Mrub_1867, Mrub_1868, and Mrub_1869 genes are predicted orthologs of the b2279, b2280, and b2281 genes found in \u3cem\u3eEscherichia coli\u3c/em\u3e coding for the NADH dehydrogenase subunits K, J, and I respectively

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_1867, Mrub_1868, and Mrub_1869. We predict that Mrub_1867 (DNA coordinates 1927237..1927527 on the reverse strand), Mrub_1868 (DNA coordinates 1927524..1928123 on the reverse strand), and Mrub_1869 (DNA coordinates 1928248..1928781 on the reverse strand) are subunits of the NADH: ubiquinone oxidoreductase complex (KEGG map number 00190). This complex catalyzes the translocation of H+ across the cytoplasmic membrane and transfers electrons from NADH to ubiquinone during oxidative phosphorylation. The respective E. coli K12 MG1655 orthologs are predicted to be b2279, b2280, and b2281 which have the gene identifiers NuoK, NuoJ, and NuoI

A Systematic Approach to Estimate the Life Cycle Cost and Effort of Project Management for Technology Centric Systems Development Projects

25th International Forum on COCOMO and Systems/Software Cost Modeling presentatio

Drawing Planar Graphs with Few Geometric Primitives

We define the \emph{visual complexity} of a plane graph drawing to be the number of basic geometric objects needed to represent all its edges. In particular, one object may represent multiple edges (e.g., one needs only one line segment to draw a path with an arbitrary number of edges). Let $n$ denote the number of vertices of a graph. We show that trees can be drawn with $3n/4$ straight-line segments on a polynomial grid, and with $n/2$ straight-line segments on a quasi-polynomial grid. Further, we present an algorithm for drawing planar 3-trees with $(8n-17)/3$ segments on an $O(n)\times O(n^2)$ grid. This algorithm can also be used with a small modification to draw maximal outerplanar graphs with $3n/2$ edges on an $O(n)\times O(n^2)$ grid. We also study the problem of drawing maximal planar graphs with circular arcs and provide an algorithm to draw such graphs using only $(5n - 11)/3$ arcs. This is significantly smaller than the lower bound of $2n$ for line segments for a nontrivial graph class.Comment: Appeared at Proc. 43rd International Workshop on Graph-Theoretic Concepts in Computer Science (WG 2017

Parental education and inequalitties in child mortality: a global systematic review and meta-analysis

The educational attainment of parents, particularly mothers, has been associated with lower levels of child mortality, yet there is no consensus on the magnitude of this relationship globally. We aimed to estimate the total reductions in under-5 mortality that are associated with increased maternal and paternal education, during distinct age intervals. This study is a comprehensive global systematic review and meta-analysis of all existing studies of the effects of parental education on neonatal, infant, and under-5 child mortality, combined with primary analyses of Demographic and Health Survey (DHS) data

An investigation of minimisation criteria

Minimisation can be used within treatment trials to ensure that prognostic factors are evenly distributed between treatment groups. The technique is relatively straightforward to apply but does require running tallies of patient recruitments to be made and some simple calculations to be performed prior to each allocation. As computing facilities have become more widely available, minimisation has become a more feasible option for many. Although the technique has increased in popularity, the mode of application is often poorly reported and the choice of input parameters not justified in any logical way

Holographic Scanning Laser Acoustic Microscopy (HOLOSLAM): A New QNDE Tool

Acoustic microscopy is the name given to high frequency, 10 MHz to 3 GHz ultrasonic visualization. The scanning laser acoustic microscopy (SLAM) is an important branch of acoustic microscopy which uses ultrasound in the frequency range of 10 to 200 MHz to produce high resolution ultrasonic images.1,2 In contrast to other visual observation techniques, SLAM provides direct access to the structural elastic properties of solid materials and biological tissues. By using this technique, valuable insight can be gained into mechanisms responsible for the changes of elastic architecture over areas tens of microns in diameter

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

Background: The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results: Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion: Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection

DNA content of a functioning chicken kinetochore

© The Author(s) 2014. In order to understand the three-dimensional structure of the functional kinetochore in vertebrates, we require a complete list and stoichiometry for the protein components of the kinetochore, which can be provided by genetic and proteomic experiments. We also need to know how the chromatin-containing CENP-A, which makes up the structural foundation for the kinetochore, is folded, and how much of that DNA is involved in assembling the kinetochore. In this MS, we demonstrate that functioning metaphase kinetochores in chicken DT40 cells contain roughly 50 kb of DNA, an amount that corresponds extremely closely to the length of chromosomal DNA associated with CENP-A in ChIP-seq experiments. Thus, during kinetochore assembly, CENP-A chromatin is compacted into the inner kinetochore plate without including significant amounts of flanking pericentromeric heterochromatin. © 2014 The Author(s).Wellcome Trust [grant number 073915]; Wellcome Trust Centre for Cell Biology (core grant numbers 077707 and 092076); Darwin Trust of Edinburg

Rapidly measured indicators of recreational water quality and swimming-associated illness at marine beaches: a prospective cohort study

<p>Abstract</p> <p>Introduction</p> <p>In the United States and elsewhere, recreational water quality is monitored for fecal indicator bacteria to help prevent swimming-associated illnesses. Standard methods to measure these bacteria take at least 24 hours to obtain results. Molecular approaches such as quantitative polymerase chain reaction (qPCR) can estimate these bacteria faster, in under 3 hours. Previously, we demonstrated that measurements of the fecal indicator bacteria <it>Enterococcus </it>using qPCR were associated with gastrointestinal (GI) illness among swimmers at freshwater beaches. In this paper, we report on results from three marine beach sites.</p> <p>Methods</p> <p>We interviewed beach-goers and collected water samples at marine beaches affected by treated sewage discharges in Mississippi in 2005, and Rhode Island and Alabama in 2007. Ten to twelve days later, we obtained information about gastrointestinal, respiratory, eye, ear and skin symptoms by telephone. We tested water samples for fecal indicator organisms using qPCR and other methods.</p> <p>Results</p> <p>We enrolled 6,350 beach-goers. The occurrence of GI illness among swimmers was associated with a log₁₀-increase in exposure to qPCR-determined estimates of fecal indicator organisms in the genus <it>Enterococcus </it>(AOR = 2.6, 95% CI 1.3-5.1) and order <it>Bacteroidales </it>(AOR = 1.9, 95% CI 1.3-2.9). Estimates of organisms related to <it>Clostridium perfringens </it>and a subgroup of organisms in the genus <it>Bacteroides </it>were also determined by qPCR in 2007, as was F+ coliphage, but relationships between these indicators and illness were not statistically significant.</p> <p>Conclusions</p> <p>This study provides the first evidence of a relationship between gastrointestinal illness and estimates of fecal indicator organisms determined by qPCR at marine beaches.</p