Natural Variants of the Cellular Slime Mold Acrasis rosea

SYNOPSIS. Twenty different isolates of the cellular slime mold Acrasis rosea, obtained from diverse sources and geographic regions, were studied to determine similarities and differences in their development and structure in culture and their sensitivity or resistance to selected chemicals incorporated into the culture media. Six different classes of fruiting were defined based on the size, distribution, and type of sorocarps formed on the yeast, Rhodotorula, streaked on agar. In the course of these studies a significant mutant, NC-18V (variant), developed spontaneously from the wild type, normal parent strain NC-18N. The mutant differed considerably from all other Acrasis isolates, appeared several times in purified parental cultures, and represents the first laboratory derived variant of A. rosea to be described. Purified strains of the variant (V) and normal (N) cultures were obtained by single-spore isolation. Normal and variant amebae were mixed in ratios of 10:1 and 100:1 (N:V) and spore and stalk cells were selected from different sorocarps in various regions of the culture plate for analysis. The results of these selection experiments clearly indicate that the individual variant amebae have increased migratory ability and that they develop smaller, morphologically different, and more numerous sorocarps that form at distances further from the food source than NC-18N. Some isolates of Acrasis no longer were able to fruit and were classified as “non-fruiters” and a few other isolates formed only a few, small sorocarps on rare occasions. These isolates were mixed together in various combinations of 2 and 3 to screen for cell interaction, but no synergism contributing to fruiting was found. Although fruiting of many A. rosea isolates was inhibited by exposure to continuous light or constant darkness, some “escape”fruiting was noted in certain isolates even when small inocula were used. Single spore isolates of these escape fruiters still fruited in continuous light or dark, but fruiting was always greatly enhanced by a routine 12 hr light : 12 hr dark incubation cycle. It was shown by biochemical studies that actidione, crystal violet, malachite green, ethyl violet, and 5-fluorodeoxyuridine selectively killed some isolates and permitted a classification of isolates as either sensitive or resistant. In a further study of cell interaction between 2 different sets of Acrasis isolates with contrasting biochemical and morphologic markers the formation of neotypes or recombinants could not be demonstrated. The results of this study clearly indicate the existence of significant variation in A. rosea and the potential for application of these differences to developmental studies.     

A natural fusion of flavodiiron,rubredoxin, and rubredoxin oxidoreductase domains is a self-sufficient water-forming oxidase of Trichomonas vaginalis

Microaerophilic pathogens such as Giardia lamblia, Entamoeba histolytica, and Trichomonas vaginalis have robust oxygen consumption systems to detoxify oxygen and maintain intracellular redox balance. This oxygen consumption results from H₂O-forming NADH oxidase (NOX) activity of two distinct flavin-containing systems: H₂O-forming NOXes and multicomponent flavodiiron proteins (FDPs). Neither system is membrane bound, and both recycle NADH into oxidized NAD⁺ while simultaneously removing O₂ from the local environment. However, little is known about the specific contributions of these systems in T. vaginalis. In this study, we use bioinformatics and biochemical analyses to show that T. vaginalis lacks a NOX–like enzyme and instead harbors three paralogous genes (FDPF1–3), each encoding a natural fusion product between the N-terminal FDP, central rubredoxin (Rb), and C-terminal NADH:Rb oxidoreductase domains. Unlike a “stand-alone” FDP that lacks Rb and oxidoreductase domains, this natural fusion protein with fully populated flavin redox centers directly accepts reducing equivalents of NADH to catalyze the four-electron reduction of oxygen to water within a single polypeptide with an extremely high turnover. Furthermore, using single-particle cryo-EM, we present structural insights into the spatial organization of the FDP core within this multidomain fusion protein. Together, these results contribute to our understanding of systems that allow protozoan parasites to maintain optimal redox balance and survive transient exposure to oxic conditions.     

生物废水处理系统的细胞自动机模型

建立了活性污泥处理生物废水的细胞自动机模型,对活性污泥生物量与有机物浓度动态进行了研究,提出了计算活性污泥回流循环比的方法.结果表明,在Moore邻居模型下废水达标排放所需时间较Von. Neumann邻居模型少,不同生长阶段的微生物浓度波动具有时滞性.稳定期有机物浓度和生物量不受活性污泥初始浓度的影响.活性污泥处理生物废水的细胞自动机模型有助于为污水处理提供理论依据.     

物种灭绝对不同时间尺度栖息地毁坏响应的空间模拟

人类活动所引起的栖息地毁坏已成为当前物种多样性丧失的最主要的原因之一。空间显含模型相对于空间隐含模型来说,更加接近于现实,因此,通过元胞自动机,模拟了物种多样性对万年、千年、百年时间尺度人类活动所引起的栖息地毁坏的响应。研究结果表明：万年时间尺度上,物种是由强到弱的灭绝;而在千年时间尺度上,物种灭绝的序受集合种群结构的影响较大;在百年时间尺度上。物种由于栖息地毁坏过于剧烈和迅速,来不及作出响应。在栖息地完全毁坏时集体灭绝。因此,物种灭绝序不只是受竞争-侵占均衡机制的影响,还受不同时间尺度（不同速率）栖息地毁坏的影响。以及集合种群结构的影响。     

集合种群动态对生境毁坏空间异质性的响应

首次将分形几何(Fractal geometry)与元胞自动机(Cellular automata)相结合,研究了破碎化生境中集合种群的空间分布格局动态,以及集合种群动态对生境毁坏空间异质性的响应。研究发现:(1)各个物种种群在生境中的分布具有很好的分形特征,物种的计盒维数(Box dimension)不仅可以很好地反映种群的空间分布结构,也能很好地反映种群动态。(2)如果将空间因素考虑进来的话,生境毁坏的灭绝债务(Time debt)将大于空间隐含模式所模拟的结果。(3)物种灭绝同时存在强物种灭绝和弱物种灭绝。并且只有在生境随机毁坏下,才与空间隐含的模拟结果比较接近,即强物种中将是最强物种率先灭绝。而在边缘毁坏这种比较集中成块的开发方式下,将是较强的物种灭绝。(4)边缘毁坏相对随机毁坏有利于物种,尤其是弱物种的长期续存。     

Biotechnological challenges of bioartificial kidney engineering

With the world-wide increase of patients with renal failure, the development of functional renal replacement therapies have gained significant interest and novel technologies are rapidly evolving. Currently used renal replacement therapies insufficiently remove accumulating waste products, resulting in the uremic syndrome. A more preferred treatment option is kidney transplantation, but the shortage of donor organs and the increasing number of patients waiting for a transplant warrant the development of novel technologies. The bioartificial kidney (BAK) is such promising biotechnological approach to replace essential renal functions together with the active secretion of waste products. The development of the BAK requires a multidisciplinary approach and evolves at the intersection of regenerative medicine and renal replacement therapy. Here we provide a concise review embracing a compact historical overview of bioartificial kidney development and highlighting the current state-of-the-art, including implementation of living-membranes and the relevance of extracellular matrices. We focus further on the choice of relevant renal epithelial cell lines versus the use of stem cells and co-cultures that need to be implemented in a suitable device. Moreover, the future of the BAK in regenerative nephrology is discussed.     

Deep learning for computational biology

Technological advances in genomics and imaging have led to an explosion of molecular and cellular profiling data from large numbers of samples. This rapid increase in biological data dimension and acquisition rate is challenging conventional analysis strategies. Modern machine learning methods, such as deep learning, promise to leverage very large data sets for finding hidden structure within them, and for making accurate predictions. In this review, we discuss applications of this new breed of analysis approaches in regulatory genomics and cellular imaging. We provide background of what deep learning is, and the settings in which it can be successfully applied to derive biological insights. In addition to presenting specific applications and providing tips for practical use, we also highlight possible pitfalls and limitations to guide computational biologists when and how to make the most use of this new technology.     

Thrombospondin-1 (TSP1)-producing B Cells Restore Antigen (Ag)-specific Immune Tolerance in an Allergic Environment

Restoration of the antigen (Ag)-specific immune tolerance in an allergic environment is refractory. B cells are involved in immune regulation. Whether B cells facilitate the generation of Ag-specific immune tolerance in an allergic environment requires further investigation. This paper aims to elucidate the mechanism by which B cells restore the Ag-specific immune tolerance in an allergic environment. In this study, a B cell-deficient mouse model was created by injecting an anti-CD20 antibody. The frequency of tolerogenic dendritic cell (TolDC) was assessed by flow cytometry. The levels of cytokines were determined by enzyme-linked immunosorbent assay. The expression of thrombospondin-1 (TSP1) was assessed by quantitative real-time RT-PCR, Western blotting, and methylation-specific PCR. The results showed that B cells were required in the generation of the TGF-β-producing TolDCs in mice. B cell-derived TSP1 converted the latent TGF-β to the active TGF-β in DCs, which generated TGF-β-producing TolDCs. Exposure to IL-13 inhibited the expression of TSP1 in B cells by enhancing the TSP1 gene DNA methylation. Treating food allergy mice with Ag-specific immunotherapy and IL-13 antagonists restored the generation of TolDCs and enhanced the effect of specific immunotherapy. In conclusion, B cells play a critical role in the restoration of specific immune tolerance in an allergic environment. Blocking IL-13 in an allergic environment facilitated the generation of TolDCs and enhanced the therapeutic effect of immunotherapy.     

湖泊生态系统弹性系数理论及其应用

在湖泊生态系统健康评价的基础上,分析城市湖泊营养状态的特殊性,论证得出响应型和非响应型湖泊的生态系统健康指数(EHI)与营养状态指数(TSI)近似呈二次函数关系.提出湖泊生态系统弹性系数,对生态系统健康指数(EHI)做出适当改进.改进后的生态系统健康指数(EHI′)能够更好地反映各类型湖泊的健康状态,完善了Xu等的EHI理论并扩展了其应用范围,是目前最为接近Costanza对HI定义的可量化计算的数学公式和方法,并成功用于厦门杏林湾生态系统健康评价.     

锡林郭勒盟煤电基地开发生态脆弱性评价

内蒙古锡林郭勒盟国家大型煤电基地的建设,对我国华北和华东区域能源安全具有重要的作用。但随着锡盟大型煤电基地的开发,其对锡林郭勒盟这一具有重要生态屏障功能的典型草原区的生态环境造成不利影响。通过对区域生态敏感性、生态弹性及生态压力的系统研究,建立了基于生态敏感性、生态弹性及生态压力的生态脆弱性评价模型,对该区域生态脆弱性进行了评价。结果表明,锡盟地区总体生态环境质量较好,但呈现由东北向西南递减的特征。研究为锡林郭勒盟国家大型煤电基地的开发建设,区域协调发展与生态环境保护提供理论支持。