High-throughput RNAi in Caenorhabditis elegans: genome-wide screens and functional genomics

The phenomenon of RNA-mediated interference (RNAi) was first discovered in the nematode Caenorhabditis elegans, in which introduction of double-stranded RNA causes specific inactivation of genes with corresponding sequences. Technical advances in RNAi methodology and the availability of the complete genome sequence have enabled the high-throughput, genome-wide RNAi analysis of this organism. Several groups have used large-scale RNAi to systematically examine every C. elegans gene for knock-down phenotypes, providing basal information to be mined in more detailed studies. Now, in addition to functional genomic RNAi analyses, high-throughput RNAi is also routinely used for rapid, genome-wide screens for genes involved in specific biological processes. The integration of high-throughput RNAi experiments with other large-scale data, such as DNA microarrays and protein-protein interaction maps, enhances the speed and reliability of such screens. The accumulation of RNAi phenotype data dramatically accelerates our understanding of this organism at the genetic level.     

Isotyping of component C4 of human complement using differences in the functional activity of isotypes C4A and C4B

The difference in the functional activity of the isotypes A and B of component C4 of human complement was used to determine their ratio and to detect the inherited deficiency of the isotypes. ELISA methods were developed for the quantitative assay of component C4 (conventional sandwich method) and its functional activity. When determining the functional activity, the classic pathway of the complement and therefore of component C4 was activated on activators sorbed on ELISA microplates: immunoglobulin IgG3 or liposaccharide of theShigella sonnei cell walls, which activates the complement by binding component C1. The nascent fragment C4b is covalently bound to the target activator; C4Ab binds better to the target protein (immunoglobulin), and C4Bb to the target carbohydrate (liposaccharide). Therefore, when immunoglobulin is a target activator, isotype C4A is bound and determined; and when the complement is activated with liposaccharide, isotype C4B is determined. The radio of the activities determined by the two methods indicates the deficiency in the individual isotypes of component C4 or its absence. The rabbit polyclonal monospecific antibodies against the human component C4 and the conjugates of these antibodies with horseradish peroxidase were used in the methods described.     

Hepatitis C virus infection protein network

A proteome‐wide mapping of interactions between hepatitis C virus (HCV) and human proteins was performed to provide a comprehensive view of the cellular infection. A total of 314 protein–protein interactions between HCV and human proteins was identified by yeast two‐hybrid and 170 by literature mining. Integration of this data set into a reconstructed human interactome showed that cellular proteins interacting with HCV are enriched in highly central and interconnected proteins. A global analysis on the basis of functional annotation highlighted the enrichment of cellular pathways targeted by HCV. A network of proteins associated with frequent clinical disorders of chronically infected patients was constructed by connecting the insulin, Jak/STAT and TGFβ pathways with cellular proteins targeted by HCV. CORE protein appeared as a major perturbator of this network. Focal adhesion was identified as a new function affected by HCV, mainly by NS3 and NS5A proteins.     

Deficiencies in C4A and C4B isotypes of human complement revealed by isoelectrofocusing and chemical reactivity of activated forms

An approach is proposed to detect deficiencies in isotypes A and B of the C4 component of human complement, based on the calculation of the ratio of their IEA activities and the ratio of their quantities determined by isoelectrofocusing of their desialated forms with chemiluminescent detection in an immunoblot. The ratios of the quantities and activities of C4A/C4B practically coincided when determined in blood serum of 20 patients, many of which had inherited deficiencies in the C4 component isotypes.     

Plant Functional Type Effects on Trace Gas Fluxes in the Shortgrass Steppe

Plant community structure is expected to regulate the microbial processes of nitrification and denitrification by controlling the availability of inorganic N substrates. Thus it could also be a factor in the concomitant release of NO and N2O from soils as a result of these processes. C3 and C4 plants differ in several attributes related to the cycling of nitrogen and were hypothesized to yield differences in trace gas exchange between soil and atmosphere. In this study we estimated fluxes of NO, N2O and CH4 from soils of shortgrass steppe communities dominated by either C3 plants, C4 plants or mixtures of the two types. We collected gas samples weekly from two sites, a sandy clay loam and a clay, throughout the growing seasons of 1995 and 1996. Plant functional type effects on gas fluxes at the clay site were not apparent, however we found several differences among plant communities on the sandy clay loam. CH4 uptake from atmosphere to soil was significantly greater on C4 plots than C3 plots in both years. NO fluxes were significantly greater from C4 plots than from C3 plots in 1995. NO fluxes from C3 and mixed plots were not significantly different between 1995 and 1996, however fluxes from C4 plots were significantly greater in 1995 compared to 1996. Results indicate that under certain environmental conditions, particularly when factors such as moisture and temperature are not limiting, plant community composition can play an important role in regulating trace gas exchange.     

小陇山黑河自然保护区水曲柳叶片功能性状及碳氮磷化学计量对海拔的响应

【目的】水曲柳是小陇山林区的主要珍贵阔叶用材树种,探讨其叶片性状对小生境变化的适应性,为深入研究影响该树种的主要环境因子提供理论基础。【方法】以小陇山黑河自然保护区内天然水曲柳为研究对象, 采用梯度取样法,设置4个海拔梯度,对其14种叶功能性状和叶片营养元素含量进行差异显著性和相关性分析。【结果】随海拔的升高,水曲柳叶片的叶片厚度、叶干物质含量和叶绿素含量逐渐增大,分别在海拔1 741 m和1 926 m处达到最大,而比叶面积、最大净光合速率、蒸腾速率、叶片C和N含量却逐渐减少,除叶片C含量外均在海拔1 268 m处达到最大。叶面积、气孔导度和叶片C∶N随着海拔的升高呈现先增加后降低的趋势,胞间CO2浓度、C∶P和N∶P呈现先降低后升高的趋势。海拔平均每上升200 m,功能性状和C∶N平均增值介于1.13%～30.72%之间,而比叶面积、最大净光合速率和C、N含量分别减小值介于2.22%～15.75%之间。各海拔叶片N∶P介于4.36～6.89之间,远低于14,且与最大净光合速率呈极显著正相关。最大净光合速率与比叶面积、C和N含量、C∶P和N∶P呈极显著正相关,与叶片厚度、叶干物质含量和叶绿素含量呈极显著负相关,比叶面积与叶干物质含量呈极显著负相关,与C和N含量和C∶P呈极显著正相关。【结论】海拔显著影响水曲柳叶功能性状及叶片元素含量,保护区内1 700 m以下有利于水曲柳叶片发育和养分含量的增加,是其生长的最适分布区。     

No evidence that sex and transposable elements drive genome size variation in evening primroses

Genome size varies dramatically across species, but despite an abundance of attention there is little agreement on the relative contributions of selective and neutral processes in governing this variation. The rate of sex can potentially play an important role in genome size evolution because of its effect on the efficacy of selection and transmission of transposable elements (TEs). Here, we used a phylogenetic comparative approach and whole genome sequencing to investigate the contribution of sex and TE content to genome size variation in the evening primrose (Oenothera) genus. We determined genome size using flow cytometry for 30 species that vary in genetic system and find that variation in sexual/asexual reproduction cannot explain the almost twofold variation in genome size. Moreover, using whole genome sequences of three species of varying genome sizes and reproductive system, we found that genome size was not associated with TE abundance; instead the larger genomes had a higher abundance of simple sequence repeats. Although it has long been clear that sexual reproduction may affect various aspects of genome evolution in general and TE evolution in particular, it does not appear to have played a major role in genome size evolution in the evening primroses.     

冬种绿肥和秸秆还田对双季稻区土壤团聚体和有机质官能团的影响

为探讨外源有机物料在提升土壤有机碳和改良土壤肥力中的作用机理,依托中国农业科学院衡阳红壤实验站的长期定位试验,研究了冬种绿肥和秸秆还田模式(CK,冬闲;MV,冬种紫云英;S,早稻秸秆全量还田;DS,早、晚稻秸秆全量还田;SMV,冬种紫云英+早稻秸秆全量还田;DSMV,冬种紫云英+早、晚稻秸秆全量还田)对土壤团聚体和有机质官能团的影响。结果表明: 双季稻土壤超大团聚体(>2 mm)和大团聚体(0.25～2 mm)含量最多,为72.1%～81.8%,且两者中有机碳含量高达12.1～20.7 g·kg^-1,占总有机碳的22.7%～59.0%。水稻土中有机物官能团以多糖为主,其次为脂肪碳和芳香碳,各官能团的丰度受紫云英种植和秸秆还田的影响。与其他处理相比,DSMV显著增加了水稻土中超大团聚体(>2 mm)和大团聚体(0.25～2 mm)的含量,并促进了两种团聚体内芳香碳等惰性碳的积累。因此,DSMV更有利于土壤团聚体和有机质稳定性的提升,在实际农业生产中具有较大的应用潜力。     

青藏高原多年冻土区不同水分条件的高寒草甸根系功能性状对增温的响应

在青藏高原多年冻土广泛分布的风火山地区,选择小嵩草（Kobresia pygmea）草甸和藏嵩草（Kobresia tibetica）沼泽化草甸为研究对象,采用开顶增温室（Open top chambers, OTCs）模拟气候变暖,探讨模拟增温对土壤水分差异的两种草甸地下生物量及根系功能性状的影响。结果显示,（1）增温显著增加小嵩草草甸0—20 cm根系生物量,主要是由于表层（0—10 cm）根系生物量显著增加,而对藏嵩草沼泽化草甸根系生物量无影响。（2）增温显著增加了小嵩草草甸根组织密度,同时提高了藏嵩草沼泽化草甸10—20 cm的比根长和比根面积（3）增温降低了小嵩草草甸的根系碳含量及10—20 cm根系氮含量,增加了藏嵩草沼泽化草甸的碳含量及10—20 cm根系氮含量,显著提高了小嵩草草甸和藏嵩草沼泽化草甸深层（10—20 cm）根系碳氮比。这些结果预示着增温使得土壤水分较低的小嵩草草甸朝着资源保守的慢速生长型发展,以适应暖干化的环境;土壤水分较高的藏嵩草沼泽化草甸朝着资源获取的快速生长型发展,加速利用土壤中的养分满足植物生长需要。可见,土壤水分可以调节高寒草甸对气候变暖的演变趋势,强调了水分的重要性。     

南亚热带森林常见种和偶见种的功能多样性特征

群落特征可能取决于物种在功能实体功能特征的独特组合（FE）中的分布。了解这些分布是保护生物多样性和维持生态系统功能的基础。鼎湖山南亚热带常绿阔叶林群落物种丰富,根据物种的多度来区分常见种（每hm²超过一个个体）和偶见种（每hm²少于一个个体）。基于功能实体,分别计算功能实体数量、功能冗余度、功能脆弱度和功能过度冗余度来描述每个样方中常见种和偶见种的功能多样性。采用Wilcoxon检验检测常见种和偶见种功能性状的差异,通过线性回归分析常见种和偶见种的功能多样性与物种数量的关系,采用冗余分析（RDA）影响常见种和偶见种的功能多样性的环境因子。研究结果表明：（1）鼎湖山南亚热带常绿阔叶林群落中功能性状在常见种和偶见种间差异显著。（2）群落中数量较低的偶见种保持着较高比例的功能实体数量。功能实体数量、功能冗余度与常见种和偶见种数量显著正相关,功能过度冗余度与偶见种数量显著正相关,功能脆弱度与常见种和偶见种的物种数量呈显著负相关。（3）海拔是影响常见种功能多样性最关键的地形因子,凹凸度是影响偶见种功能多样性最关键的地形因子。土壤含水量是影响常见种功能多样性最关键的土壤因子,速效钾是影响偶见种功能多样性最关键的环境因子。研究结果表明,尽管物种丰富的热带森林具有较高的功能冗余,但其提供的保险效应不能抵消生态系统的功能脆弱性。减少具有独特功能实体和偶见种的损失是避免热带森林生态系统功能损失的有效和必要的方法。     

Soil salinity determines the relative abundance of C3/C4 species in Argentinean grasslands

Aim The C₄ and crassulacean acid metabolism (CAM) pathways are adaptations to compensate for high rates of photorespiration and water and carbon deficiency. This is the first attempt to compare the relative abundance of C₃ vs. C₄ + CAM species in temperate and subtropical grasslands across a latitudinal gradient in central Argentina. We predict that under the same rainfall regime, C₄ + CAM plants will have larger soil coverage in highly saline soils than in neighbouring non‐saline ones. Location Data were taken from three phytogeographical provinces in the Santa Fe province of Argentina: Chaquenian, Pampean and Espinal. Methods The salinity of the soil was estimated through aqueous solution conductivity. The proportions of species belonging to C₃/C₄ + CAM photosynthetic pathways were compared among halophyte and non‐halophyte communities with a χ² homogeneity test. The sum of cover percentages corresponding to the C₃ and C₄ + CAM photosynthetic pathways were calculated and compared using analysis of variance (ANOVA). Results The soil conductivity values were higher in the halophyte than in the non‐halophyte communities for the same phytogeographical area. The C₄ + CAM plants had much higher soil coverage values in halophyte than in non‐halophyte communities in the Pampean and Espinal phytogeographical provinces. The differences were not statistically significant in the Chaquenian province. Main conclusions Soil drought provoked by soil salinity results in a much higher soil cover by C₄ + CAM plants in regions with positive to neutral water balance (i.e. Pampean and Espinal). This differential abundance pattern in C₄ + CAM functional group is not observed in areas where a pronounced water deficit exists per se (Chaquenian region), and therefore C₄ + CAM plants predominate in all environments regardless of soil salinity. Our results suggest that one of the main environmental forces driving the upsurge of C₄ species in Argentinean grasslands might have been the strong local soil salinity gradient.     

Unraveling the relative contribution of inter‐ and intrapopulation functional variability in wild populations of a tadpole species

Functional traits are increasingly recognized as an integrative approach by ecologists to quantify a key facet of biodiversity. And these traits are primarily expressed as species means in previous studies, based on the assumption that the effects of intraspecific variability can be overridden by interspecific variability when studying functional ecology at the community level. However, given that intraspecific variability could also have important effects on community dynamics and ecosystem functioning, empirical studies are needed to investigate the importance of intraspecific variability in functional traits. In this study, 256 Scutiger boulengeri tadpole individuals from four different populations are used to quantify the functional difference between populations within a species, and the relative contribution of inter‐ and intrapopulation variability in functional traits. Our results demonstrate that these four populations differ significantly in functional attributes (i.e., functional position, functional richness, and low functional overlap), indicating that individuals from different populations within a species should be explicitly accounted for in functional studies. We also find similar relative contribution of inter‐ (~56%) and intrapopulation (~44%) variation to the total variability between individuals, providing evidence that individuals within populations should also be incorporated in functional studies. Overall, our results support the recent claims that intraspecific variability cannot be ignored, as well as the general idea of “individual level” research in functional ecology.     

Traits related to carbon sequestration of common plant species in a Stipa grandis steppe in Nei Mongol under different land-uses

为了探究植物与固碳相关属性在不同功能群、器官和物种间的差异, 以及这些属性对不同土地利用方式的响应, 2012年8月对内蒙古大针茅草原的4个样地(长期无干扰样地、长期自由放牧样地、4年围封样地和4年围封割草样地)进行了群落调查, 并采集样地中的常见植物, 测定了与植物固碳相关的属性, 包括全碳含量、全氮含量、碳氮比、纤维素含量、木质素含量和酸性洗涤纤维含量等。以常见植物为对象, 在功能群水平研究了各土地利用方式下全碳含量、全氮含量和碳氮比的差异; 针对各样地的共有种——糙隐子草(Cleistogenes squarrosa)、大针茅(Stipa grandis)、冷蒿(Artemisia frigida)、羊草(Leymus chinensis)和猪毛菜(Salsola collina), 从物种和器官水平分析了不同土地利用方式下植物的固碳相关属性。结果表明: 大针茅草原植物不同功能群、物种和器官间的固碳相关属性存在极显著差异, 不同土地利用方式下大针茅草原不同功能型、物种和器官的固碳相关属性有显著差异。与其他利用方式相比, 4年围封割草对植物与固碳相关属性的影响最为明显, 功能群、器官和物种水平的植物氮含量均有下降。糙隐子草和猪毛菜的这些属性对长期自由放牧的响应敏感, 且方向相反。     

Specific molecular alterations in the norpA-encoded phospholipase C of Drosophila and their effects on electrophysiological responses in vivo

A large number of mutants in the norpA gene, which encodes the phospholipase C (PLC) involved in Drosophila phototransduction, is available for the investigation of the effects of specific amino acid substitutions in PLC on biochemical and electrophysiological properties of these mutants. Of the 47 norpA mutants screened for PLC protein content, all but one (H43) displayed drastically decreased amounts of the protein suggesting that almost any mutational alteration has a deleterious effect on the integrity of the protein. Three new amino acids were identified in the catalytic domains X and Y that are important for PLC catalytic activity and the generation of photoreceptor responses (ERG). One of them was found substituted in H43, which showed a low specific PLC activity, a pronounced decrease in ERG sensitivity, and a wild-type-like response termination time. The response termination times obtained from three mutants was found to be approximately inversely proportional to the amount of PLC. In addition, we show that (i) the specific PLC activity is a key factor determining the photoreceptor sensitivity; (ii) the catalytic activity and response termination are separable functions of PLC; and (iii) a mutation in the putative G alpha-interacting C2 domain causes a preferentially strong defect in latency.     

Rational Design of Hydroxyl‐Rich Ti3C2Tx MXene Quantum Dots for High‐Performance Electrochemical N2 Reduction

To enable an efficient and cost‐effective electrocatalytic N₂ reduction reaction (NRR) the development of an electrocatalyst with a high NH₃ yield and good selectivity is required. In this work, Ti₃C₂T_x MXene‐derived quantum dots (Ti₃C₂T_x QDs) with abundant active sites enable the development of efficient NRR electrocatalysts. Given surface functional groups play a key role on the electrocatalytic performance, density functional theory calculations are first conducted, clarifying that hydroxyl groups on Ti₃C₂T_x offer excellent NRR activity. Accordingly, hydroxyl‐rich Ti₃C₂T_x QDs (Ti₃C₂OH QDs) are synthesized as NRR catalysts by alkalization and intercalation. This material offers an NH₃ yield and Faradaic efficiency of 62.94 µg h^?1 mg^?1_cat. and 13.30% at ?0.50 V, respectively, remarkably higher than reported MXene catalysts. This work demonstrates that MXene catalysts can be mediated through the optimization of both QDs sizes and functional groups for efficient ammonia production at room temperature.