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Is your spit making you fat?
One of the central pursuits of modern human genetics is to move beyond genomic correlation. That is, to demonstrate experimentally why a specific genetic variant may be associated with a disease. New work in Nature Genetics from an international team lead by Philippe Froguel at Imperial College in London does just this – demonstrating an interesting link between saliva and obesity. Basically, all humans express amylase, a salivary enzyme that breaks down complex carbohydrates into absorbable sugars. The researchers found that people with more copies of the gene had a significantly decreased risk of developing obesity. People with fewer copies expressed less amylase, and it was hypothesized that this alteration in gastrointestinal carbohydrate metabolism affected insulin signaling, blood sugar levels, as well as the microbial community in the gut. This finding has implications for the rational design of digestive enzyme-based therapies for obesity and other metabolic disorders.
Froguel, Philippe, et al. “Low copy number of the salivary amylase gene predisposes to obesity.” Nature Genetics vol. 46, p. 492-497 (2014).
Viral Evolution
By Mubasher Ahmed, Genetics ‘15
Viral evolution is an emerging field in biology that has great implications for human health. T7 is a phage virus, meaning it infects bacteria, and is a powerful model system in evolutionary virology. In a recent experiment, a team of biologists sought to understand the degree to which genetic elements engineered into the T7 phage genome affected the phage’s rate of propagation. In this context, the genetic elements are sequences of DNA that are inserted between genes that allow for researchers to manipulate gene regulatory networks. This allows biologists to probe how phenotypes change when gene-gene interactions are perturbed. Previous studies had shown that such genomic elements led to decreased fitness for the virus, but these investigators hoped to better understand how exactly such a system would evolve in laboratory conditions.
To address their questions, the scientists grew both T7 viruses with and without design elements in each of two conditions. One condition was in a nutritious broth that used one intestinal bacterium as a host, and the other in a glucose sugar medium that had a different host bacterium. Both T7 strains were allowed to grow for 700-1000 generations in the glucose media and 100 generations in the broth media. Limitless bacteria were provided for the phages in order to encourage growth, and the researchers hypothesized that their experiment would allow enough time for the maladapted viruses to slough off deleterious design elements through evolutionary adaptation. (more…)
The hunter-gatherer gut microbiome
By: Jenny Cade, Biochemistry and Molecular Biology ‘15
In a paper published in Nature Communications on April 15, researchers profiled the gut microbiota of a group of hunter-gatherers in Tanzania known as the Hadza. They compared the results to those of people living in Italy, and found that the two groups have very different species composition. The Hadza don’t only have different kinds of gut microbes than Westerners, but a more diverse collection of microbes as well. The researchers say that this is most likely due to the dramatic difference between hunter-gatherer and Western diets.
Origin of the Y Chromosome
By Marisa Sanchez, Molecular and Cellular Biology ‘15
The genomes of male and female mammals differ by one chromosome. The Y chromosome is only present in males, and is responsible for initiating the physiological and morphological differences between the sexes. This has not always been the case though; at one point, the X and Y were identical, and over time the Y chromosome began to differentiate from the X chromosome and shrink in size. The Y chromosome today only has 20 genes, whereas the X chromosome has over 1,000 genes. (more…)
“No Ecosystem is an Island”
By Daniel Friedman, Genetics ’14
For years, ecologists have modeled the biodiversity of natural forests as if they were oceanic islands, adrift in an unlivable sea of humanity. However, research published in April in Nature by C. Mendenhall et al. suggest that this is not the most accurate or predictive way to think about these pockets of nature. By comparing bat diversity on countrysides and oceanic islands, they find that fragmented land ecosystems behave markedly different than their oceanic counterparts. They find that forest “islands” maintain species at higher overall levels of biodiversity than ocean islands, and also gain/lose species in unique patterns. This has relevance to humanity’s actions to support biodiversity on land, and suggests the need for new models, metrics, and strategies of conservation.
Mendenhall, C., Karp, D., Meyer, C., Hadly, E., Daily, G., “Predicting biodiversity change and averting collapse in agricultural landscapes”, Nature, 2014.
Image from Abu Shawka, 2009. Creative Commons.
Green Tea Can Improve Your Memory
By Marisa Sanchez, Molecular and Cellular Biology ’15
Green tea has been said to have several health benefits including helping prevent certain types of cancer and inflammation. In a new study done by Dr. Beglinger and Dr. Borgwardt at the University of Basel in Switzerland, they have found that green tea extract enhances cognitive functions, particularly the working memory because green tea extract increases the brain’s effective connectivity, the causal influence that one part of the brain exerts on another part. (more…)
Lab Engineered Cartilage used in Nose Reconstruction
By Ashley Chang, Genetics ’15
Researchers at the University of Basel in Switzerland have successfully used lab-engineered cartilage for nose reconstruction. This study was conducted on five patients between ages 76 and 88 who had significant nasal damage after skin cancer surgery. One year after the replacement, all of them note significant improvement in the ability to breathe as well as cosmetic appeal, and no patients had significant side effects. This is a groundbreaking study as it opens of the possibility of engineered cartilage replacement in other areas, such as the knee, and of tissue-engineering as a whole. (more…)
Grass-fed or grain-fed?
By Jenny Cade, Biochemistry & Molecular Biology ’15
Eating grass-fed beef and pasture-raised chicken is the eco-friendly thing to do–right? Maybe not, according to a recent paper published in the Proceedings in the National Academy of Science. The study proposes that intensifying livestock production by transitioning from pure grazing to mixed systems–where animals are fed high-energy food like grains–could reduce livestock greenhouse gas emissions by 23% by 2030. Currently, livestock account for 14.5% of all anthropogenic greenhouse gas emissions, so such a reduction would be significant.
In contrast, a comment piece that appeared in Nature last month calls for increasing grazing to make livestock systems more sustainable. Of eight strategies that the authors outline to reduce the environmental and economic costs of raising livestock, “Feed animals less human food” is number one.
“The Eukaryotic Ribosome”
This is a submission from UC Davis CBS Professor Sean Burgess. It comes from a future publication that relates the human quest to visualize the inner workings of the cell, molecular biology, with the quest to visualize the interior of the mind, art.
Title:
The Eukaryotic Ribosome
Caption:
The basic mechanism of ribosome based-protein synthesis is conserved among all domains of life. The ribosome comes in two parts. The small subunit interacts with the mRNA and decodes the interaction with the aminoacyl tRNAs. The large subunit contains the active site of peptidyl transferase. The two subunits together form three pockets for three forms of tRNA. The A site is where the aminoacyl tRNA binds, the P site holds that peptidyl tRNA when the A site is occupied. The E site contains the deacylated tRNA following peptidyl transferase. The ribosome is a huge conglomeration of RNA and proteins. The RNA appears to do all the heavy lifting for the main catalytic event of protein synthesis. So what came first, the protein or the ribosome?
Obtaining the crystal structure of the ribosome was a tour de force effort. The Nobel Prize for solving its structure was awarded in 2009.
Top: Willi Baumeister: Mortaruru with Red Overhead (1953), The Art Book, Phaidon Press Limited, 1994.
Bottom: The 60S (PDB: 305H) and 40S (PDB: 1S1H) subunits of the eukaryotic ribosome. Ben-Shem et al. (2010) Science, 330 (6008): 1203-1209. The image was generated by S.M.B. using MacPymol using coordinates from the Protein Databank (http://helixweb.nih.gov/cginbin/pdb). MacPyMOL is a product of Schrodinger, LLC. Copyright (C) 2009-2010.
Fecundity Decrease in Drosophila simulans in the absence of Wolbachia
By: Jack Taylor, Biochemistry and Molecular Biology ’15
Sponsor: Michael Turelli, Ph.D.
Ecology and Evolution
Many species of arthropods host Wolbachia, maternally transmitted bacteria that often influence host reproduction. This manipulation of host reproduction has contributed to Wolbachia becoming a normally-present infection of many Drosophila simulans. The Y36 isofemale line, a population of Drosophila simulans created from a single female collected in 2010 in Yolo County, produces flies which have an unusual phenotype when reciprocally crossed with uninfected simulans populations denoted U. The cross between Y36 male and U female produces female offspring with significantly lower fecundity than the reciprocal cross (Y36 female with U male). It is possible that this effect is a result of a paternal defect gene that is masked by the Wolbachia infection. Ten separate sublines were created from the Y36 isofemale line. The goal of my experiment was to determine whether this phenotype is still present among each of the ten sublines and if there is any variation in the phenotype among the sublines. Analysis of the data indicates that the qualitative effect of the phenotype has been preserved across the sublines but suggests that there is quantitative variation amongst them.