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‘CSI’ conservation uses tiger spit and conch fritters

Futurity.org - Thu, 2019-04-18 19:30

Scientists have come up with a new way to collect DNA from endangered species—extract it from degraded and left-behind materials, including feces, saliva, and even food products.

The near impossibility of collecting DNA samples from rare and elusive animals has hobbled wildlife detectives aiming to protect these endangered species. The researchers say their proof of concept, which appears in Methods in Ecology and Evolution, could revolutionize conservation approaches and policies worldwide.

“It’s CSI meets conservation biology,” says coauthor Dmitri Petrov, professor in the School of Humanities and Sciences at Stanford University.

Looming extinctions

The specter of extinction hangs over more than a quarter of all animal species, according to the best estimate of the International Union for Conservation of Nature, which maintains a list of threatened and extinct species. Conservationists have documented extreme declines in animal populations in every region of Earth.

“Conservation needs answers fast, and our research was not providing them fast enough.”

Helping species recover often depends on collecting DNA samples, which can reveal valuable information about details including inbreeding, population history, natural selection, and large-scale threats such as habitat destruction and illegal wildlife trade.

However, current approaches tend to require relatively large amounts of DNA or expensive and often inefficient strategies for extracting the material. Getting meaningful information rapidly from lower-concentration, often degraded and contaminated DNA samples requires expensive and specialized equipment.

Tigers and conchs

A solution may lie in an ongoing collaboration between Stanford’s Program for Conservation Genomics, including the labs of Petrov and coauthors Elizabeth Hadly and Stephen Palumbi, and India’s National Centre for Biological Sciences, including the lab of coauthor Uma Ramakrishnan, a molecular ecologist and former Fulbright faculty fellow at Stanford.

“I have been working on tiger conservation genetics for over a decade, but have been frustrated at how slow and unreliable the process of generating genetic data can be,” Ramakrishnan says. “Conservation needs answers fast, and our research was not providing them fast enough.”

The researchers looked at endangered wild tigers in India and overfished Caribbean queen conchs, examining tiger feces, shed hair, and saliva found on killed prey, as well as fried conch fritters purchased in US restaurants. All of the samples were too impure, mixed, or degraded for conventional genetic analysis.

“Our goal was to find extremely different species that had strong conservation needs, and show how this approach could be used generally,” says Palumbi, professor of marine biology. “The King of the Forest—tigers—and Queen of the Caribbean—conch—were ideal targets.”

Tiny bits of DNA

Together, the team improvised a new approach, using a sequencing method that amplifies and reads small bits of DNA with unique differences in each sample. Doing this simultaneously across many stretches of DNA in the same test tubes allowed the researchers to keep the total amount of DNA needed to a minimum.

Making the procedure specific to tiger and conch DNA allowed for the use of samples contaminated with bacteria or DNA from other species.

The technology proved highly effective at identifying and comparing genetic characteristics. For example, the method worked with an amount of tiger DNA equivalent to about one-one-hundred-thousandth the amount of DNA in a typical blood sample. The method had a higher failure rate in conchs because the researchers did not have whole genomes at their disposal.

The approach’s effectiveness, speed and affordability—implementation could cost as little as $5 per sample—represents a critical advance for wildlife monitoring and forensics, field-ready testing, and the use of science in policy decisions and wildlife trade, the researchers say.

“It is easy to implement and so can be done in labs with access to more or less basic equipment,” says coauthor Meghana Natesh of the National Centre for Biological Sciences and Sastra University in India. “If a standard procedure is followed, the data generated should be easy to share and compare across labs. So monitoring populations across states or even countries should be easier.”

The scientists have made their methods freely available. “We are working to expand the method so that it can identify other species and other characteristics, such as diet and pathogens,” Hadly says.

The Wildlife Conservation Trust, the US Department of State, the Wellcome Trust / DBT India Alliance, the Summit Foundation, and the Smithsonian Institution funded the work, which appears in
Methods in Ecology and Evolution.

Source: Stanford University

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In Divided Washington, Relief and Disappointment at Mueller’s Report

NY Times - Thu, 2019-04-18 19:29
The stoic feelings of progressive Washington were similarly subdued in the city’s more conservative corners.

Sarah Sanders to Mueller: False comments were a slip of tongue

CNN - Thu, 2019-04-18 19:25
White House press secretary Sarah Sanders admitted to federal investigators that she provided reporters baseless information related to former FBI Director James Comey's dismissal, according to special counsel Robert Mueller's redacted report. CNN's Jim Acosta reports.

Analysis: Why Democrats shouldn't pursue impeachment now

CNN - Thu, 2019-04-18 19:22
• Opinion: The speech Donald Trump will never give • Kellyanne Conway's husband calls for Congress to remove 'cancer' of Trump

Paranoia, lies and fear: Trump’s presidency laid bare by Mueller report

Washington Post - Thu, 2019-04-18 19:13
The 448-page report reveals a vivid portrait of a president and his aides on the brink of obstructing justice.

Sarah Sanders made an important admission to Mueller's team

CNN - Thu, 2019-04-18 19:12
A section of the Mueller report says that White House press secretary Sarah Sanders lied when she said people inside the FBI did not like then-FBI director James Comey and that was part of the justification for firing Comey.

Netflix, Which Made ‘Kimmy Schmidt’ in Brooklyn, to Expand Production Studios There

NY Times - Thu, 2019-04-18 19:07
The streaming company said it would spend up to $100 million on six soundstages in Brooklyn, adding to New York City’s growing role in the film industry.

Trump’s efforts to obstruct were clear, Democrats say, but question of impeachment isn’t

Washington Post - Thu, 2019-04-18 18:56
The Mueller report’s findings and the special counsel’s deferral to Congress increase pressure on Democrats and 2020 presidential candidates from the party’s left flank.

This Genetic Mutation Makes People Feel Full — All the Time

NY Times - Thu, 2019-04-18 18:55
Two new studies confirm that weight control is often the result of genetics, not willpower.

Jason Momoa shaved his beard and people are freaking out

CNN - Thu, 2019-04-18 18:51
Before you ask "Why is this news?" remember that it's Jason Momoa.

Rain on other side of the planet foreshadows California heat

Futurity.org - Thu, 2019-04-18 18:50

When heavy rain falls over the Indian Ocean and Southeast Asia and the eastern Pacific Ocean, it is a good indicator that temperatures in central California will reach 100°F in four to 16 days, according to new research.

Heat waves are common in California’s Central Valley, a 50-mile-wide oval of land that runs 450 miles from just north of Los Angeles up to Redding. The valley is home to half of the nation’s tree fruit and nut crops, as well as extensive dairy production, and heat waves can wreak havoc on agricultural production. The dairy industry had a heat wave-induced economic loss of about $1 billion in 2006, for instance. The ability to predict heat waves and understand what causes them could inform protective measures against damage.

“We want to know more about how extreme events are created,” says corresponding author Richard Grotjahn, professor in the land, air, and water resources department at the University of California, Davis.

“We know that such patterns in winter are sometimes linked with areas of the tropics where thunderstorms are enhanced. We wondered if there might be similar links during summer for those heat waves.”

The scientists analyzed the heat wave data from June through September from 1979 to 2010. Fifteen National Climatic Data Center stations located throughout the valley collected the data. From these data, the researchers identified 24 heat waves. They compared these instances to the phases of a large, traveling atmospheric circulation pattern called the Madden-Julian Oscillation, or MJO.

The MJO manifests as heavy rain that migrates across the tropical Indian and then Pacific oceans, and researchers have shown that it influences winter weather patterns.

“It’s well known that tropical rainfall, such as the MJO, has effects beyond the tropics,” says the paper’s first author Yun-Young Lee of the Asia-Pacific Economic Cooperation Climate Center in Busan, South Korea. “So a question comes to mind: Is hot weather in the Central California Valley partly attributable to tropical rainfall?”

Lee and Grotjahn found that, yes, enhanced rainfall in the tropics preceded each heat wave in specific and relatively predictable patterns. They also found that hot weather in the valley is most common after more intense MJO activity in the eastern Pacific Ocean, and next most common after strong MJO activity in the Indian Ocean.

“The more we know about such associations to large-scale weather patterns and remote links, the better we can assess climate model simulations and therefore better assess simulations of future climate scenarios,” Grotjahn says.

The National Science Foundation, the National Aeronautics and Space Administration, the Department of Energy Office of Science, the United States Department of Agriculture’s National Institute of Food and Agriculture, and the APEC Climate Center in the Republic of Korea funded the research.

The work appears in Advances in Atmospheric Sciences.

Source: UC Davis

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Excerpts and Analysis From the Mueller Report

NY Times - Thu, 2019-04-18 18:48
The Justice Department released a redacted version of the special counsel’s report on Thursday. Times reporters uncovered the biggest findings and shared excerpts and analysis.

We finally know how general anesthesia works

Futurity.org - Thu, 2019-04-18 18:44

In a new study,researchers found that to knock you out, different anesthesia drugs hijack the neural circuitry that makes you fall sleep.

The discovery of general anesthesia 170 years ago was a medical miracle, enabling millions of patients to undergo invasive, life-saving surgeries without pain.

General anesthesia drugs induce unconsciousness by activating a tiny cluster of cells at the base of the brain called the supraoptic nucleus (shown in red), while the rest of the brain remains in a mostly inactive state (blue). (Credit: Duke)

For the study, which appears in Neuron, researchers traced this neural circuitry to a tiny cluster of cells at the base of the brain responsible for churning out hormones to regulate bodily functions, mood, and sleep.

The finding is one of the first to suggest a role for hormones in maintaining the state of general anesthesia, and provides valuable insights for generating newer drugs that could put people to sleep with fewer side effects.

Ever since the first patient went under general anesthesia in 1846, scientists have tried to figure out exactly how it works. The prevailing theory was that many of these drugs tamp down the brain’s normal activities, resulting in the inability to move or feel pain.

Similar theories revolved around sleep, the sister state to general anesthesia. However, research over the last decade has shown that sleep is a more active process than previously recognized, with entire sets of neurons clocking in to work while you catch your Z’s.

Fan Wang, a professor of neurobiology at Duke University School of Medicine, and Li-Feng Jiang-Xie, a graduate student in her laboratory, wondered whether the predominant view of general anesthesia was also one-sided.

“Perhaps rather than simply inhibiting neurons, anesthetics could also activate certain neurons in the brain,” says Jiang-Xie.

To test their new theory, Jiang-Xie and Luping Yin, a postdoctoral fellow in the Wang lab, put mice under general anesthesia with several different but commonly used drugs. Then they used molecular markers to track down the neurons commonly activated by the anesthetics.

They found a cluster of actively firing neurons buried in a tiny brain region called the supraoptic nucleus, known to have leggy projections that release large amounts of hormones like vasopressin directly into the bloodstream.

“Most of the anesthesia-activated cells were a kind of hybrid cell that connects the nervous system and the endocrine system,” says Jiang-Xie. “That took us by surprise and led us into unexplored territory for understanding the neural pathways of general anesthesia.”

Next, the researchers tapped a sophisticated technique developed in the Wang lab to turn on or off this specialized group of cells with chemicals or light. When they switched on the cells in mice, the animals stopped moving and fell into a deep slumber called slow wave sleep, typically associated with unconsciousness.

Then the research team killed off this group of cells. The mice continued to move around, unable to fall asleep.

Finally, the researchers performed similar experiments on mice under general anesthesia. They found that artificially pre-activating the neuroendocrine cells made the mice stay under general anesthesia for longer periods of time. Conversely, when they silenced these cells, the mice woke up from anesthesia more easily.

The study also revealed a previously unexpected role of the brain’s hormone-secreting cells in promoting deep sleep.

“Many people, particularly those with Alzheimer’s disease, have difficulty falling to sleep, yet current medications have troublesome side effects,” says Yin. “If we can find ways to manipulate this neural circuitry, perhaps by targeting hormones or small peptides, then it could lead to the development of better sleeping pills.”

The W.M Keck Foundation, the Brain Research Foundation, the National Institutes of Health, and a Human Frontier Science Fellowship funded the work.

Source: Duke University

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Trump asked his lawyer to cross legal lines. The Mueller report shows how he pushed back.

Washington Post - Thu, 2019-04-18 18:35
The report produced a few surprises, including that President Trump's attempts to impede the investigation were “mostly unsuccessful” because officials refused to help him. Former White House counsel Donald McGahn was a major player on that front.

Trump asked his lawyer to cross legal lines. The Mueller report shows how he pushed back.

Washington Post - Thu, 2019-04-18 18:35
The report produced a few surprises, including that President Trump's attempts to impede the investigation were “mostly unsuccessful” because officials refused to help him. Former White House counsel Donald McGahn was a major player on that front.

System restores some pig brain function hours after death

Futurity.org - Thu, 2019-04-18 18:33

Researchers restored circulation and cellular activity in a pig’s brain four hours after its death, the team reports.

The finding challenges long-held assumptions about the timing and irreversible nature of the cessation of some brain functions after death.

Researchers isolated the brain of a postmortem pig from a meatpacking plant and circulated a specially designed chemical solution. They observed many basic cellular functions once thought to cease seconds or minutes after oxygen and blood flow cease, the scientists report.

“The intact brain of a large mammal retains a previously under-appreciated capacity for restoration of circulation and certain molecular and cellular activities multiple hours after circulatory arrest,” says senior author Nenad Sestan, professor of neuroscience, comparative medicine, genetics, and psychiatry at Yale University.

Immunofluorescent stains for neurons (green), astrocytes (red), and cell nuclei (blue) in a region of the hippocampus of a pig’s brain left untreated 10 hours after death (left) or subjected to perfusion with the BrainEx technology. Ten hours postmortem, neurons and astrocytes undergo cellular disintegration unless the BrainEx system salvages them. (Credit: Stefano G. Daniele & Zvonimir Vrselja; Sestan Laboratory; Yale School of Medicine)

Researchers also stress, however, that the brain lacked any recognizable global electrical signals associated with normal brain function.

“At no point did we observe the kind of organized electrical activity associated with perception, awareness, or consciousness,” says co-first author Zvonimir Vrselja, associate research scientist in neuroscience.

“Clinically defined, this is not a living brain, but it is a cellularly active brain.”

The nature of death

Scientists usually consider cellular death within the brain a swift and irreversible process. Cut off from oxygen and a blood supply, the brain’s electrical activity and signs of awareness disappear within seconds, while energy stores are depleted within minutes. Current understanding maintains that a cascade of injury and death molecules activate, leading to widespread, irreversible degeneration.

However, researchers in Sestan’s lab, whose research focuses on brain development and evolution, observed that the small tissue samples they worked with routinely showed signs of cellular viability, even when the tissue was harvested multiple hours postmortem.

Intrigued, they obtained the brains of pigs processed for food production to study how widespread this postmortem viability might be in the intact brain. Four hours after the pig’s death, they connected the vasculature of the brain to circulate a uniquely formulated solution they developed to preserve brain tissue, utilizing a system they call BrainEx. They found the system preserved neural cell integrity, and restored certain neuronal, glial, and vascular cell functionality.

Why it matters

The new system can help solve a vexing problem—the inability to apply certain techniques to study the structure and function of the intact large mammalian brain—which hinders rigorous investigations into topics like the roots of brain disorders, as well as neuronal connectivity in both healthy and abnormal conditions.

“Previously, we have only been able to study cells in the large mammalian brain under static or largely two-dimensional conditions utilizing small tissue samples outside of their native environment,” says co-first author Stefano G. Daniele, an MD/PhD candidate.

“For the first time, we are able to investigate the large brain in three dimensions, which increases our ability to study complex cellular interactions and connectivity.”

While the advance has no immediate clinical application, the new research platform may one day be able to help doctors find ways to help salvage brain function in stroke patients, or test the efficacy of novel therapies targeting cellular recovery after injury, the authors say.

“This line of research holds hope for advancing understanding and treatment of brain disorders and could lead to a whole new way of studying the postmortem human brain,” says Andrea Beckel-Mitchener, chief of functional neurogenomics at the NIH’s National Institute of Mental Health, which co-funded the research.

Ethical standards

The researchers says that it is unclear whether this approach can be applied to a recently deceased human brain. The chemical solution used lacks many of the components natively found in human blood, such as the immune system and other blood cells, which makes the experimental system significantly different from normal living conditions. However, the researchers stress that any future study involving human tissue or possible revival of global electrical activity in postmortem animal tissue should be done under strict ethical oversight.

“Restoration of consciousness was never a goal of this research,” says coauthor Stephen Latham, director of Yale’s Interdisciplinary Center for Bioethics. “The researchers were prepared to intervene with the use of anesthetics and temperature-reduction to stop organized global electrical activity if it were to emerge. Everyone agreed in advance that experiments involving revived global activity couldn’t go forward without clear ethical standards and institutional oversight mechanisms.”

There is an ethical imperative to use tools developed by the Brain Initiative to unravel mysteries of brain injuries and disease, says Christine Grady, chief of the Department of Bioethics at the NIH Clinical Center.

“It’s also our duty to work with researchers to thoughtfully and proactively navigate any potential ethical issues they may encounter as they open new frontiers in brain science,” she says.

The research appears in Nature. The National Institutes of Health’s BRAIN Initiative funded the research.

Source: Yale University

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North Face climbers likely killed in Banff National Park avalanche

CNN - Thu, 2019-04-18 18:33
Three professional mountain climbers are missing and are presumed dead after an avalanche at Canada's Banff National Park, according to park officials and the outdoor-gear brand sponsoring them.
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