A protein microarray representing 149 Yersinia pestis proteins was developed to profile antibody responses in EV76-immunized rabbits. Antibodies to 50 proteins were detected. There are 11 proteins besides F1 and V antigens to which the predominant antibody response occurred, and these proteins show promise for further evaluation as candidates for subunit vaccines and/or diagnostic antigens.Plague, one of the most dangerous diseases, is caused by Yersinia pestis. The increasing possibility of antibiotic-resistant Y. pestis strains means that a vaccine effective against bubonic and pneumonic plague is urgently needed (12,14,18). The current interest is in developing plague vaccines that consist of purified protein subunits, with improved protection and reduced side effects (25,31,34). The F1 or V single-subunit vaccine and the F1 plus V combination vaccine have been shown to provide effective protection against bubonic and pneumonic plague in animal models (1,31,34). There may still exist other Y. pestis antigens that provide protection. These novel vaccine candidates in conjunction with F1 and V can be developed as multicomponent subunit vaccines (21). It may improve protection against F1-and/or V-antigen mutant but virulent strains. Therefore, evaluation of Y. pestis proteins beside F1 and V for their efficacy in inducing specific antibody in the infected animals or human patients is urgently needed for plague vaccine development.Genomic sequences of Y. pestis CO92 (27), KIM (9), and 91001 (30) have been released in the past 3 years. Decoding of whole-genome sequence provides unprecedented opportunities for vaccine design. The microarray immobilized with multiple antigens, using a simple fluorescence analysis, allows high-throughput parallel detection and quantification of multiple specific antibodies in a miniaturized, low-sample-consumption format. In this study, a microarray representing 149 Y. pestis proteins was developed to profile the serum antibodies of rabbits that were immunized with live plague vaccine, providing an overall picture of the immunogenicity of the proteins tested.Construction of an antigen microarray representing 149 Y. pestis proteins. In our present work, 202 genes were selected for cloning and expression (additional information is available at http://bioinflab.org/journals/ruifu/supplementary_TableS1 .pdf/). The digested PCR products of specific genes were cloned into expression plasmid vector pET-32a (Novagen), and recombinant plasmids were transformed into BL21(DE3) cells. According to sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, 172 genes were successfully expressed in Escherichia coli. The expressed proteins were subjected to purification in a 96-well format using Ni-NAT agarose (QIA-GEN) according to Brauns' method with a few modifications (5). For quality control, the purified proteins were printed onto silylated glass slides (CEL) and incubated with Cy5-labeled antibody specific for the six-His tag. Only the proteins giving a signal-to-background ratio of ...

The concentration characteristics, sources, and potential ecological risk assessment of 16 PAHs were investigated in the surface water from the Songhua River Basin, Northeast China. A total of 48 river water samples, including 16 from the main streams and 32 from the tributaries, were collected. Samples were separated into dissolved phases and suspended particle matter (SPM) via filtration with 0.47 μm glass fiber filters. Each phase was analyzed for PAHs. The total PAH concentration in the dissolved phase in the water ranged from 32.5 to 108 ng L and from 0.3 to 62.3 μg g (dry weight) in the suspended particle matter (SPM). The total PAH concentration in the main stream was lower than in the tributaries; the volume of annual runoff of rivers had a significant effect on the ƩPAH in the rivers. The 2- and 3-ring PAHs dominated in both the dissolved phase and SPM, indicating a relatively recent local source of PAHs in the study area. The concentrations of PAHs in the Songhua River Basin are lower when compared with the values previously reported in the literature from other rivers around the world. The sources of PAHs were assessed by diagnostic ratios and principal component analysis (PCA), and the ecological risk of the PAHs was assessed based on the risk quotient (RQ). The diagnostic ratios and PCA indicated that the main sources of PAHs originated from pyrogenic and petrogenic sources, and pyrogenic sources had a greater impact. The ecological risk assessment indicated that the PAHs presented low ecosystem risk in the Songhua River Basin.

BackgroundSpecies delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With the advent of molecular approaches in species delimitation, this hidden diversity has received much recent attention. In addition to DNA barcoding approaches, analytical tools based on the multi-species coalescence model (MSC) have been developed for species delimitation. Musa itinerans is widely distributed in subtropical Asia, and at least six varieties have been documented. However, the number of evolutionarily distinct lineages remains unknown.ResultsUsing genome resequencing data of five populations (making up four varieties), we examined genome-wide variation and found four varieties that were evolutionary significant units. A Bayesian Phylogenetics and Phylogeography (BP&P) analysis using 123 single copy nuclear genes support three speciation events of M. itinerans varieties with robust posterior speciation probabilities; However, a Bayes factor delimitation of species with genomic data (BFD*) analysis using 1201 unlinked single nucleotide polymorphisms gave decisive support for a five-lineage model. When reconciling divergence time estimates with a speciation time scale, a modified three-lineage model was consistent with that of BP&P, in which the speciation time of two varieties (M. itinerans var. itinerans and M. itinerans var. lechangensis) were dated to 26.2 kya and 10.7 kya, respectively. In contrast, other two varieties (M. itinerans var. chinensis and M. itinerans var. guangdongensis) diverged only 3.8 kya in the Anthropocene; this may be a consequence of genetic drift rather than a speciation event.ConclusionOur results showed that the M. itinerans species complex harbours high cryptic species diversity. We recommend that M. itinerans var. itinerans and M. itinerans var. lechangensis be elevated to subspecies status, and the extremely rare latter subspecies be given priority for conservation. We also recommend that the very recently diverged M. itinerans var. chinensis and M. itinerans var. guangdongensis should be merged under the subspecies M. itinerans var. chinensis. Finally, we speculate that species delimitation of recently diverged lineages may be more effective using genome-wide bi-allelic SNP markers with BFD* than by using unlinked loci and BP&P.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1410-6) contains supplementary material, which is available to authorized users.