never get covid-19 — Quartz

“Being exposed to the SARS-CoV-2 virus doesn’t always result in infection, and we’ve been keen to understand why,” study author Rhia Kundu said in a statement, using the scientific name for the coronavirus. “We found that high levels of pre-existing T cells, created by the body when infected with other human coronaviruses like the common cold, can protect against COVID-19 infection.”

The study, which examined 52 people who lived with someone who contracted the coronavirus, found that those who didn’t get infected had significantly higher levels of T cells from previous common cold coronavirus infections. T cells are part of the immune system and believed to protect the body from infection. “Our study provides the clearest evidence to date that T cells induced by common cold coronaviruses play a protective role against SARS-CoV-2 infection,” study author Ajit Lalvani said in a statement.

Researchers cautioned that the findings should not be relied upon as a protection strategy. “While this is an important discovery, it is only one form of protection, and I would stress that no one should rely on this alone,” Kundu said. “Instead, the best way to protect yourself against COVID-19 is to be fully vaccinated, including getting your booster dose.” And the findings on the subject have been inconsistent, with other studies actually suggesting that previous infection with some coronaviruses have the opposite effect.

A major question that has come from the so-called ‘never COVID’ group is whether genetics plays a role in preventing infection. In fact, the question has spurred a team of international researchers to look for people who are genetically resistant to COVID-19 in the hopes that their findings could improve therapeutics. “What we are doing essentially is that we are testing the hypothesis that some people might not be able to get infected because of their genetic and inborn makeup, meaning that they might be genetically resistant to COVID,” says Spaan, who is a member of the COVID Human Genetic Effort.

The effort has sequenced genetic data from about 700 individuals so far, but enrollment is ongoing and researchers have received thousands of inquiries, according to Spaan. The study has several criteria, including laboratory test confirmation that the person has not had previous COVID-19 infection, intense exposure to the virus without access to personal protective equipment like masks and an unvaccinated status at the time of exposure, among others. So far, the group doesn’t know what the genetic difference could be – or if it even exists at all, though they believe it does.

“We do not know how frequent it is actually occurring,” Spaan says. “Is it like a super rare individual with a very, very rare mutation? Or is that something more common?” But the hypothesis is “embedded in human history,” according to Spaan. “COVID is not quite the first pandemic that we are dealing with,” Spaan says. “Humans have been exposed to viruses and other pathogens across time from the early beginning, and these infections have left an imprint on our genetic makeup.”

Those who haven’t gotten the coronavirus are “very much at risk,” says Murphy of Northwestern University. “I think every unvaccinated person is going to get it before this is over.” Experts stressed that research to determine why some people get COVID-19 while others don’t is still very much underway, and no one should rely on any of the hypotheses for protection. Instead, those who haven’t gotten the coronavirus should continue mitigation measures that have been proven to work, like vaccination and mask-wearing.

“You don’t ever want to have COVID,” Murphy says. “You just don’t know which people are going to get really sick from this and die or who’s going to get long COVID, which is hard to diagnose and difficult to treat and very real.” But with coronavirus cases on the rise and mitigation measures like mask mandates dropping left and right, it’s not an easy task.

COVID19: Face masks could return as cases spike Financial Mirror

06:48 Tue, 21 Jun
19:35 Mon, 20 Jun
21:11 Fri, 17 Jun
13:24Physics
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Mutations In Animals Shed New Light on The Process of Aging

Genetic changes – known as somatic mutations – occur in all cells throughout the lifespan of an organism. While most of these mutations are harmless, some of them can impair normal cell functioning or even start a cell on the path to cancer.

Since the 1950s, scientists have speculated that these mutations may also play a role in aging processes. However, due to technological limitations, they could not properly test this hypothesis.

Now, a research team led by the Wellcome Sanger Institute has analyzed the genomes of 16 mammal species – ranging from mice, rats, and rabbits to horses, tigers, and giraffes – in order to shed more light on the role of these genetic changes in ageing.

They found that, despite huge variations in lifespan and size, different animal species tend to end their natural life with surprisingly similar numbers of somatic mutations. However, the results suggest that the longer the lifespan of a species, the slower the rate at which the mutations occur, thus lending support to the hypothesis that somatic mutations may play a crucial role in ageing.

“To find a similar pattern of genetic changes in animals as different from one another as a mouse and a tiger was surprising. But the most exciting aspect of the study has to be finding that lifespan is inversely proportional to the somatic mutation rate,” said study lead author Alex Cagan, a postdoctoral researcher on somatic evolution at the Wellcome Institute.

“This suggests that somatic mutations may play a role in ageing, although alternative explanations may be possible. Over the next few years, it will be fascinating to extend these studies into even more diverse species, such as insects or plants.”

“Animals often live much longer in zoos than they do in the wild, so our vets’ time is often spent dealing with conditions related to old age. The genetic changes identified in this study suggest that diseases of old age will be similar across a wide range of mammals, whether old age begins at seven months or 70 years, and will help us keep these animals happy and healthy in their later years,” added study co-author Simon Spiro, a wildlife veterinary pathologist at the Zoological Society of London.

Nevertheless, understanding the exact causes of ageing remains an unsolved question. Although somatic mutations appear to play a fundamental role in ageing, other processes such as protein aggregation and epigenetic changes are also likely to contribute to the molecular damage in our cells and tissues that is a well-known marker of old age. Further research is needed to compare the rates of all of these processes across species with different lifespans.

By Andrei Ionescu

Source: Mutations in animals shed new light on the process of aging • Earth.com

Critics:

By Catherine Barnette

Mutations can occur during the life of an animal (acquired—affecting only a single cell) or can be inherited from a parent (present in all of the body’s cells). When a cell is affected by a mutation, all cells arising from that cell are likely to carry the mutation. In the case of an acquired mutation, this may be only a small number of cells. In the case of a reproductive cell, the mutation will affect all of the offspring’s cells.

The effects of mutations depend on the size and location of the mutation. Much of an animal’s genetic code consists of what is called non-coding DNA. These non-coding regions do not contain genes that code for protein production. Mutations in this area may have no effect on the animal or its offspring.

If an acquired mutation occurs in a coding region of DNA, the effects will vary depending on the mutation. Perhaps the most concerning effect of an acquired mutation is the formation of cancer. For example, solar radiation damage can lead to cell mutations that may result in squamous cell carcinoma or other cancers.

Inherited mutations are mutations that occurred in a parent animal’s reproductive cells. These mutations are part of the genetic code that is found in every one of the offspring’s cells. For this reason, inherited mutations can have significant effects if found in vital, coding regions of the DNA.

A marker is a specific segment of DNA with known characteristics. While the specific sequences may vary between individual, there is enough consistency in the genetic code at that particular site on the genome to allow comparison between individuals. Markers are often located in non-coding areas of the DNA where a specific base pattern repeats many times and these repeating segments are known and mapped.

When a mutation occurs in a marker region, the mutation can be easily identified because the normal pattern of the repeating segment is known. Even if the marker region is located in non-coding DNA and the mutation has no visible effects, analyzing the marker region will allow scientists to see that a mutation has occurred.

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What Old Dogs Can Teach Us About Aging

For many of us, our dogs are our constant companions. Whether collie or retriever, purebred or mutt, dogs climb mountains with us, travel on airplanes with us, and eat the scraps off our plate.  

And as we get older, so do they. In fact, dogs experience a lot of the same age-related changes that humans do, from greying hair and creaky joints to more serious conditions like cancer or cognitive decline. Today, scientists are learning how comparing different dog breeds can give us new insights into the aging process — for both our canine companions and their owners. 

Old Dogs, New Tricks

One major project currently underway is the Dog Aging Project. Headquartered at the University of Washington, the project is working with dogowners across the country, gathering info about their pets’ lives, lifespans and medical ailments.  The project has more than 32,000 dogs already enrolled, though co-director Daniel Promislow says it’s kind of just getting started. “Over this past year, we’ve sort of launched into the next phase, which is pretty exciting,” says Promislow. One key development:

Building out their logistics network, like where to store computer data and physical samples and how to make that data easy to sort through. The second development? Time.  The scientists behind the project hope that this wealth of data could soon be used to see which health problems are commonly found together, and even figure out how long problem may lead to another.

 “Once we move into this longitudinal phase, which we’re now doing, we can identify how something that happens early in a dog’s life eventually impact his health late in life. That’s the real power of discovery,” says Promislow. “Years in the future, a veterinarian could enter some information about the clinical history of a dog and know that a particular diagnosis was more or less likely.” 

They’re also collecting DNA samples from the dogs, which could help reveal the underlying genetic causes of disease. Beyond that, dogs in particular present a rare opportunity for researchers thanks to the artificial selection pressures that have shaped them.

It’s All in the Genes

Exactly when and where dogs were first domesticated is a matter of debate, but scientists think it was at least 14,000 years ago. Since that fateful day, breeders have shaped our canine companions by repeatedly choosing for specific traits like intelligence, attitude, or speed. The signs of this artificial selection and in-breeding are visible in dogs genetics or, more specifically, the amount of variation in their genetics.

“Across all dogs, it’s about the same as us genetically,” says Promislow. “But within a single breed it’s like having a whole bunch of full siblings. Or even closer.” This means that specific breeds of dogs may have traits built into their genes.

Variation in a gene known as IGF1, for instance, accounts for nearly half of all size differences between breeds.  What does this actually mean for researchers, though? Essentially, if a particular problem shows up frequently in a given breed, it may be due to something in that breed’s genes.

The IGF1 gene has been implicated as influencing both size and lifespan, possibly helping explain why large dogs tend to die younger than small ones, though it’s still being researched. Meanwhile, variants in a gene called SLC2A9 may be behind the high rate of urinary problems in Dalmatians, whereas a gene region called CDKN2A/B could contribute to the high rate of certain cancers in Bernese Mountain Dogs.  

Looking at cancer in particular helped kickstart another major project, the Golden Retriever Lifetime Study, says geneticist Janet Patterson-Kane, the project’s principal investigator.

The research team has recruited a one-time cohort of over 3,000 golden retrievers and have been going since 2012. By looking at just one specific breed, they can zero in on the effects of individual genes.  Plus, the fact that researchers are studying one breed helps them see things beyond just genetics, as well.

Because the dogs are quite similar genetically, you may be more likey to tease out the influence of something environmental or dietary to their health, says Patterson-Kane. “There’s a power in taking dogs that are quite similar to each other, and then you’re looking at the factors acting upon that,” says Patterson-Kane. 

Lessons for Humans

What’s more, studying how dogs age could help us not only help our pets, but ourselves, too. The SLC2A9 gene that causes Dalmatian urinary problems also exists in humans, for example, and could be the target of future research.  And with regards to environmental exposure, because our canine companions get exposed to a lot of what humans do — like home pesticides, second-hand smoke, or even asbestos — and suffer the same problems humans do, a dog’s health may serve as warnings for their owners.

 Studies suggest that a pet dog contracting a type of lung cancer called mesothelioma could be an early warning sign of asbestos exposure for the humans in the household.  Both The Dog Aging Project and The Golden Retriever Lifetime Study are still ongoing, though the researchers behind the latter say they’re now coming to the end of many of their enrollee dogs’ natural lifespan. “We are losing a lot of dogs right now.

It’s just one of those sobering things,” says Patterson-Kane. “But those samples from those dogs are a legacy to those dog’s lives. And after they’re gone, we’re still going to be getting those samples out looking at that data.” The hope is that more researchers, not just veterinarians but also people in other fields, will be able to use the group’s data. 

The Dog Aging Project, meanwhile, is continuing to recruit new dogs. “The Dog Aging Project welcomes dogs of all ages, from puppies to geriatric dogs,” says Promislow, adding that the research project takes dogs from all around the country. “What better way to discover the cool things that science can do then, by doing it through this dog who you love and who’s a part of the family?”

By James Gaines

Source: What Old Dogs Can Teach Us About Aging | Discover Magazine

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