结核分枝杆菌Rv1385的抗原表位预测分析

结核分枝杆菌生长缓慢,难以获得足量的天然蛋白抗原。而利用基因工程技术制备重组蛋白抗原,存在着表达量低、不易纯化,以及特异性较低等不利因素。随着生物信息技术的发展,研究者可根据生物信息学软件预测,选择合成优势抗原肽段,而不需克隆整个蛋白,具有简便、经济、特异性高等特点。因此,本研究应用生物信息学方法,预测结核分枝杆菌Rv1385蛋白的抗原表位并分析其优势表位,对了解Rv1385蛋白的免疫学特性及其与结核分枝杆菌致病的关系具有重要意义。首先,从NCBI数据库下载Rv1385的氨基酸序列,然后采用生物信息学软件PSIPRED Server预测蛋白质二级结构;BepiPred 1.0 Server和ABCpred预测该蛋白的B细胞抗原表位;BIMAS、SYFPEITHI及NetCTLpan 1.1 Server预测该蛋白的CTL表位;SYFPEITHI和NetMHCIIpan 3.2 Server预测该蛋白的Th细胞表位。最后综合分析预测结核分枝杆菌Rv1385的优势候选抗原表位。结果显示,Rv1385蛋白二级结构中,α螺旋占51.8%,β折叠占41.6%,无规卷曲占6.6%;共有4个B细胞抗原位点,位于109～124、152～169、178～192、198～209氨基酸区段;3个CTL表位,位于263～271、87～95、240～248氨基酸区段;5个Th表位,位于77～91、87～101、234～247、70～84、46～60氨基酸区段。生物信息学分析显示Rv1385含有潜在的B细胞和T细胞抗原表位,为该蛋白抗原表位的进一步研究及应用奠定了基础。     

Negative interactions determine Clostridioides difficile growth in synthetic human gut communities

Understanding the principles of colonization resistance of the gut microbiome to the pathogen Clostridioides difficile will enable the design of defined bacterial therapeutics. We investigate the ecological principles of community resistance to C. difficile using a synthetic human gut microbiome. Using a dynamic computational model, we demonstrate that C. difficile receives the largest number and magnitude of incoming negative interactions. Our results show that C. difficile is in a unique class of species that display a strong negative dependence between growth and species richness. We identify molecular mechanisms of inhibition including acidification of the environment and competition over resources. We demonstrate that Clostridium hiranonis strongly inhibits C. difficile partially via resource competition. Increasing the initial density of C. difficile can increase its abundance in the assembled community, but community context determines the maximum achievable C. difficile abundance. Our work suggests that the C. difficile inhibitory potential of defined bacterial therapeutics can be optimized by designing communities featuring a combination of mechanisms including species richness, environment acidification, and resource competition.     

Recovery of rhythmic activity in a central pattern generator: analysis of the role of neuromodulator and activity-dependent mechanisms

The pyloric network of decapods crustaceans can undergo dramatic rhythmic activity changes. Under normal conditions the network generates low frequency rhythmic activity that depends obligatorily on the presence of neuromodulatory input from the central nervous system. When this input is removed (decentralization) the rhythmic activity ceases. In the continued absence of this input, periodic activity resumes after a few hours in the form of episodic bursting across the entire network that later turns into stable rhythmic activity that is nearly indistinguishable from control (recovery). It has been proposed that an activity-dependent modification of ionic conductance levels in the pyloric pacemaker neuron drives the process of recovery of activity. Previous modeling attempts have captured some aspects of the temporal changes observed experimentally, but key features could not be reproduced. Here we examined a model in which slow activity-dependent regulation of ionic conductances and slower neuromodulator-dependent regulation of intracellular Ca²⁺ concentration reproduce all the temporal features of this recovery. Key aspects of these two regulatory mechanisms are their independence and their different kinetics. We also examined the role of variability (noise) in the activity-dependent regulation pathway and observe that it can help to reduce unrealistic constraints that were otherwise required on the neuromodulator-dependent pathway. We conclude that small variations in intracellular Ca²⁺ concentration, a Ca²⁺ uptake regulation mechanism that is directly targeted by neuromodulator-activated signaling pathways, and variability in the Ca²⁺ concentration sensing signaling pathway can account for the observed changes in neuronal activity. Our conclusions are all amenable to experimental analysis.     

Algal Bloom,Succession, and Drawdown of Silicate in the Chukchi Sea in Summer 2010

Ecosystems - The Chukchi Sea is the inflow shelf between the Arctic and the Pacific. A comprehensive research on algal dynamics, physical–biological interactions, and impacts on nutrient...     

紫茎泽兰在中国的气候生态位稳定且其分布范围仍有进一步扩展的趋势

明确入侵物种气候生态位的时空动态格局, 不仅有助于理解入侵物种生态位的变化趋势, 还可以使物种分布模型更真实地预测物种的扩散动态。本文使用恶性入侵植物紫茎泽兰(Ageratina adenophora)在原产地及我国的分布点和环境因子数据, 结合生态位分析及物种分布模型, 分析了紫茎泽兰入侵至我国后其气候生态位的时空变化特征、地理分布格局变化及其限制因子。结果表明: (1)紫茎泽兰入侵至我国后其气候生态位在时间和空间上虽略有扩张, 但仍保持较高的稳定性。尤其是入侵的初始阶段(1980年之前)稳定性最高(NS = 0.995), 此后其气候生态位的稳定性逐渐降低, 具体表现为该植物在中国更倾向于分布在潮湿(高最暖季降水量)、寒冷(低最干季平均温)且平均日较差低的生境。(2)过去50年里紫茎泽兰的适宜分布范围显著增加(151.77%-271.14%), 且其适宜分布区的重心在2010年之前表现出向东北(贵州西南部、四川南部)扩散的趋势, 2010年以后表现出向西南(云南北部、贵州北部)扩散的趋势。在扩散过程中, 该物种的气候生态位稳定性也表现出随着纬度的增加而逐渐降低的趋势。(3)未来气候变化情景下, 紫茎泽兰的适宜分布范围将进一步增加(111.97%), 到2040年该物种基本可以扩散至其整个潜在适宜分布区, 仅在藏东南地区有小范围的适宜生境受扩散限制无法达到。     

广西弄岗北热带喀斯特季节性雨林监测样地种群空间点格局分析

种群的空间分布格局是由多种机制的交互作用而形成,是探究生物多样性维持机制的基础。北热带喀斯特季节性雨林是我国北热带石灰岩山地具有地带性特征的植被,其生境的典型特征在于土层浅薄、岩石裸露率高、贮水能力低和周期性水淹,以及富钙强碱性环境等。本研究基于广西弄岗北热带喀斯特季节性雨林15 ha动态监测样地的第一次调查资料,采用双关联g(r)函数点格局方法,分析了雨林中出现个体数≥15株的160个种的种群空间分布格局以及不同类群间种群分布的差异。研究表明:160种木本植物中有146种在0–10 m的尺度上呈聚集分布,且随着空间尺度的增大,聚集度呈下降趋势;物种的种群聚集度与其物种多度、平均胸径和最大胸径成负相关;常绿物种的种群聚集度与落叶物种间差异不显著;不同生活型间的种群聚集度差异显著,总体表现为亚乔木层物种高于乔木层,灌木层物种显著高于亚乔木层;剔除生境异质性后大部分物种表现为随机分布,仅少部分物种的种群表现为聚集分布。这表明物种的功能属性如物种多度、生活型等可较好地预测物种的分布格局。此外,物种种群的分布格局还受生境异质性的影响,且不同物种受生境异质性影响的程度不同。     

Isolation and Identification of Three Novel Antioxidant Peptides from the Bactrian Camel Milk Hydrolysates

The aim of this study was isolation and purification of antioxidant peptides from Bactrian camel milk (BCM) hydrolysate. Trypsin, pepsin, alcalase, and pap     

Isolation and Identification of a Novel Antioxidant Peptide from Chickpea (Cicer arietinum L.) Sprout Protein Hydrolysates

International Journal of Peptide Research and Therapeutics - Chickpea (Cicer arietinum L.) is the second most widely cultivated leguminous plant in the world. In this study, the chickpea sprout...     

The Community Dynamics of Major Bioleaching Microorganisms During Chalcopyrite Leaching Under the Effect of Organics

To determine the effect of organics (yeast extract) on microbial community during chalcopyrite bioleaching at different temperature, real-time polymerase chain reaction (PCR) was employed to analyze community dynamics of major bacteria applied in bioleaching. The results showed that yeast extract exerted great impact on microbial community, and therefore influencing bioleaching rate. To be specific, yeast extract was adverse to this bioleaching process at 30°C due to decreased proportion of important chemolithotrophs such as Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. However, yeast extract could promote bioleaching rate at 40°C on account of the increased number and enhanced work of Ferroplasma thermophilum, a kind of facultative bacteria. Similarly, bioleaching rate was enhanced under the effect of yeast extract at 50°C owing to the work of Acidianus brierleyi. At 60°C, bioleaching rate was close to 100% and temperature was the dominant factor determining bioleaching rate. Interestingly, the existence of yeast extract greatly enhanced the relative competitiveness of Ferroplasma thermophilum in this complex bioleaching microbial community.