Hidden markov model for the prediction of transmembrane proteins using MATLAB

Since membranous proteins play a key role in drug targeting therefore transmembrane proteins prediction is active and challenging area of biological sciences. Location based prediction of transmembrane proteins are significant for functional annotation of protein sequences. Hidden markov model based method was widely applied for transmembrane topology prediction. Here we have presented a revised and a better understanding model than an existing one for transmembrane protein prediction. Scripting on MATLAB was built and compiled for parameter estimation of model and applied this model on amino acid sequence to know the transmembrane and its adjacent locations. Estimated model of transmembrane topology was based on TMHMM model architecture. Only 7 super states are defined in the given dataset, which were converted to 96 states on the basis of their length in sequence. Accuracy of the prediction of model was observed about 74 %, is a good enough in the area of transmembrane topology prediction. Therefore we have concluded the hidden markov model plays crucial role in transmembrane helices prediction on MATLAB platform and it could also be useful for drug discovery strategy. AVAILABILITY: The database is available for free at bioinfonavneet@gmail.comvinaysingh@bhu.ac.in.     

Drought and aquatic community resilience: the role of eggs and seeds in sediments of temporary wetlands

1. A long‐lived bank of propagules consisting of eggs, seeds and spores is one mechanism that allows aquatic communities to survive drought. A drying (drought) event is, for aquatic organisms in a temporary wetland, a phase from which communities must recover. Such a dry phase is often considered a disturbance but should not be considered adverse or catastrophic for the organisms that have evolved to live in temporarily wet habitats. 2. This paper explores the parallels between the egg bank of zooplankton and the seed bank of aquatic plants as means of survival in temporary wetlands. The resilience of communities in temporary wetland ecosystems is assessed by examining dormancy, hatching, germination, establishment and reproduction of animals and plants from the egg and seed banks of wetlands with a range of wetting and drying regimes. 3. Both the zooplankton and aquatic plants of the temporary wetlands studied rely on their egg and seed banks as a means for surviving drying. These communities recover after the disturbance of drying by means of specific patterns of dormancy, dormancy breakage, hatching, germination, establishment and reproduction. Spatial and temporal patterns of species richness allow resilience through dormancy, as not all species are present at all sites and not all species hatch and germinate at the same time. Multiple generations in the egg and seed bank and complexity of environmental cues for dormancy breakage also contribute to the ecosystem's ability to recover after a drying event. A persistent egg and seed bank allows species‐rich communities to hatch, germinate and develop rapidly once dormancy is broken. Rapid establishment of species‐rich communities that reproduce rapidly and leave many propagules in the egg and seed bank also facilitates community recovery on flooding of a temporary wetland after a drying event. 4. To maintain the diversity of temporary wetland communities through droughts and floods we need to manage the dry and wet phases of wetlands. To conserve a wide range of wetland types, we need to maintain a variety of hydrological patterns across the landscape.     

Metapopulation dynamics in an aphid-parasitoid system

Metapopulation theory makes a number of predictions concerning the effects of dispersal on the persistence of predator-prey or host-parasitoid systems. While the stabilising effects of dispersal have been shown in a number of laboratory studies, evidence from field studies remains scarce due to a lack of suitable model systems. I describe a host-parasitoid system that shows a classical metapopulation structure with frequent extinctions and colonisations consisting of the aphidiid Lysiphlebus hirticornisand the aphid Metopeurum fuscoviride. Both the parasitoid and the aphid are specialists on their respective hosts. I followed the dynamics of host and parasitoid on individually marked tansy (Tanacetum vulgare) plants, the host of M. fuscoviride. Dynamics of host and parasitoid populations were characterized by frequent extinctions and colonisations. Mean longevity of aphid colonies was only 3.1 weeks. Parasitism by L. hirticorniswas a main cause of extinction for the aphid as rates of parasitism often reached 100%, in particular towards the end of the field season. Patchiness in this system occurs at two spatial scales. Aphid colonies form on single tansy ramets = shoots but movements of aphid individuals among ramets within a particular tansy genet are frequent. Because aphids can persist on a genet for a large numer of generations, it is argued that local populations form on genets rather than ramets. The number of host and parasitoid extinctions described in this study exceeds the number of extinctions usually observed in field studies of host-parasitoid metapopulations. It is suggested that aphid-parasitoid systems such as the one studied in this paper may be good models to test the predictions of metapopulation theory.     

Prediction of Translation Initiation Sites on the Genome of Synechocystis sp. Strain PCC6803 by Hidden Markov Model

We developed a computer program, GeneHackerTL, which predictsthe most probable translation initiation site for a given nucleotidesequence. The program requires that information be extractedfrom the nucleotide sequence data surrounding the translationinitiation sites according to the framework of the Hidden MarkovModel. Since the translation initiation sites of 72 highly abundantproteins have already been assigned on the genome of Synechocystissp. strain PCC6803 by amino-terminal analysis, we extractednecessary information for GeneHackerTL from the nucleotide sequencedata. The prediction rate of the GeneHackerTL for these proteinswas estimated to be 86.1%. We then used GeneHackerTL for predictionof the translation initiation sites of 24 other proteins, ofwhich the initiation sites were not assigned experimentally,because of the lack of a potential initiation codon at the amino-terminalposition. For 20 out of the 24 proteins, the initiation siteswere predicted in the upstream of their amino-terminal positions.According to this assignment, the processed regions representa typical feature of signal peptides. We could also predictmultiple translation initiation sites for a particular genefor which at least two initiation sites were experimentallydetected. This program would be e.ective for the predictionof translation initiationsites of other proteins, not only inthis species but also in other prokaryotes as well.     

植冠与土壤种子库储存种子的萌发特性及策略

为明确黄土丘陵沟壑区植物种子库如何调控种子萌发来提高个体适合度,选择研究区7种具有种子库的主要物种为研究对象,以刚成熟和室内储存种子为对照,比较植冠宿存(5个宿存期)和土壤埋藏(5a埋藏期)对植物种子萌发特性的影响,探讨植冠种子库与土壤种子库储存下的种子萌发策略。结果表明:7种植物种子经过不同种子库储存后萌发特性表现出明显的种间差异,黄刺玫(Rosa xanthina)和水栒子(Cotoneaster multiflorus)种子萌发力表现为植冠宿存不变型、土壤储存增强型,土壤储存明显提高水栒子种子萌发速率;达乌里胡枝子(Lespedeza davurica)和狼牙刺(Sophora davidii)种子萌发力表现为植冠宿存增强型、土壤储存减弱型,种子萌发历时表现为植冠宿存延长型,土壤种子库储存还可加快达乌里胡枝子萌发速率、缩短萌发历时;茭蒿(Artemisia giralaii)和铁杆蒿(Artemisia gmelinii),种子萌发率随植冠宿存时间先升高后降低,随土壤储存时间先降低后升高,土壤储存可推迟其萌发,铁杆蒿种子萌发速率在植冠与土壤储存后均加快;紫丁香(Syringa oblata)种子萌发率随植冠宿存先升高后降低,土壤储存明显加快其种子启动萌发与速率。在黄土丘陵沟壑区,植物种子经过植冠或土壤种子库储存,或增加、加快、提早萌发充分利用有利条件提高占据性,或减少、减缓、推迟萌发分摊不利条件的风险;而且该区植物植冠与土壤储存后种子萌发特性间的关系,体现各自适应环境与应对干扰的分工与协作策略,主要表现为:单一主导型和相辅相成型。     

广义隐Markov模型在基因识别中的应用

广义隐Markov模型(GHMM)是基因识别的一种重要模型,但是其计算量比传统的隐Markov模型大得多,以至于不能直 接在基因识别中使用。根据原核生物基因的结构特点,提出了一种高效的简化算法,其计算量是序列长度的线性函数。在此 基础上,构建了针对原核生物基因的识别程序GeneMiner,对实际数据的测试表明,此算法是有效的。     

链霉菌基因组中放线菌型整合性接合元件的识别

【目的】链霉菌染色体重组和外源DNA片段插入是影响其遗传多样性的主要因素。旨在考察放线菌型整合性接合元件(AICE)在链霉菌遗传多样性中所发挥的作用。【方法】基于AICE的特征性模块, 采用隐马尔科夫模型预测链霉菌基因组序列中的AICEs。【结果】在已全测序的12条链霉菌染色体和35个质粒中, 共识别出29个AICEs, 其中12个为首次报道。Streptomyces coelicolor基因组中发现了4个AICEs, 而其近缘的Streptomyces lividans却没有。【结论】AICEs都整合在链霉菌染色体的核心区, 且都具有典型的整合环出、复制和接合转移等核心模块, 这些可自行转移的元件在链霉菌基因组可塑性中扮演了重要角色。     

A brief review of computational gene prediction methods

With the development of genome sequencing for many organisms, more and more raw sequences need to be annotated. Gene prediction by computational methods for finding the location of protein coding regions is one of the essential issues in bioinformatics. Two classes of methods are generally adopted: similarity based searches and ab initio prediction. Here, we review the development of gene prediction methods, summarize the measures for evaluating predictor quality, highlight open problems in this area, and discuss future research directions.     

基于序列拓扑和二阶隐马尔可夫模型的跨膜蛋白亚细胞定位预测

现有蛋白质亚细胞定位方法针对水溶性蛋白质而设计,对跨膜蛋白并不适用。而专门的跨膜拓扑预测器,又不是为亚细胞定位而设计的。文章改进了跨膜拓扑预测器TMPHMMLoc的模型结构,设计了一个新的二阶隐马尔可夫模型;采用推广到二阶模型的Baum-Welch算法估计模型参数,并把将各个亚细胞位置建立的模型整合为一个预测器。数据集上测试结果表明,此方法性能显著优于针对可溶性蛋白设计的支持向量机方法和模糊k最邻近方法,也优于TMPHMMLoc中提出的隐马尔可夫模型方法,是一个有效的跨膜蛋白亚细胞定位预测方法。     

隐马尔可夫模型-改进的预测蛋白质二级结构方法

引入蛋白质二级结构预测的新方法：隐马尔可夫模型,其中将蛋白质的二级结构分成三类：H(指α-螺旋),E(β-折叠)及O(包括转角,卷曲及其结构)．该方法属于统计方法,但考虑了相邻氮基酸之间的相互作用(体现在状态传输概率)．通过模型的改进及参数的确定后,我们编制了程序HMMPS．用它来预测蛋白质二级结构,具有很高的准确度．其中关于H,F和O的准确率分别达到80．1％．72.0％和63．2％这表明．我们的方法是较为可靠的。     

Seeds of alpine plants are short lived: implications for long-term conservation

Background and Aims

Alpine plants are considered one of the groups of species most sensitive to the direct and indirect threats to ecosystems caused by land use and climate change. Collecting and banking seeds of plant species is recognized as an effective tool for providing propagating material to re-establish wild plant populations and for habitat repair. However, seeds from cold wet environments have been shown to be relatively short lived in storage, and therefore successful long-term seed conservation for alpine plants may be difficult. Here, the life spans of 69 seed lots representing 63 related species from alpine and lowland locations from northern Italy are compared.

Methods

Seeds were placed into experimental storage at 45 °C and 60 % relative humidity (RH) and regularly sampled for germination. The time taken in storage for viability to fall to 50 % (p₅₀) was determined using probit analysis and used as a measure of relative seed longevity between seed lots.

Key Results

Across species, p₅₀ at 45 °C and 60 % RH varied from 4·7 to 95·5 d. Seed lots from alpine populations/species had significantly lower p₅₀ values compared with those from lowland populations/species; the lowland seed lots showed a slower rate of loss of germinability, higher initial seed viability, or both. Seeds were progressively longer lived with increased temperature and decreased rainfall at the collecting site.

Conclusions

Seeds of alpine plants are short lived in storage compared with those from lowland populations/related taxa. The lower resistance to ageing in seeds of alpine plants may arise from low selection pressure for seed resistance to ageing and/or damage incurred during seed development due to the cool wet conditions of the alpine climate. Long-term seed conservation of several alpine species using conventional seed banking methods will be problematic.