Category Archives: Genome

UW Genome Sciences - Wednesday Evenings at the Genome: Dr. Jesse Bloom
July 9, 2014 "Constraints on the Evolution of Influenza Virus" Due to technical difficulties, the associated slides for this presentation are unavailable.

By: UWGenomeSciences

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UW Genome Sciences - Wednesday Evenings at the Genome: Dr. Jesse Bloom - Video

UW Genome Sciences - Wednesday Evenings at the Genome: Dr. Sam Miller
July 30, 2014 "How Bacteria Cause Disease: Warfare and Detente Alter the Balance of Human Defense Microbial Invaders"

By: UWGenomeSciences

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UW Genome Sciences - Wednesday Evenings at the Genome: Dr. Sam Miller - Video

UW Genome Sciences - Wednesday Evenings at the Genome: Dr. David Raible
July 17, 2013 "Not Just a Fish Tale: Zebrafish Models to Cure Hearing Loss"

By: UWGenomeSciences

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UW Genome Sciences - Wednesday Evenings at the Genome: Dr. David Raible - Video

Full of Excuses ~ Break Me Down ~ The Human Genome (Official Music Video)
http://www.fullofexcuses.ca Premiere Video from the Canadian Alternative Rock Band ``Full of Excuses`` from Kamloops British Columbia. This is second single from the album ``The Human Genome``...

By: FOETVROCKS

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Full of Excuses ~ Break Me Down ~ The Human Genome (Official Music Video) - Video

Researchers have succeeded in sequencing the genome of a rare tapeworm that resided in the brain of a British man for four years.

There have only been 300 reports of the worm, known as Spirometra erinaceieuropaei, since 1953 and it has never appeared in the UK before. As the parasite is so rare it is not known exactly how it entered the man's body, although it is possible that it could have been caused by the man consuming tiny crustaceans from lakes, eating raw meat from amphibians and reptiles or by using a raw frog poultice, which is a Chinese remedy to cause sore eyes.

Although the man is now systemically well now, the worm causes sparganosis in humans, which is an inflammation of bodily tissues. When the parasite is inside the brain this can cause seizures, memory loss and headaches.

In this case, the worm in the man's brain was found to be only 1cm long, but before it was diagnosed and removed, it had travelled 5cm from the right side of the brain to the left. It took four years of eliminating other diseases, followed by regular MRI scans to discover what was causing the man's headaches and seizures. Comparing the MRI scans, it is possible to see the worm travelling slowly across the brain.

Even when the parasite was spotted, it wasn't possible to identify it as Spirometra erinaceieuropaei. "The key thing in this case was that the pathologist recognised it was a parasite," Matt Berriman tells WIRED.co.uk. It was removed using precision surgery and placed on a histology slide. "They pulled it out essentially with a biopsy needle."

Researchers then had to go about identifying the worm. This took several months -- and not just because we're not used to seeing such parasites in the UK. Even in countries like China and Korea where the parasite originates, it is so rare that there is very little information known about it.

"The clinical histology slide offered us a great opportunity to generate the first genome sequence of this elusive class of tapeworms," says Hayley Bennett from the Wellcome Trust Sanger Institute. Bennett, who was first author of the study detailing the genetic findings from the parasite, points out that because they only had a very tiny piece of DNA to work with -- "just 40 billionths of a gram" -- they had to make some very tough calls about exactly they wanted to find out from the DNA.

In all creatures there is one particular gene known as "the barcode of life" that can be sequenced in order to determine the exact species of the animal. When they did this to the parasite, the researchers discovered that it was a Spirometra erinaceieuropaei worm, and that of the two known sparganosis-causing worm species, the one in the man's brain was the more benign of the pair.

They also managed to generate sufficient DNA sequence data to put together a draft genome, which is now being used to investigate known and potential treatment targets.

"We made a couple of sequencing libraries -- one was very good," says Berriman. This was enough to piece together the draft genome quite nicely. He admits though that "this is not a good example about how to build a genome". Ideally to make a reference genome you wouldn't need to use a histology slide at all, he says.

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Genome of man's rare brain worm detailed in online 'WormBase'

FRIDAY, Nov. 21, 2014 (HealthDay News) -- Scientists say they've mapped the genome -- the genetic "blueprint" -- of a tapeworm extracted from a British man's brain, in hopes it might help others with this very rare infection.

As reported Nov. 21 in the journal Genome Biology, the tapeworm was removed from the brain of a 50-year-old British man of Chinese ethnicity.

"This infection is so rare worldwide and completely unexpected in this country that the patient was not diagnosed ... until the worm was pulled out from the brain," study lead author Hayley Bennett, of the Wellcome Trust Sanger Institute in the United Kingdom, said in a journal news release.

As the researchers explained, most tapeworms live in the gut, causing symptoms such as weight loss, weakness and abdominal pain. However, some species travel to areas such as the eyes, spinal cord and brain.

In this study, researchers sequenced the genome of a 1-centimeter larval tapeworm removed from the man's brain. He had been complaining of symptoms such as headaches, seizures, altered smell and memory problems. The man survived the surgery and is recovering, Bennett's team said.

Through sequencing the tapeworm's genome, researchers identified it as a rare species called Spirometra erinaceieuropaei, typically found in China, Japan, South Korea and Thailand. Infection can occur when a person eats undercooked frogs or snakes, uses frog meat for treating wounds, or drinks contaminated water.

The researchers believe the gene study might lead to improved drug treatment for people with the parasite. By sequencing the tapeworm's genome, they pinpointed genes that provide resistance to a drug called benzimidazole, and other genes that suggest a possible sensitivity to another tapeworm drug, praziquantel.

The researchers also identified a number of genes that may offer targets for drugs that are already on the market but used to treat other conditions.

"We were also surprised at how large the genome was; it is much bigger than those of other known flatworms, and roughly a third of the size of the human genome," Bennett said.

"By comparing the genome to other tapeworms we can see that certain gene families are expanded -- these possibly underpin this worm's success in a large variety of host species," she added. "The data gave us a first look at a whole group of tapeworms that have not been sequenced before."

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Ick! Tapeworm infecting man's brain yields genetic secrets

A genome of a rare species of tapeworm found living inside a patient's brain has been sequenced for the first time, in research published in the open access journal Genome Biology. The study provides insights into potential drug targets within the genome for future treatments.

Tapeworms are parasites that are most commonly found living in the gut, causing symptoms such as weakness, weight loss and abdominal pain. However, the larvae of some species of tapeworm are able to travel further afield to areas such as the eyes, the brain and spinal cord.

A 50-year-old man of Chinese ethnicity was admitted to hospital in the East of England after reporting symptoms of headaches, seizures, altered smell and memory impairment. The patient had lived in the UK for 20 years but visited his homeland often. After testing negative for a range of diseases and not presenting any other abnormalities, doctors began to take a series of MRI images of his brain. Over the course of four years, they noticed a lesion migrate at least 5 cm across his brain, and after taking a biopsy from his left thalamus, they discovered a 1 cm long ribbon-shaped larval worm. The patient, who remains anonymous, was cured of his infection by the operation and is now recovering.

Small samples of the worm were sent to researchers at the Wellcome Trust Sanger Institute, where they began to investigate its genome. Through sequencing its DNA, they identified it as Spirometra erinaceieuropaei, a rare tapeworm species typically found in China, South Korea, Japan and Thailand, and known to cause infection by ingesting undercooked frogs or snakes, using frog meat for treating wounds, and ingesting contaminated water.

The researchers sequenced the worm's entire genome for the first time, measuring it as 1.26 billion base pairs long, which is currently the largest reported genome for any flatworm. This was despite the fact they had such a small sample to work from after removal from the patient's brain. By investigating specific sections of the worm's genome, they were also able to identify genes for resistance to certain treatments, and other potential drugs targets.

Lead author Hayley Bennett from the Wellcome Trust Sanger Institute said: "This infection is so rare worldwide and completely unexpected in this country that the patient was not diagnosed with sparganosis until the worm was pulled out from the brain. We were also surprised at how large the genome was, it is much bigger than those of other known flatworms, and roughly a third of the size of the human genome. By comparing the genome to other tapeworms we can see that certain gene families are expanded -- these possibly underpin this worm's success in a large variety of host species. The data gave us a first look at a whole group of tapeworms that have not been sequenced before."

Through investigating specific parts of the genome for sensitivity to known tapeworm treatments, the researchers found that the tapeworm had genes providing resistance to benzimidazole, but possible sensitivity to another tapeworm drug praziquantel.

The team also investigated the genome to find potential targets which could be exploited by drugs already on the market but known for treating other diseases. They found a number of genes which are targets for known cancer drugs, suggesting that these treatments could be re-purposed for treating this type of infection.

The researchers also identified twenty expanded gene families with unknown function, which they say demonstrates how little is known about this order of tapeworms, and could explain its ability to live in a wide range of hosts (crustaceans, reptiles, amphibians and mammals) as well as in aquatic environments. They have made all their data publicly available so as to help other researchers.

Hayley Bennett said: "We think that it is important to make the genomic data available as is it offers a resource predicting whether other drugs can be repurposed for use in really rare infections such as in this case."

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Tapeworm found living inside a patient's brain: Worm removed and sequenced

Evolution in the sequencing of the human genome
A history of the Human Genome Project. How the process began in the late 70 #39;s and culminated in the full sequence of the Human Genome in 2002 - 2003. The nex...

By: William Orfanos

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Evolution in the sequencing of the human genome - Video

PUBLIC RELEASE DATE:

19-Nov-2014

Contact: Shane Canning shane.canning@biomedcentral.com 44-203-192-2243 BioMed Central @biomedcentral

Pioneering use of whole genome sequencing in real time to help control a hospital outbreak is reported in an article published in the open access journal Genome Medicine. The research corroborates the use of the technique as a rapid and cost-effective way of tracking and controlling the spread of drug-resistant hospital pathogens.

Acinetobacter baumannii is a multi-drug resistant pathogen found in hospitals across the globe and emerged as a significant threat to casualties in the Iraq and Afghanistan wars. It affects severely ill patients, particularly trauma and burns patients, often leading to pneumonia and bloodstream infections. Healthcare-associated infections (HAIs) are estimated to cost the UK 1 billion a year and, at any given time, one in every 15 patients will have a HAI.

Whole genome sequencing, which sequences an organism's entire DNA, is thought to be a promising new addition to the toolkit for controlling HAIs. Conventional methods are often applied retrospectively and yield limited information about a pathogen's DNA, making it difficult to compare whether patients are carrying the same bacteria and track transmission of outbreaks.

In this paper the researchers from the University of Birmingham, University of Warwick, and the National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, report how whole genome sequencing was used to control an outbreak of A. baumannii at Queen Elizabeth Hospital Birmingham in 2011. The outbreak began following the admittance of a military patient from Afghanistan with blast injuries and lasted for 80 weeks - making it one of the longest outbreaks ever described for this pathogen. The patient was carrying a novel strain of the bacterium that had not previously been observed in the region's hospitals. After first using traditional methods to try and contain the pathogen, the researchers decided to switch to whole genome sequencing mid-way through the outbreak.

Sampling patients and the environment, the researchers were able to identify 74 patients belonging to the outbreak. They then determined the detailed genetic makeup of the bacteria carried by each of these patients and used this data, with information about the ward that the patients were housed in, and the date of their first positive tests, to identify nearly 70 possible transmission events. Armed with this detailed information, the researchers were able to pinpoint transmission hot spots within the hospital, which included an operating theatre and a specialised bed for burns patients.

Deep cleaning of these transmission sites followed and new decontamination protocols were put in place by the hospital. In May 2013 the outbreak was declared closed. Lead author of the study, Mark Pallen from the University of Warwick, said: "We have demonstrated how whole genome sequencing can be applied in a clinically helpful timeframe to track and control the spread of drug-resistant hospital pathogens. In this case, it helped understand and control what was probably longest running A. baumannii outbreak ever seen in this country."

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Real-time genome sequencing helps control hospital outbreak

Chuck Bednar for redOrbit.com Your Universe Online

An international research consortium investigating the functional genome of the mouse have managed to map the creatures so-called mission control centers, and found new clues as to why certain processes and systems in the rodents prevent the results of mouse studies from being successfully replicated in humans.

Members of the Mouse ENCODE project, a project designed to complement the National Human Genome Research Institutes (NHGRI) Encyclopedia of DNA Elements (ENCODE) program, were able to produce an exhaustive description of the functional genome elements of mice, and compared that information to the human genome. Their findings produced similarities between the two mammals, as well as some significant differences.

ENCODE, which began in 2003, analyzed specific components in the human genome responsible for gene expression, or the process of coding for proteins that carry out a cells function. The Mouse ENCODE study looked at 100 mouse cell types and tissues to annotate the regulatory elements of the mouse genome and compared them to the human genome useful research, since mice are so often used as model organisms in clinical studies.

According to the National Institutes of Health (NIH), which oversees the NHGRI, the researchers reported their findings in four separate studies published in the journal Nature and other prominent scientific journals. In those papers, the authors examined the genetic and biochemical programs involved in regulating both mouse and human genomes, finding that the systems responsible for controlling gene activity in each have many similarities that have been conserved through the evolutionary process.

Their findings could provide new insight into genetic regulation and other systems essential to mammalian biology, the NIH said. Furthermore, their work could provide new information to determine in which cases the mouse will continue to be an appropriate model for studies involving the effect of drugs and disease on humans, as well as help explain some of the limitations of this model and why the results of such studies sometimes fail to translate to people.

The mouse has long been a mainstay of biological research models, said NHGRI Director Dr. Eric Green. These results provide a wealth of information about how the mouse genome works, and a foundation on which scientists can build to further understand both mouse and human biology. The collection of mouse ENCODE data is a tremendously useful resource for the research community.

This is the first systematic comparison of the mouse and human at the genomic level, added Dr. Bing Ren, a professor of cellular and molecular medicine at University of California, San Diego (UCSD) and co-senior author of the Consortiums primary Nature study. We have known that the mouse was mostly a good model for humans [and] this allows us to study human disease by studying those aspects of mouse biology that reflect human biology.

Among the discoveries made during the course of the research was the discovery as to why the immune system, metabolism and stress response of mice are so different from humans, the Centre for Genome Regulation (CGR), one of the institutions involved in the project, explained. They compared various processes involved in gene expression, including gene transcription and chromatin modification, and repeated those investigations in various different tissues and cell types from both mice and humans.

Our lab took part in analyzing the group of RNA or transcriptome, that results from transcription, the process by which the instructions in the genes are read, said Alessandra Breschi, a CGR researcher and one of the first co-authors of the main study. We have discovered that human and mice transcriptome contains both preserved and divergent elements. Surprisingly we have found that the differences seem bigger between species rather than between fabrics when initially we thought that the gene activity in the same kinds of tissues would be similar.

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Comparing The Genomes Of Mice And Humans To Aid Clinical Research