Researchers identify gene required for nerve regeneration

A gene that is associated with regeneration of injured nerve cells has been identified by scientists at Penn State and Duke University. The team, led by Melissa Rolls, an assistant professor of biochemistry and molecular biology at Penn State, has found that a mutation in a single gene can entirely shut down the process by which axons — the parts of the nerve cell that are responsible for sending signals to other cells — regrow themselves after being cut or damaged. “We are hopeful that this discovery will open the door to new research related to spinal-cord and other neurological disorders in humans,” Rolls said. The journal Cell Reports published an early online copy of the paper (Nov. 1), and also will include the paper in the monthly issue of the journal, which will be published Nov. 29.

UC Santa Barbara Scientists Learn How to Unlock the Destiny of a Cell: A Gift for the Tin Man?

Scientists have discovered that breaking a biological signaling system in an embryo allows them to change the destiny of a cell. The findings could lead to new ways of making replacement organs.

The discovery was made in the laboratory of Joel H. Rothman, a professor in the Department of Molecular, Cellular, and Developmental Biology at UC Santa Barbara. The studies were reported in the interdisciplinary journal Genes and Development, and were carried out by Ph.D student Nareg Djabrayan, in collaboration with Rothman and two other members of the laboratory, Ph.D student Erica Sommermann and postdoctoral fellow Nathaniel Dudley.

"At some point along the way toward becoming part of a complete individual, cells become destined to choose a particular identity and long-term profession," Rothman noted. "Once a cell chooses who it will be, it locks onto that identity for the remainder of its life."

A cell that is destined to become a heart cell functions exclusively in the heart until it dies, and never chooses later to change jobs by becoming, for example, a brain cell. “If Oz’s wizard possessed the powers he claimed, and had a spare brain lying around, he could switch it to a heart as a gift for the Tin Man. And he could reverse the trick for the Scarecrow,” Rothman said.

Similarly, the researchers have found a way to unlock cells’ destinies and lead them to take on a new profession.

Scientists Build ‘Mechanically Active’ DNA Material That Responds With Movement When Stimulated

Artificial muscles and self-propelled goo may be the stuff of Hollywood fiction, but for UC Santa Barbara scientists Omar Saleh and Deborah Fygenson, the reality of it is not that far away. By blending their areas of expertise, the pair have created a dynamic gel made of DNA that mechanically responds to stimuli in much the same way that cells do.

The results of their research were published online in the Proceedings of the National Academy of Sciences.

"This is a whole new kind of responsive gel, or what some might call a ‘smart’ material," said Saleh, associate professor of materials, affiliated with UCSB’s Biomolecular Science and Engineering program. "The gel has active mechanical capabilities in that it generates forces independently, leading to changes in elasticity or shape, when fed ATP molecules for energy — much like a living cell."

Their DNA gel, at only 10 microns in width, is roughly the size of a eukaryotic cell, the type of cell of which humans are made. The miniscule gel contains within it stiff DNA nanotubes linked together by longer, flexible DNA strands that serve as the substrate for molecular motors.

"DNA gives you a lot more design control," said Fygenson, associate professor of physics and also affiliated with UCSB’s BMSE program. "This system is exciting because we can build nano-scale filaments to specifications." Using DNA design, she said, they can control the stiffness of the nanotubes and the manner and extent of their cross-linking, which will determine how the gel responds to stimuli.

BeerSci: What Beer’s Key Ingredient Reveals About Our Own Genomes

The yeast S. cerevisiae is instrumental in brewing ale. But did you know that it’s also instrumental in helping scientists better understand cells?

Humans have been exploiting S. cerevisiae's fermentation prowess for thousands of years. Without it we wouldn't have beer, bread or wine. In addition to its uses in food production, S. cerevisiae is also an amazing tool for molecular and cell biology, one that is helping scientists suss out the rules of how our cells work and gain clues to what happens at the molecular level when things go wrong.

That’s because S. cerevisiae is one of the simplest eukaryotic cells—cells like those that make up your dog, your houseplants or your local bartender. In fact, in 1996 S. cerevisiae became the first eukaryote to have its genome sequenced. According to the Saccharomyces Genome Database, S. cerevisiae's genome has some 12,100,000 base pairs and some 6,600 open reading frames (that is, places in the genome that could possibly contain a gene).

Most of you, I am sure, remember that there are two general kinds of cells: prokaryotic and eukaryotic. That is, “no nucleus” and “has a nucleus.” That’s all true, but the differences between the two kinds of cells are much more profound than that. Bacteria — prokaryotes — organize their genetic material in a completely different (and much simpler) way than do eukaryotes. Prokaryotes usually only have a chunk of DNA for a genome — usually circular — and a few extra chunks, called plasmids, kicking around in the cytosol. Those plasmids are really useful in doing things like sharing genes between bacteria, and its how one antibiotic-resistant strain of bacteria can pass along antibiotic resistance to a bunch of nigh-unrelated strains of bacteria in, say, your intestines. The genes in bacteria are generally read exactly as they are found in the DNA, kind of like how you’re reading this sentence. No intervening clumps of letters to clutter things up.

Eukaryotes, on the other hand, bundle up all that DNA (and they have a lot of it) into a protein-DNA complex called chromatin, then wind that chromatin into individual chromosomes. Further, the genes are constructed in such a way that they must be heavily processed before they can ever “code” for a functional protein. Much of what we understand about eukaryotic cellular processes and eukaryotic gene expression, we learned by studying the molecular mechanics of S. cerevisiae.

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Attack! Silent watchmen charge to defend the nervous system

In many pathologies of the nervous system, there is a common event - cells called microglia are activated from surveillant watchmen into fighters. Microglia are the immune cells of the nervous system, ingesting and destroying pathogens and damaged nerve cells. Until now little was known about the molecular mechanisms of microglia activation despite this being a critical process in the body. Now new research from the Montreal Neurological Institute and Hospital – The Neuro - at McGill University provides the first evidence that mechanisms regulated by the Runx1 gene control the balance between the surveillant versus activated microglia states. The finding, published in the Journal of Neuroscience, has significant implications for understanding and treating neurological conditions.

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Scientists discover novel diabetes and obesity therapy, and potential cause of major side effects from hedgehog inhibitors used as a cancer treatment

Cancer, diabetes, and excess body weight have one thing in common: they alter cellular metabolism. Scientists from the Max Planck Institute of Immunobiology and Epigenetics in Freiburg and the Medical University of Vienna together with an international research team have jointly resolved a new molecular circuit controlling cellular metabolism. The previously unknown signalling pathway, acting downstream of the hedgehog protein enables muscle cells and brown fat cells to absorb sugars without relying on insulin. Substances that selectively activate the signalling pathway could thus be utilized in the treatment of diabetes and obesity. With their results, the researchers are also able to explain why various new anti-cancer agents have induced mysterious pronounced side effects in the clinics.

Fruit flies’ eyes shrink a little to see

I spy, with my mechanical eye. It seems a simple mechanical change plays a role in sensory perception in fruit flies, and possibly in many other animals, including humans.

The eyes of the common fruit fly (Drosophila melanogaster) contain clusters of light-sensitive cells organised into rods. When light strikes one of these cells, it triggers a series of chemical reactions. These cause a protein called a transient receptor potential (TRP) ion channel to open. When it’s open, the TRP allows charged particles to flow into the cell, causing the cell to send a signal to the fly’s brain.

TRP channels play a part in sensory perception in many animals, from nematodes to humans. But nobody knew how the chemical signals make the TRP channel open.

Researchers have discovered a way to generate new human neurons from another type of adult cell found in our brains. The discovery, reported in the October 5th issue of Cell Stem Cell, a Cell Press publication, is one step toward cell-based therapies for the treatment of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s.

Bioengineers Introduce ‘Bi-Fi’ — The Biological ‘Internet’

If you were a bacterium, the virus M13 might seem innocuous enough. It insinuates more than it invades, setting up shop like a freeloading houseguest, not a killer. Once inside it makes itself at home, eating your food, texting indiscriminately. Recently, however, bioengineers at Stanford University have given M13 a bit of a makeover.

The researchers, Monica Ortiz, a doctoral candidate in bioengineering, and Drew Endy, PhD, an assistant professor of bioengineering, have parasitized the parasite and harnessed M13’s key attributes — its non-lethality and its ability to package and broadcast arbitrary DNA strands — to create what might be termed the biological Internet, or “Bi-Fi.” Their findings were published online Sept. 7 in the Journal of Biological Engineering

Using the virus, Ortiz and Endy have created a biological mechanism to send genetic messages from cell to cell. The system greatly increases the complexity and amount of data that can be communicated between cells and could lead to greater control of biological functions within cell communities. The advance could prove a boon to bioengineers looking to create complex, multicellular communities that work in concert to accomplish important biological functions.

Making it easier to make stem cells

The process researchers use to generate induced pluripotent stem cells (iPSCs)—a special type of stem cell that can be made in the lab from any type of adult cell—is time consuming and inefficient. To speed things up, researchers at Sanford-Burnham turned to kinase inhibitors. These chemical compounds block the activity of kinases, enzymes responsible for many aspects of cellular communication, survival, and growth. As they outline in a paper published September 25 in Nature Communications, the team found several kinase inhibitors that, when added to starter cells, help generate many more iPSCs than the standard method. This new capability will likely speed up research in many fields, better enabling scientists around the world to study human disease and develop new treatments.