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Scientists find link between genome and microbiome in Crohn’s disease patients

Scientists find link between genome and microbiome in Crohn’s disease patients | Amazing Science | Scoop.it
Genes linked to Crohn’s disease, an inflammatory bowel disease, might make people’s immune cells miss out on helpful messages sent by friendly gut bacteria.

 

Good gut bacteria might not help people with Crohn’s disease.

Protective microbial messages go unread in mice and in human immune cells with certain defective genes, researchers report online May 5 in Science. The findings are the first to tie together the roles of genes and beneficial microbes in the inflammatory bowel disease, says biologist Brett Finlay of the University of British Columbia in Vancouver, who was not involved in the new work.

 

“This is a major step forward in this area,” he says. Human genes and friendly microbes work together to control inflammation, he says. “And when you muck that up, things can go awry.”

 

In Crohn’s disease, the immune system riles up too easily, trigging chronic inflammation. Scientists don’t know why exactly people’s immune systems go haywire. But researchers have linked the disease to glitches in nearly 200 genes, including ATG16L1 and NOD2, which typically help kill bad bacteria in the gut.

 

Researchers have also reported that people with Crohn’s have a different collection of gut microbes compared with that of healthy people, says study coauthor and Caltech microbiologist Sarkis Mazmanian.But though “there’s a huge body of literature on the genome and on the microbiome,” he says, “no one knew what the interplay was between the two.”

 

So his team explored a potential link using a friendly gut microbe called Bacteroides fragilis. The bacteria send out calming messages that tell the immune system to tone down inflammation. Like letters inside envelopes, these messages travel in protective pouches called outer membrane vesicles, or OMVs.

 

Feeding OMVs to mice typically protects them from developing inflamed colons, or colitis — but not mice lacking the Crohn’s-linked genes ATG16L1 and NOD2. When researchers treated those mice with a colitis-causing chemical, they succumbed to the disease, even after eating OMVs.

 

Mice with defective versions of ATG16L1 and NOD2 “can’t reap the benefits of the beneficial microbiota,” Mazmanian says.Immune cells from human patients with the defective genes didn’t respond to OMVs either.

 

The findings suggest that the genes that kill bad bacteria also work with good bacteria to keep people’s immune systems from going out of control, says gastroenterologist Balfour Sartor of the University of North Carolina School of Medicine in Chapel Hill. The work “opens up a new mechanism for protection,” he says.

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The octopus genome and the evolution of cephalopod neural and morphological novelties

The octopus genome and the evolution of cephalopod neural and morphological novelties | Amazing Science | Scoop.it

Coleoid cephalopods (octopus, squid and cuttlefish) are active, resourceful predators with a rich behavioural repertoire. They have the largest nervous systems among the invertebrates and present other striking morphological innovations including camera-like eyes, prehensile arms, a highly derived early embryogenesis and a remarkably sophisticated adaptive colouration system. To investigate the molecular bases of cephalopod brain and body innovations, a group of scientists now sequenced the genome and multiple transcriptomes of the California two-spot octopus, Octopus bimaculoides. They found no evidence for hypothesized whole-genome duplications in the octopus lineage. The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians, except for massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc-finger transcription factors.

 

Extensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described, as well as in genes participating in a broad range of other cellular functions. The researchers identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers and the nervous system. They also found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions.

 

In summary, the present analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems.

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How Craig Venter is fighting ageing with genome sequencing

How Craig Venter is fighting ageing with genome sequencing | Amazing Science | Scoop.it

Nine years ago, Craig Venter sequenced the first complete individual human genome - his own. Now, he's finally starting to decode what it means for his future. 


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Small handheld device tracks disease mutations within minutes

QuantuMDx Group is one of the most exciting biotechs to emerge from the UK and is developing a low cost, simple-to-use, handheld laboratory for 15-minute diagnosis of disease at the patient's side, for commercialisation in 2015. The robust device, which reads and sequences DNA and converts it into binary code using a tiny computer chip, is ideally suited to help address the humanitarian health burden by offering molecular diagnostics at a fraction of the price of traditional testing.

 

Rapidly & accurately detecting and monitoring emerging drug resistance of infectious diseases such as malaria, TB and HIV will enable health professionals to immediately prescribe the most effective drug against that disease. Once the device has passed regulatory approval, it will be available in developed countries for infectious disease testing and rapid cancer profiling and, in time, be available over-the-counter at pharmacies.

 

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Meraculous: Full Genome Alignment With Supercomputers in Mere Minutes

Meraculous: Full Genome Alignment With Supercomputers in Mere Minutes | Amazing Science | Scoop.it
A team of scientists from Berkeley Lab, JGI and UC Berkeley, simplified and sped up genome assembly, reducing a months-long process to mere minutes. This was primarily achieved by “parallelizing” the code to harness the processing power of supercomputers, such as NERSC’s Edison system.

 

Genomes are like the biological owner’s manual for all living things. Cells read DNA instantaneously, getting instructions necessary for an organism to grow, function and reproduce. But for humans, deciphering this “book of life” is significantly more difficult.

 

Nowadays, researchers typically rely on next-generation sequencers to translate the unique sequences of DNA bases (there are only four) into letters: A, G, C and T. While DNA strands can be billions of bases long, these machines produce very short reads, about 50 to 300 characters at a time. To extract meaning from these letters, scientists need to reconstruct portions of the genome—a process akin to rebuilding the sentences and paragraphs of a book from snippets of text.

But this process can quickly become complicated and time-consuming, especially because some genomes are enormous. For example, while the human genome contains about 3 billion bases, the wheat genome contains nearly 17 billion bases and the pine genome contains about 23 billion bases. Sometimes the sequencers will also introduce errors into the dataset, which need to be filtered out. And most of the time, the genomes need to be assembled de novo, or from scratch. Think of it like putting together a ten billion-piece jigsaw puzzle without a complete picture to reference.

 

By applying some novel algorithms, computational techniques and the innovative programming language Unified Parallel C (UPC) to the cutting-edge de novo genome assembly tool Meraculous, a team of scientists from the Lawrence Berkeley National Laboratory (Berkeley Lab)’s Computational Research Division (CRD), Joint Genome Institute (JGI) and UC Berkeley, simplified and sped up genome assembly, reducing a months-long process to mere minutes. This was primarily achieved by “parallelizing” the code to harness the processing power of supercomputers, such as the National Energy Research Scientific Computing Center’s (NERSC’s) Edison system. Put simply, parallelizing code means splitting up tasks once executed one-by-one and modifying or rewriting the code to run on the many nodes (processor clusters) of a supercomputer all at once.

 

“Using the parallelized version of Meraculous, we can now assemble the entire human genome in about eight minutes using 15,360 computer processor cores. With this tool, we estimate that the output from the world’s biomedical sequencing capacity could be assembled using just a portion of NERSC’s Edison supercomputer,” says Evangelos Georganas, a UC Berkeley graduate student who led the effort to parallelize Meraculous. He is also the lead author of a paper published and presented at the SC Conference in November 2014.  

 

“This work has dramatically improved the speed of genome assembly,” says Leonid Oliker computer scientist in CRD. “The new parallel algorithms enable assembly calculations to be performed rapidly, with near linear scaling over thousands of cores. Now genomics researchers can assemble large genomes like wheat and pine in minutes instead of months using several hundred nodes on NERSC’s Edison.”

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A global network of millions of genomes could be medicine’s next great advance

A global network of millions of genomes could be medicine’s next great advance | Amazing Science | Scoop.it

Noah is a six-year-old child suffering from a disease without a name. This year, his physicians will begin sending his genetic information across the Internet to see if there’s anyone, anywhere, in the world like him. A match could make a difference. Noah is developmentally delayed, uses a walker, speaks only a few words. And he’s getting sicker. MRIs show that his cerebellum is shrinking. His DNA was analyzed by medical geneticists at the Children’s Hospital of Eastern Ontario. Somewhere in the billions of DNA letters is a misspelling, and maybe the clue to a treatment. But unless they find a second child with the same symptoms, and a similar DNA error, his doctors can’t zero in on which mistake in Noah’s genes is the crucial one.

 

Programmers in Toronto recently began testing a system for trading genetic information with other hospitals. These facilities, in locations including Miami, Baltimore, and Cambridge, U.K., also treat children with so-called ­Mendelian disorders, which are caused by a rare mutation in a single gene. The system, called MatchMaker Exchange, represents something new: a way to automate the comparison of DNA from sick people around the world. One of the people behind this project is David Haussler, a bioinformatics expert based at the University of California, Santa Cruz. The problem Haussler is grappling with now is that genome sequencing is largely detached from our greatest tool for sharing information: the Internet. That’s unfortunate because more than 200,000 people have already had their genomes sequenced, a number certain to rise into the millions in years ahead. The next era of medicine depends on large-scale comparisons of these genomes, a task for which he thinks scientists are poorly prepared. “I can use my credit card anywhere in the world, but biomedical data just isn’t on the Internet,” he says. “It’s all incomplete and locked down.” Genomes often get moved around in hard drives and delivered by FedEx trucks.

 

Haussler is a founder and one of the technical leaders of the Global Alliance for Genomics and Health, a nonprofit organization formed in 2013 that compares itself to the W3C, the standards organization devoted to making sure the Web functions correctly. Also known by its unwieldy acronym, GA4GH, it’s gained a large membership, including major technology companies like Google. Its products so far include protocols, application programming interfaces (APIs), and improved file formats for moving DNA around the Web. But the real problems it is solving are mostly not technical. Instead, they are sociological: scientists are reluctant to share genetic data, and because of privacy rules, it’s considered legally risky to put people’s genomes on the Internet.

 

But pressure is building to use technology to study many, many genomes at once and begin to compare that genetic information with medical records. That is because scientists think they’ll need to sort through a million genomes or more to solve cases—like Noah’s—that could involve a single rogue DNA letter, or to make discoveries about the genetics of common diseases that involve a complex combination of genes. No single academic center currently has access to information that extensive, or the financial means to assemble it.

 

Haussler and others at the alliance are betting that part of the solution is a peer-to-peer computer network that can unite widely dispersed data. Their standards, for instance, would permit a researcher to send queries to other hospitals, which could choose what level of information they were willing to share and with whom. This control could ease privacy concerns. Adding a new level of complexity, the APIs could also call on databases to perform calculations—say, to reanalyze the genomes they store—and return answers.

 

The largest labs can now sequence human genomes to a high polish at the pace of two per hour. The first genome took about 13 years just 2 decades ago. Back-of-the-envelope calculations suggest that fast machines for DNA sequencing will be capable of producing 85 petabytes of data this year worldwide, twice that much in 2019, and so on. For comparison, all the master copies of movies held by Netflix take up 2.6 petabytes of storage.

 

“This is a technical question,” says Adam Berrey, CEO of Curoverse, a Boston startup that is using the alliance’s standards in developing open-source software for hospitals. “You have what will be exabytes of data around the world that nobody wants to move. So how do you query it all together, at once? The answer is instead of moving the data around, you move the questions around. No industry does that. It’s an insanely hard problem, but it has the potential to be transformative to human life.”

 

Last summer Haussler’s alliance launched a basic search engine for DNA, which it calls Beacon. Currently, Beacon searches through about 20 databases of human genomes that were previously made public and have implemented the alliance’s protocols. Beacon offers only yes-or-no answers to a single type of question. You can ask, for instance, “Do any of your genomes have a T at position 1,520,301 on chromosome 1?” “It’s really just the most basic question there is: have you ever seen this variant?” says Haussler. “Because if you did see something new, you might want to know, is this the first patient in the world that has this?” Beacon is already able to access the DNA of thousands of people, including hundreds of genomes put online by Google.

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Web resource: 1000 Fungal Genomes Project (2016)

Web resource: 1000 Fungal Genomes Project (2016) | Amazing Science | Scoop.it

Sequencing unsampled fungal diversity.  Efforts to sequence 1000+ fungal genomes. Also see the Google+ site for more discussion opportunities.

 

This project is in collaboration with the work of the JGI and you can find links on this site to the nomination page for submitting candidate species to the project.


Via Kamoun Lab @ TSL, Arjen ten Have
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Tick genome reveals secrets of a successful bloodsucker

Tick genome reveals secrets of a successful bloodsucker | Amazing Science | Scoop.it

With tenacity befitting their subject, an international team of nearly 100 researchers toiled for a decade and overcame tough technical challenges to decipher the genome of the blacklegged tick (Ixodes scapularis)The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, contributed primary support to the research, which appears in the online, open-access journal Nature Communications.


“Ticks spread more different kinds of infectious microbes to people and animals than any other arthropod group,” said NIAID Director Anthony S. Fauci, M.D. “The spiral-shaped bacterium that causes Lyme disease is perhaps the best known microbe transmitted by ticks; however, ticks also transmit infectious agents that cause human babesiosis, anaplasmosis, tick-borne encephalitis and other diseases. The newly assembled genome provides insight into what makes ticks such effective disease vectors and may generate new ways to lessen their impact on human and animal health.”


Catherine A. Hill, Ph.D., of Purdue University, headed the team of investigators. Aside from the logistical challenges of coordinating activities of dozens of workers across many time zones, the researchers’ focus was a creature that is extremely difficult to maintain and that lives a long time — up to two years in the wild and nine months in the lab, Dr. Hill noted. Ixodes ticks have three blood-feeding life stages, and during each one, they feed on a different vertebrate animal. During feeding, ticks ingest blood for hours or days at a time. After mating, adult female ticks rapidly imbibe a large blood meal during which they expand hugely. “Because genes may switch on or off depending on the life stage of the tick, we needed to culture and collect ticks at each stage for analysis. This was not easy to do,” said Dr. Hill.


Another challenge was the sheer size of the tick genome — some 2.1 billion DNA base pairs — and expansive regions where sequences are repeated. “The degree of DNA repetition — approximately 70 percent of the total — made assembling the full genome in the correct order very difficult,” Dr. Hill said. In the end, the team determined the order and sequence of about two-thirds of the total genome. “We determined the sequence for 20,486 protein-coding genes,” she said, “of which 20 percent may be unique to ticks. Those tick-specific genes are like guideposts that say ‘start here’ as we look for new ways to counter infectious ticks.”


Although the latest research represents just a first look at the tick genome, the scientists have already identified genes and protein families that shed light on why Ixodes ticks succeed so well as parasites and hint at the reasons they excel at spreading pathogens, Dr. Hill noted. For example, compared with other blood-feeders, ticks have many more proteins devoted to consuming, concentrating and detoxifying their iron-containing food. Although mosquitoes — which quickly siphon up relatively small amounts of blood through a tube-like mouthpiece — have several proteins dedicated to blood digestion, ticks have many more proteins involved in this process. Other genes code for proteins that help ticks concentrate the blood and rapidly excrete excess water that accompanies large blood meals. Still other genes allow ticks to quickly expand their stiff outer coats to accommodate a 100-fold increase in total body size during blood feeding.


Other peculiarities of the tick’s lifestyle reflected in the genome include genes associated with the multifaceted sensory systems that the parasite uses when “questing” for a host during each of its separate blood-feeding stages. Compared with mosquitoes, ticks appear to have fewer genes used to detect hosts, and, unlike a mosquito’s “smell” receptors, ticks may use “taste” receptors to locate their food sources. Each of the newly identified proteins is a potential target for new, tick-specific interventions, explained Dr. Hill. “The genome gives us a code book to the inner workings of ticks. With it, we can now begin to hack their system and write a counter-script against them.”


In an effort to explain variations in Lyme disease prevalence across the United States, the team also examined genetic diversity within and among I. scapularis populations gathered from five states in the Northeast and Midwest and three in the South. Some have speculated that ticks in the Northeast and Midwest spread the bacteria that cause Lyme disease more easily than those in the South, or that the two populations perhaps comprise separate species. The genetic analysis showed that there is only one species of I. scapularis, said Dr. Hill, but subtle genetic differences were detected, and these may help explain some of the variance in the ability of populations to transmit disease and, therefore, affect disease prevalence.

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Illumina will launch a new company, Grail, to develop blood tests to revolutionize cancer detection

Illumina will launch a new company, Grail, to develop blood tests to revolutionize cancer detection | Amazing Science | Scoop.it

The world’s largest DNA sequencing company says it will form a new company to develop blood tests that cost $1,000 or less and can detect many types of cancer before symptoms arise.


Illumina, based in San Diego, said its blood tests should reach the market by 2019, and would be offered through doctors’ offices or possibly a network of testing centers.


The spin-off’s name, Grail, reflects surging expectations around new types of DNA tests that might do more to defeat cancer than the more than $90 billion spent each year by doctors and hospitals on cancer drugs. Illumina CEO Jay Flatley says he hopes the tests could be a “turning point in the war on cancer.”


The startup will be based in San Francisco and has raised more than $100 million from Illumina as well as Bill Gates, Jeff Bezos’s venture fund, Bezos Expeditions, and Arch Venture Partners. Illumina will retain majority control.


The testing concept being pursued by Illumina, sometimes called a “liquid biopsy,” is to use high-speed DNA sequencing machines to scour a person’s blood for fragments of DNA released by cancer cells. If DNA with cancer-causing mutations is present, it often indicates a tumor is already forming, even if it’s too small to cause symptoms or be seen on an imaging machine.


Illumina didn’t invent the idea for the tests, which were first developed by academic centers including at Johns Hopkins University (see “Spotting Cancer in a Vial of Blood”) and in Hong Kong (see “Liquid Biopsy”). But Flatley says only recently has gene-sequencing become inexpensive enough to try to make the cancer screening tests affordable.


Illumina has established spin-offs in Silicon Valley to address consumer markets for DNA data. A DNA test able to pick up many kinds of cancer could be revolutionary because tumors caught early can often be cured with surgery or radiation. Since the 1970s, the largest declines in cancer deaths rates are due to either behavioral changes, like declining tobacco use, or because of effective screening tests, principally colonoscopies and pap smear. New drugs have helped, too, though their impact on survival has generally been modest.


Expectations that cancer blood tests will quickly turn into a multibillion-dollar industry has attracted growing interest from investors. For instance, last week, a startup called Guardant, run by former Illumina executives, also said it had raised $100 million.


Guardant’s test isn’t an early detection test, but is instead used to measure tumor DNA in patients already battling cancer and can be prescribed in place of an invasive tissue biopsy (see “The Great Cancer Test Experiment”). Other companies bidding for a share of the testing market include Personal Genome Diagnostics, a spin-off of Johns Hopkins University, as well as Trovagene, Boreal Genomics, and Natera.



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Broad Institute: Genome misfolding unearthed as a new path to cancer 

Broad Institute: Genome misfolding unearthed as a new path to cancer  | Amazing Science | Scoop.it

In a landmark study, researchers from the Broad Institute and Massachusetts General Hospital reveal a completely new biological mechanism that underlies cancer. By studying brain tumors that carry mutations in the isocitrate dehydrogenase (IDH) genes, the team uncovered some unusual changes in the instructions for how the genome folds up on itself. Those changes target key parts of the genome, called insulators, which physically prevent genes in one region from interacting with the control switches and genes that lie in neighboring regions. When these insulators run amok in IDH-mutant tumors, they allow a potent growth factor gene to fall under the control of an always-on gene switch, forming a powerful, cancer-promoting combination.


The findings, which point to a general process that likely also drives other forms of cancer, appear in the December 23rd advance online issue of the journal Nature“This is a totally new mechanism for causing cancer, and we think it will hold true not just in brain tumors, but in other forms of cancer,” said senior author Bradley Bernstein, an institute member at the Broad Institute and a professor of pathology at Massachusetts General Hospital. “It is well established that cancer-causing genes can be abnormally activated by changes in their DNA sequence. But in this case, we find that a cancer-causing gene is switched on by a change in how the genome folds.”


When extended from end to end, the human genome measures some six and a half feet. Although it is composed of smaller, distinct pieces (the chromosomes), it is now recognized that the pieces of the genome fold intricately together in three dimensions, allowing them to fit compactly within the microscopic confines of the cell. More than mere packaging, these genome folds consist of a series of physical loops, like those of a tied shoelace, that bring distant genes and gene control switches into close proximity.


By creating these loops — roughly 10,000 of them in total — the genome harnesses form to regulate function. “It has become increasingly clear that the functional unit of the genome is not a chromosome or even a gene, but rather these loop domains, which are physically separated — and thereby insulated — from neighboring loop domains,” said Bernstein.


But Bernstein’s group did not set out to study this higher-order packing of the genome. Instead, they sought a deeper molecular understanding of glioma, a form of brain cancer, including the highly aggressive form, glioblastoma. Relatively little progress has been made in the last two decades in treating these often incurable malignancies. In order to unlock these tumors’ biology, Bernstein and his colleagues combed through vast amounts of data from recent cancer genome projects, including the Cancer Genome Atlas (TCGA). They detected an unusual trend in IDH-mutant tumors: When a growth factor gene, called PDGFRA, was switched on, so was a faraway gene, called FIP1L1. When PDGFRA was turned off, so, too, was FIP1L1.


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Spacefaring tardigrade (water bear) has largest contribution of foreign DNA in its genome

Spacefaring tardigrade (water bear) has largest contribution of foreign DNA in its genome | Amazing Science | Scoop.it

Sequencing reveals that the genome of the Tardigrade has been published, revealing approximately 6,000 genes of foreign origin.


The tardigrade, also known as the water bear, is renowned for many reasons. The nearly indestructible micro-organism is known to have the capacity to survive extreme temperatures (-272C to 151C), and is the only animal able to survive in the vacuum of space.


Today, with the publication of its genome in PNAS, the humble water bear can add another item to its exhaustive list of superlatives. Sequencing of the genome, performed by a team of researchers at the University of North Carolina at Chapel Hill, has revealed that a massive portion of the tiny organism’s genome is of foreign origin. Indeed, nearly 17.5% of the water bear’s genome is comprised of foreign DNA, translating to a genetic complement of approximately 6,000 genes. These genes are primarily of bacterial origin, though genes from fungi and plants have also been identified.


Horizontal gene transfer, defined as the shifting of genetic material materially (thus horizontally) between organisms is widespread in the microscopic world. In humans, however, the process does occur, but in a limited fashion, and via transposons and viruses. Other microscopic animals are also known to have large complements of foreign genes.


The authors of the newly published work have proposed a method by which this extremely extensive gene transfer may have occurred. Tardigrades have long been known to undergo, and survive, the process of desiccation (extreme drying out). The authors therefore postulated that during this drying out process and the subsequent rehydration, the tardigrade’s genome may have undergone significant sheering and breakage, resulting in a general loss of integrity and leakiness experienced by the water bear’s nucleus. In turn, this compromised nuclear integrity may have enabled foreign genetic material to readily integrate the genome, in much the same way as scientists perform gene transfer through the process of electroporation.


For now, the tardigrade has a dual claim to fame, being the only known animal to survive the vacuum of space, and being the animal with the largest genetic complement. Only with the study of other micro-organisms will we be able to validate if the humble tardigrade maintains its two, current, great claims to fame.


"Animals that can survive extreme stresses may be particularly prone to acquiring foreign genes—and bacterial genes might be better able to withstand stresses than animal ones," said Boothby, a postdoctoral fellow in Goldstein's lab. After all, bacteria have survived the Earth's most extreme environments for billions of years.


The team speculates that the DNA is getting into the genome randomly but what is being kept is what allows tardigrades to survive the harshest of environments, e.g. stick a tardigrade in a - 80 celsius freezer for a year or 10 and it starts running around in 20 minutes after thawing.


This is what the team thinks happens: when tardigrades are under conditions of extreme stress such as desiccation - or a state of extreme dryness—Boothby and Goldstein believe that the tardigrade's DNA breaks into tiny pieces. When the cell rehydrates, the cell's membrane and nucleus, where the DNA resides, becomes temporarily leaky and DNA and other large molecules can pass through easily. Tardigrades not only can repair their own damaged DNA as the cell rehydrates but also stitch in the foreign DNA in the process, creating a mosaic of genes that come from different species.

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Cheap DNA sequencing is here, writing DNA inexpensively is next

Cheap DNA sequencing is here, writing DNA inexpensively is next | Amazing Science | Scoop.it

Twist Bioscience dramatically scaled down the equipment for synthesizing DNA in a lab, making the process cheaper and faster. The stamp-sized wafers contain 100 microwells. Each of these contains 100 nanowells in which DNA can be synthesized.


AT TWIST BIOSCIENCE’S office in San Francisco, CEO Emily Leproust pulled out of her tote bag two things she carries around everywhere: a standard 96-well plastic plate ubiquitous in biology labs and her company’s invention, a silicon wafer studded with a similar number of nanowells.


Twist’s pitch is that it has dramatically scaled down the equipment for synthesizing DNA in a lab, making the process cheaper and faster. As Leproust gave her spiel, I looked from the jankety plastic plate, the size of two decks of cards side by side, to the sleek stamp-sized silicon wafer and politely nodded along. Then she handed me a magnifying lens to look down the wafer’s nanowells. Inside each nanowell was another 100 microscope holes.


That’s when I actually got it. The 96-well plate was not equivalent to the wafer, the entire plate was equivalent toone nanowell on the wafer. To put a number on it, traditional DNA synthesis machines can make one gene per 96-well plate; Twist’s machine can make 10,000 genes on a silicon wafer set the same size as the plate.


But who wants to order 10,000 genes? Until recently, that question might have been met with silence. “It was a lonely time,” says Leproust of her early fundraising efforts for Twist. Fast forward a couple years, though, and Twist has just signed a deal to sell at least 100 million letters of DNA—equivalent to tens of thousands of genes—to Ginkgo Bioworks, a synthetic biology outfit that inserts genes into yeast to make scents like rose oil or flavors like vanillin. Ginkgo is at the forefront of a wave of synthetic biology companies, bolstered by new gene-editing technologies like Crispr and investor interest.


“We’re Intel and Ginkgo is Microsoft,” says Leproust, which sounds exactly the kind of rhetoric you hear all the time in startupland. But her words reveal Twist’s specific ambition to be the driver behind synthetic biology innovations. Synthesizing genes in a lab allows biologists to design—down to the letter—the ones they want to test. Companies out there are already tinkering with DNA in various cells to create spider silk, cancer treatments, biodegradable plastic, diesel fuel—and Twist’s founders thinks the company can become the driving technology behind that new world.


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Genomics and Precision Agriculture: The Future of Farming

Genomics and Precision Agriculture: The Future of Farming | Amazing Science | Scoop.it

For nearly 400 years, Thanksgiving has been a time in North America when families come together to celebrate food and agriculture. As we reflect on yet another year, agricultural scientists at USDA continue to keep a wary eye on the future. At the end of what may be the hottest year on record, a period of drought has threatened the heart of one of the most important agricultural production zones in the United States. Water demands are increasing, and disease and pest pressures are continually evolving. This challenges our farmers’ ability to raise livestock and crops.  How are science and technology going to address the problems facing our food supply? 


To find answers, agricultural scientists turn to data—big data.  Genomics, the field of science responsible for cataloging billions of DNA base pairs that encode thousands of genes in an organism, is fundamentally changing our understanding of plants and animals.  USDA has already helped to fund and collect genomes for 25 crop plant species, important livestock and fish species, and numerous bacteria, fungi, and insect species related to agricultural production. Other USDA-supported research projects expanding these efforts are currently underway, including genome sequencing of 1,000 breeds of bulls and 5,000 insect species in the i5K initiative. But classifying and understanding DNA is only part of the story.


Even if neighboring farmers were to raise identical varieties of tomato, small variations in the environment can reduce crop performance and/or increase pests and disease. So, scientists and farmers are increasingly using technology like satellites, drones, sensors, and laser-guided tractors to collect thousands of data points about the environmental conditions in a field, such as temperature, humidity, soil composition, or slope of the land. Using these “precision agriculture” techniques, farmers could reduce their environmental footprint by matching land management practices to the unique environments on their farm.


In the long term, USDA researchers are hoping to combine precision agriculture and genomics in a remarkable way—to develop crops with combinations of genes that lead to the best performance in specific environments. To support this goal, USDA continues to lead the way in collecting and maintaining open access to these types of agriculture data.  As a result, your local farmer’s market or grocery store may one day have even more varieties of produce to choose from on Thanksgiving, with each optimized for the farm or field on which it was grown.


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Why are carrots orange? Genome sequencing gives clues

Why are carrots orange? Genome sequencing gives clues | Amazing Science | Scoop.it
The humble supermarket carrot owes its deep orange colour to a newly-found gene, according to an analysis of the full carrot genome.

 

Carrots are members of the Apiaceae family of plants, which include celery, parsley, fennel, coriander, dill and parsnip. They are related to crops in the sunflower, artichoke and lettuce — the latter which it split from about 72 million years ago. Historically, carrots had small white roots with a woody interior. They most likely came from areas of Iran and Afghanistan, where they still grow today.

 

Initially they were grown for their aromatic leaves, but over hundreds of years farmers turned a naturally occurring subspecies of the carrot into a larger, less woody root. Domesticated yellow and purple carrots were found in Central Asia around 1,000 years ago, and an orange version emerged in late 16th century Holland, most probably from crossing yellow carrots with purple ones.

 

By using NGS technologies, researchers sequenced the genomes of 35 different carrot specimens and subspecies, both wild and cultivated, in an attempt to understand how carrots evolved into those we find in our fridge. They found a gene responsible for the high concentration of beta-carotene in the orange carrot taproot. They also identified more than 32,000 genes in a typical orange carrot.

 

The genome could help breed carrots that have high levels of beta-carotene and are pest resistant.

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Scientists Want To Sequence The Genome Of Leonardo Da Vinci

Scientists Want To Sequence The Genome Of Leonardo Da Vinci | Amazing Science | Scoop.it

Five hundred years ago, Leonardo da Vinci was pioneering pretty much every field of study going, from poetry to mathematics, engineering, anatomy, science, astronomy, and geology. He wasn’t bad at painting either, apparently. Seemingly inspired by his feverishly creative spirit, scientists have hatched a mad plan to sequence his genome and attempt to piece together his incredible life.

 

The Leonardo Project is bringing together a wealth of scientists, historians, archeologists and art experts from universities around the world. They have recently outlined a few of their plans in a special edition of the Human Evolution journal.

 

The team is going to look for traces of DNA and fingerprints on his books, notepads, paintings, and equipment. They then hope to pair this with information from the hair, bones, fingerprints, and skin cells of his known past and present relatives. As you can imagine, this is no small feat. Much of the work will include tracking the history and final resting place of Leonardo’s family from the 14th century right up to now.

 

Rhonda Roby, a geneticist on the project, spoke to Gizmodo about some of the challenges in finding the physical remnants of Da Vinci, saying: “More and more techniques are being developed to recover DNA from people touching things.” “I also think there’s a possibility of biological material inside paintings,” she added. “The challenge would be actually getting that material out without damaging the artwork.”

 

The legacy of Da VInci’s work in science, engineering, and culture is nothing short of superhuman. But despite this, very little is known about the man himself. One of the things that will be revealed from this genome sequencing is the appearance of the Renaissance polymath. By fitting together bits of the genetic jigsaw, they’ll be able to get a fair idea of his eye color, skin tone, hair color, weight, height, and face shape. They also reckon they’ll be able to get a fair idea of his diet, his health, and his personality.

 

There’re no plans to clone the great polymath just yet, though.

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Skeletal stem cells form the blueprint of the face structure

Skeletal stem cells form the blueprint of the face structure | Amazing Science | Scoop.it

Timing is everything when it comes to the development of the vertebrate face. In a new study published in PLoS Genetics, USC Stem Cell researcher Lindsey Barske from the laboratory of Gage Crump and her colleagues identify the roles of key molecular signals that control this critical timing.

 

Previous work from the Crump and other labs demonstrated that two types of molecular signals, called Jagged-Notch and Endothelin1 (Edn1), are critical for shaping the face. Loss of these signals results in facial deformities in both zebrafish and humans, revealing these as essential for patterning the faces of all vertebrates.

 

Using sophisticated genetic, genomic and imaging tools to study zebrafish, the researchers discovered that Jagged-Notch and Edn1 work in tandem to control where and when stem cells turn into facial cartilage. In the lower face, Edn1 signals accelerate cartilage formation early in development. In the upper face, Jagged-Notch signals prevent stem cells from making cartilage until later in development. The authors found that these differences in the timing of stem cells turning into cartilage play a major role in making the upper and lower regions of the face distinct from one another.

 

"We've shown that the earliest blueprint of the facial skeleton is set up by spatially intersecting signals that control when stem cells turn into cartilage or bone. Logically, therefore, small shifts in the levels of these signals throughout evolution could account for much of the diversity of shapes we see within the skulls of different animals, as well as the wonderful array of facial shapes seen in humans," said Barske, lead author and A.P. Giannini postdoctoral research fellow.

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Genomics for the masses: AstraZeneca launches project to sequence 2 million genomes

Genomics for the masses: AstraZeneca launches project to sequence 2 million genomes | Amazing Science | Scoop.it
Drug company aims to pool genomic and medical data in hunt for rare genetic sequences associated with disease.

 

One of the world’s largest pharmaceutical companies has launched a massive effort to compile genome sequences and health records from two million people over the next decade. In doing so, AstraZeneca and its collaborators hope to unearth rare genetic sequences that are associated with disease and with responses to treatment.

 

It’s an unprecedented number of participants for this type of study, says Ruth March, vice-president and head of personalized health care and biomarkers at AstraZeneca, which is headquartered in London. “That’s necessary because we’re going to be looking for very rare differences among individuals.”

 

To achieve that ambitious goal, AstraZeneca will partner with research institutions including the Wellcome Trust Sanger Institute in Hinxton, UK, and Human Longevity, a biotechnology company founded in San Diego, California, by genomics pioneer Craig Venter. AstraZeneca also expects to draw on data from 500,000 participants in its own clinical trials, and medical samples that it has accrued over the past 15 years.

 

In doing so, AstraZeneca will be following a burgeoning trend in genetics research. For years, geneticists pursued common variations in human DNA sequences that are linked to complex diseases such as diabetes and heart disease. The approach yielded some important insights, but these common variations often accounted for only a small percentage of the genetic contribution to individual diseases.

 

Researchers are now increasingly focusing on the contribution of unusual genetic variants to disease. Combinations of these variants can hold the key to an individual's traits, says Venter.

 

The hunt for important rare variants has led AstraZeneca to partner with the Institute for Molecular Medicine Finland, says Aarno Palotie, who heads the Human Genomics Program there. Finland’s population was geographically isolated until recently, he notes, which makes for a unique genetic make-up. As a result, some variations that are very rare in other populations may be more common in Finland, making them easier to detect and study.

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We're finally cracking the secrets of what makes us sick

We're finally cracking the secrets of what makes us sick | Amazing Science | Scoop.it

For the data in our genome to be useful, we need to process not just the 3 billion base pairs of DNA that make up each person's genome but also the genomes of many people. The Precision Medicine Initiative is starting with the genomes of at least one million people. That's a mind-boggling amount of data already, and we'll eventually end up needing even more: "many millions" of genomes, saysDr. Eric Schadt, founding director of the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai.

We're still figuring out how to decode it all.

 

At Mount Sinai, scientists are trying to "collect as much information on as many patients as we can, integrate it, build predictive models from it, and then derive from those models more refined diagnoses, risk assessments, and plans for treatment than has been possible before," Schadt told Nature Biotechnology in 2012.

 

The team at Icahn is collecting genetic information from patients and trying to incorporate that data with everything from their clinical history to the bacteria on and around them in order to develop predictive models that will calculate how a disease will affect a person.

 

"The technology advances [that make that possible] have been astounding," says Schadt. "The ability to generate sequencing data has moved at a super-Moore's law rate," faster than even computing technology, he says. The supercomputers we have now can process genetic information in ways that would have been "just impossible 10 years ago." Scientists all over the country are pushing for new ways to understand genomic data.

 

Deep Genomics, a startup run by Brendan Frey, is leveraging artificial intelligence to help decode the meaning of the genome.

Specifically, the company is using deep learning: the process by which a computer takes in data and then, based on its extensive knowledge drawn from analyzing other data, interprets that information.

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HPV Genomes Show Greater Diversity Than Expected Among Cervical Cancer Patients

HPV Genomes Show Greater Diversity Than Expected Among Cervical Cancer Patients | Amazing Science | Scoop.it
Human papillomaviruses are associated with invasive cervical cancer as well as more benign disorders such as skin warts. Although more than 180 HPV genomes have been sequenced, there has been little research on the diversity of HPV genomes within the same patient, primarily because the virus is thought to have a low mutation rate.

Of the 13 HPV genotypes thought to be carcinogenic, HPV16 is responsible for about half of all invasive cervical cancer cases worldwide. In the study, the researchers sequenced HPV16 genomes from 10 patients with cervical cancer and one with non-malignant genital warts.

To date, most genomic studies of papillomaviruses have used Sanger sequencing to look at the "most prevalent, consensus sequence" during chronic infection, but Sanger sequencing may "not be appropriate to capture the dynamics of slowly evolving viruses, such as PVs," the authors wrote.

So, they decided to turn to next-generation sequencing. The authors extracted DNA from 10 clinical samples of invasive cervical cancer and one case of genital warts caused by HPV16. They used long PCR to generate 8-kb long amplicons — the size of the HPV genome — and sequenced them using Thermo Fisher's Ion Torrent PGM.

The authors generated both a consensus genome and also de novo assembled each sample using CLC software.

Comparing the clinical samples to the reference sequence, the researchers observed 190 changes, with the E2 gene containing the largest number of changes. Two samples had duplication events in the L1 gene and L2 gene, respectively.

The team also performed a phylogenetic analysis using consensus sequences from the PGM data as well as 20 HPV16 genomes from GenBank. From the eleven clinical samples, the researchers identified three types of HPV: HPV16_A1, HPV16_A2, and HPV16_D. In addition, these types correlated with specific tumor types, with squamous cell carcinomas associated with the A type and adenocarcinomas associated with the D types.

To analyze intra-host variation, the researchers performed de novo assembly. They were able to generate one contiguous sequence for four samples, with the remaining seven samples in three to eight contigs.

The researchers identified between three and 125 polymorphic sites per genome. In the most diverse sample, 31 of the 125 polymorphic sites represented more than 10 percent of the reads in that position. In the least diverse sample, only one polymorphic site represented more than 5 percent of the reads at that position.

Next, the team calculated a "diversity index" for each sample, defined as the "probability of a randomly chosen genome to be identical to the consensus genome." The median value for the samples was just 40 percent.

The authors suggest a number of factors could contribute to the diversity observed, including both innate and adaptive immune responses. For instance, the APOBEC3G family of proteins have been shown to target papillomavirus DNA, " which may partially account for the broad diversity of human PVs." In addition, "polymorphisms observed in the E6 gene could be a result of an immune selective pressure," the authors wrote.

In the future, more research will need to be done on HPV infection to monitor viral diversity in asymptomatic, productive, benign, premalignant and malignant infections. "The possible role of oncovirus intralesion diversity generated during chronic infections should be explored as a differential factor for increased oncogenic potential," they wrote.
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Scientists uncover the key role of a single gene on how groups of animals diverge

Scientists uncover the key role of a single gene on how groups of animals diverge | Amazing Science | Scoop.it

A study by researchers at the Wellcome Trust Centre for Human Genetics at Oxford University has uncovered the key role played by a single gene in how groups of animals diverge to form new species. The study, published today in the journal Nature, restored fertility to the normally-infertile offspring of two subspecies of mice, by replacing part of the Prdm9 gene with the equivalent human version. Despite the nearly 150 million years of evolution separating mice and humans, these 'humanized' mice were completely fertile.


New animal species form when groups of animals become isolated and as a result, begin to separate through evolution (a process known as speciation). When these isolated populations meet later, they might be able to breed with each other, but the male offspring are often infertile. Horses and donkeys are an example of such speciation: they can interbreed, but their offspring, mules, are infertile.


'Our work studied similar infertility in hybrid house mice, whose two parents come from different subspecies found in Western and Eastern Europe', says Dr Ben Davies from the Nuffield Department of Medicine, the first author on the study. These two sub-species are therefore on the verge of splitting into two entirely different species, since like mules, their offspring are infertile.


Dr Davies and his colleagues studied the Prdm9  gene: this gene is already known to have a role in infertility in mice from different species, and  is in fact the only known speciation gene in mammals. However, how speciation might link up to infertility was unknown.

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NIST simulates fast, accurate DNA sequencing through graphene nanopore

NIST simulates fast, accurate DNA sequencing through graphene nanopore | Amazing Science | Scoop.it

Researchers at the National Institute of Standards and Technology (NIST) have simulated a new concept for rapid, accurate gene sequencing by pulling a DNA molecule through a tiny chemically activated hole in graphene—an ultrathin sheet of carbon atoms—and detecting changes in electrical current.


The NIST simulation study suggests the method could identify about 66 million bases per second with 90 percent accuracy and no false positives. If demonstrated experimentally, the NIST method might ultimately be faster and cheaper than conventional DNA sequencing, meeting a critical need for applications such as forensics.


Conventional sequencing, developed in the 1970s, involves separating, copying, labeling and reassembling pieces of DNA to read the genetic information. The new NIST proposal is a twist on the more recent “nanopore sequencing” idea of pulling DNA through a hole in specific materials, originally a protein (see “First full genome of a living organism sequenced and assembled using smartphone-size device“).


This concept—pioneered 20 years ago at NIST—is based on the passage of electrically charged particles (ions) through the pore. The idea remains popular but poses challenges such as unwanted electrical noise, or interference, and inadequate selectivity.

By contrast, NIST’s new proposal is to create temporary chemical bonds and rely on graphene’s capability to convert the mechanical strains (rather than charged particles) from breaking those bonds into measurable blips in electrical current.


“This is essentially a tiny strain sensor,” says NIST theorist Alex Smolyanitsky, who came up with the idea and led the project. “We did not invent a complete technology. We outlined a new physical principle that can potentially be far superior to anything else out there.”


Graphene is popular in nanopore-sequencing proposals due to its electrical properties and miniaturized thin-film structure. In the new NIST method, a graphene nanoribbon (4.5 by 15.5 nanometers) has several copies of a base attached to the nanopore (2.5 nm wide). DNA’s genetic code is built from four kinds of bases, which bond in pairs as cytosine–guanine and thymine–adenine.


In simulations of how the sensor would perform at room temperature in water, cytosine is attached to the nanopore to detect guanine. A single-strand (unzipped) DNA molecule is pulled through the pore. When guanine passes by, hydrogen bonds form with the cytosine. As the DNA continues moving, the graphene is yanked and then slips back into position as the bonds break.


The NIST study focused on how this strain affects graphene’s electronic properties and found that temporary changes in electrical current indeed indicate that a target base has just passed by. To detect all four bases, four graphene ribbons, each with a different base inserted in the pore, could be stacked vertically to create an integrated DNA sensor.


The researchers combined simulated data with theory to estimate levels of measurable signal variations. Signal strength was in the milliampere range, stronger than in the earlier ion-current nanopore methods.


Based on the performance of 90 percent accuracy without any false positives (i.e., errors were due to missed bases rather than wrong ones), the researchers suggest that four independent measurements of the same DNA strand would produce 99.99 percent accuracy, as required for sequencing the human genome.


The study authors concluded that the proposed method shows “significant promise for realistic DNA sensing devices” without the need for advanced data processing, microscopes, or highly restricted operating conditions. Other than attaching bases to the nanopore, all sensor components have been demonstrated experimentally by other research groups. Theoretical analysis suggests that basic electronic filtering methods could isolate the useful electrical signals. The proposed method could also be used with other strain-sensitive membranes, such as molybdenum disulfide.

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The Next Next Thing in NGS Sequencing

The Next Next Thing in NGS Sequencing | Amazing Science | Scoop.it

Though it may seem to be navigating by perceptibly unfixed stars, next-generation sequencing (NGS) is journeying ever more adventurously into the obscure, the rare, and the confoundingly heterogeneous domains within life’s molecular codescapes. 


NGS is already capable of producing billions of short reads, and it can do so quickly and economically. And NGS is reaching well beyond genomics. For example, it is revolutionizing transcriptomics through advances in RNA sequencing (RNA-Seq). Yet, despite this dazzling progress, a number of significant challenges remain.


These challenges were discussed at a recent Oxford Global event, the “Seventh Annual Next Generation Sequencing Congress”. The event provided a window through which attendees could browse the NGS field’s most daunting obstacles. It also displayed technologies that could allow these obstacles to be circumvented.


New capabilities and applications include the removal of toxic, unwanted transcripts from RNA-Seq libraries as well as the mapping of under-explored alternative splicing spaces. NGS is also making progress toward sequencing mitochondrial DNA. Mitochondria are increasingly recognized in disease development, yet sequencing the DNA from these organelles is complicated because mitochondria harbor considerable genetic complexity and heterogeneity.


Another area bedeviled by heterogeneity is tumor analysis. Fortunately, it appears that heterogeneous tumor samples could be subjected to sorting procedures that could isolate pure populations of cells. These populations would be more amenable to sequencing.

Finally, NGS is enhancing its single-molecule capabilities. One emerging approach involves coupling nanopore technology and mass spectrometry (MS).

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Humans may harbor more than 100 genes from other organisms

Humans may harbor more than 100 genes from other organisms | Amazing Science | Scoop.it

You’re not completely human, at least when it comes to the genetic material inside your cells. You—and everyone else—may harbor as many as 145 genes that have jumped from bacteria, other single-celled organisms, and viruses and made themselves at home in the human genome. That’s the conclusion of a new study, which provides some of the broadest evidence yet that, throughout evolutionary history, genes from other branches of life have become part of animal cells.


“This means that the tree of life isn’t the stereotypical tree with perfectly branching lineages,” says biologist Alastair Crisp of the University of Cambridge in the United Kingdom, an author of the new paper. “In reality, it’s more like one of those Amazonian strangler figs where the roots are all tangled and crossing back across each other.”


Scientists knew that horizontal gene transfer—the movement of genetic information between organisms other than parent-to-offspring inheritance—is commonplace in bacteria and simple eukaryotes. The process lets the organisms quickly share an antibiotic-resistance set of genes to adapt to an antibiotic, for instance. But whether genes have been horizontally transferred into higher organisms—like primates—has been disputed. Like in bacteria, it’s been proposed that animal cells could integrate foreign genetic material that’s introduced as small fragments of DNA or carried into cells by viruses. But proving that a bit of DNA in the human genome originally came from another organism is tricky.


Crisp and his colleagues analyzed the genome sequences of 40 different animal species, ranging from fruit flies and roundworms to zebrafish, gorillas, and humans. For each gene in the genomes, the scientists searched existing databases to find close matches—both among other animals and among nonanimals, including plants, fungi, bacteria, and viruses. When an animal’s gene more closely matched a gene from a nonanimal than any other animals, the researchers took a closer look, using computational methods to determine whether the initial database search had missed something.


In all, the researchers pinpointed hundreds of genes that appeared to have been transferred from bacteria, archaea, fungi, other microorganisms, and plants to animals, they report online today in Genome Biology. In the case of humans, they found 145 genes that seemed to have jumped from simpler organisms, including 17 that had been reported in the past as possible horizontal gene transfers.

“I think what this shows it that horizontal gene transfer is not just confined to microorganisms but has played a role in the evolution of many animals,” Crisp says, “perhaps even all animals.


The paper doesn’t give any hints as to how the genes—which now play established roles in metabolism, immune responses, and basic biochemistry—may have been transferred or the exact timeline of the jumps, he says. That will take more work.

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Samuel Viana's curator insight, December 11, 2015 6:11 AM

Cientistas encontraram no nosso próprio genoma  genes que aparentam provir de origens completamente díspares: desde vírus ou fungos.

 

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Bacteria from the sea join the fight against cancer and infections

Bacteria from the sea join the fight against cancer and infections | Amazing Science | Scoop.it

For decades, bacteria have served society by producing antibiotics – the chemical compounds that can cure infectious diseases. However, it is possible that many natural microorganisms carry the recipes for the medicines of the future hidden in their genetic material, without this part of their genetic code being activated or “switched on”.


But now, biotechnologists from SINTEF and NTNU are developing technology that will make it easier to find – and exploit – these hidden and unutilized medicine factories in bacteria that exist in the natural environment. The hunt will concentrate on marine bacteria, and is one of the projects run by the new Norwegian Centre for Digital Life.


“Our aim is to identify novel compounds that are capable, for example, of killing cancer cells or antibiotic-resistant bacteria. The technology that we are developing will reduce the time taken to search for these and to make the production process more efficient,” says Alexander Wentzel, a senior scientist at SINTEF.


As a strategy, scientists will clip out genetic material from a large number of microorganisms before they transfer their DNA to cultivable bacteria; organisms whose characteristics have already been studied and will be optimized by the researchers in the INBioPharm project. The alterations will enable these organisms to switch on production of new substances that cannot be produced in the microorganism from which the DNA has been extracted.


With the aid of systems biology and synthetic biology (see fact-box), the project will develop the microorganisms in a way which, when they are cultivated, will produce small test quantities of all the possible products, and later, enable mass-production of the most promising substances.


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Genetics: Big hopes for big data

Genetics: Big hopes for big data | Amazing Science | Scoop.it

Technology is allowing researchers to generate vast amounts of information about tumors. The next step is to use this genomic data to transform patient care.


Adrian Lee has dedicated his career to studying breast cancer, which is to say he is actually tackling many different diseases at once. “No two breast cancers are the same,” says Lee, a pharmacologist and chemical biologist at the University of Pittsburgh in Pennsylvania. “Cancer is way more complex than we know.”


Lee is using genomic technology to fully describe cancers of the breast and apply that knowledge to guide treatment decisions for individual patients. “We can now analyse multiple variables from a single specimen, such as changes in DNA, changes in RNA and changes in methylation,” he says. “Genome-wide scans allow for better systems biology and allow us to learn what's gone wrong in a particular tumor.”


Sequencing tumors is faster, cheaper and easier than ever. With many researchers collecting sequence data and uploading these to public databases such as the The Cancer Genome Atlas (TCGA), opportunities to describe the many different cancers that arise in breast tissue are upon us. “The challenge used to be generating the data,” says Nicholas Navin, a geneticist at The University of Texas MD Anderson Cancer Center in Houston. “Those issues have been resolved. Now the challenge is data processing and data analysing — interpreting the mutations and communicating those to oncologists.”


At the University of Pittsburgh, researchers are working to link the molecular signatures of people with breast cancer to a host of clinical data, including demographic information associated with risk such as age, ethnicity and body weight. They are mining electronic health records for clinical correlates, treatment interactions and outcomes. “We've got a big haystack and we're trying to find the needle,” says Lee. “But we're also trying to incriminate the needle, by linking it to lots of things.” Collecting all that data from patients' electronic records adds up, Lee says. It takes infrastructure — Pittsburgh has already accumulated 5 petabytes, or 5 million gigabytes, which is enough data to overload around 40,000 new iPhone 6 devices.


Making the connection between the reams of data coming out of sequencing laboratories and the individual women fighting breast cancer takes big-time computing power. Big data needs researchers who are comfortable with statistical noise and those who are old hands at the iterative process required to create flexible computer programs.


Big-data researchers take a large data set and look for patterns. The idea is to identify mutations that can be targeted with drug treatment. It is the essence of personalized medicine: screen a patient's tumour for a set of biomarkers to choose the best treatment to fight the cancer. Big-data researchers believe that analysing the data of the thousands of tumours that have come before will reveal patterns that can improve screening and diagnosis, and inform treatment.


Lee and his colleagues have illustrated how big-data science led to a rethink of breast cancer1. They used two public databases — TCGA and METABRIC (Molecular Taxonomy of Breast Cancer International Consortium), which contain data on the entire set of genes, RNA transcripts and proteins of thousands of breast-cancer tumours — to parse out potential differences in the molecular signatures of breast tumours in younger compared with older women. Women who are diagnosed before the age of 40 tend to have worse disease: they are more likely to have later-stage cancers, poorer prognoses and worse survival outcomes than older women.


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