Daily Archives: December 10, 2014

Fronteres del Coneixement: The Human Genome Diversity Group, Institut de Biologia Evolutiva
Fronteres del Coneixement, s una srie de vdeos de divulgaci cientfica, en la que es mostra el dia a dia de cinc grups de recerca de cinc diferents lnies d #39;investigaci a l #39;Institut...

By: IBE LCATM

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Fronteres del Coneixement: The Human Genome Diversity Group, Institut de Biologia Evolutiva - Video

Tsunamaru - Daidai Genome [Insane] + DT
AR 9.6 My blog : http://ehgur5146.blog.me/

By: dh jeong

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Tsunamaru - Daidai Genome [Insane] + DT - Video

December 8th - Susie Maidment - Cosmic Genome Science Advent Calendar
A look back into the archive with a section of Dr Susie Maidment #39;s episode of Science School where she brought in her stegosaurus tail spike to show us. Every day a new free science clip...

By: The Incomplete Map of the Cosmic Genome

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December 8th - Susie Maidment - Cosmic Genome Science Advent Calendar - Video

Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of hospital-acquired infections, with the largest burden of infections occurring in under-resourced hospitals. While genome sequencing has previously been applied in well-resourced clinical settings to track the spread of MRSA, transmission dynamics in settings with more limited infection control is unknown. In a study published online today in Genome Research, researchers used genome sequencing to understand the spread of MRSA in a resource-limited hospital with high transmission rates.

Patients from two intensive care units (ICUs) in a hospital in northeast Thailand were tested over a three-month period for MRSA. During this time, 46 patients and 5 staff members tested positive at least once (16% adult and 34% pediatric patients). The genetic similarity of the MRSA isolates precluded the use of conventional low-resolution genotyping approaches for distinguishing transmission from one person to another. Therefore, whole genome sequencing was performed on a total of 76 patient isolates, including up to two repeat isolates from patients who tested positive for MRSA in the first screen. None of the patients or staff members that tested positive for MRSA had symptoms of an infection but rather were carriers.

"A striking feature of the phylogenetic tree based on S. aureus whole genome sequencing was the presence of multiple distinct clades," said senior author Sharon Peacock from the University of Cambridge and Wellcome Trust Sanger Institute. "This suggested that multiple clades of the same lineage were circulating in the hospital at the same time."

Examining single base changes in the genomes of MRSA isolates allowed researchers to infer the most likely transmission routes between infected patients. Transmission events were observed between patients within the ICU, and also between patients and staff members. These results are in contrast to a previous study performed in the UK where patient-to-patient MRSA transmission in the ICU was rare.

"Our long term goal is to use such information to inform infection control practice," said Peacock. "The degree of transmission we demonstrated in our study has directly led to the prioritization of improved hand hygiene practices at the study hospital."

Genome sequencing also revealed that MRSA clades were dynamic in the ICU over the three-month period, with some clades more prevalent early in the study and others later.

Deep sequencing of isolates taken from a single patient carrying MRSA for the longest period revealed that although all isolates were of the same clade, there were small genetic differences between them, suggesting bacterial diversity within a single carrier. This lends further support to previous work suggesting that understanding transmission networks will require measures of within-host bacterial diversity as well as traditional 'shoe-leather epidemiological' data.

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The above story is based on materials provided by Cold Spring Harbor Laboratory. Note: Materials may be edited for content and length.

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Genome sequencing traces MRSA spread in high transmission setting

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9-Dec-2014

Contact: Sarah Collins sarah.collins@admin.cam.ac.uk 44-012-237-65542 University of Cambridge @Cambridge_Uni

Researchers from the University of Cambridge have used genome sequencing to monitor how the spread of methicillin-resistant Staphylococcus aureus (MRSA) occurs in under-resourced hospitals. By pinpointing how and when MRSA was transmitted over a three-month period at a hospital in northeast Thailand, the researchers are hoping their results will support evidence-based policies around infection control.

MRSA is a common cause of hospital-acquired infections, with the largest burden of infections occurring in under-resourced hospitals in the developing world. Whereas genome sequencing has previously been applied in well-resourced clinical settings to track the spread of MRSA, how transmission occurs in resource-limited settings is unknown. In a new study published today (9 December) in the journal Genome Research, researchers used genome sequencing to understand the spread of MRSA in a hospital with high transmission rates.

"In under-resourced hospitals and clinics, formal screening procedures for MRSA are not in place," said Professor Sharon Peacock of the University of Cambridge and the Wellcome Trust Sanger Institute, who led the research. "Filling gaps in our understanding of how MRSA spreads in such settings is important, since this not only highlights the problem but also provides direction to interventions that tackle this and other hospital-based pathogens."

The team of researchers from the UK, Thailand and Australia monitored all patients on two intensive care units (ICUs) at a hospital in northeast Thailand over a three-month period in order to track how and when MRSA was transmitted. During this time, five staff members and 46 patients tested positive at least once, which represented 16% of adult and 34% of paediatric patients.

Conventional bacterial genotyping approaches do not provide enough discrimination between closely-related MRSA strains to be able to pinpoint transmission from one person to another, but whole genome sequencing addresses this problem. A total of 76 MRSA populations, or isolates, were sequenced, including up to two repeat isolates from patients who tested positive for MRSA in the first screen. None of the patients or staff members who tested positive for MRSA were asymptomatic carriers.

By conventional typing, all of the MRSA identified belonged to sequence type 239, the dominant MRSA lineage worldwide. But, based on sequence data, there was considerable genetic diversity - including the presence or absence of clinically important genes such as those coding for antiseptic resistance and antibiotic resistance.

"A striking result from sequence data was the presence of multiple distinct clades, which suggests that several different variants of MRSA were circulating through the hospital at the same time," said Peacock. "We also confirmed numerous transmission events between patients after admission to the ICU, and identified a 'super-spreader' in each unit."

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Using genome sequencing to track MRSA in under-resourced hospitals

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9-Dec-2014

Contact: Kevin Jiang kevin.jiang@uchospitals.edu 773-795-5227 University of Chicago Medical Center @UChicagoMed

The availability of a trace nutrient can cause genome-wide changes to how organisms encode proteins, report scientists from the University of Chicago in PLoS Biology on Dec. 9. The use of the nutrient - which is produced by bacteria and absorbed in the gut - appears to boost the speed and accuracy of protein production in specific ways.

"This is in some sense a 'you are what you eat' hypothesis,"' said senior study author D. Allan Drummond, PhD, assistant professor of biochemistry and molecular biology at the University of Chicago. "This nutrient that is absorbed through the gut looks like it can cause the recoding of an entire genome over evolutionary time."

All known organisms store the blueprint of life in their DNA, and use the information to produce proteins - the structural components and molecular engines for almost every function in a cell. To accomplish this, copies of relevant DNA regions must first be made. These copies are strings of chemical letters that serve as instructions, and are read three letters at a time by molecules known as transfer RNA (tRNA). Each tRNA has a preference for a specific three letter combination, or codon, and is attached to a single amino acid. As the instructions are read, tRNAs sequentially bind to their corresponding codon and deposit their amino acid, creating a protein.

tRNAs possess a special property known as "wobble" - a flexibility in one of the binding positions - that allows them to pair with multiple codons. This means that different spellings of genetic code can be used to create the exact same protein, similar to how sentences can be written using different synonyms. However, this flexibility comes with a cost. Some codons are less reliably read and can introduce more mistakes. As such, certain codons are thought to be favored by natural selection.

To investigate the mechanisms that underlie this process and the evolutionary consequences, Drummond, together with Tao Pan, PhD, professor of biochemistry and molecular biology, and colleagues from Cornell University, analyzed and compared thousands of genes in a dozen different species of fruit fly. They looked for the frequency at which certain codons were used to encode proteins, and how this affected the accuracy and speed of protein production.

To their surprise, they found that the availability of queuine - a trace nutrient produced by bacteria that is only available when absorbed through the gut - played a major role in determining which codons were optimal. Flies which had abundant queuine possessed a higher proportion of tRNAs with a specific modification: a portion of their wobble-binding sites was replaced with a queuine-derived molecule known as queuosine (Q).

The team found that these Q-tRNAs were able to read and process certain codons much faster and more accurately than unmodified tRNAs, and caused changes throughout the flies' genomes. Species with access to plentiful queuine favored codon spellings that were optimized for Q-tRNAs. Species with access to less queuine favored other codon spellings.

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Nutrient availability can cause whole-genome recoding