tool

New, automated tool successfully classifies and relates proteins in unprecedented way

For the first time, researchers haveautomatically grouped fluorescently tagged proteins fromhigh-resolution images of cells. This technical feat opens a new way toidentify disease proteins and drug targets by helping to show whichproteins cluster together inside a cell.The approach, developed by Carnegie Mellon University, outperformsexisting visual methods to localize proteins inside cells...

GATA: a graphic alignment tool for comparative sequence analysis

Sometimes apotential target for a drug seems very promising on paper; things areoften very different in reality. Its the case of telomerase inhibitorsto treat cancer; they are supposed to strip the "immortal" (able todivide indefinitely) aspect of cancer cells. Yet, something in the cellseems to block their function, preventing them to inhibit completelythe...

Researchers add new tool to tumor-treatment arsenal

A new study demonstrates the potential effectiveness of treating tumors by combining agents that damage DNA with a drug that sensitizes cancer cells to these agents. The research, led by George Thomas, PhD, professor at the University of Cincinnati's (UC) Genome Research Institute, and Heidi Lane of Novartis Institutes for Biomedical Research, appears in the March 25, 2005, issue of the jo...

Agilent Technologies releases automated literature search tool for biology researchers

Agilent Technologies Inc. (NYSE: A) today released an automated literature search tool for the multidisciplinary study of biological systems. The tool is available as a free plug-in to Cytoscape 2.1, an open-source bioinformatics platform that enables researchers to form a visual map of complex biological networks, increasing their understanding of molecular pathways and the biological causes of...

Carnegie Mellon scientists develop tool that uses MRI to visualize gene expression in living animals

In a first, Carnegie Mellon University scientists have "programmed" cells to make their own contrast agents, enabling unprecedented high-resolution, deep-tissue imaging of gene expression. The results, appearing in the April issue of Nature Medicine, hold considerable promise for conducting preclinical studies in the emerging field of molecular therapeutics and for monitoring the delivery of ther...

Researchers develop rapid diagnostic tool for pathogen identification

Researchers at Columbia University's Mailman School of Public Health and the Columbia Genome Center have designed and developed a sensitive new diagnostic technology platform, called “Mass Tag PCR,?that can simultaneously screen for multiple infectious agents. The new technology is addressed in a paper published in the February issue of the Centers for Disease Control and Prevention's (CDC) Emerg...

Institute for Systems Biology Symposium Addresses Need for Better Computational Tools

The Institute for Systems Biology announced today at its 2005 international symposium on Computational Challenges in Systems Biology that ISB's Human Proteome Folding Project launched on IBM's World Community Grid in November 2004 has already predicted 50,000 protein structures. "This project showcases the enormous power of collaborations," stated Dr. Richard Bonneau, senior scientist at t...

Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

The current goal to reduce sickness and death from infections that patients acquire in hospitals has created a renewed focus on identifying ways to reduce the problem at its source. Hospital water for drinking, bathing, showering, to make ice cubes or to rinse medical equipment is increasingly being recognized as a significant source of microbes that may contribute to many of these life-threateni...

Software Tool for Converting Scientific Text into a Database of Functional Relationships

Ariadne Genomics, Inc. today announced the launch of MedScan?Text-to-Knowledge Suite 2.0, a Natural Language Processing-based tool for automated extraction of biological facts from scientific literature, MEDLINE abstracts, and other text sources. A demo version of MedScan is available at www.ariadnegenomics.com. MedScan leverages hand-crafted dictionaries of protein and chemical names, and...

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information

In the March 3 issue of Nature, Johns Hopkins researchers report that two proteins best known for very different activities actually come together to turn the liver into a sugar-producing factory when food is scarce. Because the liver's production of sugar is a damaging problem in people with diabetes, the proteins' interaction might be a target for future drugs to fight the disease, the research...

Newly discovered protein an important tool for sleeping sickness research

Sixty million people in 36 countries of sub-Saharan Africa are threatened daily by a deadly parasitic disease known as African sleeping sickness. The disease is caused by organisms called trypanosomes, which are spread by the tsetse fly. African sleeping sickness affects approximately 500,000 people in sub-Saharan Africa, a quarter of whom will die this year. Because the trypanosome has an except...

Computational Tool Predicts How Drugs Work In Cells, Advancing Efforts To Design Better Medicines

The ability to select and develop compounds that act on specific cellular targets has just gained a computational ally ?a mathematical algorithm that predicts the precise effects a given compound will have on a cell’s molecular components or chemical processes. Using this tool, drug developers can design compounds that will act on only desired gene and protein targets, eliciting therapeutic respo...

Improved statistical tools reveal many linked loci

An innovative new statistical method, described in the open-access journal PLoS Biology, streamlines the computation required to identify all the potential locations in the genome that influence a particular physical trait, or phenotype. Thanks to the new method developed by John Storey, Joshua M. Akey, and Leonid Kruglyak, researchers have a more efficient genome-mining technique to help them id...

Mosaic mouse technique offers a powerful new tool to study diseases and genetics

A powerful laboratory technique used by fruit fly geneticists for more than a decade is now available to scientists studying genes and diseases in mice. Writing in the May 6 edition of the journal Cell, researchers from Stanford University describe a streamlined method for creating a "genetic mosaic mouse"--a rodent whose body is genetically engineered to produce small clusters of cells w...

Virginia Tech group adds tools to DNA-targeted anti-cancer drugs

Chemistry and biology researchers at Virginia Tech have enhanced the abilities of the molecules they are creating to deliver killing blows to cancer cells. The man-made molecular complexes enter cancer cells and, when signaled, deliver killing medicine or cause the cell to change. The new supermolecules have more units that will absorb light - providing more control over the range of light freque...

New tool reveals secrets of migrating cells

Called two-photon laser-scanning microscopy, it has revealed, for...

New mitochondrial DNA gene chip may be early cancer diagnosis tool

A pilot study at the National Institute of Standards and Technology (NIST), in support of the National Cancer Institute's Early Detection Research Network (EDRN), has validated the measurement accuracy of new techniques that use mitochondrial DNA as an early indicator for certain types of cancer. Additional results suggest that a relatively simple diagnostic test using a DNA microarray "chip" cou...

Nanoparticles, nanoshells, nanotubes: How tiny specks may provide powerful tools against cancer

They're but a tiny speck, existing in a variety of forms: particles, tubes, shells, even a soccerball-like shape. They also share a common prefix: "nano," connoting their size, a billionth of a meter or roughly 25-millionth of an inch. Today, cancer researchers are exploring the potential of such nanostructures to exquisitely target cancer cells without harming surrounding tissue, and to...

New tools used to control foodborne hepatitis A outbreaks related to green onions

Novel use of genetic testing methods helped public health officials control and limit the further spread of four outbreaks of foodborne hepatitis A virus in 2003 related to the consumption of green onions, according to a detailed analysis published in the October 15 issue of The Journal of Infectious Diseases, now available online. The authors of the study, Joseph J. Amon, PhD, MSPH, and c...

MWG Biotech expands siMAX?siRNA portfolio with new scales, lengths and design tools

University of Utah researchers showed that a fruit fly gene is crucial for determining when juveniles begin to mature into adults, and how the transformation initially proceeds. Understanding this process in humans may help explain how adorable children become surly teenagers. When the DHR4 gene is disabled, fruit flies prematurely begin metamorphosis ?maturation from an immature larva to...

UF study first to quantify validity of DNA I.D. tool using marine snails

A trendy holiday gift within a decade may be a hand-held device that instantly identifies any species from a snippet of animal tissue, says a University of Florida researcher. That may be possible thanks to scientific advances that include the first test quantifying the effectiveness of a DNA identification tool among brightly colored shells. With an error rate as low as 4 percent, two UF...

Biotechnology's newest chemical tool

Exploiting biology's own chemical toolbox, researchers have developed a new technique that will allow them to modify specific sequences within a DNA molecule. The approach will not only help reveal the impact of biochemical alterations to DNA, but could have far-reaching implications for DNA-based medical diagnosis and nanobiotechnology. Combining chemistry with biotechnology, Saulius Kl...

Biotechnology's newest chemical tool

Funded by the Future and Emerging Technologies initiative of the IST programme, the CYBERHAND project aims to hard wire this hand into the nervous system, allowing sensory feedback from the hand to reach the brain, and instructions to come from the brain to control the hand, at least in part. Coordinated by Professor Paolo Dario with Professor Maria Chiara Carrozza leading the development...

Carnegie Mellon U. transforms DNA microarrays with standard Internet communications tool

A standard Internet protocol that checks errors made during email transmissions has now inspired a revolutionary method to transform DNA microarray analysis, a common technology used to understand gene activation. The new method, which blends experiment and computation, strengthens DNA microarray analysis, according to its Carnegie Mellon University inventor, who is publishing his findings in the...

Scientists develop protein-sequence analysis tool

With more and more protein sequence data available, scientists are increasingly looking for ways to extract the small subset of information that determines a protein's function. In addition to sorting out what makes related proteins differ, such information can also help scientists engineer proteins to do new jobs. Now scientists at the U.S. Department of Energy's Brookhaven National Labor...

Swiss researchers develop all-in-one remote control gene expression tool

In an article appearing online today in the journal Nature Methods, researchers at the EPFL (Ecole Polytechnique Fédérale de Lausanne) unveil a powerful new tool that will facilitate genetic research and open up new avenues for the clinical treatment of genetic disease. The researchers have combined several gene manipulation techniques and incorporated them into a single lentiviral vector...

Powerful new tool for studying brain development

Scientists at St. Jude Children's Research Hospital have given investigators around the world free access to a powerful tool for studying brain development. The Internet-based tool, called the mouse Brain Gene Expression Map (BGEM), is one of the largest gene expression maps of an organ ever developed, according to the St. Jude researchers. They say the map will likely help scientists discover th...

New RNAi tools enable systematic studies of gene function

An international public-private research team led by scientists at the Broad Institute of MIT and Harvard announced today the construction and availability of an extensive library of molecular reagents to silence most human and mouse genes. As described in the March 24 issue of Cell, this library consists of small RNA molecules that can switch off genes individually, allowing the user to d...

Discovery of new molecular tools for biosynthesis could lead to advances in use of pectin

Most people know pectin as a common household gelling agent in making jams and jellies, but its uses are vast. It has anticancer properties, for instance, and may have a role in important biological functions including plant growth and development and defense against disease. Despite the importance of pectin as a major component in the primary walls of plants, scientists have known relativ...

Tool developed to silence genes in specific tissues using RNAi

Researchers at The University of Texas M. D. Anderson Cancer Center say they have jumped a significant hurdle in the use of RNA interference (RNAi), believed by many to be the ultimate tool to both decode the function of individual genes in the human genome and to treat disease. Reporting in the journal Genes and Development, investigators have developed a simple way to use the RNAi appro...

Scientists develop malaria forecasting tool to predict disease risk

A new tool to predict epidemics of malaria up to five months in advance has been developed by a scientist at the University of Liverpool. The model uses predictions of climate variability to indicate the level of risk of an epidemic up to five months in advance of the peak malaria season ?the earliest point at which predictions have ever been made. The model will assist doctors and health...

New tool tracks brain development in babies

Researchers have used a new technique to monitor brain development in infants and detect disturbances in white matter, according to a study in the July issue of Radiology. Carola van Pul, Ph.D., and colleagues from Máxima Medical Center in Veldhoven, the Netherlands, studied seven normal infants and 10 infants with perinatal hypoxic ischemia, a type of brain injury caused by a period of ox...

Mitochondrial DNA sequencing tool updated

High-tech laboratory tools, like computers, are often updated publicly as their analytical capabilities expand. In the September issue of the Journal of Molecular Diagnostics, NIH grantees report they have developed a second generation "lab on a silicon chip" called the MitoChip v2.0 that for the first time rapidly and reliably sequences all mitochondrial DNA. Mitochondria, the energy-producing...

Hopkins researchers develop new tool to watch real-time chemical activity in cells

Attempts to identify potential drugs that interfere with the action of one particular enzyme linked to heart disease and similar health problems led scientists at Johns Hopkins to create a new tool and new experimental approach that allow them to see multiple, real-time chemical reactions in living cells. Their report on the work is published July 21 in the journal ACS Chemical Biology. <p...

Use of stone hammers sheds light on geographic patterns of chimpanzee tool use

In a finding that challenges a long-held belief regarding the cultural spread of tool use among chimpanzees, researchers report that chimpanzees in the Ebo forest, Cameroon, use stone hammers to crack open hard-shelled nuts to access the nutrient-rich seeds. The findings are significant because this nut-cracking behavior was previously known only in a distant chimpanzee population in extreme west...

A new tool against brain disease

American and South African scientists working at the epicenter of the AIDS epidemic in South Africa have discovered how the human immunodeficiency virus (HIV) "exhausts" killer T cells that would otherwise attack the virus. The researchers found that HIV can simply "turn off" fully functional T cells by flipping a molecular switch on the cells. In test tube studies, however, the scientists showed...

K-Staters design and build a low-cost remote sensing tool for environmental studies

A Kansas State University research team is prototyping a small, inexpensive remote-control plane as a sensing tool, also known as an unmanned aerial vehicle, to collect environmental data. The team plans to test it over the Konza Prairie Biological Station near Manhattan this summer. If the sensing tool performs as the team hopes, it will be made available to climate scientists, who would...

Mobile DNA part of evolution's toolbox

The repeated copying of a small segment of DNA in the genome of a primeval fish may have been crucial to the transition of ancient animals from sea to land, or to later key evolutionary changes in land vertebrates. The discovery is "tantalizing evidence" that copied DNA elements known as retroposons could be an important source of evolutionary innovations, says the director of the research, Howar...

With record resolution and sensitivity, tool images how life organizes in a cell membrane

What's the difference between a lifeless sack of chemicals and a living cell? It's all in the way they're organized, according to Stanford biophysical chemist Steven Boxer. With colleagues at Stanford, the University of California-Davis and Lawrence Livermore National Laboratory, he has developed a way to image cell membranes with unprecedented resolution-on the order of 100 nanometers, a scale l...

Recycled paper and compost could both be key tools to control plant disease

New research by the University of Warwick should have gardeners and commercial growers competing for both recycled paper and organic waste composts. The University's plant research department, Warwick HRI, is finding that recycled paper based composts are proving to be a major weapon in the fight against a range of plant diseases. A University of Warwick research team under Professor Ralp...