Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

Synthesis and biological characterization of new aryloxyindole-4,9-diones as potent trypanosomicidal agents

A new indole-4,9-dione and their phenoxy derivatives were synthesized and evaluated in vitro against the epimastigote form of Trypanosoma cruzi, Y strain. All of these novel compounds were found to be extremely potent and selective that the standard drug nifurtimox. Interestingly, phenoxyindole-4,9-dione 9d displayed excellent nanomolar inhibitory activity, IC₅₀ = 20 nM, and high selectivity index, SI = 625. In silico studies using MOE program were performed to generate a preliminary pharmacophore model.     

Phytoplankton and physical-chemical features of Tavropos Reservoir,Greece

Phytoplankton biomass values in Tavropos Reservoir, ranging from 92 to 1071 mg m^–3, are within a range characteristic of oligotrophic waters. The seasonal sequence of biomass shows three annual peaks, differing from the monoacmic pattern seen in oligotrophic lakes. This sequence was profoundly affected by changes in water withdrawal and inflow rates. Diatoms, cryptophytes, chrysophytes and dinoflagellates, in that order, were the major constituents of the reservoir phytoplankton. The succession, from diatoms and chrysophytes in late winter-spring, to centric diatoms in late spring-summer and again to diatom-chrysophytes in late autumn was similar to that in oligotrophic lakes.     

Evaluating effect of arbuscular mycorrhizal fungal consortia and Azotobacter chroococcum in improving biomass yield of Jatropha curcas

This study was conducted to study the long-term impact of bioinoculants, Azotobacter chroococcum and arbuscular mycorrhizal fungi (AMF) on growth and biomass yield of Jatropha curcas grown in nursery and in field conditions. The experiment was set up in a randomized block design, and the following treatments was designed (T₁ = control, T₂ = Azotobacter, T₃ = inoculation with AMF, and T₄ = inoculation with Azotobacter + AMF). Data on various growth attributes (shoot height and shoot diameter) and biochemical parameters [leaf relative water content (LRWC), sugars, protein, and photosynthetic pigments] were recorded up to 6 months in the nursery and in the field (18 months). Results pertaining to morpho-physiological traits showed Azotobacter and AMF consortia increase shoot height, shoot diameter, LRWC, sugars, proteins, and photosynthetic pigments over control under nursery conditions. Besides enhancing the plant growth, these bioinoculants helped in better establishment of Jatropha plants under field conditions. A significant improvement in the shoot height, shoot diameter, fruit yield/plant, and seed yield (g)/plant was evident in 18-month-old Jatropha plants under field conditions when Azotobacter and AMF were co-inoculated. This work supports the application of bioinoculants for establishment of Jatropha curcas in semi-arid regions.     

气候变化下中国八种梧桐属树种潜在适生区模拟

中国梧桐属（Firmiana）在世界梧桐属中占比较大，且除梧桐外其余种均为中国特有且分布范围狭窄的植物种，灭绝风险大，研究气候变化对中国梧桐属树种的影响对于维护生物多样性具有重要的意义。结合多时期第六次国际气候耦合模式比较计划（CMIP6）气候变量数据和中国八种梧桐属树种的分布数据，基于R语言kuenm程序包优化的最大熵（Maxent）模型模拟分析中国八种梧桐属树种在多尺度下的潜在适生区，得出梧桐属最适宜的模拟尺度、潜在适生区的面积变化和迁移方向、梧桐属多样性保护关键区域及保护空缺。结果表明：（1）梧桐属最适宜的模拟尺度为亚洲；（2） Maxent模型的接收者操作特征曲线下面积（AUC）值均大于0.9，表明模型对梧桐属潜在适生区预测结果具有较高准确度；（3）气候变化影响下除云南梧桐（Firmiana major）外其它树种的潜在适生区都将在未来有所扩大；（4）中国八种梧桐属树种潜在适生区迁移方向主要为东西向，南北向大跨度迁移较少，纬度变化不大；（5）丹霞梧桐（Firmiana danxiaensis）的稳定潜在适生区最小；（6）中国梧桐属多样性保护关键区域主要分布于广西壮族自治区及云南、广东、海南等省区；（7）中国梧桐属多样性保护空缺区域主要分布于广西壮族自治区中部及海南省北部；（8）梧桐属多样性保护关键区域正在为人造地表所侵蚀。研究分析气候变化对中国八种梧桐属树种的影响及其潜在适生区变化、中国梧桐属多样性保护状态，可为中国梧桐属建立多样性保护廊道提供相关建议，为制定多样性保护规划及相应措施提供参考。     

<Emphasis Type="Italic">Artemisia lerchiana</Emphasis> as a producer of essential oil

Abstrac  The composition of essential oil of Artemisia lerchiana Web. plants growing in Volgograd oblast was studied. Sampling was performed from plots contrasting in climatic and soil characteristics. Essential oil was obtained by hydrodistillation. The content of essential oil in shoot biomass increased gradually during shoot formation, flower bud formation, and flowering beginning and then decreased. The highest content of essential oil varied from 1.1 to 1.5% of plant dry weight at the stage of flower bud formation. More than thirty compounds were identified by gas chromatography-mass spectrometry. The following major components were found: camphor, borneol, bornylacetate, camphene, and 1,8-cineole. Some of compounds (sesquiterpenes and sesquiterpenoids) were identified for the first time. The time-course of accumulation of essential oil components strongly depended on habitat edaphic factors and climatic conditions during the year of sampling. The results permit a conclusion that A. lerchiana is a valuable producer of essential oils. Original Russian Text ? E.B. Kirichenko, Yu.V. Orlova, D.V. Kurilov, 2008, published in Fiziologiya Rastenii, 2008, Vol. 55, No. 6, pp. 934–941.