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.     

Influence of Phytase Transgenic Corn on the Intestinal Microflora and the Fate of Transgenic DNA and Protein in Digesta and Tissues of Broilers

An experiment was conducted to investigate the effect of phytase transgenic corn (PTC) on intestinal microflora, and the fate of transgenic DNA and protein in the digesta and tissues of broilers. A total of 160 1-day-old Arbor Acres commercial male broilers were randomly assigned to 20 cages (8 chicks per cage) with 10 cages (replicates) for each treatment. Birds were fed with a diet containing either PTC (54.0% during 1–21 days and 61.0% during 22–42 days) or non-transgenic isogenic control corn (CC) for a duration of 42 days. There were no significant differences (P>0.05) between birds fed with the PTC diets and those fed with the CC diets in the quantities of aerobic bacteria, anaerobic bacteria, colibacillus and lactobacilli, or microbial diversities in the contents of ileum and cecum. Transgenic phyA2 DNA was not detected, but phyA2 protein was detected in the digesta of duodenum and jejunum of broilers fed with the PTC diets. Both transgenic phyA2 DNA and protein fragments were not found in the digesta of the ileum and rectum, heart, liver, kidney, and breast or thigh muscles of broilers fed with the PTC diets. It was concluded that PTC had no adverse effect on the quantity and diversity of gut microorganisms; Transgenic phyA2 DNA or protein was rapidly degraded in the intestinal tract and was not transferred to the tissues of broilers.     

囊萼花属─—中国玄参科新记录属及—新种

报道了我国玄参科的一个新记录属──囊萼花属ＣｙｒｔａｎｄｒｏｍｏｅａＺｏｌｌ，该属为印度－马来西亚分布，它经过泰国北部，缅甸与我国发生连系，到达我国云南贡山、屏边、金平。全世界有１１—１２种，我国（云南）首次记录两种，其中一种为新种。     

Growth form and distribution of introduced plants in their native and non-native ranges in Eastern Asia and North America

There is a growing interest in understanding the influence of plant traits on their ability to spread in non-native regions. Many studies addressing this issue have been based on relatively small areas or restricted taxonomic groups. Here, we analyse a large data base involving 1567 plant species introduced between Eastern Asia and North America or from elsewhere to both regions. We related the extent of species distributions in each region to growth form and the distinction between upland and wetland habitats. We identified significant relationships between geographical distribution and plant traits in both native and exotic ranges as well as regional differences in the relationships. Range size was larger for herbaceous graminoids and forbs, especially annuals compared to perennials, than for woody species, and range size also was larger for plants of wetland compared to upland habitats. Distributions were more extensive in North America than in Eastern Asia, although native plants from both regions had broader distributions than non-natives, with exotics from elsewhere intermediate. Growth form and environment explained more of the variance in distribution of plants in North America than in Eastern Asia. The influence of growth form and habitat on distribution suggests that these traits might be related to tolerance of ecological conditions. In addition, the smaller extents of species in non-native compared to native areas suggest roles for dispersal limitation and adaptation to region-specific ecological conditions in determining distribution.     

FlhF regulates the number and configuration of periplasmic flagella in Borrelia burgdorferi

The Lyme disease bacterium Borrelia burgdorferi has 7–11 periplasmic flagella (PF) that arise from the cell poles and extend toward the midcell as a flat-ribbon, which is distinct from other bacteria. FlhF, a signal recognition particle (SRP)-like GTPase, has been found to regulate the flagellar number and polarity; however, its role in B. burgdorferi remains unknown. B. burgdorferi has an FlhF homolog (BB0270). Structural and biochemical analyses show that BB0270 has a similar structure and enzymatic activity as its counterparts from other bacteria. Genetics and cryo-electron tomography studies reveal that deletion of BB0270 leads to mutant cells that have less PF (4 ± 2 PF per cell tip) and fail to form a flat-ribbon, indicative of a role of BB0270 in the control of PF number and configuration. Mechanistically, we demonstrate that BB0270 localizes at the cell poles and controls the number and position of PF via regulating the flagellar protein stability and the polar localization of the MS-ring protein FliF. Our study not only provides the detailed characterizations of BB0270 and its profound impacts on flagellar assembly, morphology and motility in B. burgdorferi, but also unveils mechanistic insights into how spirochetes control their unique flagellar patterns.     

Effect of fertilizers on Cd accumulation and subcellular distribution of two cosmos species (Cosmos sulphureus and Cosmos bipinnata)

Addition of fertilizer amendments is regarded as an ideal approach to enhancing phytoextraction. However, there is little information available on the influence of common fertilizers on Cd accumulation of two newly reported Cd accumulators, Cosmos sulphureus and Cosmos bipinnata (C. sulphureus and C. bipinnata). The effects of N (CO(NH₂)₂), NP (CO(NH₂)₂ + Ca(H₂PO₄)₂), and NPK (CO(NH₂)₂ + Ca(H₂PO₄)₂ + KCl) fertilizers on Cd accumulation and subcellular distribution of C. sulphureus and C. bipinnata were studied in a 70-d pot experiment. The results showed that Cd uptake of C. sulphureus and C. bipinnata with NPK fertilizer was significantly higher than control, N, and NP fertilizers, especially 3.8- and 4.7-fold higher than control (p < 0.05). Compared with C. bipinnata, C. sulphureus achieved higher biomass and Cd uptake in aboveground parts under fertilizer treatments, especially NPK fertilizer. The Cd subcellular distribution revealed that segregation of Cd to Cd-rich granules (MRG) might play an important role in Cd detoxification in both species. C. sulphureus is more likely than C. bipinnata to separate the Cd in MRG and reduce the partition in the heat-denatured protein fraction, especially with NPK fertilizer. Therefore, C. sulphureus combined with NPK fertilizers could be an effective method to remediate Cd-polluted farmland soils in China.     

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。     

Modelling Infectious Hematopoietic Necrosis Virus Dispersion from Marine Salmon Farms in the Discovery Islands,British Columbia,Canada

Finite volume ocean circulation and particle tracking models are used to simulate water-borne transmission of infectious hematopoietic necrosis virus (IHNV) among Atlantic salmon (Salmo salar) farms in the Discovery Islands region of British Columbia, Canada. Historical simulations for April and July 2010 are carried out to demonstrate the seasonal impact of river discharge, wind, ultra-violet (UV) radiation, and heat flux conditions on near-surface currents, viral dispersion and survival. Numerical particles released from infected farm fish in accordance with IHNV shedding rates estimated through laboratory experiments are dispersed by model oceanic flows. Viral particles are inactivated by ambient UV radiation levels and by the natural microbial community at rates derived through laboratory studies. Viral concentration maps showing temporal and spatial changes are produced and combined with lab-determined minimum infectious dosages to estimate the infective connectivity among farms. Results demonstrate that neighbouring naïve farms can become exposed to IHNV via water-borne transport from an IHNV diseased farm, with a higher risk in April than July, and that many events in the sequence of farm outbreaks in 2001-2002 are consistent with higher risks in our farm connectivity matrix. Applications to other diseases, transfers between farmed and wild fish, and the effect of vaccinations are also discussed.