Recognition of bacteria named entity using conditional random fields in Spark

Background

Microbe plays a crucial role in the functional mechanism of an ecosystem. Identification of the interactions among microbes is an important step towards understand the structure and function of microbial communities, as well as of the impact of microbes on human health and disease. Despite the importance of it, there is not a gold-standard dataset of microbial interactions currently. Traditional approaches such as growth and co-culture analysis need to be performed in the laboratory, which are time-consuming and costly. By providing predicted candidate interactions to experimental verification, computational methods are able to alleviate this problem. Mining microbial interactions from mass medical texts is one type of computational methods. Identification of the named entity of bacteria and related entities from the text is the basis for microbial relation extraction. In the previous work, a system of bacteria named entities recognition based on the dictionary and conditional random field was proposed. However, it is inefficient when dealing with large-scale text.

Results

We implemented bacteria named entity recognition on Spark platform and designed experiments for comparison to verify the correctness and validity of the proposed system. The experimental results show that it can achieve higher F-Measure on the comparison of correctness. Moreover, the predicting speed is much faster than the previous version in large-scale biomedical datasets, and the computational efficiency is improved remarkably by about 3.1 to 6.7 times.

Conclusions

The system for bacteria named entity recognition solves the inefficiency of the previous proposed system on large-scale datasets. The proposed system has good performance in accuracy and scalability.

     

Molecular studies of cellulose synthase supercomplex from cotton fiber reveal its unique biochemical properties

Science China Life Sciences - Cotton fiber is a highly elongated and thickened single cell that produces large quantities of cellulose, which is synthesized and assembled into cell wall...     

基于全基因组SNP分子标记分析青海云杉遗传结构

以张掖龙渠青海云杉（Picea crassifolia）无性系种子园中的106个青海云杉亲本无性系为研究材料,采用改良CTAB法,提取的青海云杉基因组DNA,构建SLAF文库并进行高通量测序,之后分析SLAF测序数据和筛选SNP位点,基于邻接法分析得到样品的聚类情况。研究得出：将测序的水稻日本晴reads与其参考基因组进行比对,显示本试验双端比对效率为95.33%,说明SLAF建库成功。本研究中所测序列的Q30较高,碱基测 序错误率低,测序质量高;本研究共开发4 058 883个SLAF标签,标签的平均测序深度为21.21×。共开发 12 275 765个青海云杉SNP标记,各青海云杉样本的SNP数量为1 890 934~4 487 841。利用已开发的高质量青海云杉SNP标记,构建了106个青海云杉的系统发育树,发现来自不同种源的青海云杉在各组中分布比较均匀,不同种源的青海云杉多聚为一类。通过SNP标记和主成分分析,这些无性系来源于同一个祖先的可能性较大,表明无性系间亲缘关系相近。为今后遗传多样性的分析、遗传图谱的构建等提供了基础数据,也为青海云杉初级种子园去劣疏伐提供依据,为高世代种子园的营建奠定基础。     

Molecular characterization and expression analysis reveal the roles of Cys2/His2 zinc-finger transcription factors during flower development of Brassica rapa subsp. chinensis

Plant Molecular Biology - Conserved motif, gene structure, expression and interaction analysis of C2H2-ZFPs in Brassica rapa, and identified types of genes may play essential roles in flower...     

Pancreatic acinar cells-derived cyclophilin A promotes pancreatic damage by activating NF-κB pathway in experimental pancreatitis

Inflammation triggered by necrotic acinar cells contributes to the pathophysiology of acute pancreatitis (AP), but its precise mechanism remains unclear. Recent studies have shown that Cyclophilin A (CypA) released from necrotic cells is involved in the pathogenesis of several inflammatory diseases. We therefore investigated the role of CypA in experimental AP induced by administration of sodium taurocholate (STC). CypA was markedly upregulated and widely expressed in disrupted acinar cells, infiltrated inflammatory cells, and tubular complexes. In vitro, it was released from damaged acinar cells by cholecystokinin (CCK) induction. rCypA (recombinant CypA) aggravated CCK-induced acinar cell necrosis, promoted nuclear factor (NF)-κB p65 activation, and increased cytokine production. In conclusion, CypA promotes pancreatic damage by upregulating expression of inflammatory cytokines of acinar cells via the NF-κB pathway.     

Characterization of a Novel Cotton Subtilase Gene GbSBT1 in Response to Extracellular Stimulations and Its Role in Verticillium Resistance

Verticillium wilt is a disastrous vascular disease in plants caused by Verticillium dahliae. Verticillium pathogens secrete various disease-causing effectors in cotton. This study identified a subtilase gene GbSBT1 from Gossypium babardense and investigated the roles against V. dahliae infection. GbSBT1 gene expression is responsive to V. dahliae defense signals, jasmonic acid, and ethylene treatments. Moreover, the GbSBT1 protein is mainly localized in the cell membrane and moves into the cytoplasm following jasmonic acid and ethylene treatments. Silencing GbSBT1 gene expression through virus-induced GbSBT1 gene silencing reduced the tolerance of Pima-90 (resistant genotype), but not facilitated the infection process of V. dahliae in Coker-312 (sensitive genotype). Moreover, the ectopically expressed GbSBT1 gene enhanced the resistance of Arabidopsis to Fusarium oxysporum and V. dahliae infection and activated the expression levels of defense-related genes. Furthermore, pull-down, yeast two-hybrid assay, and BiFC analysis revealed that GbSBT1 interacts with a prohibitin (PHB)-like protein expressed in V. dahliae pathogens during infection. In summary, GbSBT1 recognizes the effector PHB protein secreted from V. dahliae and is involved in Verticillium-induced resistance in cotton.     

N fertilization affects on soil respiration, microbial biomass and root respiration in Larix gmelinii and Fraxinus mandshurica plantations in China

The response of belowground biological processes to soil N availability in Larix gmelinii (larch) and Fraxinus mandshurica (ash) plantations was studied. Soil and root respiration were measured with Li-Cor 6400 and gas-phase O₂ electrodes, respectively. Compared with the control, N fertilization induced the decreases of fine root biomass by 52% and 25%, and soil respiration by 30% and 24% in larch and ash plantations, respectively. The average soil microbial biomass C and N were decreased by 29% and 42% under larch stand and 39% and 47% under ash stand, respectively. While the fine root tissue N concentration under fertilized plots was higher 26% and 12% than that under control plots, respectively, the average fine root respiration rates were increased by 10% and 13% in larch and ash stands under fertilized plot, respectively. Soil respiration rates showed significantly positive exponential relationships with soil temperature, and a seasonal dynamic. These findings suggest that N fertilization can suppress fine root biomass at five branch orders (<2 mm in diameter), soil respiration, and soil microbial biomass C and N, and alter soil microbial communities in L. gmelinii and F. mandshurica plantations.     

TNFAIP3 Facilitates Degradation of Microbial Antigen SEB in Enterocytes

Background and Aims

The enterocytes have the potential to absorb noxious substances, such as microbial products, from the gut lumen. How the enterocytes process the substances to harmless materials is not fully understood. This study aims to elucidate the role of ubiquitin E3 ligase TNFAIP3 (TNFAIP3) in facilitating the degradation of endocytic microbial products in enterocytes.

Methods

Human intestinal epithelial cell line, HT-29 cells, was cultured to monolayers using as an in vitro model to observe the endocytosis and degradation of microbial products, Staphylococcal enterotoxin B (SEB) in epithelial cells. The RNA interference was employed to knock down the TNFAIP3 gene in HT-29 cells to observe the role of TNFAIP3 in the degradation of endocytic SEB. The role of TNFAIP3 in facilitating the endosome/lysosome fusion was observed by immunocytochemistry.

Results

Upon the absorption of SEB, the expression of TNFAIP3 was increased in HT-29 cells. Silencing the TNFAIP3 gene in HT-29 cells resulted in a large quantity of SEB to be transported across the HT-29 monolayers to the transwell basal chambers; the transportation was via the intracellular pathway. TNFAIP3 was required in the fusion of SEB-carrying endosomes and lysosomes.

Conclusions

TNFAIP3 plays a critical role in the degradation of endocytic SEB in enterocytes.     

Mining Temporal Protein Complex Based on the Dynamic PIN Weighted with Connected Affinity and Gene Co-Expression

The identification of temporal protein complexes would make great contribution to our knowledge of the dynamic organization characteristics in protein interaction networks (PINs). Recent studies have focused on integrating gene expression data into static PIN to construct dynamic PIN which reveals the dynamic evolutionary procedure of protein interactions, but they fail in practice for recognizing the active time points of proteins with low or high expression levels. We construct a Time-Evolving PIN (TEPIN) with a novel method called Deviation Degree, which is designed to identify the active time points of proteins based on the deviation degree of their own expression values. Owing to the differences between protein interactions, moreover, we weight TEPIN with connected affinity and gene co-expression to quantify the degree of these interactions. To validate the efficiencies of our methods, ClusterONE, CAMSE and MCL algorithms are applied on the TEPIN, DPIN (a dynamic PIN constructed with state-of-the-art three-sigma method) and SPIN (the original static PIN) to detect temporal protein complexes. Each algorithm on our TEPIN outperforms that on other networks in terms of match degree, sensitivity, specificity, F-measure and function enrichment etc. In conclusion, our Deviation Degree method successfully eliminates the disadvantages which exist in the previous state-of-the-art dynamic PIN construction methods. Moreover, the biological nature of protein interactions can be well described in our weighted network. Weighted TEPIN is a useful approach for detecting temporal protein complexes and revealing the dynamic protein assembly process for cellular organization.