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,
who is also a professor of biology at MIT. his reporter is a very important tool.
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,
existing approaches have offered limited insight into this fundamental biological control. Creating a system that dynamically visualizes methylation at the level of a single cell intrigued Yonatan Stelzer
In his study, Shan-Lu Liu, an associate professor in the Department of Molecular Microbiology and Immunology in the School of medicine and an investigator in the Bond Life sciences Center at MU, targeted IFITM proteins
Jingyou Yu, a doctoral student in MU pathobiology graduate program, conducted experiments to show that IFITM proteins, particularly IFITM2 and IFITM3, block HIV cell-to-cell transmission.
who is also a graduate student in pathobiology, and discovered that IFITM proteins specifically interact with the HIV-1 envelope glycoprotein
#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 John van der Oost at Wageningen University, describe the unexpected biological features of this new system
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
and their natural biological function was described initially in 2010 and 2011. 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.
In the new study, Zhang and his collaborators searched through hundreds of CRISPR systems in different types of bacteria,
says Zhang, the W. M. Keck Assistant professor in Biomedical engineering in MIT Department of Brain and Cognitive sciences.
leaving lunt endsthat often undergo mutations as they are rejoined. With the Cpf1 complex the cuts in the two strands are offset, leaving short overhangs on the exposed ends.
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,
and proteins can be used to create materials that exhibit dynamic behaviors found in biological tissues like growth, morphogenesis, and healing.
Alvaro Mata, Director of the Institute of Bioengineering at QMUL and lead author of the paper
Detailed in a paper published in Genome Medicine on September 28th this technology could prove highly useful in settings where lab equipment
First, it expands our knowledge of the biological role of Vitamin b12, which was understood already to help convert fat into energy,
says Catherine Drennan, a professor of chemistry and biology at MIT. The findings are detailed this week in the journal Nature.
of which exactly three are bound to the genetic material something Drennan says surprised her. hat the best part about science,
says Rowena Matthews, a professor emerita of biological chemistry at the University of Michigan, who has read the paper.
says Zhen Gu, corresponding author of a paper on the work and an assistant professor in the joint biomedical engineering program at North carolina State university and the University of North carolina at Chapel hill. irst,
lead author of the paper and a Ph d. student in the joint biomedical engineering program. Here how the process works.
Reading and Assembling Contextual and Holistic Mechanisms From Textwill create a computer system that reads papers, extracts information on biochemical pathways,
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,
fast, individualized and precise biomedical care. he REACH project is applied to cancer biology, but we have an even bigger vision than that,
although cancer biology is big enough, Morrison said. If big data is a two-part challenge,
Others on the UA research team include Ryan Gutenkunst, assistant professor of molecular and cellular biology; Guang Yao, assistant professor of molecular and cellular biology;
and Kobus Barnard, professor of computer science. Morrison, who also has a strong, academic background in developmental psychology, said,
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
and is just as sensitive as the gold-standard polymerase chain reaction (PCR) assays, which are used widely in clinical laboratories.
The researchers evaluated the new test in two sets of biological samples for example, from blood, stool and nasal secretions from patients at St louis Children Hospital.
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,
a biological material from living or recently living organisms, as a replacement for graphite, has drawn recent attention because of its high carbon content, low cost and environmental friendliness.
Nanocarbon architectures derived from biological materials such as mushrooms can be considered a green and sustainable alternative to graphite-based anodes,
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
are based on analyses of DNA mutations in cancer tissue samples from patients with metastasized cancer,
The pattern of mutations is analysed in a computer program which has been trained to find possible primary tumour localizations.
In recent years, researchers have discovered several ways of using genome sequencing of tumours to predict
Associate professor Aron Eklund from DTU Systems Biology explains: e are pleased very that we can now use the same sequencing data together with our new algorithms to provide a much faster diagnosis for cancer cases that are difficult to diagnose,
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,
called mitochondria. his study marks an important contribution to research on LHON, and in efforts toward an effective therapy.
and it is mutations within this MITOCHONDRIAL DNA (mtdna) that lead to LHON, as well as a host of other diseases.
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.
The most common mutation behind LHON impairs a mitochondrial gene called ND4. 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.
But viruses evolved to invade the body cells and penetrate the nucleus, which contains the bulk of our DNA,
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.
the researchers loaded the virus with a defective copy of the ND4 gene carrying the same mutation that causes about 70 percent of LHON cases.
The presence of the virally encoded ND4 mutation in the eye was confirmed by essentially doing an eye exam to look for the red fluorescent marker.
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.
distinguished professor of chemistry and biochemistry and materials science and engineering, was published recently by the journal ACS Nano.
Assistant professor of Mechanical and Biomedical engineering AT SEAS, founder of the Harvard Biodesign Lab AT SEAS, and author on the paper. he device is a minimally invasive way to deliver a patch
Jeff Karp, Ph d.,a bioengineer at Brigham and Women Hospital and a cofounder of Gecko Biomedical, developed the glue product in his lab at Brigham and Women Hospital.
Indeed, bioinformatic analysis led him to predict the existence of a mysterious protein: COCO, a ecombinationalhuman molecule that is normally expressed within photoreceptors during their development.
Trajan Chief executive officer Stephen Tomisich said Trajan is driven by a passion to develop technologies that will impact human wellbeing. hilst this first iteration of the hemapen provides a DBS format ready for Liquid Chromatography-Mass Spectrometry (LC-MS) analysis,
A report on the work by Jeffrey Watson and co-authors from the UA departments of Biomedical engineering
or replaced by modern techniques that give the physician an indication of the elasticity of a biological tissue.
sensitive test for HIV mutations Tests that can distinguish whether HIV-positive people are infected with a drug-resistant strain
if a mutation is present and then make many copies of those combined probes (amplification) for detection.
and quantitative PCR (polymerase chain reaction) amplification into a single system, said Anubhav Tripathi, professor of engineering at Brown and corresponding author on the paper. ach HIV contains about 10,000 nucleotides,
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.
The experiments reported in the paper show that the LRA test was sensitive enough to find a commonly sought K103n mutation in concentrations as low as one mutant per 10,000 strands of ormalviral RNA.
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.
those pairs that perfectly match the target HIV RNA containing a mutation that causes drug resistance can rapidly become fused together,
quick and accurate HIV drug resistance mutation detection system for use in developing nations. e met soon thereafter
and other methods on patient samples to detect additional mutations and address specific HIV challenges related to mutation detection,
such as enormous genomic diversity, Kantor said, nd work on incorporation of such methods onto a point-of-care device that would satisfy the infrastructure and low-cost needs of resource limited settings. s
#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.
With the retroviruses safely removed via genetic engineering, however, the door is now open on the possibility that humans could one day receive lifesaving organ transplants from pigs.
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 is currently collaborating with Church on further genetic modifications of his pigs. f Church and his team are able to produce pigs from genetically engineered embryos lacking PERVS by the use of CRISPR-Cas9,
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.
professor of neuroscience in Penn School of veterinary medicine and Perelman School of medicine, provides important clues for understanding how a father life experiences may affect his children brain development and mental health through a purely biological and not behavioral means. t remarkable to
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.
we could prevent that. ptogenetics uses genetic modification to alter cells so that they can be activated by light.
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.
Conducting nanoscale biomolecular research could lead to low-cost DNA sequencing technologies, and in turn create targeted drug delivery systems
Biologists construct phylogenetic trees to capture the evolutionary relationship between species, and help us better understand the functions and interactions of genes, the origin and spread of diseases, the co-evolution of hosts and parasites and migration of human populations.
or de novo genome assembly. 7 petabytes of Lustre-based high-performance storage from Aeon, and 6 petabytes of durable storage for data reliability.
#Biomarker finder adjusts on the fly A Rice university laboratory has developed a continuously tunable method to find and quantify DNA and RNA biomarkers.
Rice bioengineer David Zhang and his colleagues have developed a unique way to adjust their nucleic acid probe reagents on the fly
and take a reliable count of target sequences. The work is detailed in an open-access paper this week in Nature Methods.
especially mutations, has become critically important for the detection of diseases and design of therapies to treat them.
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.
In previous work, the lab designed probes that find single-nucleotide mutations in DNA while using ompetingprobes to bind to healthy sequences
and effectively get them out of the way. This time the lab is developing synthetic DNA rotectorsthat mimic the target sequence
there may be two biomarker sequences of interest, but the high expression of one would outshine the low expression of another.
Because the unit brightness of each biomarker can be adjusted, the researchersnew method allows the simultaneous and accurate observation of many biomarkers. n principle,
we should be able to tune indefinitely, he said. ut we be trading off time and labor and cost versus what people actually need.
Probe design is complicated by the fact that researchers often look for many biomarkers at once, and that those biomarkers interact with each other,
Zhang said. n an age of advancing science and big data, we want to look at hundreds or thousands or millions of different DNA biomarker signatures. esearchers have to decide in advance
whether to measure how sensitive the target sequences are to their probes, or how specific they will be when binding,
In one of many successful tests, the lab designed molecules to detect mutation sequences in historic biopsy samples preserved in wax from cancer patients.
One of the researchersgoals is to design noninvasive cancer diagnostics that detect DNA biomarkers in blood samples for early screening and early recurrence detection.
faster and cheaper answers for researchers and clinicians who are looking at hundreds or thousands of different mutations,
ew insights into the biology of blood cancers and disorders that originate in the bone marrow have only been made possible by the latest advances in technology.
borrowing tools from the developing field of optogenetics, which so far has been used mainly in brain science.
we could prevent that. ptogenetics uses genetic modification to alter cells so that they can be activated by light.
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.
#Mini-kidney organoids re-create disease in lab dishes Stem-cell biology and gene editing advances offer hope for kidney regeneration,
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.
resulted from combining stem cell biology with leading-edge gene-editing techniques. The journal Nature Communications reports the findings today, Oct 23.
Those with mutations in polycystic kidney disease genes formed balloon like, fluid filled sacks, called cysts, from kidney tubules.
The organoids with mutations in podocalyxin, a gene linked to glomerulonephritis, lost connections between filtering cells. utation of a single gene results in changes kidney structures associated with human disease,
The researchers found that genetically matched kidney organoids without disease-linked mutations showed no signs of either disease.
RISPR can be used to correct gene mutations explained Freedman. ur findings suggest that gene correction using CRISPR may be a promising therapeutic strategy.
Bonventre and colleagues introduced into healthy human pluripotent stem cells either the gene mutations associated with polycystic kidney disease
The scientists then coaxed the stem cells to differentiate into mature kidney cells that self-assembled into functional organoids with the physical complications related to their genetic mutations;
Rice chemist Jeffrey Hartgerink, lead author Vivek Kumar and their colleagues reported their discovery in the American Chemical Society journal ACS Biomaterials Science and Engineering.
says the molecular biologist Prof. Dr. Susanne Schoch from the department of Neuropathology at the University of Bonn.
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.
associate professor of biomedical engineering at Duke university. any labs across the world are using these tools on the assumption that theye getting specific effects,
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
assistant professor of biostatistics and bioinformatics at Duke. inding a change in sequence or gene activity is relatively straightforward
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
who all work together in adjacent laboratories and offices in Duke Center for Genomic and Computational biology, for help with these more specialized techniques.
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,
Small says. nderstanding how this gene works may help us treat many macular diseases more effectively in the future. cientists already know how to create new retinal cells from a patient skin,
said Robert Mckenna, Ph d.,a professor of biochemistry and molecular biology in the UF College of Medicine,
Biological Crystallography and Chemical engineering Science. The chemistry of sequestering works this way: The enzyme, carbonic anhydrase, catalyzes a chemical reaction between carbon dioxide and water.
#Bioengineers cut in half time needed to make high-tech flexible sensors Bioengineers at the University of California,
The new fabrication process will allow bioengineers to broaden the reach of their research to more clinical settings.
a bioengineering professor at the Jacobs School of engineering at UC San diego. Researchers describe their work in the journal Sensors. clinical need is
investigator Shingo Kajimura, Phd, an assistant professor of cell and tissue biology in UCSF School of dentistry. He holds a joint appointment in UCSF Diabetes Center and Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research.
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
#Biologist uncovers fundamental new strategy for destroying cancer cells University of Virginia cell biologist John Herr believes that the most ground-breaking findings always start with an insight built on basic science.
and within the egg and the sperm, said Herr, a professor of cell biology in the School of medicine.
He used his research to launch three biotech companies centered on forensic science, fertility assessment and contraception methods.
Ovastasis focuses on protein biomarkers that are specific to the reproductive cells, in this case, the egg.
The difference is that Ovastasis plans to use those protein biomarkers as targets for a novel female birth control medication. he identification of drug targets that are selective to the egg
and opens opportunities for biological drug strategies that selectively target the gametes in the ovary and testis,
It was through the same research into egg biomarkers that Herr and his team uncovered a fundamental,
and acquire their own unique set of biomarkers as they begin to form specific organs.
Like Ovastasis, Neoantigenics is focused on creating a targeted drug that will affect only those cells identified by the correct cell surface biomarkers.
the biomarker that is found only on growing eggs and tumor cells. The monoclonal antibodies to SAS1B can be thought of as a homing mechanism to guide a miniscule warhead selectively to the surface of cancer cells.
The same biomarkers that will help limit the area of impact for Ovastasis birth control will also help Neoantigenics confine the toxic effects of cancer treatment to growing egg and tumor cells.
Herr said. ithout a deep level of understanding of the fundamental biology, commercial applications are not possible.
and Differentiation in the Institute of Molecular and Cellular Biosciences have established a technique to isolate hipsc-derived liver progenitor cells (LPCS, cells
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