Interrogation of rabbit miRNAs and their isomiRs

Rabbit (Oryctolagus cuniculus) is the only lagomorph animal of which the genome has been sequenced. Establishing a rabbit miRNA resource will benefit subsequent functional genomic studies in mammals. We have generated small RNA sequence reads with SOLiD and Solexa platforms to identify rabbit miRNAs, where we identified 464 pre-miRNAs and 886 mature miRNAs. The brain and heart miRNA libraries were used for further in-depth analysis of isomiR distributions. There are several intriguing findings. First, several rabbit pre-miRNAs form highly conserved clusters. Second, there is a preference in selecting one strand as mature miRNA, resulting in an arm selection preference. Third, we analyzed the isomiR expression and validated the expression of isomiR types in different rabbit tissues. Moreover, we further performed additional small RNA libraries and defined miRNAs differentially expressed between brain and heart. We conclude also that isomiR distribution profiles could vary between brain and heart tissues.     

Disorder transitions and conformational diversity cooperatively modulate biological function in proteins

Structural differences between conformers sustain protein biological function. Here, we studied in a large dataset of 745 intrinsically disordered proteins, how ordered‐disordered transitions modulate structural differences between conformers as derived from crystallographic data. We found that almost 50% of the proteins studied show no transitions and have low conformational diversity while the rest show transitions and a higher conformational diversity. In this last subset, 60% of the proteins become more ordered after ligand binding, while 40% more disordered. As protein conformational diversity is inherently connected with protein function our analysis suggests differences in structure‐function relationships related to order‐disorder transitions.     

Cell-mediated and glucocorticoid-mediated target cell lysis do not appear to share common pathways

Target cell lysis by cytolyic lymphocytes follows a sequence of events that culminate in osmotic destruction of the target. Although it is clear that killer cell derived components play a crucial role in target cell lysis it is not clear to what extent the target itself is involved in its destruction. Recent observations have pointed to the possibility that glucocorticoid mediated and cell mediated lysis may utilize common pathways of cell lysis. In analyzing this question we found that cell lines that have nonfunctional glucocorticoid receptors like S49-78 and S49-88 are good targets for both NK and thymus-derived killer (TK) cells. Cell lines that are glucocorticoid sensitive such as Q1(4)6 are sensitive to NK-mediated lysis as its derivative HL4-6-3 which contains glucocorticoid receptors but is glucocorticoid resistant. An intriguing exception to this is the glucocorticoid-resistant mutant S49-4RD which is relatively resistant to both NK and TK lysis compared with parent S49. The resistance of S49-4RD to cell-mediated lysis we show here is most likely due to a defect in the target which results in its failure to trigger the cytolytic machinery in the killer cell rather than in its resistance to lysis per se. In support of this we demonstrate that lysis of S49-4RD by cytolytic granules from TK cells is normal. Moreover TK cells lyse S49-4RD as efficiently as its parent in the presence of the lectin Con A. The conclusion that S49-4RD has a defect in its ability to induce killer cells to initiate the cytolytic reaction is also in agreement with the finding that TK-S49-4RD conjugates show inefficient reorientation of the Golgi apparatus in the effector.     

MicroRNA与肿瘤相关的信号转导通路

信号转导通路在细胞代谢、生长、增殖、应激、发育和凋亡等生命活动中具有极为重要的作用。干扰这些通路将可能影响细胞的正常发育, 甚至导致肿瘤。MicroRNA(miRNA)是近年来在真核生物中发现的、在转录后水平负调节基因表达的一类长度约22个核苷酸的非编码小RNA, 其靶基因数目众多, 生物学功能广泛。在多种肿瘤中发现了miRNA的异常表达, 提示后者与肿瘤发生有关, 可能机制为调控癌基因或肿瘤抑制基因的表达。此外亦发现miRNA的靶基因有许多作用于肿瘤相关的信号转导通路。miRNA在肿瘤发生过程中的重要调控功能预示其将成为人类癌症诊断和治疗方面的新星。     

A dictionary on microRNAs and their putative target pathways

While in the last decade mRNA expression profiling was among the most popular research areas, over the past years the study of non-coding RNAs, especially microRNAs (miRNAs), has gained increasing interest. For almost 900 known human miRNAs hundreds of pretended targets are known. However, there is only limited knowledge about putative systemic effects of changes in the expression of miRNAs and their regulatory influence. We determined for each known miRNA the biochemical pathways in the KEGG and TRANSPATH database and the Gene Ontology categories that are enriched with respect to its target genes. We refer to these pathways and categories as target pathways of the corresponding miRNA. Investigating target pathways of miRNAs we found a strong relation to disease-related regulatory pathways, including mitogen-activated protein kinase (MAPK) signaling cascade, Transforming growth factor (TGF)-beta signaling pathway or the p53 network. Performing a sophisticated analysis of differentially expressed genes of 13 cancer data sets extracted from gene expression omnibus (GEO) showed that targets of specific miRNAs were significantly deregulated in these sets. The respective miRNA target analysis is also a novel part of our gene set analysis pipeline GeneTrail. Our study represents a comprehensive theoretical analysis of the relationship between miRNAs and their predicted target pathways. Our target pathways analysis provides a ‘miRNA-target pathway’ dictionary, which enables researchers to identify target pathways of differentially regulated miRNAs.     

单羧酸转运蛋白家族及其生物学功能

单羧酸转运蛋白家族是哺乳动物细胞膜上一类重要的跨膜转运蛋白,负责乳酸,短链脂肪酸等单羧酸类化合物的跨膜转运,涉及多种生物学功能,包括促进营养物质吸收、影响代谢动态平衡、调节胞内pH值以及参与药物输送等.迄今为止,单羧酸转运蛋白家族已发现有1 4个成员,各亚型间具有底物差异性和组织分布特异性.研究单羧酸转运蛋白家族的生化特征、组织分布、生物学功能及基因表达调控,将为人和动物的营养代谢稳衡和疾病治疗提供新的方法.     

Characterization of cadmium-responsive MicroRNAs and their target genes in maize (Zea mays) roots

MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness. Considering that miRNAs can modulate gene expression, this study was designed to identify differentially expressed miRNAs that could be modulating biological processes involved with beef tenderness. Deep sequence analysis of miRNA libraries from longissimus thoracis muscle allowed the identification of 42 novel and 308 known miRNAs. Among the known miRNAs, seven were specifically expressed in skeletal muscle. Differential expression analysis between animals with high (H) and low (L) estimated breeding values for shear force (EBVSF) revealed bta-mir-182 and bta-mir-183 are up-regulated (q value < 0.05) in animals with L EBVSF, and bta-mir-338 is up-regulated in animals with H EBVSF. The number of bovine predicted targets for bta-mir-182, bta-mir-183 and bta-mir-338 were 811, 281 and 222, respectively, which correspond to 1204 unique target genes. Among these, four of them, MEF2C, MAP3K2, MTDH and TNRC6B were common targets of the three differentially expressed miRNAs. The functional analysis identified important pathways related to tenderness such as apoptosis and the calpain–calpastatin system. The results obtained indicate the importance of miRNAs in the regulatory mechanisms that influence muscle proteolysis and meat tenderness and contribute to our better understanding of the role of miRNAs in biological processes associated with beef tenderness.     

Mechanisms common to biological macromolecules and gels

Functional Biological macromolecules arising from folding, cross-connection and solvation of long chain biopolymers forming three-dimensional networks may be regarded as Gels. Both involve identical internal competitive forces that are selectively influenced by external conditions and conspire to adjust conformations and modulate activities. In spite of important differences in size, chemical composition, polymer bonding, density and configuration, biological macromolecules indeed manifest some of the essential physical-chemical properties of gels when involved in equilibria and rate processes. This result represents a presumptive evidence for common underlying mechanisms in functional molecules and gels. Thus, the present and highly perfectible model explains why and how, depending on initial conditions, a system may respond differently to an external parameter, and similarly to different parameters. Moreover, the fact that any localized change in one of the competitive forces gives to a pressure in the system as a whole provides an explanation for the mechanism of the transmission of information.     

From biological pathways to regulatory networks

This paper presents a general theoretical framework for generating Boolean networks whose state transitions realize a set of given biological pathways or minor variations thereof. This ill-posed inverse problem, which is of crucial importance across practically all areas of biology, is solved by using Karnaugh maps which are classical tools for digital system design. It is shown that the incorporation of prior knowledge, presented in the form of biological pathways, can bring about a dramatic reduction in the cardinality of the network search space. Constraining the connectivity of the network, the number and relative importance of the attractors, and concordance with observed time-course data are additional factors that can be used to further reduce the cardinality of the search space. The networks produced by the approaches developed here should facilitate the understanding of multivariate biological phenomena and the subsequent design of intervention approaches that are more likely to be successful in practice. As an example, the results of this paper are applied to the widely studied p53 pathway and it is shown that the resulting network exhibits dynamic behavior consistent with experimental observations from the published literature.     

Cytotoxic T lymphocyte-induced loss of target cell adhesion and lysis involve common and separate signaling pathways

Recently, we demonstrated that an early event in the CTL-target cell (TC) interaction is loss of TC adherence to substrate. This loss of adhesion is Ag-specific, but distinct from the lytic event because it can ensue in nominally Ca2+-free medium. In this study, we examine further the mechanism of CTL-induced loss of adhesion, concentrating mainly on the signal transduction pathway. Based on the differential sensitivity of CTL to extracellular Ca2+, protein kinase C activation/depletion and inhibition by anti-Lyt-2 (CD8) or anti-CTL receptor (TCR) reagents, we demonstrate that CTL-induced loss of adhesion can be initiated through multiple activation pathways. Although CTL-mediated lysis is restricted to a Ca2+ and protein kinase C-dependent signaling mechanism, CTL-induced loss of adhesion is initiated in the presence or absence of extracellular Ca2+ or functional protein kinase C activity. Furthermore, although under physiologic conditions, anti-CD8 or anti-TCR reagents strongly block both CTL activities, under non-lytic conditions, they fail to inhibit the ability of CTL to promote loss of adhesion. These findings implicate the participation of additional CTL-TC ligand interactions resulting in loss of adhesion, and thus, provide further evidence to support the hypothesis that CTL-induced loss of adhesion can be initiated through multiple triggering pathways.     

MicroRNAs and their role in viral infection

Recently, a class of about 22 nucleotides (nt) small RNA has been discovered in many eukaryotes, termed microRNAs (miRNAs), which have a variety of functions. Many recent findings have demonstrated that viruses can also encode their own miRNAs. Meanwhile, other findings reveal a relationship between host miRNA and viral infection. These findings suggest a tight relationship between host and viral infection via miRNA pathway. This article introduces the miRNAs encoded by viruses and reviews the advances of the interaction of the mammalian host miRNAs and viral infection.     

MicroRNAs and their role in viral infection

Recently,a class of about 22 nucleotides (nt)small RNA has been discovered in many eukaryotes,termed microRNAs (miRNAs),which have a variety of functions.Many recent findings have demonstrated that viruses can also encode their own miRNAs.Meanwhile,other findings reveal a relationship between host miRNA and viral infection.These findings suggest a tight relationship between host and viral infection via miRNA pathway.This article introduces the miRNAs encoded by viruses and reviews the advances of the interaction of the mammalian host miRNAs and viral infection.