Allele-specific targeting of hsa-miR-657 to human IGF2R creates a potential mechanism underlying the association of ACAA-insertion/deletion polymorphism with type 2 diabetes

The biological mechanism of a recent discovered association of type 2 diabetes with the ACAA-insertion/deletion polymorphism at the 3′UTR of the IGF2R gene has remained unclear. A very recently emerging novel polymorphic control layer by microRNAs (miRNAs) makes it possible to elucidate this issue. In this study, a prediction by web tools MicroInspector and miRanda demonstrated that DNA sequence polymorphism (DSPs) ACAA-insertion/deletion in IGF2R 3′UTR is located within the hsa-miR-657 and hsa-miR-453 binding sites. And luciferase reporter assay revealed that hsa-miR-657 acts directly at the 3′UTR of the IGF2R. Furthermore, ACAA-deletion exerted a further repression compared with ACAA-insertion, indicating that hsa-miR-657 regulates IGF2R gene expression in a polymorphic control manner. Importantly, we also demonstrated that hsa-miR-657 can translationally regulate the IGF2R expression levels in Hep G2 cells. Thus, our findings testify the possibility that the ACAA-insertion/deletion polymorphism may result in the change of IGF2R expression levels at least in part by hsa-miR-657-mediated regulation, contributing to the elucidation for the pathogenesis of type 2 diabetes and raise the possibility that miRNAs or in combination with functional DNA sequence polymorphism may be valuable in the treatment of human type 2 diabetes.     

Rational design of cationic antimicrobial peptides by the tandem of leucine-rich repeat

Antimicrobial peptides represent ancient host defense effector molecules present in organisms across the evolutionary spectrum. Lots of antimicrobial peptides were synthesized based on well-known structural motif widely existed in a variety of lives. Leucine-rich repeats (LRRs) are sequence motifs present in over 60,000 proteins identified from viruses, bacteria, and eukaryotes. To elucidate if LRR motif possesses antimicrobial potency, two peptides containing one or two LRRs were designed. The biological activity and membrane–peptide interactions of the peptides were analyzed. The results showed that the tandem of two LRRs exhibited similar antibacterial activity and significantly weaker hemolytic activity against hRBCs than the well-known membrane active peptide melittin. The peptide with one LRR was defective at antimicrobial and hemolytic activity. The peptide containing two LRRs formed α-helical structure, respectively, in the presence of membrane-mimicking environment. LRR-2 retained strong resistance to cations, heat, and some proteolytic enzymes. The blue shifts of the peptides in two lipid systems correlated positively with their biological activities. Other membrane-peptide experiments further provide the evidence that the peptide with two LRRs kills bacteria via membrane-involving mechanism. The present study increases our new understanding of well-known LRR motif in antimicrobial potency and presents a potential strategy to develop novel antibacterial agents.     

A Simple Evaluation of Soil Quality of Waterlogged Purple Paddy Soils with Different Productivities

Evaluation of soil quality can be crucial for designing efficient farming systems and ensuring sustainable agriculture. The present study aimed at evaluating the quality of waterlogged purple paddy soils with different productivities in Sichuan Basin. The approach involved comprehensive analyses of soil physical and chemical properties, as well as enzyme activities and microbial community structure measured by phospholipid fatty acid analysis (PLFA). A total of 36 soil samples were collected from four typical locations, with 12 samples representing high productivity purple paddy soil (HPPS), medium productivity purple paddy soil (MPPS) and low productivity purple paddy soil (LPPS), respectively. Most measured soil properties showed significant differences (P ≤ 0.05) among HPPS, MPPS and LPPS. Pearson correlation analysis and principal component analysis were used to identify appropriate soil quality indicators. A minimum data set (MDS) including total nitrogen (TN), available phosphorus (AP), acid phosphatase (ACP), total bacteria (TB) and arbuscular mycorrhizal fungi was established and accounted for 82.1% of the quality variation among soils. A soil quality index (SQI) was developed based on the MDS method, whilst HPPS, MPPS and LPPS received mean SQI scores of 0.725, 0.536 and 0.425, respectively, with a ranking of HPPS > MPPS > LPPS. HPPS showed relatively good soil quality characterized by optimal nutrient availability, enzymatic and microbial activities, but the opposite was true of LPPS. Low levels of TN, AP and soil microbial activities were considered to be the major constraints limiting the productivity in LPPS. All soil samples collected were rich in available N, K, Si and Zn, but deficient in available P, which may be the major constraint for the studied regions. Managers in our study area should employ more appropriate management in the LPPS to improve its rice productivity, and particularly to any potential limiting factor.     

Flavobacterium qiangtangensis sp. nov., Isolated from Qiangtang Basin in Qinghai-Tibetan Plateau,China

A flexirubin-type yellow-pigmented, non-gliding, non-flagellated, gram-negative bacterium strain, designated F3^T, was isolated from a drilling core sample of the Qiangtang basin, Qinghai-Tibetan plateau, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain F3^T belongs to the genus Flavobacterium, with the highest 16S rRNA gene sequence similarity to the Flavobacterium noncentrifugens CGMCC 1.10076^T (94.92 %). Strain F3^T grew optimally at temperature about 20 °C, at pH about 7.0–8.0, at NaCl concentration 0 % (w/v). The DNA G+C content of the isolate was 35.5 mol%. The major polar lipid was phosphatidylethanolamine, predominant cellular fatty acids of the strain was iso-C_15:0 (22.02 %), while the major menaquinone was menaquinone 6. Due to the phenotypic and genetic distinctiveness and several other characteristic studied in this article, we consider F3^T as a novel species of the genus Flavobacterium, and propose to name it Flavobacterium qiangtangensis sp. nov. The type strain is F3^T (=CGMCC 1.12706^T = JCM 19739^T).     

Caffeine-induced Ca2+ oscillations in type I horizontal cell of carp retina: A mathematical model

Oscillations in intracellular free Ca²⁺ concentration ([Ca²⁺]_i) have been observed in a variety of cell types. In the present study, we constructed a mathematical model to simulate the caffeine-induced [Ca²⁺]_i oscillations based on experimental data obtained from isolated type I horizontal cell of carp retina. The results of model analysis confirm the notion that the caffeine-induced [Ca²⁺]_i oscillations involve a number of cytoplasmic and endoplasmic Ca²⁺ processes that interact with each other. Using this model, we evaluated the importance of store-operated channel (SOC) in caffeine-induced [Ca²⁺]_i oscillations. The model suggests that store-operated Ca²⁺ entry (SOCE) is elicited upon depletion of the endoplasmic reticulum (ER). When the SOC conductance is set to 0, caffeine-induced [Ca²⁺]_i oscillations are abolished, which agrees with the experimental observation that [Ca²⁺]_i oscillations were abolished when SOC was blocked pharmacologically, verifying that SOC is necessary for sustained [Ca²⁺]_i oscillations.     

An S-Curve-Based Approach of Identifying Biological Sequences

The main idea of S-curve diagram is to assign different angle values (from 0° to 180°) to different nucleotide acid residues or to different protein amino acids, and then according to cos α _j and sin α _j , the values are accumulated to construct an S-curve diagram, which is in strict one-to-one correspondence with the biological sequence. In addition, the S-curve diagram proves to be without the degeneracy phenomenon, so that both the degeneracy problem represented by diagrams and the problem of visualization for biological sequence data are solved. Meanwhile, a new approach to differentiate the similarity of biological sequences—the degree of similarity—is put forward on the basis of the S-curve diagram. To put it in detail, the least square approach is first adopted to obtain a straight line equation according to the S-curve diagram, then according to the distance formula of the point to the straight line, the average ratio of square sum for the distance between the S-curve and the straight line is calculated, and finally, the similarity of the biological sequences is presented by the new standard—the degree of similarity. As is shown by the experimental results, the S-curve diagram can better represent biological sequences (such as protein’s) within Cartesian coordinate system, and the mutation point of biological sequence. Thus, it turns out that the new standard—the degree of similarity is of obviously great advantage.     

MicroRNA-27a Negatively Modulates the Inflammatory Response in Lipopolysaccharide-Stimulated Microglia by Targeting TLR4 and IRAK4

microRNA, a family of small non-coding RNA, plays significant roles in regulating gene expression, mainly via binding to the 3′-untranslated region of target genes. Although the role of miRNA in regulating neuroinflammation via the innate immune pathway has been studied, its role in the production of inflammatory mediators during microglial activation is poorly understood. In this study, we investigated the effect of miR-27a on lipopolysaccharide (LPS)-induced microglial inflammation. miR-27a expression was found to be rapidly decreased in microglia by real-time polymerase chain reaction (real-time PCR) after LPS stimulation. Over-expression of miR-27a significantly decreased the production of inflammatory cytokines, such as interleukin-6 (IL-6), interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and nitric oxide (NO), whereas knockdown of miR-27a increased the expression of these inflammatory factors. We also demonstrated by loss- and gain-of-function studies that miR-27a directly suppressed the expression of toll-like receptor 4 (TLR4) and interleukin-1 receptor-associated kinase 4 (IRAK4)—a pivotal adaptor kinase in the TLR4/MyD88 signaling pathway—by directly binding their 3′-UTRs: knocking down TLR4 or IRAK4 in microglia significantly decreased TLR4 or IRAK4 expression and inhibited the downstream production of inflammatory mediators. Moreover, the inflammatory cytokines IL-6 and IL-1β were regulated by IRAK4, whereas TNF-α and NO were more dependent on TLR4 activation. Thus, miR-27a might regulate the LPS-induced production of inflammatory cytokines in microglia independently of TLR4 and IRAK4. Taken together, our results suggest that miR-27a is associated with microglial activation and the inflammatory response.     

聚乙二醇沉淀剂有效分离尿外泌体

尿外泌体是病毒大小的胞外囊泡,是非侵入性获得肾及泌尿生殖道细胞生理病理信息的重要靶标。聚乙二醇沉淀 剂可经济高效地分离富集血清等外泌体,但未见用于尿外泌体富集的详细报道。本研究采用聚乙二醇沉淀剂分离鉴定尿外泌体,并对其RNA组分进行检测,以期建立一个经济、高效、简便的尿外泌体分离富集方法。采集10例健康志愿者晨尿20 mL,聚乙二醇沉淀剂分离尿外泌体。透射电镜观察到直径30～100 nm双层膜包绕的囊性小泡,中央有直径5～15 nm高电子密度区。Western印迹检测到外泌体标记蛋白CD63、CD9、TSG101、ADAM10和内标蛋白β-肌动蛋白的表达。纳米粒径仪测定粒子直径介于30～130 nm,并可见25.37 nm和95.07 nm二个粒子峰。qRT-PCR扩增得到β-肌动蛋白和RNU6 RNA产物带。上述结果表明,聚乙二醇沉淀剂可分离富集尿外泌体,该法简单、高效,不需要超速离心机等昂贵设备,且采用该法富集到的外泌体可用于后续蛋白质与核酸分析。该方法可望加速液体活检应用,尤其是肾及泌尿生殖道病变的无创检测。