miRNA qPCR检测方法研究进展及其应用

miRNA是目前国际研究的热点领域之一,而miRNA表达检测是miRNA研究的基础内容。针对miRNA序列短小的特点,开发出了多种检测方法,其中miRNA qPCR定量检测是应用最广泛的方法。就miRNA抽提,miRNA qPCR定量检测原理及miRNA qPCR定量检测流程包括引物设计、反应体系设置、内参基因筛选等方面进行了深入探讨,并对miRNA定量检测研究方法的发展趋势进行了展望,以期为研究者进行miRNA qPCR定量检测提供参考。     

单细胞真核生物的miRNA系统及其进化意义

miRNA 系统在高等多细胞真核生物中得到了广泛深入的研究。近年来,人们在单细胞真核生物上的miRNA研究也取得了重要进展。这不仅丰富了人们对miRNA在整个生物界中的认识,更重要的是对于揭示miRNA这一表达调节系统是如何在生物界中起源进化的问题具有重要意义。该文结合作者在最低等单细胞真核生物——贾第虫上的研究结果,对该领域的研究进展作一概述,并对有关miRNA这一系统的起源进化问题进行了探讨。     

miRNA定量检测方法的研究进展

MicroRNA(miRNA)是广泛存在于真核生物当中的一类长度为18～25个核苷酸的小分子RNA,由DNA转录产生。作为一种内源性非编码小分子RNA, mi RNA在许多生命活动中起着重要作用,如当机体内的某些mi RNA表达下调时,就会更容易罹患癌症和其他一系列疾病。这一现象提示,人们可通过对mi RNA进行定量检测来实现对相关疾病的早期诊断。本文综述了基于杂交、扩增和测序原理的mi RNA检测技术的研究进展,并对mi RNA的研究方法及方向予以了阐述。     

miRNA在植物发育与环境适应性中的作用

植物miRNA是广泛分布于植物基因组的非编码小分子RNA．是真核生物基因表达的一类负调控因子,主要通过指导靶基因的切割或降低靶基因的翻译从转录后水平上来抑制植物基因表达．从而影响植物形态发生、发育过程和适应环境的能力。本文综述了植物miRNA形成、作用机理、功能等方面研究的最新进展,总结了现有miRNA研究方法的优缺点,提出了miRNA在植物适应养分和元素毒害胁迫过程中的调节作用．拓宽了该领域研究的思路。     

植物microRNA的生物信息学预测与分析

microRNAs(miRNAs)是一类广泛存在于真核生物中调控基因转录后表达的非编码小分子RNA。大量研究表明,miRNA在调节多种生物途径中起着重要的作用,采用生物信息学方法预测与分析miRNA是当前发现和鉴定植物miRNA的重要策略之一。研究内容总结了生物信息学预测植物miRNA及其靶基因的方法策略,阐述了生物信息学在植物miRNA研究中的重要作用,为今后的研究奠定了基础。     

miRNA及其功能

microRNA(miRNA,微RNA)是近年来才引起广泛关注的在真核生物中发现的一类5′端带磷酸基团,3′端带羟基长度为22nt左右的内源性非编码调控RNA。新的miRNA的寻找以及它们的生物起源、作用机制以及功能等研究工作正处于积极的进展之中。     

微RNA在肿瘤发病相关信号通路中的作用

微RNA(microRNA,miRNA)是一类长约20～22nt的单链非编码RNA,它广泛存在于真核生物中并具有多种生物学功能。研究发现,miRNA在多种肿瘤细胞中表达异常,提示miRNA可能与肿瘤发生有关。MiRNA可以调控其靶基因参与的信号通路,而信号通路的异常和紊乱则在肿瘤的发生中起至关重要的作用。因此,有关miRNA调控信号通路的研究将为肿瘤的诊断和治疗带来福音。     

哺乳动物早期发育相关microRNAs的研究进展

本文简要总结了近年来哺乳动物早期发育相关microRNA(miRNA)的研究进展。miRNA是真核生物中一类长度约为18～25 nt的内源性非编码单链小RNA分子,其调控基因表达是近年来在动植物体内发现的一种新的生物学调节机制。通过荧光定量PCR检测、miRNA的过表达、抑制或基因敲除实验以及生物信息学分析等发现,miRNA在哺乳动物植入前胚胎前的发育过程中有重要作用,参与胚胎细胞的增殖、分化、基因印记以及重编程甲基化等,与动物生殖或发育异常相关,是表观遗传学的研究热点之一。     

人源microRNA前体的全基因组预测

microRNA（miRNA）是一类不编码蛋白的调控小分子RNA,在真核生物中发挥着广泛而重要的调控功能.由于miRNA的表达具有时空特异性,因而通过计算方法预测miRNA而后有针对性的实验验证是miRNA发现的一条重要途径.降低假阳性率是miRNA预测方法面临的重要挑战.本研究采用集成学习方法构建预测miRNA前体的分类器SVMbagging,对训练集、测试集和独立测试集的结果表明,本研究的方法性能稳健、假阳性率低,具有很好的泛化能力,尤其是当阈值取0.9时,特异性高达99.90%,敏感性在26%以上,适合于全基因组预测.采用SVMbagging在人全基因组中预测miRNA前体,当取阈值0.9时,得到14933个可能的miRNA前体.通过与高通量小RNA测序数据的比较,发现其中4481个miRNA前体具有完全匹配的小RNA序列,与理论估计的真阳性数值非常接近.最后,对32个可能的miRNA进行实验验证,确定其中2条为真实的miRNA.     

昆虫microRNA的研究进展

MicroRNA (miRNA)是20世纪90年代发现的一类由内源基因编码的长度约21~24 nt的非编码单链RNA分子, 广泛存在于真核生物中, 对基因的转录后调控起着非常重要的作用。本文简要介绍了miRNA的产生与调控机制, 同时从昆虫miRNA的发现鉴定、 靶基因预测与功能验证, 昆虫miRNA的序列特征与进化, 果蝇和非果蝇类昆虫miRNA生物学功能以及供昆虫miRNA研究的网络平台等方面对昆虫miRNA的最新进展进行了综述, 旨在为进一步研究昆虫miRNA提供借鉴和参考。对昆虫miRNA的研究表明其参与调控细胞分化、 增殖及凋亡、 胚胎发育、 器官发生、 形态构建、 生理代谢、 环境协调、 行为认知、 免疫防御等几乎所有的生物过程。因此, 深入研究其生物功能、 调控网络和开发应用等可能成为今后一段时间昆虫miRNA研究的重要内容。     

Frequencies of paired open-closed durations of ion channels. Method of evaluation from single-channel recordings.

The probability of the occurrence of consecutive closed-open or open-closed intervals of specified durations in single-channel recordings may be of enormous help in the establishment of the kinetic scheme that describes the behavior of the channel. The relevant probability functions are linear combinations of products of exponential functions of the closed durations and the open durations. A method is presented for the evaluation of the coefficients of the exponential functions using a set of auxiliary functions that are each orthogonal to all but one of the exponential functions. The coefficients in the probability functions may then be obtained from the experimental data by multiplication by the auxiliary functions and subsequent simple integration operations. Furthermore, the variance to be expected in the evaluated numerical magnitude of the parameters, due to the stochastic nature of the transitions in the channel conductance, is also readily estimated by use of the above auxiliary functions. The procedure is illustrated by analysis of synthetic data obtained from computer simulated experiments.     

Integrating ecosystem functions into restoration ecology—recent advances and future directions

Including ecosystem functions into restoration ecology has been repeatedly suggested, yet there is limited evidence that this is taking place without bias to certain habitats, species, or functions. We reviewed the inclusion of ecosystem functions in restoration and potential relations to habitats and species by extracting 224 publications from the literature (2004–2013). Most studies investigated forests, fewer grasslands or freshwaters, and fewest wetlands or marine habitats. Of all studies, 14% analyzed only ecosystem functions, 44% considered both biotic composition and functions, 42% exclusively studied the biotic component, mostly vascular plants, more rarely invertebrates or vertebrates, and least often microbes. Most studies investigating ecosystem functions focused on nutrient cycling (26%), whereas productivity (18%), water relations (16%), and geomorphological processes (14%) were less covered; carbon sequestration (10%), decomposition (6%), and trophic interactions (6%) were rarely studied. Monitoring of ecosystem functions was common in forests and grasslands, but the functions considered depended on the study organisms. These associations indicate research opportunities for certain habitats, species, and functions. Overall, the call to include ecosystem functions in restoration has been heard; however, a lack of clarity about the ecosystem functions to be included and deficits of feasible field methods are major obstacles for a functional approach. Restoration ecology should learn from recent advances in rapid assessment of ecosystem functions, and by a closer integration with biodiversity–ecosystem functioning research. Not all functions need to be measured in all ecosystems, but more functions than the few commonly addressed would improve the understanding of restored ecosystems.     

Betaine use by rhizosphere bacteria: genes essential for trigonelline, stachydrine, and carnitine catabolism in Rhizobium meliloti are located on pSym in the symbiotic region.

Rhizobium meliloti is known to use betaines synthesized by its host, Medicago sativa, as osmoprotectants and sources of energy. It is shown in the present report that the symbiotic megaplasmid (pSym) of R. meliloti RCR2011 encodes functions essential to the catabolism of three betaines, trigonelline (nicotinic acid N-methylbetaine), stachydrine (proline betaine or dimethylproline), and carnitine (gamma-trimethyl-beta-hydroxybutyrobetaine). Preliminary evidence is presented showing that functions on pSym also influence the catabolism of choline and its oxidative product, glycine betaine. Genes implicated in betaine catabolism are found in the symbiotic region of pSym. Trigonelline catabolism functions lie between two clusters of symbiotic genes, nifKDH and nok/fixVI'. Stachydrine and carnitine functions lie to the right of trigonelline catabolism functions, immediately to the right of fixVI'. Information necessary to choline and glycine betaine catabolism is probably encoded to the right of stachydrine catabolism functions.     

Evolutionary innovations and the organization of protein functions in genotype space

The organization of protein structures in protein genotype space is well studied. The same does not hold for protein functions, whose organization is important to understand how novel protein functions can arise through blind evolutionary searches of sequence space. In systems other than proteins, two organizational features of genotype space facilitate phenotypic innovation. The first is that genotypes with the same phenotype form vast and connected genotype networks. The second is that different neighborhoods in this space contain different novel phenotypes. We here characterize the organization of enzymatic functions in protein genotype space, using a data set of more than 30,000 proteins with known structure and function. We show that different neighborhoods of genotype space contain proteins with very different functions. This property both facilitates evolutionary innovation through exploration of a genotype network, and it constrains the evolution of novel phenotypes. The phenotypic diversity of different neighborhoods is caused by the fact that some functions can be carried out by multiple structures. We show that the space of protein functions is not homogeneous, and different genotype neighborhoods tend to contain a different spectrum of functions, whose diversity increases with increasing distance of these neighborhoods in sequence space. Whether a protein with a given function can evolve specific new functions is thus determined by the protein's location in sequence space.     

Bifurcation Analysis of Models with Uncertain Function Specification: How Should We Proceed?

When we investigate the bifurcation structure of models of natural phenomena, we usually assume that all model functions are mathematically specified and that the only existing uncertainty is with respect to the parameters of these functions. In this case, we can split the parameter space into domains corresponding to qualitatively similar dynamics, separated by bifurcation hypersurfaces. On the other hand, in the biological sciences, the exact shape of the model functions is often unknown, and only some qualitative properties of the functions can be specified: mathematically, we can consider that the unknown functions belong to a specific class of functions. However, the use of two different functions belonging to the same class can result in qualitatively different dynamical behaviour in the model and different types of bifurcation. In the literature, the conventional way to avoid such ambiguity is to narrow the class of unknown functions, which allows us to keep patterns of dynamical behaviour consistent for varying functions. The main shortcoming of this approach is that the restrictions on the model functions are often given by cumbersome expressions and are strictly model-dependent: biologically, they are meaningless. In this paper, we suggest a new framework (based on the ODE paradigm) which allows us to investigate deterministic biological models in which the mathematical formulation of some functions is unspecified except for some generic qualitative properties. We demonstrate that in such models, the conventional idea of revealing a concrete bifurcation structure becomes irrelevant: we can only describe bifurcations with a certain probability. We then propose a method to define the probability of a bifurcation taking place when there is uncertainty in the parameterisation in our model. As an illustrative example, we consider a generic predator–prey model where the use of different parameterisations of the logistic-type prey growth function can result in different dynamics in terms of the type of the Hopf bifurcation through which the coexistence equilibrium loses stability. Using this system, we demonstrate a framework for evaluating the probability of having a supercritical or subcritical Hopf bifurcation.     

Unusual catalytic activities and functions of cholinesterases

Cholinesterases (acetylcholinesterase and butyrylcholinesterase) have been shown to exhibit not only esterase activity but also an amine sensitive aryl acylamidase and a metallo-carboxypeptidase activities. There is also evidence to indicate that they have functions in the substantia nigra of brain, in neural cell differentiation, cell division and tumorigenesis, cell-adhesion and detoxication mechanisms. Butyrylcholinesterase is suggested to act as a back-up enzyme in acetylcholinesterase knock-out mice. Cholinesterases have catalytic or non-catalytic roles in these functions. Partial sequence homology to many other proteins having different functions and a metal binding site which can influence functions are probably factors that confer the non-cholinergic functions and activities on cholinesterases.     

京津冀地区县域耕地景观多功能性评价

随着城镇化发展和农业产业化升级,耕地景观功能由单一的生产功能向经济功能、生态功能、文化功能拓展,耕地景观多功能性成为新的学术热点。已有研究往往侧重于探讨耕地功能的多指数耦合,缺乏耕地景观多重功能空间定量化与相互关联的分析。以京津冀地区为研究区,对耕地景观的粮食供给功能、生境维持功能、景观连通功能、土壤保持功能、景观美学功能和人口承载功能六项功能及其冷热点聚集区分别空间定量化,评价县域尺度耕地景观多功能性,并识别耕地景观多种功能的空间关联。研究结果表明,京津冀中部平原地区粮食供给功能显著,南部平原地区景观连通功能突出,燕山与太行山山脉土壤保持功能、维持生境功能最高,山前平原地带人口承载功能相对重要。2010年京津冀地区耕地景观功能总体呈现南高北低的分布格局,但功能高低值分布规律差异明显,各功能全部处于高值或低值的样本极少;耕地景观不同功能间的权衡与协同关系数量相当,景观连通功能与粮食供给功能呈现明显协同关系,而与土壤保持功能呈现较强权衡关联。     

Space for people,plants, and livestock? Quantifying interactions among multiple landscape functions in a Dutch rural region

Rural landscapes are often multifunctional, meaning that at one single location different goods and services are being provided. Multifunctionality is spatially heterogeneous as not all areas are equally suitable to supply multiple goods and services. This suitability depends on favourable biophysical and socio-economic conditions and interactions among landscape functions. The objective of this paper is to identify and quantify interactions among landscape functions in a diverse and dynamic rural region, the Gelderse Vallei in the Netherlands. To be able to study these interactions first seven landscape functions (residential, intensive livestock, cultural heritage, tourism, plant habitat, arable production, and leisure cycling) are quantified and mapped using landscape indicators. These landscape function maps are subsequently aggregated to identify and quantify multifunctionality. The results of these analyses are used to study three aspects of landscape function interactions (a) influence of landscape characteristics on function interactions, (b) interrelations among landscape functions and (c) effect of multifunctionality on the different landscape functions. Landscape functions do not equally interact with one another, some landscape functions are affected negatively by the presence of other functions while other landscape functions benefit from multifunctionality. At multifunctionality hot spots different landscape functions are present that are enhancing one another. Additionally, in our study area it appears that mainly locations with landscape functions that sub-optimally provide goods and services are strongly multifunctional. Quantification and an improved understanding of landscape interactions will help to design and evaluate spatial policies related to the provision of multiple goods and services by the landscape.