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Thursday 29 March 2012

1000 Genomes Project and AWS

Data from the 1000 Genomes project - The world's largest set of data on human genetic variation produced by the international 1000 Genomes Project — is now publicly available on the Amazon Web Services (AWS) cloud (http://aws.amazon.com/1000genomes/). See the NIH press realease for more information: (http://1.usa.gov/Hnt1f7). 1000 genomes data may also be downloaded from the NCBI though ftp (http://bit.ly/Hlj3wM) or through the Aspera protocol (http://1.usa.gov/d9ON7X)

1000 Genomes Project and AWS

The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research. The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year.
The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: s3.amazonaws.com/1000genomes

Accessing 1000 Genomes Data

AWS is making the 1000 Genomes Project data publicly available to the community free of charge. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. Learn more about Public Data Sets on AWS.
All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket.
You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP.

Analyzing 1000 Genomes Data

Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse.
Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow.

Other Sources
The 1000 Genomes project data are also freely accessible through the 1000 Genomes website, and from each of the two institutions that work together as the project Data Coordination Centre (DCC).
 
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Wednesday 28 March 2012

nanoscale sensor to electronically read the sequence of a single DNA molecule

Researchers have devised a nanoscale sensor to electronically read the sequence of a single DNA molecule, a technique that is fast and inexpensive and could make DNA sequencing widely available.
The various levels of electrical signal from the sequence of a DNA strand pulled through a nanopore reader (top) corresponds to specific DNA nucleotides, thymine, adenine, cytosine and guanine (bottom). (Credit: University of Washington)
The technique could lead to affordable personalized medicine, potentially revealing predispositions for afflictions such as cancer, diabetes or addiction.
"There is a clear path to a workable, easily produced sequencing platform," said Jens Gundlach, a University of Washington physics professor who leads the research team. "We augmented a protein nanopore we developed for this purpose with a molecular motor that moves a DNA strand through the pore a nucleotide at a time."
The researchers previously reported creating the nanopore by genetically engineering a protein pore from a mycobacterium. The nanopore, from Mycobacterium smegmatis porin A, has an opening 1 billionth of a meter in size, just large enough for a single DNA strand to pass through.
To make it work as a reader, the nanopore was placed in a membrane surrounded by potassium-chloride solution, with a small voltage applied to create an ion current flowing through the nanopore. The electrical signature changes depending on the type of nucleotide traveling through the nanopore. Each type of DNA nucleotide -- cytosine, guanine, adenine and thymine -- produces a distinctive signature.
The researchers attached a molecular motor, taken from an enzyme associated with replication of a virus, to pull the DNA strand through the nanopore reader. The motor was first used in a similar effort by researchers at the University of California, Santa Cruz, but they used a different pore that could not distinguish the different nucleotide types.
Gundlach is the corresponding author of a paper published online March 25 by Nature Biotechnology that reports a successful demonstration of the new technique using six different strands of DNA. The results corresponded to the already known DNA sequence of the strands, which had readable regions 42 to 53 nucleotides long.
"The motor pulls the strand through the pore at a manageable speed of tens of milliseconds per nucleotide, which is slow enough to be able to read the current signal," Gundlach said.
Gundlach said the nanopore technique also can be used to identify how DNA is modified in a given individual. Such modifications, referred to as epigenetic DNA modifications, take place as chemical reactions within cells and are underlying causes of various conditions.
"Epigenetic modifications are rather important for things like cancer," he said. Being able to provide DNA sequencing that can identify epigenetic changes "is one of the charms of the nanopore sequencing method."
Coauthors of the Nature Biotechnology paper are Elizabeth Manrao, Ian Derrington, Andrew Laszlo, Kyle Langford, Matthew Hopper and Nathaniel Gillgren of the UW, and Mikhail Pavlenok and Michael Niederweis of the University of Alabama at Birmingham.
The work was funded by the National Human Genome Research Institute in a program designed to find a way to conduct individual DNA sequencing for less than $1,000. When that program began, Gundlach said, the cost of such sequencing was likely in the hundreds of thousands of dollars, but "with techniques like this it might get down to a 10-dollar or 15-minute genome project. It's moving fast."

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Tuesday 27 March 2012

Saturday 24 March 2012

Diatom Biosensor Could Shine Light On Future Nanomaterials

A glow coming from the glassy shell of microscopic marine algae called diatoms could someday help us detect chemicals and other substances in water samples. And the fact that this diatom can glow in response to an external substance could also help researchers develop a variety of new, diatom-inspired nanomaterials that could solve problems in sensing, catalysis and environmental remediation.

A side and front view of the microscopic marine diatom Thalassiosira pseudonana. PNNL scientists used this species to develop a fluorescent biosensor that changes its glow in the presence of the sugar ribose. (Credit: Nils Kröger, Universität Regensburg)



Fluorescence is the key characteristic of a new biosensor developed by researchers at the Department of Energy's Pacific Northwest National Laboratory. The biosensor, described in a paper published this week in the scientific journal PLoS ONE, includes fluorescent proteins embedded in a diatom shell that alter their glow when they are exposed to a particular substance.
"Like tiny glass sculptures, the diverse silica shells of diatoms have long intrigued scientists," said lead author and molecular biologist Kate Marshall, who works out of PNNL's Marine Sciences Laboratory in Sequim, Wash. "And the way our biosensor works could make diatoms even more attractive to scientists because it could pave the way for the development of novel, synthetic silica materials."
Diatoms are perhaps best known as the tiny algae that make up the bulk of phytoplankton, the plant base of the marine food chain that feeds the ocean's creatures. But materials scientists are fascinated by diatoms for another reason: the intricate, highly-ordered patterns that make up their microscopic shells, which are mostly made of silica. Researchers are looking at these minuscule glass cages to solve problems in a number of areas, including sensing, catalysis and environmental remediation.
PNNL Laboratory Fellow and corresponding author Guri Roesijadi found inspiration for this biosensor in previous work by other researchers, who showed it's possible to insert proteins in diatom shells through genetic engineering. Using that work as a starting point, Roesijadi, Marshall and their PNNL colleagues aimed to use fluorescent proteins to turn diatoms into a biosensor. They specifically aimed to create a reagent-less biosensor, meaning one that detects a target substance on its own and without depending on another chemical or substance.
Well-equipped diatom
As a test case, the PNNL team inserted genes for their biosensor into Thalassiosira pseudonana, a well-studied marine diatom whose shell resembles a hatbox. The new genes allowed the diatoms to produce a protein that is the biosensor.
At the heart of the biosensor is the ribose-binding protein, which, as the name suggests, attaches to the sugar ribose. Each ribose-binding protein is then flanked by two other proteins -- one that glows blue and another that glows yellow. This three-protein complex attaches to the silica shell while the diatom grows.
In the absence of ribose, the two fluorescent proteins sit close to one another. They're close enough that the energy in the blue protein's fluorescence is easily handed off, or transferred, to the neighboring yellow protein. This process, called fluorescence resonance energy transfer, or FRET, is akin to the blue protein shining a flashlight at the yellow protein, which then glows yellow.
But when ribose binds to the diatom, the ribose-binding protein changes its shape. This moves the blue and yellow fluorescent proteins apart in the process, and the amount of light energy that the blue protein shines on the yellow protein declines. This causes the biosensor to display more blue light.
Microscopic light show
Regardless of whether or not ribose is bound to the diatom's biosensor, the biosensor always emits some blue or yellow glow when it's exposed to energy under a microscope. But the key difference is how much of each kind of light is displayed.
The PNNL team distinguished between light from the two proteins with a fluorescence microscope that was equipped with a photon sensor. The sensor allowed them to measure the intensities of the unique wavelengths of light given off by each of the fluorescent proteins. By calculating the ratio of the two wavelengths, they could determine if the diatom biosensor was exposed to ribose, and how much of ribose was present.
The team also succeeded in making the biosensor work with the shell alone, after it was removed from the living diatom. Removing the living diatom provides researchers greater flexibility in how and where the silica biosensor can be used. The Office of Naval Research, which funded the research, believes biosensors based on modifying a diatom's silica shell may prove useful for detecting threats such as explosives in the marine environment.
"With this research, we've made our important first steps to show it's possible to genetically engineer organisms such as diatoms to create advanced materials for numerous applications," Marshall said.
Co-authors on the paper include scientists at EMSL, DOE's Environmental Molecular Sciences Laboratory at PNNL's Richland, Wash., campus. They used EMSL's mass spectrometry capabilities to verify the team had the correct ribose-binding and fluorescent proteins before adding them to the diatoms.

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Shiny New Tool for Imaging Biomolecules

At the heart of the immune system that protects our bodies from disease and foreign invaders is a vast and complex communications network involving millions of cells, sending and receiving chemical signals that can mean life or death. At the heart of this vast cellular signaling network are interactions between billions of proteins and other biomolecules. These interactions, in turn, are greatly influenced by the spatial patterning of signaling and receptor molecules. The ability to observe signaling spatial patterns in the immune and other cellular systems as they evolve, and to study the impact on molecular interactions and, ultimately, cellular communication, would be a critical tool in the fight against immunological and other disorders that lead to a broad range of health problems including cancer. Such a tool is now at hand.

Gold triangle nanoparticles paired tip-to-tip in a bow-tie formation, serve as optical antennas. When a protein (green) bound to a fluorescently labeled SOS-catalyst passes through the the gaps between opposing tips of the triangles (plasmonic hot spots) fluorescence is amplified. (Credit: Image courtesy of DOE/Lawrence Berkeley National Laboratory)


Researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley, have developed the first practical application of optical nanoantennas in cell membrane biology. A scientific team led by chemist Jay Groves has developed a technique for lacing artificial lipid membranes with billions of gold "bowtie" nanoantennas. Through the phenomenon known as "plasmonics," these nanoantennas can boost the intensity of a fluorescent or Raman optical signal from a protein passing through a plasmonic "hot-spot" tens of thousands of times without the protein ever being touched.
"Our technique is minimally invasive since enhancement of optical signals is achieved without requiring the molecules to directly interact with the nanoantenna," Groves says. "This is an important improvement over methods that rely on adsorption of molecules directly onto antennas where their structure, orientation, and behavior can all be altered."
Groves holds joint appointments with Berkeley Lab's Physical Biosciences Division and UC Berkeley's Chemistry Department, and is also a Howard Hughes Medical Institute investigator. He is the corresponding author of a paper that reports these results in the journal NanoLetters. The paper is titled "Single Molecule Tracking on Supported Membranes with Arrays of Optical Nanoantennas." Co-authoring the paper were Theo Lohmuller, Lars Iversen, Mark Schmidt, Christopher Rhodes, Hsiung-Lin Tu and Wan-Chen Lin.
Fluorescent emissions, in which biomolecules of interest are tagged with dyes that fluoresce when stimulated by light, and Raman spectroscopy, in which the scattering of light by molecular vibrations is used to identify and locate biomolecules, are work-horse optical imaging techniques whose value has been further enhanced by the emergence of plasmonics. In plasmonics, light waves are squeezed into areas with dimensions smaller than half-the-wavelength of the incident photons, making it possible to apply optical imaging techniques to nanoscale objects such as biomolecules. Nano-sized gold particles in the shape of triangles that are paired in a tip-to-tip formation, like a bow-tie, can serve as optical antennas, capturing and concentrating light waves into well-defined hot spots, where the plasmonic effect is greatly amplified. Although the concept is well-established, applying it to biomolecular studies has been a challenge because gold particle arrays must be fabricated with well-defined nanometer spacing, and molecules of interest must be delivered to plasmonic hot-spots.
"We're able to fabricate billions of gold nanoantennas in an artificial membrane through a combination of colloid lithography and plasma processing," Groves says. "Controlled spacing of the nanoantenna gaps is achieved by taking advantage of the fact that polystyrene particles melt together at their contact point during plasma processing. The result is well-defined spacing between each pair of gold triangles in the final array with a tip-to-tip distance between neighboring gold nanotriangles measuring in the 5-to-100 nanometer range."
Until now, Groves says, it has not been possible to decouple the size of the gold nanotriangles, which determines their surface plasmon resonance frequency, from the tip-to-tip distance between the individual nanoparticle features, which is responsible for enhancing the plasmonic effect. With their colloidal lithography approach, a self-assembling hexagonal monolayer of polymer spheres is used to shadow mask a substrate for subsequent deposition of the gold nanoparticles. When the colloidal mask is removed, what remains are large arrays of gold nanoparticles and triangles over which the artificial membrane can be formed.
The unique artificial membranes, which Groves and his research group developed earlier, are another key to the success of this latest achievement. Made from a fluid bilayer of lipid molecules, these membranes are the first biological platforms that can combine fixed nanopatterning with the mobility of fluid bilayers. They provide an unprecedented capability for the study of how the spatial patterns of chemical and physical properties on membrane surfaces influence the behavior of cells.
"When we embed our artificial membranes with gold nanoantennas we can trace the trajectories of freely diffusing individual proteins as they sequentially pass through and are enhanced by the multiple gaps between the triangles," Groves says. "This allows us to study a realistic system, like a cell, which can involve billions of molecules, without the static entrapment of the molecules."
As molecules in living cells are generally in a state of perpetual motion, it is often their movement and interactions with other molecules rather than static positions that determine their functions within the cell. Groves says that any technique requiring direct adsorption of a molecule of interest onto a nanoantenna intrinsically removes that molecule from the functioning ensemble that is the essence of its natural behavior. The technique he and his co-authors have developed allows them to look at individual biomolecules but within the context of their surrounding community.
"The idea that optical nanoantennas can produce the kinds of enhanced signals we are observing has been known for years but this is the first time that nanoantennas have been fabricated into a fluid membrane so that we can observe every molecule in the system as it passes through the antenna array," Groves says. "This is more than a proof-of-concept we've shown that we now have a useful new tool to add to our repertoire."
This research was primarily supported by the DOE Office of Science.

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Wednesday 21 March 2012

Need for Speed: Molecular Ticket Determines RNA’s Destination and Speed Inside Egg Cell

Like any law-abiding train passenger, a molecule called oskar RNA carries a stamped ticket detailing its destination and form of transport, scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, have found. They show that for this molecule, moving in the right direction isn't enough: speed is of the essence. Their study, published online March 18 in Nature Structural & Molecular Biology, also provides clues as to how a single molecule could receive tickets for different destinations, depending on what type of cell it is in


Oskar RNA (red) is transported to the posterior pole in a normal fruit fly egg cell (top), but not in an oocyte with a mutated SOLE tag (bottom). (Credit: Copyright EMBL/S.Gosh)

For a fruit fly embryo to develop properly, oskar RNA produced by the mother has to enter the egg cell, or oocyte, as it matures, and be taken to one of its ends -- the posterior pole. Researchers in Anne Ephrussi's group at EMBL have now found that this movement is more complicated than it seemed. When oskar is processed for transport by a mechanism called splicing, two different tags -- SOLE and EJC -- are attached to it, next to each other, at a specific spot. Ephrussi and colleagues found that both tags have to be in place for oskar to reach the right destination. Together, they seem to form a ticket that marks oskar for transport to the posterior pole, differentiating it from the many other RNAs that enter the oocyte bound for different destinations.
When they genetically altered the SOLE tag, the scientists found that oskar didn't go to the oocyte's posterior pole, as it should. But surprisingly, it did still move, and seemingly in the right direction. The problem, the researchers realised, was that oskar is racing towards a moving target. As the oocyte grows, it becomes longer, in effect taking the posterior pole further and further away as oskar is carried towards it. With a defective SOLE tag, oskar seemed unable to move fast enough to overcome the oocyte's growth. So somehow this 'ticket' affects the speed of transport, too.
Ephrussi and colleagues are now investigating how SOLE and EJC interact with each other, and how they might influence the cellular machinery that transports oskar. The scientists would also like to explore an interesting possibility raised by their current findings. They discovered that the SOLE tag is only formed if the RNA molecule is spliced. Since some RNAs can be spliced at different spots along their length, this means the same RNA could potentially be issued with tickets for different destinations -- for instance, in different cell types -- depending on which parts of it are spliced.

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Thursday 15 March 2012

How Muscle Cells Seal Their Membranes

Every cell is enclosed by a thin double layer of lipids that separates the distinct internal environment of the cell from the extracellular space. Damage to this lipid bilayer, also referred to as plasma membrane, disturbs the cellular functions and may lead to the death of the cell. For example, downhill walking tears many little holes into the plasma membranes of the muscle cells in our legs. To prevent irreparable damage, muscle cells have efficient systems to seal these holes again. Researchers at Karlsruhe Institute of Technology (KIT) and Heidelberg University have succeeded for the first time in observing membrane repair in real-time in a living organism.


Repair of the plasma membrane of a cell: For the first time, researchers have observed the relevant repair mechanisms in zebrafish. (Credit: Institute of Toxicology and Genetics, KIT)
The results were published in the recent issue of the journal Developmental Cell. Using a novel high-resolution imaging method, Prof. Uwe Strähle and Dr. Urmas Roostalu for the first time observed membrane repair in real time in a living animal. They tagged repair proteins with fluorescent proteins in muscle of the transparent zebrafish larvae. With a laser, the researchers burned tiny holes into the plasma membrane of muscle cells and followed the repair of the holes under the microscope. They showed that membrane vesicles together with two proteins Dysferlin and Annexin A6 rapidly form a repair patch. Other Annexins accumulate subsequently on the injured membrane. These studies by Karlsruhe and Heidelberg researchers suggest that the cell assembles a multilayered repair patch from the inside that seals off the cell's interior from the extracellular environment. Moreover, it was found that there is a specialized membrane area that supplies rapidly the membrane that is needed for sealing the plasma membrane hole.
This animal model for membrane repair will contribute to the identification of new proteins in this sealing process and will help elucidate the underlying mechanisms. The results may contribute to the development of therapies for human myopathies and open up new possibilities in biotechnology.
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Tuesday 13 March 2012

DST JRF & RA Jobs in University of Calcutta, Kolkata

Recruitment for the post of Junior Research Fellow and Research Associate for DST funded project in S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata
Project Title: Molecular Genetic Studies of Cognitive Function Among Parkinson’s Disease Patients of India.
1. Post: Junior Research Fellow
No. of Post: One
Eligibility: M.Sc in Life Sciences, preferably Neuroscience with NET qualification.
2. Post: RA
No. of Post: One
Eligibility: PhD/MD with publications in peer reviewed journals.
Date and Time: March 21, 2012 at 3:00 pm.
Venue: S. N. Pradhan Centre for Neurosciences, 5th Floor, 35, Ballygunge Circular Road, Kolkata – 700 019.
Candidates are requested to bring with them two sets of Bio-data, containing academic qualification and research / teaching experience (if any) with original and attested copies of certificates.

for further info:
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Jobs for Scientist / Senior Scientist Positions in CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow

Applications are invited for the following posts:
1. Post: Scientist / Senior Scientist (Agronomy / Soil Science)
Essential Qualification: Ph.D. submitted in the area of Agronomy / Soil Science for Scientist or Ph.D. in the area of Agronomy / Soil Science with two years postdoctoral research experience in related area for Senior Scientist.


2. Post: Scientist / Sr. Scientist (Plant Biochemistry/Plant Biotechnology)
Essential Qualification: Ph.D. submitted in the area of Plant Biochemistry/Plant Biotechnology for Scientist or Ph.D. in the area of Plant Biochemistry/Plant Biotechnology with two years postdoctoral research experience in related area for Senior Scientist.


3. Post: Scientist / Senior Scientist (Structural Chemistry)
Essential Qualification: Ph.D. submitted in the area of Crystallography for Scientist or Ph.D in the area of Crystallography with minimum two years postdoctoral research experience in related area for Senior Scientist.


4. Post: Scientist / Senior Scientist (For CSIR-800 Rural Sector Program)
Essential Qualification: M.Sc. in Agricultural Sciences with MBA (1st class) in Rural Management or Ph.D. submitted in the area of Agricultural Sciences for Scientist position or M.Sc. in Agricultural Sciences with MBA (1st class) in Rural Management with three years experience in relevant area or Ph.D. in the area of Agricultural Sciences with two years research experience in Agriculture extension
related activities for Senior Scientist.


5. Post: Scientist / Senior Scientist (Agronomy)
Essential Qualification: Ph.D. submitted in the area of Agronomy for Scientist or Ph.D. in the area of Agronomy with two years postdoctoral research experience in related area for Senior Scientist.


6. Post: Scientist / Senior Scientist (Publications)
Essential Qualification: Ph.D. submitted in the area of Botany/Chemistry/Biochemistry for Scientist or Ph.D. in the area of Botany/Chemistry/Biochemistry with two years postdoctoral research experience in related area for Senior Scientist.

Applications on prescribed form duly completed in all respects alongwith a recent passport size photograph, attested copies of certificates of educational qualification, experience certificate, reprints of published papers, community certificate (in the case of SC/ST/OBC etc.) and application fee of Rs. 100/- only for general and OBC category candidates (no fee is payable by the candidates belonging to SC/ST community, Physically Handicapped persons and regular employees of CSIR) through an a/c payee Bank Draft issued by State Bank of India (SBI) with a six months validity, drawn in favour of Director, Central Institute of Medicinal and Aromatic Plants, Lucknow or Director, CIMAP, Lucknow payable at State Bank of India, Main Branch, Lucknow should be sent to the Administrative Officer, CIMAP, Post Office-CIMAP, Lucknow so as to reach us on or before 25th April 2012.

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Senior Research Fellow Jobs in Entomology at GBPUAT, Pantnagar

Vacancies for the post of Senior Research Fellow in Department of Entomology, G. B. Pant University of Agriculture & Technology, Pantnagar


Applications are invited for the following post:
Post: Senior Research Fellow

Project Title: Evaluation of Imidacloprid 600FS as seed treatment for early season insect control and plant health effects in rice.

Consolidated Fellowship: Rs. 16000/- month

Applicants holding M.Sc. (Ag) in Entomology may send their application to Dr. S.N. Tiwari, Principal Investigator, Department of Entomology, College of Agriculture, G.B.P.U.A.&T. Pantnagar – 263145 up to 10 AM of 15.03.2012 and appear for interview on 15.03.12 at 11.00 AM in the Department of Entomology, College of Agriculture, Pantnager – 263145.

for further info:
http://www.gbpuat.ac.in/news/15%20March%202012%20SRF%20advertisement.pdf
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Vacancy for Senior Research Fellow in Plant Pathology / Zoology at GBPUAT, Pantnagar

Applications are invited for the following post:

Post: Senior Research Fellow

No. of Post: One

Project Title: To study efficacy of new coded compounds CHA7178 on chick pea/ pigeon pea with special references to pod borer (H. armigera) and Spodoptera.

Essential qualification: M.Sc. Entomology/Plant Pathology/Zoology with specialization in Entomology/ Plant Protection with specialization in Entomology.

Desirable: Experience in Apiculture with publication. Good knowledge of computers
Emoluments (Fixed) P.M.: Rs. 16000/-

Age Limit: Maximum 35 years for male and 40 years for female

Eligible candidates may send their application on plain paper to the principal investigator (By name) on or before 19.03.12 in the prescribed format along with the passport size photographs. Candidates fulfilling the qualification should appear for test/ interview on 20.03.12 at 10:00 AM.

for further info:
http://www.gbpuat.ac.in/news/19%20March%202012%20Cheminova_ADVERTISEMENT_NOTICE.pdf

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Vacancy for the post of Senior Research Fellow on contract basis in Indian Institute of Forest Management, Bhopal

Walk-in-Interview for the following post:
Post: Senior Research Fellow
Qualification & Experience: The candidate should have Post Graduate Degree in Forestry/Agriculture (all disciplines)/Environment/Botany/Natural Resource Management or related field with not less than 50% marks from a recognized University/Institute and two years relevant experience. Preference shall be given to the candidate qualified NET and publication in professional journals.
Consolidated monthly emoluments: Rs.16,000/- + 20% HRA (Rs.3,200) and Rs.400/- as reimbursement of medical insurance premium per month.
Interview Schedule: The Interview will be conducted on 26.03.2012 at 12.00 Noon in Room No.39, IIFM, Nehru Nagar, Bhopal.
Candidates should bring with them updated CV/Resume along with self attested copies of all certificates/testimonials and their originals.

for further info:
http://www.iifm.ac.in/vacancies/advt12.pdf


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Sending out an SOS: How Telomeres Incriminate Cells That Can't Divide

The well-being of living cells requires specialized squads of proteins that maintain order. Degraders chew up worn-out proteins, recyclers wrap up damaged organelles, and-most importantly-DNA repair crews restitch anything that resembles a broken chromosome. If repair is impossible, the crew foreman calls in executioners to annihilate a cell. As unsavory as this last bunch sounds, failure to summon them is one aspect of what makes a cancer cell a cancer cell.

This microscope image shows chromosomes in human lung cells exhibiting telomere damage caused by colcemid, a drug that arrests cell division. The Salk scientists discovered the molecular pathway that initiates a stress response upon treatment with chemotherapy drugs, resulting in a cessation of cell growth or cell death. (Credit: Courtesy of Jan Karlseder, Professor, Molecular and Cellular Biology Laboratory, Makoto Hayashi, research associate and James Fitzpatrick, Waitt Advanced Biophotonics Center)
 A recent study from scientists at the Salk Institute for Biological Studies showed exactly how cells sense the possibility that their DNA is damaged as a first step to responding to the failure to divide properly. That study, published March 11 in Nature Structural and Molecular Biology, found that if cells take too long to undergo cell division, structures at the tips of their chromosomes, known as telomeres, send out a molecular SOS signal.
These findings have dual implications for cancer chemotherapy. First, they show how a class of anti-cancer drugs that slows cell division -- known as mitotic inhibitors -- kills cells. This class includes the common chemotherapy drugs Vinblastine, Taxol and Velcade. More significantly, the findings suggest ways to make therapy with those inhibitors more potent.
"How mitotic inhibitors work as cancer therapy has been a 25-year-old question," says Jan Karlseder, a professor in Salk's Molecular and Cell Biology Laboratory and the study's senior author. "These drugs are widely used, but it was unclear why they actually kill cancer cells."
The Karlseder lab has long been fascinated by the roles played by telomeres in aging and cancer. Often described as the genomic equivalent of the plastic caps that keep shoelaces from fraying, telomeres form a protective protein/DNA cap on each end of linear chromosomes, masking those ends from vigilant but apparently myopic repair proteins, who might mistake exposed chromosome ends for broken DNA.
Initially, the group searched for specific proteins that might keep telomeres intact during cell division. To do so, they genetically eliminated candidate proteins one by one and then examined cells using fluorescence microscopy to detect whether telomeres became damaged. What they found was unexpected -- namely, that any manipulation that crippled and prolonged cell division produced increased numbers of punctate telomere blobs indicative of "unprotected" telomeres.
Treating cells with mitotic inhibitors used in cancer chemotherapy did the very same thing. Those studies established a link between arrested mitosis, telomere perturbation and cell death.
They then confirmed that as cells stalled in mitosis, telomeric shoelace caps started to disintegrate. "Normally the ends of chromosomes are covered by the protein TRF2, which protects the telomere," says Makoto Hayashi, a postdoctoral fellow in the Karlseder lab and the study's first author. "But we found that, during mitotic arrest TRF2 dissociates from telomeres, exposing chromosome ends as damaged DNA. That likely activates a DNA damage signal."
The clincher came when the investigators found that the longer cells endured telomere distress, the more massively they induced what ought to be everyone's most treasured gene, the tumor suppressor p53.
"DNA damage signals occurring during mitotic arrest likely predispose cells to upregulate p53 in the following phase," says Hayashi. "This then either halts the cell cycle to enable DNA repair to occur or commits cells to a suicide pathway called 'apoptosis'."
Karlseder notes that p53 and proteins it mobilizes constitute the most frequently mutated pathway in cancer. "A functional p53 pathway is a healthy sign, as it is the cell's first responder to DNA breaks or telomere dysfunction," he says, "Without it, chromosomes could become unstable and could fuse to one another or break, leading to a loss of genome integrity and uncontrolled growth."
This work suggests novel strategies that could be used in combinatorial cancer chemotherapy regimes, which rely on the synergy between two or more drugs. The theory is that a multi-pronged approach might pack more of a wallop than a sledgehammer alone, as evidenced by the highly effective "triple cocktail" of drugs now used to treat AIDS.
"To make therapy more effective and reduce side effects, we might be able to use more moderate levels of mitotic inhibitors, which at high doses can cause severe side effects, paired with a different drug that sensitizes cells to the DNA damage response," says Karlseder. "That could improve the chances of catching 100 percent of the tumor cells."
Prior to this study telomeres were already celebrated for the fact that they regulate aging by acting as a cellular clock, which ticks down a cell's age. "Every time a cell divides, a little bit of the telomere cap is lost until it is gone, signaling that cells cannot divide anymore," explains Karlseder. "This limitation ensures that cells do not become immortal or cancerous."
Recent studies show, however, that among their other insidious activities, cancer cells figure out how to set back the telomere clock and keep them immortal. "They do this by switching on pathways that specifically lengthen telomeres," says Karlseder. "These pathways therefore represent an important potential target for therapy."
Also contributing to this study were Anthony Cesare, of the Karlseder Lab; James Fitzpatrick, director of Salk's Waitt Advanced Biophotonics Core Facility; and Eros Lazzerini-Denchi, of The Scripps Research Institute in La Jolla.
Funding for the study came from the National Institutes of Health, the Human Frontier Science Program and the Japan Society for the Promotion of Science.
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How the Human Body Controls Viruses Thought to Cause a Variety of Cancers

New research from the Trudeau Institute addresses how the human body controls gamma-herpesviruses, a class of viruses thought to cause a variety of cancers. The study, carried out in the laboratory of Dr. Marcia Blackman, awaits publication in The Journal of Immunology. Led by postdoctoral fellow Mike Freeman, with assistance from other laboratory colleagues, the study describes the role of white blood cells in controlling gamma-herpesvirus infections and has implications for the treatment and prevention of certain cancers.

One of the many factors that can contribute to the development of cancer is infection with cancer-causing viruses, among them gamma-herpesviruses like the Epstein Barr virus and Kaposi's sarcoma-associated herpesvirus. With more than 95 percent of the human population infected with one or both of these viruses, it is important to understand their infection cycles and how immune responses keep them in check in the majority of individuals.
Gamma-herpesvirus infections are characterized by two distinct phases. In the initial, active phase, the immune system responds by attacking the virus. The virus, however, has developed a clever mechanism for "sneaking" past the immune response to conceal itself within the body, a process researchers refer to as latent infection. While in hiding, the virus persists in a quiet, inactive state. Occasionally, it can start to reactivate and begin to multiply again, increasing the risk of cancer development.
The chance that cancer will develop is greatly increased if the immune system is weakened, such as with immunosuppression following transplantation or as a consequence of other diseases, such as AIDS.
Researchers around the globe are asking important questions about the nature of these viruses and working in their labs to answer them. Among those questions: How do the viruses escape the immune response to establish lifelong latency? What triggers their reactivation in some people? Can we develop therapies to control reactivation and prevent the development of cancer?
The key finding of the Blackman study is that the mechanism by which a type of white blood cell, called a CD8 T cell, controls the virus differs between the initial active phase of infection and long-term latent infection. These novel findings will accelerate efforts to develop therapies to control gamma-herpesvirus infections and prevent the development of virus-associated cancers.

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Monday 12 March 2012

job opening - biosquare

Biotech Marketing Executive -Job Opening

Location: Hyderabad, AP

Job Description / Responsibilities: Sales & promotion of catalog products to government & non-government research institutes , Pharma Biotech Industries and Clinical Research Organizations (CROs) , to achieve annual sales target.

Job Title: Biotech sales & Marketing Executive

Desired Candidate Profile /Desired profile of the job-seeker :
1.BSc. Bio-technology , B.Tech in Bio-technology or MSc. in Biotechnology
2. At least one year institutional sale experience. Freshers are prefferable.
3.Fluency in English, Hindi & Telugu
4.Good Verbal & Written Communication Skills
5. Experience Required: 0-1 years Intersted candidates may send their resume to Biosquarebio@gmail.com You can reach us at Ph: 8886103232.
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Undergraduate Research & Innovation Program (UGRI- 2012),IIT RAJASTHAN


      Indian Institute of Technology Rajasthan started the Undergraduate Research and Innovation (UGRI) Programme in 2011 with the objective to promote research and innovation among a diverse group of undergraduate students. We are continuing this programme in the current academic year (2011-2012) to help selected students improve their professional knowledge and skills. We encourage students across the country to utilize the UGRI Programme for their academic and professional developments.
This year’s UGRI Programme will begin on May 8, 2012 and end on July 20, 2012 (for the duration of 10 weeks).

Financial Assistance and Accommodation :
      Selected students will be provided accommodation at student hostel in IITR. During this period, a remuneration of Rs. 8000 per month will be offered as Financial Assistance. Furthermore, the students will receive an additional Rs. 2000 for preparing posters and interim reports. However, the students will have to bear the expenses of their boarding and lodging as per institute rules.

Minimum Eligibility Criteria for students to apply :
  • Must have completed 5th Semester of BE/B.Tech/Dual Degree or 1st Year of MSc/ MA.
  • Minimum academic score : 70% or a CPI of 7.5 on a 10 point scale for Engineering and 65% or 7.0 CPI for Science programmes. The student should not have any backlogs.
    • Minimum score of 60% throughout their academic career
Instructions and procedure for on-line application
      Candidates willing to apply for UGRI Programme this year need to fill up an online application form and provide two project preferences in accordance with the proposals available on the website. Candidates also need to submit a one page write-up on “how they can contribute to the project” they are interested in. The students may also propose a new problem or project which he or she would like to take up during this internship. The submitted proposal must comprise title and a brief write up describing the idea the student would like to work on. The write up should not exceed 800 words. Preference will be given to those candidates who will be selecting the research topic from the given list of proposals.

Selection Process :
      Students will be selected purely on the basis of academic achievements and the merit of the proposal submitted. If required, the faculty member in charge may adopt any objective mechanism for comparison. The list of short-listed candidates will be announced latest by the second week of April 2012, and they will be intimated through email. Interested students must confirm their participation through email on or before 25th April 2012.

Other important guidelines for the students :
  • The selected candidate should submit a No-objection Certificate from HOD/Principal of his/her institute at the time of joining.
  • Selected student must stay on the campus for a minimum period of 60 days to be able to receive the certificate.
  • The student should have a health insurance valid all through their stay at IITJ.
Important instructions about the proposal submission by students :
  • Project could be a theoretical (system design, algorithm development etc.) or an experimental one.
  • The proposal should not comprise more than 800 words (one A4 size Page).
  • The proposal must be neatly typewritten (without any typographical errors). This file is to be uploaded in the PDF format only.
  • The proposal should clearly outline the work under headings such as "Objective", "Methodology" and "Innovation". Under the ‘Innovation’ heading, please explain why you think your idea is innovative.
  • Proposals related to Energy, Health, Environment, and ICT (Information, Communication and Technologies) will be given preference. However, students are free to submit proposals concerning any area of Engineering/Science/Arts.
  • Students are encouraged to take into consideration the expertise of the faculty members of the institute (http://www.iitj.ac.in/iitf/dofa.do) while drafting the proposal.


    Important Dates:
    Start of the on-line application process
    13th February 2012
    Last date for the receipt of application
    30th March 2012
    Declaration of the final list of candidates
    15th April 2012
    Last date for the acceptance of Internship Offer
    25th April 2012
    Commencement of Programme
    08th May 2012
    Poster Presentation and Award Ceremony
    20th July 2012


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Sunday 11 March 2012

How a Bacterial Pathogen Breaks Down Barriers to Enter and Infect Cells

Scientists from the Schepens Eye Research Institute, a subsidiary of Mass. Eye and Ear and affiliate of Harvard Medical School, have found for the first time that a bacterial pathogen can literally mow down protective molecules, known as mucins, on mucus membranes to enter and infect a part of the body. Their landmark study, published in the March 7, 2012 PLoS ONE, describes how they discovered that an "epidemic" strain of the bacterium Streptococcus pneumoniae, which causes conjunctivitis, secretes an enzyme to damage mucins and breach the mucosal membrane to infect and inflame the eye.

"We are excited about this finding," says Ilene Gipson, Ph.D., the study's principal investigator and a senior scientist at the Schepens. "Our discovery may ultimately lead to new ways of diagnosing, treating and preventing bacterial infections originating not only in the eye but in other parts of the body as well."
More than 80 percent of infections are contracted through the body's mucus membranes, which are the wet epithelial surfaces of the eye and the urogenital, respiratory, and gastrointestinal tracts of the body. The outer surface of all mucus membranes are protected by two types of mucin molecules -- one that is secreted and is in constant motion to sweep away trapped foreign material from the membrane surface, and the other that remains rooted in the membrane surface. The latter type of mucin molecules constitutes a physical shield that keeps potentially harmful substances from penetrating the membrane.
These membranes often encounter two types of bacterial pathogens. Some are "opportunistic." They sit on the membrane surface and only enter the tissue when there is trauma or injury that leaves a gap in the mucus membrane layer. An example of an opportunistic bacterium is Staphylococcus aureus that is often the cause of surgery related infections.
The other type of pathogen is non-opportunistic or "epidemic" and causes more invasive and aggressive infections such as occur in epidemic conjunctivitis caused by the strain of Streptococcus pneumoniae used in this study. These disease-causing bacteria enter the body even when there is no apparent injury to the protective layer. And, they can cause rapidly expanding and contagious disease.
Until the current PLoS ONE study, little has been known about how epidemic infection causing bacteria are able to cross through the mucin barrier. Experts in the study of mucins and determined to find a piece of this puzzle, the Schepens scientists hypothesized that "epidemic" bacteria must somehow remove the mucins themselves.
To test their hypothesis, the team grew "epidemic" conjunctivitis bacteria (a strain of streptococcus pneumoniae) in a culture. This bacteria causes an inflammation of the conjunctiva, the mucous membrane covering the white of the eyes and the inner side of the eyelids. They then applied the fluid that the bacteria were cultured in to cell lines that mimicked the eye's surface, including presence of intact mucins, and found that the membrane-anchored mucins were cut off and released from the surface of the cells. Removal of the mucins allowed the bacteria to enter the cells.
Using mass spectrometry, the researchers were then able to identify the enzyme, ZmpC, as the culprit. They confirmed their findings by knocking out the gene in the bacteria that produced this enzyme and demonstrated that the bacterium could no longer remove the mucins from the membrane.
According to Dr. Gipson, "This discovery is a major breakthrough in this long unsolved puzzle about how "epidemic" bacteria enter the body and has given us a new target for drugs that could even be used preventatively."
The next step in the research, according to Dr. Gipson, will be to determine if the method of enzymatically removing the surface mucins to gain entrance is used by other disease causing bacteria.
Other scientists who authored the study include: Bharathi Govindarajan, Balaraj B. Menon, Sandra Spurr-Michaud
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Clock Gene Helps Plants Prepare for Spring Flowering, Study Shows

University researchers tested computer models of gene networks in a simple cress plant to determine the role played by a protein, known as TOC1, in governing these daily cycles.
The model shows how 12 genes work together to run the plant's complex clockwork, and reset the clock at dawn and dusk each day.
Researchers found that the TOC1 protein, which was previously linked to helping plants wake up, is in fact involved in dampening gene activity in the evening.
This helps plants stay dormant at night.

Contradictory finding
"The 24-hour rhythms of biological clocks affect all living things including plants, animals and people, with wide-ranging effects on sleep, metabolism and immunity," said Professor Andrew Millar of the School of Biological Sciences.
The findings contradict what scientists had previously understood about the gene and its role in early morning activity.
Scientists in Barcelona independently reached a similar conclusion to the Edinburgh team.
The two studies pave the way for further research to define how the cycles improve plant growth and allow plants to adapt to our changing environment.
Changing seasons
These internal 24-hour cycles -- known as circadian clocks -- also allow people, animals and plants to make tiny adjustments as daylight changes, and adapt to changing seasons.
Researchers hope their discovery will bring them a step closer to understanding other seasonal rhythms that affect plants and people.
These include the flowering of staple crops such as wheat, barley and rice, and the breeding patterns of animals.
"We are now far better placed to understand how this complex process impacts on the plant's life and what happens when the rhythms are interrupted, for example by climate change," said Millar.

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Friday 9 March 2012

Protein Folding: Understanding the Dance of the Chaperones

Proteins are the molecular building blocks and machinery of cells and involved in practically all biological processes. To fulfil their tasks, they need to be folded into a complicated three-dimensional structure. Scientists from the Max Planck Institute of Biochemistry (MPIB) in Martinsried near Munich, Germany, have now analysed one of the key players of this folding process: the molecular chaperone DnaK. "The understanding of these mechanisms is of great interest in the light of the many diseases in which folding goes awry, such as Alzheimer's or Parkinson's," says Ulrich Hartl, MPIB director.
The chaperone DnaK binds to new proteins and mediates their folding. Proteins it cannot fold, DnaK transports to GroEL, a highly specialised folding machine. (Credit: MPI of Biochemistry)

The work of the researchers has now been published in Cell Reports.
Proteins are responsible for almost all biological functions. The cells of the human body continuously synthesize thousands of different proteins in the form of amino acid chains. In order to be biologically useful, these chains must fold into a complex three-dimensional pattern. When this difficult process goes wrong, it can lead to useless or even dangerous protein clumps. All cells, from bacteria to human, have therefore developed a network of molecular chaperones, proteins themselves, which help other proteins to fold properly.
MPIB scientists have now investigated the organisation of this network in the bacterium Escherichia coli. Using proteomic analyses they show how different chaperones cooperate during the folding process. "We identified the Hsp70 protein DnaK as the central player of the network," explains Ulrich Hartl. "It functions as a kind of turntable." DnaK binds to about 700 different protein chains as they are synthesised. Furthermore, DnaK mediates the folding of most of these protein chains. Those it cannot fold are transferred to yet another chaperone, the barrel-shaped GroEL. GroEL is a highly specialised folding machine. It forms a nano-cage in which a single protein chain is temporarily enclosed and allowed to fold while protected from external influences.
Disruptions in the Chaperone Network
The researchers also investigated what happens when the chaperone network is disturbed. For example, when GroEL is removed from the cells, its client proteins accumulate on DnaK, which then shuttles them to proteases to be decomposed. "Apparently, DnaK realises that the attached protein chains will never be able to mature into useful molecules," says the biochemist. Similar but even more complicated chaperone networks control the proteome of human cells. Understanding these reactions is of great interest in the light of the many neurodegenerative diseases in which folding goes awry.

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Powerful Tool to Measure Metabolites in Living Cells

By engineering cells to express a modified RNA called "Spinach," researchers have imaged small-molecule metabolites in living cells and observed how their levels change over time. Metabolites are the products of individual cell metabolism. The ability to measure their rate of production could be used to recognize a cell gone metabolically awry, as in cancer, or identify the drug that can restore the cell's metabolites to normal.

imaging S-adenosylmethionine in cells with RNA. The fluorescence markedly increases at each time point after adding methionine (bottom right). (Credit: Image courtesy of NewYork-Presbyterian Hospital/Weill Cornell Medical Center/Weill Cornell Medical College)
Researchers at Weill Cornell Medical College say the advance, described in the March 9 issue of Science, has the potential to revolutionize the understanding of the metabolome, the thousands of metabolites that provide chemical fingerprints of dynamic activity within cells.
"The ability to see metabolites in action will offer us new and powerful clues into how they are altered in disease and help us find treatments that can restore their levels to normal," says Dr. Samie R. Jaffrey, an associate professor of pharmacology at Weill Cornell Medical College. Dr. Jaffrey led the study, which included three other Weill Cornell investigators.
"Metabolite levels in cells control so many aspects of their function, and because of this, they provide a powerful snapshot of what is going on inside a cell at a particular time," he says.
For example, biologists know that metabolism in cancer cells is abnormal; these cells alter their use of glucose for energy and produce unique breakdown products such as lactic acid, thus producing a distinct metabolic profile. "The ability to see these metabolic abnormalities can tell you how the cancer might develop," Dr. Jaffrey says. "But up until now, measuring metabolites has been very difficult in living cells."
In the Science study, Dr. Jaffrey and his team demonstrated that specific RNA sequences can be used to sense levels of metabolites in cells. These RNAs are based on the Spinach RNA, which emits a greenish glow in cells. Dr. Jaffrey's team modified Spinach RNAs so they are turned off until they encounter the metabolite they are specifically designed to bind to, causing the fluorescence of Spinach to be switched on. They designed RNA sequences to trace the levels of five different metabolites in cells, including ADP, the product of ATP, the cell's energy molecule, and SAM (S-Adenosyl methionine), which is involved in methylation that regulates gene activity. "Before this, no one has been able to watch how the levels of these metabolites change in real time in cells," he says.
Delivering the RNA sensors into living cells allows researchers to measure levels of a target metabolite in a single cell as it changes over time. "You could see how these levels change dynamically in response to signaling pathways or genetic changes. And you can screen drugs that normalize those genetic abnormalities," Dr. Jaffrey says. "A major goal is to identify drugs that normalize cellular metabolism."
This strategy overcomes drawbacks of the prevailing method of sensing molecules in living cells using green fluorescent protein (GFP). GFP and other proteins can be used to sense metabolites if they are fused to naturally occurring proteins that bind the metabolite. In some cases, metabolite binding can twist the proteins in a way that affects their fluorescence. However, for most metabolites, there are no proteins available that can be fused to GFP to make sensors.
By using RNAs as metabolite sensors, this problem is overcome. "The amazing thing about RNA is that you can make RNA sequences that bind to essentially any small molecule you want. They can be made in a couple of weeks," Dr. Jaffrey says. These artificial sequences are then fused to Spinach and expressed as a single strand of RNA in cells.
"This approach would potentially allow you to take any small molecule metabolite you want to study and see it inside cells," Dr. Jaffrey says. He and his colleagues have expanded the technology to detect proteins and other molecules inside living cells.
He adds that uses of the technology to understand human biology can be applied to many diseases. "We are very interested in seeing how metabolic changes within brain neurons contribute to developmental disorders such as autism," Dr. Jaffrey says. "There are a lot of opportunities, as far as this new tool is concerned."
Co-authors of the study include Dr. Jeremy S. Paige, Mr. Thinh Nguyen Duc, and Dr. Wenjiao Song from the Department of Pharmacology at Weill Cornell Medical College.
The study was funded by the National Institute of Biomedical Imaging and Bioengineering of the NIH, and the McKnight Foundation. The Cornell Center for Technology Enterprise and Commercialization (CCTEC), on behalf of Cornell University, has filed has filed for patent protection on this technology. Dr. Samie Jaffrey is the founder and scientific advisor to Lucerna Technologies, and holds equity interests in this company. In addition, Lucerna Technologies has a license that is related to technology described here.

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Drug Helps Purge Hidden HIV

A team of researchers at the University of North Carolina at Chapel Hill has successfully flushed latent HIV infection from hiding, with a drug used to treat certain types of lymphoma. Tackling latent HIV in the immune system is critical to finding a cure for AIDS.

The results were presented March 8 at the 19th Conference on Retroviruses and Opportunistic Infections in Seattle, Washington.
While current antiretroviral therapies can very effectively control virus levels, they can never fully eliminate the virus from the cells and tissues it has infected.
"Lifelong use of antiretroviral therapy is problematic for many reasons, not least among them are drug resistance, side effects, and cost," said David Margolis, MD, professor of medicine, microbiology and immunology, and epidemiology at the University of North Carolina at Chapel Hill. "We need to employ better long-term strategies, including a cure."
Margolis' new study is the first to demonstrate that the biological mechanism that keeps HIV hidden and unreachable by current antiviral therapies can be targeted and interrupted in humans, providing new hope for a strategy to eradicate HIV completely.
In a clinical trial, six HIV-infected men who were medically stable on anti-AIDS drugs, received vorinostat, an oncology drug. Recent studies by Margolis and others have shown that vorinostat also attacks the enzymes that keep HIV hiding in certain CD4+ T cells, specialized immune system cells that the virus uses to replicate. Within hours of receiving the vorinostat, all six patients had a significant increase in HIV RNA in these cells, evidence that the virus was being forced out of its hiding place.
"This proves for the first time that there are ways to specifically treat viral latency, the first step towards curing HIV infection," said Margolis, who led the study. "It shows that this class of drugs, HDAC inhibitors, can attack persistent virus. Vorinostat may not be the magic bullet, but this success shows us a new way to test drugs to target latency, and suggests that we can build a path that may lead to a cure."
The research conducted is part of a UNC-led consortium, the Collaboratory of AIDS Researchers for Eradication (CARE), funded by the National Institute of Allergy and Infectious Diseases. The consortium is administered by the North Carolina Translational and Clinical Sciences (NC TraCS) Institute at UNC, one of 60 medical research institutions in the US working to improve biomedical research through the NIH Clinical and Translational Science Awards (CTSA) program.
Other UNC authors on the paper include Nanci Archin, PhD, Shailesh Choudary, PhD, Joann Kuruc, MSN, and Joseph Eron, MD of the medical school; Angela Kashuba, PharmD of the Eshelman School of Pharmacy; and Michael Hudgens, PhD, of the Gillings School of Global Public Health.
Funding for this research was provided by the National Institutes of Health, Merck & Co., and the James B. Pendleton Charitable Trust.

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Mission: Biodegradable plastic from waste

Non-degradable plastic waste has been a major source of concern for authorities as well as the common masses. Hyderabad-based SPC Biotech for the last five-to-six years has been doing research on bio-products, especially bio-polymers and bio-chemicals to find an alternative. IndoPLA, SPC Biotech's biodgradable polymer, can be used in all conventional conversion processes such as injection molding, blow bolding, thermo forming and extrusion. The first plant of the company started its commercial operations in 2004-05. However, concerns such as the three-to-four times costlier prices as compared to the conventional petroleum-based plastic and the use of food source as the source of raw material were plaguing the firm.

After initial study, the R&D team at SPC Biotech found a unique way to tackle the problem. They started working on agriwaste which is not fit for human consumption as basic raw material to produce bioplastics. The result was the development of a process that does bioconversion of mango kernel into polylactic acid (PLA), a biodegradable polyester, and finally created bioplastic material.

The company after developing the technology for the conversion of agriwaste into bioplastics at laboratory-scale and bench-scale approached the Department of Biotechnology (DBT), Ministry of Science and Technology under the Biotechnology Industry Partnership Programme (BIPP), for commercialising the same.

The technical expert committee recommended that technology has to be demonstrated at pilot scale and the DBT supported the same. Out of the total project cost of 100 lakh, the DBT provided funding to the tune of 50 lakh and the rest was managed by the company. The BIPP support proved to be useful for the company as it is difficult to get financial support for validating technology at pilot scale. Mr M S Shankara Prasad, managing director, SPC Biotech, while appreciating the BIPP support, says, “Thanks to the BIPP, many industries with good technologies are able to introduce their products in the market. It is difficult to get the support from regular commercial financial institutions, where they look for so many things.”

The way forward
The advantage of the green plastic is that it ultimately decomposes to water and carbon dioxide by the action of microorganisms in a natural environment. Therefore its availability at a lower price will surely help in controlling the environmental damage caused by the non degradable plastic material to a huge extent. Given the fact that the estimated plastic consumption in India is close to 30 million ton, even if five percent of this is replaced with polylactic acid-based biodegradable plastic, the requirement would be around 1.5 million ton per year. Thus, it can create more employment opportunities for people in rural areas. SPC Biotech has finished the validation of the technology on a pilot scale. Now it is in the process of commercializing it with an installed capacity of 1,000 metric ton. In the next six months, these products are expected to be available for commercial applications in a natural environment, especially in areas where recycling is difficult.
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Thursday 8 March 2012

Scientists Revolutionize Electron Microscope: New Method Could Create Highest Resolution Images Ever

Researchers at the University of Sheffield have revolutionised the electron microscope by developing a new method which could create the highest resolution images ever seen.

For over 70 years, transmission electron microscopy (TEM), which `looks through´ an object to see atomic features within it, has been constrained by the relatively poor lenses which are used to form the image.
The new method, called electron ptychography, dispenses with the lens and instead forms the image by reconstructing the scattered electron-waves after they have passed through the sample using computers.
Scientists involved in the scheme consider their findings to be a `first step´ in a `completely new epoch of electron imaging´. The process has no fundamental experimental boundaries and it is thought it will transform sub-atomic scale transmission imaging.
Project leader Professor John Rodenburg, of the University of Sheffield´s Department of Electronic and Electrical Engineering, said: "To understand how material behaves, we need to know exactly where the atoms are. This approach will enable us to look at how atoms sit next to one another in a solid object as if we´re holding them in our hands.
"We´ve shown we can improve upon the resolution limit of an electron lens by a factor of five. An extension of the same method should reach the highest resolution transmission image ever obtained; about one tenth of an atomic diameter. No longer does TEM have to be bound by the paradigm of the lens, its Achilles´ heel since its invention in 1933."
The technique is applicable to microscopes using any type of wave and has other key advantages over conventional methods. For example, when used with visible light, the new technology forms a type of image that means scientists can see living cells very clearly without the need to stain them, a process which usually kills the cells.
The new method also disposes of the need to put a lens very close to a living sample, meaning that cells can be seen through thick containers like petri dishes or flasks. This means that as they develop and grow over days or weeks, they do not have to be disturbed.
Plans are even being put into place with the European Space Agency to take the new, more robust, microscope technology to the moon in 2018 to examine the structure of moon soil.
Professor Rodenburg added: "We measure diffraction patterns rather than images. What we record is equivalent to the strength of the electron, X-ray or light waves which have been scattered by the object -- this is called their intensity. However, to make an image, we need to know when the peaks and troughs of the waves arrive at the detector -- this is called their phase.
"The key breakthrough has been to develop a way to calculate the phase of the waves from their intensity alone. Once we have this, we can work out backwards what the waves were scattered from: that is, we can form an aberration-free image of the object, which is much better than can be achieved with a normal lens.
"A typical electron or X-ray microscope image is about one hundred times more blurred than the theoretical limit defined by the wavelength. In this project, the eventual aim is to get the best-ever pictures of individual atoms in any structure seen within a three-dimensional object."
The ground-breaking results were part of a three-year study costing £4.3 million which was funded by the Engineering and Physical Sciences Research Council (EPSRC).
The investigation was carried out with the help of Phase Focus Ltd, a University of Sheffield spin-out company, and Gatan Inc.
Ptychographic electron microscopy using high-angle dark-field scattering for sub-nanometre resolution imaging was published in Nature Communications on March 6, 2012.

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Crystal Structure of Archael Chromatin Clarified

Researchers at the RIKEN SPring-8 Center in Harima, Japan have clarified for the first time how chromatin in archaea, one of the three evolutionary branches of organisms in nature, binds to DNA. The results offer valuable clues into the evolution of chromatin structure in multi-cellular organisms and promise insights into how abnormalities in such structure can contribute to cancers and gene disorders.
Polimerization of Alba2-DNA complex structure. (Credit: Image courtesy of RIKEN)


Three distinct evolutionary branches of organisms make up all natural forms of life on the planet: bacteria, archaea and eukaryotes. Among these three, the domain known as archaea includes a variety of organisms that live in harsh environments similar to those of an early Earth, thus offering arguably the greatest glimpse of what life may have looked like 4 billion years ago.
One area of great interest is the process by which DNA bind to proteins to compact and regulate the availability of genetic material, a process which is essential in all cellular organisms. In eukaryotes, proteins known as "histones" package and order DNA into a compact protein-DNA structure called chromatin. Archaea, in contrast, have no such universal chromatin proteins, instead using two or more DNA-binding proteins to package DNA. Alba is the most widespread and abundant such archaeal chromatin protein, present in the genome sequence of every archaeal species that lives in high-temperature environments (thermophilic or hyperthermophilic).
While researchers know about the existence of Alba in archaea, the question of how these proteins bind to and compact DNA has remained a mystery. To answer this question, the researchers analyzed the crystal structure of the Alba2-DNA complex from the archaea A. pernix K1 at atomic-level resolution using synchrotron radiation from the RIKEN SPring-8 facility in Harima, Japan. Their results indicate that unlike the chromatin structure of eukaryotes, Alba2 in archaea forms a hollow pipe with the duplex DNA running through it, with the hairpin structure of Alba2 stabilizing the pipe.
Published in the February 10th issue of the Journal of Biological Chemistry, this newly-discovered mechanism for compacting DNA marks a major step forward in our understanding of the evolution of chromatin structure. The results promise to clarify how abnormalities in chromatin structure can contribute to cancers and gene disorders, while also providing inspiration for the development of new types of biodevices.
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Tuesday 6 March 2012

Is Seaweed the Future of Biofuel?

As scientists continue the hunt for energy sources that are safer, cleaner alternatives to fossil fuel, an ever-increasing amount of valuable farmland is being used to produce bioethanol, a source of transportation fuel. And while land-bound sources are renewable, economists and ecologists fear that diverting crops to produce fuel will limit food resources and drive up costs.

Now, Prof. Avigdor Abelson of Tel Aviv University's Department of Zoology and the new Renewable Energy Center, and his colleagues Dr. Alvaro Israel of the Israel Oceanography Institute, Prof. Aharon Gedanken of Bar-Ilan University, Dr. Ariel Kushmaro of Ben-Gurion University, and their Ph.D. student Leor Korzen, have gone to the seas in the quest for a renewable energy source that doesn't endanger natural habitats, biodiversity, or human food sources.He says that marine macroalgae -- common seaweed -- can be grown more quickly than land-based crops and harvested as fuel without sacrificing usable land. It's a promising source of bioethanol that has remained virtually unexplored until now.
The researchers are now developing methods for growing and harvesting seaweed as a source of renewable energy. Not only can the macroalgae be grown unobtrusively along coastlines, Prof. Abelson notes, they can also clear the water of excessive nutrients -- caused by human waste or aquaculture -- which disturb the marine environment.
A human-made "ecosystem"
While biomasses grown on land have the potential to inflict damage on the environment, the researchers believe that producing biofuel from seaweed-based sources could even solve problems that already exist within the marine environment. Many coastal regions, including the Red Sea in the south of Israel, have suffered from eutrophication -- pollution caused by human waste and fish farming, which leads to excessive amounts of nutrients and detrimental algae, ultimately harming endangered coral reefs.
Encouraging the growth of seaweed for eventual conversion into biofuel could solve these environmental problems. The system that the researchers are developing, called the "Combined Aquaculture Multi-Use Systems" (CAMUS), takes into account the realities of the marine environment and human activity in it. Ultimately, all of these factors function together to create a synthetic "human-made ecosystem," explains Prof. Abelson.
Human-made fish feeders, which produce pollution in the form of excess nutrients and are generally considered harmful to the marine environment, would become a positive link in this chain. Used alongside an increased population of filter feeders such as oysters, which suck in extra particles and convert them food that the microalgae can consume, this "pollution" could be used to sustain a much greater yield of seaweed, which is needed for seaweed to become a sustainable source of fuel.
"By employing multiple species, CAMUS can turn waste into productive resources such as biofuel, at the same time reducing pollution's impact on the local ecosystem," he says.
Turning waste into opportunity
The researchers are now working to increase the carbohydrate and sugar contents of the seaweed for efficient fermentation into bioethanol, and they believe that macroalgae will be a major source for biofuel in the future. The CAMUS system could turn seaweed into a sustainable bioethanol source that is productive, efficient, and cost-effective.

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