Category Archives: Transhuman News

Fossil DNA may be rewriting the history of elephant evolution.

The first genetic analysis of DNA from fossils of straight-tusked elephants reveals that the extinct animals most closely resembled modern African forest elephants. This suggests that straight-tusked elephants were part of the African, not Asian, elephant lineage, scientists report online June 6 in eLife.

Straight-tusked elephants roamed Europe and Asia until about 30,000 years ago. Much like modern Asian elephants, they sported high foreheads, double-domed skulls and downward sloping spines. These features convinced scientists for decades that straight-tusked and Asian elephants were sister species, says Adrian Lister, a paleobiologist at the Natural History Museum in London who was not involved in the study.

For the new study, researchers extracted and decoded DNA from the bones of four straight-tusked elephants found in Germany. The fossils ranged from around 120,000 to 240,000 years old. The genetic material in most fossils more than 100,000 years old is too decayed to analyze. But the elephant fossils were unearthed in a lake basin and a quarry, where the bones would have been quickly covered with sediment that preserved them, says study author Michael Hofreiter of the University of Potsdam in Germany.

Hofreiters team compared the ancient animals DNA with the genomes of the three living elephant species Asian, African savanna and African forest and found that straight-tusked genetics were most similar to African forest elephants.

When the researchers told elephant experts what theyd found, Everybody was like, This cant possibly be true! says study coauthor Beth Shapiro of the University of California, Santa Cruz. Then it gradually became, Oh yeah, I see. The way weve been thinking about this is wrong.

If straight-tusked elephants were closely related to African forest elephants, then the African lineage wasnt confined to Africa where all elephant species originated as paleontologists previously thought. It also raises questions about why straight-tusked elephants bore so little resemblance to todays African elephants, which have low foreheads, single-domed skulls and more horizontal backbones.

Story continues after graphic

This tree shows a revision to how scientists think straight-tusked elephants fit into elephant evolution: Straight-tusked elephants shared the most common ancestors with African forest elephants, rather than Asian elephants.

Accounting for this new finding may not be as simple as moving one branch on the elephant family tree, Lister says. Its possible that straight-tusked elephants really were a sister species of Asian elephants, but they exhibit genetic similarities to African forest elephants from interbreeding before the straight-tusked species left Africa.

Its also possible that a common ancestor of Asian, African and straight-tusked elephants had particular genetic traits that were, for some reason, only retained by African and straight-tusked elephants, he says.

Lister and colleagues are now reexamining data on straight-tusked skeletons to reconcile the species skeletal features with the new information on their DNA. I will feel most comfortable if we can understand these genetic relationships in terms of the [physical] differences between all these species, he says. Then well have a complete story.

Continued here:
Ancient DNA shakes up the elephant family tree - Science News Magazine

Daniel Rochat, left, is on trial in the killing of Barbara Vernieri in 2012.(Photo: TARIQ ZEHAWI/NorthJersey.com file photo)

HACKENSACK The DNA evidence in the slaying of East Rutherford real estate agent Barbara Vernieri should exonerate Daniel Rochat, his lawyer told the jury during the defense's closing arguments on Tuesday.

Rochat, who knew Vernieri since he was a young child, is accused of beating her and setting her on fire in September 2012. Vernieri worked with Rochat and hisfather at Kurgan-Bergen Realty at the time of her death.

Jim Doyle, one of Rochat's attorneys, said the testimony ofMelissaHuyck, who was the prosecution's DNA expert, was "without a doubt one of the most disappointing things [he's] ever seen by a scientist on the stand."

During his summations, Doyle attempted to cast doubt on a number of pieces of evidence, includingthe DNA evidence, noting that Rochat's DNA was not found in Vernieri's home and Vernieri's blood was not found anywhere it was not supposed to be. It was not found in Rochat's apartment in Wood-Ridge, it was not found in the family shore house in Toms River, it was not found on his shoes, it was not found in either of his cars, he said.

From left, Daniel Rochat, accused in the killing of Barbara Vernieri in 2012, with his attorneys Jim Doyle and Richard Potter, before Superior Court Judge Margaret M. Foti.(Photo: Tariq Zehawi/NorthJersey.com)

Doyle continued his argument by sayingthe DNA that was found in the Van Winkle condo, which Rochat's father was the property manager was, was not proven to be blood and that the tests done by the crime scene unit investigators only presumed blood was present. He argued that Vernieri's DNA could have been transferred to Van Winkle at a different point in time due to how often she came into contact with Rochat and his father.

Additionally, Doyle noted that the DNA found underneath Vernieri's fingernails could belong to a number of men in the population. It was testified that one in 333 men, including Rochat and his paternal relatives,could have the same DNA profile. Doyle said that one of the detectives, Sgt. Gary Boesch, used an inappropriate tool to collect the fingernails. Boesch used a piece of computer paper to collect Vernieri's fingernail clippings and Doyle said it is possible the DNA could belong to any other male at the scene or anyone who had ever handled the paper. Doyle also told jurors to remember that the DNA of two unknown males were found in Vernieri's home.

Doyle reminded the jurors it was their job to find Rochat guilty beyond a reasonable doubt.

"Certain phrases sound trite until you have to use them," he said.

Doyle said the prosecution will argue that Rochat's conduct the day of and in the days following Vernieri's death establishes motive and conscience of guilt, but he feels differently. He said numerous people testified that Rochat's behavior was nothing out of the ordinary for him including a friend he was with when he found out about Vernieri's death.

Daniel Rochat, left, with his attorneys Jim Doyle and Richard Potter before Superior Court Judge Margaret Foti in Hackensack.(Photo: Tariq Zehawi/NorthJersey.com)

Doyle also made arguments against the prosecution's seemingly most damaging evidence. Rochat's cellphone pinged off a tower that is directly by Vernieri's home at 10:39 a.m., a time that Rochat said he was sleeping in his apartment over a mile away. The prosecution's cellphone expert testified that it would be impossible for Rochat's phone to ping on that tower due to the number of towers in the area. The defense's cellphone expert argued differently, stating that a cellphone could potentially ping on that tower almost 11 miles away.

Doyle said the Bergen County Sheriff's Office use of Verizon's Real Time Tool records, used to approximate where a cellphone is located at the time of a call, is the wrong way to determine an individual's locationand that triangulation and GPS were better tools.

According to Doyle, the prosecution is throwing motives at the wall "to see what sticks" and that they do not have a clear motive and do not really know who killed Vernieri.

Prosecutor Danielle Grootenboer will begin her closing arguments Wednesdaymorning before jury instruction anddeliberations.

Read or Share this story: https://njersy.co/2sq496V

Read the original post:
Defense attorney argues DNA evidence should exonerate Rochat - NorthJersey.com

Georgia Tech News Center

Researchers Uncover New Instruction Manual to Repair Broken DNA Georgia Tech News Center Radiation and chemotherapy can cause a DNA double-strand break, one of the most harmful types of DNA damage. The process of homologous recombination which involves the exchange of genetic information between two DNA molecules plays an ...

The rest is here:
Researchers Uncover New Instruction Manual to Repair Broken DNA - Georgia Tech News Center

The ocean might as well be Mars. Like astronomers grasping at ways to identify life on a distant planet, marine scientists have no easy method for detecting sea creatures presence in the vast watery realm.

Team members from the Monterey Bay Aquarium Research Institute collect water from Monterey Bay for eDNA analysis. (Image credit: Collin Closek)

An emerging technique analyzing DNA in skin, scales and feces animals leave behind has shown promise for revealing hidden ecosystems on land and in fresh water. But deep ocean environments have largely proven too complex for the approach. Now, Stanford scientists show progress in using this analysis to overcome complicated water movements and other obstacles to detect ocean animals in locations where the water can be more than 7,200 feet deep.

We want to know whats out there, said study lead author Elizabeth A. Andruszkiewicz, a graduate student in Stanfords Department of Civil and Environmental Engineering. Eventually, this technology may answer bigger questions, such as how communities of organisms have adapted to environmental changes over time.

Of the few previous environmental DNA, or eDNA, studies of ocean animals, all were done in relatively shallow nearshore environments. Most were done in controlled systems such as saltwater tanks, and few looked in real environments at questions of spatial distribution of eDNA.

The Stanford-led study also marks the first time the approach has been used in the deep waters of Monterey Bay, an important ecosystem in the California Current, which flows southward along the western coast of North America. In addition to being highly productive ecosystems, these areas have been the focus of relatively intensive ongoing research by institutions such as the Monterey Bay Aquarium Research Institute (a partner in the study). The resulting archived water samples and long-term datasets present unique opportunities for eDNA analysis of ecological change over time.

Sampler device is deployed to collect water in Monterey Bay. (Image credit: Collin Closek)

Collecting eDNA is fairly straightforward a basic water sample does the trick and scientists can archive these samples for long periods by freezing them. The approach promises a faster, more comprehensive and less invasive way to measure abundance and distribution of organisms. It might also be able to detect invasive species or changes in the distribution of endangered species.

This could revolutionize the way we keep track of animals, said study co-author Alexandria Boehm, professor of civil and environmental engineering and a senior fellow at the Stanford Woods Institute for the Environment.

The eDNA survey identified 72 species of vertebrates (marine fishes, mammals such as elephant seals, humpback whales, sharks and rockfishes) at study sites across 28 miles of the Monterey Bay National Marine Sanctuary.

Scientists found DNA of some creatures, such as sunfishes, salmon, seahorses and mackerel sharks, only in locations where the water was less than 600 feet deep. DNA of other animals, such as dolphins and marine smelts, turned up only in waters more than 600 feet deep. The shallowest waters held the greatest biodiversity. Taken as a whole, the findings provide a proof of concept for eDNA as an ocean sleuthing tool.

It is a remarkably powerful way to answer a simple question: What species are present in space and time in our oceans? said co-author Barbara Block, the Charles and Elizabeth Prothro Professor in Marine Sciences at Stanford. It could change how we view our planets marine biodiversity.

DNA sequencing has driven unprecedented research and discovery in fields ranging from medical diagnosis to evolutionary biology.

Pacific white-sided dolphins accompany the NOAA ship Reuben Lasker off the coast of California in June 2016 during a cruise collecting water samples for environmental DNA (eDNA) analysis. (Image credit: Collin Closek)

Preliminary studies have shown that eDNA sequencing can identify vertebrate species missed by traditional monitoring methods and can allow sampling in places inaccessible to traditional techniques such as dive surveys and fish trawls. The approach can also be used at finer resolutions, in terms of time and space, compared to traditional biomonitoring methods. This allows scientists to document changes in biodiversity over seasonal and annual cycles, as well as over different topographies.

Questions still remain about how to properly sample water for eDNA, and how to interpret sequencing results to avoid false positives and false negatives. Solving these and other challenges will bring into focus the next frontier for eDNA: counting actual numbers of sea animals and discerning their population-level identity, rather than just detecting their presence. Working with a team of geneticists, fish physiologists, oceanographers and engineers, Boehm and Block hope to realize that goal within 10 years.

Additional authors on Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding, published in PLOS ONE, are Lauren M. Sassoubre, a former postdoctoral scholar at Stanford; Hilary A. Starks of Stanfords Center for Ocean Solutions; and Francisco P. Chavez of the Monterey Bay Aquarium Research Institute.

The research was supported by a gift from the Seaver Institute to the Stanford Woods Institute for the Environments Environmental Venture Projects program, the U.S. Environmental Protection Agency and the David and Lucile Packard Foundation.

Visit link:
DNA left by ocean animals provides rare glimpse of marine ecosystems, Stanford researchers say - Stanford University News

June 13, 2017 Rif1 is shepherding DNA ends. Crystal structure of the conserved N-terminal domain of Rif1 reveals an extraordinarily elongated shape resembling a shepherds crook. Within the hook, Rif1 contains a DNA binding domain forming a protective sheath. This activity of Rif1 underpins telomere homeostasis, checkpoint suppression at chromosome ends, and DNA double-strand break repair, a function now identified as conserved in eukaryotes. The molecular gating of DNA ends offers a unified mechanism for the diverse genome stability functions of Rif1. Credit: Friedrich Miescher Institute for Biomedical Research

All cells are confronted with DNA damage, for example by exposure of the skin to UV rays, chemical byproducts of nerve cells consuming sugar, or immune cells destroying bacteria. If these DNA lesions are not - or badly - repaired, they may initiate tumor formation. Thankfully, cells have evolved an elaborate control system to correct these DNA anomalies. Uli Rass and Nico Thom at the FMI, together with colleagues at the University of Geneva (UNIGE), have now discovered the key role of a protein called Rif1 in the protection, stabilization and repair of damaged DNA. This study, published in the journal Nature Structural & Molecular Biology, uncovers a DNA maintenance function likely to be present in all eukaryotes because the region of Rif1 that enables the formation of a protective sheath around DNA lesions is similar in humans and yeast.

A multi-faceted protein

Cells have developed a complex control system to repair the DNA breaks that occur every day. This system includes patrolling proteins, molecules that set off an alarm, as well as damage-repairing enzymes. The teams of Nicolas Thom and Ulrich Rass at the FMI and the group of David Shore at UNIGE are interested in a protein called Rif1. Rif1 is involved in many processes, some of which are related to DNA replication and repair. Certain activities of Rif1, a protein present in both humans and yeast, vary from one type of organism to another, while others remain similar. It was not clear why that was the case.

The scientists thus examined the molecular structure of Rif1. "This protein is made of divergent functional elements depending on the species studied, which may explain the diversity of its activities. But there is also a common part whose function was hitherto unknown", says Stefano Mattarocci, co-first author of the study and member of the Geneva group.

A ubiquitous repair module

By studying the 3-D structure of this common region, the biologists have discovered that it is intimately involved in the protection and the repair of deteriorated DNA. "This region of Rif1 binds to the damaged strands and then recruits more Rif1 proteins that assemble to form a protective sheath around the weakened segment", notes Julia Reinert, co-first author and member of the Basel team.

This molecular plaster gates access of repair enzymes to the protected strands, while restricting access of enzymes responsible for degrading the ends of damaged DNA. All eukaryotes, that is to say organisms whose cells have a nucleus, appear to benefit from the sheath formed by Rif1, since the protective region of this protein is similar in humans and yeast.

This study has revealed the molecular mechanism allowing Rif1 to preserve the integrity of the genome. The findings contribute to a better understanding of how cells avoid the accumulation of DNA lesions, which would otherwise lead to senescence, cell death, or cancer.

Explore further: The proteins ensuring genome protection

More information: Stefano Mattarocci et al. Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends, Nature Structural & Molecular Biology (2017). DOI: 10.1038/nsmb.3420

Researchers from the University of Geneva (UNIGE), Switzerland, have discovered the crucial role of two proteins in developing a cell 'anti-enzyme shield'. This protection system, which operates at the level of molecular ...

A group from the University of Geneva, Switzerland, discovers a key factor that curbs the undesirable triggering of DNA replication.

(Phys.org) A team of scientists at the Friedrich Miescher Institute for Biomedical Research and the University of Geneva has functionally dissected the molecular processes that ensure the stability of chromosomes. They ...

Drexel University and Georgia Institute of Technology researchers have discovered how the Rad52 protein is a crucial player in RNA-dependent DNA repair. The results of their study, published today in Molecular Cell, reveal ...

A research group from the University of Seville has revealed the role that the protein Rrm3 plays in the repair of breaks that occur during the replication of DNA, by using the yeast Saccharomyces cerevisiae as a model organism. ...

An international collaboration between Osaka University and the Friedrich Miescher Institute for Biomedical Research (FMI) in Switzerland is investigating the repair process of a serious form of DNA damage that can lead to ...

Male birds tend to be better singers than femalesbut does the basis for this difference lie in the brain or in the syrinx, the bird equivalent of our larynx? The researchers behind a new study from The Auk: Ornithological ...

Animals living in areas where conditions are ideal for their species have less chance of evolving to cope with climate change, new research suggests.

The arrangement of the photoreceptors in our eyes allows us to detect socially significant color variation better than other types of color vision, a team of researchers has found. Specifically, our color vision is superior ...

Using high magnification imaging, a team of researchers has identified several never before seen structures on bacteria that represent molecular machinery. The research is published this week in the Journal of Bacteriology, ...

UNC School of Medicine researchers have cracked a long-standing mystery about an important enzyme found in virtually all organisms other than bacteria. The basic science finding may have implications for understanding cancer ...

One of the main types of fossil used to understand the first flowering plants (angiosperms) are charred flowers. These charcoals were produced in ancient wildfires, and they provide some evidence for the types of plants that ...

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Go here to see the original:
A molecular plaster to repair DNA - Phys.Org