Category Archives: Genome

Genome mufflerImpreza sti(GDB-F) Exhaust Note
Impreza Exhaust Note(no running enginracing only) http://youtu.be/yW6JgH3CqMY Car specification GDB-F ...

By: merlion177

Original post:
Genome mufflerImpreza sti(GDB-F) Exhaust Note - Video

PUBLIC RELEASE DATE:

11-Dec-2014

Contact: Tim Stephens stephens@ucsc.edu 831-459-4352 University of California - Santa Cruz @ucsc

Crocodiles are the closest living relatives of the birds, sharing a common ancestor that lived around 240 million years ago and also gave rise to the dinosaurs. A new study of crocodilian genomes led by scientists at UC Santa Cruz reveals an exceptionally slow rate of genome evolution in the crocodilians (a group that includes crocodiles, caimans, alligators, and gharials).

The UC Santa Cruz team used the crocodilian genomes, combined with newly published bird genomes, to reconstruct a partial genome of the common ancestor of crocodiles, birds, and dinosaurs. The study, part of an ambitious international collaboration to analyze the genomes of modern birds and gain insights into their evolution, is one of eight papers from the Avian Phylogenomics Consortium being published in a December 12 special issue of Science.

Richard E. (Ed) Green, lead author of the crocodilian genome paper and an assistant professor of biomolecular engineering at UC Santa Cruz, said the slow evolutionary rate in the crocodilian lineage was helpful in reconstructing the genome of the common ancestor.

"The ticking of the molecular clock in the crocodilians is much slower than in other lineages we're used to looking at, like mammals, which means we can see back into their past more cleanly," Green said.

The reconstructed genome of the common ancestor will be a valuable tool for investigating the evolution of the "archosaurs," the group that includes all dinosaurs, pterosaurs, birds, and crocodilians. (Crocodilians are actually more closely related to birds and dinosaurs than they are to other reptiles, i.e., lizards, snakes, and turtles.) Green said the genome reconstruction effort, led by UC Santa Cruz research specialist Benedict Paten, yielded about half of the genome sequence of the common ancestor with an accuracy of about 91 percent, and he expects that to improve as more data on bird and crocodile genomes become available.

The team sequenced the genomes of three crocodilian species: the American alligator, the saltwater crocodile, and the Indian gharial. Their analysis indicates that the ancestor of all archosaurs probably had an extremely slow rate of molecular evolution, and that the rate of change sped up in the bird lineage. The rate of molecular evolution of crocodilians is an order of magnitude slower than that of mammals. The most likely reason for this relates to the relatively long time between generations in crocodilians, Green said.

"When it takes longer to get from one generation to the next, you expect the evolutionary rate to be slower, and big animals tend to have long generation times," he said. "We know from fossils that the body plan of crocs has remained largely unchanged for millions of years. Mammals, however, if you go back 50 or 60 million years there were no big mammals, so we see a faster rate of evolutionary change."

Read more from the original source:
Scientists reconstruct genome of common ancestor of crocodiles, birds, dinosaurs

A 3D Map of the Human Genome
Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist....

By: cellvideoabstracts

Originally posted here:
A 3D Map of the Human Genome - Video

A Texas Tech University biologist led a team of more than 50 scientists who mapped the genomes of three crocodilians.

By mapping these genomes, scientists may better understand the evolution of birds, which are the toothy predators' closest living relatives, said David Ray, an associate professor of biology. The team completed genomes of a crocodile, an alligator and a true gharial to complete the genomic family portrait.

"One of the major finds in our case was that crocodilian genomes change very slowly when compared to birds," Ray said. "We compared both birds and crocodilians to turtles, which are the closest living relatives of the group that includes both birds and crocodilians. We found that they evolved slowly also. The best explanation for this is that the common ancestor of all three was a 'slow evolver,' which in turn suggests that rapid evolution is something that evolved independently in birds."

Research began in 2009 as an attempt to map only 1 percent of crocodilian DNA. However, shortly after starting, the price for mapping a million bases dropped from $1,000 eventually down to $1.

"We had proposed to sequence about 2.4 million bases from the three crocodilians in the original proposal," Ray said. "By the time we got the funds, it became clear that we could easily accomplish a thousand times that much and could afford to sequence an entire genome of 3 billion bases."

Ray said that when biologists look at a group of organisms, they look for what makes that group unique as well as what all members of one group of organisms share that other groups do not. The best way to do that is to examine their closest relatives.

"Technically, birds' closest relatives are the dinosaurs," he said. "So we can only look at their fossils and this can provide only limited information on their biology when compared to examining organisms that are alive today. We get insight into differences in behavior, structures that don't fossilize, and in our case, the makeup of the genome."

Ray said he and other scientists were surprised to see how genetically uniform the alligators that the group sequenced were. Initially, the group suspected severe hunting during most of the 20th century may be to blame.

"Because alligators underwent a severe population decline, we first thought that might be what happened," he said. "However, we see the same pattern in all three species and the likelihood that all three were subject to the same genetic bottlenecks is small. We suggested instead that change just occurs slowly in crocodilians. In other words, it wasn't that the genetic differences were reduced because of overhunting. Rather, the amount of variation in crocodilians is low because change simply occurs slowly in these genomes."

The DNA in alligators, crocodiles and gharials is about 93 percent identical across the genome. By comparison, a human shares about 93 percent of his or her DNA with a macaque.

Read more:
Biologists map crocodilian genomes

Science Projects On The Genetic Genome Of Organisms

By: Top Learning to Read

See the article here:
Science Projects On The Genetic Genome Of Organisms - Video

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

Read more here:
Fronteres del Coneixement: The Human Genome Diversity Group, Institut de Biologia Evolutiva - 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

See the original post here:
December 8th - Susie Maidment - Cosmic Genome Science Advent Calendar - Video

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

By: dh jeong

Continue reading here:
Tsunamaru - Daidai Genome [Insane] + DT - Video

PUBLIC RELEASE DATE:

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."

Read more from the original source:
Using genome sequencing to track MRSA in under-resourced hospitals

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.

Story Source:

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

Read more:
Genome sequencing traces MRSA spread in high transmission setting