Now that the genome (DNA) of humans and many other organisms have been sequenced, biologists are turning their attention to discovering how the many thousands of structural and control genes — the “worker bees” of living cells that can turn genes on and off — function.

To do that, they need to develop new techniques and tools. Scientists in the Optical Microscopy group at the National High Magnetic Field Laboratory at Florida State University, working in collaboration with researchers from the University of Alberta in Canada and the University of California, San Diego, have done just that, and in the process have produced back-to-back articles in the prestigious journal Nature Methods.

In the first paper, magnet-lab biologists Michael Davidson and Kristen Hazelwood worked with researchers from the University of Alberta to create two new fluorescent-protein biosensors, molecular “beacons” that can tell if there is activity within a cell. The biosensors can be used simultaneously to monitor two separate dynamic functions in a single cell — a key to understanding how different proteins and enzymes (the biomolecules that cause chemical reactions) work together to complete the daily chores that help cells grow and divide. Knowing how cells work together can help researchers learn a great deal more about tumors and developmental biology, among many other things.

The researchers improved a powerful technique used to monitor cellular dynamics called fluorescence resonance energy transfer, or FRET. The technique is used to examine a new class of biosensor molecules that tether two fluorescent proteins together through an intervening peptide (which is like a polymer). Several hundred of these new biosensors have been developed over the past few years and are being used by scientists around the world to study a variety of functions, including programmed cell death, carbohydrate metabolism, cell division, hormone stimulation, acidity changes — just about any cellular process that can occur.

“In FRET, two molecules that are fluorescent act as ‘molecular beacons’ under the microscope, transferring energy between each other if they interact in the living cell,” said Davidson, who directs the magnet lab’s Optical Microscopy program. “With FRET, we can see that happen, but until now, we have only been able to monitor one biosensor at a time.”

The new technique, called Dual FRET, is outlined in the paper “Fluorescent Protein FRET Pairs for Ratiometric Imaging of Dual Biosensors.” http://www.nature.com/nmeth/journal/v5/n5/abs/nmeth.1207.html

Further expanding the capabilities of optical microscopy, Davidson and his team worked with collaborators from the University of California, San Diego to create a new screening method for fluorescent proteins that makes them more stable under the microscope. These proteins are sensitive to light, which can bleach them out after a certain period of time. By making the proteins more stable, microscopists can observe live cell dynamics for longer periods of time. The paper describing their work, “Improving the Photostability of Bright Monomeric Orange and Red Fluorescent Proteins,” was published in the May 4 online edition of Nature Methods. http://www.nature.com/nmeth/journal/v4/n9/full/nmeth1083.html

Taken together, the new technique and tool are expected to speed up experiments and expand the utility of optical microscopy by allowing two dynamic processes inside a cell to be observed at once — and for longer periods of time.

Source: Florida State University

Now that the genome (DNA) of humans and many other organisms have been sequenced, biologists are turning their attention to discovering how the many thousands of structural and control genes — the “worker bees” of living cells that can turn genes on and off — function.

To do that, they need to develop new techniques and tools. Scientists in the Optical Microscopy group at the National High Magnetic Field Laboratory at Florida State University, working in collaboration with researchers from the University of Alberta in Canada and the University of California, San Diego, have done just that, and in the process have produced back-to-back articles in the prestigious journal Nature Methods.

This image illustrates fluorescence resonance energy transfer works. With FRET, the illuminated yellow molecules come together, signaling that they are transferring energy in the living cell. Click here for more information.

In the first paper, magnet-lab biologists Michael Davidson and Kristen Hazelwood worked with researchers from the University of Alberta to create two new fluorescent-protein biosensors, molecular “beacons” that can tell if there is activity within a cell. The biosensors can be used simultaneously to monitor two separate dynamic functions in a single cell — a key to understanding how different proteins and enzymes (the biomolecules that cause chemical reactions) work together to complete the daily chores that help cells grow and divide. Knowing how cells work together can help researchers learn a great deal more about tumors and developmental biology, among many other things.

The researchers improved a powerful technique used to monitor cellular dynamics called fluorescence resonance energy transfer, or FRET. The technique is used to examine a new class of biosensor molecules that tether two fluorescent proteins together through an intervening peptide (which is like a polymer). Several hundred of these new biosensors have been developed over the past few years and are being used by scientists around the world to study a variety of functions, including programmed cell death, carbohydrate metabolism, cell division, hormone stimulation, acidity changes — just about any cellular process that can occur.

“In FRET, two molecules that are fluorescent act as ‘molecular beacons’ under the microscope, transferring energy between each other if they interact in the living cell,” said Davidson, who directs the magnet lab’s Optical Microscopy program. “With FRET, we can see that happen, but until now, we have only been able to monitor one biosensor at a time.”

Kristin Hazelwood, National High Magnetic Field Laboratory biologist. Click here for more information.

The new technique, called Dual FRET, is outlined in the paper “Fluorescent Protein FRET Pairs for Ratiometric Imaging of Dual Biosensors.” http://www.nature.com/nmeth/journal/v5/n5/abs/nmeth.1207.html

Further expanding the capabilities of optical microscopy, Davidson and his team worked with collaborators from the University of California, San Diego to create a new screening method for fluorescent proteins that makes them more stable under the microscope. These proteins are sensitive to light, which can bleach them out after a certain period of time. By making the proteins more stable, microscopists can observe live cell dynamics for longer periods of time. The paper describing their work, “Improving the Photostability of Bright Monomeric Orange and Red Fluorescent Proteins,” was published in the May 4 online edition of Nature Methods. http://www.nature.com/nmeth/journal/v4/n9/full/nmeth1083.html

Taken together, the new technique and tool are expected to speed up experiments and expand the utility of optical microscopy by allowing two dynamic processes inside a cell to be observed at once — and for longer periods of time.

Source: Florida State University

The radioactive carbon-14 produced by above-ground nuclear testing in the 1950s and ’60s has helped researchers determine that the number of fat cells in a human’s body, whether lean or obese, is established during the teenage years. Changes in fat mass in adulthood can be attributed mainly to changes in fat cell volume, not an increase in the actual number of fat cells.

These results could help researchers develop new pharmaceuticals to battle obesity as well as the accompanying diseases such as high blood pressure and diabetes.

A new study by Lawrence Livermore National Laboratory scientist Bruce Buchholz - along with colleagues from the Karolinska Institute in Sweden; Humboldt University Berlin, Foundation of Research and Technology in Greece; Karolinska University Hospital; and Stockholm University - applied carbon dating to DNA to discover that the number of fat cells stays constant in adulthood in lean and obese individuals, even after marked weight loss, indicating that the number of fat cells is set during childhood and adolescence.

Carbon dating is typically used in archaeology and paleontology to date the age of artifacts. However, in this application, which appeared in the May 4 early online edition of the journal Nature, the scientists used the pulse of radiocarbon to analyze fat cell turnover in humans.

Radiocarbon or carbon-14 is naturally produced by cosmic ray interactions with air and is present at low levels in the atmosphere and food. Its concentration remained relatively constant during the past 4,000 years, butatmospheric testing of nuclear weapons from 1950-1963 produced a global pulse in the amount of radiocarbon in the atmosphere, Buchholz said.

In the new study, Buchholz analyzed the uptake of carbon-14 in genomic DNA within fat cells to establish the dynamics of fat cell turnover. Approximately 10 percent of fat cells are renewed annually at all adult ages and levels of body mass index.

Neither fat cell death nor its generation rate is altered in early onset obesity, suggesting a tight regulation of the number of fat cells in obese adults.

“Fat cells change in size but no one had ever measured fat cell turnover,” Buchholz said. “An increase in cell size means it can hold more mass.”

Obesity is increasing in epidemic proportions in most countries and poses a public health problem by enhancing the risks for cardiovascular diseases and metabolic disorders such as type 2 diabetes. According to the Centers for Disease Control and Prevention, the prevalence of overweight and obesity has increased sharply for both adults and children since the 1970s. Data from two National Health and Nutrition Examination surveys show that among adults aged 20-74 years the prevalence of obesity increased from 15 percent (in the 1976-80 survey) to 32.9 percent (in the 2003-04 survey).

The two surveys also show increases in overweight children and teens. For children aged 2-5 years, the prevalence increased from 5 percent to 13.9 percent; for those aged 6-11 years, prevalence increased from 6.5 percent to 18.8 percent; and for those aged 12-19 years, prevalence increased from 5 percent to 17.4 percent.

In the Nature study, the team first found that there was a direct correlation between the measures of fat mass (measured from body mass index (BMI) and fat cell volume in subcutaneous fat, which represents about 80 percent of all fat, and visceral fat.

In a study of 687 adults, the researchers found that number of fat cells increases in childhood and adolescence, but levels off and remains constant in adulthood. The group looked at whether the number of fat cells changes under extreme conditions such as drastic weight loss by radical reduction in caloric intake, such as through bariatric surgery. The treatment resulted in a significant decrease in BMI and fat cell volume; however, it did not reduce the number of fat cells two years after the surgery. Similarly, significant weight gain (15-25 percent) over several months in non-obese adult men resulted in significant increase in body fat volume but no change in number. Subsequent weight loss back to baseline resulted in a decrease in fat cell volume but no change in the number of fat cells.

“If you are overweight and you lose weight, you still have the capacity to store lipids because you still have the same number of fat cells. That may be why it’s so hard to keep the weight off,” Buchholz said.

Overweight and obesity result from an energy imbalance - eating too many calories and not getting enough physical activity. Body weight is the result of genes, metabolism, behavior, environment, culture and socioeconomic status. “This work may give us new ideas of how to deal with the diseases that go along with obesity,” Buchholz said.

Source: DOE/Lawrence Livermore National Laboratory

Research Highlights:

• Mechanism of action of compound found to induce neurotransmitter activity in brain cells
• The findings may lead researchers to develop potential novel therapies to treat Alzheimer’s disease, amyotrophic lateral sclerosis, Huntington’s disease, epilepsy, stroke/ischemia, dementia and malignant gliomas

Virginia Commonwealth University researchers have discovered how an antibiotic works to modulate the activity of a neurotransmitter that regulates brain functions, which eventually could lead to therapies to treat Alzheimer’s disease, Huntington’s disease, epilepsy, stroke, dementia and malignant gliomas. … Continue Reading »

A team of scientists has provided, for the first time, a detailed map of how the building blocks of chromosomes, the cellular structures that contain genes, are organized in the fruit fly Drosophila melanogaster. The work identifies a critical stop sign for transcription, the first step in gene expression, and has implications for understanding how the AIDS virus regulates its genes. The findings will be published in the 15 May 2008 issue of the journal Nature.

The scientists found that nucleosomes–chromosomal building blocks made up of proteins around which DNA is coiled–occur at precise locations along genes that are actively undergoing transcription. They also showed that RNA polymerase–the enzyme that reads genes as the first step in making proteins–is stopped at the first nucleosome, where it remains idle until it is directed to continue moving forward. “This discovery is important because nucleosomes are barriers to transcription and we now are seeing the impact of nucleosome organization on RNA polymerase,” said lead investigator B. Franklin Pugh, professor and Willaman Chair in Molecular Biology at Penn State University. … Continue Reading »

Researchers at the OU Cancer Institute have identified a new gene that causes cancer. The ground-breaking research appears in Nature’s cancer journal Oncogene.

The gene and its protein, both called RBM3, are vital for cell division in normal cells. In cancers, low oxygen levels in the tumors cause the amount of this protein to go up dramatically. This causes cancer cells to divide uncontrollably, leading to increased tumor formation.

Researchers used new powerful technology to genetically “silence” the protein and reduce the level of RBM3 in cancerous cells. The approach stopped cancer from growing and led to cell death. The new technique has been tested successfully on several types of cancers – breast, pancreas, colon, lung, ovarian and prostate. … Continue Reading »

A tiny modification called methylation on estrogen receptors prolongs the life of these growth-driving molecules in breast cancer cells, according to research by scientists at Emory University’s Winship Cancer Institute.

The results are published in the May 9, 2008 issue of the journal Molecular Cell.

Most breast cancers contain estrogen receptors, which enable them to grow in the presence of the hormone estrogen. Their presence can determine whether tumors will respond to the estrogen-blocking drug tamoxifen. … Continue Reading »

A new approach to estimating tumour growth based on breast screening results from almost 400,000 women is published today BioMed Central’s open access journal, Breast Cancer Research. This new model can also estimate the proportion of breast cancers which are detected at screening (screen test sensitivity). It provides a new approach to simultaneously estimating the growth rate of breast cancer and the ability of mammography screening to detect tumours. … Continue Reading »

There’s no doubt about it … the platypus is one odd duck-billed, egg-laying, lactating mammal. With adaptations like webbed feet to fit its aquatic lifestyle and the poison spurs that decorate males, the platypus represents for many a patchwork of evolutionary development. But LSU’s Mark Batzer, along with an international consortium of scientists led by Wes Warren at Washington University in Saint Louis, Mo., has taken this theory to an entirely new level, proving that platypus looks aren’t only skin-deep – their DNA is an equally cobbled-together array of bird, reptile and mammalian lineages.

The consortium conducted the first analysis of platypus DNA in what was the largest platypus population genetics study to date. … Continue Reading »

An undergraduate student at Rensselaer Polytechnic Institute has learned very quickly that a spoonful of sugar really does help the medicine go down. In fact, with his invention, the sugar may actually be the medicine.

Among the most important and complex molecules in the human body, sugars control not just metabolism but also how cells communicate with one another. Graduating senior Jeffery Martin has put his basic knowledge of sugars to exceptional use by creating a lab-on-a-chip device that builds complex, highly specialized sugar molecules, mimicking one of the most important cellular structures in the human body — the Golgi Apparatus.

“Almost completely independently he has been able to come closer than researchers with decades more experience to creating an artificial Golgi,” said Robert Linhardt, the Ann and John H. Broadbent Jr. ’59 Senior Constellation Professor of Biocatalysis and Metabolic Engineering at Rensselaer and Martin’s adviser. “He saw a problem in the drug discovery process and almost instantly devised a way to solve it.” … Continue Reading »

Prions, the infamous agents behind mad cow disease and its human variation, Creutzfeldt-Jakob Disease, also have a helpful side. According to new findings from Gerald Zamponi and colleagues, normally functioning prions prevent neurons from working themselves to death. The findings appear in the May 5th issue of the Journal of Cell Biology.

Diseases such as mad cow result when the prion protein adopts an abnormal conformation. This infectious form creates a template that induces normal copies of the protein to misfold as well. Scientists have long assumed that prions must also have a beneficial side but have been unable to pinpoint any such favorable traits.

In the new work, the authors found that mice lacking the prion protein had overactive brain cells. Their neurons responded longer and more vigorously to electrical or drug-induced stimulation than did neurons that had normal prion protein. This hyperactivity eventually led to the neurons’ death. The results might help explain why misfolded prions cause dementia: in the wrong conformation, the prion can no longer protect brain cells from deadly overexcitement.

Source: Rockefeller University

Retinas in newborn mice appear perfectly fine without any help from tiny bits of genetic material called microRNAs except for one thing — the retinas do not work.

In the first-ever study of the effects of the absence of microRNAs in the mammalian eye, an international team of researchers directed by the University of Florida and the Italian National Research Council describes a gradual structural decline in retinas that lack microRNAs — a sharp contrast to the immediate devastation that occurs in limbs, lungs and other tissues that develop without microRNAs. … Continue Reading »

For the first time, researchers from the University of Pittsburgh School of Medicine have identified genetic components of dendritic cells that are key to asthma and allergy-related immune response malfunction. Targeting these elements could result in more effective drugs to treat allergic disorders and asthma, according to a study reported in the May edition of the journal Nature Medicine.

Dendritic cells are vital to immune response in that they recognize, capture and introduce threatening organisms to T lymphocytes - other immune cells that secrete potent proteins called cytokines that surround and destroy the invaders. However, the Pittsburgh team’s study goes further to illuminate a pathway that allergens use to act directly on dendritic cells to propel differentiation into the T lymphocytes that fight back. … Continue Reading »

Using ingenious molecular espionage, scientists have found how a single key enzyme, seemingly the Swiss army knife in HIV’s toolbox, differentiates and dynamically binds both DNA and RNA as part of the virus’ fierce attack on host cells. The work is described this week in the journal Nature.

The enzyme, reverse transcriptase (RT), is already the target of two of the three major classes of existing anti-HIV drugs. The new work, using single-molecule fluorescent imaging to trace RT’s activity in real time, not only reveals novel insights into how this critical viral enzyme functions, but also clarifies how some of the anti-HIV pharmaceuticals work. … Continue Reading »

Genetic variation in the DNA of mitochondria – the “power plants” of cells – contributes to a person’s risk of developing age-related macular degeneration (AMD), Vanderbilt investigators report May 7 in the journal PLoS ONE.

The study is the first to examine the mitochondrial genome for changes associated with AMD, the leading cause of blindness in Caucasians over age 50.

“Most people don’t realize that we have two genomes,” said lead author Jeff Canter, M.D., M.P.H., an investigator in the Center for Human Genetics Research. “We have the nuclear genome – the “human genome” – that makes the cover of all the magazines, and then we also have this tiny genome in mitochondria in every cell.” … Continue Reading »

A team of McGill University scientists has discovered important differences between the brains of suicide victims and so-called normal brains. Although the genetic sequence was identical in the suicide and non-suicide brains, there were differences in their epigenetic marking – a chemical coating influenced by environmental factors. … Continue Reading »

Tumors have a unique vulnerability that can be exploited to make them more sensitive to heat and radiation, researchers at Washington University School of Medicine in St. Louis report.

The Washington University radiation oncology researchers found that tumors have a built-in mechanism that protects them from heat (hyperthermia) damage and most likely decreases the benefit of hyperthermia and radiation as a combined therapy.

By interfering with that protection, the researchers have shown that tumor cells grown in culture can be made more sensitive to hyperthermia-enhanced radiation therapy. The findings are reported in the May 1, 2008 issue of Cancer Research. … Continue Reading »

Analysis and diagnosis in a chip format are coming of age, but their practical application has been limited because until now, the sample usually had to be prepared separately and on a nonminiaturized scale. Jürgen Pipper and his team at the Institute of Bioengineering and Nanotechnology in Singapore want to change this. They have now developed a rapid test for genetic diagnosis that combines the preparation of biological samples with a polymerase chain reaction (PCR) on one chip. As they report in the journal Angewandte Chemie, the “laboratory device” for all steps in this system is a single drop containing magnetic nanoparticles, which is moved across the chip by a magnetic field.

PCR allows gene sequences to be duplicated and identified—to identify a disease trigger, for example. In this process, the sample must cycle through a specific sequence of temperatures. Because of the slow heating and cooling processes, laboratory PCR usually takes several hours. The new chip PCR requires only minutes, including for the sample preparation. … Continue Reading »

Breaking news: Think Gene has recently received a civilian report [edit: confirmed] of a Man Bear Pig sighting in Appalachian Ohio!

I would like to know the sponsoring agency for the thinkgene website.
today my students were surfing the web and found your man, bear, pig [editor: Man Bear Pig, April 1st 2008]. At first glance my students thought it was real. I encouraged them to read on and to do more research.
Anyone who post things on the web has a civic duty to clairify and correct. People that just look at photos and headlines are mislead daily.
the internet’s main goal was not for entertainment…. but for knowledge. Leave sci fi to the movie industry.

kjl

Science Dept Chair
Wellston High School

kjl, as Senior Editor of ThinkGene, thank you for alerting The Internet regarding this important Man Bear Pig sighting in Wellston, Ohio. Please accept this Certificate of Sighting on behalf of The Internet and The Movie Industry as a token of our appreciation.

Please help us by ensuring that the fine students of Wellston High School of Wellston Ohio receive their certificate. Thank you.

–Andrew Yates

Researchers have discovered how a mole develops into melanoma by showing the interaction of two key proteins involved in 60-70 percent of tumors. The Penn State scientists also demonstrate that therapeutic targeting of these proteins is necessary for drugs to effectively treat this deadly form of cancer.

“We have shown that when two proteins – (V600E)B-Raf and Akt3 – communicate with one another in a mole, they cooperate leading to the development of melanoma,” said Gavin Robertson, lead author and associate professor of pharmacology, pathology and dermatology, and director of the Foreman Foundation Melanoma Therapeutics Program at the Penn State College of Medicine Cancer Institute. “We have also shown that effective therapies for melanoma need to target both these proteins, which essentially eliminates the tumors.” … Continue Reading »