The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella

<p>Abstract</p> <p>Background</p> <p>Compelling evidence indicates that <it>Shigella </it>species, the etiologic agents of bacillary dysentery, as well as <it>enteroinvasive Escherichia coli</it>, are derived from multiple origins of <it>Escherichia coli </it>and form a single pathovar. To further understand the genome diversity and virulence evolution of <it>Shigella</it>, comparative genomic hybridization microarray analysis was employed to compare the gene content of <it>E. coli </it>K-12 with those of 43 <it>Shigella </it>strains from all lineages.</p> <p>Results</p> <p>For the 43 strains subjected to CGH microarray analyses, the common backbone of the <it>Shigella </it>genome was estimated to contain more than 1,900 open reading frames (ORFs), with a mean number of 726 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains.</p> <p>Conclusion</p> <p>These results support the hypothesis that by gain and loss of functions, <it>Shigella </it>species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships.</p

Fine mapping and candidate gene analysis of proportion of four-seed pods by soybean CSSLs

Soybean yield, as one of the most important and consistent breeding goals, can be greatly affected by the proportion of four-seed pods (PoFSP). In this study, QTL mapping was performed by PoFSP data and BLUE (Best Linear Unbiased Estimator) value of the chromosome segment substitution line population (CSSLs) constructed previously by the laboratory from 2016 to 2018, and phenotype-based bulked segregant analysis (BSA) was performed using the plant lines with PoFSP extreme phenotype. Totally, 5 ICIM QTLs were repeatedly detected, and 6 BSA QTLs were identified in CSSLs. For QTL (qPoFSP13-1) repeated in ICIM and BSA results, the secondary segregation populations were constructed for fine mapping and the interval was reduced to 100Kb. The mapping results showed that the QTL had an additive effect of gain from wild parents. A total of 14 genes were annotated in the delimited interval by fine mapping. Sequence analysis showed that all 14 genes had genetic variation in promoter region or CDS region. The qRT−PCR results showed that a total of 5 candidate genes were differentially expressed between the plant lines having antagonistic extreme phenotype (High PoFSP &gt; 35.92%, low PoFSP&lt; 17.56%). The results of haplotype analysis showed that all five genes had two or more major haplotypes in the resource population. Significant analysis of phenotypic differences between major haplotypes showed all five candidate genes had haplotype differences. And the genotypes of the major haplotypes with relatively high PoFSP of each gene were similar to those of wild soybean. The results of this study were of great significance to the study of candidate genes affecting soybean PoFSP, and provided a basis for the study of molecular marker-assisted selection (MAS) breeding and four-seed pods domestication

A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF

<p>Abstract</p> <p>Background</p> <p>New strategies for high-throughput sequencing are constantly appearing, leading to a great increase in the number of completely sequenced genomes. Unfortunately, computational genome annotation is out of step with this progress. Thus, the accurate annotation of these genomes has become a bottleneck of knowledge acquisition.</p> <p>Results</p> <p>We exploited a proteogenomic approach to improve conventional genome annotation by integrating proteomic data with genomic information. Using <it>Shigella flexneri </it>2a as a model, we identified total 823 proteins, including 187 hypothetical proteins. Among them, three annotated ORFs were extended upstream through comprehensive analysis against an in-house N-terminal extension database. Two genes, which could not be translated to their full length because of stop codon 'mutations' induced by genome sequencing errors, were revised and annotated as fully functional genes. Above all, seven new ORFs were discovered, which were not predicted in <it>S. flexneri </it>2a str.301 by any other annotation approaches. The transcripts of four novel ORFs were confirmed by RT-PCR assay. Additionally, most of these novel ORFs were overlapping genes, some even nested within the coding region of other known genes.</p> <p>Conclusions</p> <p>Our findings demonstrate that current <it>Shigella </it>genome annotation methods are not perfect and need to be improved. Apart from the validation of predicted genes at the protein level, the additional features of proteogenomic tools include revision of annotation errors and discovery of novel ORFs. The complementary dataset could provide more targets for those interested in <it>Shigella </it>to perform functional studies.</p

Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin

<p>Abstract</p> <p>Background</p> <p>Tuberculosis is an infectious bacterial disease in humans caused primarily by <it>Mycobacterium tuberculosis</it>, and infects one-third of the world's total population. <it>Mycobacterium bovis </it>bacillus Calmette-Guérin (BCG) vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated <it>M. bovis </it>BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS) to characterize potential protein-protein interactions in membrane fractions.</p> <p>Results</p> <p>Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins), which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane helixes were identified well in our work.</p> <p>Conclusions</p> <p>In this study, we utilized LC-MS/MS in combination with blue native PAGE to characterize modular components of multiprotein complexes in BCG membrane fractions. The results demonstrated that the proteomic strategy was a reliable and reproducible tool for analysis of BCG multiprotein complexes. The identification in our study may provide some evidence for further study of BCG protein interaction.</p

Nanomechanical properties of induction cladded in-situ TiC reinforced titanium matrix composite coatings

In order to reveal the correspondence between the microstructure and mechanical properties of in-situ TiC/Ti composite coatings by induction fusion coating, the nano-mechanical property variation patterns of different phase structures within the coatings were investigated by using the isolated nanoindentation test method, and the mechanical properties of the coating micro-zone structure were studied by using grid indentation test method. The isolated indentation results show that the nanoindentation hardness and elastic modulus of the in-situ TiC-reinforced phases are 21.3 GPa and 275 GPa, respectively, while the average nano hardness of the matrix phase in the α-Ti-rich and β-Ti-rich regions is 4 GPa and 6 GPa, respectively, and the average elastic modulus is 130 GPa and 155 GPa, respectively. The correspondence between the grid indentation and isolated indentation test results is good. The minimum peak obtained from the three-peak Gaussian fitting of the fractional nanoindentation test results represents the mechanical properties of the matrix phase of the coating, the middle peak reflects the comprehensive mechanical properties of the coating, and the maximum peak is lower than the real mechanical properties of the in-situ TiC reinforcement due to the influence of the reinforcement size and indentation position. Under the consideration of coating microstructure and reinforcement size, by reasonably setting the fractional indentation test conditions and selecting the appropriate test area, it can reveal comprehensive properties of the coating while obtaining real mechanical properties of different phase structures of in-situ TiC composite coatings

Collisional dynamics in laser-induced plasmas: evidence for electron-impact excitation

We have experimentally investigated the collisional dynamics in femtosecond-laser-induced plasmas and presented the evidence for electron-impact excitation through enhanced high-order harmonic (HH) generation. The measurements were carried out by using an elliptically polarized pump pulse to induce the underdense plasmas and by using a time delayed linearly polarized probe pulse to drive the HH generation from the plasmas. We found that the rise time of this enhanced HH generation was insensitive to the ellipticity degree (ED) of pump pulse but sensitive to its laser intensity (LI). With further comparison between physical scenarios and qualitative analysis, we demonstrated that the atomic excitation causing the HH enhancement should be attributed to the electron-impact excitation. i.e., the excitation from the collision between neutral atoms and electrons during the lifetime of the underdense plasma. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement11Nsciescopu

Indico MEETING tutorial

This short tutorial explains how to create a MEETING in indico, how to populate the timetable, write minutes and how to add material. If you are only interested in the timetable part, please slide to 03.39, for the minutes to 07.46 and for adding material to 08.29. &nbsp; Tell us what you think via e-learning.support at cern.ch More tutorials in the e-learning collection of the CERN Document Server (CDS) http://cds.cern.ch/collection/E-learning%20modules?ln=en All info about the CERN rapid e-learning project is linked from http://twiki.cern.ch/ELearning &nbsp;</p