Genome Digest: What researchers are learning as they sequence, map, and decode species’ genomes

Kitty can has genome?

Species: Domestic cat (Felis catus)
Genome size: 3.1 billion base pairs

Domestic cats can develop diseases like leukemia and feline immunodeficiency virus . To better understand these diseases, an international team of researchers sequenced and annotated the genomes of three domestic cats. The results, published this month (August 5) in GigaScience, include a new feline genome browser, Genome Annotation Resource Fields (GARfield), which encompasses methylation patterns in cat blood cells and more than 21,000 annotated genomic features.

A team led by investigators at Nova Southeastern University in Florida sequenced and analyzed the genomes of three cats using three different methods. While the feline genome was previously published, Nova Southeastern researcher Stephen O’Brien and his colleagues noted that their work helps to close gaps in the low-coverage shotgun sequencing methods previously used in earlier work. O’Brien’s team also uncovered several new features in the cat genome, including new retrovirus-like elements and single nucleotide variants. Approximately 55.7 percent of the genome is comprised of repetitive elements.

The analysis suggests a “highly conserved ancestral mammal genome organization,” and offers data to “connect the rich veterinary and natural history of cats to genome discovery,” the authors wrote in their paper.


Read more genome news at TheScientist

Novel approach mimicks natural evolution with ‘promiscuous reactions’ to improve the diversity of drugs

A revolutionary new scientific method developed at the University of Leeds will improve the diversity of ‘biologically active molecules’, such as antibiotics and anti-cancer agents.

The researchers, who report their findings online in the journal Nature Chemistry, took their inspiration from evolution in nature. The research may uncover new pharmaceutical drugs that traditional methods would never have found.

“Nature produces some amazing structures with really interesting biological activity, but the plant or animal did not design them. Instead the organisms gradually evolved both the chemical structures and the methods to produce them over millennia because they were of benefit. We wanted to capture the essence of this in our approach to discovering new drugs,” said George Karageorgis, a PhD student from the School of Chemistry and the Astbury Centre for Structural Molecular Biology at the University of Leeds, and first author of the study.

The traditional method for discovering new drugs involves preparing new biologically active molecules by adjusting the chemical structure of an existing one slightly and analysing the results. This trial and error method is both time consuming and limits the variety of new types of drugs that are developed.

“There is a known problem with limited diversity in drug discovery. It’s like a baker always going to the same storage cupboard and using the same ingredients, yet hoping to create something that tastes different,” said Dr Stuart Warriner from the School of Chemistry and the Astbury Centre for Structural Molecular Biology at the University of Leeds, a co-author of the research paper.

Read full story at MNT

Fears over powerful new strain of gonorrhoea

Concerns are mounting over a powerful new form of gonorrhoea after a patient was found to have the highest level of drug resistance to the disease ever reported in Australia.

It is understood the patient, a tourist from central Europe, contracted the “sex superbug” in Sydney and was eventually treated in Cairns.

The discovery of the case in Australia, which resulted in a health alert in July, has also prompted warnings in New Zealand, where sexual health clinics are on high alert amid fears the new strain will spread there.

NZ Sexual Health Society president Edward Coughlan warned the patient involved, who is believed to have left the country, had the highest level of gonorrhoea drug resistance ever reported in Australia.


Read full story on TheGuardian

For Polio, Two Vaccines Work Better Than One

A booster dose of inactivated polio vaccine bolsters the immune system and reduces viral shedding in children already treated with the oral polio vaccine, a study shows


Depending on when and where in the world you were born, you may have received a different kind of polio vaccine than someone else born into different circumstances. If you were born in the U.S. after 2000, for example, you likely received an injection of the inactivated polio vaccine (IPV), but before that, you might have received the oral polio vaccine (OPV), a live attenuated virus, administered by mouth. Starting later this year, children born in polio-affected countries will receive both vaccine types, per World Health Organization (WHO) “endgame” plans to finish the job of eradicating polio.

The results of a study published today (August 21) inScience support this approach. In a group of Northern Indian children who had already received one or more doses of OPV, a supplementary dose of IPV bolstered their immune responses and reduced their shedding of viral particles in stool, a team led by researchers at the WHO reported.


Read full story here

When the Neanderthals Disappeared

Analysis of 40 European archaeological sites suggests a gradual extinction of Neanderthals over thousands of years.  


Neanderthals overlapped with early modern humans and, based on genetic evidence, even interbred. But the extent of the overlap of the two species both in terms of time and geography is still not fully known, mainly because it has been difficult to accurately date archaeological specimens that go back more than 30,000 years. Using newer techniques, a large-scale dating effort of Neanderthal specimens from Western Europe to Russia now narrows the timing of the extinction of Neanderthals to a span of 2,000 years—between 39,000 and 41,000 years ago. The study is published today (August 20) in Nature.

“The results point to a mosaic pattern of Neanderthal extinction in Europe and provide a shorter time frame for the potential interaction of humans with Neanderthals,” said study author Ron Pinhasi, a professor of archaeology at the University College Dublin in Ireland.


Read full article on TheScientist

Amgen enters heavyweight fray for Kendall Square’s few remaining blocks of space

As if things couldn’t get more competitive in East Cambridge’s office and lab market: Drug giant Amgen Inc. is on the prowl for another 150,000 square feet of space.

The news comes a day after the Boston Business Journal first reported that Bristol-Myers Squibb (NYSE: BMY) was seeking up to 200,000 square feet of new space in East Cambridge and less than two monthsafter a Page 1 story on the stealthy push by local real estate and business development officials to relocate the U.S. headquarters of a major biotechnology firm to the neighborhood. That effort, known locally as Project Tiger, is anticipated to sweep another 400,000 square feet of office and lab space off the East Cambridge market.

Read full story at Boston Business Journal

Connecting The Dots

Extending her initial studies of social wasps, Mary Jane West-Eberhard has spent her career probing the evolutionary relationship between social behavior and developmental flexibility.


In 2003, Mary Jane West-Eberhard publishedDevelopmental Plasticity and Evolution, the culmination of many years of reflection and observation on the links between developmental biology and evolution. The seeds of this book had been planted 40 years earlier, when West-Eberhard was an earnest zoology undergraduate student at the University of Michigan.

In 1961, as a junior in college, West-Eberhard wrote a research paper for a class taught by entomologist Richard Alexander—who would later become her doctoral advisor—on the evolution of dance communication in honeybees.

Forager honeybees perform a “waggle dance” in the shape of a figure eight to communicate information to their colony mates about the direction and distance to nectar and water sources. Digging through studies of insect movement, West-Eberhard came across a University of Michigan thesis on movements of hemipteran insects—the true bugs. The student had observed that bugs placed in a maze would alternate between turning right and left—which he called “twig behavior” because it allows insects to reach an end of a branched twig. West-Eberhard proposed that honeybees performing the waggle dance employed this twig behavior, providing an example of an ancient phenotype being used in a new context.


The Scientist

How safe is eating meat?

There have been a lot of news reports about the health risks of meat eating, but are they justified? Dr Michael Mosley has been investigating the truth behind the headlines for BBC Horizon.

I like eating meat, but what was once an innocent pleasure is now a guilty one.

If you believe the headlines, regularly indulging in a steak or a bacon sandwich raises your risk of heart disease and cancer.

The threat to health comes not from eating white meat, like chicken, but from red and processed meat.

Despite the negative headlines, on average Brits still eat about 70g of red and processed meat a day, with a quarter of men eating almost twice as much.

My wife, Clare, who is a GP, has for many years been trying to cut our family’s consumption of red and processed meat. I, however, was resistant.

So we were both delighted when Horizon asked me to investigate what, if any, the risks really are.

I visited numerous experts, finding out what they themselves eat.

I also decided to go on a high-meat diet to see what effects doubling my intake to around 130g a day would have.


Read full story at BBC News

Metagenomics Mash-Up A tour of the newest software and strategies for analyzing microbial and viral communities

With sequencing reads getting longer and cheaper in the past few years, researchers have begun ambitious efforts to catalog the genomic richness and variation within complex microbial and viral communities. So-called metagenomics studies involve collecting a sample of cells from their environment, breaking them open, chopping their DNA into pieces, and running the fragments on a sequencing machine.

Metagenomic analyses are more computationally demanding than genomic analyses because you’re working with a mix of diverse genomes rather than DNA from a more homogeneous microbial population. And even more than for genomics, one of the biggest challenges for metagenomics is making sense of the resulting data, says evolutionary biologist Jonathan Eisen of the University of California, Davis. Not only do scientists want to understand what microorganisms are present in a particular environment—not easy, considering that an average of 99 percent of them have never been cultured —and at what levels, but also what their functions are and how they compare with one another. “Sequencing is cheap, but that doesn’t mean you can put a community into a sequencer and make sense of it,” Eisen says.



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