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Monthly Archives: April 2017
Keys to heart disease, diabetes, cancer may be in genome’s ‘dark matter’ – Genetic Literacy Project
Posted: April 13, 2017 at 11:23 pm
A new method lets researchers quicklyscreen the non-coding DNA of the human genome for links to diseases that are driven by changes in gene regulation.
The technique could revolutionize modern medicines understanding of the genetically inherited risks of developing heart disease, diabetes, cancer, neurological disorders, and others, and lead to new treatments.
As reported in Nature Biotechnology, the new technique relies on the gene-hacking system called CRISPR/Cas9. Originally discovered as a natural antiviral defense mechanism in bacteria, the system recognizes and homes in on the genetic code of previous intruders and then chops up their DNA. In the past several years, researchers have harnessed this biologic system to precisely cut and paste DNA sequences in living organisms.
With the new tool, Gersbach and his colleagues are exploring the 98 percent of our genetic code often referred to as the dark matter of the genome.
The technique is already producing results, identifying previously known genetic regulatory elements while also spotting a few new ones. The results also show it can be used to turn genes either on or off, which is superior to other tools for studying biology that only turn genes off. Different cell types also produced differentbut partially overlappingresults, highlighting the biological complexity in gene regulation and disease that can be interrogated with this technology.
The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post:How scientists explore our genomes dark matter
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Keys to heart disease, diabetes, cancer may be in genome's 'dark matter' - Genetic Literacy Project
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What’s a knotand what’s notin genomic mapping – Phys.org – Phys.Org
Posted: at 11:23 pm
April 11, 2017 A depiction of a part of a simulated DNA molecule within a nanochannel. The green beads are an unknotted portion of the molecule and the orange beads are a knot. Credit: Jain and Dorfman
While DNA sequencing provides precise, nucleotide-by-nucleotide genomic information, genome mapping provides a bigger-picture perspective of sequenced DNA that can provide valuable structural information. Like mapping roads to depict a city's structural information without needing to detail each home or business, genome mapping can be a powerful tool for understanding variations of large pieces of rearranged or altered DNA.
More technically, genome mapping is used to obtain large-scale genomic information with a resolution of around 2000 base pairs (bp), as opposed to the single-base resolution of sequencing. Genome mapping complements DNA sequencing, offering insight into huge, intact molecules between 150,000 and 1 million bp in length. Obtaining measurements of such large segments is not without its challenges, but new research into the physics of nanochannel mapping published this week in the journal Biomicrofluidics, may help overcome a (literal) knot in the process and advance genome mapping technology.
A team of researchers from the University of Minnesota partnered with BioNano Genomics, a company commercializing genome mapping in nanochannels, to understand the basic physics that underlies the mapping, and use that understanding to improve the technology. BioNano Genomics maps genomes by encoding DNA with sequence-specific, fluorescent labels before injecting it into nanochannels that cause the molecule to stretch out. The structural mapping information is read from the stretched DNA.
DNA knots, however, would put a kink in this method as the molecular tangle could be read incorrectly as a structural variation in the genome sequence. To better understand these nanoknots, the group uses computer simulations to model nanochannel configurations of DNA and compares the predictions to measurement-based characterizations.
"We looked at the probability that the DNA would form a knot inside the channel and predicted the size of the knots," said Kevin Dorfman, a member of the research team and lead author of the work. "This is important in mapping because knots could be incorrectly characterized as changes in DNA sequence structure when, in fact, they are just rearrangements of the DNA within the channel."
This line of research posed several challenges. The probability of forming knots is very low, and the molecules used in genome mapping are very large, requiring the team to come up with a computational pipeline capable of simulating this system at both the resolution of the knots as well as the DNA segment as a whole.
"Previous work on DNA knotting in these types of nanochannels looked at molecules that were almost an order of magnitude smaller than the ones in our study," Dorfman said. Another challenge the team faced was handling the terabytes of data from the millions of DNA chains that were generated to get meaningful statistics.
The goal of this research was to see whether or not the model's predictions of knotting were consistent with bright spots observed during experiments that could be knots on the DNA molecule.
"We found that experimental results are not consistent with equilibrium statistical mechanics, meaning that the knots in the experiments may not actually be knotswhile the way the data were processed in the experiments suggests many potential knotting events, we cannot definitively identify these events as knots," Dorfman said.
To address the discrepancy between experiments and simulations, the group will have to return to experiments, collecting dynamic data from the movement of the knots.
"The dynamic information can give us very important insights about the structure of the DNA in the channel, and potentially allow us to tell if the knots are, indeed, knots," Dorfman said.
Since knot formation is very rare, acquiring huge data sets, screening them to locate possibly knotted DNA, then analyzing those DNA molecules in detail is necessary.
The work did reveal, however, that these knots are not an intrinsic problem in genome mapping. If knot formation was frequent, this would make the processing of genome mapping data much more challenging. If the apparent knots in the experiments come from some other sources, then they can be removed by changing other parts of the experimental protocol.
Explore further: Improving accuracy in genomic mapping with time-series data
More information: "Simulations of knotting of DNA during genome mapping," Biomicrofluidics (2017). DOI: 10.1063/1.4979605
If you already have the sequenced map of an organism's genome but want to look for structural oddities in a sample, you can check the genomic barcodea series of distances between known, targeted sitesby cutting a DNA ...
Anyone who has been on a sail boat knows that tying a knot is the best way to secure a rope to a hook and prevent slippage. Similarly, knots in sewing threads prevent them slipping through two pieces of fabric. How, then, ...
Many of the processes essential to life involve proteins - long molecules which 'fold' into three-dimensional shapes allowing them to perform their biological role.
Nanotechnologies require a detailed knowledge of the molecular state. For instance, it is useful to know when and how a generic polymer, a long chain of polymers (chain of beads), knots. The study of molecular entanglement ...
Protein factors are responsible for organizing chromosomes inside the nucleus in three dimensions (3D), forming a shape like a gift bow, with proteins aggregating as the central 'knot' holding the ribbon-like loops of DNA ...
Scientists at The University of Manchester have produced the most tightly knotted physical structure ever known - a scientific achievement which has the potential to create a new generation of advanced materials.
People's ability to make random choices or mimic a random process, such as coming up with hypothetical results for a series of coin flips, peaks around age 25, according to a study published in PLOS Computational Biology.
Imagine that the way flies and butterflies drink nectar and other fluids can be imitated for use in medicine, potentially to deliver life-saving drugs to the bodyand also how this method can save their own lives in times ...
A team of scientists from the Broad Institute of MIT and Harvard, the McGovern Institute for Brain Research at MIT, the Institute for Medical Engineering & Science at MIT, and the Wyss Institute for Biologically Inspired ...
The bacterial flagellum is one of nature's smallest motors, rotating at up to 60,000 revolutions per minute. To function properly and propel the bacterium, the flagellum requires all of its components to fit together to exacting ...
Hunting is a major threat to wildlife particularly in tropical regions, but a systematic, large-scale estimate of hunting-induced declines of animal numbers has been lacking. A study published in Science on April 14 fills ...
There are many processes that take place in cells that are essential for life. Two of these, transcription and translation, allow the genetic information stored in DNA to be deciphered into the proteins that form all living ...
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Clinical trial finds no benefits of wearing silk for children with eczema – Medical News Today
Posted: at 11:23 pm
Eczema affects a large proportion of children and adolescents in the United States. New research investigates whether silk clothing improves health outcomes for children with eczema.
Eczema - also known as atopic dermatitis - is a chronic dermatological disease that causes the skin to itch and become very dry. Although the condition is not contagious, people with eczema may be vulnerable to other viral and bacterial skin diseases.
Atopic dermatitis affects approximately 30 percent of the U.S. population, according to the National Institutes of Health (NIH). Children and adolescents seem to be particularly at risk of eczema, the NIH report.
Clothing seems to play an important role in the management of the disease. Patients are routinely advised to wear cotton or smooth fabrics and avoid materials such as wool, which may worsen the itching.
Furthermore, in countries such as the United Kingdom, specialist silk clothing is available on prescription for people with eczema.
As a result, a team of researchers from the University of Nottingham in the U.K. - led by Kim Thomas and colleagues - set out to investigate the benefits of wearing silk garments for children with eczema. The study was published in the journal PLOS Medicine.
Thomas and team conducted a randomized, controlled, and observer-blind trial - that is, the nurses who evaluated the patients were unaware of the treatment that the participants were undergoing - and called it the "CLOTHES Trial."
The team recruited 300 children aged between 1 and 15 who received community and secondary care for moderate to severe eczema across five medical centers in the U.K.
Participants were randomized into two groups: one group received standard care for eczema and wore silk clothing, while the other group received standard care alone.
In the first group, the children wore the silk clothing - which was made of 100 percent sericin-free silk - for 6 months. Using the Eczema Area and Severity Index (EASI), the researchers evaluated the severity of eczema at the beginning of the study, and then at 2, 4, and 6 months, respectively.
The researchers adjusted for the children's age and the medical center from which they were recruited.
Thomas and colleagues averaged the EASI score for the two groups and found no significant difference between them.
Specifically, 25 percent of the children in the silk garments plus standard care group developed skin infections, compared with 28 percent in the group that received only standard care. The small treatment effect was considered insignificant from a statistical and clinical standpoint, as the 95 percent confidence interval varied from 1.5 points in favor of silk garments to 0.5 in favor of standard care alone - a difference too small to be considered relevant.
Additionally, the study found no difference in the quality of life between the two groups.
Furthermore, the researchers calculated the cost of using silk therapeutically per quality-adjusted life year, and they concluded that silk garments are not cost-effective. The computed yearly cost amounted to 56,881, which corresponds to around $70,550.
The researchers explain the significance of the findings:
"The CLOTHES Trial is the first large, independent [randomized, controlled trial] to have evaluated silk garments for the management of eczema. The results of this trial suggest that silk garments are unlikely to provide additional clinical or economic benefits over standard care for children with moderate to severe eczema."
However, the authors also admit a limitation of the study: although using an objective primary outcome measure - namely, the EASI score, assessed by nurses who were blinded to the treatment - minimized detection bias, it may have also ignored changes in symptoms and underestimated the beneficial effects of the treatment.
Learn how an arthritis drug successfully treated eczema.
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Silk clothing did not improve eczema in children – Science Daily
Posted: at 11:23 pm
No significant differences were observed in eczema severity for children with moderate to severe eczema who wore silk garments compared with those who wore their usual clothing, according to a randomized controlled study published in PLOS Medicine by Kim Thomas from University of Nottingham, UK, and colleagues.
Clothing may play a role in either exacerbating or soothing eczema, and patients often avoid wool garments and turn to cotton and other fine weave fabrics, including silk. In the new study, 300 children age 1 to 15 years with moderate to severe eczema were recruited from five UK centers covering a range of rural and urban settings. The participants were randomly divided into two groups: half the children received the standard of care and the other half received the standard of care plus silk garments that are claimed to be beneficial for eczema.
After 6 months, there was no significant difference in eczema severity -- based on the Eczema Area and Severity Index -- and no difference in quality of life or medication use between the groups. The researchers report that the garments are unlikely to be cost-effective even if the small differences between groups were genuine, with a computed cost per quality adjusted life year of silk garments to be GBP 56,811.
A limitation of the study is that the use of an objective outcome measure (an eczema severity score assessed by research nurses) may underestimate changes in symptoms.
The authors say: "The results of this trial suggest that silk garments are unlikely to provide additional clinical or economic benefits over standard care for children with moderate to severe eczema."
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FDA approved a new ointment for eczema that can help manage symptoms – Miami Herald
Posted: at 11:23 pm
FDA approved a new ointment for eczema that can help manage symptoms Miami Herald Eucrista, also called crisaborole, is an FDA-approved ointment used to treat mild to moderate eczema in adults and children ages 2 and older. It is not a steroid and does not cause skin thinning and other side effects that occur with prolonged steroid use. |
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New Ways to Control Eczema – Newsmax
Posted: at 11:23 pm
Diversity is required to create a healthy body politic and a healthy body, inside and out.
You've heard a lot about the various "good" and "bad" bacteria that make up your gut biome. But you may not know that your skin is also home to a wildly rich and, when healthy, very diverse bacterial soup.
Scientists have discovered that on healthy skin, harmful Staphylococcus aureus is kept in check by its friendlier cousin, Staphylococcus epidermidis.
But on people with eczema specifically atopic dermatitis (AD), the most common type of eczema there is an overgrowth of S. aureus compared to S. epidermidis.
When researchers check the biome in the inner elbow or the back of the knee on folks with AD, they find an imbalance of those microbes. And the less diversity there is the less healthy the skin.
But a skin biome transplant may be possible: When gram-negative bacteria is collected from healthy human skin and cultured in the lab, it can be put into a treatment (maybe a cream) that can knock out AD.
This breakthrough in understanding of the skin biome means that there's good news on the horizon for the 17.8 million Americans with AD.
So stay tuned for the next round of research and, in the meantime, try taking a probiotic capsule regularly. That can add healthful diversity to your skin biome, as well as your gut.
And if you have AD, avoid antibacterial soaps and household products that can further upset your skin biome.
2017 NewsmaxHealth. All rights reserved.
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Silk clothing not effective in reducing children’s eczema – Nursery World (subscription)
Posted: at 11:23 pm
13 April 2017 by Katy Morton
Researchers found that use of silk clothing does not improve children's eczema
Findings from the trial, which involved 300 children aged one to 15 years of age with moderate to severe eczema, suggest that wearing specialist silk garments does not reduce the severity of the skin condition, nor does it lessen the amount of cream and ointment needed to treat eczema.
Results of the CLOTHing for the relief of Eczema Symptoms trial (CLOTHES trial) are published in the journal PLOS Medicine.
According to researchers from the University of Nottingham, who led the trial, clothing has been thought to play a role in either soothing or making eczema symptoms worse, and specialist clothing is now available on prescription in the UK in a variety of forms, including silk.
The aim of the clinical trial was to determine whether adding silk garments to standard eczema care could reduce the severity of eczema in children with the condition.
Those who took part were split into two groups. One group continued with just their normal eczema treatments, while the other group used their normal eczema treatment and wore silk garments - long-sleeved silk vests and leggings, during the day and night. At the time of the trial, the same silk garments were available on prescription.
All the children continued regularly using emollient creams and topical steroids for controlling inflammation, and were asked not to change their standard treatment for the duration of the trial if possible.
Throughout the trial, their skin was assessed by nurses every two months using the Eczema Area and Severity Index (EASI), which measures how bad eczema is, for example how red and inflamed the skin looks, evidence of scratch marks and skin swelling. Researchers also assessed the childrens eczema symptoms, use of creams and steroids, quality of life and the number of skin infections and hospital admissions.
In terms of severity of eczema, quality of life and use of eczema medications, the researchers found no difference between the children in the two groups. The number of skin infections and hospitalisations due to eczema were also similar.
However, children who used the silk clothing did report small improvements in their eczema, but the differences were minimal.
Professor Kim Thomas from the Centre for Evidence-based Dermatology in the University of Nottinghams School of Medicine, who led the trial, said, The silk garments that we looked at as part of this trial did not appear to provide additional clinical or economic benefits over standard care for the management of children with eczema.
While some may find these results disappointing, we hope that patients and doctors will find the CLOTHES study useful in helping them to make informed decisions about how best to help children with eczema. Unfortunately, this trial suggests that silk clothing probably does not provide value for money for patients or for the NHS.
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How Living With Psoriasis Changed ‘Scandal’ Star Katie Lowes’ Life – Us Weekly
Posted: at 11:22 pm
Katie Lowes is known for her role in the hit television show, Scandal, but what fans may not know is that the actress is living with psoriasis. Lowes chatted with Stylish to talk about her battle with the autoimmune disease, and how it has affected her life.
"I was 28 years old, I was engaged to my then boyfriend, now husband [actor Adam Shapiro], and we were planning our wedding, which can be a stressful occasion," Lowes, 35, tells Stylish. "I also booked Scandal, which was the biggest job I had ever booked and it was kind of a big break for me, and all eyes were on me in Hollywood. The combination of those things really caused my symptoms to come out for the first time and also grow."
In fact, her psoriasis symptoms typically, dry, itchy patches that can appear anywhere on your skin and flake became so severe she cancelled her engagement-photo shoot. After that, "I said to myself, 'Wow, this has gotten too far. Whatever denial I'm in, I'm actually canceling important, momentous life occasions due to something that's going on with me, and I need to really get a handle on it.'"
That's when she did her research, discovered she had psoriasis and changed her whole lifestyle. "It's a lot about water and weather," she explains. "Am I traveling somewhere that's humid, or am I traveling somewhere that's dry? Am I going to workout and do a hard sweat today or something lighter, like pilates? It's also about stress and diet for me. If I'm on vacation and eating pizza 500 times a day, that can cause a flare up."
Another thing she revamped? Her beauty bag. "For sure, I changed my skincare and beauty routine. I use all-natural beauty products and products for sensitive skin, because it is a little bit about the products you use." A few of her faves? EO Botanical Body Oil in French Lavender ($6, amazon.com), Original Sprout Scrumptious Baby Cream ($29, dermstore.com) and Crystal Essence Natural Mineral Roll-On Deodorant ($5, jet.com).
And now, she's partnering up with the National Psoriasis Foundation to help create awareness. "I feel like there's so much embarrassment and shame surrounding disease," Lowes tells Stylish of the condition that Kim Kardashian and LeAnn Rimes also battle. "It's something we don't talk about, and I'm just like, 'Well, here I am. I'm an actress in Hollywood, and I'm on TV, and people look at me, yes, and I have it.'" She collaborated with the foundation on psoriasisinsidestory.com, which, she says, "is about that inside monologue that goes on in your head about that shame and embarrassment, how you feel terrible and like you're not good enough. With the website you can talk to other people who are going through it, see what helps them and realize you are not alone."
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Kadmon (KDMN) Announces Publication of Data on KD025 in Psoriasis Patients – StreetInsider.com
Posted: at 11:22 pm
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Kadmon Holdings, Inc. (NYSE: KDMN) (Kadmon or the Company) today announced the publication of clinical data from its completed Phase 2 open-label clinical trial of KD025, its oral Rho-associated coiled-coil kinase 2 (ROCK2) inhibitor, in patients with moderate to severe psoriasis. In the study, KD025 treatment improved clinical scores and skin pathology in psoriasis patients via concurrent modulation of the pro- and anti-inflammatory immune cell response. The results were published this week in the Cutting Edge section of the Journal of Immunology.
Preclinical and clinical studies by Kadmon researchers have previously demonstrated the importance of the ROCK2 signaling pathway in autoimmune disease settings. To further explore the therapeutic potential of ROCK2 inhibition, Kadmon conducted a 12-week, open-label, Phase 2 study of KD025 in 38 patients with moderate to severe psoriasis. The results demonstrated that KD025 affected the cellular mechanisms associated with psoriasis progression, as measured in both peripheral blood and the skin, leading to improvements in clinical scores of patients at 12 weeks. Specifically, KD025 significantly reduced peripheral blood levels of IL-17 and IL-23, two pro-inflammatory cytokines, and showed a correlation between changes in IL-17 levels and patients clinical scores. In addition, researchers observed a concurrent up-regulation of the immunosuppressive cytokine IL-10 and a significant increase in the percentage of Foxp3+ CD4 T cells in blood, which diminish immuno-inflammatory response. Together, these findings demonstrated the potential of selective ROCK2 inhibition to modulate pro- and anti-inflammatory immune cell responses to treat psoriasis.
We have demonstrated the molecular mechanism of action by which ROCK2 inhibition with KD025 modulates the immune system to treat psoriasis, correlating with improvements in patients clinical scores and symptoms, said Alexandra Zanin-Zhorov, PhD, Vice President, Head of Immunology at Kadmon and corresponding author of the manuscript. These results are consistent with our previously published preclinical animal models and cell-based in vitro assays and provide further evidence of the importance of ROCK2 signaling in autoimmune diseases like psoriasis.
We have demonstrated the crucial role of the ROCK2 signaling pathway in rebalancing immune response in patients, further validating the therapeutic potential of KD025 in autoimmune disease, said Harlan W. Waksal, M.D., President and CEO at Kadmon. We hope to confirm these findings in our ongoing placebo-controlled Phase 2 study of KD025 in psoriasis, which will be carried out for a longer time period in a larger patient population.
The manuscript, titled Selective Oral ROCK2 Inhibitor Reduces Clinical Scores in Patients with Psoriasis Vulgaris and Normalizes Skin Pathology via Concurrent Regulation of IL-17 and IL-10, is available on the Journal of Immunology website here.
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Consensus Study on Human Gene Editing – National-Academies.org
Posted: at 11:22 pm
Consensus Study
Background
With the conclusion of the International Summit on Human Gene Editing, the second component of the Human Gene-Editing Initiative began: a comprehensive study of the scientific underpinnings of human gene-editing technologies, their potential use in biomedical research and medicine -- including human germline editing -- and the clinical, ethical, legal, and social implications of their use.
A multidisciplinary committee of expertsbegan its information-gathering process at the summit, and over the past year performed its own independent and in-depth review of the science and policy of human gene editing by reviewing the literature and holding data-gathering meetings in the U.S. and abroad to solicit broad input from researchers, clinicians, policymakers, and the public. The committee also monitored for the latest scientific achievements of importance in this rapidly developing field.
While informed by the statement issued by the organizing committee for the international summit, the consensus study committee had broad discretion to arrive at its own findings and conclusions. The committee's report represents the official views of NAS and NAM.
Moreabout the study| Info onpublic meetings | Answers tofrequently asked questions
Human Genome Editing: Science, Ethics, and Governance
Genome editing is a powerful new tool for making precise alterations to an organisms genetic material. Recent scientific advances have made genome editing more efficient, precise, and flexible than ever before. These advances have spurred an explosion of interest from around the globe in the possible ways in which genome editing can improve human health. The speed at which these technologies are being developed and applied has led many policymakers and stakeholders to express concern about whether appropriate systems are in place to govern these technologies and how and when the public should be engaged in these decisions.
In Human Genome Editing: Science, Ethics, and Governance, a new report from the National Academy of Sciences and National Academy of Medicine, an expert committee considers important questions about the human application of genome editing including: Balancing potential benefits with unintended risks, governing the use of genome editing, incorporating societal values into clinical applications and policy decisions, and respecting the inevitable differences across nations and cultures that will shape how and whether to use these new technologies. The committee sets forth criteria that must be met before permitting clinical trials of heritable germline editing, provides conclusions on the crucial need for public education and engagement, and presents seven general principles for the governance of human genome editing.
A Report Highlights brief is available:
The following one-pagers are also available:
Watch the archived video webcast of the report release briefing, held Feb. 14, 2017.
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