Genome

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Synopsis: Biotech: Genetics: Genomics: Genome:

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,

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

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.

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.

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

'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.

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.##

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.

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 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

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

#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.

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.

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.

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.

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

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.

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.##

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,

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.

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,

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

6 Molecular Milestones Boeke's team made more than 500 tweaks to the native genome removing repeated sections

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.

and have RNA genomes. Their sequences, published this week in Science1, could be used to design new therapies against colds

"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,

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,

#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,

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.

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,

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,

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

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,

#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.#

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

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

#Fast modeling of cancer mutations Sequencing the genomes of tumor cells has revealed thousands of genetic mutations linked with cancer.

Their approach based on the genome-editing technique known as CRISPR is much faster than existing strategies

Scientists have begun recently exploiting this system to make targeted mutations in the genomes of living animals either deleting genes

The CRISPR genome-editing system presented the perfect strategy to go after those genes. CRISPR originally discovered by biologists studying the bacterial immune system involves a set of proteins that bacteria use to defend themselves against bacteriophages (viruses that infect bacteria.

MIT biological engineers have demonstrated now that a new genome-editing technique called CRISPR can disrupt a single parasite gene with a success rate of up to 100 percent in a matter of weeks.

Even though we ve sequenced the entire genome of Plasmodium falciparum half of it still remains functionally uncharacterized.

This occurs very rarely in the genome of the malaria parasite. You have to rely on this really inefficient process that occurs

The general concept of using the CRISPR/Cas9 system to edit the genome of the malaria parasite is significant

#A new way to model cancer Sequencing the genomes of tumor cells has revealed thousands of mutations associated with cancer.

The Broad Institute grew from an MIT-based flagship center for the Human Genome Project

Broad scientists have invented also powerful new tools that allow researchers to precisely manipulate the genome and measure the millions of complex chemical interactions within cells.

They plan to pioneer cutting-edge techniques such as genome editing which allows them to precisely introduce any mutations they choose.

Pandora for example comes down to this thing that they call the music genome which contains a summary of your musical tastes.

To recommend a song all you need is the last 10 songs you listened to just to make sure you don t keep recommending the same one again and this music genome.

what songs they ll like than anything captured by Pandora s music genome. Openpds preserves all that potentially useful data but in a repository controlled by the end user not the application developer or service provider.

When the cell repairs the damage produced by Cas9 it copies from the template introducing new genetic material into the genome.

Scientists envision that this kind of genome editing could one day help treat diseases such as hemophilia Huntington s disease

or replicate its genome. If enough of these blockages form the cell undergoes a type of programmed cell suicide called apoptosis

and IBM's T. J. Watson Research center have developed a prototype DNA reader that could make whole genome profiling an everyday practice in medicine.

Such game-changing technology is needed to make genome sequencing a reality. The current hurdle is to do so for less than $1000 an amount for

In the case of warfarin#the most frequently prescribed anticoagulant#there are SNP differences in specific parts of the genome that indicate

and amplified from a patient's genome. The nanoprobes are initially pink due to surface plasmonic effects involving ripples of electric charge.

and the genome fragments separate. For cases of partial complementarity#in which the fragments are mismatched by a single nucleotide#the melting temperature is lowered by an amount depending on the level of mismatch.

or DNA sequence from one animal into the genome of another plays a critical role in a wide range of medical researchncluding cancer, Alzheimer's disease, and diabetes.

#The study is online in Genome Biology o

#Mega-Canyon Discovered Beneath Greenland Ice Sheet A previously unknown canyon has been discovered in Greenland hidden beneath the ice.

#How Mya Breitbart Is Mapping The Genomes Of Entire Ecosystems Each year Popular Science seeks out the brightest young scientists and engineers and names them the Brilliant Ten.

--The Editorsuniversity of South Floridamapping the genomes of an entire ecosystem at once. Viruses are the most abundant entities on the planet and among the most mysterious.

#How Feng Zhang Modified A Cell's Genome On the fly Each year Popular Science seeks out the brightest young scientists and engineers and names them the Brilliant Ten.

--The Editorsmassachusetts Institute of technology and Broad Institutemodifying a cell's genome on the flywhen Feng Zhang was in graduate school he discovered that the tools for splicing new genes into living cells were costly time-consuming and proprietary.

So what we can do is take that genome-editing tool and target anything we want.

Once these genome-editing techniques were mastered the researchers then had to figure out ways to deliver the modified CRISPRS to the bacteria.

the researchers first placed the 5clc lesion at a specific site within the genome of a bacterial virus. They then replicated the virus within the cell.

the researchers replicated the genome containing the lesion with a variety of different types of polymerase,

By tweaking the genomes of these viruses, known as bacteriophages, researchers hope to customize them to target any type of pathogenic bacteria.

Also, each family of bacteriophages can have a different genome organization and life cycle, making it difficult to engineer them

the researchers combed through databases of phage genomes looking for sequences that appear to code for the key tail fiber section, known as gp17.

Existing techniques for editing viral genomes are fairly laborious so the researchers came up with an efficient approach in

which they insert the phage genome into a yeast cell, where it exists as an rtificial chromosomeseparate from the yeast cell own genome.

During this process the researchers can easily swap genes in and out of the phage genome. nce we had that method,

it allowed us very easily to identify the genes that code for the tails and engineer them or swap them in and out from other phages,

and precision of genome engineering A team including the scientist who first harnessed the CRISPR-Cas9 system for mammalian genome editing has identified now a different CRISPR system with the potential for even simpler and more precise genome engineering.

and demonstrate that it can be engineered to edit the genomes of human cells. his has dramatic potential to advance genetic engineering,

The Cpf1 system represents a new generation of genome editing technology. CRISPR sequences were described first in 1987

The application of the CRISPR-Cas9 system for mammalian genome editing was reported first in 2013, by Zhang and separately by George Church at Harvard university.

This could be an advantage in targeting some genomes, such as in the malaria parasite as well as in humans. he unexpected properties of Cpf1 and more precise editing open the door to all sorts of applications,

with other enzymes that may be repurposed for further genome editing advances. e

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