Quercus infectoria galls possess antioxidant activity and abrogates oxidative stress-induced functional alterations in murine macrophages

The present study reports the antioxidant activity of ethanolic extract of Quercus infectoria galls. The antioxidant potency of galls was investigated employing several established in vitro model systems. Their protective efficacy on oxidative modulation of murine macrophages was also explored. Gall extract was found to contain a large amount of polyphenols and possess a potent reducing power. HPTLC analysis of the extract suggested it to contain 19.925% tannic acid (TA) and 8.75% gallic acid (GA). The extract potently scavenged free radicals including DPPH (IC(50)~0.5 microg/ml), ABTS (IC(50)~1 microg/ml), hydrogen peroxide (H(2)O(2)) (IC(50)~2.6 microg/ml) and hydroxyl (*OH) radicals (IC(50)~6 microg/ml). Gall extract also chelated metal ions and inhibited Fe(3+) -ascorbate-induced oxidation of protein and peroxidation of lipids. Exposure of rat peritoneal macrophages to tertiary butyl hydroperoxide (tBOOH) induced oxidative stress in them and altered their phagocytic functions. These macrophages showed elevated secretion of lysosomal hydrolases, and attenuated phagocytosis and respiratory burst. Activity of macrophage mannose receptor (MR) also diminished following oxidant exposure. Pretreatment of macrophages with gall extract preserved antioxidant armory near to control values and significantly protected against all the investigated functional mutilations. MTT assay revealed gall extract to enhance percent survival of tBOOH exposed macrophages. These results indicate that Q. infectoria galls possess potent antioxidant activity, when tested both in chemical as well as biological models.     

Water quality index,Labeo rohita,and Eichhornia crassipes: Suitable bio-indicators of river water pollution

The present study investigated the water quality index (WQI) of the Kshipra river at Dewas, Madhya Pradesh, India, using native fish Labeo rohita, and plant Eichhornia crassipes. The temperature, pH, dissolved oxygen, alkalinity, turbidity, and dissolved solids were found to be within the prescribed limits. However, heavy metals concentration exceeded the limit except for Cu and Zn. Their occurrence in river water was as follows: Ni > Fe > Cd > Cr > Mn > Zn > Cu. Among these heavy metals, Cd was found to be highly bioavailable, whereas Zn was the least bioavailable metal. Based on WQI, the water was found to be unfit for drinking, and the high WQI value was due to the presence of Cr and Cd. In fish tissues (muscle, liver, gut, gills, and kidney), the highest and lowest metal pollution index was found in gills (45.03) and kidneys (12.21), respectively. Bioaccumulation of these metals resulted in significant depletion of energy reserves (protein, glucose, and glycogen) and also altered hematological parameters. Moreover, liver function tests showed hepatic damage in the exposed fish. In-plant, both the bioaccumulation and mobility factor exceeded 1 for all these metals. On the other hand, the translocation factor was found to be beyond 1 for Fe, Ni, and Zn. These high values make this plant fit for phytoextraction of Mn, Fe, Cu, Zn, and Cd and phytostabilization of Cr in water. Moreover, consumption of L. rohita from the Kshipra River does not pose a non-cancer risk as the target hazard quotient was below 1, but it may pose cancer risk because of the presence of Cr in the range of 1.402 × 10^?3 to 1.599 × 10^?3.     

土壤原生生物多样性及其生态功能研究进展

原生生物广泛分布在土壤和不同生境中, 其数量庞大、种类繁多, 在生态系统物质循环和能量流动以及维持土壤和植物健康中起着举足轻重的作用。与土壤其他生物类群相比, 原生生物分类体系和生态类型复杂, 分类鉴定困难且分子检测技术不够成熟, 目前对原生生物的认识相对不足。本文对当前原生生物的相关研究进展进行了总结和梳理, 系统阐述了原生生物的分类系统和营养功能群特征、土壤原生生物的多样性分布特征及影响因子, 重点介绍了原生生物群落在参与土壤养分循环、维持土壤和植物健康等中的功能作用, 并对未来的研究方向与应用前景进行了展望。对土壤原生生物的研究有助于我们深入认识土壤生物多样性资源, 并进行保护性地开发和利用, 维护土壤和生态系统健康。     

Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction.

Loops are regions of nonrepetitive conformation connecting regular secondary structures. We identified 2,024 loops of one to eight residues in length, with acceptable main-chain bond lengths and peptide bond angles, from a database of 223 protein and protein-domain structures. Each loop is characterized by its sequence, main-chain conformation, and relative disposition of its bounding secondary structures as described by the separation between the tips of their axes and the angle between them. Loops, grouped according to their length and type of their bounding secondary structures, were superposed and clustered into 161 conformational classes, corresponding to 63% of all loops. Of these, 109 (51% of the loops) were populated by at least four nonhomologous loops or four loops sharing a low sequence identity. Another 52 classes, including 12% of the loops, were populated by at least three loops of low sequence similarity from three or fewer nonhomologous groups. Loop class suprafamilies resulting from variations in the termini of secondary structures are discussed in this article. Most previously described loop conformations were found among the classes. New classes included a 2:4 type IV hairpin, a helix-capping loop, and a loop that mediates dinucleotide-binding. The relative disposition of bounding secondary structures varies among loop classes, with some classes such as beta-hairpins being very restrictive. For each class, sequence preferences as key residues were identified; those most frequently at these conserved positions than in proteins were Gly, Asp, Pro, Phe, and Cys. Most of these residues are involved in stabilizing loop conformation, often through a positive phi conformation or secondary structure capping. Identification of helix-capping residues and beta-breakers among the highly conserved positions supported our decision to group loops according to their bounding secondary structures. Several of the identified loop classes were associated with specific functions, and all of the member loops had the same function; key residues were conserved for this purpose, as is the case for the parvalbumin-like calcium-binding loops. A significant number, but not all, of the member loops of other loop classes had the same function, as is the case for the helix-turn-helix DNA-binding loops. This article provides a systematic and coherent conformational classification of loops, covering a broad range of lengths and all four combinations of bounding secondary structure types, and supplies a useful basis for modelling of loop conformations where the bounding secondary structures are known or reliably predicted.     

人源溶菌酶结构与功能的研究进展

人溶菌酶是一类人体内天然存在的能够溶解细菌细胞壁的碱性蛋白的总称。其作用特征是能够裂解肽聚糖中的N-乙酰氨基葡萄糖与N-乙酰氨基甲酸之间的β-(1,4)-糖苷键。人溶菌酶具有抗菌、抗炎、抗病毒和增强免疫力等多种特性,因此在国内外市场上应用广泛。本文就人溶菌酶的结构特点、表达部位、功能表达以及应用情况进行综述。     

Herbivory drives large‐scale spatial variation in reef fish trophic interactions

Trophic interactions play a critical role in the structure and function of ecosystems. Given the widespread loss of biodiversity due to anthropogenic activities, understanding how trophic interactions respond to natural gradients (e.g., abiotic conditions, species richness) through large‐scale comparisons can provide a broader understanding of their importance in changing ecosystems and support informed conservation actions. We explored large‐scale variation in reef fish trophic interactions, encompassing tropical and subtropical reefs with different abiotic conditions and trophic structure of reef fish community. Reef fish feeding pressure on the benthos was determined combining bite rates on the substrate and the individual biomass per unit of time and area, using video recordings in three sites between latitudes 17°S and 27°S on the Brazilian Coast. Total feeding pressure decreased 10‐fold and the composition of functional groups and species shifted from the northern to the southernmost sites. Both patterns were driven by the decline in the feeding pressure of roving herbivores, particularly scrapers, while the feeding pressure of invertebrate feeders and omnivores remained similar. The differential contribution to the feeding pressure across trophic categories, with roving herbivores being more important in the northernmost and southeastern reefs, determined changes in the intensity and composition of fish feeding pressure on the benthos among sites. It also determined the distribution of trophic interactions across different trophic categories, altering the evenness of interactions. Feeding pressure was more evenly distributed at the southernmost than in the southeastern and northernmost sites, where it was dominated by few herbivores. Species and functional groups that performed higher feeding pressure than predicted by their biomass were identified as critical for their potential to remove benthic biomass. Fishing pressure unlikely drove the large‐scale pattern; however, it affected the contribution of some groups on a local scale (e.g., large‐bodied parrotfish) highlighting the need to incorporate critical functions into conservation strategies.     

Expected utility maximization and selection of stable plant cultivars

Summary In most plant breeding programs, selection of the best commercially suitable cultivars for a target group of environments is based on information obtained from evaluation trials cultivated in a sample of environments. Information on the performance of cultivars collected in a sample of environments can only be approximate and, consequently, selection of the best cultivar involves choosing among cultivars that respond uncertainly in many environments. The agronomic and/or economic value of a cultivar across environments may be considered the general or overall utility of the cultivar. Data from a sample of environments therefore provides only an estimate of any cultivar's overall utility, with the overall goal of selection among all cultivars being the maximization of the expected utility. Within this frame-work, expected utility maximization, an approach to decision making that has been well developed in the disciplines of economics and statistics, can assist the plant breeder in making such decisions. This research was initiated (1) to determine how expected utility maximization might be used to develop indices that are useful for selecting broadly adapted plant cultivars, and (2) to determine how the breeder's preferences might affect choice of the best cultivar. The data used in this research were from USDA Regional Soybean Tests. The results indicated that expected utility maximization, which explicitly incorporates into the selection rule the plant breeder's preferences regarding stability, can be a useful aid in the selection of stable plant cultivars.     

黏蛋白1基因敲除小鼠模型的构建

黏蛋白1(MUC1)属黏蛋白家族成员,分布于上皮细胞膜表面,由于在免疫炎症反应以及肿瘤发生中的重要作用而日益受到重视.为了进一步深入研究MUC1的生物学功能,构建了Muc1基因敲除小鼠模型.首先,根据小鼠Muc1基因组序列设计基因剔除策略,将2个loxP位点分别插在外显子2和3两侧,构建基因剔除载体Muc1-ABRLFn-pBR322.以电穿孔方法将载体导入胚胎干细胞(ES细胞),用G418和更昔洛韦进行正负筛选获得4个同源重组的ES细胞克隆.挑选其中一个阳性ES克隆行囊胚显微注射,获得16只嵌合率大于50%的雄鼠;其次,利用嵌合雄鼠与C57BL/6J野生型雌鼠交配后获得11只floxP杂合子小鼠(10雄1雌),通过杂合子小鼠回交,并进一步与EⅡa-Cre小鼠交配,最终成功得到Muc1全身敲除小鼠,其中纯合子小鼠未出现胚胎致死现象.初步表型观察未发现Muc1基因敲除相关器官组织结构的异常改变.本研究为MUC1的生物学功能的挖掘,尤其是MUC1在肿瘤发生转移中的作用机制的揭示提供了实验平台.     

On the accuracy of analytical potentials: comment on ‘Accurate ab initio calculation of the Ar–CF4 intermolecular potential energy surface’

In a recent study of the Ar–CF₄ intermolecular interaction potential [Shen C-C, Chang R-Y. Accurate ab initio calculation of the Ar–CF₄ intermolecular potential energy surface. Mol Sim. 2010;36:1111–1122], Shen and Chang (SC) illustrated how the use of bond functions can improve the accuracy and basis-set saturation of electronic structure calculations employing perturbation and coupled-cluster theory. SC then used these ab initio data to derive analytic potential energy functions for use in chemical dynamics simulations. We critically examine these analytic potentials and comment on their usage in such simulations. Our analysis highlights the need for care and global validation when deriving analytic potential energy functions.