Stereochemical studies on cyclic peptides: Detailed energy minimization studies on hydrogen bonded all-trans cyclic pentapeptide backbones

Conformational studies have been carried out on hydrogenbonded all-trans cyclic pentapeptide backbone. Application of a combination of grid search and energy minimization on this system has resulted in obtaining 23 minimum energy conformations, which are characterized by unique patterns of hydrogen bonding comprising of β- and γ-turns. A study of the minimum energy conformationsvis-a-vis non-planar deviation of the peptide units reveals that non-planarity is an inherent feature in many cases. A study on conformational clustering of minimum energy conformations shows that the minimum energy conformations fall into 6 distinct conformational families. Preliminary comparison with available X-ray structures of cyclic pentapeptide indicates that only some of the minimum energy conformations have formed crystal structures. The set of minimum energy conformations worked out in the present study can form a consolidated database of prototypes for hydrogen bonded backbone and be useful for modelling cyclic pentapeptides both synthetic and bioactive in nature. This is part XV of the series. Part XIV in this series is Ramakrishnanet al 1987.     

A covalently bound photoisomerizable agonist. Comparison with reversibly bound agonists at electrophorus electroplaques

After disulphide bonds are reduced with dithiothreitol, trans-3- (α-bromomethyl)-3’-[α- (trimethylammonium)methyl]azobenzene (trans-QBr) alkylates a sulfhydryl group on receptors. The membrane conductance induced by this “tethered agonist” shares many properties with that induced by reversible agonists. Equilibrium conductance increases as the membrane potential is made more negative; the voltage sensitivity resembles that seen with 50 [mu]M carbachol. Voltage- jump relaxations follow an exponential time-course; the rate constants are about twice as large as those seen with 50 μM carbachol and have the same voltage and temperature sensitivity. With reversible agonists, the rate of channel opening increases with the frequency of agonist-receptor collisions: with tethered trans-Qbr, this rate depends only on intramolecular events. In comparison to the conductance induced by reversible agonists, the QBr-induced conductance is at least 10-fold less sensitive to competitive blockade by tubocurarine and roughly as sensitive to “open-channel blockade” bu QX-222. Light-flash experiments with tethered QBr resemble those with the reversible photoisomerizable agonist, 3,3’,bis-[α-(trimethylammonium)methyl]azobenzene (Bis-Q): the conductance is increased by cis {arrow} trans photoisomerizations and decreased by trans {arrow} cis photoisomerizations. As with Bis-Q, ligh-flash relaxations have the same rate constant as voltage-jump relaxations. Receptors with tethered trans isomer. By comparing the agonist-induced conductance with the cis/tans ratio, we conclude that each channel’s activation is determined by the configuration of a single tethered QBr molecule. The QBr-induced conductance shows slow decreases (time constant, several hundred milliseconds), which can be partially reversed by flashes. The similarities suggest that the same rate-limiting step governs the opening and closing of channels for both reversible and tethered agonists. Therefore, this step is probably not the initial encounter between agonist and receptor molecules.     

Palatability and feeding preferences of Uresiphita maorialis (Lepidoptera: Crambidae) for three Sophora species

In a three-hour bioassay, we tested the palatability and feeding preferences of Uresiphita maorialis (kōwhai moth) for Sophora tetraptera, Sophora microphylla and Sophora prostrata. Palatability tests showed no differences among the Sophora species. Feeding preferences, on the other hand, showed that S. tetraptera and S. microphylla leaves are preferred over S. prostrata leaves. Our results support our field observations in Wellington city parks and gardens showing that S. tetraptera and S. microphylla plants frequently have higher densities of larvae than S. prostrata.     

Biodeterioration of Mayan buildings at uxmal and tulum,Mexico

Uxmal and Tulum are two important Mayan sites in the Yucatan peninsula. The buildings are mainly composed of limestone and grey/black discoloration is seen on exposed walls and copious greenish biofilms on inner walls. The principal microorganisms detected on interior walls at both Uxmal and Tulum were cyanobacteria; heterotrophic bacteria and filamentous fungi were also present. A dark‐pigmented mitosporic fungus and Bacillus cereus, both isolated from Uxmal, were shown to be acidogenic in laboratory cultures. Cyanobacteria belonging to rock‐degrading genera Synechocystis and Gloeocapsa were identified at both sites. Surface analysis previously showed that calcium ions were present in the biofilms on buildings at Uxmal and Tulum, suggesting the deposition of biosolubilized stone. Apart from their potential to degrade the substrate, the coccoid cyanobacteria supply organic nutrients for bacteria and fungi, which can produce organic acids, further increasing stone degradation.     

毛乌素沙地南缘沙丘生物结皮对凝结水形成和蒸发的影响

在水分极度匮乏的荒漠生态系统,凝结水是除降雨之外最重要的水分来源之一,它对荒漠生态系统结构、功能和过程的维持产生重要的影响。为探明半干旱沙区生物结皮表面的凝结水形成和蒸发特征,采用自制的微型蒸渗计(直径7 cm、高5 cm的PVC管)实验观测了不同类型地表(裸沙、浅灰色藻类结皮、黑褐色藻类结皮和苔藓结皮)对凝结水形成和蒸发的影响。结果表明:(1)观测期间共有20次凝结水形成记录,除降雨天气外,几乎每天都能观测到水分凝结现象;(2)不同类型地表凝结水总量依次为(1.998±0.075),(2.326±0.083),(2.790±0.058)和(3.416±0.068) mm,生物结皮表面的凝结水总量显著大于裸沙(P < 0.05);随生物结皮的发育,不同类型生物结皮表面的凝结水总量呈增加的趋势,凝结水总量之间差异显著(P < 0.05);观测期间不同类型地表日平均凝结水量依次为(0.100±0.003),(0.116±0.004),(0.140±0.002)和(0.171± 0.003) mm,不同类型地表日平均凝结水量之间差异极显著(P < 0.01);(3)凝结水形成过程的观测结果显示,凝结水19:00开始形成,23:00-凌晨1:00形成不明显,1:00-7:00继续形成,除浅灰色藻类结皮外,太阳升出后在黑褐色藻类结皮和苔藓结皮表面继续形成少量的凝结水;凝结水7:30开始蒸发,10:30到11:00之间结束蒸发,凝结水在裸沙和浅灰色藻类结皮中的保持时间显著大于黑褐色藻类结皮和苔藓结皮中的保持时间(P < 0.05);(4)凝结水的形成受大气温度、地表温度、空气相对湿度和大气地表温度差等气象因素的影响,但其形成过程不与某一个气象因素呈简单的线性关系。     

The role of fish-poultry integration on fish growth performance,yields and economic benefits among smallholder farmers in sub-Saharan Africa,Tanzania

Aquaculture practices from sub-Saharan Africa are characterised by low production, owing to improper technology. Production can be increased through integrating fish farming with other existing on-farm activities, particularly livestock husbandry. We assessed the role of fish-poultry integration on all male Nile tilapia, Oreochromis niloticus growth performance, yields and economic benefits among smallholder farmers in sub-Saharan Africa, Tanzania. The study also compared phytoplankton species composition, abundance and biomass between the fish-poultry integration and non-integrated system. After 180 days of the experiment, all male O. niloticus cultured under fish-poultry integration exhibited significantly higher growth rates than those in the non-integrated system (p < 0.05). Gross fish yield (GFY), net fish yield (NFY) and net annual yields (NAY) obtained from fish-poultry integration were significantly higher than those from non-integrated system (p < 0.05). Partial enterprise budget analysis revealed that fish-poultry integration was more profitable than the non-integrated system. Moreover, fish-poultry integrated system produced significantly higher phytoplankton abundance and biomass than those from the non-integrated system. Results demonstrate that rural smallholder farmers can achieve higher growth rate, farm net yields and income by integrating all male O. niloticus with other on-farm activities than practising a stand-alone fish culture system.     

G-IMEx: A comprehensive software tool for detection of microsatellites from genome sequences

Microsatellites are ubiquitous short tandem repeats found in all known genomes and are known to play a very important role in various studies and fields including DNA fingerprinting, paternity studies, evolutionary studies, virulence and adaptation of certain bacteria and viruses etc. Due to the sequencing of several genomes and the availability of enormous amounts of sequence data during the past few years, computational studies of microsatellites are of interest for many researchers. In this context, we developed a software tool called Imperfect Microsatellite Extractor (IMEx), to extract perfect, imperfect and compound microsatellites from genome sequences along with their complete statistics. Recently we developed a user-friendly graphical-interface using JAVA for IMEx to be used as a stand-alone software named G-IMEx. G-IMEx takes a nucleotide sequence as an input and the results are produced in both html and text formats. The Linux version of G-IMEx can be downloaded for free from http://www.cdfd.org.in/imex.     

A Study on Mutational Dynamics of Simple Sequence Repeats in Relation to Mismatch Repair System in Prokaryotic Genomes

Mutational bias toward expansion or contraction of simple sequence repeats (SSRs) is referred to as directionality of SSR evolution. In this communication, we report the mutational bias exhibited by mononucleotide SSRs occurring in the non-coding regions of several prokaryotic genomes. Our investigations revealed that the strains or species lacking mismatch repair (MMR) system generally show higher number of polymorphic SSRs than those species/strains having MMR system. An exception to this observation was seen in the mycobacterial genomes that are MMR deficient where only a few SSR tracts were seen with mutations. This low incidence of SSR mutations even in the MMR-deficient background could be attributed to the high fidelity of the DNA polymerases as a consequence of high generation time of the mycobacteria. MMR system-deficient species generally did not show any bias toward mononucleotide SSR expansions or contractions indicating a neutral evolution of SSRs in these species. The MMR-proficient species in which the observed mutations correspond to secondary mutations showed bias toward contraction of polymononucleotide tracts, perhaps, indicating low efficiency of MMR system to repair SSR-induced slippage errors on template strands. This bias toward deletion in the mononucleotide SSR tracts might be a probable reason behind scarcity for long poly A|T and G|C tracts in prokaryotic systems which are mostly MMR proficient. In conclusion, our study clearly demonstrates mutational dynamics of SSRs in relation to the presence/absence of MMR system in the prokaryotic system.