Science Quick Picks » Biology and Biochemistry

Cloud Computing in Gene Analysis

Jorge Goncalves — Wed, 08 Sep 2010 17:40:58 +0000

Researchers at the Johns Hopkins Bloomberg School of Public Health have developed new software that greatly improves the speed at which scientists can analyze RNA sequencing data. RNA sequencing is used to compare differences in gene expression to identify those genes that switched on or off when, for instance, a particular disease is present. However, sequencing instruments can produce billions of sequences per day, which can be time-consuming and costly to analyze. The software, known as Myrna, uses “cloud computing”, an Internet-based method of sharing computer resources. Faster, cost-effective analysis of gene expression could be a valuable tool in understanding the genetic causes of disease. The findings are published in the current edition of the journal Genome Biology. The Myrna software is available for free download.

Read the full press release: Cloud Computing Method Greatly Increases Gene Analysis.

Cloud Computing in Gene Analysis is a post from Science Quick Picks, a blog dedicated to the world of Science.

Ingenuity Answers Alpha for Biological and Chemical Questions

Jorge Goncalves — Fri, 30 Jul 2010 08:55:37 +0000

Ingenuity Systems, the makers of IPA (Ingenuity Pathway Analysis), have just launched Ingenuity Answers (still in alpha version). Ingenuity Answers is an advanced search tool that enables you to quickly and reliably answer specific biological and chemical questions by identifying lists of genes (or other biological and chemical objects) that satisfy particular biological criteria. Ingenuity Answers leverages the Ingenuity Knowledge Base to allow you to ask highly focused questions involving biological details on multiple levels (genes, chemicals, cells, domains, pathways, diseases, and more) and provides answers based on demonstrated and accurate biological relationships, so you have confidence in your search results.

Just enter a keyword or type a question about genes, proteins, chemicals, drugs, cells, tissues, pathways, biological processes, diseases, biomarkers, or clinical trials. You’ll access detailed summary information and explore reported relationships and interactions between objects. You can also drill down into the supporting literature to see evidence for the results.

Ingenuity Answers Alpha for Biological and Chemical Questions is a post from Science Quick Picks, a blog dedicated to the world of Science.

Highlighting Key Discoveries: Nature Milestones

Jorge Goncalves — Mon, 14 Jun 2010 23:16:29 +0000

Nature Milestones highlights key discoveries that have shaped different scientific fields and enables the wider recognition of these classic findings that are often recognized only by those in the field.

Highlighting Key Discoveries: Nature Milestones is a post from Science Quick Picks, a blog dedicated to the world of Science.

Archaeopteryx: The Dinobird

Jorge Goncalves — Mon, 17 May 2010 09:32:46 +0000

X-Rays Reveal Chemical Link Between Birds and Dinosaurs. Researchers have found that a 150 million year old “dinobird” fossil, long thought to contain nothing but fossilized bone and rock, has been hiding remnants of the animal’s original chemistry. Using the bright X-ray beam of the Stanford Synchrotron Radiation Lightsource, located at the Department of Energy’s SLAC National Accelerator Laboratory, an international team of paleontologists, geochemists and physicists has revealed this transformative glimpse into one of the most important fossils ever discovered: the Archaeopteryx, a half-dinosaur/half-bird species.

“Archaeopteryx is to paleontology what Tutankhamen is to archaeology. It’s simply one of the icons of our field,” said University of Manchester paleontologist Phil Manning. “You would think after 150 years of study, we’d know everything we need to know about this animal. But guess what—we were wrong.”

When the first Archaeopteryx specimen was uncovered a century and a half ago, just a year after Charles Darwin published On the Origin of Species, the discovery provided the strongest evidence yet for the theory of evolution. In the intervening years, nine additional specimens have been found, including the Thermopolis specimen that the researchers studied at SSRL. Like the other Archaeopteryx specimens, this fossil has undergone extensive visual analyses and even CT scans in the past, none of which revealed that beneath the surface hid the dinobird’s chemical remains. But that was before researchers placed it under the X-ray beam at SSRL.

Using light source technology primarily utilized for advanced energy-related research in materials science, biology and other fields, the scientists traced SSRL’s hair-thin X-ray beam across the Thermopolis Archaeopteryx fossil. By recording how the X-rays interacted with the fossil, the researchers were able to identify very precisely the locations of chemical elements hidden within. From this, they created the first maps of the dinobird’s chemistry, revealing half a dozen chemical elements that were actually part of the living animal itself. In almost every element studied, the researchers found significantly different concentrations in the fossil than in the rock that surrounds it, confirming that the observed elements are indeed remnants of the dinobird and not merely chemicals that leached from the surrounding rock into the fossil.

Archaeopteryx: The Dinobird is a post from Science Quick Picks, a blog dedicated to the world of Science.

MendelWeb: All About Gregor Mendel

Jorge Goncalves — Tue, 07 Aug 2007 20:39:49 +0000

MendelWeb – An Electronic Science/Math/History Resource for the WWW. ‘MendelWeb was conceived and constructed by Roger B. Blumberg and is an educational resource for teachers and students interested in the origins of classical genetics, introductory data analysis, elementary plant science, and the history and literature of science. Constructed around Gregor Mendel’s 1865 paper “Versuche über Pflanzen-Hybriden” and a revised version of the English translation by C.T. Druery and William Bateson, “Experiments in Plant Hybridization”, MendelWeb is offered as a public sourcebook and collaborative environment compatible with a variety of guided and independent studies.’

The Mendelroom and General Moo Information. ‘Mendelroom is a virtual space designed for teachers and students who wish to share their experiences, thoughts and questions while using MendelWeb.’

MendelWeb: All About Gregor Mendel is a post from Science Quick Picks, a blog dedicated to the world of Science.

Coffee and Exercise May Help Prevent Skin Cancer

Jorge Goncalves — Wed, 01 Aug 2007 15:31:41 +0000

Caffeine and Exercise Can Team Up to Prevent Skin Cancer. ‘Regular exercise and little or no caffeine has become a popular lifestyle choice for many Americans. But a new Rutgers study has found that it may not be the best formula for preventing sun-induced skin damage that could lead to cancer. Low to moderate amounts of caffeine, in fact, along with exercise can be good for your health.

Groups of hairless mice, whose exposed skin is vulnerable to the sun, were the test subjects in experiments in which one set drank caffeinated water (the human equivalent of one or two cups of coffee a day); another voluntarily exercised on a running wheel; while a third group both drank and ran. A fourth group, which served as a control, didn’t run and didn’t caffeinate. All of the mice were exposed to lamps that generated UVB radiation that damaged the DNA in their skin cells.

Some degree of programmed cell death, also known as apoptosis, was observed in the DNA-damaged cells of all four groups, but the caffeine drinkers and exercisers showed an increase over the UVB-treated control group. Apoptosis is a way in which cells with badly damaged DNA commit suicide – UVB-damaged cells in this case.

“If apoptosis takes place in a sun-damaged cell, its progress toward cancer will be aborted,” said Allan Conney, director of Rutgers’ Cullman Laboratory.

Compared to the UVB-exposed control animals, the caffeine drinkers showed an approximately 95 percent increase in UVB-induced apoptosis, the exercisers showed a 120 percent increase, while the mice that were both drinking and exercising showed a nearly 400 percent increase.’

Coffee and Exercise May Help Prevent Skin Cancer is a post from Science Quick Picks, a blog dedicated to the world of Science.

A Fantastic Video about a Fantastic Voyage Inside a Cell

Jorge Goncalves — Mon, 30 Jul 2007 22:47:26 +0000

TED Talks – David Bolinsky: Fantastic voyage inside a cell (Video). ‘Medical animator David Bolinsky presents 3 minutes of stunning animation that show the bustling life inside a cell. Built by his company, XVIVO, to teach Harvard medical students, the clip features sweeping cinematic values and even a little drama. It communicates not only the facts of life, but life’s truth and beauty.’

TED. ‘TED stands for Technology, Entertainment, Design. It started out (in 1984) as a conference bringing together people from those three worlds. Since then its scope has become ever broader. The annual conference now brings together the world’s most fascinating thinkers and doers, who are challenged to give the talk of their lives (in 18 minutes).
This site makes the best talks and performances from TED available to the public, for free.’

A Fantastic Video about a Fantastic Voyage Inside a Cell is a post from Science Quick Picks, a blog dedicated to the world of Science.

Hormone Sensitive Bacterias

Jorge Goncalves — Thu, 19 Jul 2007 11:26:33 +0000

Engineered E. coli may lead to new drugs, detect pollutants. ‘Bacteria that respond to human hormones – the body’s chemical messengers – may enable the discovery of new treatments for hormone-related medical problems, including thyroid disease and some forms of breast cancer. Developed by Princeton chemical engineers, the sensitive bugs also may detect hormone-mimicking pollutants, which can disrupt normal processes in the body.

Hormones must be present in specific amounts to maintain health. For example, sufficient levels of the hormone estrogen are necessary for bone formation and reproduction, but too much of it has been implicated in premature puberty as well as the development of breast cancer and heart disease. The Princeton engineers hope that the bacteria can shed light on the way hormone-like compounds affect the body and eventually guide the development of drugs that can regulate hormone levels.’

Hormone Sensitive Bacterias is a post from Science Quick Picks, a blog dedicated to the world of Science.

Sequencing the Genome of Neanderthals

Jorge Goncalves — Tue, 17 Jul 2007 22:49:31 +0000

The human family tree explored. ‘It sounds as though it came out of the pages of a science fiction book or from the mind of Steven Spielberg. But as is often the case, reality is where all the action is and this time it’s happening in Leipzig, Germany. There, scientists from the Max Planck Institute for Evolutionary Anthropology are close to unlocking the secrets of the DNA belonging to Neanderthal man. Their efforts will help answer the question as to just how close a relative the Neanderthal man is to modern Man.

There has been much debate in the scientific community as to whether there is any relationship between Neanderthals and modern humans. Currently, the deliberation is divided into two main camps with some researchers believing that Neanderthals were simply replaced by early modern humans, while those in the other camp posit that the two groups may have indeed interbred.

That is why the research conducted by these European scientists is so important. By sequencing the genome of Neanderthals, scientists will be able to clarify the evolutionary relationship between humans and Neanderthals. This will also help identify those genetic changes that enabled modern humans to leave Africa and make their way across the world some 100 000 years ago.’

Sequencing the Genome of Neanderthals is a post from Science Quick Picks, a blog dedicated to the world of Science.

Fantastic Discovery: Orlistat (Xenical® or Alli®) Can Kill Cancer Cells

Jorge Goncalves — Tue, 10 Jul 2007 08:32:14 +0000

Discovery about Obesity Drug Helping Scientists Develop New Cancer Treatments. Based on their surprising discovery that an obesity drug can kill cancer cells, scientists at Wake Forest University School of Medicine have made a new finding about the drug’s effects and are working to design more potent cancer treatments.
Published online in Nature Structural and Molecular Biology, the study is the first to report how the drug orlistat (Xenical® or Alli®) binds and interacts with a protein found in tumor cells. The drug blocks the protein’s function and causes cell death.
The project started five years ago when Steven Kridel, Ph.D., an assistant professor in the Department of Cancer Biology, analyzed prostate cancer cells to see which enzymes were expressed at high levels. His hope was that treatments to inhibit those enzymes could also stop tumor growth.
“We found that a protein known as fatty acid synthase is expressed at high levels in prostate tumor cells, and is fairly absent in normal cells,” said Kridel.
Other research has shown that the protein is found in many tumor cells including breast, colon, ovarian, liver, lung and brain.
“High levels of fatty acid synthase correlate with a poor prognosis so it is a great treatment target,” said Kridel. “This makes an exciting treatment target because theoretically you don’t have to worry about harming nearby healthy tissue.”
Unfortunately, orlistat itself cannot be used as a cancer treatment because, while it can kill cancer cells in the laboratory, in humans it is designed to act only in the digestive tract.
“Understanding this drug-protein interaction is essential for designing new drugs,” said W. Todd Lowther, Ph.D., an assistant professor in the Department of Biochemistry. “We’ve used a technique known as X-ray crystallography and now have a three-dimensional snapshot of the drug interacting with the protein.”
“Our goal is to develop an orlistat-like drug that can get into the bloodstream and go to the site of a tumor,” said Lowther.’

Fantastic Discovery: Orlistat (Xenical® or Alli®) Can Kill Cancer Cells is a post from Science Quick Picks, a blog dedicated to the world of Science.

Science Quick Picks » Biology and Biochemistry

Cloud Computing in Gene Analysis

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