Daily Archives: May 13, 2017

The Chimpanzee Genome Project is an effort to determine the DNA sequence of the Chimpanzee genome. It is expected that by comparing the genomes of humans and other apes, it will be possible to better understand what makes humans distinct from other species from a genetic perspective. It will also aid in the study of diseases that affect (or, conversely, do not affect) various primate species.

Human and chimpanzee chromosomes are very similar. The primary difference is that humans have one fewer pair of chromosomes than do other great apes. Humans have 23 pairs of chromosomes and other great apes have 24 pairs of chromosomes. In the human evolutionary lineage, two ancestral ape chromosomes fused at their telomeres, producing human chromosome 2.[3] There are nine other major chromosomal differences between chimpanzees and humans: chromosome segment inversions on human chromosomes 1, 4, 5, 9, 12, 15, 16, 17, and 18. After the completion of the Human genome project, a common chimpanzee genome project was initiated. In December 2003, a preliminary analysis of 7600 genes shared between the two genomes confirmed that certain genes such as the forkhead-box P2 transcription factor, which is involved in speech development, are different in the human lineage. Several genes involved in hearing were also found to have changed during human evolution, suggesting selection involving human language-related behavior. Differences between individual humans and common chimpanzees are estimated to be about 10 times the typical difference between pairs of humans.[4]

Analysis of the genome was published in Nature on September 1, 2005, in an article produced by the Chimpanzee Sequencing and Analysis Consortium, a group of scientists which is supported in part by the National Human Genome Research Institute, one of the National Institutes of Health. The article marked the completion of the draft genome sequence.[4] A database [5] now exists containing the genetic differences between human and chimpanzee genes, with about thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. Gene duplications account for most of the sequence differences between humans and chimps. Single-base-pair substitutions account for about half as much genetic change as does gene duplication.

Typical human and chimp homologs of proteins differ in only an average of two amino acids. About 30 percent of all human proteins are identical in sequence to the corresponding chimp protein. As mentioned above, gene duplications are a major source of differences between human and chimp genetic material, with about 2.7 percent of the genome now representing differences having been produced by gene duplications or deletions during approximately 6 million years [6] since humans and chimps diverged from their common evolutionary ancestor. The comparable variation within human populations is 0.5 percent.[7]

About 600 genes have been identified that may have been undergoing strong positive selection in the human and chimp lineages; many of these genes are involved in immune system defense against microbial disease (example: granulysin is protective against Mycobacterium tuberculosis [8]) or are targeted receptors of pathogenic microorganisms (example: Glycophorin C and Plasmodium falciparum). By comparing human and chimp genes to the genes of other mammals, it has been found that genes coding for transcription factors, such as forkhead-box P2 (FOXP2), have often evolved faster in the human relative to chimp; relatively small changes in these genes may account for the morphological differences between humans and chimps. A set of 348 transcription factor genes code for proteins with an average of about 50 percent more amino acid changes in the human lineage than in the chimp lineage.

Six human chromosomal regions were found that may have been under particularly strong and coordinated selection during the past 250,000 years. These regions contain at least one marker allele that seems unique to the human lineage while the entire chromosomal region shows lower than normal genetic variation. This pattern suggests that one or a few strongly selected genes in the chromosome region may have been preventing the random accumulation of neutral changes in other nearby genes. One such region on chromosome 7 contains the FOXP2 gene (mentioned above) and this region also includes the Cystic fibrosis transmembrane conductance regulator (CFTR) gene, which is important for ion transport in tissues such as the salt-secreting epithelium of sweat glands. Human mutations in the CFTR gene might be selected for as a way to survive cholera.[9]

Another such region on chromosome 4 may contain elements regulating the expression of a nearby protocadherin gene that may be important for brain development and function. Although changes in expression of genes that are expressed in the brain tend to be less than for other organs (such as liver) on average, gene expression changes in the brain have been more dramatic in the human lineage than in the chimp lineage.[10] This is consistent with the dramatic divergence of the unique pattern of human brain development seen in the human lineage compared to the ancestral great ape pattern. The protocadherin-beta gene cluster on chromosome 5 also shows evidence of possible positive selection.[11]

Results from the human and chimp genome analyses should help in understanding some human diseases. Humans appear to have lost a functional caspase-12 gene, which in other primates codes for an enzyme that may protect against Alzheimer's disease.

The results of the chimpanzee genome project suggest that when ancestral chromosomes 2A and 2B fused to produce human chromosome 2, no genes were lost from the fused ends of 2A and 2B. At the site of fusion, there are approximately 150,000 base pairs of sequence not found in chimpanzee chromosomes 2A and 2B. Additional linked copies of the PGML/FOXD/CBWD genes exist elsewhere in the human genome, particularly near the p end of chromosome 9. This suggests that a copy of these genes may have been added to the end of the ancestral 2A or 2B prior to the fusion event. It remains to be determined if these inserted genes confer a selective advantage.

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Chimpanzee genome project - Wikipedia

San Diego-based Edico Genome has received $22 million in Series B financing to staff up and speed adoption of its Dragen genomic data platform. The round was led by new investor Dell Technologies Capital, and included previous investors Qualcomm Ventures, Axon Ventures and NuVasive CEO Greg Lucier.

Were going to extend and expand the engineering, sales and marketing teams, said Pieter van Rooyen, Edicos president and CEO in a phone interview. Our focus is to build out the team and grow revenue.

Dragen is designed around the companys field programmable gate array (FPGA), a dynamic processor that can be reprogrammed whenever necessary. The company holds nine patents on the technology, which rapidly clarifies genomic data and could make it easier to use genomics to diagnose patients.

We take the data that comes off the sequencer, which is about a 180-gig file, said van Rooyen. We process and analyze it and the output is around a one gig file, and that contains all the variants associated with a specific patient.

Dragens biggest asset is speed. According to van Rooyen, the platform can process an entire genome in 20 minutes when used from a local server as little as ten minutes when linked to the Amazon AWS cloud.

Edico is building an impressive array of partnerships to extend the technology IBM, Intel, Johns Hopkins and van Rooyen hints there are others in the pipeline. In late 2015, Dragen collaborated with Illumina, Childrens Mercy Hospital in Kansas City and Stephen Kingsmore on a groundbreaking study that showed whole genome sequencing could diagnose neonatal intensive care patients in 26 hours. The feat holds the Guinness record for fastest genetic diagnosis.

The company hopes to build on this and other early successes, believing its FPGA technology gives it a distinct edge in both speed and price. Still, theres no shortage of competition: GenomeCloud, Genalice and DNAnexus are just a few of the companies offering similar services.

Ultimately, van Rooyen and colleagues are betting the industry will standardize the genomic informatics pipeline, making data sharing more routine, and Edico will have a seat at the table.

We have a strong IP portfolio, and were in the process of becoming the industry standard for precision medicine analytics and data analysis, said van Rooyen.

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Edico Genome raises $22M to accelerate adoption of genomic analysis platform - MedCity News

Medical News Today

For anorexia nervosa, researchers implicate genetic locus on chromosome 12 Science Daily "We identified one genome-wide significant locus for anorexia nervosa on chromosome 12, in a region previously shown to be associated with type 1 diabetes and autoimmune disorders," said lead investigator, Cynthia Bulik, PhD, FAED, founding director of ... Study identifies genetic locus in anorexia nervosaUPI.com Genes linked to anorexia show deadly disease isn't just psychiatricInternational Business Times UK all 7 news articles »

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For anorexia nervosa, researchers implicate genetic locus on chromosome 12 - Science Daily

Researchersare pushing forward on a project to one day create asyntheticgenome of humans and other organisms,a development that could result in new ways to treat disease and even affect our fundamental understanding of human biology, yetalso presents challenging ethical questions. At a recent scientific meeting questions remained abouthow much should beshared with the public.

On Tuesday and Wednesday, more than 200 prominent geneticists, biologists, technologists, and enthusiasts gathered in downtown Manhattan for a meeting of GP-write, a project with the goal to understand the blueprint for life provided by the Human Genome Project.

The researchers plan to develop the scientific and technological tools necessary to synthesize genetic code inexpensively and efficiently. While the ease with which scientists can readDNA has sped up dramatically in the past 15 years, their ability to write it is much farther behind. They can synthesize small bits of DNA, and even have created small viral and bacterial genomes from scratch, but eventually the goal is to tackle genomes of more complex microbes, plants, and even humans. Accomplishing thiscould give scientists cell lines for research and the production of biologic drugs, safer and innovative therapies to treat disease, microbes that could help nourish our bodies where food is scarce, or even complex data storage.

This is the second meeting of GP-write. Last years meeting, held in Boston in May, drewcontroversy, mostly due to its opacity. Concerns about the ethics drivingan advance as dramatic as a synthetichuman genetic code, somethingthat has the capacity tocompletely redefine the core of what now joins all of humanity together as a species, as one researcher wrote, demand constant dialogue beyond the scientific community. But instead of inviting that conversation, the meetingappeared closed and secretive it was capped at 130 scientists with no members of the media present.

The meeting organizers say their hands were tied by scientific publishing rules an article outlining their work was going to be published in thejournal Science, which does not allow researchers to discuss results publicly before publication (the articlewas published the following month). Media coverage of the meeting itself, however, contained a lot of hype and few facts, since the organizers couldnt talk to the press. However, GP-writes organizers did listen to public feedback generated from those articles,Nancy Kelley, the coordinator of GP-write, told Vocativ, and broadenedthe focus of the project beyond synthesizinghuman DNA.

Though they do plan to synthesize human DNA eventually, they realized that the human part needed tobe put off until the ethical implications were fully explored, Kelleysaid.

For this years meeting, Kelley said, the project organizers wanted a moreopen meeting, and 22 reporters representing well-known magazines, newspapers, and web sites were on the list of attendees (I had recently reported on GP-write for CNBC). Some of the initial sessions were live streamed to hundreds of viewers, Kelley said. The overall vibe was congenial and collaborative.

But there was a caveat. The night before the meeting, members the media received an email that includeda media policy. Because some of the presentations contain unpublished data, we were asked, as a professional courtesy, to refrain from sharing screen shots of the slide presentations and any scientific data shared at the meeting unless you have permission from the presenter or publishing any content without permission from the scientist in question.A bolded note to the same effect was inside the packet of materials handed to all attendees. The speakerswere supposed to note on their slides whether the data was unpublished, Kelley said, but sometimes they forgot. Some people still took photos of slides, but the Twitter dialogue was relatively sparse.

For most researchers, the policy didnt seem strange. Several scientists and ethicists told Vocativ its common to limit what can be shared at scientific meetings to promote openness within the scientific community because it allows researchers to discuss their unpublished work without violating journals policies and without fear of others beating them to it.

The policy is in line with standard norms of academic discourse at scientific conferences, Barbara Evans, the director of the University of Houston Law Center and one of Tuesdays speakers who mentioned the importance of transparency in GP-write, toldVocativ via email. Its a little counterintuitive, but true, that reasonable restrictions on communicationcan serve to promote transparency, if the restrictionsencourage people to feel comfortable about sharing their original thoughts and ideas.

To others, however, the policy was less natural. There were many attendees who were not actively participating in research and might not have ever come to a scientific meeting, so they werent used to the rule, especially because there was such little unpublished data presented. And, given the number of speakers who mentioned the importance of public interface and participation, the policy couldeven seem contradictory to some journalists.

But despite opening their doors, [GP-write organizers] still have a ways to go to embrace transparency. The day before the meeting, a PR exec gave reporters new ground rules: No publishing content without permission from the scientist involved, reads Stat News email newsletter sent early Tuesday, before the meeting started.

One attendee named Bryan Bishop, whose interest in biology is strictly a hobby, tooktranscripts of the first of Tuesdays talks and postedlinks to them on Twitter. He toldVocativ he was tapped on the shoulder by one of the meeting organizers and asked to stop. The following exchange happened on Twitter:

Bishop saidhe didnt know about the media policy and toldVocativ via email: I think that everyone means well at GP-write. I dont feel offended they are still figuring how GP-write works and whats in their DNAI wasnt expecting a blanket dont post any content at all especially after hearing the Center say kind words about the virtues of transparency and inclusiveness.

If anyone is restricting the transparency of the meeting, its the scientific journals,saidEliza Strickland, a senior associate editor at engineering magazine IEEE Spectrum.I fault these journals for wielding their power in an old-fashioned andoutdated way that interferes with the free flow of scientific information, but I dont fault scientists or conference organizers for complying with their rules.

Journal policy or not,transparency has to be at the heart of GP-write, and last years firestorm showed what can happen if it appears compromised.Jeffrey Bessen, a chemistry graduate student at Harvard who is on GP-writes public outreach committee, felt the media policy is justified, but says that he understands the optics of appearing as transparent as possible. I think theres trust to be regained. That policy to me doesnt read like its not transparent, but to someone else it might.

The project organizers know this and say they are committed to it. Various sessions at the two-day meeting were dedicated to ethical concerns and public outreach; a committee met to discuss how the organizers can best have an open conversation about their work. The dialogue will be ongoing, especially if the scientists get closer to synthesizing a human genome.

Were going to continue to be as open as we possibly can, Kelley said.

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Scientists Working To Build A Human Genome Struggle With ... - Vocativ

Scientists are trying to unlock some of the secrets of spider silk by sequencing the genetic code of the spiders themselves. One new study is led by the University of Vermont and the University of Pennsylvania.

UVM biology professor Ingi Agnarsson, an expert on spiders and the properties of spider silk, is one of the researchers on that study.

"The goal of this study is trying to understand at the molecular level, the building blocks, how these materials are actually put together by the spiders to aid us in mimicking these properties in man-made materials," Agnarsson told Vermont Edition on Thursday.

Spider silk is one of the toughest materials in existence, with combined strength and elasticity that manufacturing techniques struggle to match.

"We're pretty good at making materials that are either very strong or maybe very stretchy," Agnarsson says. "But spider silk combine[s] the two, and it's in the combination of these two properties that makes them really, really tough."

Rather than just focus on the properties of the spider silk, this study actually sequenced the genome of a spider as a way to try and understand the silk better.

"A lot of the research that has been done on spider silk in the last 50 years has focused on the biomechanical properties, and we understand these pretty well," Agnarsson explains.

"So now the issue is: what is the structure of these materials that have this excellent performance? And that's where this study comes in, trying to understand the molecular makeup of these fibers whose biomechanics we have already characterized pretty well."

The spider whose genome was sequenced for this study is called a golden orb-weaver, which Agnarsson describes as "sort of the 'lab rat' of spider silk research, because they are easy to work with. They're very large spiders, so you get relatively thick fibers out of them. And they're easy to find in nature."

Agnarsson notes that golden orb-weavers don't live as far north as Vermont, but rather are common in the southern United States.

"Our first goal was simply to characterize the different types of silk they have and asking very basic questions. Like, how many types of silks do they actually make? How many types of proteins are each type of silk composed of? And what are the similarities and differences between different silk?" UVM professor Ingi Agnarsson

Thanks to the genome work of the study, Agnarsson says the information they have collected and organized could be used to help address a number of questions about spider silk.

"Our first goal was simply to characterize the different types of silk they have and asking very basic questions," Agnarsson says. "Like, how many types of silks do they actually make? How many types of proteins are each type of silk composed of? And what are the similarities and differences between different silk?"

"So we've created this huge database, this resource, that we can now basically pinpoint the molecular structure of different types of silk, and start to answer these questions of, you know, what is it that makes this particular silk very strong or that other type of silk very stretchy? And so on."

There are actually different kinds of spider silk that serve different intended purposes. Agnarsson explains that some silk might be used for creating the web structure, another for coating a spider's egg sac and yet another to bind other fibers.

One finding that Agnarsson says was surprising had to do with the location of a certain silk protein within the spider's glands.

"The silk fibers come out of the end of the abdomen of the spider where all the silk glands are, and the venom is produced in the front of the spider close to the mouth, obviously," Agnarsson says. "So there's no physical connection or proximity, but it turns out that one of the silk proteins is almost exclusively expressed in the venom glands."

While Agnarsson says they aren't sure why that happens to be the case, he does add that "silk strands themselves don't have any venomous properties as far as we know."

Agnarsson says he continues to be motivated by his personal curiosity and has a plan for building on this spider research.

"The next project is to take ... another species of spider that has a super strong, super tough silk, do the genome of that spider, and then compare the two and try to figure out what exactly is it that makes this new spider so different from other spiders," Agnarsson says.

Listen to the full conversation with Agnarsson above. Broadcast live on Thursday, May 11, 2017 during the noon hour; rebroadcast during the 7 p.m. hour.

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Secrets Of Spider Silk: New Study Uses Genome Sequencing To Examine Its Properties - Vermont Public Radio