Archives for : novembre2013

Single-cell genome sequencing gets better and better

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Researchers led by bioengineers at the University of California, San Diego have generated the most complete genome sequences from single E. coli cells and individual neurons from the human brain. The breakthrough comes from a new single-cell genome sequencing technique that confines genome amplification to fluid-filled wells with a volume of just 12 nanoliters. “Our preliminary data suggest that individual neurons from the same brain have different genetic compositions. This is a relatively new idea, and our approach will enable researchers to look at genomic differences between single cells with much finer detail,” said Kun Zhang, a professor in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering and the corresponding author on the paper.


The researchers report that the genome sequences of single cells generated using the new approach exhibited comparatively little “amplification bias,” which has been the most significant technological obstacle facing single-cell genome sequencing in the past decade. This bias refers to the fact that the amplification step is uneven, with different regions of a genome being copied different numbers of times. This imbalance complicates many downstream genomic analyses, including assembly of genomes from scratch and identifying DNA content variations among cells from the same individual.


Sequencing the genomes of single cells is of great interest to researchers working in many different fields. For example, probing the genetic make-up of individual cells would help researchers identify and understand a wide range of organisms that cannot be easily grown in the lab from the bacteria that live within our digestive tracts and on our skin, to the microscopic organisms that live in ocean water. Single-cell genetic studies are also being used to study cancer cells, stem cells and the human brain, which is made up of cells that increasingly appear to have significant genomic diversity.

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PLOS ONE: Genetic Relatedness among Hepatitis A Virus Strains Associated with Food-Borne Outbreaks

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The genetic characterization of hepatitis A virus (HAV) strains is commonly accomplished by sequencing subgenomic regions, such as the VP1/P2B junction. HAV genome is not extensively variable, thus presenting opportunity for sharing sequences of subgenomic regions among genetically unrelated isolates. The degree of misrepresentation of phylogenetic relationships by subgenomic regions is especially important for tracking transmissions. Here, we analyzed whole-genome (WG) sequences of 101 HAV strains identified from 4 major multi-state, food-borne outbreaks of hepatitis A in the Unites States and from 14 non-outbreak-related HAV strains that shared identical VP1/P2B sequences with the outbreak strains. Although HAV strains with an identical VP1/P2B sequence were specific to each outbreak, WG were different, with genetic diversity reaching 0.31% (mean 0.09%). Evaluation of different subgenomic regions did not identify any other section of the HAV genome that could accurately represent phylogenetic relationships observed using WG sequences. The identification of 2–3 dominant HAV strains in 3 out of 4 outbreaks indicates contamination of the implicated food items with a heterogeneous HAV population. However, analysis of intra-host HAV variants from eight patients involved in one outbreak showed that only a single sequence variant established infection in each patient. Four non-outbreak strains were found closely related to strains from 2 outbreaks, whereas ten were genetically different from the outbreak strains. Thus, accurate tracking of HAV strains can be accomplished using HAV WG sequences, while short subgenomic regions are useful for identification of transmissions only among cases with known epidemiological association.

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How Do Viruses Avoid Inhibition by Endogenous Cellular MicroRNAs?

See on Scoop.itHost Cell & Pathogen Interactions

From molecules to physiology

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New imaging method ‘predicts’ heart attack risk

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Scientists have created an imaging technique that can detect which patients are at high risk of heart attack. The device ‘lights up’ fatty plaques in the arteries that may rupture.

Researchers from the University of Edinburgh in the UK say the test – carried out using positron emission tomography (PET) and computed tomography (CT) – is able to “light up” dangerous fatty plaques in the arteries that are in danger of rupturing. This is a process that can cause heart attacks.

To reach their findings, the researchers analyzed 80 patients. Of these, 40 patients recently had a heart attack, while the other 40 patients had angina – restricted blood supply to the heart posing a higher risk of heart attack.

‘First step’ towards heart attack prevention

Using the PET-CT scanner, the researchers found that 90% of patients who had a heart attack showed a “lit up” yellow area in one of their blood vessels. This area corresponded exactly to the location of the plaque that caused the patients’ heart attacks, the researchers say.

The scanner also showed lit up plaques in around 40% of the patients with angina. Furthermore, the researchers found “high-risk” features in these patients that suggested a heart attack may be imminent, meaning they were in need of aggressive drug treatment or surgery.


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Gelatin Bio-Ink May Allow Printing Of Organs And Tissue

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German researchers have developed a new gelatin bio-ink that can be used by 3D printing technology to produce various types of tissue and organs.

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Glioblastoma multiforme: Incurable brain cancer gene BCL2L12 is silenced

See on Scoop.itAmazing Science

Scientists at Northwestern University say they were able to demonstrate the successful delivery of a drug that turns off a critical gene in glioblastoma multiforme (GBM), increasing survival rates significantly in animals with the deadly disease. This form of brain cancer, which ended Sen. Edward Kennedy’s life, kills approximately 13,000 Americans a year.


According to the investigators, the novel therapeutic, which is based on nanotechnology, is small and nimble enough to cross the blood-brain barrier and get to where it is needed—the brain tumor.


Designed to target a specific cancer-causing gene in cells, the drug flips the switch of the oncogene to “off,” silencing the gene, they added. This knocks out the proteins that keep cancer cells immortal.


In a study of mice (“Spherical Nucleic Acid Nanoparticle Conjugates as an RNAi-Based Therapy for Glioblastoma”), the nontoxic drug was delivered by intravenous injection. In animals with GBM, the survival rate increased nearly 20%, and tumor size was reduced three to four fold, as compared to the control group. The results were published October 30 in Science Translational Medicine.


“We preclinically evaluate an RNA interference (RNAi)–based nanomedicine platform, based on spherical nucleic acid (SNA) nanoparticle conjugates, to neutralize oncogene expression in GBM,” wrote the scientists. “In vivo, the SNAs penetrated the blood-brain barrier and blood-tumor barrier to disseminate throughout xenogeneic glioma explants. SNAs targeting the oncoprotein Bcl2Like12 (Bcl2L12)—an effector caspase and p53 inhibitor overexpressed in GBM relative to normal brain and low-grade astrocytomas—were effective in knocking down endogenous Bcl2L12 mRNA and protein levels, and sensitized glioma cells toward therapy-induced apoptosis by enhancing effector caspase and p53 activity.”


“This is a beautiful marriage of a new technology with the genes of a terrible disease,” said Chad A. Mirkin, Ph.D., a nanomedicine expert and a senior co-author of the study.


“This proof-of-concept further establishes a broad platform for treating a wide range of diseases, from lung and colon cancers to rheumatoid arthritis and psoriasis.”


The power of gene regulation technology is that a disease with a genetic basis can be attacked and treated if scientists have the right tools, pointed out Dr. Mirkin. Thanks to the Human Genome Project and genomics research over the last two decades, there is an enormous number of genetic targets; having the right therapeutic agents and delivery materials has been the challenge, he explained.


“The RNA interfering-based SNAs are a completely novel approach in thinking about cancer therapy,” said Alexander H. Stegh, Ph.D., a co-author on the study. “One of the problems is that we have large lists of genes that are somehow disregulated in glioblastoma, but we have absolutely no way of targeting all of them using standard pharmacological approaches.


That’s where we think nanomaterials can play a fundamental role in allowing us to implement the concept of personalized medicine in cancer therapy.”


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Mobile Technology and App Use by Physicians (Poll by Sermo)

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A bias persists that doctors don’t use technology enough, particularly social media and apps.  A Poll by Sermo however shows that while some doctors are reluctant to enter the digital pool, once they adopt, they adopt enthusiastically. Doctors are open to adopting more technology to manage their practices and they embrace medical reference apps.

The most popular smart phone for physicians is the iPhone according to MedCrunch. A few top apps are listed below

Medscape.  Used by over 3 million doctors, nurses and medical students worldwide, Medscape is big.  You can use it for medical news, clinical reference to things like drugs, diseases, conditions and procedures, and even provides medical education.


EpocratesRx.   This app is popular for drug interactions, research, Pill ID and medicine calculators.   The lite version is free, but you can purchase the full version for $160.


NeuroMind is a great app for neurologists, neurosurgeons and med students.  It provides basic safety checklist requirements via the World Health Organization, and has “interactive clinical decision support.”  It is the number one neuro app with over 140,000 downloads.



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New Non-Invasive Skin Biopsy Technology Makes Doctor Visits Easier

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Skin biopsies can be painful, long, and expensive. Caliber I.D. has developed a skin biopsy technology that uses lasers to perform skin biopsies.

The VivaScope system is a high-resolution medical imaging system that allows doctors to perform skin biopsies, to test for cancerous cells in moles, for example, without cutting into a patient’s skin.

For a traditional skin biopsy, a dermatologist will numb the specified area, excise a piece of skin, and send it off to a pathology lab. The pathologists in the lab then freeze, section, and stain the skin sample and look at it under a microscope. Results could take up to a week. VivaScope eliminates most of this procedure, allowing real time diagnoses.

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Genetic sequencing and modeling of cold virus illustrate cure difficulty | Vaccine News Daily

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