000 group A streptococcus genomes collected over decades. Researchers from Houston Methodist Research Institute, Houston Methodist Hospital, institutions in Finland and Iceland,
scientists are able to sequence the entire genome of the bacteria, just as is done in humans.
and its relatively small genome, which allows the genome of thousands of strains to be sequenced completely relatively rapidly.
The researchers'original hypothesis, which turned out to be correct, was that changes in the genetic make-up of the GAS pathogen had underpinned new epidemics.
the collaborating international team sequenced the genome of thousands of disease-causing strains, precisely defining every base pair mutation in the strains."
and Joseph Wu, MD, Phd, professor of cardiovascular medicine and of radiology, teamed up with a group of genome-sequencing specialists to develop the new technique:
Wilson and Wu said that the gold standard of genome sequencing involves thousands of genes, costs $1,
it makes no sense to sequence the entire 22,000-gene genome, since fewer than 200 genes are known to affect the heart,
Moreover, whole-genome sequencing typically contains mistakes, so key mutations might be missed. To meet this challenge
This approach--surveying a small subgroup of relevant genes instead of the whole genome--is used already to test for other diseases, such as cystic fibrosis.
or clpps, were developed at the Stanford Genome Technology Center. These simple probes accurately target specific parts of the genome
and can be made in large batches at low cost. Because of their simplicity, they are customized easily to target different genes.
The heart disease clpp assay was cheaper, faster and more accurate than whole-genome assays. The Stanford team next plans to test the technique on a group of 200-300 patients.
"Wilson and Wu said the genome technology group has been working on the clpp technique for a long time.""Our goal is to make genetic testing more accessible to more people,
and hepatitis C. What they have in common is that the genome does not consist of DNA, but RNA.
That mechanism is a gene variant--an allele--found in a part of the genome that controls inflammation.
sequenced the genomes of more than 100 members of a Colombian family affected with early-onset Alzheimer's.
or added to the genome. When there are too many or too few copies of a given gene or genes, due to CNVS,
One powerful single-cell analytic technique for exploring CNV is whole genome sequencing. The challenge is that,
web-based program automatically processes sequence data, maps the sequences to a reference genome, and creates CNV profiles for every cell that can then be viewed with a user friendly graphical interface.
For the vast majority of cells in this genome-wide screen, Chelsea Marie was correct; E. histolytica decimated many thousands of these independent cell cultures.
#Genome mining effort discovers 19 new natural products in four years It took two postdoctoral researchers, a lab technician,
"Postdoctoral researcher Kou-San Ju used a technique called"genome mining"to search the genomes of 10,000 strains of actinomycete bacteria for pepm,
"Genome mining has previously been used, but only with a few organisms at a time,"Ju said.""We wanted to know
The researchers then sequenced the full genomes of all 278 strains that had the gene.
The researchers describe the new findings as a proof of concept that genome mining can be used on a scale that will speed the process of drug discovery,
"Our study shows that genome mining is not only a viable route to new natural products, but that there are a tremendous number of new compounds awaiting discovery from the genomes of microbial strains,
"Ju said d
#New drug-like compounds may improve odds of men battling prostate cancer, researchers find Researchers at Southern Methodist University,
#Whole genome-sequencing uncovers new genetic cause for osteoporosis Using extensive genetic data compiled by the UK10K project,
that sophisticated analysis of the genome would reveal those genes associated with disease. The promise for the contribution genetics can make to human health lies in the discovery of novel compounds that can counter the effect of deleterious genetic variants influencing these genes s
and VIRAL DNA residing in the host genome. This characteristic property, known as proviral silencing, however, has not been understood fully.
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"artificial chromosome"separate from the yeast cell's own genome.
During this process the researchers can easily swap genes in and out of the phage genome."
"Once we had that method, it allowed us very easily to identify the genes that code for the tails
#Scientists discover new system for human genome editing A team including the scientist who first harnessed the revolutionary 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. In a study published in Cell, Feng Zhang and his colleagues at the Broad Institute of MIT and Harvard and the Mcgovern Institute for Brain Research at MIT,
and demonstrate that it can be engineered to edit the genomes of human cells.""This 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.
This could be an advantage in targeting some genomes, such as in the malaria parasite as well as in humans."
The Zhang lab also offers free online tools and resources for researchers through its website, http://www. genome-engineering. org.
with other enzymes that may be repurposed for further genome editing advances
#Cabozantinib improves survival in patients with advanced kidney cancer: Results from the METEOR trial Patients with advanced kidney cancer live for nearly twice as long without their disease progressing
researchers have discovered several ways of using genome sequencing of tumours to predict whether an individual cancer patient will benefit from a specific type of medicine.
whole-genome sequencing in six subjects, sequencing of all protein-coding regions (exomes) in 66 subjects,
and comparing variation in the number of copies of all genes across the genome in 80 subjects."
and/or deletions in ARID1A occurred in over 40 percent of the SS genome studied.
though sequences of its genome have been identified in various locations, such as the Arctic ocean, the Baltic sea, Canada, China, Germany, Hungary, Spain, Taiwan and the USA.
#Genome-edited plants, without DNA The public and scientists are at odds over the safety of genetically modified (GM) food.
Scientists at the IBS Center for Genome Engineering in South korea have created a way to genetically modify plants using CRISPR-Cas9 without the addition of DNA.
the resulting genome-edited plants could likely be exempt from current GMO regulations and given a warmer reception by the public.
IBS Director of the Center for Genome Engineering Jin-Soo Kim explains that"the targeted sites contained germline-transmissible small insertions
CRISPR is used now widely for genome editing. What's crucial in genetic engineering is for the gene editing tool to be accurate and precise,
They grew full plants from the seeds of these genome edited and regenerated plants, which had the mutation from the previous generation.
which Jin-Soo Kim points out,"paves the way for the widespread use of RNA-guided genome editing in plant biotechnology and agriculture."
"The IBS team's technique of genome editing without inserting DNA could be revolutionary for the future of the seed industry.
Researchers led by Sven Rottenberg of the Cancer Research Centre in Amsterdam also identified LRRC8D as a relevant gene in a genome-wide screen for cellular cytostatic resistance.
director of the U s. Department of energy Joint Genome Institute. hen we got microscopes, and got microbes.
and sent it to the Joint Genome Institute for sequencing. What they got back was a mess.
Brown said. hen you figure out which of these larger pieces are part of a single genome.
is called genome binning. To execute it, the researchers relied on another set of algorithms, customized for the task by Itai Sharon,
They also assembled some of the genomes manually, making decisions about what goes where based on the fact that some characteristics are consistent for a given genome.
For example, the percentage of Gs and Cs will be similar on any part of an organism DNA.
and 789 draft genomes that were roughly 90 percent complete. Some of the organisms had been glimpsed before;
By reconstructing complete or nearly complete genomes, Brown and his collaborators were able to locate 16s rrna genes
All the organisms they found have very short genomes about one million base pairs (compare that to E coli,
and genome binning make Brown and Banfield optimistic, though, that it won be long before wee mapped them all. think that much of the tree of life will come into view in the next few years,
and Evangelos Pazarentzos, Phd, a postdoctoral fellow, the research group analyzed cells from this tumor using next-generation genome sequencing in an effort to understand how the cells sidestepped erlotinib treatment.
and enhancersieces of the genome that control gene activityy chemically manipulating proteins that package DNA.
and guiding stem cell differentiation. he epigenome is associated everything with the genome other than the actual genetic sequence,
explained Gersbach. ut there also many other pieces of the genome called enhancers that aren next to any genes at all,
Reddy thought perhaps he could chemically alter the histones at the enhancers to turn them on. here are already drugs that will affect enhancers across the whole genome,
#Electrolyte Genome Could Be Battery Game-Changer A new breakthrough batteryne that has significantly higher energy,
But Lawrence Berkeley National Laboratory (Berkeley Lab) scientist Kristin Persson says she can take some of the guesswork out of the discovery process with her Electrolyte Genome.
and the Electrolyte Genome would return a short list of promising candidate molecules, dramatically speeding up the discovery timeline. lectrolytes are a stumbling block for many battery technologies,
Persson Electrolyte Genome, launched more than two years ago, uses high-throughput computer screening to calculate the properties
the Electrolyte Genome offers two other significant advantages to battery scientists. The first is that it could generate novel ideas. hile there are some amazing organic chemists out there,
The second advantage of the Electrolyte Genome is that it can add to scientistsfundamental understanding of chemical interactions. t adds explanations to why certain things work
How it works funnel method The Electrolyte Genome uses the infrastructure of the Materials Project, a database of calculated properties of thousands of known materials,
Early success stories The Electrolyte Genome first major scientific findinghat magnesium electrolytes are very prone to forming ion pairs,
#USDA Scientists, International Colleagues Sequence Upland cotton Genome U s. Department of agriculture (USDA) scientists and their partners have sequenced the genome of the world most widely cultivated and genetically complex species of cotton,
Sequencing the genome of Upland cotton (Gossypium hirsutum) will help breeders develop varieties of cotton that are equipped better to combat the pests,
The two teams sequenced the genome of the genetic standard of Upland cotton, Texas Marker-1,
#Researchers discover cancer markers may be visible early during human development Researchers at the Virginia Bioinformatics Institute have uncovered a link between the genomes of cells originating in the neural crest
Long considered unk DNAOR ark matterwithin the genome because their function was unclear microsatellites are known for their role in certain diseases such as Fragile X and Huntington disease.
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,
It a future in which diseases like muscular dystrophy, cystic fibrosis and many others are treated permanently through the science of genome engineering.
Hubbard research, published in the journal Nature Methods, demonstrates a new technology advancing the field of genome engineering.
In theory, genome engineering will eventually allow us to permanently cure genetic diseases by editing the specific faulty genes. evolutionizing health caregenome engineering involves the targeted, specific modification of an organism genetic information.
we can produce gene editing tools that are 100 times more specific for their target sequence. uture applicationsmuch of the current research in genome engineering is focused on treating monogenic diseasesiseases that involve a single geneecause theye much easier for researchers
He hopes his current work will play a role in helping genome engineering reach its full potential
#Researchers genetically engineer yeast to produce opioids After a decade work a team led by Stanford bioengineer Christina Smolke succeeded in finding more than 20 genes from five different organisms and engineering them into the genome of baker yeast.
and rossover where a new genome is formed by merging genes from two individuals. In order for the mother to determine which children were the fittest,
This includes the sequencing of their entire genome. Also, skin cell samples are cultured and made available to lab-based researchers for functional assays.
and precision of DNA 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
#Molecular diagnostics at home: Chemists design rapid, simple, inexpensive tests using DNA Chemists at the University of Montreal used DNA molecules to developed rapid,
Detailed in a paper published in Genome Medicine on September 28th this technology could prove highly useful in settings where lab equipment
such as a patient genome. In turn, it could model how a specific treatment would interact with the patient. heyl be the Microsofts and Googles of biomedicine,
Results published online in September in the journal Genome Research demonstrate that in patient samples the new test called Virocap can detect viruses not found by standard testing based on genome sequencing.
Developed in collaboration with the university Mcdonnell Genome Institute, the test sequences and detects viruses in patient samples
In the first, standard testing that relied on genome sequencing had detected viruses in 10 of 14 patients.
In recent years, researchers have discovered several ways of using genome sequencing of tumours to predict
#Transplanting from Pig to Human Never before have scientists been able to make scores of simultaneous genetic edits to an organism genome.
Wyss Institute at Harvard Universitythe 62 edits were executed by the team to inactivate native retroviruses found in the pig genome that have inhibited so far pig organs from being suitable for transplant in human patients.
latent retrovirus fragments in their genomes, present in all their living cells, that are harmless to their native hosts
and understand repetitive regions in the genome, where an estimated more than two-thirds of our own human genome resides d
or de novo genome assembly. 7 petabytes of Lustre-based high-performance storage from Aeon, and 6 petabytes of durable storage for data reliability.
drug discovery Mini-kidney organoids have now been grown in a laboratory by using genome editing to re-create human kidney disease in petri dishes.
they inactivated the cutting function of Cas9 and attached proteins that control the packaging of the genome.
By unraveling or tightly bundling these regions of the genome, they could effectively turn them on and off.
These experiments show exceptional specificity, demonstrating that the technology is capable of targeting single sequences of the genome.
The power to control the genome switches would be especially important for studying and potentially treating human diseases such as cancer,
which can be driven by mutations in control regions of the genome. The hope is that overriding one of these switches could uncover
if youe focusing on one concentrated area in the genome. But looking at how turning off one enhancer switch affects the activity
and structure of the whole genome requires more specialized techniques. Gersbach turned to Reddy and colleague Gregory Crawford
Crawford, associate professor of pediatrics, has spent more than a decade developing techniques to identify control regions across the genome
change the activity of many switches across the genome simultaneously, creating thousands of off-target effects,
it provides a blueprint for researchers to assess these effects. y integrating genomics and genome engineering,
and shows genome changes that indicate domestication by humans. The new research is published in Nature Genetics.
and difficult to get them to function correctly. ou try to put all your genes into one parcel so they go to one place in the genome,
Genome pioneer Craig Venter led a team that manufactured a genome for a germ that causes pneumonia in cows,
Retrieving small genomes from a mix of organisms Scientists from the IZW led by Alex Greenwood publish in PLOS ONE a simple way to retrieve small genomes from a mix of various organisms.
how to retrieve the genome of a specific pathogen from a mixture of DNAS in a patient and its microbial cohabitants?
Analysis of the sequences and comparison with reference data demonstrated that the complete mitochondrial genome of the rodents had been retrieved from the DNA pool.
In fact entire mitochondrial genomes and almost the entire genome sequence of a bacterium were obtained when specifically tested for the efficiency of the bycatch principle.
We can use short preserved gene sequences to yield the genome (or at least large sections of it) from pathogenic variants of influenza viruses for example or from completely new pathogens explains Greenwood.
From the intestinal bacterium Escherichia coli contained in a human urine sample the scientists retrieved 90 per cent of the genome in one go.
and have been published in the journal Genome Research. When people talk about stress they generally refer to feeling the strains of too high burdens at work or in their private life.
They are only able to reproduce inside the host's cells they have known the smallest genome of all organisms with a cell nucleus (eukaryotes) and they posses no mitochondria of their own (the cell's power plant.
Due to their phenomenal high molecular evolution rate genome analysis has so far been rather unsuccessful:
The analysis of the entire genome had several surprises in store for them: The genome resembles more that of a fungi than a microsporidium
and in addition also has a mitochondrial genome. The new species now named Mitosporidium daphniae thus represents the missing link between fungi and microsporidia.
With the help of scientists in Sweden and the U s. the Basel researchers rewrote the evolutionary history of microsporidia.
but that its genome is rather atypical for a microsporidium. It resembles much more the genome of their fungal ancestors.
Genome modificationsthe scientists thus conclude that the microsporidia adopted intracellular parasitism first and only later changed their genome significantly.
These genetic adaptations include the loss of mitochondria as well as extreme metabolic and genomic simplification. Our results are not only a milestone for the research on microsporidia
CRISPR is a technique that emerged a few years ago as a way to edit DNA anywhere within the genome.
The selected RNA serves as an adaptor that determines the target anywhere within the genome.
The Weissman team led experiments demonstrating that CRISPR molecules incorporating the Suntag can be used to precisely control gene expression of many genes within the genome.
The adaptation of the Suntag for CRISPR activation makes it possible to systematically probe the biological roles of all genes within the genome in a single experiment.
We can now sequence the entire genome of a cancer cell and what we're finding is that many cancers have mutations in the epigenetic machinery.
Work the microbiome was pioneered by Washington University scientists led by Jeffrey Gordon MD the Dr. Robert J. Glaser Distinguished University Professor and director of the Center for Genome Sciences and Systems Biology.
and director of the JP Sulzberger Columbia Genome Center, at Columbia's College of Physicians and Surgeons.
"Conventional techniques, like genome-wide association studies, must test all possible genetic mutations and variants in a disease cell, compared with a normal cell,
and mutational profile data of more than 250 patients collected by the Cancer Genome Atlas consortium.
Using a technique known as Chia-PET the researchers focused on how these proteins interact. y knowing which of the Cohesin/CTCF bound sites are coming together in physical proximity we started to go from a linear view of the genome to sets of looping interactions
but they were in similar locations as in the ESC genome. Of course the repression or enhancement role of the loops differed between ESCS and the more differentiated cells.
"We are living in a big data world thanks to the likes of the Human genome Project and post-genome technologies.
molecules that until recently were dismissed by scientists as nonfunctional noise in the genome. Now, lncrnas are thought to regulate normal cellular development
"Importantly, viral sequence information from the epidemic reveals rapid changes in the viral genome, while our target sequence remains the same.
and that mutations which could affect other parts of the genome are capable of occurring.
This work opens up the other non-coding half of the genome. Maggert explains that chromosomes are located in the nuclei of all human cells
Based on those initial reports researchers determined that only two percent of the genome (about 21000 genes) represented coding DNA.
Now thanks to Aldrich's and Maggert's investigation of heterochromatin the groundwork has been laid to study the rest of the genome.
unless biologists can look at the entire genome. We still can't--yet --but at least now we're a step closer.
and using nucleic acids bears a risk for accidental genome editing. These methods are also toxic,
#Who wins in the battle of genome sequencers? Desktop sequencers promise to democratize genomics, but it s difficult for researchers who aren t experts in sequencing technology to sort through the overheated marketing claims made in this fiercely competitive industry.
As next-generation genome sequencing heads into the clinic and public health, it ll be targeted at people who don t necessarily fully understand these issues.
The Personal Genome Machine vs Miseq videos played off the Mac vs PC ads. People are crying out for independent analysis,
and weaknesses and when it comes to genome sequencing, there s no one-size-fits-all solution,
genome by Davefayram via Flickr, sequencers from Nature New e
#Why (and how) retailers should embrace'showrooming'More evidence emerged this week suggesting the power of smartphones to reshape how retailers stock,
the FDA said it has authority to regulate software that interprets genomes, even if such services are given away free.
MIT Technology Review tested several interpretation-only sites using DNA data of anonymous donors posted publicly by the Personal Genome Project,
The information in the report is similar to that in 23andme banned ersonal Genome Service, but there are differences.
2035hat the genome will all make sense, and that the day you are allowed to see it,
Lennon says the site was modeled on Wikipedia. hat was the promise of the genome, that it should be for everybody,
If you can have a simpler mechanism that doesn't require anatomical changes that's pretty darn good says Daniel Voytas director of the Center for Genome Engineering at the University of Minnesota.
A sequencer this small might one day let police read off a genome from a spot of blood at a crime scene or permit doctors to pinpoint viruses in the midst of an epidemic.
There were a lot of smart people saying this is physically not possible to do says Jeffery Schloss head of the division of genome sciences at the National Human genome Research Institute in Bethesda Maryland.
Those bits then have to be puzzled back together to create a genome. Even with a supercomputer the puzzle often can't be solved there can be repeated too many sequences
Like having the edges of a puzzle long reads make it much easier to reassemble a genome especially of a species never studied before.
which was introduced early this year (see Does Illumina Have the First $1000 Genome?)to labs interested in sequencing hundreds of thousands of human genomes for medical research h
Overtext Web Module V3.0 Alpha
Copyright Semantic-Knowledge, 1994-2011