A predicted consensus structure for the protein kinase C2 homology (C2H) domain,the repeating unit of synaptotagmin

A secondary structure has been predicted for the protein kinase C2 regulatory domain found in homologous form in synaptotagmin, some phospholipases, and some GTP activated proteins. The proposed structure is built from seven consecutive beta strands followed by a terminal alpha helix. Considerations of overall surface exposure of individual secondary structural elements suggest that these are packed into a 2-sheet beta sandwich structure, with one of only three of the many possible folds being preferred. © 1995 Wiley-Liss, Inc.     

A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%.

To improve secondary structure predictions in protein sequences, the information residing in multiple sequence alignments of substituted but structurally related proteins is exploited. A database comprised of 70 protein families and a total of 2,500 sequences, some of which were aligned by tertiary structural superpositions, was used to calculate residue exchange weight matrices within alpha-helical, beta-strand, and coil substructures, respectively. Secondary structure predictions were made based on the observed residue substitutions in local regions of the multiple alignments and the largest possible associated exchange weights in each of the three matrix types. Comparison of the observed and predicted secondary structure on a per-residue basis yielded a mean accuracy of 72.2%. Individual alpha-helix, beta-strand, and coil states were respectively predicted at 66.7, and 75.8% correctness, representing a well-balanced three-state prediction. The accuracy level, verified by cross-validation through jack-knife tests on all protein families, dropped, on average, to only 70.9%, indicating the rigor of the prediction procedure. On the basis of robustness, conceptual clarity, accuracy, and executable efficiency, the method has considerable advantage, especially with its sole reliance on amino acid substitutions within structurally related proteins.     

用于蛋白质同源模建及三维结构预测的结构比较方法

继前面的工作把测试蛋白从三族扩大到十一族,寻求联配参数的普适“缺省值“;比较不同的主链曲率和挠率的计算方法,进一步确认主链的折红红分几何刻划方法的有效性;寻找有效的可变缺失突变惩罚函数的形式。结果表明,编制的蛋白质多重联配软件系统是满意的,可用于蛋白质三维结构预测。     

Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing--a review

A widespread class of introns is characterized by a particular RNA secondary structure, based upon four conserved nucleotide sequences. Among such "class I" introns are found the majority of introns in fungal mitochondrial genes and the self-splicing intron of the large ribosomal RNA of several species of Tetrahymena. A model of the RNA secondary structure, which must underlie the self-splicing activity, is here evaluated in the light of data on 16 further introns. The main body or "core structure" of the intron always consists of the base-paired regions P3 to P9 with the associated single-stranded loops, with P2 present also in most cases. Two minority sub-classes of core structure occur, one of which is typical of introns in fungal ribosomal RNA. Introns in which the core structure is close to the 5' splice site all have an internal guide sequence (IGS) which can pair with exon sequences adjacent to the 5' and 3' splice sites to align them precisely, as proposed by Davies et al. [Nature 300 (1982) 719-724]. In these cases, the internal guide model allows us to predict correctly the exact location of splice sites. All other introns probably use other mechanisms of alignment. This analysis provides strong support for the RNA splicing model which we have developed.     

Estimating predation risk in zooplankton communities: the importance of vertical overlap

In order to estimate predation risk in nature, two basic components of predation need to be quantified: prey vulnerability, and density risk. Prey vulnerability can be estimated from clearance rates obtained from enclosure experiments with and without predators. Density risk is a function of predator density, and the spatial and temporal overlap of the predator and prey populations. In the current study we examine the importance of the vertical component of overlap in making accurate estimates of predation risk from the invertebrate predator Mesocyclops edax on rotifer versus crustacean prey. The results indicate that assumptions of uniform predator and prey densities cause a significant underestimation of predation risk for many crustacean prey due to the coincident vertical migration of these prey with the predator. The assumption of uniformity is more reasonable for estimating predation risk for most rotifer prey.     

Excretion of total phosphorus,dissolved reactive phosphorus,ammonia, and urea by Lake MichiganMysis relicta

Rates of nutrient release byMysis relicta in Lake Michigan were measured on five nights at a 45-m station near Milwaukee, Wisconsin, U.S.A., in the summer of 1977. Nocturnal vertical migrations of the mysids were monitored with both echosounder tracings and vertical net tows. Estimates of the total areal dry mass of the mysids ranged from 600 to 1 820 mg m–2. Rates of release of dissolved reactive phosphorus, total phosphorus, ammonia, and urea were measured in dark incubations on shipboard. Excretion experiments were initiated immediately after mysids were collected from each of several vertical net hauls. The depths of maximum mysid densities corresponded approximately with a deep phytoplankton peak located in the vicinity of the thermocline. Semiquantitative demands for N and P by phytoplankton within this peak were obtained from¹⁴C estimates of primary production from a previous study, assuming a constant C:N:P ratio for the algae. These algal nutrient demands were compared to potential N and P release by the mysids to obtain a first approximation of the relative rates of nutrient supply and demand for the field phytoplankton populations. Our analysis indicates that mysids may directly supply about 1–10% of the daily N and P demands of the phytoplankton in the deep peak. However, indirect interactions betweenMysis relicta and other organisms, such as small zooplankton and fishes, could be major factors in nutrient recycling within the metalimnion and subthermocline region of Lake Michigan.Contribution No. 238, Center for Great Lakes Studies, University of Wisconsin-Milwaukee, Wisconsin.Contribution No. 238, Center for Great Lakes Studies, University of Wisconsin-Milwaukee, Wisconsin.     

Evaluation of a standpipe corer for sampling aquatic interstitial biotopes

The relative efficiencies of two sizes of a standpipe corer were evaluated. The size composition of the gravel sampled by the corer was very similar to that (below the opening size of the core chamber) of the streambed. The small corer (25 cm³ sample size) produced a mean overestimate of total numbers of only 19% even in highly heterogeneous gravels. Most of the taxa commonly in the substrates sampled did not escape from the corer. A few rare taxa were consistently over- or under-estimated and possible reasons for this are discussed.     

A Review on Additives for Halide Perovskite Solar Cells

Additives are widely adopted for efficient, stable, and hysteresis‐free perovskite solar cells and play an important role in various breakthroughs of perovskite solar cells (PSCs). Herein the various additives adopted for PSCs are reviewed and their functioning mechanism and influence on device performance is described. The main roles of additives, modulating morphology of perovskite films, stabilizing phase of formamidinium (FA) and cesium (Cs)‐based perovskites, adjusting energy level alignment in PSCs, suppressing nonradiative recombination in perovskites, eliminating hysteresis, enhancing operational stability of PSCs, are summarized.     

Achieving Balanced Crystallization Kinetics of Donor and Acceptor by Sequential‐Blade Coated Double Bulk Heterojunction Organic Solar Cells

Sequential deposition has great potential to achieve high performance in organic solar cells due to the resulting well‐controlled vertical phase separation. In this work, double bulk heterojunction organic solar cells are fabricated by sequential‐blade cast in ambient conditions. Probed by the in situ grazing incidence X‐ray diffraction and in situ UV–vis absorption measurements, the seq‐blade system exhibits a different tendency from each of the binary films during the film formation process. Due to the extensive aggregation of FOIC, the binary PBDB‐T:FOIC film displays a strong and large phase separation, resulting in low current density (J_sc) and unsatisfactory power conversion efficiency. In the seq‐blade cast system, the bottom layer PBDB‐T:IT‐M produces many crystal nuclei for the top layer PBDB‐T:FOIC, so the PBDB‐T molecules are able to crystallize easily and quickly. Balanced crystallization kinetics between polymer and small molecule and an ideal percolation network in the film are observed. In addition, the balanced crystallization kinetics are favorable toward realizing lower recombination loss through charge transport processes.