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Latest news on complex systems in life sciences, engineering, education and government
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Present in almost in every cell, microRNAs are known to target tens to hundreds of genes each and to be able to repress, or "silence," their expression. What is less well understood is how exactly miRNAs repress target gene expression. Now a team of scientists led by geneticists at the University of California, Riverside has conducted a study on plants (Arabidopsis) that shows that the site of action of the repression of target gene expression occurs on the endoplasmic reticulum (ER), a cellular organelle that is an interconnected network of membranes—essentially, flattened sacs and branching tubules—that extends like a flat balloon throughout the cytoplasm in plant and animal cells
ComplexInsight's insight:
I think this is fundamentally important. As a programmer - microRNA reminds me of microcode running on multiple parallel processes . With this work showing that ER membranes are essential for microRNA activity. The last line of the article nails it: "Our work shows that an integral membrane protein, AMP1, is required for the miRNA-mediated target gene repression to be successful. As AMP1 has counterparts in animals, our findings in plants could have broader implications." Full paper in Cell Delete the scoop?
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Learning bioinformatics usually requires solving computational problems of varying difficulty that are extracted from real challenges of molecular biology. To make learning bioinformatics fun and easy, we have founded Rosalind, a platform for learning bioinformatics through problem solving. Rosalind offers an array of intellectually stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection. Rosalind also promises to facilitate improvements in standard bioinformatics education by providing a vital teaching aid and a central homework resource. Via Chris Upton + helpers Delete the scoop?
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Biodiversity informatics is about how to develop, integrate and use information about life on Earth,” said Town Peterson, University Distinguished Professor of Ecology and Evolutionary Biology and curator in the Biodiversity Institute. “We have a lot of raw data about biodiversity, which is to say we know places where particular species have been seen. But turning those raw data into usable information is a much bigger challenge.” In Africa, as in much of the world, there is scant availability of training in this important discipline. This is about to change. With funding from the JRS Biodiversity Foundation, Peterson will lead multiple training sessions in four African nations: Ghana, South Africa, Kenya and Egypt. CLick on image or title to learn more. Delete the scoop?
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Both the number of viruses in initial flu infection, and the virus type, affects the patient's outcome. Mice infected by high concentrations developed immunity, and generated immune cells in the lungs to fight other strains. Mice that were infected with a relatively low concentration of the virus developed weaker immunity against the strain that infected them, did not build up this crucial population of immune cells in the lungs, and showed only delayed immunity toward other flu strains. This discovery could pave the way for new prophylactic strategies to fight flu infections and provides a novel basis for vaccine design. Learn more by clicking on the image or headline. Delete the scoop?
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All creatures, from bacteria to humans, monitor and transform their environments using small protein nanomachines made of thousands of atoms,” explained the senior author of the study, Stephen Michnick of the University of Montreal department of biochemistry. To understand how a protein goes from a linear chain to a unique assembled structure, Michnik's team developed a strategy to monitor protein assembly by integrating fluorescent probes throughout the linear protein chain so that they could detect the structure of each stage of protein assembly, step by step to its final structure. Learn more... Delete the scoop?
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mBio is a great source for developments in biology. This week they have a good commentary on the Sachs and Hollowell Black Queen hypothesis which has implications for how we understand the evolution of bacterial genomes and for the development of new techniques for growing bacteria in the lab. Learn More... Delete the scoop?
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This one is important to us as we start testing OLAPX and BIOLAP approaches for data analysis. The Ewing Marion Kauffman Foundation, based in Kansas City, Missouri, aims to “create the world’s largest pool of openly available, user-contributed data about health and genomics” in hopes of easing challenges with informed consent and data ownership that some biomedical researchers say are holding science back in the era of ‘big data’. Learn more... Delete the scoop?
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How the blistering pace of technological change could have a profound impact on healthcare.
ComplexInsight's insight:
The combination of sensors and automated tests in areas of genetics and proteomics enable collection of largescale comprehensive health data for the first time. That data will generate insights into human biology, our bacterial biome and how our health systems work. Advances in large scale data processing, correlation and machine learning will help over the next decade to radically change our understanding of human biology. As data is collected and in silico experimentation mapped to invitrio understanding data will change our healthcare systems over the next 30 years. This BBC article gives a good insight into how and why this is starting to happen now. Delete the scoop?
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Researchers from Johns Hopkins and Northwestern universities have discovered how to control the shape of nanoparticles that move DNA through the body and have shown that the shapes of these carriers may make a big difference in how well they work in treating cancer and other diseases. The use of computer models allowed Luijten’s team to mimic traditional lab experiments at a far faster pace. These molecular dynamic simulations were performed on Quest, Northwestern’s high-performance computing system. The computations were so complex that some of them required 96 computer processors working simultaneously for one month. “Our computer simulations and theoretical model have provided a mechanistic understanding, identifying what is responsible for this shape change,” Associate Professor Eric Luijten said. “We now can predict precisely how to choose the nanoparticle components if one wants to obtain a certain shape.”. Click on the image or the title to learn more. Delete the scoop?
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Simulation is increasingly used in biology to explore system relationships. This lab will gives students the opportunity to explore the regulation of bacterial gene expression through the use of both traditional biochemical lab techniques and modern computer simulations. While they incubate their bacteria, they use computer simulations to better understand how beta-galactosidase expression is regulated in E. coli. Thw dynamic model helps them make predictions as to the outcome of the experiment. There are computer simulations for different types of gene regulatory systems to explore and make predictions about how gene expression is controlled in each circumstance. Biology lessons were always cool - but they just got a whole lot cooler. Click on the image or headline to learn more. Delete the scoop?
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From - Lab Manager Magazine® : An Indiana University team of researchers has conducted the most in-depth and diverse genetic analysis of the defense systems that trillions of micro-organisms in the human body use to fend off viruses. Led by IU Bloomington assistant professor of informatics and computing Yuzhen Ye, the team of bioinformaticists and biologists reconstructed arrays of clusters of regularly interspaced short palindromic repeats -- CRISPRs -- which function as immune systems to the bacteria that play a vital role in human health. Between genomic repeats, CRISPR locations carry short strands of foreign DNA called spacers, which provide a history of past exposures to outside invaders like plasmids and bacteriophages (viruses that infect bacteria), and allow the bacteria to fight off viruses they have already encountered. This is an incredibly interesting piece of research and demonstrates the applications of CRISPRs to tracing the virus exposure of individuals and it indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes and human health. Learn more... Delete the scoop?
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(Phys.org) -- As the interface between the cell and its environment, the cell membrane, which consists of fats and proteins, fulfils a variety of vital functions. Scientists at the Max Planck Institute of Biochemistry in Martinsried near Munich have performed the first comprehensive analysis of the molecular structure of this boundary layer, and revealed precisely how it is organised. In yeast cells, the entire membrane is made up of independent domains, each containing just one or a few protein types. If a protein is relocated to an inappropriate domain, it may even fail to function. The study shows that the membrane is a kind of patchwork quilt and should help scientists to gain a better understanding of basic cellular processes. Learn more... Delete the scoop?
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Bio-Linux is an operating system set up for bioinformatics with a vast number of programs pre-installed. It can be obtained for free from the NERC Environmental Bioinformatics Centre. You can obtain a USB drive from NERC and boot from that ... Via Dr Richard Badge Delete the scoop?
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the GisAgents blog is always a great read. Nice link to new algorithm for population synthesis that fuses remote-sensing data with partial and sparse demographic surveys. The algorithm addresses non-binding constraints and complex sampling designs by translating population synthesis into a computationally efficient procedure for constrained network growth. Click on image or title to learn more.