Enhanced resistance to sclerotinia stem rot in transgenic soybean that overexpresses a wheat oxalate oxidase

Sclerotinia stem rot (SSR), caused by the oxalate-secreting necrotrophic fungal pathogen Sclerotinia sclerotiorum, is one of the devastating diseases that causes significant yield loss in soybean (Glycine max). Until now, effective control of the pathogen is greatly limited by a lack of strong resistance in available commercial soybean cultivars. In this study, transgenic soybean plants overexpressing an oxalic acid (OA)-degrading oxalate oxidase gene OXO from wheat were generated and evaluated for their resistance to S. sclerotiorum. Integration and expression of the transgene were confirmed by Southern and western blot analyses. As compared with non-transformed (NT) control plants, the transgenic lines with increased oxalate oxidase activity displayed significantly reduced lesion sizes, i.e., by 58.71–82.73% reduction of lesion length in a detached stem assay (T₃ and T₄ generations) and 76.67–82.0% reduction of lesion area in a detached leaf assay (T₄ generation). The transgenic plants also showed increased tolerance to the externally applied OA (60 mM) relative to the NT controls. Consecutive resistance evaluation further confirmed an enhanced and stable resistance to S. sclerotiorum in the T₃ and T₄ transgenic lines. Similarly, decreased OA content and increased hydrogen peroxide (H₂O₂) levels were also observed in the transgenic leaves after S. sclerotiorum inoculation. Quantitative real-time polymerase chain reaction analysis revealed that the expression level of OXO reached a peak at 1 h and 4 h after inoculation with S. sclerotiorum. In parallel, a significant up-regulation of the hypersensitive response-related genes GmNPR1-1, GmNPR1-2, GmSGT1, and GmRAR occurred, eventually induced by increased release of H₂O₂ at the infection sites. Interestingly, other defense-related genes such as salicylic acid-dependent genes (GmPR1, GmPR2, GmPR3, GmPR5, GmPR12 and GmPAL), and ethylene/jasmonic acid-dependent genes (GmAOS, GmPPO) also exhibited higher expression levels in the transgenic plants than in the NT controls. Our results demonstrated that overexpression of OXO enhances SSR resistance by degrading OA secreted by S. sclerotiorum and increasing H₂O₂ levels, and eliciting defense responses mediated by multiple signaling pathways.

     

31° South: The physiology of adaptation to arid conditions in a passerine bird

Arid environments provide ideal ground for investigating the mechanisms of adaptive evolution. High temperatures and low water availability are relentless stressors for many endotherms, including birds; yet birds persist in deserts. While physiological adaptation probably involves metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we took an intraspecific approach that focused on a species that is resident over a mesic to arid gradient, the Karoo scrub‐robin (Cercotrichas coryphaeus). Specifically, we integrated environmental (climatic and primary productivity), physiological (metabolic rates: a measure of energy expenditure), genotypic (genetic variation underlying the machinery of energy production) and microbiome (involved in processing food from where energy is retrieved) data, to infer the mechanism of physiological adaptation. We that found the variation in energetic physiology phenotypes and gut microbiome composition are associated with environmental features as well as with variation in genes underlying energy metabolic pathways. Specifically, we identified a small list of candidate adaptive genes, some of them with known ties to relevant physiology phenotypes. Together our results suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly microbiota composition may facilitate adaptation to local conditions and provide an explanation to the high avian intraspecific divergence observed in harsh environments.     

猪伪狂犬病病毒流行株HLJ-01的分离鉴定及致病性分析

【背景】自2011年以来,猪伪狂犬病毒(pseudorabies virus,PRV)发生变异,经典的疫苗株已不能完全抵抗PRV变异株的感染,国内多个猪场出现伪狂犬病的暴发,PRV变异毒株开始在我国大规模流行。【目的】通过分离PRV流行变异毒株,并对其进行遗传进化和致病性分析,为PRV流行病学调查及疫苗研制提供实验数据。【方法】采集黑龙江某猪场感染PRV的脑组织病料,根据GenBank PRV gE和gB保守序列设计引物,进行PCR鉴定。通过对gE和gC基因进行序列测定和遗传进化分析。利用BHK-21细胞分离病毒,采用噬斑纯化方法对病毒进行纯化。通过电镜、间接免疫荧光对病毒进行鉴定,测定病毒生长曲线并进行致病性研究。【结果】经PCR和测序鉴定分离株为PRV流行株,将其命名为HLJ-01。遗传进化分析结果显示,该分离毒株与我国近几年分离的流行变异株位于同一分支;氨基酸序列分析结果显示,gE和gC存在国内流行变异株的特征序列,表明该分离毒株为流行变异株。生长曲线显示,分离株HLJ-01在感染48h时滴度最高(10^8.5TCID₅₀/mL)。电镜观察结果显示,病毒颗粒直径约150nm,呈球形,有囊膜,囊膜外有放射状纤突,呈现典型PRV病毒特征。动物感染实验结果显示,10^7.0TCID₅₀剂量感染组死亡率为100%;10^6.0TCID₅₀剂量感染组死亡率为80%;10^5.0TCID₅₀剂量感染组死亡率为60%。仔猪在接种病毒后均出现PRV感染的典型症状和病理变化,证实分离毒株对仔猪有较强致病力。【结论】分离获得一株猪伪狂犬病毒,经鉴定该分离株为流行变异株,而且具有较强的致病力,这为PRV流行病学分析及疫苗候选株的筛选奠定了基础。     

Avianbase: a community resource for bird genomics

Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released by the Avian Phylogenomics Consortium.Access to complete genome sequences provides the first step towards the understanding of the biology of organisms. It is the template that underpins the phenotypic characteristics of individuals and ultimately separates species due to the accumulation and fixation of mutations over evolutionary timescales. In terms of the available genomic datasets for species, birds, as our more distant relatives, have been historically underrepresented. The high cost of sequencing and annotation in the past led to a bias towards accumulating data for species that are either established model organisms or economically significant (that is, chicken, turkey and duck, representing two sister orders within the Galloanseriformes clade from the large and diverse phylogeny of birds). The recent release of genome assemblies and initial predictions of protein-coding genes [1-4] for 44 bird species, including representatives from all major branches of the bird phylogeny, is, therefore, highly significant.One of the major challenges with the release of this number of newly sequenced genomes and the many more to come [5] is how to make these available to the various research communities in a way that supports basic research. Providing access to the sequences and initial annotations in the format of text files will limit the potential usage of the data as they require significant resources, including bioinformatics personnel and computer infrastructure in place to access and mine - for example, searching for genes belonging to certain protein families or searching for orthologous genes. These overheads pose a serious bottleneck that can hinder research and requires concerted action by the relevant research communities.Once genomes are submitted to public databases, genome-wide annotations are frequently generated and released either via the Ensembl project [6] or by the National Center for Biotechnology Information [7] and sequence and annotation are then made visually available online in integrated views via the Ensembl or the University of California Santa Cruz (UCSC) genome browsers [8]. These systems provide search facilities, sequence alignment tools like BLAT/BLAST and various analysis tools to facilitate subsetting and computational retrieval of the data, including UCSC’s Table Browser or Ensembl’s Perl and REST APIs and BioMart system.While these systems have become almost indispensable for research, not all sequenced genomes are annotated and displayed in genome browsers. Full genome annotation remains time consuming and resource intensive: a full evidence-based Ensembl genebuild takes approximately 4 months. Thus, the list of species represented is currently limited and depends on various factors, including the completeness of the assembled genome sequence and the overall demand in the scientific community for the resources, including whether the species is a model organism (for example, human or mouse), economically important (for example, farmed animals) or of specific phylogenetic interest. Many of the recently sequenced bird genomes do not obviously fall within these categories.     

Epigallocatechin-3-gallate (EGCG) as a pro-osteogenic agent to enhance osteogenic differentiation of mesenchymal stem cells from human bone marrow: an in vitro study

The proliferation and osteogenic capacity of mesenchymal stem cells (MSCs) needs to be improved for their use in cell-based therapy for osteoporosis. (?)-Epigallocatechin-3-gallate (EGCG), one of the green tea catechins, has been widely investigated in studies of osteoblasts and osteoclasts. However, no consensus on its role as an osteogenic inducer has been reached, possibly because of the various types of cell lines examined and the range of concentrations of EGCG used. In this study, the osteogenic effects of EGCG are studied in primary human bone-marrow-derived MSCs (hBMSCs) by detecting cell proliferation, alkaline phosphatase (ALP) activity and the expression of relevant osteogenic markers. Our results show that EGCG has a strong stimulatory effect on hBMSCs developing towards the osteogenic lineage, especially at a concentration of 5 μM, as evidenced by an increased ALP activity, the up-regulated expression of osteogenic genes and the formation of bone-like nodules. Further exploration has indicated that EGCG directes osteogenic differentiation via the continuous up-regulation of Runx2. The underlying mechanism might involve EGCG affects on osteogenic differentiation through the modulation of bone morphogenetic protein-2 expression. EGCG has also been found to promote the proliferation of hBMSCs in a dose-dependent manner. This might be associated with its antioxidative effect leading to favorable amounts of reactive oxygen species in the cellular environment. Our study thus indicates that EGCG can be used as a pro-osteogenic agent for the stem-cell-based therapy of osteoporosis.     

Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh,Ihh and Dhh) in Vertebrates

The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – Shh; Indian hedgehog – Ihh; and Desert hedgehog – Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the Hh orthologs. Our results provide new insights on the evolutionary history of the Hh gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots.     

皮状丝孢酵母同步利用葡萄糖/木糖的糖转运动力学简

皮状丝孢酵母（ Trichosporon cutaneum）能够同步利用葡萄糖和木糖生产油脂。以2脱氧葡萄糖（2 DOG）为底物,考察皮状丝孢酵母糖跨膜运输的转运动力学。结果表明：2 DOG转运符合米氏方程,表观米氏常数Km为0.19 mmol/L,最大转运速率Vmax为14.1 nmol/（ min＆#183;mg）。葡萄糖和木糖均竞争性抑制2 DOG转运,葡萄糖表观抑制常数Ki远低于木糖,表明存在一个共用转运体系,且该转运体系对葡萄糖亲和力更高。大量木糖与2 DOG同时转运到胞内,进一步说明木糖与葡萄糖共运输。代谢抑制剂和pH对糖转运有明显影响,说明质子/底物同向运输系统是该酵母的主要糖转运系统。     

Association of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Elements with Specific Serotypes and Virulence Potential of Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) strains (n = 194) representing 43 serotypes and E. coli K-12 were examined for clustered regularly interspaced short palindromic repeat (CRISPR) arrays to study genetic relatedness among STEC serotypes. A subset of the strains (n = 81) was further analyzed for subtype I-E cas and virulence genes to determine a possible association of CRISPR elements with potential virulence. Four types of CRISPR arrays were identified. CRISPR1 and CRISPR2 were present in all strains tested; 1 strain also had both CRISPR3 and CRISPR4, whereas 193 strains displayed a short, combined array, CRISPR3-4. A total of 3,353 spacers were identified, representing 528 distinct spacers. The average length of a spacer was 32 bp. Approximately one-half of the spacers (54%) were unique and found mostly in strains of less common serotypes. Overall, CRISPR spacer contents correlated well with STEC serotypes, and identical arrays were shared between strains with the same H type (O26:H11, O103:H11, and O111:H11). There was no association identified between the presence of subtype I-E cas and virulence genes, but the total number of spacers had a negative correlation with potential pathogenicity (P < 0.05). Fewer spacers were found in strains that had a greater probability of causing outbreaks and disease than in those with lower virulence potential (P < 0.05). The relationship between the CRISPR-cas system and potential virulence needs to be determined on a broader scale, and the biological link will need to be established.