Category Archives: Genome

Who owns the genome of a cow? That is, the complete genetic material encoded in the DNA of the animal.

That's the basis of hearing underway this week before the Federal Court in Melbourne.

In 2010, the Australian Patent Office granted a patent titled 'Compositions, methods and systems for inferring bovine traits', to commodities giant Cargill USA and Branhaven LLC.

When Meat and Livestock Australia (MLA) found out about the patent early last year it launched an appeal along with Dairy Australia.

MLA believes the patent's broad claims potentially mean it extends to around two thirds of the bovine genome, including almost every economically valuable trait, such as beef tenderness, marbling in meat, and milk production.

It has raised serious concern at MLA and Dairy Australia because the two organisations invest a significant amount of their levy payers' money into cattle research, with an increasing focus on genomics.

The organisations believe the patent will maintain the high price of genomic testing for beef and dairy farmers, while also having a chilling effect on Australian research into cattle genomics.

Barrister Katrina Howard SC, on behalf of MLA, argued before Justice Jonathan Beach on Monday that the claims in the patent granted to Cargill USA and Branhaven LLC used scientific and statistical tools that would have been well known and understood by a person skilled in genomic mapping at the patent's priority date, 2003.

But on Tuesday, Branhaven's legal counsel argued the methods used to identify these traits had never been used at the time of the patent's priority date, that they were theoretical at the time, and their significant investment in applying them and identifying the traits represents a real invention.

Two years ago, the High Court unanimously ruled a patent could not be granted over genetic information, because it is a discovery of nature, not an invention.

Cargill Australia is not defending MLA's appeal, but the USA-based parent company is the joint owner of the patent. In the courtroom this week, only Branhaven's legal representatives are fighting the appeal.

Information about Branhaven is sparse, but in joint press releases with Cargill USA, it is described as a "private holding company focused on acquiring companies with strong intellectual properties".

Today the court will hear evidence from a panel of expert geneticists from Australia and the USA, who'll give evidence in a 'hot tub', or concurrent style.

The hearing will run until Thursday with a decision to be handed down later.

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Legal fight over cattle genome underway in Melbourne's Federal Court - ABC Online

May 16, 2017 Credit: Harry Taylor, Natural History Museum

Scientists from the University of Aberdeen are part of an international team which has been working to better understand the biology of a snail species that transmits a disease infecting 200 million people, killing around 200,000 each year in developing countries.

Schistosomiasis, also known as 'snail fever' or bilharzia, ranks second only to malaria in impact of a parasitic disease on human global health. It is caused by parasites (schistosomes) contracted from tropical freshwater snails, the most significant of which is 'Biomphalaria glabrata', subject of the large scale genome study published in Nature Communications this week.

The consortium led by the University of New Mexico, is made up of over 100 academics from across Europe, the USA, Africa and Australia. The UK consortium consists of scientists from the universities of Aberdeen, Aberystwyth, Brunel, Kingston, Westminster, the Natural History Museum, London (WHO Collaborating Centre), and the European Bioinformatics Institute.

Scientists have identified a number of crucial processes in the snail's biology that is helping them to understand how it transmits this lethal parasite, enabling them to uncover new ways to potentially stop transmission.

The Aberdeen University team, led by Dr Catherine Jones (who represents the UK consortium on the international steering committee), Dr Les Noble and Dr Anne Lockyer, working in collaboration with colleagues at Brunel University, are largely concerned with characterising snail genes which, amongst other functions, detoxify mollusc pesticides and control reproductive processes.

This information promises new control strategies; for example, design of novel selective pesticides which inhibit specific detoxification genes which may allow targeting of only this species of freshwater snail.

Conventional mollusc pesticides have a broad spectrum effect, also killing fish and other aquatic life crucial to maintain the healthy ecosystems on which local people are dependent.

Additionally, the increased knowledge of genes involved in snail reproduction could allow development of strategies which disrupt egg production and so limit numbers.

Dr Jones, from the University's School of Biological Sciences, said: "This disease is a gigantic problem for global health killing around 200,000 people each year and blighting the lives of millions more. Children are particularly susceptible to the disease, as they tend to be in closer contact with water infected by the parasite.

"Our team and the wider international consortium have for the first time analysed the entire genetic make up of this nuisance species, and as a result now have a much better understanding of this snail's biology, and how they transmit the disease.

"Going forward, we can suggest specific strategies which could be explored further with a view to, hopefully, reducing transmission of schistosomiasis, helping the World Health Organisation in its aim to eliminate this disease by 2025."

Explore further: New protein could be key in fighting debilitating parasitic disease

More information: Coen M. Adema et al. Whole genome analysis of a schistosomiasis-transmitting freshwater snail, Nature Communications (2017). DOI: 10.1038/ncomms15451

A naturally occurring protein has been discovered that shows promise as a biocontrol weapon against schistosomiasis, one of the world's most prevalent parasitic diseases, Oregon State University researchers reported today ...

Large-scale programmes to treat a life-threatening disease could improve the health of millions despite concerns about their long-term effects, a study suggests.

Schistosomiasis (also known as snail fever) affects more than 250 million people worldwide. Individuals become infected after skin contact with the schistosome parasite in contaminated water, and, without treatment, experience ...

Researchers at Oregon State University have discovered a group of genes in one species of snail that provide a natural resistance to the flatworm parasite that causes schistosomiasis, and opens the door to possible new drugs ...

In the late 1970s, a new drug held the promise of wiping out a disease that currently affects more than 250 million people. Nearly 40 years later, the drug, praziquantel, has yet to make a dent in the global burden of schistosomiasis, ...

(Medical Xpress) -- Infections from certain parasites can compromise the immune system, leaving it less able to fight other diseases.

Large families and strong social ties help animals live longer, new research suggests.

The beginnings of agriculture changed human history and has fascinated scientists for centuries.

Clocks and calendars, sports scores and stock-market tickers - our society is saturated with numbers. One of the first things we teach our children is to count, just as we teach them their ABCs. But is this evidence of a ...

Human teeth evolved from the same genes that make the bizarre beaked teeth of the pufferfish, according to new research by an international team of scientists.

Scientists from the University of Aberdeen are part of an international team which has been working to better understand the biology of a snail species that transmits a disease infecting 200 million people, killing around ...

Findings of a new study solve a key mystery about the chemistry of how plants tell time so they can flower and metabolize nutrients.

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Understanding the chemical commerce of this species, the species-specific pheromones it produces for various life needs, would enable their use in eliminating this beautiful snail. Remember that pheromones are both species specific and synergistic (not unlike fish oil benefits).

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Scientists decode genome of deadly tropical snail - Phys.Org

Q. How do you view the relationship between history and theology when it comes to Adams existence, his sin, the Fall etc.?

A. I am purposefully ambiguous if not agnostic because I cant make up my mind on the basis of the Bible. There are elements in the Bible the genealogies for instance that suggest a real man and historical person. There are other elements in Gen 1-3, like a talking snake, a man named Dusty and a woman named Momma of all Living Beings that sound like ANE stories in some ways. The genre, as you know, of Gen 1-11 is a much debated question but after reading the discussions I simply dont know what to decide. I see the text functioning as a revelation of the vocation of Adam and Eve in this world; I see it telling us that humans are exiled for their sins; I see it telling us that Adam and Eves sin followed by a murdering son; these are what I see. As such, I side with the many Jewish texts that inform us Adam was seen as a moral archetypal human who was told how to live before God and chose not to. I dont oppose original sin etc but Im unconvinced anyone in the Bible explicitly teaches it. Im not Eastern and Im not Western; Im convinced that Adam and Eve sinned and Im convinced the Bible says we are sinners and need redemption.

Q. In evaluating the genetics arguments in the first half of the book, if you were to discuss the strengths and weaknesses of the argument of Dennis Venema from a Biblical and theological point of view, what would you say?

A. Nothing, I like what Dennis wrote.

See the rest here:
Adam and the Genome The Dialogue Part Three - Patheos (blog)

MSUToday

$1.5M NSF grant to explore secrets of electric fish genome MSUToday Electric fish have been a model biology system since the 18th century. Their potential, though, has been mostly isolated to neurological studies. Thanks to the recent availability of electric fish genome sequences, Michigan State University researchers ... and more »

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$1.5M NSF grant to explore secrets of electric fish genome - MSUToday

Researchers have used whole genome sequencing to identify DNA abnormalities that cause genetic diseases in cats, such as progressive retinal atrophy and Niemann-Pick type 1, a fatal disorder in domestic felines.

Whole genome sequencing, which is the process of determining an organisms complete DNA sequence, can be used to identify DNA anomalies that cause disease. Identifying disease-causing DNA abnormalities allows clinicians to better predict an effective course of treatment for the patient.

Findings from the studies could help feline preservationists implement breeding strategies in captivity for rare and endangered species such as the African black-footed cat.

The researchers worked with the 99 Lives Cat Genome Sequencing Consortium to identify the genetic variants. Leslie Lyons, a professor of comparative medicine in the College of Veterinary Medicine at the University of Missouri, established the project to improve health care for cats through research.

The database has genetically sequenced more than 50 felines and includes DNA from cats with and without known genetic health problems. The goal of the database is to identify DNA that causes genetic disorders and have a better understanding of how to treat diseases.

In the first study, Lyons and her team used the 99 Lives consortium to identify a genetic mutation that causes blindness in the African black-footed cat, an endangered species often found in US zoos.

The team sequenced three catstwo unaffected parents and an affected offspringto determine if the mutation was inherited or spontaneous. The genetic mutation identified was located the IQCB1 gene and is associated with progressive retinal atrophy, an inherited degenerative retinal disorder that leads to blindness. The affected cat had two copies of the genetic mutation, indicating that it was an inherited disorder.

African black-footed cats are closely related to domestic cats, so it was a good opportunity to use the 99 Lives database, Lyons says.

When sequencing DNA, we are looking for the high priority variants, or genetic mutations that result in disease. Variants in the IQCB1 gene are known to cause retinal degeneration in humans. We evaluated each gene of the African black-footed cat, one at a time, to look for the genetic mutation that is associated with vision loss.

In another study representing the first time precision medicine has been applied to feline health, Lyons and her team used whole genome sequencing and the 99 Lives consortium to identify a lysosomal disorder in a 36-week-old silver tabby kitten that was referred to the university Veterinary Health Center.

The kitten was found to have two copies of a mutation in the NPC1 gene, which causes Niemman-Pick type 1, a fatal disorder. The NCP1 gene identified is not a known variant in humans; it is a rare mutation to the feline population.

Genetics of the patient is a critical aspect of an individuals health care for some diseases, Lyons says. Continued collaboration with geneticists and veterinarians could lead to the rapid discovery of undiagnosed genetic conditions in cats. The goal of genetic testing is to identify disease early, so that effective and proactive treatment can be administered to patients.

Identification of both the IQCB1 gene in the African black-footed cat and the NCP1 in the silver tabby will help to diagnose other cats and allow them to receive appropriate treatment. Using results of the black-footed cat study, zookeepers will be implementing species survival plans to help manage the cats in captivity in North America.

The first studyappears in Scientific Reports. Funding came fromthe University of Missouri, College of Veterinary Medicine Clinician Scientific Grant. The second study is publishedin the Journal of Veterinary Internal Medicine.

Source: University of Missouri

Read more here:
Genomes reveal cause of disease in rare cats - Futurity - Futurity: Research News

Science Daily

Genome sequence of fuel-producing alga announced Science Daily The report, in Genome Announcements, comes after almost seven years of research, according to Dr. Tim Devarenne, AgriLife Research biochemist and principal investigator in College Station. In addition to sequencing the genome, other genetic facts ...

Excerpt from:
Genome sequence of fuel-producing alga announced - Science Daily

A study published last month details one of the most diverse canine genome maps produced to date tracing the relationship between breeds. In examining the genomes of over 1,000 dogs, the map provided insight into two interesting findings.

The first showed that canines bred to perform similar functions, such as dogs from the herding or working groups, dont necessarily share the same origins.

Herding breeds are my favorite, holding beloved traits like intelligence and agility. So its surprising that these dogs may be more different than they seem.

The reason behind this convergence may also be why geneticists had difficulty mapping out herding dog lineages in the past. Study author Elaine Ostranger believes this happened because herding dogs emerged through selective breeding at multiple times in many different places.

In retrospect, that makes sense, says Elaine. What qualities youd want in a dog that herds bison are different from mountain goats, which are different from sheep, and so on.

The second finding shed light on an ancient type of dog that may have come to the Americas thousands of years before Christopher Columbus. Researchers have looked for the genetic legacy of these dogs in the DNA of modern American breeds, but have found little evidence until now.

Most of the breeds studied originated in Europe and Asia. But domestic dogs first came to the Americas thousands of years ago, when people crossed the Bering land bridge linking Alaska and Siberia. These New World dogs later disappeared when European and Asian dogs arrived in the Americas.

But the way two South American breeds, the Peruvian hairless dog and the xoloitzcuintli, are clustered together on the map suggest they could share genes not found in any of the others. This means those genes could have come from dogs that were present in the Americas pre-Columbus.

I think our view of the formation of modern dog breeds has historically been one-dimensional, says Bob Wayne, an evolutionary biologist at the University of California. We didnt consider that the process has a deep historical legacy.

Researchers now think that dog breeds underwent two major periods of diversification. Thousands of years ago, dogs were selected for their skills. This changed a few hundred years ago, when animals were bred for physical traits instead.

Bob says that, when it comes to genetics, studying dogs is a unique opportunity since no other animal has had the same level of intense deliberate breeding.

While its interesting to learn more about our dogs and where they came from, the scientists had practical reasons for creating this genetic database. They hope that this information can help future studies of canine and human diseases.

Read more:
New Canine Genome Map - The Bark (blog)

Q. What promoted you to do this co-authored book?

A. While I never made the sciences anything central to my own intellectual interests over the years science pops up as important to some biblical discussion I am engaged in, not least when I was teaching undergraduates at North Park. Many of them were science majors and many of them had some solid commitments to science and it made them wonder how solid their faith could be. Over the years I read various books, L. Duane Thurmond to Francis Collins to my co-bloggers (RJSs) posts to John Walton to Dennis Venema. The last of whom I met at BioLogos event, told him how much I appreciated his work. Unknown to me Dennis had the idea of applying for a BioLogos grant, we worked on it together, we were successful and we were launched to write this book.

Q. Q. At first blush this appears to be a dialogue book, but in fact it isnt. Each of you do your own presentations with really not much apparent interaction. Why did you decide to do it this way? You dont question his genetics arguments, and he doesnt really question your Biblical and theological ones.

A. When I was a child I was somehow given a police hat a little cheap plastic one. One day I was discovered in the middle of a (not at all busy) street standing in the middle of the street stopping a car and then waving it along. I soon learned that was wrong and dangerous and I was told I was not a policeman. A parable: I have no business, as I didnt have any business directing cars as a child because I had a police hat, telling scientists what to say and they have no business telling me what to say. Each of us can hold the other a bit accountable, and that is in fact what happened in this book. Just because we are theologians and know the truth of the gospel doesnt mean we are to tell scientists what to do. But we can see in scientists where they infringe upon our territory and they can see it in us at times infringing on their territory. The book, thus, lets the science be science and the Bible be the Bible. The biggest problem for this discussion is that too many Bible people think they can tell scientists what to think when it is clear (to some of us) that the Bible is not making claims about science.

More:
Adam and the Genome The Dialogue Part One - Patheos (blog)

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.

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