计算识别microRNA及其靶基因

小RNA的发现为基因调控系统研究提供了新的方向。在多数物种中已经发现了大量的小RNA。这一领域已经成为了近来研究的热点,在研究起始阶段,计算学方法已经成为实验研究中不可或缺的工具,许多发现是由生物学实验与计算学方法共同合作来完成的。在这篇综述中,我们总结了前人关于小RNA及其靶基因识别的理论知识。最后,讨论了关于预测小RNA及其靶基因的计算学方法和相关软件。     

Genome Editing in Methanotrophic Bacteria: Potential Targets and Available Tools

Microbiology - Aerobic methanotrophic bacteria are prokaryotic microorganisms possessing methane monooxygenases, unique enzymes that determine their ability to utilize methane (CH4) as a growth...     

Macrophages Recognize Size and Shape of Their Targets

Recognition by macrophages is a key process in generating immune response against invading pathogens. Previous studies have focused on recognition of pathogens through surface receptors present on the macrophage''s surface. Here, using polymeric particles of different geometries that represent the size and shape range of a variety of bacteria, the importance of target geometry in recognition was investigated. The studies reported here reveal that attachment of particles of different geometries to macrophages exhibits a strong dependence on size and shape. For all sizes and shapes studied, particles possessing the longest dimension in the range of 2–3 µm exhibited highest attachment. This also happens to be the size range of most commonly found bacteria in nature. The surface features of macrophages, in particular the membrane ruffles, might play an important role in this geometry-based target recognition by macrophages. These findings have significant implications in understanding the pathogenicity of bacteria and in designing drug delivery carriers.     

Identification of microRNAs,phasiRNAs and Their Targets in Pineapple

MicroRNAs (miRNAs) are small non-coding RNAs that regulate their target mRNA levels by directing cleavage or repressing its translation. Besides its outstanding nutritional and medicinal significances, pineapple serves as a model for studying genome evolution in cereal crops as well as obligate crassulacean acid metabolism (CAM) photosynthesis. Thus, studying miRNAs in pineapple is critical for better understanding their roles in this plant species. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in pineapple by analyzing small RNA profiles from flowers, fruits and leaves. The analyses have identified 131 conserved miRNAs that could be grouped into 37 families and 16 novel miRNAs. Three TAS3 loci and forty five 21 nucleotide (nt) PHAS loci, and seventy three 24 nt PHAS loci were also identified. The putative targets of the identified miRNAs and phasiRNAs were predicted. The presented results provide a comprehensive view of small regulatory RNAs and their targets in pineapple.     

大蒜内生细菌的分离及拮抗菌筛选与鉴定

利用常规分离方法对大蒜鳞茎进行内生细菌的分离,采用对峙法和平板涂布法对分离的内生菌进行拮抗试验研究,并对菌株DSP6进行16S rDNA全序列鉴定。结果表明:分离得到19株内生细菌,其中10株菌对2种以上植物病原真菌有不同程度的抑制作用,占分离菌总数的52.6%,DSN7对番茄早疫病的抑菌圈半径最大,为13mm;17株菌对5种病原细菌中至少1种有抑制作用,占分离菌总数的89.5%,其中菌株DSP3对大肠杆菌的抑菌圈半径最大,达到10 mm;菌株DSP6对供试的9种病原菌有较强的抑菌作用,且抑菌圈平均半径最大,为6.88mm;16S rDNA全序列鉴定显示,菌株DSP6与芽孢杆菌属Bacillus axarquiensis相似性为100%,表明菌株DSP6为Bacillus axarquiensis。     

The Genetic Improvement of Entomopathogenic Nematodes and Their Symbiont Bacteria: Phenotypic Targets, Genetic Limitations and an Assessment of Possible Hazards

The methodologies of classical genetics and genetic engineering can be used for the genetic improvement of entomopathogenic nematodes (EPNs) and their symbiont bacteria. Many of the complex behavioural and physiological traits which are targets for genetic improvement are likely to be controlled polygenically, thus selective breeding for improvements to these traits would be appropriate. Much basic research needs to be carried out before researchers will be able to effect improvements to EPNs and their symbionts by genetic engineering. There is a lack of basic information on the genetics and biochemistry of the characteristics that might be altered by transgenic methods in EPNs, and their bacteria, and existing transformation protocols need to be made more effective.     

附睾小体功能蛋白及sRNA研究进展

精液质量是反映男性生殖健康最基本和最重要的指标。哺乳动物的精子需在附睾中经历一系列复杂的结构与功能的变化才能成熟并具有潜在受精能力。精子成熟是由大量转录因子、激素等信号分子协同调控的复杂生理过程。近年来越来越多的证据表明附睾小体(epididymosomes)中的功能蛋白和sRNAs(small RNAs)可参与调节精子成熟及受精等过程。本文主要综述了附睾小体中功能蛋白及两类主要的sRNAs(tRNAs和miRNAs)的生物学作用,以期为男性不育等疾病的治疗提供一定的理论指导和新的治疗思路。     

Predicting Chemical Environments of Bacteria from Receptor Signaling

Sensory systems have evolved to respond to input stimuli of certain statistical properties, and to reliably transmit this information through biochemical pathways. Hence, for an experimentally well-characterized sensory system, one ought to be able to extract valuable information about the statistics of the stimuli. Based on dose-response curves from in vivo fluorescence resonance energy transfer (FRET) experiments of the bacterial chemotaxis sensory system, we predict the chemical gradients chemotactic Escherichia coli cells typically encounter in their natural environment. To predict average gradients cells experience, we revaluate the phenomenological Weber''s law and its generalizations to the Weber-Fechner law and fold-change detection. To obtain full distributions of gradients we use information theory and simulations, considering limitations of information transmission from both cell-external and internal noise. We identify broad distributions of exponential gradients, which lead to log-normal stimuli and maximal drift velocity. Our results thus provide a first step towards deciphering the chemical nature of complex, experimentally inaccessible cellular microenvironments, such as the human intestine.     

Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations

Temporal lobe epilepsy (TLE) is a prevalent neurological disorder resulting in disruptive seizures. In the case of drug resistant epilepsy resective surgery is often considered. This is a procedure hampered by unpredictable success rates, with many patients continuing to have seizures even after surgery. In this study we apply a computational model of epilepsy to patient specific structural connectivity derived from diffusion tensor imaging (DTI) of 22 individuals with left TLE and 39 healthy controls. We validate the model by examining patient-control differences in simulated seizure onset time and network location. We then investigate the potential of the model for surgery prediction by performing in silico surgical resections, removing nodes from patient networks and comparing seizure likelihood post-surgery to pre-surgery simulations. We find that, first, patients tend to transit from non-epileptic to epileptic states more often than controls in the model. Second, regions in the left hemisphere (particularly within temporal and subcortical regions) that are known to be involved in TLE are the most frequent starting points for seizures in patients in the model. In addition, our analysis also implicates regions in the contralateral and frontal locations which may play a role in seizure spreading or surgery resistance. Finally, the model predicts that patient-specific surgery (resection areas chosen on an individual, model-prompted, basis and not following a predefined procedure) may lead to better outcomes than the currently used routine clinical procedure. Taken together this work provides a first step towards patient specific computational modelling of epilepsy surgery in order to inform treatment strategies in individuals.     

Allelopathic Bacteria and Their Impact on Higher Plants

The impact of allelopathic, nonpathogenic bacteria on plant growth in natural and agricultural ecosystems is discussed. In some natural ecosystems, evidence supports the view that in the vicinity of some allelopathically active perennials (e.g., Adenostoma fasciculatum, California), in addition to allelochemicals leached from the shrub's canopy, accumulation of phytotoxic bacteria or other allelopathic microorganisms amplify retardation of annuals. In agricultural ecosystems allelopathic bacteria may evolve in areas where a single crop is grown successively, and the resulting yield decline cannot be restored by application of minerals. Transfer of soils from areas where crop suppression had been recorded into an unaffected area induced crop retardation without readily apparent symptoms of plant disease. Susceptibility of higher plants to deleterious rhizobacteria is often manifested in sandy or so-called skeletal soils. Evaluation of phytotoxic activity under controlled conditions, as well as ways to apply allelopathic bacteria in the field, is approached. The allelopathic effect may occur directly through the release of allelochemicals by a bacterium that affects susceptible plant(s) or indirectly through the suppression of an essential symbiont. The process is affected by nutritional and other environmental conditions, some may control bacterial density and the rate of production of allelochemicals. Allelopathic nonpathogenic bacteria include a wide range of genera and secrete a diverse group of plant growth-mediating allelochemicals. Although a limited number of plant growth-promoting bacterial allelochemicals have been identified, a considerable number of highly diversified growth-inhibiting allelochemicals have been isolated and characterized. Some species may produce more than one allelochemical; for example, three different phyotoxins, geldanamycin, nigericin, and hydanthocidin, were isolated from Streptomyces hygroscopicus. Efforts to introduce naturally produced allelochemicals as plant growth-regulating agents in agriculture have yielded two commercial herbicides, phosphinothricin, a product of Streptomyces viridochromogenes, and bialaphos from S. hygroscopicus. Many species of allelopathic bacteria that affect growth of higher plants are not plant specific, but some do exhibit specificity; for example, dicotyledonous plants were more susceptible to Pseudomonas putida than were monocotyledons. Differential susceptibility of higher plants to allelopathic bacteria was noted also in much lower taxonomical categories, at the subspecies level, in different cultivars of wheat, or of lettuce. Therefore, when test plants are employed to evaluate bacterial allelopathy, final evaluation must include those species that are assumed to be suppressed in nature. The release of allelochemicals from plant residues in plots of ‘continuous crop cultivation’ or from allelopathic living plants may induce the development of specific allelopathic bacteria. Both the rate by which a bacterium gains from its allelopathic activity through utilizing plant excretions, and the reasons for the developing of allelopathic bacteria in such habitats, are important goals for further research.     

深海细菌及其适压机制

深海是以高压为主要特征的极端环境。在深海中适压生活的细菌在分类上多属于蛋白细菌(Pro-teobacteria)类群的γ分支。深海细菌对高压的适应可表现为嗜压或耐压,其适压的机制包括细胞膜脂成分中不饱和脂肪酸的增加,此外,细菌细胞的呼吸链系统也与耐压有关。     

Bromodomains：表观遗传医学新靶点及其抑制剂

Bromodomains（BRDs）是一类能够特异性识别乙酰化赖氨酸残基的保守蛋白结构域,存在于染色质及与转录相关的蛋白 中,其功能包括染色质重塑和转录调控,并在细胞内由乙酰化介导的蛋白-蛋白相互作用中发挥极为重要的作用,是多种疾病（包括癌 症、炎症和自身免疫病）的表观遗传医学靶点。介绍BRDs 的生物学功能、结构及分类,主要从BET bromodomain 抑制剂和非BET bromodomain 抑制剂两个方面对BRDs 抑制剂的研究进展作一综述,为高活性和选择性的BRDs 抑制剂研发提供参考。     

Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress

Salinity is a major limiting factor for agricultural production worldwide. A better understanding of the mechanisms of salinity stress response will aid efforts to improve plant salt tolerance. In this study, a combination of small RNA and mRNA degradome sequencing was used to identify salinity responsive-miRNAs and their targets in barley. A total of 152 miRNAs belonging to 126 families were identified, of which 44 were found to be salinity responsive with 30 up-regulated and 25 down-regulated respectively. The majority of the salinity-responsive miRNAs were up-regulated at the 8h time point, while down-regulated at the 3h and 27h time points. The targets of these miRNAs were further detected by degradome sequencing coupled with bioinformatics prediction. Finally, qRT-PCR was used to validate the identified miRNA and their targets. Our study systematically investigated the expression profile of miRNA and their targets in barley during salinity stress phase, which can contribute to understanding how miRNAs respond to salinity stress in barley and other cereal crops.