414 research outputs found
We have the technology to save peer review - now it is up to our communities to implement it
Today marks the beginning of Peer Review Week 2017. Here on the Impact Blog, weâll be featuring posts covering a variety of perspectives on and issues relating to peer review, and which also consider this yearâs theme of âTransparencyâ. To kick things off, Jon Tennant, Daniel Graziotin and Sarah Kearns consider what can be done to address the various shortcomings and problems of the peer review process. While there is obviously substantial scope for improvement, none of the ideas proposed here are beyond our current technical and social means. The key challenge may lie in galvanising our scholarly communities
A defined medium to investigate sliding motility in a Bacillus subtilis flagella-less mutant
BACKGROUND: We have recently shown that undomesticated strains of Bacillus subtilis can extensively colonize the surfaces of rich, semi-solid media, by a flagellum-independent mechanism and suggested that sliding motility is responsible for surface migration. Here we have used a flagella-less hag null mutant to examine and confirm sliding motility. RESULTS: Using a defined semi-solid medium we determined that a B. subtilis hag mutant colonized the surface in two stages, first as tendril-like clusters of cells followed by a profuse pellicle-like film. We determined the levels of macro- and micro-nutrients required for the tendril-to-film transition. Sufficient levels of each of the macronutrients, glycerol, Na-glutamate, and Na-phosphate, and inorganic nutrients, K(+), Mg(2+), Fe(2+ )and Mn(2+), were required for robust film formation. The K(+ )requirement was quantified in more detail, and the thresholds for complete tendril coverage (50 ÎźM KCl) or film coverage (2â3 mM KCl) were determined. In addition, disruption of the genes for the higher affinity K(+ )transporter (KtrAB), but not the lower affinity K(+ )transporter (KtrCD), strongly inhibited the formation of both tendrils and films, and could be partially overcome by high levels of KCl. Examination of hag tendrils by confocal scanning laser microscopy revealed that tendrils are multicellular structures, but that the cells are not as highly organized as cells in wild-type B. subtilis pellicles. CONCLUSION: These results suggest that B. subtilis can use sliding motility to colonize surfaces, using a tendril-like growth mode when various macronutrients or micronutrients are limiting. If nutrients are balanced and sufficient, the surfaces between tendrils can be colonized by robust surface films. Sliding motility may represent a strategy for nutrient-deprived cells to colonize surfaces in natural environments, such as plant roots, and the media described here may be useful in investigations of this growth phenotype
Concordance between ER, PR, Ki67, and HER2âlow expression in breast cancer by MammaTyper RTâqPCR and immunohistochemistry:implications for the practising pathologist
Background: There are limited data on the role of multigene tests and their correlation with immunohistochemistry (IHC), especially on core biopsy. MammaTyper is a quantitative conformite Europeeanne (CE) marked, National Institute for Health and Care excellence (NICE) approved, in in vitro diagnostic quantitative realâtime polymerase chain reaction (RTâqPCR) test for assessment of mRNA expression of four biomarkers (ESR1, PGR, ERBB2, MKI67).Methods: We evaluated the concordance of MammaTyper with oestrogen receptor (ER), progesterone receptor (PR), HER2, and Ki67 by IHC on 133 core needle biopsies of breast cancer. HER2 was positive if IHC 3+ or 2+ and fluorescence in situ hybridization (FISH)âamplified. Global and hotspot Ki67 expression was analysed using a cutoff of âĽ20% assessed manually and by digital image analysis. Agreements were expressed as overall percent agreement (OPA), positive percent agreement (PPA), negative percent agreement (NPA), and Cohen's kappa. Results: RTâqPCR results of ESR1 were highly concordant with IHC with OPA of 94.7% using 1% cutoff and 91.7% when the low ERâpositive category was included. The PPA and NPA between RTâqPCR and IHC for PR was 91.5% and 88.0%, respectively, when using the 1% cutoff. For ERBB2/HER2, the OPA was 95% and the PPA was 84.6%. 40 of 72 HER2 IHC score 0 tumours were classified as ERBB2 low. Best concordance between MKI67 by MammaTyper and Ki67 IHC was achieved using hotspot digital image analysis (OPA: 87.2%, PPA: 90.6%, NPA: 80%).Conclusion: RTâqPCRâbased assessment of the mRNA expression of ESR1, PGR, ERBB2, and MKI67 showed high concordance with IHC, suggesting that the MammaTyper test on core needle biopsies represents a reliable, efficient, and reproducible alternative for breast cancer classification and refining HER2 low categorisation
Multi-species integrative biclustering
We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surprisingly high degree of conservation of regulatory modules across these three species and allows data and insights from well-studied organisms to complement the analysis of related but less well studied organisms
Carbonyl Reduction by YmfI Completes the Modification of EF-P in \u3cem\u3eBacillus subtilis\u3c/em\u3e to Prevent Accumulation of an Inhibitory Modification State
Translation elongation factor P (EFâP) in Bacillus subtilis is required for a form of surface migration called swarming motility. Furthermore, B. subtilis EFâP is postâtranslationally modified with a 5âaminopentanol group but the pathway necessary for the synthesis and ligation of the modification is unknown. Here we determine that the protein YmfI catalyzes the reduction of EFâPâ5 aminopentanone to EFâPâ5 aminopentanol. In the absence of YmfI, accumulation of 5âaminopentanonated EFâP is inhibitory to swarming motility. Suppressor mutations that enhanced swarming in the absence of YmfI were found at two positions on EFâP, including one that changed the conserved modification site (Lys 32) and abolished postâtranslational modification. Thus, while modification of EFâP is thought to be essential for EFâP activity, here we show that in some cases it can be dispensable. YmfI is the first protein identified in the pathway leading to EFâP modification in B. subtilis, and B. subtilis encodes the first EFâP ortholog that retains function in the absence of modification
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