Category Archives: Transhuman News

August 16, 2017 Adult C. elegans worms can be seen with embryos inside them. Credit: Adam Klosin, CRG

Cell division is key for renewing the cells in our tissues and organs. There are two particular processes in which cell division is crucial: embryonic development and tumorigenesis. A fault in the process that copies DNA during cell division can cause genetic changes, so impaired DNA replication is a well-known cancer hallmark and a driver of genomic instability.

Now, scientists at the Centre for Genomic Regulation (CRG) in collaboration with the Josep Carreras Leukaemia Research Institute (IJC) and The Institute for Health Science Research Germans Trias i Pujol (IGTP) have discovered that impaired DNA replication can also cause large epigenetic changes. Their study, which was performed in worms (the model organism Caenorhabditis elegans), suggests that these genome-wide epigenetic alterations establish new gene expression states that may be inherited for up-to five generations. This is a striking example of trans-generational inheritance of epigenetic changes meaning that two individuals may differ in gene expression only because of the stress experienced by their ancestors.

The researchers, led by ICREA research professor and group leader at the CRG Ben Lehner, also identified the mechanism causing these epigenetic changes. "For the correct function of cells and ultimately the health of the organism, it is important to keep certain genes active and others silenced. Inside cells, there are DNA-protein complexes called heterochromatin that prevent genes from becoming activated when they should not be. Initially, we noticed that a gene artificially inserted into the worm genome and normally silenced by heterochromatin was activated in animals that carried mutations in proteins involved in the copying of DNA," explains Tanya Vavouri CRG alumna currently group leader at IJC and IGTP and coauthor of this study. "We found that this was caused by loss of heterochromatin and that other genes also silenced by heterochromatin were activated too. Unexpectedly, the gene was inappropriately activated for five generations in animals that did not carry the mutation in DNA replication but had ancestors that did," she adds.

"Our results show that impaired DNA replication not only causes genetic alterations but also genome-wide epigenetic changes that can be stably inherited," says Ben Lehner, senior author of the paper. An important question in epigenetics is the extent to which epigenetic states are transmitted between generations. Lehner and collaborators are addressing this and other questions from many different angles. They previously reported that some temperature-induced gene expression changes can also be inherited between generations. "We hope that our work will change the way people think about the impact of replication stress during tumorigenesis and embryonic development as well as about inter-generational inheritance," he concludes.

Explore further: Environmental 'memories' passed on for 14 generations

More information: A. Klosin, K. Reis, C. Hidalgo-Carcedo, E. Casas, T. Vavouri, B. Lehner. "Impaired DNA replication derepresses chromatin and generates a transgenerational inherited epigenetic memory". Science Advances. 3, e1701143 (2017). DOI: 10.1126/sciadv.1701143

Provided by: Center for Genomic Regulation

Scientists at the Centre for Genomic Regulation (CRG) in Barcelona and the Josep Carreras Leukaemia Research Institute and The Institute for Health Science Research Germans Trias i Pujol (IGTP) in Badalona, Spain, have discovered ...

Studies of human populations suggest that our health and longevity could be affected by the diets and experiences of our grandparents. For example, studies of a small community in northern Sweden where detailed historical ...

We are more than the sum of our genes. Epigenetic mechanisms modulated by environmental cues such as diet, disease or lifestyle take a major role in regulating the DNA by switching genes on and off. It has been long debated ...

Researchers at RIKEN have uncovered a mechanism by which the effects of stress in the fly species Drosophila are inherited epigenetically over many generations through changes to the structure of chromatin, the material that ...

According to epigeneticsthe study of inheritable changes in gene expression not directly coded in our DNAour life experiences may be passed on to our children and our children's children. Studies on survivors of traumatic ...

USC scientists have discovered how two different structural apparatuses collaborate to protect repetitive DNA when it is at its most vulnerable while it is being unzipped for replication.

A small team of researchers affiliated with several institutions in France has discovered why medium-sized ants have more trouble climbing out of sand pits than larger or smaller ants. In their paper published in the journal ...

Scientists at the University of Stirling have discovered a new type of plant growing in Shetland - with its evolution only having occurred in the last 200 years.

It's already known some fish have big hearts - at least during the winter.

Cell division is key for renewing the cells in our tissues and organs. There are two particular processes in which cell division is crucial: embryonic development and tumorigenesis. A fault in the process that copies DNA ...

New technologies for analyzing DNA may transform how imperiled species are considered and managed for conservation protection, according to a study published today in the journal Science Advances and led by the University ...

Markus Knaden and Bill Hansson, and their colleagues at the Department of Evolutionary Neuroethology, study ecologically relevant odors in the natural environment of insects, especially vinegar flies. In this new study they ...

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Impaired DNA replication can cause epigenetic changes inherited for several generations - Phys.Org

An Oxford man was recently charged with a November 2014 robbery of a New Milford gas station after he was linked to the crime through DNA evidence, police said.

Michael Warga, 25, of 43B Christian St., was arraigned last week in Bantam Superior Court and charged with first-degree robbery, first-degree burglary and fourth-degree larceny.

The charges stem from a November 2014 robbery of the Valero gas station at 28 Danbury Road, according to an affidavit. In investigating the incident, police determined that a man entered the store, held an employee at gunpoint and demanded he open the cash register.

Once the cash register drawer was opened the male took the money and then told (the employee) not to do anything, count from one to (50) without moving and nothing bad would happen to him, wrote New Milford Detective Mark Lynch in the affidavit. The male then fled out of the store.

The suspect was seen in surveillance footage wearing a dark zippered hooded sweatshirt, blue jeans, boots, dark gloves and a dark hat, according to the affidavit.

K-9 Officer Michael Lafond and his partner, Kira, began to search the area and found a black hat, two black gloves and a black article of clothing that seemed to be a jacket or sweatshirt. These items were later brought to the Connecticut Forensic Laboratory, where they returned a DNA profile, which was entered into state and national databases, police said.

The DNA profile from a glove was found to match those from similar robberies under investigation in Naugatuck and Prospect, according to the affidavit. Two further robberies in Ansonia were thought to have been committed by the same person.

In March 2017, a positive match for Warga, incarcerated at the Bridgeport Correctional Center, was determined to correspond for the aforementioned cases.

Warga was found to have a criminal history in Florida and Connecticut, according to the affidavit, with past charges including larceny, possession of marijuana and assault.

A warrant had already been completed for a DNA sample for Warga, according to the affidavit. In May 2017, that sample was compared to the DNA collected on the hat and gloves gathered from the November 2014 robbery and the resulting report showed that Michael Wargas DNA was located on all of the aforementioned items, according to the affidavit.

Wargas case was transferred to Litchfield Superior Court last week, according to court records, and bail was set at $10,000. He is next scheduled to appear in court Aug. 31.

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DNA evidence prompts New Milford police to charge Oxford man in 2014 robbery - Danbury News Times

August 16, 2017 Liquid biopsy for cancer. Credit: Victor Velculescu et al., Science Translational Medicine 2017

In a bid to detect cancers early and in a noninvasive way, scientists at the Johns Hopkins Kimmel Cancer Center report they have developed a test that spots tiny amounts of cancer-specific DNA in blood and have used it to accurately identify more than half of 138 people with relatively early-stage colorectal, breast, lung and ovarian cancers. The test, the scientists say, is novel in that it can distinguish between DNA shed from tumors and other altered DNA that can be mistaken for cancer biomarkers.

A report on the research, performed on blood and tumor tissue samples from 200 people with all stages of cancer in the U.S., Denmark and the Netherlands, appears in the Aug. 16 issue of Science Translational Medicine.

"This study shows that identifying cancer early using DNA changes in the blood is feasible and that our high accuracy sequencing method is a promising approach to achieve this goal," says Victor Velculescu, M.D., Ph.D., professor of oncology at the Johns Hopkins Kimmel Cancer Center.

Blood tests for cancer are a growing part of clinical oncology, but they remain in the early stages of development. To find small bits of cancer-derived DNA in the blood of cancer patients, scientists have frequently relied on DNA alterations found in patients' biopsied tumor samples as guideposts for the genetic mistakes they should be looking for among the masses of DNA circulating in those patients' blood samples.

To develop a cancer screening test that could be used to screen seemingly healthy people, scientists had to find novel ways to spot DNA alterations that could be lurking in a person's blood but had not been previously identified.

"The challenge was to develop a blood test that could predict the probable presence of cancer without knowing the genetic mutations present in a person's tumor," says Velculescu.

The goal, adds Jillian Phallen, a graduate student at the Johns Hopkins Kimmel Cancer Center who was involved in the research, was to develop a screening test that is highly specific for cancer and accurate enough to detect the cancer when present, while reducing the risk of "false positive" results that often lead to unnecessary overtesting and overtreatments.

The task is notably complicated, says Phallen, by the need to sort between true cancer-derived mutations and genetic alterations that occur in blood cells and as part of normal, inherited variations in DNA.

As blood cells divide, for example, Velculescu says there is a chance these cells will acquire mistakes or mutations. In a small fraction of people, these changes will spur a blood cell to multiply faster than its neighboring cells, potentially leading to pre-leukemic conditions. However, most of the time, the blood-derived mutations are not cancer-initiating.

His team also ruled out so-called "germline" mutations. While germline mutations are indeed alterations in DNA, they occur as a result of normal variations between individuals, and are not usually linked to particular cancers.

To develop the new test, Velculescu, Phallen and their colleagues obtained blood samples from 200 patients with breast, lung, ovarian and colorectal cancer. The scientists' blood test screened the patients' blood samples for mutations within 58 genes widely linked to various cancers.

Overall, the scientists were able to detect 86 of 138 (62 percent) stage I and II cancers. More specifically, among 42 people with colorectal cancer, the test correctly predicted cancer in half of the eight patients with stage I disease, eight of nine (89 percent) with stage II disease, nine of 10 (90 percent) with stage III and 14 of 15 (93 percent) with stage IV disease. Of 71 people with lung cancer, the scientists' test identified cancer among 13 of 29 (45 percent) with stage I disease, 23 of 32 (72 percent) with stage II disease, three of four (75 percent) with stage III disease and five of six (83 percent) with stage IV cancer. For 42 patients with ovarian cancer, 16 of 24 (67 percent) with stage I disease were correctly identified, as well as three of four (75 percent) with stage II disease, six of eight (75 percent) with stage III cancer and five of six (83 percent) with stage IV disease. Among 45 breast cancer patients, the test spotted cancer-derived mutations in two of three (67 percent) patients with stage I disease, 17 of 29 (59 percent) with stage II disease and six of 13 (46 percent) with stage III cancers.

They found none of the cancer-derived mutations among blood samples of 44 healthy individuals.

Despite these initial promising results for early detection, the blood test needs to be validated in studies of much larger numbers of people, say the scientists.

Velculescu and his team also performed independent genomic sequencing on available tumors removed from 100 of the 200 patients with cancer and found that 82 (82 percent) had mutations in their tumors that correlated with the genetic alterations found in the blood.

The Johns Hopkins-developed blood test uses a type of genomic sequencing the researchers call "targeted error correction sequencing." The sequencing method is based on deep sequencing, which reads each chemical code in DNA 30,000 times. "We're trying to find the needle in the haystack, so when we do find a DNA alteration, we want to make sure it is what we think it is," says Velculescu.

Such deep sequencing, covering more than 80,000 base pairs of DNA, has the potential to be very costly, but Velculescu says sequencing technology is becoming cheaper, and his research team may eventually be able to reduce the number of DNA locations they screen while preserving the test's accuracy.

He says the populations that could benefit most from such a DNA-based blood test include those at high risk for cancer including smokersfor whom standard computed tomography scans for identifying lung cancer often lead to false positivesand women with hereditary mutations for breast and ovarian cancer within BRCA1 and BRCA2 genes.

Explore further: Blood biopsy test reads platelets to detect human lung cancer

More information: J. Phallen el al., "Direct detection of early-stage cancers using circulating tumor DNA," Science Translational Medicine (2017). stm.sciencemag.org/lookup/doi/ scitranslmed.aan2415

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Scientists develop blood test that spots tumor-derived DNA in people with early-stage cancers - Medical Xpress

The story you are about to read is true. I know because it happened to me.

It started months ago when our daughters gave us gift certificates for DNA screening through Ancestry. com.

Like most of us, I knew that DNA has been used for years to catch criminals, clear innocent persons of crimes, determine paternity and identify the remains of deceased persons.

Frankly, the TV ads about tracing DNA to find your genetic makeup seemed like a fad, much like buying the name of a star out in space.

I never had a college course in molecular biology so I went online to learn that DNA was first observed by a German biochemist named Frederich Miescher in 1869.

But no one realized the importance of the deoxyribonucleic acid molecule until 1953 when James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin figured out the structure of DNA a double helix which they discovered could carry biological information.

Appropriately, Watson, Crick and Wilkins were awarded the Nobel Prize in Medicine in 1962.

Even after reading about DNA, I remained skeptical about how a half-teaspoonful full of saliva in a mail-order test tube could tell me where my ancestors lived and which ethnic groups I came from.

My test results arrived three weeks later. Somewhat to my surprise, my genetic makeup was 37 percent British, 32 percent Irish and 31 percent other European regions. My genetic community was identified as the early settlers of Central Appalachia East Kentucky and parts of Ohio, West Virginia, and Virginia. The system found 787 DNA matches to me out of a pool of 156,880 other descendants from that region. It also linked me directly to both of my grandmothers, my parents and one grandfather.

I wrote earlier about recently confirming my relationship to my biological grandfather, Harry Paul Temple of Sandusky, Ohio, who died in 1960.

So I queried the surname of Temple and came up with George Washington Temple, Harrys father and my great-grandfather, as a likely relative.

Ancestry.com had no independent information about my kinship with this other family.

Incredibly, they connected my bloodlines with those of the Temple family solely through my DNA.

In a word, wow!

Keith Kappes can be reached at kkappes@journal-times.com or by telephone at 356-0912.

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Wednesday's Post: The science of DNA is simply amazing - Journal-Times

In BriefA group of biohackers at the University of Washington found away to sequence gene bases to implant malware through a laboratorycomputer. Though still in its early stages, they have invented asci-fi device of biopunk ingenuity. Welcome to the World of Biohacking

Biologists pay scrupulous attention to DNA synthesis, not just out of a need for precision, but also as a precaution. Scientists dont want to create or spread a dangerous stretch of genetic code that, with a little bit of criminal ingenuity, could be used to make a toxin or an infectious disease. But recently, a group of biohackers has found a way to cross biology with the digital by resequencing DNA, not to infect humans or animals, but computers.

A group of researchers from the University of Washington has shown that, for the first time, its possible to encode malicious software into physical strands of DNA. And so, when a gene sequencer performs an analysis, the output transforms into a program which corrupts gene-sequencing software to gain control of an entire computer.

This is a far cry from a criminal implementation. Researchers agree that this new method could be integrated into real-world applications once DNA sequencing grows more powerful and ubiquitous.

We know that if an adversary has control over the data a computer is processing, it can potentially take over that computer, said Tadayoshi Kohno, Computer Science Professor at the University of Washington in an interview with WIRED, noting the similarity to traditional hacker attacks. That means when youre looking at the security of computational biology systems, youre not only thinking about the network connectivity and the USB drive and the user at the keyboard but also the information stored in the DNA theyre sequencing. Its about considering a different class of threat, he added.

While, currently, this feels more like an alternate take on Neal Stephensons Snow Crashthan an imminent cyber threat, the means for disseminating this bio-delivered code are already coming into being. University labs, for one, are employing increasingly centralized services for students and professors working with college-owned (and expensive) gene sequencing equipment. And as other, non-academic environs like corporations, medical facilities, and government-run facilities follow suit, this DNA-malware delivery trick will become feasible. Additionally, the DNA-malware delivery will come from outside sources, which could provide the perfect window for malware insertion.

Called an exploit by hackers, this specific kind of computer attack is known as a buffer overflow which fills the space in a computers memory allocated for the gene sequence and then spills out into other parts of the computers memory until it can plant its own commands.

So far, challenges to the process like squeezing the code into a few hundred DNA bases and the tendency of redundant base patterns to cause DNA to fold into itself have limited the digital translation to a mere 37% success rate. Clearly, DNA-hacking is still only a reality for readers of biopunk sci-fi, but wed be naive to dismiss it as the next generations problem (or boon). After all, Seth Shipman of a Harvard team recently encoded a video in a DNA sample. Once perfected, DNA storage could replace magnetic encoding in flash memory because DNA maintains its structure for much longer.

DNA coding and bio-exploitation might sound like fiction today, but, like the cell phones origins in Star Trek canon, its only a matter of doing.

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Researchers Hacked Into DNA and Encoded it With Malware - Futurism

Like middle-aged women dying their hair fluorescent colors and young women dying their hair iron gray, DNA testing has become fashionable even without necessarily leading to positive results.

Do we really need to know more about our ancestral heritage, as if we're characters out of "Game of Thrones" and desperate to figure out whether to pledge allegiance to wolves, dragons or the incestuous Lannisters, thereby becoming part of some larger powerful dynasty?

While finding out information about your grandparents' hometown might be fun, shrines to bloodlines aren't such a good idea, especially when neo-Nazis armed with their hand- painted homemade shields (as if arts and crafts have replaced Sturm und Drang) might just change their goal from world domination to "extreme ancestry."

In an increasingly diverse world, why are we trying to locate our individual genetic pattern anyhow? Is it because, when you go to the website for a popular DNA testing service called "23 and Me," you're greeted with the motto "Everyone Has a DNA Story"?

Maybe your family is perfect, but my first reaction was that a lot of DNA stories should be put on "do not resuscitate" orders they should not be revived but, like sleeping dogs, left to lie.

Remember, it wasn't until about 60 years ago that you could tell if your DNA matched the rest of your family's. There was a reason why Homer (not from the "The Simpsons" but the "The Odyssey") observed, "It's a wise child that knows its own father."

Illustrating "Everyone Has a DNA Story" is a cheerful white woman in athletic gear, sporting an iPod and an unfocused gaze. Next to her is the following text: "Scandinavian 34.5 percent and lactose intolerant."

So the mysteries solved by hundreds of years of science are that Blondie is partly Scandinavian and gets gassy when she eats cheese? For that she needed to know what land masses her distant relatives traversed to get her family to, say, Milwaukee?

At another popular site run by Ancestry.com, a white woman cheerfully announces "Holy crow! I'm related to George Washington." We learn that "Emily found a presidential cousin who could be hiding in your family tree?"

I think my family tree was the one cut down by the young George Washington. Not that I'm bitter.

Families have a wide assortment of pasts. Some people have excruciatingly detailed family histories and can trace their lineage back to amoebas, presumably wearing tiny distinctive crests or tartans when they separated in the primordial muck. They're very proud of being able to point to the first traces of these organisms, as if dissemination were somehow an acquired skill, like the bro-sis couple in "Game of Thrones."

Some family trees don't fork. But they do spoon.

But enough about white supremacists, neo-Nazis, the KKK and other groups giving the lunatic fringe a bad reputation; the rest of us have to start seeing the points at which our lives connect rather than disconnect.

Sniffing out ethnic or racial bloodlines and tracking individual family trace molecules won't bring us closer as a community or as a nation.

Discovering our collective human blueprints might.

You do that through education, by sharing values and understanding history. You don't do it by swabbing the inside of your cheek.

Those who believe in the superiority of an ethnic white heritage are a feeble and fearful group. Fueled by fanatical beliefs they cannot render in intelligible terms and driven by degraded ideologies the origins of which are rooted in superstition, bigotry and pathology, they want to blame their failures on somebody as long as that person doesn't look like their kin.

Threatening, lazy and impotent, metaphorically if not literally, they regard every successful woman, every successful person of color, every successful recent immigrant, every successful person who is slightly different in any way (queer, non-fundamentalist-Christian, artistic, funny or well-dressed) as repudiation.

There must be an excuse for the fact that they have nothing to strive for, except a past that might have an ancestor hiding in a branch somewhere.

They might believe that branch is currently the executive one. Let's prove them wrong. The past is done and the future doesn't belong to them. It's not about any single group's DNA, resume, IQ or ZIP code. It's about all of us.

Gina Barreca is an English professor at UConn and author of "If You Lean In, Will Men Just Look Down Your Blouse?" and eight other books. She can be reached at ginabarreca.com.

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Gina Barreca: White Supremacists Wrong, It's Not Our DNA - Hartford Courant