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Archive - Nov 12, 2019

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Batty Microbiomes Defy Predictions

Right now, there are trillions of bacteria living in your gut, making up about one percent of your body weight. They're supposed to be there--we need them to help us digest food and fight off diseases. The same is true for most mammals; in general, just about every mammal from dogs to dolphins relies on a community of helpful bacteria, called a microbiome, living inside them for health and survival. Many animals have even evolved along with their gut bacteria to work together better, to the point that closely related host species typically share more similar microbiomes. But a new study has identified one group of mammals that seems to buck that trend: bats. A new paper, published online on November 12, 2019 in mSystems, reveals that the microbiomes of closely-related bats can be totally different from each other, which suggests that having a community of helpful gut bacteria may not be so important for this already eccentric group of mammals. The open-access article is titled “Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome.” "It shifts the paradigm we've been operating under, that animals require microbes for digestion and nutrient acquisition. That's true for us, but it may not be true for all species," says lead author Holly Lutz, PhD, a research associate at Chicago's Field Museum and post-doctoral researcher at the University of California, San Diego. "The trends we're seeing suggest that bats may not depend on bacteria the same way many other mammals do, and that they can survive just fine without a strict suite of bacteria in their guts to help them digest their food." To learn about the relationships between bats and their microbes, Dr. Lutz and her colleagues took samples of bacteria from the skin, tongues, and guts of 497 bats from 31 different species in Kenya and Uganda.

Anthrax Toxin May Be Effective Weapon in Fighting Bladder Cancer

Anthrax may soon help more people win the fight against bladder cancer, which the Centers for Disease Control and Prevention (CDC) says strikes approximately 72,000 Americans each year and kills about 16,000, and is one of the most expensive cancers to treat. The current treatments for bladder cancer are invasive for patients - who often must sit for hours at a time with a bladder full of an agent designed to kill cancer cells and tumors. Bladder cancer also is one of the most reoccurring for people diagnosed with the disease. Now, researchers at Purdue University have come up with a way to combine the anthrax toxin (image) with a growth factor to kill bladder cancer cells and tumors. The research was published online on October 4, 2019 in the International Journal of Cancer. "We have effectively come up with a promising method to kill the cancer cells without harming the normal cells in the bladder," said R. Claudio Aguilar, PhD, an Associate Professor and the Assistant Head of Biological Sciences in Purdue's College of Science. "It is basically like creating a special solution that targets cancer cells, while leaving healthy cells alone." Dr. Aguilar said the bladder has its own protective layer, which saves the good cells from the anthrax mixture but offers no protection for the cancer cells and tumors. He said the Purdue system works within minutes - instead of the usual hours for bladder cancer treatment - to target the cancer cells in the bladder. "We have seen outstanding results with our treatment," said Dr. Aguilar, who works as part of a team focused on cell identity and signaling at the Purdue University Center for Cancer Research. "It is fast and effective, both of which are critical for people dealing with this devastating disease." Dr. Aguilar and his group worked with the Purdue teams led by Dr.

Frequent Technical Bias Occurs in RNA-Seq Expression Studies, Leading to Widespread Misinterpretation of Gene Expression Data; Authors Present Approach to Removing This Bias

Reproducibility is a major challenge in experimental biology, and with the increasing complexity of data generated by genomic-scale, this concern is immensely amplified. RNA-seq, one of the most widely used methods in modern molecular biology, allows in a single test the simultaneous measurement of the expression level of all the genes in a given sample. New research, published online on November 12, 2019 in the open-access journal PLOS Biology by Shir Mandelbaum, Zohar Manber, Orna Elroy-Stein, and Ran Elkon from Tel Aviv University, identifies a frequent technical bias in data generated by RNA-seq technology, which recurrently leads to false results. The article is titled “Recurrent Functional Misinterpretation of RNA-Seq Data Caused By Sample-Specific Gene Length Bias.” Analyzing dozens of publicly available RNA-seq datasets, which profiled the cellular responses to numerous different stresses, Dr. Mandelbaum and colleagues noticed that sets of particularly short or long genes repeatedly showed changes in expression level (as shown by the apparent number of RNA transcripts from a given gene). Puzzled by this recurring pattern, the authors then asked whether it reflects some universal biological response common to many different triggers or if it, rather, stems from some experimental artefact. To tackle this question, they compared replicate samples from the same biological condition. Differences in gene expression between replicates can reflect technical effects that are not related to the experiment's biological factor of interest. Unexpectedly, the same pattern of particularly short or long genes showing changes in expression level was observed in these comparisons between replicates, demonstrating that this pattern is the result of a technical bias that seemed to be coupled with gene length.