Pathway analysis identifies perturbation of genetic networks induced by butyrate in a bovine kidney epithelial cell line

Ruminant species have evolved to metabolize the short-chain volatile fatty acids (VFA), acetate, propionate, and butyrate, to fulfill up to 70% of their nutrient energy requirements. The inherent VFA dependence of ruminant cells was exploited to add a level of increased sensitivity to the study of the role of butyrate gene-response elements in regulatory biochemical pathways. Global gene expression profiles of the bovine kidney epithelial cells regulated by sodium butyrate were investigated with high-density oligonucleotide microarrays. The detailed mechanisms by which butyrate induces cell growth arrest and apoptosis were analyzed using the Ingenuity Pathways Knowledge Base. The functional category and pathway analyses of the microarray data revealed that four canonical pathways (Cell cycles: G2/M DNA damage checkpoint, and pyrimidine metabolism; G1/S checkpoint regulation and purine metabolism) were significantly perturbed. The biologically relevant networks and pathways of these genes were also identified. IGF2, TGFB1, TP53, E2F4, and CDC2 were established as being centered in these genomic networks. The present findings provide a basis for understanding the full range of the biological roles and the molecular mechanisms that butyrate may play in animal cell growth, proliferation, and energy metabolisms. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. Mention of trade names or commercial products in this publication is solely for providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.     

Cloning of two classes of PR genes and the development of SNAP markers for powdery mildew resistance loci in chestnut rose (<Emphasis Type="Italic">Rosa roxburghii</Emphasis> Tratt)

Pathogenesis-related (PR) genes were isolated from chestnut rose (Rosa roxburghii Tratt) using a PCR approach with degenerate primers designed for the conserved regions of two PR gene families: class 2 (β-1,3-glucanase) and class 5 (osmotin). Thirteen PR2 and ten PR5 genes were obtained, with a nucleotide identity that ranged from 40.1 to 99.7% and from 99.2 to 99.8%, respectively. Sequence comparison revealed the presence of single nucleotide polymorphisms (SNPs) in these sequences with, on an average, one SNP in every 64-bp fragment for the PR2 genes and one in every 68-bp fragment for the PR5 genes. A total of 23 primers were used to genotype these SNPs for use in developing single nucleotide-amplified polymorphisms (SNAP) markers. One marker (Glu7) was found to be linked to powdery mildew resistance loci. Based on genetic mapping of a segregating F₁ population, we determined that 16 of the 23 SNAP markers formed one group and subsequently detected a quantitative trait locus that accounted for 12% of the variation in the powdery mildew resistance phenotype. The results of this study provide a first insight into the genomic structure of PR genes and show that the candidate gene approach in combination with SNAP markers is an attractive strategy to search for powdery mildew resistance loci in chestnut rose.     

A bioinformatics approach to identifying tail-anchored proteins in the human genome

Intracellular proteins with a carboxy-terminal transmembrane domain and the amino-terminus oriented toward the cytosol are known as 'tail-anchored' proteins. Tail-anchored proteins have been of considerable interest because several important classes of proteins, including the vesicle-targeting/fusion proteins known as SNAREs and the apoptosis-related proteins of the Bcl-2 family, among others, utilize this unique membrane-anchoring motif. Here, we use a bioinformatic technique to develop a comprehensive list of potentially tail-anchored proteins in the human genome. Our final list contains 411 entries derived from 325 unique genes. We also analyzed both known and predicted tail-anchored proteins with respect to the amino acid composition of the transmembrane segments. This analysis revealed a distinctive composition of the membrane anchor in SNARE proteins.     

Photo-luminescent hydroxyapatite coatings through a bio-mimetic process

Hydroxyapatite (HAp) is the major inorganic component in natural bones. Because HAp has the advantages of excellent biocompatibility, free of cell toxicity, and forming strong bonding to bone osteoinductively, it has been widely studied and prepared in many forms for orthopedic and dental applications. In the recent years, silicon based bio-chip was extensively studied. To improve the biocompatibility and search for novel application of bio-chip are not only an important aim but also a challenge. In the previous literatures, it's reported that HAp is relatively difficult to be coated onto a Si(1 0 0) substrate. In this study, we successfully manufactured crystalline HAp on to Si(1 0 0) using simplified supersaturated solution and investigated the structural characteristics through the measurements of XRD, FTIR, FE-SEM, and XPS. The photo-luminescent properties of the coatings were also studied.     

Calmodulin-dependent activation of calcineurin by chlorogenic acid

Chlorogenic acid (CGA) has been proved to be an activator of calcineurin (CN) in our previous research. In this study, the activation mechanism of CN by CGA was further explored. The results showed that although the purified CN was inactive in vitro if only Ca(2+)/calmodulin (CaM) existed without Mn(2+)/Ni(2+), CGA activated the inactive CN potently. It was found that CN's activity increased as the concentration of CGA increased and reached a plateau of 4- to 6-fold higher activity using p-nitrophenyl phosphate (pNPP) or phosphopeptide (32)P-RII as substrate. And the activation was CaM-dependent. Moreover, the fluorescent emission of CN had a 17 nm red shift in the presence of 128 muM CGA, and the quenching constant was 1.21x10(12) M(-1) . s(-1), which indicated that CGA bound to CN statically and changed its conformation. According to the kinetic analysis, CGA preferred to activate CN in a substrate noncompetitive manner. When Mn(2+) or Ni(2+) presented, CGA also activated CN with CaM-dependency by improving CN's affinity for Mn(2+) or Ni(2+). In addition, the inhibition of CN by Zn(2+) was partially eliminated by CGA chelation. Our findings suggested the activation of CN by CGA was in a CaM-dependent and substrate noncompetitive manner. This might provide the basis for the further study of CN-targeted activators.     

乌勇布拉克盐湖嗜盐古菌絮凝效果筛选及活性检测

【目的】从嗜盐古菌中筛选可产生生物絮凝剂的菌株,对发酵液、上清液、菌悬液、胞外聚合物的絮凝作用进行检测,筛选能够适应高盐废水处理,且具有广谱盐度及pH作用范围的微生物絮凝剂。【方法】以新疆乌勇布拉克干盐湖沉积物为研究对象,利用纯培养方法对嗜盐古菌进行分离,对絮凝菌株进行初筛及16S rRNA基因测序,构建系统进化树,初步判断菌株分类地位;复筛检测不同生物材料的絮凝效果;选择絮凝效果较好的生物材料,检测其盐度、pH的絮凝效果稳定性。【结果】采用纯培养方法共分离到28株嗜盐古菌,絮凝初筛共筛选出16株嗜盐古菌,分布于碱线菌属(Natrinema)、盐缓长菌属(Halopiger)和盐土生菌属(Haloterrigena)。菌株发酵液、上清液、菌悬液、胞外聚合物具有不同程度的絮凝效果。菌株A279-1、A133、RP33、NGA0064、RM-152、A389的发酵液、上清液的絮凝效果较好,其中菌株A389的发酵液絮凝率为61.06%,上清液为67.92%。所有菌株菌悬液的絮凝率达到80%以上。菌株所产胞外聚合物表现出较好的絮凝效果,菌株RM-152所产胞外聚合物的絮凝率最高,达89.86%,其次是A389 (81.53%)。菌株A389所产胞外聚合物的产量最大,达12.53 g/L,具有广泛的盐度和pH适应性。【结论】乌勇布拉克干盐湖沉积物中蕴含丰富的可产生微生物絮凝剂的嗜盐古菌资源。嗜盐古菌菌株发酵液、上清液、菌悬液及胞外聚合物均具有良好的絮凝作用,尤其是胞外聚合物表现出较好的絮凝效果,具有广谱的盐度和pH耐受性。嗜盐古菌所产生物絮凝剂的发现对于后续高盐废水功能材料开发具有重要应用价值。     

Oxygen isotope temperature calibrations for modern Tridacna shells in western Pacific

Coral Reefs - The oxygen isotope ratio of carbonate in Tridacna shell (δ18Oshell) is assumed to be precipitated in isotopic equilibrium with surrounding seawater and thus reflects a...     

The branch-thorn occurrence of Lycium ruthenicum is associated with leaf DNA hypermethylation in response to soil water content

Molecular Biology Reports - Lycium ruthenicum is an eco-economic shrub which can exist in two forms, thorny and thornless under varying soil moisture conditions. The aim of this study was to...