New vistas in GPCR 3D structure prediction

Human G-protein coupled receptors (hGPCRs) comprise the most prominent family of validated drug targets. More than 50% of approved drugs reveal their therapeutic effects by targeting this family. Accurate models would greatly facilitate the process of drug discovery and development. However, 3-D structure prediction of GPCRs remains a challenge due to limited availability of resolved structure. The X-ray structures have been solved for only four such proteins. The identity between hGPCRs and the potential templates is mostly less than 30%, well below the level at which sequence alignment can be done regularly. In this study, we analyze a large database of human G-protein coupled receptors that are members of family A in order to optimize usage of the available crystal structures for molecular modeling of hGPCRs. On the basis of our findings in this study, we propose to regard specific parts from the trans-membrane domains of the reference receptor helices as appropriate template for constructing models of other GPCRs, while other residues require other techniques for their remodeling and refinement. The proposed hypothesis in the current study has been tested by modeling human β2-adrenergic receptor based on crystal structures of bovine rhodopsin (1F88) and human A2A adenosine receptor (3EML). The results have shown some improvement in the quality of the predicted models compared to Modeller software.     

农田周围生态保留带中普通田鼠的种群生态学：种群数量动态及结构

于2003年5月~2004年11月,采用标志重捕法对栖息在生态保留带的普通田鼠种群结构和数量动态进行了跟踪研究。结果表明,两年中种群密度夏季最大分别达到410个体/hm2和641个体/hm2,春季最少分别达到166个体/hm2和153个体/hm2,种群数量从7月份开始增长,8月份种群密度减少并于11月份开始重新增长。种群中雌性个体数量比较多,雌性在种群中的居留时间较长,同时存活率比雄性高,这导致种群数量的季节变化。种群周转率比较高,在两个捕鼠期间种群中的80%个体被更新,这表明普通田鼠在生态保留带中的活动非常频繁,不断与周围的其他种群进行交流,提高了种群对环境的适应能力。种群中雌雄个体的巢区之间没有年间变化,活动巢区比较小,巢区长度2003年平均为11 m,最长为37.5 m,2004年平均为13 m,最长为52 m。Pearson相关指数表明种群数量和生态保留带年龄、覆盖率和高度之间没有相关性。     

阿尔泰山两河源自然保护区森林生态系统朽木生地衣群落的数量分类

应用双向指示种分析和除趋势对应分析对阿尔泰山两河源国家级自然保护区的朽木生地衣群落进行了数量分类。初步结果表明,该自然保护区朽木生地衣共有43种,隶属于5目、14科、20属,它们组成了以下4个地衣群落。群落(Ⅰ):分布在样点1、2、3、4、5中,包括15种地衣种类,命名为对开蜈蚣衣+半羽蜈蚣衣+红心黑蜈蚣衣群落。群落(Ⅱ):分布在样点6、7、8、9、11中,包括25种地衣,命名为尖头石蕊+粉石蕊+矮石蕊群落。群落(Ⅲ):由样点10、12、13、14、16组成,常见的地衣种类有19个种,命名为蜡黄橙衣+茎口果粉衣+冷杉粉衣群落。群落(Ⅳ):包括样点15、17、18、19和20,由22个地衣种组成。命名为疑小梅衣+同色黄烛衣+脱落网衣群落。群落Ⅰ和群落Ⅱ的相似性最高为0.723,其次为群落Ⅰ和群落Ⅲ为0.609,群落Ⅲ和群落Ⅳ之间的相似性最低为0.262。群落Ⅲ的多样性最大为1.954;其次为群落Ⅱ和群落Ⅰ,分别为1.742和我1.685,群落Ⅳ的多样性最低为0.543。各群落的相似性和多样性之间的差异与其所处环境和朽木树种的多样性有关。同时发现在研究地区的朽木生地衣群落的分布与海拔高度、朽木腐蚀程度、朽木大小、森林郁闭度等因子具有密切的关系。     

新疆博格达山岩面生地衣群落结构特征

根据对新疆博格达山岩面生地衣群落20个样点(20m×20m)调查的数据,以各地衣种的盖度为指标结合双向指示种分析方法(TWINSPAN)和除趋势对应分析法(DCA)对博格达山岩面生地衣群落进行数量分类并分析了群落结构特征及其多样性和相似性。采用典范对应分析法(CCA)对各群落的物种分布格局与环境因子的关系进行研究。结果表明,TWINSPAN分析和DCA排序将分布在博格达山的37种岩面生地衣分为以下5个群丛。群丛1:斑纹网衣(Lecidea tessellate Florke)+粉芽盾衣(Peltula euploca(Ach.)Poelt)+杜瑞氏黄梅(Xanthoparmelia durietzii Hale)群丛,有25个种,总覆盖度为30.145%,多样性为4.025;群丛2:袋衣(Hypogymnia physodes(L.)Nyl.)+白边平茶渍(Aspicilia sublaqueata(H.Magn.)J.C.Wei)+砖孢胶衣(Collema subconveniens Nyl.)群丛,有17个种,地衣总盖度为15.885%,多样性为3.196;群丛3:聚茶渍(Lecanora accumulate H.Magn.)+丽石黄衣(Xanthoria elegans(Link)Th.Fr.)+亚洲平茶渍(Aspicilia asiatica(H.Magn.)Yoshim.)群丛,有30个种,地衣总盖度为37.87%,多样性为4.357;群丛4:中华石果衣(Endocarpon sinense H.Magn.)+伴藓大孢蜈蚣衣(Physconia muscigena(Ach.)Poelt.)+垫脐鳞衣(Rhizoplaca melanophthalma(DC.)LeuckertPoelt)群丛,有24个种,地衣总盖度为30.458%,多样性为3.912;群丛5:石胶衣(Collema flaccidum(Ach.)Ach.)+短绒皮果衣(Dermatocarpon vellereum Zschacke)+绿黑地图衣(Rhizocarpon viridiatrum(Wulfen)Korber.)群丛,有18个种,地衣总盖度为19.331%,多样性为3.515。CCA排序结果反映,该地区岩面生地衣的分布与海拔高度、光照强度、岩石pH和人为干扰有关,其中影响最大的因素是海拔高度,其次为光照强度和干扰。坡向和岩石大小对地衣种类分布的影响不显著。     

Genetic analysis of the pnp-deaD genetic region reveals membrane lipoprotein NlpI as an independent participant in cold acclimatization of Salmonella enterica serovar Typhimurium

Plasmid pAMI7 of the methylotrophic bacterium Paracoccus aminophilus JCM 7686 (Alphaproteobacteria) encodes a functional type II restriction-modification (R-M) system designated PamI. Homologous systems were identified in the genomes of distinct taxonomic groups of Bacteria and Archaea, which provides evidence that horizontal gene transfer has contributed to the wide dissemination of R-M modules - even between domains. Analysis of the cleavage specificity of the R.PamI endonuclease revealed that this protein is an isoschizomer of restriction enzyme NcoI. Interestingly, bioinformatic analyses suggest that R.PamI and NcoI are accompanied by methyltransferases of different methylation specificities (C5-methylcytosine and N4-methylcytosine methyltransferases, respectively), which possibly exemplifies recombinational shuffling of genes coding for individual components of R-M systems. The PamI system can stabilize plasmid pAMI7 in a bacterial population, most probably at the postsegregational level. Therefore, it functions in an analogous manner to plasmid-encoded toxin-antitoxin (TA) systems. Since the TA system of pAMI7 is nonfunctional, it is highly probable that this lack is compensated by the stabilizing activity of PamI. This indicates the crucial role of the analyzed R-M system in the stable maintenance of pAMI7, which is, to our knowledge, the first report of 'symbiosis' between a R-M system and a plasmid in the Alphaproteobacteria.     

Variation of toxigenic Vibrio cholerae O1 in the aquatic environment of Bangladesh and its correlation with the clinical strains

The diversity of toxigenic V. cholerae O1 in the aquatic environment of Bangladesh is not known. A total of 18 environmental and 18 clinical strains of toxigenic V. cholerae O1 were isolated simultaneously from four different geographical areas and tested for variation by the pulsed-field gel electrophoresis method. Environmental strains showed diversified profiles and one of the profiles was common to some environmental strains and most clinical strains. It appears that one clone has an advantage over others to cause disease. These findings suggest that the study of the molecular ecology of V. cholerae O1 in relation to its environmental reservoir is important in identifying virulent strains that cause disease.     

Stability of entomopathogenic bacteria, <Emphasis Type="Italic">Xenorhabdus nematophila</Emphasis> and <Emphasis Type="Italic">Photorhabdus luminescens</Emphasis>, during in vitro culture

The entomopathogenic nematode–bacteria complexes Heterorhabditis bacteriophora/Photorhabdus luminescens and Steinernema carpocapsae/Xenorhabdus nematophila are mass produced for use as biological insecticides. Stability of the bacterial partner in culture is essential for maintaining traits important for both biological control and production. Two geographically distinct strains of each bacterial species were isolated from their nematode partners and serially subcultured on in vitro media to assess trait stability. Subculturing resulted in a shift to secondary cell production in one P. luminescens strain and both X. nematophila strains within ten in vitro culture cycles. However, when cell phenotypic variation was controlled in X. nematophila strains by regular selection for primary variants, no trait change was detected in the primary variant after prolonged subculture. When P. luminescens cell phenotypic variation was controlled by selection for primary variants, changes in the primary variant of both strains were noted including reductions in cell and inclusion body size and inclusion body prevalence. Bacterial ability to cause lethal infections following injection into the hemocoel of Tenebrio molitor larvae declined by more than half in primary variants of one P. luminescens strain. Conversely, yield was enhanced, with the subcultured P. luminescens strains showing 53.5 and 75.8% increases in primary cell density. Field adapted traits of primary variant P. luminescens strains tend to deteriorate during in vitro culture as tradeoffs for gains in yield. In vitro producers of the P. luminescens/H. bacteriophora complex must weigh the need for superior bacterial yield against the need to preserve traits important for biological control.     

Breeding Potential of Some Exotic Tomato Lines: A Combined Study of Morphological Variability,Genetic Divergence,and Association of Traits

Tomato (Solanum lycopersicum L.) is called ‘the poor man’s orange’ due to its low price and improved nutritional values. An experiment was conducted to study the breeding potential of some exotic tomato lines by assessing various qualitative and quantitative traits conferring yield and quality attributes. Among the qualitative traits, greater variability was observed for growth type, stem hairiness, and fruit shape and size. A determinate growth habit was observed in the genotype AVTO9802 while the genotype AVTO0102 produced yellow color fruits. A significant (p ≤ 0.01) variation was also observed for the studied quantitative traits. Based on yield and traits attributed to yield, the genotypes AVTO0314, GPB0107, GPB0120 and AVTO9802 were selected as promising genotypes. The differences between the genotypic and phenotypic coefficients of variation (GCV and PCV) of the studied quantitative traits were very low. This suggests that the apparent variation was mainly due to the genotypes. The higher GCV and PCV values were observed for the number of primary branches plant⁻¹ (NPB), number of fruits cluster⁻¹ (NFC), individual fruit weight (IFW) and total soluble solids (TSS). High heritability was recorded for all quantitative traits in a broad sense. However, the individual fruit diameter showed the highest heritability (99.56). The highest (102.75) genetic advance (GA) was observed for the number of fruits plant⁻¹ (NFP). High heritability coupled with high GA as percentage of mean were recorded for the traits NFP, NFC, fruit yield plant⁻¹ (FYP) and IFW. FYP showed a significant positive correlation with NFC (0.714***) and a negative correlation with days to the first harvest (−0.539***) and plant height (−0.492**). Principal component analysis revealed that the first four components explained 78.5% of the total variation among the genotypes. Thus, the promising genotypes (AVTO0314, GPB0107, GPB0120, AVTO9802 and AVTO0102) isolated from this study can be used for developing high-yielding and high-quality tomato varieties.     

Identification of QTLs for Yield and Associated Traits in F₂ Population of Rice

Identification of quantitative trait loci (QTLs) controlling yield and yield-related traits in rice was performed in the F₂ mapping population derived from parental rice genotypes DHMAS and K343. A total of 30 QTLs governing nine different traits were identified using the composite interval mapping (CIM) method. Four QTLs were mapped for number of tillers per plant on chromosomes 1 (2 QTLs), 2 and 3; three QTLs for panicle number per plant on chromosomes 1 (2 QTLs) and 3; four QTLs for plant height on chromosomes 2, 4, 5 and 6; one QTL for spikelet density on chromosome 5; four QTLs for spikelet fertility percentage (SFP) on chromosomes 2, 3 and 5 (2 QTLs); two QTLs for grain length on chromosomes 1 and 8; three QTLs for grain width on chromosomes1, 3 and 8; three QTLs for 1000-grain weight (TGW) on chromosomes 1, 4 and 8 and six QTLs for yield per plant (YPP) on chromosomes 2 (3 QTLs), 4, 6 and 8. Most of the QTLs were detected on chromosome 2, so further studies on chromosome 2 could help unlock some new chapters of QTL for this cross of rice variety. Identified QTLs elucidating high phenotypic variance can be used for marker-assisted selection (MAS) breeding. Further, the exploitation of information regarding molecular markers tightly linked to QTLs governing these traits will facilitate future crop improvement strategies in rice.