A simple, inexpensive blood test could soon help doctors halt organ rejection before it impairs transplanted hearts and kidneys. “In the past, we couldn’t spot rejection episodes until they harmed the organ,” said Atul Butte, MD, PhD, who is co-senior author of the new research and an associate professor of medical informatics and of pediatrics at the Stanford University School of Medicine, in addition to director of the Center for Pediatric Bioinformatics at Lucile Packard Children’s Hospital… (Source: Health News from Medical News Today)

Mechanisms providing for temporally complex patterns of maternal mRNA translation after fertilization are poorly understood. We employed bioinformatics analysis to compare populations of mRNAs enriched specifically on polysomes at the metaphase II (MII) stage oocyte and late one-cell stages and a detailed deletion/truncation series to identify elements that regulate translation. We used the Bag4 3′ untranslated region (UTR) as a model. Bioinformatics analysis revealed one conserved motif, subsequently confirmed by functional studies to be a key translation repressor element. The deletion/truncation studies revealed additional regulatory motifs, most notably a strong translation activator element of <30 nt. Analysis of mRNA secondary structure suggests that secondary structure plays a ke…

The catalytic domain of metalloelastase (matrix metalloproteinase-12 or MMP-12) is unique among MMPs in exerting high proteolytic activity upon fibrils that resist hydrolysis, especially elastin from lungs afflicted with chronic obstructive pulmonary disease or arteries with aneurysms. How does the MMP-12 catalytic domain achieve this specificity? NMR interface mapping suggests that -elastin species cover the primed subsites, a strip across the β-sheet from β-strand IV to the II–III loop, and a broad bowl from helix A to helix C. The many contacts may account for the comparatively high affinity, as well as embedding of MMP-12 in damaged elastin fibrils in vivo. We developed a strategy called BINDSIght, for bioinformatics and NMR discovery of specificity of interactions, to …

Conclusions:
The MultiRTA method yields competitive performance but with a significantly simpler and physically interpretable model compared with previous prediction methods. A MultiRTA prediction webserver is available at http://bordnerlab.org/MultiRTA. (Source: BMC Bioinformatics – Latest articles)

Conclusions:
Fast and accurate prediction of microbial phenotypes based on genomic protein domain content is feasible and has the potential to provide novel biological insights. First results of a systematic check for annotation errors indicate that our approach may also be applied to semi-automatic correction and completion of the existing phenotype annotation. (Source: BMC Bioinformatics – Latest articles)

Conclusions:
We illustrate that DDSD is insensitive to shape deformation of flexible molecules and more effective at capturing molecular structures than traditional shape descriptors. The presented algorithm is robust and does not require any prior knowledge of the flexible regions. (Source: BMC Bioinformatics – Latest articles)

Forty-five individuals have recently joined DF/HCC. See below to learn more about these scientists and their research interests.
    Reza Abdi, MD (BWH) Cancer Immunology Research focus: The lab focuses on identifying antigen dependent and independent factors which may result in development and progression of chronic renal allograft dysfunction. They research the roles of chemokines in the pathogenesis of allograft rejection, ischemia renal injuries and diabetes, and are planning to carry out novel approaches to study the role of chemokines in allograftrejection.   Andrew Bellizzi, MD (BWH) Gastrointestinal Malignancies Research focus: The lab conducts clinical and translational research in gastrointestinal, pancreatobiliary, and head and neck path…

Contact: angelo.facchiano@isa.cnr.it (Source: Bioinformatics)

(No abstract is available for this citation) (Source: Bioinformatics)

(No abstract is available for this citation) (Source: Bioinformatics)