who also is an investigator in the Center for the Genetics of Host Defense and holder of the George L. Macgregor Distinguished Chair in Biomedical science.
#A better way to read the genome UCONN researchers have sequenced the RNA of the most complicated gene known in nature,
They published their findings on Sept. 30 in Genome Biology. If your genome was a library
and each gene was a book, some genes would be straightforward reads -but some would be more like a"Choose Your Own Adventure"novel.
"Graveley will speak about the research at the Oxford Nanopore Minion Community Meeting at the New york Genome Center on Dec 3.
that can be gleaned by combing the genome of a large collection of leukemia tissue samples. By analyzing genetic material in chronic lymphocytic leukemia (CLL) and normal tissue from more than 500 patients,
researchers identified dozens of genetic abnormalities that may drive the disease, including two that had never before been linked to human cancer.
as its ever-churning genome spawns new groups and subgroups of tumor cells in a single patient.
reading the genetic code letter by letter in sections of DNA that hold the code for making proteins.
or byproducts,"says senior author Inder Verma, professor of genetics and holder of Salk's Irwin and Joan Jacobs Chair in Exemplary Life science."
The researchers narrowed in on the 4, 700 genes in the human genome related to cellular signaling--specifically,
A 10-year national project called the Cancer Genome Atlas mapped the genomes of hundreds of patients for over 20 different cancers
From the Cancer Genome Atlas data, the Salk team found that genetic alterations of Epha2 were detected in 54 out of 230 patients with adenocarcinoma.
In research that appeared today in Nature Genetics, a Weizmann Institute of Science team has revealed now one of the drivers of a particularly deadly subset of melanomas-one that is still seeing a rise in new cases.
which consists of more than 500 melanoma genomes and exomes-protein-building sequences-making it the largest melanoma dataset to date.
Indeed, the melanoma genome sequences contained mutations in known tumor suppressor genes, but there was also a new gene that stood out in the team's search, named RASA2.
#Gene on-off switch works like backpack strap A research team based in Houston's Texas Medical center has found that the proteins that turn genes on by forming loops in human chromosomes work like the sliding plastic adjusters on a grade-schooler
and allow researchers to reprogram cells by directly modifying the loops in genomes. The study,
is by the same team that published the first high-resolution 3-D maps showing how the human genome folds inside the nucleus of a cell.
Every human cell contains a genome, a linear string of DNA. Sequences of DNA bases spell out genes,
and coming into contact during genome folding. Last year, the team showed that it was possible to map the positions of these loops,
and the researchers created the first atlas of loops in the human genome. But the group couldn't explain how the loops were forming."
"said senior author Erez Lieberman Aiden, a geneticist and computer scientist with joint appointments at Baylor and Rice."
"The human genome contains more than 20,000 genes. In any given cell, only a fraction of these are active,
"Aiden, assistant professor of genetics at Baylor and of computer science and computational and applied mathematics at Rice, said Sanborn
and high-performance computation to predict how a genome will fold. The team confirmed their predictions by making tiny modifications in a cell's genome
and showing that the mutations changed the folding pattern exactly as expected. Rao likened the result to a new form of genome surgery:
a procedure that can modify how a genome is folded by design and with extraordinary precision.""We found that changing even one letter in the genetic code was enough to modify the folding of millions of other letters,
"said Rao, a graduate student in the Aiden lab and at Stanford university.""What was stunning was that once we understood how the loops were forming,
the results of these changes became extremely predictable.""Sanborn said the discovery also explains a puzzling pattern that the team noticed
and the genome is flexible at that scale, "said Sanborn.""If I were a protein,
The basic idea is that the tri-glide protein complex lands on the genome and pulls the strand from each side so that a loop forms in the middle--just like the loop someone might make
"Aiden said that one of the most astonishing implications of the new model is that loops on different chromosomes tend not to become entangled."
when two bits of the genome wiggled around and then met inside the cell nucleus, "Aiden said."
"But this process would lead to interweaving loops and highly entangled chromosomes. This is a big problem
if you need those chromosomes to separate again when the cell divides.""The tri-glide takes care of that,
genetics and disease diagnosis. But carrying out such analyses requires expensive lab equipment, making its application out of reach for many people who live in resource-limited places.
however, could make analysis of genetic material possible at a much lower cost. David Sinton and colleagues wanted to see
Professor Peter Waterhouse, a plant geneticist at QUT, discovered the gene in the ancient Australian native tobacco plant Nicotiana benthamiana, known as Pitjuri to indigenous Aboriginals tribes.
which for decades has been used by geneticists as a model plant upon which to test viruses and vaccines.
which for decades has been used by geneticists as a model plant upon which to test viruses and vaccines."
"By sequencing its genome and looking through historical records we have been able to determine that the original plant came from the Granites area near the Western australia and Northern territory border,
"Professor Waterhouse, a molecular geneticist with QUT's Centre for Tropical Crops and Biocommodities, said scientists could use this discovery to investigate other niche
Professor Waterhouse said the team's findings also have implications for future genetic research back here On earth."
When you consider that the human genome codes for over 600 different forms of just the E3 ligases alone,
This is currently the strategy with gene therapy as well, to flood an area with many nonspecific actors to wash out the importance of their individual incompetence,
The study was initiated in Japan by a group of geneticists at the Okayama University Institute of Plant science
or retains it in the ear. he Japanese geneticists found that the cell walls were much thinner in brittle crop and much thicker in non-brittle crop.
and the natural spreading of the species. After the Japanese geneticists had proved the gene formation was linked to the brittle characteristic,
despite consistent human genetics, suggesting a pivotal role for an environmental factor, "commented Chassaing.""Food interacts intimately with the microbiota
which can activate pro-inflammatory gene expression by the immune system, said Chassaing and colleagues. These changes in bacterial expression triggered chronic colitis in mice genetically prone to this disorder,
#quid teethplastic self-heals with water Scientists derived the genetic code of squid ring teeth to develop a polymer that self-heals with a single drop of water.
and the selective uptake of serotonin. he researchers found that they could produce induced serotonergic neurons from fibroblasts by introducing four genes that control the development of serotonin neurons. hese genes change how the human genome,
Jewett says. ur new protein-making factory holds promise to expand the genetic code in a unique and transformative way, providing exciting opportunities for synthetic biology and biomolecular engineering,
which plays a key role in controlling gene expression and, thereby helps regulate the cell's development, growth and function."
"When I showed the results to our clinical geneticists, initially they were floored, "said Stephen Scherer, Ph d.,principal investigator on the current study and Director of The Centre for Applied Genomics (TCAG) at Sickkids."
"In light of the findings, we suggest that genomic analyses be integrated into the standard of practice for diagnostic assessment of cerebral palsy."
"CNVS are structural alterations to an individual genome that lead to deletion, additions, or some reorganization of gene sequences that produces aberrant genetic products.
This study will provide the impetus to make genetic testing a standard part of the comprehensive assessment of the child with cerebral palsy."
"When I showed the results to our clinical geneticists, initially they were floored, "said Dr. Scherer."
"In light of the findings, we suggest that genomic analyses be integrated into the standard of practice for diagnostic assessment of cerebral palsy."
"CNVS are structural alterations to an individual genome that lead to deletion, additions, or some reorganization of gene sequences that produces aberrant genetic products.
This study will provide the impetus to make genetic testing a standard part of the comprehensive assessment of the child with cerebral palsy. e
In one proof-of-principle demonstration, the team edited the genetic code of a standard human antibody to replace one of its target-grappling elements structure that normally would bind to a virus
whether genetic material has been delivered successfully to cells that they are trying to alter genetically. Cells that did not receive the new gene could be induced to undergo cell death
However, genetics may hold the key to developing more effective treatments. My colleagues and I recently discovered that one specific gene may allow us to decode the function of all genes involved in the disease.
A similar technique, called optogenetics, is currently in practice and uses light pulses to control neurons. Just like a switch in your house turns your lights on and off,
I think we have shot a better with noninvasive sonogenetics approaches than with optogenetics.""Chalasani told the Guardian,
using gene therapy and a therapeutic virus, it may be possible to make target human neurons temporarily susceptible to the ultrasound signal in a clinical setting for certain neurological treatments."
as long as they share a few genetic characteristics with known viruses. According to Kristine Wylie, assistant professor of pediatrics at the university Mcdonnell Genome Institute,
published in Genome Research, ne of the exciting things of using this high-throughput sequencing is the amount of data we are able to generate in a short amount of time.
Researchers can scan the virus genetic sequences and look for a match from conserved genes that have been gathered in public repositories such as the Viral Genome Project.
Virocap has the capacity to detect a vast array of viruses, from the big, bad scary ones such as Ebola or SARS, to the everyday rhinoviruses and noroviruses that cause colds and gastrointestinal flu.
Virocap can help to add previously unidentified VIRAL DNA to the database of known viruses. he more genome coverage we have,
music to create an environment that is constantly adapting to the mood or genus of human activity.
Researchers used data from different people's genotypes and metabolism to build personalized models that simulate how a drug will affect a particular set of cells in the body."
they were looking at a tiny part of a real genome, only about one turn of the double helix.
and all 3. 3 feet (1 meter) of this genetic information must fit into the nucleus of a cell,
and to understand how these loops of genetic code act in real-time, the team created computer simulations that revealed the supercoiled loops wriggling over time.
#Nanoparticles Penetrate Mucus Barrier to Bring Gene therapy to Lung Parenchyma A collaboration between researchers at Johns hopkins university
and other conditions affecting the lungs by offering the ability for gene therapy to be delivered directly into pulmonary tissue through inhalation.
#Optogenetics With Closed-Loop Control for Complex Brain Experiments Wee excited about optogenetics, the new technology that allows scientists to selectively control the firing of genetically modified neurons within living animalsbrains.
The so-called ptoclamptechnique involves continuous monitoring of the electrical activity of the neuronal cells excited via optogenetics
One of the most critical biological and medical tools available today, it lies at the core of genome analysis. Reading the exact make-up of genes,
These are called ucleotidesand are strung together in various combinations that contain the cell genetic information, such as genes.
In addition, a gene therapy is administered that lowers the cellular defense against reactive oxygen species. Both the phthalocyanine
During the procedures, mice receiving the gene therapy also continued to grow and gain weight, indicating a lack of side effects."
The collaborative effort also includes Kang Zhang, a professor of ophthalmology and chief of Ophthalmic Genetics at UC San diego and a corresponding author on this study y
One of the most critical biological and medical tools available today, it lies at the core of genome analysis. Reading the exact make-up of genes,
"and are strung together in various combinations that contain the cell's genetic information, such as genes. Essentially
The so called DNA chip card employs electrochemical DNA chips and overcomes the complicated procedures associated with genetic testing of conventional methods.
"We have installed new genetic information in the yeast Pichia pastoris, so that our cells are able to produce Nootkatone from sugar,
The genome of the yeast cells has been extended with four foreign genes derived from the cress Arabidopsis thaliana, the Egyptian henbane Hyoscyamus muticus, the Nootka cypress Xanthocyparis nootkatensis and from baker's yeast Saccharomyces cerevisiae.
and reform into spindles that are used by the dividing cell to move chromosomes. For chromosome migration to occur,
the microtubules attached to them must disassemble, carrying the chromosomes in the process. The dynamic instability that makes it possible for microtubules to transition from a rigid polymerized
or"assembled"nucleotide state to a flexible depolymerized or"disassembled"nucleotide state is driven by guanosine triphosphate (GTP) hydrolysis in the microtubule lattice."
#Super-small needle technology for the brain Microscale needle-electrode array technology has enhanced brain science and engineering applications, such as electrophysiological studies, drug and chemical delivery systems, and optogenetics.
including recording/stimulation electrodes, glass pipettes, and optogenetic fibers.""He added:""This has the potential to reduce invasiveness drastically
"Other approaches have tried to define the paleome by comparing genome sequences and finding the gene portfolio that seemed to be similar in all of these sequences.
This just defines the minimal genome. Our definition of the paleome takes a more comprehensive approach.
The team's approach to define the paleome is based on a genome-scale computational model for cellular growth in E coli.
and gene expression processes in the cell. Using this model the researchers simulated the growth of a well-studied strain of E coli across 333 different growth conditions.
We are hoping to use this paleome as a starter kit to rapidly build a new generation of genome-scale cellular growth models for other organisms,
Its a future in which diseases like muscular dystrophy, cystic fibrosis and many others are treated permanently through the science of genome engineering.
"demonstrates a new technology advancing the field of genome engineering. The method significantly improves the ability of scientists to target specific faulty genes
and then edit them, replacing the damaged genetic code with healthy DNA. There is a trend in the scientific community to develop therapeutics in a more rational fashion,
In theory, genome engineering will eventually allow us to permanently cure genetic diseases by editing the specific faulty gene (s). Revolutionizing health care Genome engineering involves the targeted
specific modification of an organisms genetic information. Much like how a computer programmer edits computer code, scientists could one day replace a persons broken
Future applications Currently much of the research in the field of genome engineering is focused on treating monogenic diseasesdiseases that involve a single geneas theyre much easier for researchers to successfully target.
He hopes his current work will play a role in helping genome engineering reach its full potential
"Our research shows how the structure of our genetic material-DNA-can be changed and used in a way we didn't realise."
#Water heals a bioplastic (w/video) A drop of water self-heals a multiphase polymer derived from the genetic code of squid ring teeth,
#Proteins assemble and disassemble on command Scientists have deciphered the genetic code that instructs proteins to either self-assemble
Because the laboratory identified the genetic sequences that encode this behavior, they were able to point out a long list of human proteins that likely exhibit it."
whether genetic material has been delivered successfully to cells that scientists are trying to genetically alter. Cells that did not receive the new gene could be induced to undergo cell death,
or to study the 3-D structure of normal chromosomes by testing whether two genes located far from each other on a chromosome fold in such a way that they end up next to each other,
the researchers say
#New frontiers in 3d printing Three dimensional printing is revolutionizing the production of new devices and structures, including soft robots,
The current gold standard for Ebola virus detection relies on a method called polymerase chain reaction (PCR) to amplify the virus's genetic material for detection.
and separates the two strands of the DNA double helix as it passes through a central pore in the structureand how the helicase coordinates with the two'polymerase'enzymes that duplicate each strand to copy the genome."
and C bases of the genetic code) to the side-by-side split ends as they move out of the helicase to form two new complete double helix DNA strands.
Professor Peter Waterhouse, a plant geneticist at QUT, discovered the gene in the ancient Australian native tobacco plant Nicotiana benthamiana, known as Pitjuri to indigenous Aboriginals tribes.
which for decades has been used by geneticists as a model plant upon which to test viruses and vaccines."
"By sequencing its genome and looking through historical records we have been able to determine that the original plant came from the Granites area near the Western australia and Northern territory border,
"Professor Waterhouse, a molecular geneticist with QUT's Centre for Tropical Crops and Biocommodities, said scientists could use this discovery to investigate other niche
Professor Waterhouse said the team's findings also have implications for future genetic research back here On earth."
to study the genomes of seven family members. Dr Bally and Professor Waterhouse have lodged a patent on their study (Organisms with Modified Growth Characteristics and Methods of Making Them) and a research paper,
the researchers replicated the genome containing the lesion with a variety of different types of polymerase,
researchers have recently been able to develop precise treatments for cancer by sequencing tumor genomes
Genetic research has identified hundreds of genes that are involved, which impedes diagnosis and, ultimately, drug development. There simply may be too many targets, each with too small an effect.
This includes the sequencing of their entire genome. Also, skin cell samples are cultured and made available to lab-based researchers for functional assays.
of which exactly three are bound to the genetic material something Drennan says surprised her. hat the best part about science,
and Christopher J. Martyniuk of the Center for Environmental and Human Toxicology and Department of Physiological Sciences, UF Genetics Institute, University of Florida.
#Octopus Genome Offers Insights Into One Of Ocean's Cleverest Oddballs Scientists have sequenced just the first genome of an octopus,
"The octopus has a very large genome. It's nearly the size of the human genome,
"says Carrie Albertin, a biologist at the University of Chicago. As technology to sequence DNA has gotten faster and cheaper,
Wednesday, in the journal Nature, they report on the genetic code of Octopus bimaculoides aka the California two-spot octopus.
For example, scientists had thought the octopus genome got so big because at some point the whole genome just copied itself.
But no, says Albertin.""As we started to dig into the data, we were seeing more and more signs that there was no duplication."
"We were surprised really as we were poking through the octopus genome to see that there were just 150 or 160 of these genes,
because scientists are busy working on those genomes too g
#Genetically Modified Yeast Yields Narcotics, Raises Regulation Questions When bioengineer Christina Smolke started her own research lab,
"said Samuel Pfaff, a professor in Salk's Gene expression Laboratory.""These are just raw signals you can see through the eyepiece of a microscope.
In response, Francis Collins, the director of the National institutes of health (and leader of the U s. effort to sequence the human genome),
and the editing process can cause damage to the entire genome. The NIH's stance means those safety problems won't be solved on the U s s dime
the researchers uncovered the genetic code for the proteins that allow the teeth to heal themselves when broken.
the researchers uncovered the genetic code for the proteins that allow the teeth to heal themselves when broken.
the enzyme used in the CRISPR/Cas9 genome-editing technique, employed on a stand of DNA.
Some argue that editing the human genome could have unintended consequences that could be passed down to future generations,
a group of European researchers were able to store information in DNA, our genetic material. The promise of this discovery was huge.
or identifying the components of genetic material, is getting dramatically cheaper. For example, you can have the 3 billion bases in your own DNA sequenced for as little as $1000.
or on them it seems there certainly would be room to put your social security number in the genome of some bacteria or virus. However,
if you did manage to incorporate your personal information into the HPV genome (you couldn't add much-the genome is very small) remember using today technology the DNA has to be extracted,
#Gene on-off switch works like backpack strap A research team based in Houston Texas Medical center has found that the proteins that turn genes on by forming loops in human chromosomes work like the sliding plastic adjusters on a grade-schooler backpack.
and allow researchers to reprogram cells by directly modifying the loops in genomes. The study,
is by the same team that published the first high-resolution 3-D maps showing how the human genome folds inside the nucleus of a cell.
Every human cell contains a genome, a linear string of DNA. Sequences of DNA bases spell out genes,
and coming into contact during genome folding. Last year, the team showed that it was possible to map the positions of these loops,
and the researchers created the first atlas of loops in the human genome. But the group couldn explain how the loops were forming. or months
said senior author Erez Lieberman Aiden, a geneticist and computer scientist with joint appointments at Baylor and Rice. hen one day,
The human genome contains more than 20,000 genes. In any given cell, only a fraction of these are active,
Aiden, assistant professor of genetics at Baylor and of computer science and computational and applied mathematics at Rice, said Sanborn
and high-performance computation to predict how a genome will fold. The team confirmed their predictions by making tiny modifications in a cell genome
and showing that the mutations changed the folding pattern exactly as expected. Rao likened the result to a new form of genome surgery:
a procedure that can modify how a genome is folded by design and with extraordinary precision. e found that changing even one letter in the genetic code was enough to modify the folding of millions of other letters,
said Rao, a graduate student in the Aiden lab and at Stanford university. hat was stunning was that once we understood how the loops were forming,
the results of these changes became extremely predictable. Sanborn said the discovery also explains a puzzling pattern that the team noticed
and the genome is flexible at that scale, said Sanborn. f I were a protein,
The basic idea is that the tri-glide protein complex lands on the genome and pulls the strand from each side so that a loop forms in the middle just like the loop someone might make
Aiden said that one of the most astonishing implications of the new model is that loops on different chromosomes tend not to become entangled. n the old model,
when two bits of the genome wiggled around and then met inside the cell nucleus, Aiden said. ut this process would lead to interweaving loops and highly entangled chromosomes.
This is a big problem if you need those chromosomes to separate again when the cell divides. he tri-glide takes care of that,
he said. ven in a big pile of backpacks, you can use your tri-glide to make a loop without any risk of entanglement. u
#CRISPR brings precise control to gene expression Researchers have demonstrated the exceptional specificity of a new way to switch sequences of the human genome on
or off without editing the underlying genetic code. Originally discovered as an antiviral system in bacteria,
CRISPR/Cas9 is one of the hottest topics in genetic research today. By engineering a version of that system,
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's switches would be especially important for studying and potentially treating human diseases such as cancer, cardiovascular disease, neurodegenerative conditions and diabetes,
which can be driven by mutations in control regions of the genome. The hope is that overriding one of these switches could uncover
This presents problems for gene therapy treatments and fundamental science projects where researchers want to alter the function of specific genes without causing unintended side effects.
if you're 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,
Reddy has focused his career on investigating how gene switches work across the human genome, how those switches differ between individuals and the implications of these insights for human traits and diseases.
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,
"By integrating genomics and genome engineering, we have developed a method to comprehensively interrogate how this genetic silencing system works
Overtext Web Module V3.0 Alpha
Copyright Semantic-Knowledge, 1994-2011