土地利用/覆被变化对生物栖息地连接度的影响——以巩义地区黄鼬、蒙古兔和黄喉貂为例

土地利用/覆被变化通过改变生物栖息地而对物种分布产生影响。以河南省巩义市为研究区域,选取分布在该区域的哺乳动物黄鼬(Mustela sibirica)、蒙古兔(Lepus tolai)和黄喉貂(Martes flavigula)为目标物种,首先依据其生物特性和生态需求,确定了这3个物种的扩散能力;其次,基于景观连接度原理,分析了1990—2011年研究区土地利用整体变化和各类型变化情况,及其对单一物种和多物种栖息地连接度变化的影响。研究结果表明:(1)土地利用整体变化使得栖息地连接度增加,变化范围为22.22%—45.46%;(2)各土地利用类型变化对栖息地连接度的影响差异显著,连接度的升高和降低与栖息地斑块面积增加和减少密切相关;(3)基于多目标物种栖息地整体连接度空间分布图,确定了研究区目标物种保护的关键区域。     

Experimental field test of the influence of generalist stingless bees (Meliponini) on the topology of a bee–flower mutualistic network in the tropics

1. Generalists are assumed to play a key role in structuring and stabilising animal–plant mutualistic networks. Until now, analyses on the effects of generalists have been based on empirical field data or simulations. The present natural field experiment manipulated the abundance of a generalist and abundant stingless bee [Melipona (Eomelipona) marginata] to determine the effects on the mutualistic network. 2. Networks were generated, and associated metrics were used for comparing replicate plots with and without the insertion of stingless bee nests. 3. Unweighted metrics and the basic qualitative structural pattern of networks (high nestedness, very low modularity and specialisation) was not affected by experimental variation in stingless bee abundance because they exert strong basal effects on the plant–pollinator community under natural conditions of abundance. Still, increased abundance caused significant variation in weighted nestedness and modularity and community-level specialisation. 4. Supporting predictions of neutral models, increased abundance of the stingless bee led to an increase in most of its specific metrics, expressing the expansion of its realised trophic niche. 5. During this process, specialist and other generalist bees were affected in different ways. More plant species became even more dependent on this stingless bee (increased asymmetry). 6. Long-term effects could not be inferred directly from instantaneous values of network metrics. Nonetheless, the increased abundance of the generalist stingless bee may both reduce the local level of ecological specialisation in the short term and affect the spatial distribution of less abundant and/or specialist bee species and plants in the long term.     

in silico analyses of metabolic pathway and protein interaction network for identification of next gen therapeutic targets in Chlamydophila pneumoniae

Chlamydophila pneumoniae, the causative agent of chronic obstructive pulmonary disease (COPD), is presently the fifth mortality causing chronic disease in the world. The understanding of disease and treatment options are limited represents a severe concern and a need for better therapeutics. With the advancements in the field of complete genome sequencing and computational approaches development have lead to metabolic pathway analysis and protein-protein interaction network which provides vital evidence to the protein function and has been appropriate to the fields such as systems biology and drug discovery. Protein interaction network analysis allows us to predict the most potential drug targets among large number of the non-homologous proteins involved in the unique metabolic pathway. A computational comparative metabolic pathway analysis of the host H. sapiens and the pathogen C pneumoniae AR39 has been carried out at three level analyses. Firstly, metabolic pathway analysis was performed to identify unique metabolic pathways and non-homologous proteins were identified. Secondly, essentiality of the proteins was checked, where these proteins contribute to the growth and survival of the organism. Finally these proteins were further subjected to predict protein interaction networks. Among the total 65 pathways in the C pneumoniae AR39 genome 10 were identified as the unique metabolic pathways which were not found in the human host, 32 enzymes were predicted as essential and these proteins were considered for protein interaction analysis, later using various criteria''s we have narrowed down to prioritize ribonucleotide-diphosphate reductase subunit beta as a potential drug target which facilitate for the successful entry into drug designing.     

Insights into the molecular regulatory network of pathomechanisms in osteochondroma

Osteochondroma is a benign autosomal dominant hereditary disease characterized by abnormal proliferation of cartilage in the long bone. It is divided into solitary osteochondroma and hereditary multiple exostoses (HMEs). The exostosin-1 (EXT-1) and exostosin-2 (EXT-2) gene mutations are well-defined molecular mechanisms in the pathogenesis of HME. EXT-1 and EXT-2 encode glycosyltransferases that are necessary for the synthesis of heparin sulfate. Accumulating evidence suggests that mutations in the EXT family induce changes in isolated hypogonadotropic hypogonadism-parathyroid hormone-related protein, bone morphogenetic protein, and fibroblast growth factor signaling pathways. Studies have also found that a large number of microRNAs (miRNAs) are abnormally expressed in osteochondroma tissues, and some of them also participate in several major signaling pathways. The regulation of miRNA expression could be another breakthrough in the treatment of osteochondroma. Although the pathogenesis of osteochondroma is very complicated, significant progress has been made in recent years. It is hoped that the pathogenesis of osteochondroma will be clearly understood and the most effective methods for the prevention and treatment of osteochondroma will be determined. This review provides an update on the recent progress in the interpretation of the underlying molecular mechanisms of osteochondroma.     

Developmental sequence of bone-resorbing cells induced by intramuscular implantation of mineral-containing bone particles into rainbow trout,Oncorhynchus mykiss

Mineral-containing bone particles (BPs) were implanted intramuscularly into rainbow trout (Oncorhynchus mykiss) to investigate the sequence of appearance of bone-resorbing cells. A fibrous substance first surrounded the implanted BPs and was gradually replaced by connective tissue containing capillaries. Two weeks after BP implantation, relatively small multinucleated cells (type-1 cells), whose cytoplasm stained deeply with hematoxylin, appeared along the surfaces of the BPs. At later stages (after 4–8 weeks), the majority of cells which appeared to be resorbing the BPs were multinucleated cells whose cytoplasm stained deeply with eosin (type-2 cells). Type-2 cells contained more nuclei than type-1 cells. Electron-microscopical observations revealed that type-2 cells had the characteristic features of osteoclasts: the presence of numerous mitochondria, vacuoles and granules, and a differentiation of the cell membrane and cytoplasm into a ruffled border and clear zone, respectively. A tartrate-resistant acid phosphatase activity, which is an established characteristic of osteoclasts in terrestrial vertebrates, but which had not previously been examined in teleosts, was demonstrated histochemically in the type-2 cells. Development of type-2 cells was closely correlated with the development of connective tissue. These findings suggest that the development of a capillary network around the implanted BPs enables circulating osteoclast-progenitors to reach the surface of the BPs.     

The Short-chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family

The Short-chain Dehydrogenases/Reductases Engineering Database (SDRED) covers one of the largest known protein families (168 150 proteins). Assignment to the superfamilies of Classical and Extended SDRs was achieved by global sequence similarity and by identification of family-specific sequence motifs. Two standard numbering schemes were established for Classical and Extended SDRs that allow for the determination of conserved amino acid residues, such as cofactor specificity determining positions or superfamily specific sequence motifs. The comprehensive sequence dataset of the SDRED facilitates the refinement of family-specific sequence motifs. The glycine-rich motifs for Classical and Extended SDRs were refined to improve the precision of superfamily classification. In each superfamily, the majority of sequences formed a tightly connected sequence network and belonged to a large homologous family. Despite their different sequence motifs and their different sequence length, the two sequence networks of Classical and Extended SDRs are not separate, but connected by edges at a threshold of 40% sequence similarity, indicating that all SDRs belong to a large, connected network. The SDRED is accessible at https://sdred.biocatnet.de/.     

Cytokine array analysis of peritoneal fluid between women with endometriosis of different stages and those without endometriosis

Cytokines are key mediators of intercellular communication and are likely to promote the development and progression of endometriosis. Previous studies provided evidence that endometriosis develops as a result of the pathogenetic factors in the peritoneal environment, especially the peritoneal fluid (PF). We determined different cytokine expression in peritoneal fluid between women with minimal/mild and moderate/severe endometriosis and those without endometriosis using the cytokine array. As a result, 78 cytokines were found to have a threefold change, including 74 increases and four decreases in endometriosis compared with the control group; 96 cytokines had a threefold change including 91 increases and five decreases in minimal and mild endometriosis compared with the control group; 83 cytokines had a threefold change including 14 increases and 69 decreases in moderate and severe endometriosis compared with minimal and mild endometriosis. The cytokine networks were produced by Pathway Studio software and revealed that most cytokines are involved in cell binding, interaction and protein synthesis and transportation regulation. Among them activin A, Smad7 and β-nerve growth factor are the most interesting as they may be involved in the pathogenesis of endometriosis. These results suggest that cytokines are very important factors in the development of endometriosis. The findings of differentially expressed cytokines improves our knowledge of the pathogenesis and development of endometriosis and these findings warrant further studies to develop potential targets for the diagnosis and treatment of endometriosis.