Genomics

Bacterial genome (7)
Genetic analysis (11)
Genetic material (83)
Genome (761)
Genome sequence (27)
Genomics (84)
Human genome (68)
Proteomics (6)

Synopsis: Biotech: Genetics: Genomics:

When the scientists corrected a loss-of-function PKC mutation in the genome of a colon cancer cell line

"highly sensitive whole-genome sequencing of single neurons and a new technology that identifies inserted bits of DNA caused by retrotransposons,

"says Christopher Walsh, MD, Phd, chief of Genetics and Genomics at Boston Children's and co-senior author on the paper."

which developed methods to sequence the genomes of single neurons, and represents the first time single neurons have been sequenced in their entirety.

#Genome wide expression changes in vascular tissue identified due to infection/diet Source: Boston University Medical Centeralthough it has been shown that a diet high in fat

These findings which currently appear inbmc Genomics suggest that future therapies for this disease may need to be individualized.

In this study the researchers used four experimental groups to compare genome-wide expression changes in vascular tissue.

In collaboration with the Clinical and Translational Science Institute (CTSI) at Boston University the researchers performed genome-wide microarray profiling

It examines the entire genome rather than known specific gene point mutations. Robust mutation panels vastly improve monitoring

Since the entire genome was surveyed, the researchers were able to identify a non-coding region of the genome as a"hotspot,

"which may be generating previously unrecognized chromosomal control elements in prostate cancer. The other 19"hotspots"were involved rich in genes in replication

the first such finding regarding this gene in a mammalian species. Myc is found in the genomes of all animals,

Genome-wide patterns of gene expression showed that Myc heterozygotes had significant differences in pathways related to metabolism and the immune system.

The agreement will integrate genomics research conducted at Columbia with Biogen idec understanding of disease mechanisms and pathways,

founding director of Columbia University Institute for Genomic Medicine. his collaboration marries the exceptional drug development expertise of Biogen with cutting-edge genomics expertise at Columbia University Medical center.

and Columbia to investigate the genomes of patients showing unusual treatment responses or unique disease presentations and to explore the connections among genes, pathways,

and complete whole-genome sequencing projects rapidly. It will allow for rapid population-scale DNA sequencing across a broad range of disease areas, focusing on diseases with significant unmet clinical need such as amyotrophic lateral sclerosis (ALS) and idiopathic pulmonary fibrosis.

which could help explain how non-genetic material is inherited. Non-genetic material is material that is not part of the chromosomes, the chains in the cell nucleus

which contain the genes. Genes are the sequence of nucleic acids which provide the assembly instructions for a living organism,

with the first completion of the sequencing of the genome for one species of the bacterium, Streptomyces coelicolor.

unravelling the secrets of the genome revealed a new mystery. It was known that the bacterium produced four different antibiotics

but the genome sequence revealed the potential for around 20. The known antibiotics represented only 20%of the possible total.

'hitherto lying undetected within the genome.''We could see the genes were there, but there was no product,

'Meanwhile, the genomes of other streptomycete species had been sequenced and all had shown the same pattern, with between 12 and 15'cryptic pathways'.'

and the Marburg virus The device identifies individual viruses based on size variations resulting from distinct genome lengths and other factors.

Taylor and coauthor Jeremy Bruenn professor of biological sciences research viral##fossil genes##â##chunks of genetic material that animals and other organisms acquire from viruses during infection.

One fossil gene called VP35 appeared in the same spot in the genomes of four different rodent species:

##These rodents have billions of base pairs in their genomes so the odds of a viral gene inserting itself at the same position in different species at different times are very small##Taylor says.##

##The genetic material in the VP35 fossil was more closely related to Ebola than to Marburg indicating that the lines leading to these viruses had begun already diverging from each other in the Miocene.

Topping the list was p53 a protein often called the##guardian of the genome ##because it causes damaged out of control cells to commit suicide

They also found a close relative of ptena in the amoeba which they called lpten that performs the same functions of ptena but to a lesser degreeâ a possible bench player in the amoeba s genome.

The repulsive forces formed by the layered strands of genetic material exert a large amount of pressure on the capsid

or months says Mark Pallen professor of microbial genomics at University of Warwick Medical school. Plus relying on laboratory culture means using techniques that date back to the 1880s.

while also giving us key insights into their genome sequences and the lineages that they belong to.

Last year they used metagenomics to obtain an outbreak strain genome from stool samples from an E coli outbreak

and to recover TB genomes from Hungarian mummies approximately 200 years-old. Earlier this year they recovered the genome of Brucella melitensis

which causes an infection called brucellosis in livestock and humans from a 700-year-old skeleton from Sardinia Italy.

Collaborators at the Genome Institute at Washington University School of medicine used DNA sequencing to tally the bacterial populations in 922 stool samples from 58 premature infants.

Ismagilov and his colleagues obtained enough genetic material to sequence a high-quality draft genome of the organism.

By conducting a genome-wide study of these particular retrievers with a naturally occurring cleft palate,

The team set out to identify the hereditary mutations that account for the other 60 percent by sequencing part of the genome of 184 patients with hereditary melanoma caused by unknown mutations.

and is a prime example of how genomics can transform public health, says Julia Newton Bishop,

and the fact that now all of its genome has been sequenced. The Ruth L. Kirschstein National Research Service Award and the National institutes of health National Institute of General Medical supported the work e

They documented for the first time the presence of genetic material for the bluetongue virus in female midges that were collected during two consecutive winter seasons.

A second component a single short strand of genetic material (DNA) then binds to the Neutravidin creating a small molecular complex. he system is still in its infancy.

What Smolke s team has done now is to carefully reprogram the yeast genome the master instruction set that tells every organism how to live to behave like a poppy

Since she wanted to produce several different opioids her team hacked the yeast genome in slightly different ways to produce each of the slightly different opioid formulations such as oxycodone or hydrocodone.

Published in the journal Science the findings will help scientists understand how plant genomes evolve in the context of domestication.

Broccoli cauliflower Brussels sprouts Chinese cabbage turnip collared greens mustard canola oil all these are different incarnations of the same plant genus Brassica. hole-genome sequencing efforts like this one allow us to address two fundamental

questionssays Eric Lyons assistant professor in the School of Plant Sciences at University of Arizona. ow does stored the genetic information in the genome help us understand the functions of the organism

and what does the structure of the genome tell us about the evolution of genomes in general?

(or Brassica napus) genome contains a large number of genes more than 100000 due to the fact that it arose from a merger between two parent species Brassica rapa (Chinese cabbage)

and others. he rapeseed genome has a very interesting historysays Haibao Tang a senior scientist of bioinformatics. s a result of the merger event it ended up with four copies of each gene.

The genome defines what Brassicas are.?It also defines what kids hate to eatlyons says. he bitterness in some cultivars such as broccoli

and we find that precisely those genes that code for those compounds were lost from the rapeseed genome. he sequencing effort provides scientists

and nuclear genomes of these parasitic ants and their host in an effort to confirm speciation

They also combined 33 new transcriptomes a set of RNA molecules with 13 genomes both

of which hold genetic material for organisms. The researchers identified 2696 genes by breaking down the DNA down and piecing it back together Kawahara says.

#Rice genome could answer the 9 billion-people question Researchers have sequenced the complete genome of African rice a hardy crop that could help feed the world s growing population. ice feeds

Now with the completely sequenced African rice genome scientists and agriculturalists can search for ways to cross Asian

The African rice genome is especially important because many of the genes code for traits that make African rice resistant to environmental stress such as long periods of drought high salinity in the soils

and flooding. ow that we have a precise knowledge of the genome we can identify these traits more easily

what geneticists call physical maps a tool that enables scientists to understand the structure of the genome.

and donated it to the Rice Genome Project making sequencing of that complete genome possible.

Much of the evolutionary analysis of the genome was performed by plant sciences doctoral candidate Muhua Wang and by Carlos Machado of the University of Maryland.

Yeisoo Yu a research associate professor in Wing s research group at the Arizona Genomics Institute led the sequencing effort.

In analyzing the 33000 genes that make up the African rice genome the researchers discovered that during the process of domestication Africans

Additionally the sequenced genome helps resolve questions about whether African rice originally was domesticated in one region or in several locations across Africa.

By comparing the genome with what is known about the genetic structure of wild varieties Wing

From 1998 to 2005 Wing led the US effort to help sequence the genome of Asian rice which is the only other domesticated rice species. Those results were published in the journal Nature in 2005

and analyzing the genomes of the wild relatives of African and Asian rice. y understanding the entire genus at a genome level we have a whole new pool of genetic variation that can be used to combat pests

and plant pathogenswing says. One example would be adding disease resistance genes from all of the wild rice varieties to a species of cultivated rice creating a new super-crop that is resistant to diseases and pests.

Whereas biological motors are made of protein researchers are trying to create synthetic motors based on DNA the genetic materials in cells that consist of a sequence of four chemical bases:

but now we have data on almost all the RNA molecules in a cell more than 10000 different RNASASSMANN says. e are the first to determine on a genome-wide basis the structures of the RNA molecules in a plant

because it is the first plant species to have its full genome sequenced and has the greatest number of genetic tools available.

or a few RNAS you can t get a pattern. ow that we have genome-wide information for a particular organism we can start to abstract patterns of how RNA structure influences gene expression and ultimately plant function.

he complex Rddm machinery is composed of several proteins that guide the genome in response to growth developmental and stress signals.

Studies of a fungus called Cryptococcus show the process of sexual reproduction can result in extra bundles of genetic material

because if there are two identical genomes coming together the end product should be the same as if the fungi had cloned just itself through asexual reproductionsays Heitman. e were trying to get a sense of is it just spinning its wheels

Plant senescence is estimated to involve 10 percent of genes in the genome. Plants use an expedited hypersensitive process to thwart pathogens by sacrificing infected cells to protect the surrounding healthy tissues.

or#fancy#poultry breeders to identify at fine resolution the exact location of the mutation in the genome in blue egg laying chickens.

This makes it possible for genetic material from a retrovirus to become permanently incorporated into the DNA of an infected cell.

and diversity of species. It s quite remarkable#retroviruses are considered generally to integrate at random locations in the genome

Because the genomes of horses and donkeys differ by approximately one in every 200 base pairs (differences called single nucleotide polymorphisms

The Cornell Center for Vertebrate Genomics Zweig Memorial Fund and Morris Animal Foundation funded the research h

It seems to be a key gene in the barley genome, he says. Hickey has declined to patent the DNA marker preferring the information to be freely available to other researchers.

Evolution occurs when an individual experiences a spontaneous beneficial mutation in its genome that improves its ability to adapt to its environment.

for Integrative Genomics. Lang is first author on the paper which appears in the journal Nature.

Less than a tenth of 1%of the genome is actually going to be affected. It is not part of

Mitochondria carry their own genomes, but some of the cellular components needed for respiration are produced partly by the nucleus,

and the two genomes communicate well, aging is kept at bay. But another molecule called NAD+keeps SIRT1 on the job;

#Secret code discovered in human DNA Genomes use the genetic code to write two separate languages. A secret second code hiding within DNA

However, the revelation made by the research team led by John Stamatoyannopoulos of the University of Washington indicates that genomes use the genetic code to write two separate languages.##

##Now we know that this basic assumption about reading the human genome missed half of the picture.##

And it s those duons that are expected to change the way physicians interpret human genomes and give clues for the treatments of diseases.##

Scientists have predicted the end of chemotherapy after launching a landmark project to map 100,000 genomes to find the genes responsible for cancer and rare diseases.

Britain is the first country in the world to embark on a program to map the genomes of thousands of people in the hope of finding

Prof Farrer also predicted that genome sequencing to find the causes of the disease will become standard within our lifetime.

The first human genome was sequenced in 2003 following 13 years of work at a cost of 2 billion.

A genome consists of a person s 20,000 or so genes and the DNA in between.

Each genome consists of a code of 3 billion letters. Over the next four years, about 75,000 patients with cancer and rare diseases, plus their close relatives, will have their whole genetic codes,

or genomes, sequenced. Cancer patients will have the DNA of both healthy and tumour cells mapped,

A 78 million partnership between Genomics England, the body set up by the Department of health to oversee the project,

whose genome contains man-made DNA building blocks opens the door for tailor-made organisms that could be used to produce new drugs and other products.

RNA is a genetic material similar to DNA, except it has a different chemical backbone and replaces the base thymine with uracil (U). Living things translate DNA into proteins through a series of steps.

Now that the scientists have demonstrated an organism can incorporate artificial DNA letters into its genome, the next step will be showing it can convert the DNA into new proteins,

"The research paves the way for"designer"organisms with custom-made genomes that are capable of performing useful tasks, like making drugs.

which have man-made DNA sequences in their genomes. The researchers are now working on expanding the DNA alphabet of yeast cells,

which yields a quantitative measurement of the activity of every gene in the human genome simultaneously about 20000 genes in total.

#Synthetic yeast chromosome paves the way for designer genomes A chunk of the genetic blueprint for yeast has been created

and some of these former students were co-authors on the study Unraveling the Human genome: 6 Molecular Milestones Boeke's team made more than 500 tweaks to the native genome removing repeated sections

and so-called junk DNA (not known to encode proteins the molecules that perform vital tasks inside cells) including so-called jumping genes

The research will lead to a better understanding of the rules of genome structure and behavior in yeast one of the most important model systems for understanding biological processes they added.

Ultimately the researchers plan to synthesize a complete yeast genome with all 16 chromosomes. Boeke's team plans to synthesize larger chromosomes

Despite its utility the work poses questions about the ethics of creating man-made genomes especially in more complex organisms such as animals.

Synthesizing plant and animal genomes is a long way off Boeke said but the day will come.

#The genomics of the sniffles: Nature News Genome sequences of the cold virus could reveal new secrets behind its prowess.

Heidi Ledford Rhinvirus capsid A human rhinovirus capsidj-Y Sgro/UW Madison Bang in the middle of sniffle season, researchers have released the full genome sequences of more than 100 strains of the viruses

responsible for most common colds. The viruses all belong to the rhinovirus family, and have RNA genomes. Their sequences, published this week in Science1,

could be used to design new therapies against colds or to determine, for example, why one strain can cause more severe symptoms than another."

"says Stephen Liggett, director of cardiopulmonary genomics at the University of Maryland Medical center in Baltimore,

"Sniffle-omics All this havoc is caused by a tiny virus only about 30 nanometres in diameter, with a genome that is a mere 7,

000 bases long a minute speck compared with the human genome, which has more than three billion bases.

Although the genomes of a few strains of cold virus had been sequenced, no one had compiled the full sequences of the 99 strains frequently studied by researchers.

Rhinovirus genome tree The human rhinovirus genome tree (click for larger image. Science Liggett, Palmenberg and their colleagues decided to fill this gap by sequencing the reference-library strains,

and the previously reported HRV-C genomes with one another to look for patterns and evolutionary relationships (see human rhinovirus genome tree, right).

The results suggest that three of the strains may comprise a further new rhinovirus species. The sequences also indicate that

the viruses may exchange portions of their genomes a phenomenon that, until now, had not been described in rhinoviruses.

In addition, all of the strains have extremely variable RNA sequences in one specific region of the genome.

Palmenberg also believes that the genome is structured to allow ribosomes the molecular machines that read RNA and produce a protein,

to rapidly skip over regions of the genome that do not code for proteins. The mechanism may make the viruses more competitive by allowing them to synthesize their proteins more quickly,

variable viral genome sequences may not prove to be the primary determinant of virulence.""Ultimately, the immune status of the patient may have a greater impact,

#Neanderthal genome to be unveiled: Nature News The entire genome of a 38,000-year-old Neanderthal has been sequenced by a team of scientists in Germany.

The group is already extracting DNA from other ancient Neanderthal bones and hopes that the genomes will allow an unprecedented comparison between modern humans and their closest evolutionary relative.

The three-year project, which cost about#5 million (US$6. 4 million), was carried out at the Max Planck Institute for Evolutionary Anthropology in Leipzig.

computational biologist Richard Green, is coordinating the analysis of the genome's 3 billion base pairs.

Comparisons with the human genome may uncover evidence of interbreeding between Neanderthals and humans, the genomes

The genome may also deliver more details about how these species developed their different physical traits,

"says Edward Rubin, director of the US Joint Genome Institute in Walnut creek, California, which is also sequencing Neanderthal DNA

Almost all of the Neanderthal genome to be unveiled in Chicago comes from DNA extracted from a single bone originally discovered in a cave near Vindija in Croatia.

and so is well on the way to creating a library of Neanderthal genomes that would allow stronger comparisons with modern humans.

Pääbo says that his group will publish a first draft of the entire Neanderthal genome later this year,

However, some published human genomes had all their base pairs read eight to ten times before publication.

The team says that its single-read of the Neanderthal genome is sufficient for publication

from sequencing its genome to crossbreeding coffee plants with resistant strains. Caused by the fungus Hemileia vastatrix,

And in the United kingdom, Harry Evans is working on the genome of H.#vastatrix at CABI in Egham.

Genetic analysis revealed that some microbes in the upper atmosphere are thought related to bacteria to catalyse ice-crystal formation and cloud condensation2.

April 2009 Paper reports successful derivation of human ips cells without the integration of genetic information into the cell genome.

#Genomes link Aboriginal australians to Indians Some Aboriginal australians can trace as much as 11%of their genomes to migrants who reached the island around 4, 000 years ago from India,

This scenario is the result of a large genetic analysis outlined today in the Proceedings of the National Academy of Sciences1.

Irina Pugach, a postdoctoral researcher in Stoneking s laboratory, discovered signs of the Indian migration by comparing genetic variation across the entire genomes of 344 individuals, including Aboriginal australians from the Northern territory, highlanders

Pugach confirmed an ancient association between the genomes of Australians New Guineans and the Mamanwa#a Negrito group from the Philippines.

because it is absent from New Guinean and Mamanwa genomes, and it is too uniformly spread across the northern Aboriginal genomes to have come from European colonists.

The genetic mingling coincided with the arrival in Australia of microliths#small stone tools that formed the tips of weapons

and not anything like the dense, genome-wide study we carried out. A few smaller studies of MITOCHONDRIAL DNA and the Y chromosome have hinted at recent gene flow between India and Australia2, 3,

but a genome-wide study in 2010 missed it by not including any Indian populations4,

and a project that sequenced a full Aboriginal genome dismissed signs of gene flow from India as a spurious result5.

and a co-author of the earlier genome-wide study, welcomes the latest research, but warns that the finding is"definitely not representative of Australia,

Aled Edwards leads the Structural genomics Consortium at the University of Toronto, Canada, in which some drug companies contribute both chemical analysis and screening support,

The synthetic shell contains no genetic material and so it cannot infect the animals. But it will spur the immune system to produce antibodies that would protect them from the real virus. In 2001,

It costs less than US$1, 500 per person to have the important parts of his clients genomes sequenced.

which will be touting for customers at a meeting of the American College of Medical Genetics and Genomics in Phoenix, Arizona, on 19-23 march.

which provides genetic analysis software on its cloud-based platform and allows users to upload and run their own algorithms.

Seven Bridges Genomics, based in Cambridge, Massachusetts, aims to be accessible to people with no expertise in bioinformatics,

Ingenuity Systems in Redwood City, California, allows users to upload a list of mutations in a person s genome,

and is optimized to run genome-analysis software. Knome of Cambridge Massachusetts, announced last year that it plans to sell $125, 000 genome-analysis machines for use in customers labs (see Nature 490,157;

2012). ) It seems unlikely that any single analysis company will rule the market; the range of customers who need to interpret sequence data is growing,

and assembled the complete genome of the new virus. The virus was found in every one of the eight horses,

especially in the context of precision medicine and whole-genome sequencing.""Industry and academia often do things together,

While some recent AD genome-wide association studies (GWAS), which search the entire human genome for small variations,

have suggested that MAPT is associated with increased risk for AD, other studies have found no association.

#In 2001 Chun was the first to report that the brain contains many distinct genomes within its cells#much like the colorful tiles in an artist#s mosaic.#

while others hunt for the virus own genetic material. Some assays can measure the presence or absence of longer-lasting antibodies that can linger for decades after an infection.

Traditional methods for mapping HIV genetic material use long strings of these nucleotides, called oligomers, to find and bind to complementary strands of DNA or RNA in sample tissues.

allowing researchers to create an image of precisely where the viral genetic material is dispersed throughout the tissue sample.

#Bacteria become genomic tape recorders MIT engineers have transformed the genome of the bacterium E coli into a long-term storage device for memory.

The new strategy described in the Nov 13 issue of the journal Science overcomes several limitations of existing methods for storing memory in bacterial genomes says Lu the paper s senior author.

After the DNA is produced the recombinase inserts the DNA into the cell s genome at a preprogrammed site.

We can target it anywhere in the genome which is why we re viewing it as a tape recorder

If the DNA is inserted into a nonfunctional part of the genome sequencing the genome will reveal

Instead the vast majority of this genetic material is found within the trillions of microorganisms that call our bodies home.

Immunologists geneticists and genomics researchers drive Progress to this wealth of information clinicians contribute patient-based insights and gain potential targets for therapeutics.

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