Weibing Shi

Copyright © 2015 Xinwang Wang et al.This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Transcriptome analysis was conducted in two popular Lagerstroemia cultivars: “Natchez ” (NAT), a white flower and powdery mildew resistant interspecific hybrid and “Carolina Beauty ” (CAB), a red flower and powdery mildew susceptible L. indica cultivar. RNA-seq reads were generated from Erysiphe australiana infected leaves and de novo assembled. A total of 37,035 unigenes from 224,443 assembled contigs in both genotypes were identified. Approximately 85 % of these unigenes have known function. Of them, 475 KEGG genes were found significantly different between the two genotypes. Five of the top ten differentially expressed genes (DEGs) involved in the biosynthesis of secondary metabolites (plant defense) and four in flavonoid biosynthesi...

Endocrine disrupters include a broad spectrum of chemicals such as industrial chemicals, natural estrogens and androgens, synthetic estrogens and androgens. Phytoestrogens are widely present in diet and food supplements; mycoestrogens are frequently found in grains. As human beings and animals are commonly exposed to phytoestrogens and mycoestrogens in diet and environment, it is important to understand the potential beneficial or hazardous effects of estrogenic compounds. Many bioassays have been established to study the binding of estrogenic compounds with estrogen receptor (ER) and provided rich data in the literature. However, limited assays can offer structure information with regard to the ligand/ER complex. Our current study surveys the global structure dynamics changes for ERα ligand binding domain (LBD) when phytoestrogens and mycoestrogens bind. The assay is based on the structure dynamics information probed by hydrogen deuterium exchange mass spectrometry and offers a uni...

Transcriptome analysis was conducted in two popular Lagerstroemia cultivars: "Natchez" (NAT), a white flower and powdery mildew resistant interspecific hybrid and "Carolina Beauty" (CAB), a red flower and powdery mildew susceptible L. indica cultivar. RNA-seq reads were generated from Erysiphe australiana infected leaves and de novo assembled. A total of 37,035 unigenes from 224,443 assembled contigs in both genotypes were identified. Approximately 85% of these unigenes have known function. Of them, 475 KEGG genes were found significantly different between the two genotypes. Five of the top ten differentially expressed genes (DEGs) involved in the biosynthesis of secondary metabolites (plant defense) and four in flavonoid biosynthesis pathway (antioxidant activities or flower coloration). Furthermore, 5 of the 12 assembled unigenes in benzoxazinoid biosynthesis and 7 of 11 in flavonoid biosynthesis showed higher transcript abundance in NAT. The relative abundance...

In order to find an excellent kind of heat transfer element under vacuum condition, the heat transfer performance of tube bundles of different materials in vacuum state was studied through experiments, of which include stainless steel tube, brass tube, Ni-based implanted steel tube and ion implanted brass tube. The relative curves prove that the condensation heat transfer coefficient and the overall heat transfer coefficient of four kinds of bundles all increase with the rising vacuum and increasing Re value, especially of the Ni-based implanted steel tube and the ion implanted brass tube. Under higher vacuum (0.07MPa), for larger Re value (24613), it was found that the condensation heat transfer coefficient of Ni-based implanted steel tube bundle is about 3 times that of the stainless steel tube bundle, the condensation heat transfer coefficient of ion implanted brass tube bundle is about 2.4 times that of the common brass tube bundle as well. Therefore, it is believed that partly dropwise condensation was achieved on the surface of these two implanted tube bundles, and ion implantation is proved to be an effective method of dropwise condensation attainment. According to the conclusion, it is considered that the Ni-based steel tube can substitute more expensive brass tube as heat transfer component to some extent.

Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts. Methane production in the rumen is strongly connected to microbial hydrogen production through fermentation processes. In this study, we investigate the contribution that rumen bacteria make to methane yield phenotypes in sheep. Using deep sequence metagenome and metatranscriptome datasets in combination with 16S rRNA gene amplicon sequencing from HMY and LMY...

Gene set enrichment analysis of metagenome and metatranscriptome datasets. Pathways with genes differentially present or expressed based on nominal P value (NOM P val â ¤0.05) are shown, ranked by normalised enrichment score (NES). Corrected P values for false discovery rate (FDR q val) and familywise-error rate (FEWER P val) are shown. (PDF 88Â kb)

Insect guts represent unique natural biocatalyst systems for biocatalyst discovery and biomass deconstruction mechanism studies. In order to guide the further research for enzyme discovery and biodiversity analysis, we carried out comprehensive xylanase and cellulase activity assays for the gut contents of three insect species representing different orders and food sources. The three insect species are grasshopper (Acrididae sp.), woodborer

Entomopathogenic fungi can infect and kill spider mite eggs but their ovicidal activities are poorly understood. Here we gain histopathogenical and molecular insights into the ovicidal activities of Beauveria bassiana and Isaria fumosorosea against the two-spotted spider mite, Tetranychus urticae. Scanning electronic microscopy indicated successful adhesion and germination of fungal conidia on egg shell at 24h post-spray (HPS). Germ tubes of both fungi could penetrate into egg shell with penetration pegs at 48 HPS. Interestingly, the germ tubes of B. bassiana may elongate on egg surface to locate appropriate sites for penetration, acting as 'searching' hyphae. Aside from the normal penetration, the germ tubes of I. fumosorosea can be completely or partially embedded into egg shell for a distance of extension, forming shell humps. Light microscopy of ultrathin sections of infected eggs showed shrunken (affected) or disrupted embryos at 48-96 HPS despite little effect on egg cleavage at 24 HPS. However, distinguishable hyphal cells were hardly found inside the embryos lacking oxygen although fungal outgrowths were abundant on unhatched (killed) eggs. In PCR with specific probes, the 18S rDNA signals of B. bassiana (412 bp) and I. fumosorosea (454 bp) in the DNA extracts from surface-cleaned mite eggs increased at 0-96 HPS, confirming fungal colonization in the infected eggs. We consider that the colonization on shell surface and underside could rely upon extending hyphae for uptake of egg nutrition, resulting in embryo disruption. Our observations add knowledge to microbial control of spider mites.

Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional characterization. Here we propose a workflow to address this challenge by combining phylogenomic guided DNA synthesis with high-throughput mass spectrometry and apply it to the systematic characterization of GH1 β-glucosidases, a family of enzymes necessary for biomass hydrolysis, an important step in the conversion of lignocellulosic feedstocks to fuels and chemicals. We synthesized and expressed 175 GH1s, selected from over 2000 candidate sequences to cover maximum sequence diversity. These enzymes were functionally characterized over a range of temperatures and pHs using nanostructure-initiator mass spectrometry (NIMS), generating over 10,000 data points. When combined with HPLC-based sugar profiling, we observed GH1 enzymes active over a broad temperature range and toward many different β-linked disaccharides. For some GH1s we also ob...

High abundance proteins like ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) impose a consistent challenge for the whole proteome characterization using shot-gun proteomics. To address this challenge, we developed and evaluated Polyethyleneimine Assisted Rubisco Cleanup (PARC) as a new method by combining both abundant protein removal and fractionation. The new approach was applied to a plant insect interaction study to validate the platform and investigate mechanisms for plant defense against herbivorous insects. Our results indicated that PARC can effectively remove Rubisco, improve the protein identification, and discover almost three times more differentially regulated proteins. The significantly enhanced shot-gun proteomics performance was translated into in-depth proteomic and molecular mechanisms for plant insect interaction, where carbon re-distribution was used to play an essential role. Moreover, the transcriptomic validation also confirmed the reliability of PARC analysis. Finally, functional studies were carried out for two differentially regulated genes as revealed by PARC analysis. Insect resistance was induced by over-expressing either jacalin-like or cupin-like genes in rice. The results further highlighted that PARC can serve as an effective strategy for proteomics analysis and gene discovery.

ABSTRACT We have recently carried out comprehensive proteomics analysis of cattle rumen microbiota to study the molecular mechanisms of biomass deconstruction and utilization. The study includes four treatments of high fiber to low fiber in the treatments in a 72 day feeding trial. Metagenome sequencing was first carried out to derive the gene models for proteomics data search. Enzyme assays revealed that the cellulytic enzyme activities are higher in the high fiber biomass treated time point. MudPIT-based shot-gun proteomics was carried out to characterize both the soluble and fiber portion of the rumen material. The proteome profiling highlighted that microbial diversity and enzyme profile change dramatically in response to the feeding content. Furthermore, cluster analysis and protein co-regulatory network modeling of protein abundance revealed that several groups of enzymes are coordinatively regulated in response to the high fiber biomass feeding. Each group of these coordinative enzymes includes multiple glycoside hydrolase (GH) families and functional category, indicating the synergistics toward biomass deconstruction. More importantly, the protein profiling correlates with the metagenome analysis in a way that some co-regulating enzymes were found in the same operon in metagneome sequences. The results highlighted both the regulation mechanisms and the reliability of proteomics data. Based on the network modeling, we have cloned and characterized multiple enzymes toward reverse design of a biorefinery process for efficient biomass utilization. Overall, the systems biology analysis revealed the potential mechanisms for efficient biomass degradation in cattle rumen, which can be used for both animal nutrition and biotechnology applications.