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Genome sequencing reveals severe inbreeding of mountain gorillas

Genome sequencing reveals severe inbreeding of mountain gorillas | Amazing Science | Scoop.it

The most extensive genetic analysis of mountain gorillas ever conducted has found the critically endangered apes burdened with severe inbreeding and at risk of extinction but the researchers still see reasons for optimism about their survival.


Twenty-three scientists from six countries unveiled on Thursday the first complete genetic map of the mountain gorilla, a close genetic cousin to humans inhabiting two isolated areas in central Africa. “We found extremely high levels of inbreeding,” said geneticist Chris Tyler-Smith of Britain’s Wellcome Trust Sanger Institute.


The study in the journal Science revealed a substantial loss of genetic diversity from inbreeding caused by mating with close relatives due to small population size, with mountain gorillas inheriting identical segments from both parents in about a third of their genome.


Inbreeding can increase threats from disease and environmental change by reducing the genetic ability to adapt and cause a larger hardship of harmful mutations. “Mountain gorillas are critically endangered and at risk of extinction, and our study reveals that as well as suffering a dramatic collapse in numbers during the last century, they had already experienced a long decline going back many thousands of years,” University of Cambridge geneticist Aylwyn Scally said.


The researchers were surprised that many of the most harmful mutations, those that can stop genes from working and cause serious health conditions, were less common than in other gorilla subspecies. “We have shown that although low in genetic diversity they have not yet crossed any genetic threshold of no return. They can continue to survive and will return to larger numbers if we help them,” Scally said.


There are only about 880 mountain gorillas, living in mist-covered forests of the Virunga volcanic mountain range on the borders of Rwanda, Uganda and the Democratic Republic of Congo and Uganda’s Bwindi Impenetrable National Park. The study was based on blood samples from seven Virunga gorillas.

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Detection of Pathogens and Novel Viruses Carried by New York City Rats

Detection of Pathogens and Novel Viruses Carried by New York City Rats | Amazing Science | Scoop.it

No one was under the illusion that New York’s rats were clean creatures, but a study published this week in mBio found dozens of viruses that have never been described by science, some of which may be potentially harmful to humans. “While a subset of the agents we identified are known to cause disease in humans, many more are novel viruses whose zoonotic potential cannot be inferred from available data,” Cadhla Firth, the lead researcher of the team from Columbia University, wrote. “It is therefore possible that human infection with some of the agents identified here may already be occurring, and the risk of future zoonotic transmission should not be disregarded.”


Beyond that, the researchers found many, many pathogens that are well known and are very bad for people, pets, and sometimes even zebras. So, in an attempt to scare the bejesus out of everyone, I quickly analyzed the 32 species of clinically important microbes that were identified. 

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Age-related leukemia almost inevitable: 70% of people over 90 have genetic mutations that could lead to leukemia

Age-related leukemia almost inevitable: 70% of people over 90 have genetic mutations that could lead to leukemia | Amazing Science | Scoop.it

It is "almost inevitable" that your blood will take the first steps towards leukemia as you age, researchers show. The cancer is often associated with children, but some types become more common with age. The study, published in the journal Cell Reports, showed 70% of healthy people in their 90s had genetic errors that could lead to leukemia. The researchers warn that the number of cases could soar as life expectancy increases.


The team at the Wellcome Trust Sanger Institute, outside Cambridge, analysed the blood of 4,219 people. They focused on accurately testing for errors in the DNA that are linked to the blood cancers. If one blood cell in a hundred carried such a mutation they would pick it up.


The results were a surprise. They suggest 20% of people in their 50s have potentially cancerous mutations rising to 70% in people in their 90s. One of the researchers, Dr George Vassiliou, told the BBC News website: "We had suspected people had these mutations, but didn't expect they would be an almost inevitable consequence of aging. "What it is saying is that a lot more people than expected are starting on the path to leukemia, but thankfully only a few make it to the end."

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Development of an Epigenome Browser to Help Understanding the Functional Complexity of the Genome

Development of an Epigenome Browser to Help Understanding the Functional Complexity of the Genome | Amazing Science | Scoop.it

Advances in next-generation sequencing platforms have reshaped the landscape of functional genomic and epigenomic research as well as human genetics studies. Annotation of noncoding regions in the genome with genomic and epigenomic data has facilitated the generation of new, testable hypotheses regarding the functional consequences of genetic variants associated with human complex traits1. Large consortia, such as the US National Institutes of Health (NIH) Roadmap Epigenomics Consortium3 and ENCODE4, have generated tens of thousands of sequencing-based genome-wide data sets, creating a useful resource for the scientific community5. The WashU Epigenome Browser68 continues to provide a platform for investigators to effectively engage with this resource in the context of analyzing their own data.


The newly developed Roadmap Epigenome Browser (http://epigenomegateway.wustl.edu/browser/roadmap/) is based on the WashU Epigenome Browser and integrates data from both the NIH Roadmap Epigenomics Consortium and ENCODE in a visualization and bioinformatics tool that enables researchers to explore the tissue-specific regulatory roles of genetic variants in the context of disease. The browser takes advantage of the over 10,000 epigenomic data sets it currently hosts, including 346 'complete epigenomes', defined as tissues and cell types for which we have collected a complete set of DNA methylation, histone modification, open chromatin and other genomic data sets9.


Data from both the NIH Roadmap Epigenomics and ENCODE resources are seamlessly integrated in the browser using a new Data Hub Cluster framework. Investigators can specify any number of single nucleotide polymorphism (SNP)-associated regions and any type of epigenomic data, for which the browser automatically creates virtual data hubs through a shared hierarchical metadata annotation, retrieves the data and performs real-time clustering analysis. Investigators interact with the browser to determine the tissue specificity of the epigenetic state encompassing genetic variants in physiologically or pathogenically relevant cell types from normal or diseased samples.


The epigenomic annotation of two noncoding SNPs can be identified from genome-wide association studies of people with multiple sclerosis10, by clustering the histone H3K4me1 profile of SNP-harboring regions and RNA-seq signal of their closest genes across multiple primary tissues and cellsThus, reference epigenomes provide important clues into the functional relevance of these genetic variants in the context of the pathophysiology of multiple sclerosis, including inflammation11.

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Is whole-genome sequencing for newborns coming?

Is whole-genome sequencing for newborns coming? | Amazing Science | Scoop.it

The advent and refinement of sequencing technologies has resulted in a decrease in both the cost and time needed to generate data on the entire sequence of the human genome. This has increased the accessibility of using whole-genome sequencing and whole-exome sequencing approaches for analysis in both the research and clinical contexts. The expectation is that more services based on these and other high-throughput technologies will become available to patients and the wider population. Some authors predict that sequencing will be performed once in a lifetime, namely, shortly after birth. The Public and Professional Policy Committee of the European Society of Human Genetics, the Human Genome Organization Committee on Ethics, Law and Society, the PHG Foundation and the P3G International Pediatric Platform address herein the important issues and challenges surrounding the potential use of sequencing technologies in publicly funded newborn screening (NBS) programs. This statement presents the relevant issues and culminates in a set of recommendations to help inform and guide scientists and clinicians, as well as policy makers regarding the necessary considerations for the use of genome sequencing technologies and approaches in NBS programs. The primary objective of NBS should be the targeted analysis and identification of gene variants conferring a high risk of preventable or treatable conditions, for which treatment has to start in the newborn period or in early childhood.


The development of next-generation sequencing (NGS) technologies has substantially reduced both the cost and the time required to sequence an entire human genome. The prospect of the availability of NGS technologies and consequently the greater facility to conduct whole-genome sequencing (WGS) have led some to predict that the use of this technology will change the current practice of medicine and public health by enabling more accurate, sophisticated and cost-effective genetic testing.1 It is anticipated that in the short term, the implementation of WGS in the clinic will improve diagnosis and management of some disorders with a strong heritable component,2 as well as improve personalized diagnosis and personalized drug therapy and treatment.


Presently, NGS is being used for targeted sequencing of sets of genes to help guide cancer treatment, and a number of cancer centers are considering using WGS or whole-exome sequencing (WES) in the future. During pregnancy, noninvasive prenatal testing for aneuploidy is also being done using NGS.3 In the clinic, WGS and WES are also being used to identify the causes of rare genetic diseases especially in children4 and in individuals with ‘atypical manifestations, (that) are difficult to confirm using clinical or laboratory criteria alone, or otherwise require extensive or costly evaluation’.5 Disorders for which WGS has been used as a diagnostic tool are usually genetically heterogeneous and have variable phenotypic expression such as intellectual disability, congenital malformations and mitochondrial dysfunctions.5 Other foreseen applications include tissue matching, disease risk predictions, reproductive risk information, forensics or even recreational genomic information, such as genealogy or nonmedically related traits.


Nonetheless, Goldenberg and Sharp6 predict that ‘it is likely that the earliest applications of whole-genome sequencing will be restricted to settings in which genetic testing is already a routine part of clinical or public health practice, such as state newborn screening (NBS) programs’.6 In truth, it should be noted that DNA testing, per se, is not a routine part of NBS and that only a very small proportion of babies, depending on the country, have a DNA test (as opposed to a biochemical test).7


Furthermore, the above prediction could be criticized as the routine nature of NBS with its often implied consent, together with its public health context, and the particular vulnerability of the population tested, would make it an unsuitable context into which to first welcome a WGS approach.

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Viruses In Our Genome: Forty Million Years In the Making

Viruses In Our Genome: Forty Million Years In the Making | Amazing Science | Scoop.it

Each year, billions of people get infected with viruses–with common ones like influenza and cold viruses, and rarer ones like polio and Ebola. The viruses don’t stay all that long inside of us. In most cases, our immune systems wipe them out, except for a few refugees that manage to escape to a new host and keep their species alive. In some cases, the viruses kill their unfortunate hosts, and end their own existence as well. But in some exquisitely rare cases, viruses meld with the genome of their hosts and become part of the genetic legacy their hosts pass down to future generations.


Scientists know this melding has happened because viruses have distinctive genes. When scientists scan the human genome, they sometimes come across a stretch of DNA that bears the hallmarks of viruses. The easiest type of virus to recognize are retroviruses, a group that includes HIV. Retroviruses make copies of themselves by infecting cells and then using an enzyme to insert their genes into their host cell’s DNA. The cell then reads the inserted DNA and makes new molecules that assemble into new viruses.


Humans carry about 100,000 pieces of DNA that came from retroviruses–known as endogenous retroviruses. All told, they come to an estimated 5 to 8 percent of the entire human genome. That’s several times more DNA that makes up all 20,000 of our protein-coding genes.


Gkikas Magiorkinis, a University of Oxford virologist, and his colleagues have now carried out large-scale survey of endogenous retroviruses in humans, apes, and Old World monkeys–a group of species that all descend from a common primate ancestor that lived some 40 million years ago. They catalogued the viruses in each species and compared them to the versions in the other primates. They were able to reconstruct the history of our viral DNA in unprecedented detail, even coming up with estimates for the rate at which the viruses inserted new copies into our genome.


The scientists can trace our viral DNA to 30 to 35 separate invasions. Once each virus established itself in our ancestors’ DNA, it produced copies of itself scattered through the genome. The rate at which new copies were inserted rose and fell over time, and at different rates in different branches of the primate tree. Here’s an overall look at the history of the viruses. 


Our monkey-like ancestors 40 million years ago acquired new virus copies at a fast clip–much faster than in our own lineage in the past couple million years. One virus in particular, known as HERV-H, was responsible for most of the new copies. It may have evolved adaptations that made it into a superspreader inside the genome.


In the past million years, only a single virus has continued to multiply–known as HERV-K. Today, you can find some HERV-K copies in some people and not in others. The pattern of these copies suggests that as recently as 250,000 years ago, HERV-K was still making new copies.


It’s possible that HERV-K is completely dead now. There’s no evidence that HERV-K or any other endogenous retrovirus is actively spreading or causing cancer. It’s hard to say at this point why humans have put the brakes on endogenous retroviruses. But Magiorkinis has one suggestion: our ancestors may have reduced their odds of picking up new viruses.

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Global ENIGMA consortium finds that common genetic variants influence human brain structures

Global ENIGMA consortium finds that common genetic variants influence human brain structures | Amazing Science | Scoop.it

In the largest collaborative study of the brain to date, about 300 researchers in a global consortium of 190 institutions identified eight common genetic mutations that appear to age the brain an average of three years. The discovery could lead to targeted therapies and interventions for Alzheimer’s disease, autism, and other neurological conditions.


Led by the Keck School of Medicine of the University of Southern California (USC), an international team known as the Enhancing Neuro Imaging Genetics through Meta Analysis (ENIGMA) Network, pooled brain scans and genetic data worldwide to pinpoint genes that enhance or break down key brain regions in people from 33 countries.


This is the first high-profile study since the National Institutes of Health (NIH) launched its Big Data to Knowledge (BD2K) centers of excellence in 2014. The research was published Wednesday, Jan. 21, in the peer-reviewed journal Nature.


“Our global team discovered eight genes that may erode or boost brain tissue in people worldwide,” said Paul Thompson, Ph.D., Keck School of Medicine of USC professor and principal investigator of ENIGMA. ” Any change in those genes appears to alter your mental bank account or brain reserve by 2 or 3 percent. The discovery will guide research into more personalized medical treatments for Alzheimer’s, autism, depression and other disorders.”


The study could help identify people who would most benefit from new drugs designed to save brain cells, but more research is necessary to determine if the genetic mutations are implicated in disease. The ENIGMA researchers screened millions of “spelling differences” in the genetic code to see which ones affected the size of key parts of the brain in magnetic resonance images (MRIs) from 30,717 individuals.


The MRI analysis focused on genetic data from seven regions of the brain that coordinate movement, learning, memory and motivation. The group identified eight genetic variants associated with decreased brain volume, several found in over one-fifth of the world’s population.  People who carry one of those eight mutations had, on average, smaller brain regions than brains without a mutation but of comparable age; some of the genes are implicated in cancer and mental illness.


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End of cancer-genome project prompts to rethink: Should effort switch from sequencing to functional analysis?

End of cancer-genome project prompts to rethink: Should effort switch from sequencing to functional analysis? | Amazing Science | Scoop.it

A mammoth US effort to genetically profile 10,000 tumors has officially come to an end. Started in 2006 as a US$100-million pilot, The Cancer Genome Atlas (TCGA) is now the biggest component of the International Cancer Genome Consortium, a collaboration of scientists from 16 nations that has discovered nearly 10 million cancer-related mutations.


The question is what to do next. Some researchers want to continue the focus on sequencing; others would rather expand their work to explore how the mutations that have been identified influence the development and progression of cancer.


“TCGA should be completed and declared a victory,” says Bruce Stillman, president of Cold Spring Harbor Laboratory in New York. “There will always be new mutations found that are associated with a particular cancer. The question is: what is the cost–benefit ratio?”


Stillman was an early advocate for the project, even as some researchers feared that it would drain funds away from individual grants. Initially a three-year project, it was extended for five more years. In 2009, it received an additional $100 million from the US National Institutes of Health plus $175 million from stimulus funding that was intended to spur the US economy during the global economic recession.


On 2 December, Staudt announced that once TCGA is completed, the NCI will continue to intensively sequence tumours in three cancers: ovarian, colorectal and lung adenocarcinoma. It then plans to evaluate the fruits of this extra effort before deciding whether to add back more cancers. But this time around, the studies will be able to incorporate detailed clinical information about the patient’s health, treatment history and response to therapies. Because researchers can now use paraffin-embedded samples, they can tap into data from past clinical trials, and study how mutations affect a patient’s prognosis and response to treatment. Staudt says that the NCI will be announcing a call for proposals to sequence samples taken during clinical trials using the methods and analysis pipelines established by the TCGA.


The rest of the International Cancer Gene Consortium, slated to release early plans for a second wave of projects in February, will probably take a similar tack, says co-founder Tom Hudson, president of the Ontario Institute for Cancer Research in Toronto, Canada. A focus on finding sequences that make a tumour responsive to therapy has already been embraced by government funders in several countries eager to rein in health-care costs, he says. “Cancer therapies are very expensive. It’s a priority for us to address which patients would respond to an expensive drug.”


The NCI is also backing the creation of a repository for data not only from its own projects, but also from international efforts. This is intended to bring data access and analysis tools to a wider swathe of researchers, says Staudt. At present, the cancer genomics data constitute about 20 petabytes (10**15 bytes), and are so large and unwieldy that only institutions with significant computing power can access them. Even then, it can take four months just to download them.

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How DNA Sequencing In Sewers Could Detect Disease Outbreaks

How DNA Sequencing In Sewers Could Detect Disease Outbreaks | Amazing Science | Scoop.it

Disease prevention and mapmaking have been inextricably intertwined since 1854, when an English physician named John Snow plotted a cholera outbreak on a grid to locate–and shut down–a bacteria-tainted water pump, inventing the modern science of epidemiology along the way.

In 2010 geneticist Eric Schadt, then the chief scientific officer at DNA sequencer maker Pacific Biosciences, had a brainstorm as to how to update Snow’s breakthrough for the modern age. The germs that infect us–everything from influenza to measles to bubonic plague–wind up in our waste. Why not look for them by using DNA technology to sequence raw sewage?


Snippets of DNA in wastewater could then be matched to known pathogens–and specific physical locations. Public health officials would no longer have to wait for someone to spike a fever to know that Ebola virus was in Manhattan–they would be alerted by the sequences coming from the sewers, and they would know within a few blocks where it was.


Schadt tried the project out using samples from the San Francisco sewers, but bringing sewage back to PacBio’s expensive, heavy sequencers was impractical at best. Christopher Mason, a Weill Cornell Medical College professor, has picked up a simpler version of the idea, applying swabs to surfaces all over New York City to create a “Pathomap” of germs that will be unveiled early next year.


But Schadt, who now heads a sweeping Carl Icahn-funded genomics effort at the Mount Sinai School of Medicine in Manhattan, still wants a more detailed map produced automatically from sewage. Possible? One new DNA sequencer, made by Oxford Nanopore, is a thumb drive that can take sequences on the spot. Who knows what another generation of innovation could bring? Says Mason: “It’s futuristic, but not unrealistic.”



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Singapore scientists develop genome-wide mutation hunting computational software for genomic medicine

Singapore scientists develop genome-wide mutation hunting computational software for genomic medicine | Amazing Science | Scoop.it

Phen-Gen is the first computer analysis software that cross-references a patient’s symptoms and a person’s genome sequence, to better aid doctors in diagnosing diseases. The software was created by a team of scientists at A*STAR’s Genome Institute of Singapore (GIS), led by Dr. Pauline Ng. Results from the research were published in the prestigious journal Nature Methods on 4th August 2014.
 
Phen-Gen can detect faulty genes responsible for diseases by up to 88 per cent, yielding results in 15 to 30 minutes. It has been proven to be faster and more efficient compared to current methods analysing genomes for this purpose.
 
One area that Dr Ng is currently working on is incorporating the Phen-Gen technique in the diagnosis of rare diseases. Rare diseases are often hard to diagnose based on symptoms alone. By using Phen-Gen, doctors are able to make a more accurate diagnosis based on a patient’s unique genetic code.
 
Dr Ng’s team is working with doctors in local and international hospitals to incorporate Phen-Gen to diagnose patients with rare disorders.  “We aim to translate scientific research to help people directly,” said senior author Pauline Ng. “To this end, GIS has created a programme to help diagnose patients with rare disorders. Phen-Gen works with both exome and whole genome sequencing data. It is the first algorithm to leverage disease symptoms and give genome-wide predictions.”
 
Most rare diseases, such as those that affect neurological, brain or cardiac development, manifest early in life. “There is little else more satisfying than the opportunity to help a sick patient, and through our research at GIS, we want others in the world to benefit as well,” said first author Dr. Asif Javed. “The program is also downloadable online for those who prefer to keep their DNA information private.”
 
The Executive Director of the GIS, Prof. Ng Huck Hui, commented “As we enter the genomics era with more powerful Next-Generation Sequencing technologies that can analyse the human genomes at a reduced cost, data analytics becomes a bottleneck. Dr. Pauline Ng’s group has taken on this exciting challenge to develop analytics capabilities. In partnership with the Singapore hospitals, the GIS has initiated a research project on sequencing patients with undiagnosed conditions or congenital disorders. The Phen-Gen method is timely as it fills an urgent gap in hospitals for accurate diagnosis of rare diseases.”

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Tooth loss in birds occurred about 116 million years ago

Tooth loss in birds occurred about 116 million years ago | Amazing Science | Scoop.it

The absence of teeth or "edentulism" has evolved on multiple occasions within vertebrates including birds, turtles, and a few groups of mammals such as anteaters, baleen whales and pangolins. Where early birds are concerned, the fossil record is fragmentary. A question that has intrigued biologists is: Based on this fossil record, were teeth lost in the common ancestor of all living birds or convergently in two or more independent lineages of birds? A research team led by biologists at the University of California, Riverside and Montclair State University, NJ, has found an answer. Using the degraded remnants of tooth genes in birds to determine when birds lost their teeth, the team reports in the Dec. 12 issue ofScience that teeth were lost in the common ancestor of all living birds more than 100 million years ago.


"One of the larger lessons of our finding is that 'dead genes,' like the remnants of dead organisms that are preserved in the fossil record, have a story to tell," said Mark Springer, a professor of biology and one of the lead authors of the study along with Robert Meredith at Montclair State University who was previously a graduate student and postdoctoral researcher in Springer's laboratory. "DNA from the crypt is a powerful tool for unlocking secrets of evolutionary history."


Springer explained that edentulism and the presence of a horny beak are hallmark features of modern birds. "Ever since the discovery of the fossil bird Archaeopteryx in 1861, it has been clear that living birds are descended from toothed ancestors," he said. "However, the history of tooth loss in the ancestry of modern birds has remained elusive for more than 150 years."


All toothless/enamelless vertebrates are descended from an ancestor with enamel-capped teeth. In the case of birds, it is theropod dinosaurs. Modern birds use a horny beak instead of teeth, and part of their digestive tract to grind up and process food.

Tooth formation in vertebrates is a complicated process that involves many different genes. Of these genes, six are essential for the proper formation of dentin (DSPP) and enamel (AMTN, AMBN, ENAM, AMELX, MMP20).


The researchers examined these six genes in the genomes of 48 bird species, which represent nearly all living bird orders, for the presence of inactivating mutations that are shared by all 48 birds. The presence of such shared mutations in dentin and enamel-related genes would suggest a single loss of mineralized teeth in the common ancestor of all living birds.


Springer, Meredith, and other members of their team found that the 48 bird species share inactivating mutations in both dentin-related (DSPP) and enamel-related genes (ENAMAMELX, AMTNMMP20), indicating that the genetic machinery necessary for tooth formation was lost in the common ancestor of all modern birds.

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Human genomes are extraordinarily individual, study finds

Human genomes are extraordinarily individual, study finds | Amazing Science | Scoop.it

In 2001 scientists announced the successful decoding of the first human genome. Since then, thousands more have been sequenced. The price of a genetic analysis will soon fall below the 1,000 dollar mark. Given this rapid pace of development, it’s easy to forget that the technology used only reads a mixed product of genetic information.


The analytical methods commonly employed do not take into account the fact that every person has two sets of genetic material. “So they are ignoring an essential property of the human genome. However, it’s important to know, for example, how mutations are distributed between the two chromosome sets,” says Margret Hoehe from the Max Planck Institute for Molecular Genetics, who carried out the study.


Hoehe and her team have developed molecular genetic and bioinformatic methods that make it possible to sequence the two sets of chromosomes in a human separately. The researchers decoded the maternal and paternal parts of the genome in 14 people and supplemented their analysis with the genetic material of 372 Europeans from the 1000 Genomes Project. “Fourteen people may not sound like a lot, but given the technical challenge, it is an unprecedented achievement,” says Hoehe.


The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person - and are therefore individual in the truest sense of the word.


Some of the many variants that alter the genome also have an effect at the protein level. The researchers have now identified a set of 4,000 genes that are altered by mutations so that their proteins occur especially frequently in two different forms in humans. These genes mainly control signal transmission between cells, the immune system and gene activity. This dual gene and protein arrangement has the advantage that it allows the activity of genes to be more flexibly adjusted and altered. By using the more favourable variant, the body is better able to adapt to changes in its own processes and to environmental conditions. If the duality of genes goes awry and the wrong protein form is used, this can trigger pathogenic mechanisms. This is probably why those 4,000 genes include many disease genes.


These findings will change the interpretation of genetic analyses and the prediction of diseases. Moreover, individualised medicine cannot ignore the “dual nature” of human genomes. “Our investigations at the protein level have shown that 96 percent of all genes have at least 5 to 20 different protein forms. This results in tremendous individual diversity in possible interactions between genes, and shows how daunting the challenge is to develop individually tailored therapies,” says Hoehe.

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For $25 a year, Google will keep a copy of any genome in the cloud

For $25 a year, Google will keep a copy of any genome in the cloud | Amazing Science | Scoop.it

Google is approaching hospitals and universities with a new pitch. Have genomes? Store them with us. The search giant’s first product for the DNA age is Google Genomics, a cloud computing service that it launched last March but went mostly unnoticed amid a barrage of high profile R&D announcements from Google, like one late last month about a far-fetched plan to battle cancer with nanoparticles (see “Can Google Use Nanoparticles to Search for Cancer?”).


Google Genomics could prove more significant than any of these moonshots. Connecting and comparing genomes by the thousands, and soon by the millions, is what’s going to propel medical discoveries for the next decade. The question of who will store the data is already a point of growing competition between Amazon, Google, IBM, and Microsoft.


Google began work on Google Genomics 18 months ago, meeting with scientists and building an interface, or API, that lets them move DNA data into its server farms and do experiments there using the same database technology that indexes the Web and tracks billions of Internet users.


“We saw biologists moving from studying one genome at a time to studying millions,” says David Glazer, the software engineer who led the effort and was previously head of platform engineering for Google+, the social network. “The opportunity is how to apply breakthroughs in data technology to help with this transition.”


Some scientists scoff that genome data remains too complex for Google to help with. But others see a big shift coming. When Atul Butte, a bioinformatics expert at Stanford heard Google present its plans this year, he remarked that he now understood “how travel agents felt when they saw Expedia.”


The explosion of data is happening as labs adopt new, even faster equipment for decoding DNA. For instance, the Broad Institute in Cambridge, Massachusetts, said that during the month of October it decoded the equivalent of one human genome every 32 minutes. That translated to about 200 terabytes of raw data.


This flow of data is smaller than what is routinely handled by large Internet companies (over two months, Broad will produce the equivalent of what gets uploaded to YouTube in one day) but it exceeds anything biologists have dealt with. That’s now prompting a wide effort to store and access data at central locations, often commercial ones. The National Cancer Institute said last month that it would pay $19 million to move copies of the 2.6 petabyte Cancer Genome Atlas into the cloud. Copies of the data, from several thousand cancer patients, will reside both at Google Genomics and in Amazon’s data centers.


The idea is to create “cancer genome clouds” where scientists can share information and quickly run virtual experiments as easily as a Web search, says Sheila Reynolds, a research scientist at the Institute for Systems Biology in Seattle. “Not everyone has the ability to download a petabyte of data, or has the computing power to work on it,” she says.

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corneja's curator insight, November 27, 2014 7:20 PM

"Our genome in the cloud"... it sounds like the title of a song. Google is offering to keep genome data in the cloud.

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Genome Study Predicts DNA of a Whole Country

Genome Study Predicts DNA of a Whole Country | Amazing Science | Scoop.it
Large genome databases are starting to reveal critical health information—even about people who have not contributed their DNA.


The CEO of an Icelandic gene-hunting company says he is able to identify everyone from that country who has a deadly cancer risk, but has been unable to warn people of the danger because of ethics rules governing DNA research. The company, DeCode Genetics, based in Reykjavík, says it has collected full DNA sequences on 10,000 individuals. And because people on the island are closely related, DeCode says it can now also extrapolate to accurately guess the DNA makeup of nearly all other 320,000 citizens of that country, including those who never participated in its studies.That’s raising complex medical and ethical issues about whether DeCode, which is owned by the U.S. biotechnology company Amgen, will be able to inform members of the public if they are at risk for fatal diseases.


Kári Stefánsson, the doctor who is founder and CEO of DeCode, says he is worried about mutations in a gene called BRCA2 that convey a sharply increased risk of breast and ovarian cancers. DeCode’s data can now identify about 2,000 people with the gene mutation across Iceland’s population, and Stefánsson said that the company has been in negotiations with health authorities about whether to alert them. “We could save these people from dying prematurely, but we are not, because we as a society haven’t agreed on that,” says Stefánsson. “I personally think that not saving people with these mutations is a crime. This is an enormous risk to a large number of people.” The Icelandic Ministry of Welfare said a special committee had been formed to regulate such “incidental” findings and would propose regulations by the end of the year.


The technique used by DeCode to predict people’s genes offers clues to the future of so-called precision medicine in other countries, including the U.S., where this year President Barack Obama called for researchers to assemble a giant database of one million people (see “U.S to Develop DNA Study of One Million People”). A large enough U.S. database could also be used to infer genes of people whether or not they had joined it, says Stefánsson, and could raise similar questions about whether and how to report health hazards to the public. “This technique can be applied to any population,” says Myles Axton, chief editor of Nature Genetics, the journal in which DeCode today presented some of its findings. He said the tiny island’s detailed genealogical records are why “it was achieved first in Iceland.”


“The rule is that you can only use and expose genetic data if you have the permission from the individual in question,” says Gísli Pálsson, an anthropologist at the University of Iceland. “But this is beyond informed consent. People are not even in the studies, they haven’t submitted any consent or even a sample, yet the company claims to have knowledge about these people and that there is a health risk.” The life expectancy of women with the BRAC2 mutation is 12 years less than for women without it because 86 percent of those who have it will develop cancer. Men are also affected because the mutation raises the chance of prostate cancer. Stefansson says many of those deaths could be avoided by preventive surgery, like a mastectomy. “We could in Iceland, at the push of a button, find all women with a mutation in the BRCA2 gene,” says Stefánsson. “It is one tiny little example of what you can do. You can use this in preventive medicine like never before.”

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British Isles mapped out by genetic ancestry: Finest-scale DNA survey of any country reveals historic migrations

British Isles mapped out by genetic ancestry: Finest-scale DNA survey of any country reveals historic migrations | Amazing Science | Scoop.it

Researchers have found genetic signatures among Britons that betray their historical roots in particular locales of the UK, leading to the finest-scale map of genetic variation yet created. The analysis — which shows a snapshot of clusters of genetic variation in the late 1800s, when people were less likely to migrate far from their region of birth — reflects historical waves of migration by different populations into the island. “The patterns we see are extraordinary,” says Peter Donnelly, director of the Wellcome Trust Centre for Human Genetics in Oxford, UK, who co-led the study published 18 March in Nature1. “The genetic effects we’re looking at are the result of, probably, thousands of years of history.”


Today, few Britons have ancestors from just one local region of the UK, so it is hard to identify patterns of genetic variation specific to any one place. But Donnelley and his team found 2,039 Britons of European ancestry who lived in rural areas and knew that their four grandparents were all born within 80-kilometres of each other. Since these volunteers’ DNA was a mosaic of their grandparents’, who themselves were to known be strongly linked to one British region in the late nineteenth century, Donnelley hoped to find genetic variation that clustered neatly with their grandparents' geographic location.


So it proved: a statistical model lumped participants into 17 groups based only on their DNA, and these groupings matched geography. People across central and southern England fell into the largest group, but many groupings were more isolated, such as the split between Devonians and Cornish in Britain’s southwest. People who trace their ancestry to the Orkney Islands, off the northeast coast of Scotland, fell into three distinct categories. They are likely so differentiated because the islands made it hard for different populations to mingle.


As well as geographic barriers like these, the patchwork was formed by migrations into and around Britain, Donnelley says. The team analyzed the genomes of 6,209 people from continental Europe to understand their ancestors’ contributions to Britons’ ancestry. This confirmed the flow of Anglo-Saxons from present-day Germany into Britain after the departure of the Romans in 410 ad. They interbred with local residents instead of replacing them wholly, as some historians and archaeologists have suggested. Danish Vikings, who occupied Britain between 700s and 1100s ad, by contrast, left little signature in most Britons’ genomes.


Now that DNA signatures linked to historical local settlement are known, Donnelly says Britons or people with British heritage could conceivably use their genomes to trace the homelands of their ancestors.The team’s study should also help researchers find genetic variations linked to disease by ruling out the differences that are due to geography. Graham Coop, a population geneticist at the University of California, Davis, says it should be possible to also map the British ancestry of people from more diverse genetic backgrounds, such as Americans. However, he says, "it gets trickier the further back that ancestry is in your family tree, as less and less of your genome is from any one ancestor."


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Wyatt Fratnz's curator insight, March 19, 10:33 PM

This item shows us how migration has changed over time, starting from years when people wouldn't travel far from their house, until today,  when people travel everywhere. This study shows that these different patterns are evident through DNA tests. Different ethnicities are linked to significant settlements and regions that benefit them.

 

This is a great foundation that shows how migration works and why it works that way. It branches out from here, to many different specifics of the field of migration.

Jacqueline Garcia pd1's curator insight, March 23, 7:54 PM

In this article and photo we can better understand the population clusters within a region where groups of people have made settlements. I think that we can learn a lot from this and realize that our ancestors have dictated where we live and raise our future generations. 

Pilar Moral's curator insight, March 26, 1:09 PM

MIGRATIONS

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Well Preserved Baby Woolly Rhino Found In Siberia Stuns Scientists

Well Preserved Baby Woolly Rhino Found In Siberia Stuns Scientists | Amazing Science | Scoop.it

Scientists are very excited over the recent discovery of a baby woolly rhinoThe pristine specimen of the tiny extinct rhino--the only one of its type ever found--was discovered in permafrost along the bank of a stream in Siberia's Sakha Republic, The Siberian Times reported.


"At first we thought it was a reindeer's carcass, but after it thawed and fell down we saw a horn on its upper jaw and realized it must be a rhino," Alexander 'Sasha' Banderov, the hunter who made the discovery, told the Times. "The part of the carcass that stuck out of the ice was eaten by wild animals, but the rest of it was inside the permafrost and preserved well."


Scientists estimate that the rhino--which has been dubbed Sasha--was 18 months old when it died some 10,000 years ago, according to the Times. The specimen includes the animal's wool, an ear, an eye, nostrils, and skull and mouth.


"We are hoping Sasha the rhino will give us a lot of answers to questions of how they grew and developed, what conditions they lived in, and which of the modern day animals is the closest to them," Albert Protopopov, head of the Mammoth Fauna Department at the Academy of Sciences in Sakha Republic, told the Times. "We will concentrate on the DNA, because the carcass was kept frozen and chances are high we will get a better preserved DNA. We are hoping to report first results in a week or two." The genomic information might be used to recreate the species, similar to ongoing experiments with mammoth remains.

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Researchers Produce First Map of New York City Subway System Microbes

Researchers Produce First Map of New York City Subway System Microbes | Amazing Science | Scoop.it

The microbes that call the New York City subway system home are mostly harmless, but include samples of disease-causing bacteria that are resistant to drugs — and even DNA fragments associated with anthrax and Bubonic plague — according to a citywide microbiome map published today by Weill Cornell Medical College investigators.


The study, published in Cell Systems, demonstrates that it is possible and useful to develop a "pathogen map" — dubbed a "PathoMap" — of a city, with the heavily traveled subway a proxy for New York's population. It is a baseline assessment, and repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large scale health management for New York, says the study's senior investigator, Dr. Christopher E. Mason, an assistant professor in Weill Cornell's Department of Physiology and Biophysics and in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine (ICB).


The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Dr. Mason says. The majority of the 637 known bacterial, viral, fungal and animal species he and his co-authors detected were non-pathogenic and represent normal bacteria present on human skin and human body. Culture experiments revealed that all subway sites tested possess live bacteria.


Strikingly, about half of the sequences of DNA they collected could not be identified — they did not match any organism known to the National Center for Biotechnology Information or the Centers for Disease Control and Prevention. These represent organisms that New Yorkers touch every day, but were uncharacterized and undiscovered until this study. The findings underscore the vast potential for scientific exploration that is still largely untapped and yet right under scientists' fingertips.


"Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract," Dr. Mason says. "These bacteria may even be helpful, since they can out-compete any dangerous bacteria."


But the researchers also say that 12 percent of the bacteria species they sampled showed some association with disease. For example, live, antibiotic-resistant bacteria were present in 27 percent of the samples they collected. And they detected two samples with DNA fragments of Bacillus anthracis (anthrax), and three samples with a plasmid associated with Yersinia pestis (Bubonic plague) — both at very low levels. Notably, the presence of these DNA fragments do not indicate that they are alive, and culture experiments showed no evidence of them being alive.


Yet these apparently virulent organisms are not linked to widespread sickness or disease, Dr. Mason says. "They are instead likely just the co-habitants of any shared urban infrastructure and city, but wider testing is needed to confirm this."


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U.S. proposes effort to analyze genome from 1 million people

U.S. proposes effort to analyze genome from 1 million people | Amazing Science | Scoop.it

The United States has proposed analyzing genetic information from more than 1 million American volunteers as part of a new initiative to understand human disease and develop medicines targeted to an individual’s genetic make-up.


At the heart of the “precision medicine” initiative, announced on Friday by President Barack Obama, is the creation of a pool of people – healthy and ill, men and women, old and young – who would be studied to learn how genetic variants affect health and disease.


Officials hope genetic data from several hundred thousand participants in ongoing genetic studies would be used and other volunteers recruited to reach the 1 million total.


“Precision medicine gives us one of the greatest opportunities for new medical breakthroughs we’ve ever seen,” Obama said, promising that it would “lay a foundation for a new era of life-saving discoveries.”


The near-term goal is to create more and better treatments for cancer, Dr. Francis Collins, director of the National Institutes of Health (NIH), told reporters on a conference call on Thursday. Longer term, he said, the project would provide information on how to individualize treatment for a range of diseases.


The initial focus on cancer, he said, reflects the lethality of the disease and the significant advances against cancer that precision medicine has already made, though more work is needed.


The president proposed $215 million in his 2016 budget for the initiative. Of that, $130 million would go to the NIH to fund the research cohort and $70 million to NIH’s National Cancer Institute to intensify efforts to identify molecular drivers of cancer and apply that knowledge to drug development.


A further $10 million would go to the Food and Drug Administration to develop databases on which to build an appropriate regulatory structure; $5 million would go to the Office of the National Coordinator for Health Information Technology to develop privacy standards and ensure the secure exchange of data.


The effort may raise alarm bells for privacy rights advocates who have questioned the government’s ability to guarantee that DNA information is kept anonymous. Obama promised that “privacy will be built in from day one.”

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Risto Suoknuuti's curator insight, February 13, 6:59 PM

I wellcome this inititive in the name of all camcer patients who have suffered current hard and heavy teatments exspeacially remembering those of us who did not survive. Give them more hope.

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Genome-wide search in C.elegans reveals that >750 worm genes are involved in long-term memory

Genome-wide search in C.elegans reveals that >750 worm genes are involved in long-term memory | Amazing Science | Scoop.it

A new Princeton University study has identified more than 750 genes involved in long-term memory in the worm — part of research aimed at finding ways to retain cognitive abilities during aging, including compounds.


The new study, published in the journal Neuron, included many genes that had not been found previously and that could serve as targets for future research, said senior author Coleen Murphy, an associate professor of molecular biology at Princeton and the Lewis-Sigler Institute for Integrative Genomics.


The researchers then scanned the genomes of both trained worms and non-trained worms, looking for genes turned on by CREB. The researchers detected 757 CREB-activated genes in the long-term memory-trained worms, and showed that these genes were turned on primarily in worm cells called the AIM interneurons. They also found CREB-activated genes in non-trained worms, but the genes were not turned on in AIM interneurons and were not involved in long-term memory. CREB turns on genes involved in other biological functions such as growth, immune response, and metabolism. Throughout the worm, the researchers noted distinct non-memory (or “basal”) genes in addition to the memory-related genes.


“There is a pretty direct relationship between CREB and long-term memory,” Murphy said, “and many organisms lose CREB as they age.” By studying the CREB-activated genes involved in long-term memory, the researchers hope to better understand why some organisms lose their long-term memories as they age.


Worms are a perfect system in which to explore that question, Murphy said. The worm Caenorhabditis elegans has only 302 neurons, whereas a typical mammalian brain contains billions of the cells. “Worms use the same molecular machinery that higher organisms, including mammals, use to carry out long-term memory,” said Murphy. “We hope that other researchers will take our list and look at the genes to see whether they are important in more complex organisms.”


The next step, said Murphy, is to find out what these newly recognized long-term memory genes do when they are activated by CREB. For example, the activated genes may strengthen connections between neurons.

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Transformative Genomics: England Begins Daunting Task of Sequencing 100,000 Genomes by 2017

Transformative Genomics: England Begins Daunting Task of Sequencing 100,000 Genomes by 2017 | Amazing Science | Scoop.it
Genomics England begins its 100,000 Genome Project to speed time to diagnosis and inform personalized treatment regimens


The project, titled 100,000 Genomes, is a transformative research project aimed at finding new ways to identify and care for patients, and could ultimately change how patients are treated in the National Health Service, according to Professor Mark Caulfield, lead scientist of Genomics England“The overall impact of the work of Genomics England could be to transform the NHS provision of diagnostic tests and then care to a whole range of patients,” says Caulfield. “This could itself have an impact on how services are commissioned, with perhaps greater emphasis on testing of the broader population in order to achieve earlier diagnosis and more effective intervention for patients most at risk from developing very serious illnesses”, Prof Caulfield said.


Genomics is the study of genes and how they work. A genome is a complete map of a person’s DNA. It “contains all the information needed to build and maintain the organism,” according to Genome Home Reference, a service of the U.S. National Library of Medicine. Genomics lends insight into the cause of diseases and how diseases develop in each individual. Currently, medical researchers use genomics in an effort to develop personalized treatments for diseases. Also useful in public health, genomics helps track infectious diseases. It can help in understanding how infections spread and in many cases allow the pinpointing of the source and nature of an outbreak.


Genomics England has procured Illumina, a global leader in gene sequencing, to sequence and analyze the genomes. After analysis, results will be sent to NHS for review and possible clinical application. Some 75,000 participants are expected to take part in the 100,000 Genome Project, and recruitment will begin in early February 2015. Clinicians will refer eligible patients who wish to be involved in this project to one of 11 designated genomic medical centers. A genome project of this magnitude is not without challenges.


Referring to these inherent challenges, Jim Davies, Chief Technology Officer of Genomics England, said“The data we need for Genomics England is large and complex: to get to 100,000 genomes we’ll be collecting 10 petabytes of sequence data, and detailed, relevant health data on up to 100,000 people.” Additional challenges include the need for informed patient consent, which means educating people about what a genome is and how learning about it might impact their lives, and ensuring data privacy.

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jean marc mosselmans's curator insight, March 22, 3:42 PM

the race for the genome sequencing could strangely be the wrong one, as epigenetic is now demonstrating activation and silencing of our genes through methylation activated by.. our own lifestyle

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House fly genome reveals an expanded immune system combatting many animal pathogens

House fly genome reveals an expanded immune system combatting many animal pathogens | Amazing Science | Scoop.it

Scientists have sequenced the house fly genome for the first time, revealing robust immune system genes, as one might expect from an insect that thrives in pathogen-rich dung piles and garbage heaps.

The research, published Oct. 13, 2014, in the journal Genome Biology, will increase our understanding of house fly genetics and biology and of how flies quickly adapt to resist insecticides, which could lead to novel control methods.

Adult house flies (Musca domestica) carry and transmit more than 100 human and animal diseases, including salmonellosis, anthrax, typhoid fever, tuberculosis, cholera and diarrhea as well as parasites such as pinworms, roundworms, hookworms and tapeworms. House fly larvae are important animal waste decomposers and live in close contact with many animal pathogens.

“Anything that comes out of an animal, such as bacteria and viruses, house flies can take from that waste and deposit on your sandwich,” said Jeff Scott, the paper’s lead author and a Cornell professor of entomology. “House flies are the movers of any disgusting pathogenic microorganism you can think of,” Scott added.

The genome, roughly twice the size of the fruit fly’s genome, revealed an expanded number of immune response and defense genes. The researchers also discovered an expansion in the number of cytochrome P450s, which help the flies metabolize environmental toxins. “House flies have a lot more of these enzymes than would be expected based on other insects they are related to,” said Scott, noting that the house fly’s close relative, Glossina morsitans (tsetse fly), has half as many cytochrome P450s. These enzymes are more ancient than insecticides. “We don’t have a clear handle on why house flies need so many,” Scott said.

The M. domestica genome also revealed many genes for chemoreceptors, which detect certain chemical stimuli in the environment. These receptors are important in sensing food and moving in ways critical for survival, allowing house flies to detect a wide variety of different things, Scott said.

“If you think of the genome like a phone book, we now have the phone number of every gene,” said Scott. “We now can study every gene. For any scientific question, we have a highway to get us there.”

One of those questions will focus on controlling house flies and developing new toxins that disrupt the fly’s internal balance by poisoning them or using RNAi to turn off specific genes and killing them, Scott said.

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Plants with pocket-sized genomes: Record for smallest plant genome found

Plants with pocket-sized genomes: Record for smallest plant genome found | Amazing Science | Scoop.it
Members of Genlisea, a genus of carnivorous plants, possess the smallest genomes known in plants. To elucidate genomic evolution in the group as a whole, researchers have now surveyed a wider range of species, and found a new record-holder.


The genus Genlisea (corkscrew plants) belongs to the bladderwort family (Lentubulariaceae), a family of carnivorous plants. Some of the 29 species of Genlisea that have been described possess tiny genome sizes. Indeed, the smallest genome yet discovered among flowering plants belongs to a member of the group. The term 'genome' here refers to all genetic material arranged in a set of individual chromosomes present in each cell of a given species. An international team of researchers, led by Professor Günther Heubl of LMU's Department of Biology, has now explored, for the first time, the evolution of genome size and chromosome number in the genus. Heubl and his collaborators studied just over half the known species of Genlisea, and their findings are reported in the latest issue of the journal Annals of Botany.


"During the evolution of the genus, the genomes of some Genlisea species must have undergone a drastic reduction in size, which was accompanied by miniaturization of chromosomes, but an increase in chromosome number," says Dr. Andreas Fleischmann, a member of Heubl's research group. Indeed, the chromosomes of the corkscrew plants are so minute that they can only just be resolved by conventional light microscopy. With the aid of an ingenious preparation technique, Dr. Aretuza Sousa, a specialist in cytogenetics and cytology at the Institute of Systematic Botany at LMU, was able to visualize the ultrasmall chromosomes of Genlisea species by fluorescence microscopy. Thanks to this methodology, the researchers were able to identify individual chromosomes and determine their number, as well as measuring the total DNA content of the nuclear genomes of selected representatives of the genus.


The LMU researchers also discovered a new record-holder. Genlisea tuberosa, a species that was discovered only recently from Brazil, and was first described by Andreas Fleischmann in collaboration with Brazilian botanists, turns out to have a genome that encompasses only 61 million base pairs (= Mbp; the genome size is expressed as the total number of nucleotide bases found on each of the paired strands of the DNA double helix) Thus G. tuberosa possesses now the smallest plant genome known, beating the previous record by 3 Mbp. Moreover, genome sizes vary widely between different Genlisea species, spanning the range from ~60 to 1700 Mbp.

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Discovering the Undiscovered: The time is right to apply genomic technologies to discover new life on Earth

Discovering the Undiscovered: The time is right to apply genomic technologies to discover new life on Earth | Amazing Science | Scoop.it

In a perspective piece published November 6 in the journal Science,Eddy Rubin, Director of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, along with Microbial Program Head Tanja Woyke, discusses why the time is right to apply genomic technologies to discover new life on Earth. In this perspective they propose the division of microbial life on Earth into three categories: explored, unexplored, and undiscovered. The first can be grown in the laboratory. The second encompasses the uncultivated organisms from environmental samples known only by their molecular signatures. The third, the focus of the perspective, is the yet-undiscovered life that up until now has eluded detection.


“We are poised, armed with a new toolkit of powerful genomic technologies to generate and mine the increasingly large datasets to discover new life that may be strikingly different from those that we catalogued thus far,” said Rubin. “Nature has been tinkering with life for at least three billion years and we now have a new set of ways to look for novel life that have so far eluded discovery.”


“Massive-scale metagenomic sequencing of environmental DNA and RNA samples should, in principle, generate sequence data from any entity for which nucleic acids can be extracted,” Rubin noted. “Analysis of these data to identify outliers to previously defined life represents a powerful means to explore the unknown.”


In addition, Rubin pointed to the advent of single-cell sequencing with microfluidic and cell sorting approaches, focused specifically on cells that lack genes that match previously identified ones, as another approach in the search for completely novel organisms.


“We also need to choose particularly suitable environmental niches so that we are not just looking, ‘under the street lamp’ — at environments that we have already previously studied.”


Rubin suggested targets for the discovery of novel life including extreme, inhospitable and isolated environments that are expected to be preferred niches for early life, potentially sheltered from more modern microbial competitors. This would include low oxygen subsurface sites with environmental conditions predating the Great Oxidation Event that occurred about 2.3 billion years ago when the atmosphere went from very low to high oxygen concentrations. Support for the idea that isolated low-oxygen environments may be preferred niches for early life comes from observations that anaerobic niches deep within Earth’s crust tend to harbor ancient branches within the domains of life.


Exploring the “undiscovered” classification is expected to be a boon for enriching the public data portals, Rubin said. He also noted that lurking among these difficult ones may well be the discovery of a “fourth domain” of life, to which a reasonable mariner, ancient or contemporary, may proclaim, “full speed ahead.”


Rubin presented recent work on “microbial dark matter” at the DOE Joint Genome Institute’s 2014 Genomics of Energy and Environment Meeting that can be viewed at http://bit.ly/JGIUM9Rubin. The DOE JGI’s 10th Annual Meeting will be held March 24-26, 2015 and the list of preliminary speakers can be found here: http://usermeeting.jgi.doe.gov/.

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Dahl Winters's curator insight, December 18, 2014 8:00 AM

A big use of big data - exploring the genomes of life on Earth.  One of the biggest data sets in the world is the one we carry around with us and on us every day.

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Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing

Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing | Amazing Science | Scoop.it

Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process.


A group of scientists now applied next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. The scientists conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.

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Centipede Genome Yields Surprises: Loss of Light Receptor Genes and Circadian Clock

Centipede Genome Yields Surprises: Loss of Light Receptor Genes and Circadian Clock | Amazing Science | Scoop.it

A team of scientists has sequenced the genome of the centipede for the first time and found that it has around 15,000 genes -- about 7,000 fewer than humans do.


Arthropods -- the most species-rich group of animals on Earth -- are divided into four classes, including insects, crustaceans, chelicerates and myriapods. The latter group, which includes centipedes, is the only class for which no genome had yet been sequenced, scientists said in a study, published in the journal PLOS Biology.


“With genomes in hand from each of the four classes of living arthropod, we can now begin to build a picture of the genetic make-up of their common ancestor,” Frank Jiggins, of the University of Cambridge's genetics department, and one of the researchers involved in the study, said in a statement. “For example, by comparing flies and mosquitoes with centipedes, we have shown that the innate immune systems of insects are much older than previously appreciated.”


As part of the study, the scientists sequenced the genome of “Strigamia maritima,” a northern European centipede. They found that its genome is more conserved than that of many other arthropods, such as the fruit fly, suggesting that the centipede has evolved more slowly from their common ancestor. Despite their name, centipedes do not have hundred legs. Strigamia maritima, which lives in coastal habitats, can have between 45 and 51 pairs of legs, but the number of pairs is always odd.


The researchers also discovered that the centipedes have lost the genes encoding all of the known light receptors used by animals, as well as the genes controlling the circadian rhythm, or the body clock.


“Strigamia live underground and have no eyes, so it is not surprising that many of the genes for light receptors are missing, but they behave as if they are hiding from the light. They must have some alternative way of detecting when they are exposed,” Michael Akam of the University of Cambridge and one of the lead researchers of the study, said in the statement.

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Bernadette Cassel's curator insight, January 1, 6:47 PM


SUR ENTOMONEWS

→  Le premier génome de myriapode séquencé