554 research outputs found
A suggested classification for two groups of Campylobacter myoviruses
Most Campylobacter bacteriophages isolated to date have long contractile tails and belong to the family Myoviridae. Based on their morphology, genome size and endonuclease restriction profile, Campylobacter phages were originally divided into three groups. The recent genome sequencing of seven virulent campylophages reveal further details of the relationships between these phages at the genome organization level. This article details the morphological and genomic features among the campylophages, investigates their taxonomic position, and proposes the creation of two new genera, the “Cp220likevirus” and “Cp8unalikevirus” within a proposed subfamily, the “Eucampyvirinae”.AMK would like to thank Andre Villegas for developing "extractUpStreamDNA". The authors are thankful to Denis Arutyunov and Jessica Sacher for helpful discussions and help with phage preparations, and to Cheryl Nargang for her help with nucleotide sequencing and analysis of gp047 homolog from phage F336. The bacteriophage receptor-binding protein studies were funded by an Alberta Innovates Scholar Award (CMS) and a Natural Sciences and Engineering Research Council of Canada Strategic Grant (CMS). RL and AMK are chair and vice chair, respectively, of the prokaryotic virus subcommittee of the ICTV (International Committee for Taxonomy of Viruses)
A Cognitive Model of an Epistemic Community: Mapping the Dynamics of Shallow Lake Ecosystems
We used fuzzy cognitive mapping (FCM) to develop a generic shallow lake
ecosystem model by augmenting the individual cognitive maps drawn by 8
scientists working in the area of shallow lake ecology. We calculated graph
theoretical indices of the individual cognitive maps and the collective
cognitive map produced by augmentation. The graph theoretical indices revealed
internal cycles showing non-linear dynamics in the shallow lake ecosystem. The
ecological processes were organized democratically without a top-down
hierarchical structure. The steady state condition of the generic model was a
characteristic turbid shallow lake ecosystem since there were no dynamic
environmental changes that could cause shifts between a turbid and a clearwater
state, and the generic model indicated that only a dynamic disturbance regime
could maintain the clearwater state. The model developed herein captured the
empirical behavior of shallow lakes, and contained the basic model of the
Alternative Stable States Theory. In addition, our model expanded the basic
model by quantifying the relative effects of connections and by extending it.
In our expanded model we ran 4 simulations: harvesting submerged plants,
nutrient reduction, fish removal without nutrient reduction, and
biomanipulation. Only biomanipulation, which included fish removal and nutrient
reduction, had the potential to shift the turbid state into clearwater state.
The structure and relationships in the generic model as well as the outcomes of
the management simulations were supported by actual field studies in shallow
lake ecosystems. Thus, fuzzy cognitive mapping methodology enabled us to
understand the complex structure of shallow lake ecosystems as a whole and
obtain a valid generic model based on tacit knowledge of experts in the field.Comment: 24 pages, 5 Figure
Service provision and barriers to care for homeless people with mental health problems across 14 European capital cities
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
Predicting the effect of climate change on temperate shallow lakes with the ecosystem model PCLake
Ethnic Variation in Inflammatory Profile in Tuberculosis
PMCID: PMC3701709This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
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Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset
Diabetes like many diseases and biological processes is not mono-causal. On the one hand multifactorial studies with complex experimental design are required for its comprehensive analysis. On the other hand, the data from these studies often include a substantial amount of redundancy such as proteins that are typically represented by a multitude of peptides. Coping simultaneously with both complexities (experimental and technological) makes data analysis a challenge for Bioinformatics
Current challenges in software solutions for mass spectrometry-based quantitative proteomics
This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.
Spatiotemporal expansion of primary progenitor zones in the developing human cerebellum
We present histological and molecular analyses of the developing human cerebellum from 30 days after conception to 9 months after birth. Differences in developmental patterns between humans and mice include spatiotemporal expansion of both ventricular and rhombic lip primary progenitor zones to include subventricular zones containing basal progenitors. The human rhombic lip persists longer through cerebellar development than in the mouse and undergoes morphological changes to form a progenitor pool in the posterior lobule, which is not seen in other organisms, not even in the nonhuman primate the macaque. Disruptions in human rhombic lip development are associated with posterior cerebellar vermis hypoplasia and Dandy-Walker malformation. The presence of these species-specific neural progenitor populations refines our insight into human cerebellar developmental disorders
Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences
The authors propose that short repeat sequences may play an important role in causing the pervasive clustering of mutations across diverse genomes from prokaryotes to humans
Validation of previously identified serum biomarkers for breast cancer with SELDI-TOF MS: a case control study
<p>Abstract</p> <p>Background</p> <p>Serum protein profiling seems promising for early detection of breast cancer. However, the approach is also criticized, partly because of difficulties in validating discriminatory proteins. This study's aim is to validate three proteins previously reported to be discriminative between breast cancer cases and healthy controls. These proteins had been identified as a fragment of inter-alpha trypsin inhibitor H4 (4.3 kDa), C-terminal-truncated form of C3a des arginine anaphylatoxin (8.1 kDa) and C3a des arginine anaphylatoxin (8.9 kDa).</p> <p>Methods</p> <p>Serum protein profiles of 48 breast cancer patients and 48 healthy controls were analyzed with surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). Differences in protein intensity between breast cancer cases and controls were measured with the Mann-Whitney U test and adjusted for confounding in a multivariate logistic regression model.</p> <p>Results</p> <p>Four peaks, with mass-to-charge ratio (<it>m/z</it>) 4276, 4292, 8129 and 8941, were found that were assumed to represent the previously reported proteins. <it>M/</it>z 4276 and 4292 were statistically significantly decreased in breast cancer cases compared to healthy controls (p < 0.001). M/<it>z </it>8941 was decreased in breast cancer cases (p < 0.001) and <it>m/z </it>8129 was not related with breast cancer (p = 0.87). Adjustment for sample preparation day, sample storage duration and age did not substantially alter results.</p> <p>Conclusion</p> <p><it>M/z </it>4276 and 4292 both represented the previously reported 4.3 kDa protein and were both decreased in breast cancer patients, which is in accordance with the results of most previous studies. <it>M/z </it>8129 was in contrast with previous studies not related with breast cancer. Remarkably, <it>m/z </it>8941 was decreased in breast cancer cases whereas in previous studies it was increased. Differences in patient populations and pre-analytical sample handling could have contributed to discrepancies. Further research is needed before we can conclude on the relevance of these proteins as breast cancer biomarkers.</p
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