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Archive - Aug 5, 2014

Caltech Scientists Make Tissues Transparent with Broad Implications

In general, our knowledge of biology—and much of science in general—is limited by our ability to actually see things. Researchers who study developmental problems and disease, in particular, are often limited by their inability to look inside an organism to figure out exactly what went wrong and when. Now, thanks to techniques developed at Caltech, scientists can see through tissues, organs, and even an entire body. The techniques offer new insight into the cell-by-cell makeup of organisms—and the promise of novel diagnostic medical applications. "Large volumes of tissue are not optically transparent—you can't see through them," says Viviana Gradinaru (BS, 2005), an assistant professor of biology at Caltech and the principal investigator whose team has developed the new techniques, which are explained in a paper appearing online on July 31, 2014 in the journal Cell. Lipids throughout cells provide structural support, but they also prevent light from passing through the cells. "So, if we need to see individual cells within a large volume of tissue"—within a mouse kidney, for example, or a human tumor biopsy—"we have to slice the tissue very thin, separately image each slice with a microscope, and put all of the images back together with a computer. It's a very time-consuming process and it is error-prone, especially if you look to map long axons or sparse cell populations such as stem cells or tumor cells," she says. The researchers came up with a way to circumvent this long process by making an organism's entire body clear, so that it can be peered through—in 3-D—using standard optical methods such as confocal microscopy. The new approach builds off a technique known as CLARITY that was previously developed by Gradinaru and her collaborators to create a transparent whole-brain specimen.

Wisconsin Scientists Uncover Novel Process for Creation of Possible Alternative to Fossil Fuels

A team of researchers at the University of Wisconsin (UW)-Madison, and collaborators, have identified the genes and enzymes that create a promising compound — the 19-carbon furan-containing fatty acid (19Fu-FA). The compound has a variety of potential uses as a biological alternative for compounds currently derived from fossil fuels. Researchers from the Great Lakes Bioenergy Research Center (GLBRC), which is headquartered at UW-Madison and funded by the U.S. Department of Energy, discovered the cellular genomes that direct 19Fu-FA's synthesis and published the new findings online on August 4, 2014 in the journal PNAS. "We've identified previously uncharacterized genes in a bacterium that are also present in the genomes of many other bacteria," says Dr. Tim Donohue, GLBRC director and UW-Madison bacteriology professor. "So, we are now in the exciting position to mine these other bacterial genomes to produce large quantities of fatty acids for further testing and eventual use in many industries, including the chemical and fuel industries." The novel 19Fu-FAs were initially discovered as "unknown" products that accumulated in mutant strains of Rhodobacter sphaeroides (see image), an organism being studied by the GLBRC because of its ability to overproduce hydrophobic, or water-insoluble, compounds. These types of compounds have value to the chemical and fuel industries as biological replacements for plasticizers, solvents, lubricants, or fuel additives that are currently derived from fossil fuels. The team also provides additional evidence that these fatty acids are able to scavenge toxic reactive oxygen species, showing that they could be potent antioxidants in both the chemical industry and cells. Cellular genomes are the genetic blueprints that define a cell's features or characteristics with DNA.

Pyruvate Oxidation Is Critical Determinant of Pancreatic Islet Number and Beta-Cell Mass

Researchers at the University at Buffalo, led by Dr. Mulchand Patel and also at Lawson Health Research Institute and Western Ontario, London, Canada, led by Dr. David Hill, collaboratively evaluated the role of the mitochondrial multienzyme pyruvate dehydrogenase complex in the regulation of pancreatic beta-cell development and maturation in the immediate postnatal period in mice. This study, reported in the August 2014 issue of Experimental Biology and Medicine, demonstrated that the pyruvate dehydrogenase complex is not only required for insulin gene expression and glucose-stimulated insulin secretion, but also directly influences beta-cell (see image) growth and maturity. This places glucose metabolism as a direct regulator of beta-cell mass and plasticity. Glucose metabolism within the pancreatic beta-cells is crucial for insulin gene expression and hormone exocytosis, but there is increasing evidence that glucose metabolic pathways are also important for beta-cell development and the maintenance of beta-cell mass in adult life. A targeted deletion of glucokinase in mouse beta-cells not only prevents glucose-stimulated insulin secretion, but also prevents beta-cell proliferation and is associated with increased apoptosis. A direct manipulation of glucose availability to the embryonic pancreas in tissue culture showed that it was necessary for both alpha- and beta-cell development through the regulation of the transcription factors Neurogenin 3 (Neurog3) and NeuroD.

Scientists Study Butterflies’ Ability to Suck Wide Range of Liquids for Applications to Fluidics Advances

New discoveries about how butterflies feed could help engineers develop tiny probes that siphon liquid out of single cells for a wide range of medical tests and treatments, according to Clemson University researchers. The National Science Foundation recently awarded the project $696,514. It was the foundation’s third grant to the project, bringing the total since 2009 to more than $3 million. The research has brought together Clemson’s materials scientists and biologists who have been focusing on the proboscis (see image), the mouthpart that many insects use for feeding. For materials scientists, the goal is to develop what they call “fiber-based fluidic devices,” among them probes that could eventually allow doctors to pluck a single defective gene out of a cell and replace it with a good one, said Dr. Konstantin Kornev, a Clemson materials physics professor. “If someone were programmed to have an illness, it would be eliminated,” he said. Researchers published some of their findings about the butterfly proboscis online on June 15, 2014 in The Journal of Experimental Biology, with a correction following in the same journal on July 1, 2014. The scientists are now advancing to a new phase in their studies. Much remains unknown about how insects use tiny pores and channels in the proboscis to sample and handle fluid. “It’s like the proverbial magic well,” said Clemson entomology professor Dr. Peter Adler. “The more we learn about the butterfly proboscis, the more it has for us to learn about it.” Dr. Kornev said he was attracted to butterflies for their ability to draw various kinds of liquids. “It can be very thick like nectar and honey or very thin like water,” he said. “They do that easily.

Anti-Cancer Molecule May Also Help Pneumonia Patients

The tip of an immune molecule known for its ability to fight cancer may also help patients survive pneumonia, scientists report. A synthesized version of the tip of tumor necrosis factor (TNF) (see image) appears to work like a doorstop to keep sodium channels open inside the air sacs of the lungs so excess fluid can be cleared, according to a study published online on July 16, 2014 in the American Journal of Respiratory Critical Care Medicine. This TIP peptide is attracted to the sugar coating at the mouth of the sodium channel. Once the two connect, they move inside the small but essential number of cells that help keep the lungs clear by taking up sodium, said Dr. Rudolf Lucas, vascular biologist at the Medical College of Georgia (MCG) at Georgia Regents University and the study's corresponding author. Inside these cells, TIP binds to the most critical part of the sodium pump, the alpha subunit, and fluid starts moving again. Sodium comes in the channel, water follows, and the sodium pump pushes the fluid into the body's natural drainage network, called the lymphatic system. "The more sodium you take up, the more water will be taken up by these cells," Dr. Lucas said. "That is the way it's supposed to work.” Fluid in the lungs' 266 million air sacs interferes with breathing as well as the important transfer of oxygen from air sacs to capillaries so it can be distributed throughout the body. TNF, known for its tumor-killing capacity, actually has been viewed as a "bad guy" in the lungs where it can block the sodium channel. In fact, excessive TNF production can put patients into shock. "We found that there is another side on the tip of this molecule, which recognizes sugar groups and this side counteracts that side," Dr. Lucas said.

Triple Therapy Revs Up Immune System against Glioblastoma

A triple therapy for glioblastoma, including two types of immunotherapy and targeted radiation, has significantly prolonged the survival of mice with these brain cancers, according to a new report by scientists at the Johns Hopkins Kimmel Cancer Center. Mice with implanted, mouse-derived glioblastoma cells lived an average of 67 days after the triple therapy, compared with mice that lasted 24 days when they received only the two immunotherapies. Half of the mice who received the triple therapy lived 100 days or more and were protected against further tumors when new cancer cells were re-injected under the animals' skins. The combination treatment described in an open-access article published on July 11, 2014 in PLOS ONE consists of highly focused radiation therapy targeted specifically to the tumor and strategies that lift the brakes and activate the body's immune system, allowing anti-cancer drugs to attack the tumor. One of the immunotherapies is an antibody that binds to and blocks an immune checkpoint molecule on T cells called CTLA-4, allowing the T-cells to infiltrate and fight tumor cells. The second immunotherapy, known as 4-1BB, supplies a positive "go" signal, stimulating anti-tumor T cells. None of the treatments are new, but were used by the Johns Hopkins team to demonstrate the value of combining treatments that augment the immune response against glioblastomas, the most common brain tumors in human adults. The prognosis is generally poor, even with early treatment. "We're trying to find that optimal balance between pushing and pulling the immune system to kill cancer," said Charles Drake, M.D., Ph.D., an associate professor of oncology, immunology, and urology, and medical oncologist at the Johns Hopkins Kimmel Cancer Center.