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Archive - Jan 2017

January 11th

CRISPR-Cas9 Edits to Address X-Linked Chronic Granulomatous Disease Are Maintained Long-Term in Mice

Researchers have harnessed the CRISPR-Cas9 technology to correct mutations in the blood stem cells of patients with a rare immunodeficiency disorder, with the engineered cells successfully engrafted in mice for up to five months. The study paves the way for CRISPR-Cas9 as a powerful gene editing tool with potential therapeutic applications for inherited diseases - leading to more widely available gene therapy techniques. In particular, CRISPR-Cas9 holds promise for advancing ex vivo gene therapy, which tweaks disease-causing mutations in patient cells at the lab bench and implants them back into the body. However, scientists' ability to selectively modify DNA errors without introducing additional mutations into a patient's genome remains a challenge. Suk See De Ravin, Ph.D., from the National Institute of Allergy and Infectious Diseases, and colleagues applied an ex vivo gene editing approach using the CRISPR-Cas9 platform to chronic granulomatous disease (CGD), a genetic disorder with limited treatment options that leads to life-threatening infections and often requires long-term antibiotics. CGD is caused by defects in the NOX2 protein, a key molecule that helps the immune system destroy harmful bacteria. While stem cell transplantation offers a potential therapy for CGD, the procedure carries a risk of toxicity and potentially lethal complications. The authors repaired the NOX2 mutation in stem cells from CGD patients, confirming their ability to differentiate into immune cells with restored antimicrobial function. When implanted into mice, the pool of altered cells maintained their gene edits long-term, with no signs of side effects. With further development, CRISPR-Cas9-based gene therapy may offer a new clinical strategy for CGD, and perhaps other blood disorders.

New Research Explores Effect of Winter Dormancy on Cold-Blooded Cognition in Amphibians

Unlike mammals, amphibians who rest up during the winter do not forget the memories they made beforehand - this is the surprising discovery of new scientific research. The new study, published online on January 11, 2017 in Scientific Reports, reveals that the processes involved in winter dormancy may have a fundamentally different impact on memory in amphibians and mammals. The open-accesss article is titled “The Effect of Brumation on Memory Retention.” Researchers from the University of Lincoln (UK) and two universities in Vienna, Austria, discovered that brumation - the period of winter dormancy that is observed in cold-blooded animals, similar to the process of hibernation in mammals - does not seem to adversely affect the memory of salamanders. This key finding differs dramatically from previous studies of mammals, which show that hibernation often causes animals to forget some of the memories they formed prior to their period of inactivity. Dr. Anna Wilkinson, from the School of Life Sciences at the University of Lincoln, led the study in collaboration with colleagues from the University of Vienna and the University of Veterinary Medicine Vienna. Dr. Wilkinson said: "Long-term torpor is an adaptive strategy that allows animals to survive harsh winter conditions. However, the impact that this has on cognitive function is poorly understood. We know that in mammals, hibernation causes reduced synaptic activity and can cause them to lose some of the memories they formed prior to hibernation, but the effect of brumation on memory has been unexplored, until now."

The researchers trained twelve salamanders to navigate a maze and remember the path they needed to take to reach a reward. Half of the animals were then placed into brumation for 100 days, while the other half remained under normal keeping conditions.

January 11th

Exosome Release from Tumor Cells Promoted by PKM2 Phosphorylation of Synaptosome-Associated Protein 23

In a study published online on January 9, 2017 in Nature Communications, a research team led by Dr. Ke Zen and Dr. Chen-Yu Zhang from Nanjing University in China reports that pyruvate kinase type M2 (PKM2) promotes tumor cell exosome release through phosphorylating synaptosome-associated protein 23 (SNAP-23). The open-access article is titled “Pyruvate Kinase Type M2 Promotes Tumour Cell Exosome Release Via Phosphorylating Synaptosome-Associated Protein 23.” As a mechanism to communicate with the microenvironment, tumor cells actively release large numbers of microvesicles (MVs), particularly exosomes. These tumor-released MVs, which are abundant in the body fluids of patients with cancer, play a critical role in promoting tumor growth and progression. The mechanism underlying the active exocytosis of exosomes by tumor cells, however, remains incompletely understood. It has been reported that cellular exocytosis activity is increased during tumorigenesis, but the molecular basis to switch on the exocytosis process in tumor cells has not been identified. In the present study, the Nanjing University team showed that PKM2, an enzyme involved in the tumor cell's reliance on aerobic glycolysis (Warburg effect), plays a critical role in promoting the release of exosomes from the tumor cell. Specifically, the researchers identify SNAP-23, which controls the dock and release of secretory granules or exosome-containing multivesicular bodies (MVBs), is a substrate of PKM2 in tumor cells. During exocytosis, phosphorylated PKM2 is recruited to secretory granules or MVBs near cell membranes where it associates with SNAP-23 and phosphorylates SNAP-23 at Ser95, leading to upregulation of exocytosis in tumor cells.

Genetic Opposites Attract When Chimps Choose Mates

When it comes to hookups in the animal world, casual sex is common among chimpanzees. In our closest animal relatives both males and females mate with multiple partners. But when taking the plunge into parenthood, they're more selective than it seems. A study appearing online on January 11, 2017 in the journal Royal Society Open Science reveals that chimps are more likely to reproduce with mates whose genetic makeup differs most from their own. The open-access article is titled “Chimpanzees Breed with Genetically Dissimilar Mates.” Many animals avoid breeding with parents, siblings, and other close relatives, said first author Kara Walker, Ph.D., a postdoctoral Associate in Evolutionary Anthropology at Duke University. But chimpanzees are unusual in that even among nonrelatives and virtual strangers they can tell genetically similar mates from more distant ones. The researchers aren't sure yet exactly how the chimps make this discrimination, but it might be a best guess based on appearance, smell, or sound, said senior author Anne Pusey, Ph.D., Professor of Evolutionary Anthropology at Duke. Researchers took DNA samples from the feces of roughly 150 adult chimpanzees in Gombe National Park, Tanzania, and analyzed eight to eleven variable sites across the genome. From these, they were able to estimate the genetic similarity between every possible male-female pair. In chimpanzees, as in other animals, only some sexual encounters lead to offspring. When the researchers compared pairs that produced infants with those that didn't, they found that females conceived with sires that were less similar to them than the average male. Chimps are somehow able to distinguish degrees of genetic similarity among unfamiliar mates many steps removed from them in their family tree, the study shows.

Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis & Anti-TB Host Defense

University of Texas (UT) Southwestern Medical Center researchers have identified a protein that is central to the immune system’s ability to recognize and destroy the bacterium responsible for the global tuberculosis (TB) epidemic. The new finding, reported in the January 11, 2017 issue of Cell Host & Microbe, could someday lead to the development of immunity-based therapies to treat tuberculosis – which typically takes months to eradicate and has become increasingly resistant to antibiotics – by strengthening this immune pathway, said Dr. Michael Shiloh, Assistant Professor of Internal Medicine and Microbiology. The article is titled “The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-Tuberculous Host Defense.” According to the World Health Organization, TB is a top infectious disease killer worldwide and is estimated to have infected 9.5 million people and caused 1.5 million deaths in 2014. That year, tuberculosis surpassed HIV as the world’s most lethal infection. “The protein Smurf1 functions in specialized white blood cells called macrophages in both mice and humans, thereby suggesting a conserved evolutionary pathway,” said Dr. Shiloh, co-senior author of the study along with Dr. Beth Levine, Director of the University’s Center for Autophagy Research. In 2011, UT Southwestern researchers in Dr. Levine’s laboratory identified the protein Smurf1 as important for the elimination of viruses and damaged mitochondria from cells via a cellular housekeeping process called autophagy. Dr. Levine is also a Professor of Internal Medicine and Microbiology; a Howard Hughes Medical Institute Investigator; and holder of the Charles Cameron Sprague Distinguished Chair in Biomedical Science.

New Transplant Technique Restores Vision in Mice; “Results Are a Proof of Concept for Using iPSC-Derived Retinal Tissue to Treat Retinal Degeneration”

Retinal degeneration is largely a hereditary disease that is characterized by the death of photoreceptors--the light-sensitive neurons in the eye--which eventually leads to blindness. While many have attempted to treat the disease through retinal transplants, and some have shown that transplanting graft photoreceptors to the host without substantial integration can rescue retinal function, until now, no one has conclusively succeeded in transplanting photoreceptors that functionally connect to host cells and send visual signals to the host retina and brain. The research team led by Masayo Takahashi, Ph.D., of the RIKEN Center for Developmental Biology in Japan, studied this problem using a mouse model for end-stage retinal degeneration in which the outer nuclear layer of the retina is completely missing. This is an important issue because in clinical practice this type of therapy would most likely target end-stage retinas in which the photoreceptors are dead and the next neurons up the chain do not have any input. The Takahashi group has recently shown that 3D retinal sheets derived from mouse embryonic stem cells develop normal structure connectivity. "Using this method was a key point," explains first author Michiko Mandai, Ph.D. "Transplanting retinal tissue instead of simply using photoreceptor cells allowed the development of more mature, organized morphology, which likely led to better responses to light." The new results were published in the January 10, 2017 issue of Stem Cell Reports. The open-access article is titled “iPSC-Derived Retina Transplants Improve Vision in rd1 End-Stage Retinal-Degeneration Mice.” (iPSC stands for induced pluripotent stem cells).

UW-Madison Launches $1 Million Microbiome Initiative

We are not alone. Each of us carries a wide array of microbial species that outnumber our cells tenfold. Recent studies have shown that the complement of microorganisms, the microbiome, is an important determinant of human health and disease. The microbiomes of other animals, plants, soil, bodies of water, and the atmosphere play similarly important roles. Our understanding of the diversity and roles of these microbiomes is limited, a fact that led the White House Office of Science and Technology Policy to launch the National Microbiome Initiative last year. Stakeholders, including the University of Wisconsin (UW)–Madison, have responded with new commitments to develop a comprehensive understanding of microbiomes across all ecosystems. A new UW–Madison Microbiome Initiative comes with $1 million in grant funding administered by the vice chancellor for research and graduate education to support interdisciplinary research, infrastructure, and research community enhancements related to the microbiome. “Microbiome science has the potential to revolutionize areas such as health care, agriculture, biomanufacturing, environmental management, and more,” says Marsha Mailick (photo), Ph.D., UW–Madison’s Vice Chancellor for Research and Graduate Education. “The potential of microbiome research is enormous — it could create revolutionary technologies. By providing seed funding for microbiome projects at UW–Madison, we hope to position our faculty to be more competitive when applying for federal funding for their research in this area.” “Microbes influence our everyday existence in immeasurable ways. They are master chemists who have provided us with the air that we breathe.

Nanotechnology Used to Deliver Gene-Silencing RNAs to Plants to Offer Significant Crop Protection Against Viruses

Researchers at the University of Surrey (UK) and University of Queensland (Australia) have developed a revolutionary new crop protection technique which offers an environmentally-friendly alternative to genetically-modified crops and chemical pesticides. The breakthrough research, published online on January 9, 2017 in Nature Plants, could have huge benefits for agriculture and positively impact communities around the world. Plant pests and pathogens are estimated to reduce global crop yields by 30 to 40 per cent a year, constraining global food security. At the same time, the need for higher production, regulatory demands, pesticide resistance, and concern about global warming driving the spread of disease all mean there is a growing need for new approaches to crop protection. The researchers have found that by combining clay nanoparticles with designer “RNAs” (molecules with essential roles in gene biology), it is possible to silence certain genes within plants. The spray the scientists have developed -- known as BioClay -- has been shown to give plants virus protection for at least 20 days following a single application. When sprayed with BioClay, the plant “thinks” it is being attacked by a disease or pest insect and responds by protecting itself. The latest research overcomes the instability of “naked” RNAs sprayed on plants, which has previously prevented these molecules from being used effectively for virus protection. By loading the agents on to clay nanoparticles, they do not wash off, enabling them to be released over an extended period of time before degrading. The BioClay technology, which is based on nanoparticles used in the development of human drug treatments, has a number of advantages over existing chemical-based pesticides.

January 10th

Mechanism for Coping with Ribosomes Stalled on mRNAs with Premature Stop Codons

New research from the Case Western Reserve University School of Medicine describes a mechanism by which an essential quality control system in cells identifies and destroys faulty genetic material. The findings were published online on December 23, 2016 in Nature Communications. The open-access article is titled ATP Hydrolysis by UPF1 Is Required for Efficient Translation Termination at Premature Stop Codons.” Kristian Baker Ph.D., Associate Professor in the Center for RNA Molecular Biology at Case Western Reserve University School of Medicine, led the study that provided evidence for direct communication between the cell's protein synthesis machinery - the ribosome - and the protein complex that recognizes and destroys defective genetic intermediates called messenger RNAs (mRNAs). "We aimed to understand how cells are able to recognize mRNA that is defective and distinguish it from normal mRNA. For most cells, this process is critical for survival, but we didn't yet understand how it works, especially when the difference between the two is very subtle," said Dr. Baker. "Our findings clearly show that surveillance machinery involved in identifying faulty mRNA functionally interacts with the ribosome, the apparatus responsible for synthesizing proteins in the cell. It is now clear that these two elements communicate and work closely together to recognize and eliminate aberrant mRNA from the cell." Cells convert sections of DNA encoding genes into mRNA that serves as a blueprint for the synthesis of a protein.

Bacteria Not Initially Sensitive to Phage Become Sensitive After Molecular Exchange of Membrane Vesicles from Sensitive Bacteria

Bacteriophages (phages) are probably the most abundant entities in nature, often exceeding bacterial densities by an order of magnitude. As viral predators of bacteria, phages have a major impact on bacterial communities by reducing some bacteria and enabling others to flourish. Phages also occasionally package host DNA and deliver it to other bacteria, in a process known as horizontal gene transfer (HGT). The biology of phage infection has been extensively studied since the beginning of the 20th century. However, the fate of phages in complex bacterial communities resembling their natural ecosystem has not been studied at the cellular level. To investigate the biology of phage infection in complex bacterial communities, researchers followed phage dynamics in communities harboring phage-resistant (R) and phage-sensitive (S) bacteria, a common scenario in nature. Now, in new research, published online on December 29, 2016 in Cell, researchers at the Hebrew University of Jerusalem's Faculty of Medicine provide the first demonstration of a mechanism by which bacteria entirely resistant to a given phage become susceptible to it upon co-incubation with sensitive bacteria. The researchers show how phage-sensitive bacteria harboring phage receptor can deliver the receptor to nearby phage-resistant cells that lack the phage receptor, via a molecular transfer they call "acquisition of sensitivity" (ASEN). This process involves a molecular exchange driven by membrane vesicles (MVs), in which phage-resistant cells transiently gain phage attachment molecules released from neighboring phage-sensitive cells. By exploiting this novel delivery system, phages can invade bacteria lacking their receptor.