Category Archives: Transhuman News

August 2, 2017 by David Salisbury Molecular model of the lesion that the bacterial toxin yatakemycin forms on DNA. Credit: Elwood Mullins / Vanderbilt

One of the most potent toxins known acts by welding the two strands of the famous double helix together in a unique fashion which foils the standard repair mechanisms cells use to protect their DNA.

A team of Vanderbilt University researchers have worked out the molecular details that explain how this bacterial toxinyatakemycin (YTM)prevents DNA replication. Their results, described in a paper published online July 24 by Nature Chemical Biology, explain YTM's extraordinary toxicity and could be used to fine-tune the compound's impressive antimicrobial and antifungal properties.

YTM is produced by some members of the Streptomyces family of soil bacteria to kill competing strains of bacteria. It belongs to a class of bacterial compounds that are currently being tested for cancer chemotherapy because their toxicity is extremely effective against tumor cells.

"In the past, we have thought about DNA repair in terms of protecting DNA against different kinds of chemical insults," said Professor of Biological Sciences Brandt Eichman. "Now, toxins like YTM are forcing us to consider their role as part of the ongoing chemical warfare that exists among bacteria, which can have important side effects on human health."

Cells have developed several basic types of DNA repair, including base excision repair (BER) and nucleotide excision repair (NER). BER generally fixes small lesions and NER removes large, bulky lesions.

A number of DNA toxins create bulky lesions that destabilize the double helix. However, some of the most toxic lesions bond to both strands of DNA, thereby preventing the cell's elaborate replication machinery from separating the DNA strands so they can be copied. Normally, this distorts the DNA's structure, which allows NER enzymes to locate the lesion and excise it.

"YTM is different," said postdoctoral fellow Elwood Mullins. "Instead of attaching to DNA with multiple strong covalent bonds, it forms a single covalent bond and a large number of weaker, polar interactions. As a result, it stabilizes the DNA instead of destabilizing it, and it does so without distorting the DNA structure so NER enzymes can't find it."

"We were shocked by how much it stabilizes DNA," Eichman added. "Normally, the DNA strands that we used in our experiments separate when they are heated to about 40 degrees [Celsius] but, with YTM added, they don't come apart until 85 degrees."

The Streptomyces bacteria that produce YTM have also evolved a special enzyme to protect their own DNA from the toxin. Surprisingly, this is a base excision repair enzymecalled a DNA glycosylasethat is normally limited to repairing small lesions, not the bulky adducts caused by YTM. Nevertheless, studies have shown that it is extremely effective.

It so happens that one of Streptomyces' competitors, Bacillus cereus, has managed to co-opt the gene that produces this particular enzyme. In Bacillus, however, the enzyme it producescalled AlkDprovides only limited protection.

In 2015, Eichman and Mullins reported that, unlike other BER enzymes, AlkD can detect and excise YTM lesions. At the time, they had no idea why it wasn't as effective as its Streptomyces counterpart. Now they do. It turns out that AlkD tightly binds the product that it forms from a YTM lesion, inhibiting the downstream steps in the BER process that are necessary to fully return the DNA to its original, undamaged state. This drastically reduces the effectiveness of the repair process as a whole.

In recent years, biologists have discovered that animals and plants host thousands of different species of commensal bacteria and this microscopic community, called the microbiome, plays a surprisingly important role in their health and well-being. Normally, these bacteria are beneficialfor example, converting indigestible foods into digestible formsbut they can also cause problems, such as the stomach bacteria Heliobacter pylori that can cause inflammation that produces ulcers.

"We know that bacteria produce compounds like YTM when they are under stress," Eichman observed. "The negative effects this has on their hosts is an unfortunate side effect. So it is very important that we learn as much as we can about how these bacterial toxins work and how bacteria defend against them."

Explore further: New class of DNA repair enzyme discovered

More information: Elwood A Mullins et al. Toxicity and repair of DNA adducts produced by the natural product yatakemycin, Nature Chemical Biology (2017). DOI: 10.1038/nchembio.2439

This year's Nobel Prize in chemistry was given to three scientists who each focused on one piece of the DNA repair puzzle. Now a new study, reported online Oct. 28 in the journal Nature, reports the discovery of a new class ...

Tucked within its double-helix structure, DNA contains the chemical blueprint that guides all the processes that take place within the cell and are essential for life. Therefore, repairing damage and maintaining the integrity ...

Day in and day out, in our bodies, the DNA in cells is damaged for a variety of reasons, and thus intercellular DNA-repair systems are fundamental to the maintenance of life. Now scientists from the UNC School of Medicine ...

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 - ...

Every day our bodies come under a barrage of toxic agents cigarette smoke, the sun, free radicals and other carcinogenic substances that create damaging lesions in our DNA that can initiate cancer and other human ...

Food poisoning caused by Bacillus cereus can lead to diarrhea which is probably caused by a 3-component toxin which is produced by this bacteria strain and which perforates and kills cells.

One of the most potent toxins known acts by welding the two strands of the famous double helix together in a unique fashion which foils the standard repair mechanisms cells use to protect their DNA.

The hardest thing about concrete just might be the problem of how to make the ubiquitous building material in an environmentally friendly manner. Recent laboratory results at Princeton University indicate that the challenge ...

A chemical process that allows color images to be printed on specially coated paper and then erased so that different images can be printed on the same paper has been developed by researchers at Rice, Yonsei and Korea universities.

Unlike the rigid plastic models from chemistry class, real chains of molecules can bend and stretch, like beads on an elastic cord. Some polymers, like DNA, are especially stretchy, a characteristic that can complicate attempts ...

By some estimates, bacterial strains resistant to antibioticsso-called superbugs - will cause more deaths than cancer by 2050.

Jean-Sabin McEwen knocks out a web search for "North Dakota," "night sky" and "flaring," and quickly finds a picture from space showing a glowing cluster bigger than Minneapolis. It's from oil and gas fields burning off methane, ...

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

Originally posted here:
Deciphering potent DNA toxin's secrets - Phys.Org

SmartNews Keeping you current The York Gospels (York Minster)

smithsonian.com July 31, 2017

In 2010, bioarchaeologist Matthew Collins of the University of Copenhagen and his colleagues realized that the parchment used in medieval manuscripts, which is made of scraped and stretched animal skins, was actually a repository of information about the history of domestic animals in Europe.

ChrisBaraniukatNew Scientistreports that Collins and histeam have since begun collecting the dry eraser waste of skinsleft when conservators gently cleaned the manuscripts. Using these scraps,they've been able to draw out the DNA and proteins of the animal that sourced the parchment as well as that of any bookworms and humansthat hadcome in contact with the page since.

At a recent symposium on bioarchaeology at Oxfords Bodleian Library, the researchers presentedan unpublished paperwhere they applied DNA techniques as well as traditional techniques to the 1,000-year-old York Gospels, an Anglo-Saxon manuscript, which is one of the few manuscripts to survive the Norman Conquest and the Protestant Reformation.

Ann Gibbons at Science reports that analysis of the parchment led to several surprises. For instance, the 167 folio pages of the York Gospels were made mainly from female calves, which is unusual since its believed they would normally be allowed to grow up and reproduce. But documents report that a cattle disease struck the region around the time the manuscript was produced, meaning there may have been many stillborn or sick calves around to provide the material.

Gibbons also reports that 20 percent of the DNA extracted from theYork Gospelswas human most of it from the bacteria that lived on the skin and noses of priests who took an oath by kissing certain pages. That and other bacteria could give some insight into the health of people in Middle Ages York.

A similar analysis of a Gospel of Luke manuscript by Collins and his colleagues revealedthe book was made from the skins of eight-and-a-half calves, ten-and-a-half sheep, and half a goat, as well as a cover from roe deer and a strap from fallow or red deer. Such mixed parchment suggests that scribes had to carefully manage their resources since their favored skin was not always available.

There are so many possibilities raised by the developing techniques thatGibbons reports researchers dont even know what questions to ask.Bookworm DNA could help determine what region a book was produced or traveled to; parchment DNA could help trace the changes in livestock types and breeds over time; its even possible to find the DNA of specific historical individuals who handled a book during their lifetime.

While scholars have long mined medieval manuscripts to learn about the development of language and writing styles from the texts and gleaninformation about daily life from the illustrations (and paw prints), this new lens into the manuscripts offers a whole new way to mine information frommanuscripts and bringlost chapters ofhistory to life.

Like this article? SIGN UP for our newsletter

Jason Daley is a Madison, Wisconsin-based writer specializing in natural history, science, travel, and the environment. His work has appeared in Discover, Popular Science, Outside, Mens Journal, and other magazines.

Visit link:
Medieval Manuscripts Are a DNA Smorgasbord - Smithsonian

It's now cheaper than ever to map the human genome. But most healthy people don't seem to care all that much about their DNA.

A startup called Helix is trying to change that. The company launches this month with more than a dozen genetic tests in categories ranging from health to entertainment.

Bay Area-based Helix is a spinout of Illumina, a biotech company that develops DNA sequencing machines. Helix's mission is to make genomics relevant to millions more people than have used services like 23andMe, or have taken genetic tests for medical reasons.

It is hoping to reach that broader audience by partnering with a variety of brands that use genetic data in their marketing campaigns.

Examples of apps on Helix's e-commerce store include EverlyWell's "Breast Milk DHA+", which offers new moms the opportunity to find out about the DHA in their breast milk, and Dot One's "personalized scarf," which puts the pattern of a user's genetic code into a scarf. The company also offers health applications, like an inherited diabetes and cholesterol test, and its other categories are fitness, entertainment, nutrition, and ancestry.

The goal for Helix is to reach a new user-base who might not be aware of genetics or are fearful of the consequences of sharing their sensitive health data with companies (there are some gaps in the laws that protect people from discrimination based on their genetics). To convince these people, Thurston said, "utility must surpass fear." In other words, these tests need to be useful or entertaining enough to convince users to give Helix a shot.

Helix is positioning itself as an "app store," because takes on the task of sequencing a users' DNA in its San Diego lab then curates the apps that can take advantage of that information. Helix provides exome sequencing, which is more extensive than "genotyping" services offered by 23andMe, Ancestry.com and the like.

Read this article:
Start-up Helix wants you to care about your DNA -- and it's enlisting help from marketers - CNBC

Tanya Eiserer, WFAA 10:29 PM. CDT August 01, 2017

Wendy Birdsall (Photo: WFAA)

Wendy Birdsall has survived so much.

Homelessness. Crack addiction. Run-ins with the law. Being raped 11 years go.

They say what doesn't kill you makes you stronger, says Birdsall, 43.

Clean now for seven years and attending Southern Methodist University, Birdsall hadn't thought of that rape in years. Last month, she came home to find a card on her door telling her to call an investigator. She thought at first perhaps something from her past had come back to haunt her.

When she finally met with the investigator, she learned that police had a suspect in her rape. His name is Roy Gutierrez, a suspect in a series of attacks dating back more than a decade.

I was really shocked that they found the guy, she says.

When she saw his picture, she says knew it was the man who attacked her the same man accused of raping a young woman behind a building on the edge of Deep Ellum in June.

All these years, I had no idea what his name was, she says.

Roy Gutierrez is a suspect in a series of attacks dating back more than a decade. (Photo: WFAA)

Seeing his picture took her back to a dark traumatic place in her life. What really upsets her is to find that his DNA had been matched to her case nearly two years after her attack. She did not know about the DNA match until last month.

It's not clear why the case wasn't filed against him at the time.

Part of me is angry, really angry, she says.

The only explanation shes received so far is that there are cracks in the criminal justice system. That is hardly a comfort to victims.

Every single girl after that that was a victim, did not have to be a victim, she says.

A recent search of police records revealed that Gutierrez had been suspected in seven rapes between 2004 and 2007, according to court documents.

Gutierrez is currently in the Dallas County jail. He is charged with two counts of aggravated sexual assault one for the Deep Ellum case and the other for Birdsalls case.

On that night in November 2006, Birdsall and her boyfriend got into an argument outside. A white car pulled up. The man inside asked, Hey are you alright? You need me to take you somewhere.

Birdsdall says she was so mad at her boyfriend that she got in the car. Before she knew it, the man was driving to a place way out of the area.

I knew in the pit of my stomach something was wrong, she says. At that time, I was not a Christian. I started praying to God, If youre real, help me.'

The man pulled into a wooded area. He raped her at gunpoint in the car. He ordered her out of the vehicle and raped her again. When he turned his back to retrieve his gun, she ran as fast as she could. He fired his gun at her at least twice.

I kept running, Birdsall said. I was so terrified.

She ran to several houses, but no one would answer. She heard a car and knew it had to be her attacker, so she jumped a 10-foot fence. The homeowner came out and called the police.

The next year, in 2007, Gutierrez was identified as a potential suspect in a series of attacks that had occurred over a two-year period, according to 2007 police report.

There had been several rapes involving a Hispanic male in a small silver car. In each case, the rapist had picked up the victims and taken them to same wooded area.

On Sept. 21, 2007, an officer drove to that area in the early morning hours, looking for possible victims. When he got there, he saw a vehicle matching the suspects vehicle description.

The officer saw Gutierrez getting out of the car. The officer saw an undressed woman in the back seat.

She told police that she had gotten into an argument with her boyfriend in East Dallas and that she had packed her clothing when he drove up and offered her a ride.

She told police that he drove her to a wooded area and tried to rip her dress off, saying, It goes off like this.

She told police that he threatened to stab her and raped her, saying, You like this, dont you.

Gutierrez was arrested at the scene. He was charged with aggravated sexual assault. He pleaded guilty in a plea deal to aggravated assault.

He violated probation and served five years in prison. Gutierrez was released in 2014.

Birdsall says it took years for her to understand that the rape was not her fault. She says she plans to testify against him to make sure he cant do it to anyone else. She says she forgave him for what he did, not for him, but for herself.

I am a survivor, she says. Im not a victim. Im an overcomer.

A one-time high school dropout, she graduated from El Centro with honors. She celebrated seven years drug-free last week.

Shes scheduled to graduate next year with degrees in applied psychology and health management.

My life is a walking testimony, she says. I know for a fact that somebody upstairs loves me.

2017 WFAA-TV

Read more:
Rape survivor upset about lengthy delay after DNA matches suspect - WFAA

DNA evidence further vindicates...

YAKIMA, Wash. - A Yakima rape victim could be another step closer to finding justice, thanks to a man who was wrongfully convicted of attacking her more than 20 years ago. Ted Bradford was convicted of rape in the late 1990's. He confessed to the crime during an interrogation because he wanted to end the questioning and he thought biological evidence would exonerate him. But, at the time, crime labs couldn't test a DNA sample that small and a jury convicted Bradford of rape. After he served his sentence, the Pacific Northwest chapter of The Innocence Project took up his case. They had DNA evidence tested and it did not match Bradford. Still, the DNA was not matched to a suspect... until now. KXLY4 News profiled Bradford in a special report about the Innocence Project in 2016. Bradford told us of his ongoing litigation against the Yakima Police investigator who handled his case. That civil case was thrown out, but is under review by the U.S. Court of Appeals.His attorneys in that caseused that DNA sample to help find who they believe is the real suspect. The attorneys narrowed down a list of possible suspects to a family member of the victim. They then hired a private investigator who collected a DNA sample from the man's trash. That sample was tested at a private lab and the results came back this summer. According to a news release issued Monday, "[the DNA sample] was compared to the DNA sample collected from items the rapist left at the scene. The lab results demonstrated that the two samples had a nearly 100 percent probability of having originated from the same person." "The news was overwhelming," said Jackie McMutrie, founder of Innocence Project Northwest. "It is a tragedy that more reliable police practices and a thorough investigation could have prevented the heartbreaking losses suffered by Ted and his family." The attorneys brought their information to the Yakima Police Department, the Yakima Prosecuting Attorney and the State Attorney General. It's up to the prosecutor now to determine if new charges will be filed. The prosecutor told the Seattle Times that it's not clear yet if they'll do that. The Times said the statute of limitations on the crime expires next year. "I cannot express my gratitude to [civil attorney] Mike [Wampold] and the rest of his team, and the living, breathing saints at the Innocence Project Northwest," Bradford said. "They've worked for years to help me win my freedom. Now through Mike Wompold's dogged determination, we know who the bad guy is and we hope he will be held accountable for his horrible crime." For more information about the case, visit http://www.justiceforted.com.

Link:
DNA evidence further vindicates previously exonerated man - KXLY Spokane