#Closing the loop with optogenetics Optogenetics provides a powerful tool for studying the brain by allowing researchers to activate neurons using simple light-based signals.
Optogenetics technology places genes that express light-sensitive proteins into mammalian cells that normally lack such proteins.
which closes the loop in optogenetic systems. The technique uses a computer to acquire and process the neuronal response to the optical stimulus in real-time
electrical stimulation or even light-plus-optogenetics through fiber optics, will all be closed loop. That means they will be responsive to the moment-to-moment needs of the nervous system.
However, now scientists from the RIKEN Molecular genetics Laboratory have revealed the mechanism underlying the memory of innate immunity.
Some of the most notorious antibiotic-resistant strains and species belong to the genus Staphylococcus. They are classified typically as pathogenic or non-pathogenic based on production of the enzyme coagulase.
a transcription factor a protein able to influence gene expression known as Er81. Fast-spiking interneurons are part of a general class of neurons
and genetic materials and serve as a vehicle for communication between cells. In the nervous system, exosomes guide the direction of nerve growth,
the development of new synthetic materials for the delivery of therapeutic proteins and genetic material. In 2015, he received a Faculty Early Career development (CAREER) award from the National Science Foundation (NSF),
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.
but also other cellular features such as gene expression, post translational modification, and cell function, said Huang. he acoustic power intensity
DNA methylation is essential for the proper control of gene expression and cell identityhat enables cells with the same genetic material to become, for example, a nerve cell, a muscle cell or a skin cell.
Certain diseases, including cancer, involves changes in DNA methylation patterns, and the ability to document these alterations aid in the development of novel therapies. ethylation is really key in development,
The differences between a muscle cell and a brain cell are attributable to differences in gene expression; that is, which genes are turned on and off.
DNA methylationhe addition of methyl groups to the DNAS an epigenetic mechanism that controls gene expression. In most cases, methylated genes are switched off,
#New system for human genome editing has potential to increase power 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.
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. his has dramatic potential to advance genetic engineering,
but also shows that Cpf1 can be harnessed for human genome editing and has remarkable and powerful features.
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
of which exactly three are bound to the genetic material something Drennan says surprised her. hat the best part about science,
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.
an instructor of pediatrics. light genetic variations among viruses often can be distinguished by currently available tests
In addition, because the test includes detailed genetic information about various strains of particular viruses, subtypes can be identified easily.
In all the research team included 2 million unique stretches of genetic material from viruses in the test.
their genetic material could easily be added to the test, Storch said. The researchers plan to conduct additional research to validate the accuracy of the test,
Now, researchers at DTU Systems Biology have combined genetics with computer science and created a new diagnostic technology based on advanced self learning computer algorithms whichn the basis of a biopsy from a metastasisan with 85 per cent certainty identify the source of the disease
In recent years, researchers have discovered several ways of using genome sequencing of tumours to predict
A method to identify the tissue of origin from the somatic mutations of a tumour specimen in BMC Medical Genomics i
#Scientists test new gene therapy for vision loss from a mitochondrial disease NIH-funded study shows success in targeting MITOCHONDRIAL DNA in mice Researchers funded by the National institutes of health have developed a novel mouse model for the vision disorder
and found that they can use gene therapy to improve visual function in the mice. LHON is one of many diseases tied to gene mutations that damage the tiny energy factories that power our cells,
said John Guy, M d.,professor of ophthalmology and director of the ocular gene therapy laboratory at the Bascom Palmer Eye Institute, University of Miami Miller School of medicine.
and using it to test an investigational gene therapy is described today in the Proceedings of the National Academy of Sciences.
Dr. Guy began to research a possible gene therapy approach for delivering a substitute copy of the gene into mitochondria about 15 years ago.
In most studies and applications of gene therapy viruses have become the preferred vessel for delivering genes into cells.
This modified virus has been the key to creating a mouse that replicates LHON and to an investigational gene therapy for LHON that is currently in clinical trials.
To develop a gene therapy for LHON, the team packaged the normal human ND4 gene into the same stealthy virus. This combination,
and is testing the safety of the same gene therapy approach (without the red fluorescent protein) in people with LHON.
or building blocks, in its genetic material, and a drop of blood from a patient with resistant HIV can contain thousands to millions of copies of HIV.
LRA works by sending in many copies of a pair of short engineered probes of genetic material to complement the RNA in the HIV sample.
#Transplanting from Pig to Human Never before have scientists been able to make scores of simultaneous genetic edits to an organism genome.
Artistic rendering shows pig chromosomes (background) which reside in the nucleus of pig cells and contain a single strand of RNA,
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.
Church is the Robert Winthrop Professor of Genetics at Harvard Medical school and a Wyss core faculty member.
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
#Stressed dads affect offspring brain development through sperm microrna More and more, scientists have realized that DNA is not the only way that a parent can pass on traits to their offspring.
and then amplified the RNA in each single cell to look for gene expression levels. They found that, indeed,
borrowing tools from the developing field of optogenetics, which so far has been used mainly in brain science.
A protein called channelrhodopsin was delivered to heart cells using gene therapy techniques so that they could be controlled by light.
as gene therapy moves into the clinic and with miniaturization of optical devices, use of this all-optical technology may become possible.
such as genomics, finance and the social sciences. Some of the domains already being served by Comet include:
or de novo genome assembly. 7 petabytes of Lustre-based high-performance storage from Aeon, and 6 petabytes of durable storage for data reliability.
But finding a specific biomarker in a massive amount of genetic code is hard. Zhang and his team at Rice Bioscience Research Collaborative have become specialists in finding such needles in haystacks.
borrowing tools from the developing field of optogenetics, which so far has been used mainly in brain science.
We wanted to use it to very precisely control the activity of millions of cells. protein called channelrhodopsin was delivered to heart cells using gene therapy techniques
as gene therapy moves into the clinic and with miniaturization of optical devices, use of this all-optical technology may become possible.
the researchers found that the genetic alteration that confers these benefits turns on a set of molecules called PARP9-DTX3L.
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.
or environmental factors and not genetics. f there were a way to reverse silencing of the RGS10 protein,
and epigenetic program controlling the self-renewal of stem cells, and on a practical side, it could allow us to inexpensively produce large numbers of immune cells,
#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 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
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 An alternative strategy was developed to switch on
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
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,
it provides a blueprint for researchers to assess these effects. y integrating genomics and genome engineering,
first mapped the gene causing North carolina macular dystrophy on chromosome 6 in 1992. The current findings ultimately required an international team of 20 investigators using data from the Human genome Project
and an elaborate computer analysis to identify the actual mutations in INTERGENIC DNA near the PDRM13 gene. ndividuals with this disease have normal eyes except that they fail to form maculas,
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
said Andrzej Joachimiak, an Argonne Distinguished Fellow, head of the Structural biology Center, co-principal investigator at the Center for Structural genomics of Infectious diseases and a corresponding author on the new study.
A link to epigenetics To identify which polymerase was at the top of the helicase,
Oonnell suggests. hanges to nucleosomes carry epigenetic information that instructs different cells to become the different tissues of the body,
and other organs during embryonic development, Oonnell says. o we can speculate that Pol-e interaction with nucleosomes could play a role in assigning different epigenetic identities to the two new daughter cells after cell division,
and shows genome changes that indicate domestication by humans. The new research is published in Nature Genetics.
The plant endosperm has been an important factor in the establishment of a mutualistic relationship with humanso facilitate their survival and spread,
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,
who leads a German consortium developing transgenic pigs. t very cumbersome. Creating a good pig is really like winning the lottery. n the United states,
Since last year, some of the genetic engineering has been carried out in collaboration with Synthetic Genomics, a California company started by DNA sequencing entrepreneur J. Craig Venter.
who runs the mammalian synthetic biology program for Synthetic Genomics. o one is so naïve as to think, h,
The organs he used before had three genetic alterations, but the next ones will have seven. f they survive,
Genome pioneer Craig Venter led a team that manufactured a genome for a germ that causes pneumonia in cows,
Romesberg lab could claim to have made the first living thing with an expanded genetic code. eople would ask what the big deal is said,
#Stimulating Neurons with Sound Over the past five years, optogenetics method for stimulating genetically engineered neurons with lightas taken the life sciences by storm.
Study coauthor Sreekanth Chalasani, a molecular neurobiologist at the Salk Institute, explained that sonogenetics will complement optogenetics,
People using optogenetics in mammals for instance, must surgically insert a probe, whereas stimulation with ultrasound will require no such surgery. his is said noninvasive,
the amplified ultrasound waves also do appear to affect some other neurons. t not he same thing at this point as optogenetics, where it really an all-or-none thing,
The team found a similar gene expression profile to that of kidneys of first-trimester human fetuses, for example,
Just a few years ago, sequencing a human genome cost $95m. Now, the price is $1 000.
In line with women's health, connected care plays a crucial role in keeping the world's XX-chromosomes healthy.
The researchers also hope to explore the unexpected conformational changes for insights into epigenetics the field that studies how genes are expressed and moderated.
#Protein found in insect blood helps power pests immune responses Pest insects may be sickened to learn to that researchers at Kansas State university have discovered a genetic mechanism that helps compromise their immune system.
It is recognized often by a genetic mechanism in the mosquito's immune system which kills the parasite.
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.
It is therefore possible to yield plenty of genetic information with just a tiny fragment. 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. Capflank opens doors to completely new possibilities e g. in the genetic analysis of pathogens.
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.
As their next task his team wants to retrieve simple and well characterised DNA VIRUSES such as the elephant herpes virus.
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
--and the transmission of these mutations to children--could provide valuable insights for genetic counseling. These mutations cause more than 200 diseases and contribute to others such as diabetes cancer Parkinson's disease and Alzheimer's disease.
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.
and responds by activating cellular gene expression programs. Observations that fructose potently activates Chrebp in rodent livers
Ribosomes common to all living organisms are the machines that read the genetic code producing proteins based on the instructions therein.
One protein directs epigenetic players Every single human cell contains every single human gene. But depending on the cell only some of these genes need to be expressed or turned on.
Now scientists know that there are tiny proteins--epigenetic proteins--that sit atop the genetic code inside cells.
Now UNC researchers discovered that one gene-regulating protein called Bre1 must be maintained in the proper amount for other epigenetic players to do their jobs properly.
All this supporting staff is part of epigenetics--epi meaning on or above--a field that focuses on the environment and the players that allow our genes to act.
I think epigenetics is a new frontier of cancer research says Brian Strahl Ph d. a professor of biochemistry and biophysics in the UNC School of medicine.
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.
We're not just finding this in cancer cell lines in the lab but in cancer patients.
or denies access to the genetic information inside our cells. This is what Strahl studies. His goal is to figure out precisely how histones contribute to basic biological functions
or further prevent access to our genetic information--our DNA. And this access or denial ultimately affects genes
Nasty environmental stuff such as cigarette smoke can mess up the epigenetic machinery. Yet these chemical tags are not ultimately in charge of the genes.
what had been an epigenetic mystery. Scientific literature on Bre1 had been mixed. Some studies indicated that Bre1 had a role as a tumor suppressor Strahl said.
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.
A study published by Cell Press October 9th in the American Journal of Human genetics shows that neurodevelopmental disorders caused by distinct genetic mutations produce similar molecular effects in cells suggesting that a one-size-fits-all therapeutic approach could be effective
the Clyde and Helen Wu Professor of Chemical Biology (in Biomedical Informatics and the Institute for Cancer Genetics), chair of the Department of 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,
by jointly analyzing the gene expression and mutational profile data of more than 250 patients collected by the Cancer Genome Atlas consortium.
The CUMC team found two genes--C/EBPD and KLHL9--that appear to activate glioblastoma's master regulators.
C/EBPD, had already been identified by the labs of Dr. Califano and of Antonio Iavarone, MD, professor of neurology and of pathology & cell biology (in the Institute for Cancer Genetics),
As the instructions for all cell processes the DNA must be accessible to the cell transcription machinery yet be compressed tightly enough to fit inside the nucleus. Scientists have theorized long that the way DNA is packaged affects gene expression.
and repressing gene expression. or the first time we see that the structure of the chromosomes contributes to gene controlsays Whitehead Member Richard Young who is also a professor of biology at MIT. n the past there have been all kinds of ideas around how the structure might affect gene control
elements to highly condensed chromosomes. Working in mouse embryonic stem cells (ESCS) the Young lab examined the scaffolding landscape found within topologically associated domains.
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
which led us to these domains these super enhancer domains where gene expression enhancement is contained within the loopsays Jill Dowen a postdoctoral researcher in Young lab. Dowen
and CTCF acting as the purse strings to create a DNA loop that cradles proteins enhancing or repressing gene expression.
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.
although they may switch their contents and therefore their effect on gene expression. The researchers plan to study the loop structure
and its effects. think wee filled in a major gap in the understanding of how gene expression is linked to the local organization of chromosomessays Hnisz. t will be exciting to explore
Using brain scans from the ENIGMA Consortium and genetic information from The Mouse Brain Library he was able to identify a novel gene,
The study has just been published in the journal BMC Genomics. David, who works in Dr Reinmar Hager's lab at the Faculty of life sciences, says:"
"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
"said Ranjan J. Perera, Ph d.,associate professor and scientific director of Analytical Genomics and Bioinformatics at Sanford-Burnham's Lake Nona campus in Orlando."
The team used the technology to study motions of proteins on the surface of the HIV virus (called envelope proteins) that are key to the virus's ability to infect human immune cells carrying CD4 receptor proteins.
CD4 receptor proteins help HIV bind to a cell. The envelope consists of three gp120
"that open up like a flower in the presence of CD4, exposing the gp41 subunit that is essential for subsequent aspects of the mechanism that causes infection."
"Many scientists believe that the particles remain in one conformation until they come across a CD4-positive cell.
when no CD4 was present--they change shape all the time.""The researchers were then able to watch how the viruses responded
when synthetic CD4 was introduced. They also saw that antibodies known to exhibit some effectiveness acted to prevent gp120 from opening,
"Importantly, viral sequence information from the epidemic reveals rapid changes in the viral genome, while our target sequence remains the same.
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