Boltzmann probability of RNA structural neighbors and riboswitch detection

MOTIVATION: We describe algorithms implemented in a new software package, RNAbor, to investigate structures in a neighborhood of an input secondary structure S of an RNA sequence s. The input structure could be the minimum free energy structure, the secondary structure obtained by analysis of the X-ray structure or by comparative sequence analysis, or an arbitrary intermediate structure. RESULTS: A secondary structure T of s is called a delta-neighbor of S if T and S differ by exactly delta base pairs. RNAbor computes the number (N(delta)), the Boltzmann partition function (Z(delta)) and the minimum free energy (MFE(delta)) and corresponding structure over the collection of all delta-neighbors of S. This computation is done simultaneously for all delta < or = m, in run time O (mn3) and memory O(mn2), where n is the sequence length. We apply RNAbor for the detection of possible RNA conformational switches, and compare RNAbor with the switch detection method paRNAss. We also provide examples of how RNAbor can at times improve the accuracy of secondary structure prediction. AVAILABILITY: http://bioinformatics.bc.edu/clotelab/RNAbor/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

绒山羊和绵羊KAP6.1基因CDS区克隆与分析

目的:克隆绒山羊、绵羊KAP6.1基因CDS全序列,分析序列特征和蛋白结构。方法:RT-PCR法克隆基因并测序,生物信息学软件分析序列特征和结构。结果:绒山羊、绵羊KAP6.1基因CDS序列全长252 bp,编码83个氨基酸;绒山羊、绵羊KAP6.1蛋白在基本理化特性、二级结构以及空间三维结构上的差异较小。结论:绒山羊与绵羊KAP6.1蛋白结构上的差异将会在一定程度上影响其功能。     

The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA.

BACKGROUND:. The translation elongation factor EF-Tu in its GTP-bound state forms a ternary complex with any aminoacylated tRNA (aa-tRNA), except initiator tRNA and selenocysteinyl-tRNA. This complex delivers aa-tRNA to the ribosomal A site during the elongation cycle of translation. The crystal structure of the yeast Phe-tRNAPhe ternary complex with Thermus aquaticus EF-Tu-GDPNP (Phe-TC) has previously been determined as one representative of this general yet highly discriminating complex formation. RESULTS: The ternary complex of Escherichia coli Cys-tRNACys and T. aquaticus EF-Tu-GDPNP (Cys-TC) has been solved and refined at 2.6 degrees resolution. Conserved and variable features of the aa-tRNA recognition and binding by EF-Tu-GTP have been revealed by comparison with the Phe-TC structure. New tertiary interactions are observed in the tRNACys structure. A 'kissing complex' is observed in the very close crystal packing arrangement. CONCLUSIONS: The recognition of Cys-tRNACys by EF-Tu-GDPNP is restricted to the aa-tRNA motif previously identified in Phe-TC and consists of the aminoacylated 3' end, the phosphorylated 5' end and one side of the acceptor stem and T stem. The aminoacyl bond is recognized somewhat differently, yet by the same primary motif in EF-Tu, which suggests that EF-Tu adapts to subtle variations in this moiety among all aa-tRNAs. New tertiary interactions revealed by the Cys-tRNACys structure, such as a protonated C16:C59 pyrimidine pair, a G15:G48 'Levitt pair' and an s4U8:A14:A46 base triple add to the generic understanding of tRNA structure from sequence. The structure of the 'kissing complex' shows a quasicontinuous helix with a distinct shape determined by the number of base pairs.     

Protein secondary structure: entropy, correlations and prediction

MOTIVATION: Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone or by non-local tertiary interactions? To answer this question, we measure the entropy densities of primary and secondary structure sequences, and the local inter-sequence mutual information density. RESULTS: We find that the important inter-sequence interactions are short ranged, that correlations between neighboring amino acids are essentially uninformative and that only one-fourth of the total information needed to determine the secondary structure is available from local inter-sequence correlations. These observations support the view that the majority of most proteins fold via a cooperative process where secondary and tertiary structure form concurrently. Moreover, existing single-sequence secondary structure prediction algorithms are almost optimal, and we should not expect a dramatic improvement in prediction accuracy. AVAILABILITY: Both the data sets and analysis code are freely available from our Web site at http://compbio.berkeley.edu/     

Arby: automatic protein structure prediction using profile-profile alignment and confidence measures

MOTIVATION: Arby is a new server for protein structure prediction that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The methods used include a threading approach, which makes use of structural information, and a profile-profile alignment approach that incorporates secondary structure predictions. The combination of the different methods with the help of empirically derived confidence measures affords reliable template selection. RESULTS: According to the recent CAFASP3 experiment, the server is one of the most sensitive methods for predicting the structure of single domain proteins. The quality of template selection is assessed using a fold-recognition experiment. AVAILABILITY: The Arby server is available through the portal of the Helmholtz Network for Bioinformatics at http://www.hnbioinfo.de under the protein structure category.     

pRNA导入型Ribozyme的设计和体外转录制备

目的:枯草杆菌的包装RNA分子pRNA是新型纳米分子载体,将其同锤头型核酶Ribozyme重组可以构建结构稳定、能进入细胞、主动识别结合和剪切基因RNA的pRNA-Ribozyme.由于目前100 nt以上的RNA分子采用化学合成制备较为困难,实验采用基因重组构建并体外转录制备170 nt的pRNA-Ribozyme....     

XdomView: protein domain and exon position visualization

SUMMARY: The relationship between intron distribution in the eukaryotic gene and protein structural elements is essential for understanding the origin and evolution of genes. XdomView is a web-based viewer mapping protein structural domains and intron positions in eukaryotic homologues to its tertiary structure. The association of sequence signals to 3D structure in XdomView provides a valuable visualization environment for eukaryotic gene organization, gene evolution, protein folding and protein structure classification. AVAILABILITY: Freely available from http://surya.bic.nus.edu.sg/xdom.     

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

MOTIVATION: As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. RESULT: We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. AVAILABILITY: Source code available from http://mastr.binf.ku.dk/     

Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles

Secondary structure predictions are increasingly becoming the workhorse for several methods aiming at predicting protein structure and function. Here we use ensembles of bidirectional recurrent neural network architectures, PSI-BLAST-derived profiles, and a large nonredundant training set to derive two new predictors: (a) the second version of the SSpro program for secondary structure classification into three categories and (b) the first version of the SSpro8 program for secondary structure classification into the eight classes produced by the DSSP program. We describe the results of three different test sets on which SSpro achieved a sustained performance of about 78% correct prediction. We report confusion matrices, compare PSI-BLAST to BLAST-derived profiles, and assess the corresponding performance improvements. SSpro and SSpro8 are implemented as web servers, available together with other structural feature predictors at: http://promoter.ics.uci.edu/BRNN-PRED/.     

Land-use and soil depth affect resource and microbial stoichiometry in a tropical mountain rainforest region of southern Ecuador

Global change phenomena, such as forest disturbance and land-use change, significantly affect elemental balances as well as the structure and function of terrestrial ecosystems. However, the importance of shifts in soil nutrient stoichiometry for the regulation of belowground biota and soil food webs have not been intensively studied for tropical ecosystems. In the present account, we examine the effects of land-use change and soil depth on soil and microbial stoichiometry along a land-use sequence (natural forest, pastures of different ages, secondary succession) in the tropical mountain rainforest region of southern Ecuador. Furthermore, we analyzed (PLFA-method) whether shifts in the microbial community structure were related to alterations in soil and microbial stoichiometry. Soil and microbial stoichiometry were affected by both land-use change and soil depth. After forest disturbance, significant decreases of soil C:N:P ratios at the pastures were followed by increases during secondary succession. Microbial C:N ratios varied slightly in response to land-use change, whereas no fixed microbial C:P and N:P ratios were observed. Shifts in microbial community composition were associated with soil and microbial stoichiometry. Strong positive relationships between PLFA-markers 18:2n6,9c (saprotrophic fungi) and 20:4 (animals) and negative associations between 20:4 and microbial N:P point to land-use change affecting the structure of soil food webs. Significant deviations from global soil and microbial C:N:P ratios indicated a major force of land-use change to alter stoichiometric relationships and to structure biological systems. Our results support the idea that soil biotic communities are stoichiometrically flexible in order to adapt to alterations in resource stoichiometry.     

DNA conformation and energy in nucleosome core: a theoretical approach

DNA conformation in complex with proteins is far from its canonical B-form. The affinity of complex formation and structure of DNA depend on its attachment configuration and sequence. In this article, we develop a mechanical model to address the problem of DNA structure and energy under deformation. DNA in nucleosome core particle is described as an example. The structure and energy of nucleosomal DNA is calculated based on its sequence and positioning state. The inferred structure has remarkable similarity with X-ray data. Although there is no sequence-specific interaction of bases and the histone core, we found considerable sequence dependency for the nucleosomal DNA positioning. The affinity of nucleosome formation for several sequences is examined and the differences are compatible with observations. We argue that structural energy determines the natural state of nucleosomal DNA and is the main reason for affinity differences in vitro. This theory can be utilized for the DNA structure and energy determination in protein–DNA complexes in general.

An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:17     

A simple and fast secondary structure prediction method using hidden neural networks

MOTIVATION: In this paper, we present a secondary structure prediction method YASPIN that unlike the current state-of-the-art methods utilizes a single neural network for predicting the secondary structure elements in a 7-state local structure scheme and then optimizes the output using a hidden Markov model, which results in providing more information for the prediction. RESULTS: YASPIN was compared with the current top-performing secondary structure prediction methods, such as PHDpsi, PROFsec, SSPro2, JNET and PSIPRED. The overall prediction accuracy on the independent EVA5 sequence set is comparable with that of the top performers, according to the Q3, SOV and Matthew's correlations accuracy measures. YASPIN shows the highest accuracy in terms of Q3 and SOV scores for strand prediction. AVAILABILITY: YASPIN is available on-line at the Centre for Integrative Bioinformatics website (http://ibivu.cs.vu.nl/programs/yaspinwww/) at the Vrije University in Amsterdam and will soon be mirrored on the Mathematical Biology website (http://www.mathbio.nimr.mrc.ac.uk) at the NIMR in London. CONTACT: kxlin@nimr.mrc.ac.uk     

Fully automated ab initio protein structure prediction using I-SITES,HMMSTR and ROSETTA

MOTIVATION: The Monte Carlo fragment insertion method for protein tertiary structure prediction (ROSETTA) of Baker and others, has been merged with the I-SITES library of sequence structure motifs and the HMMSTR model for local structure in proteins, to form a new public server for the ab initio prediction of protein structure. The server performs several tasks in addition to tertiary structure prediction, including a database search, amino acid profile generation, fragment structure prediction, and backbone angle and secondary structure prediction. Meeting reasonable service goals required improvements in the efficiency, in particular for the ROSETTA algorithm. RESULTS: The new server was used for blind predictions of 40 protein sequences as part of the CASP4 blind structure prediction experiment. The results for 31 of those predictions are presented here. 61% of the residues overall were found in topologically correct predictions, which are defined as fragments of 30 residues or more with a root-mean-square deviation in superimposed alpha carbons of less than 6A. HMMSTR 3-state secondary structure predictions were 73% correct overall. Tertiary structure predictions did not improve the accuracy of secondary structure prediction.     

Analysis of conservation and substitutions of secondary structure elements within protein superfamilies

MOTIVATION: Structural alignments of superfamily members often exhibit insertions and deletions of secondary structure elements (SSEs), yet conserved subsets of SSEs appear to be important for maintaining the fold and facilitating common functionalities. RESULTS: A database of aligned SSEs was constructed from the structure-based alignments of protein superfamily members in the CAMPASS database. SSEs were classified into several types on the basis of their length and solvent accessibility and counts were made for the replacements of SSEs in different types at structurally aligned positions. The results, summarized as log-odds substitution matrices, can be used for two types of comparisons: (1) structure against structure, both with secondary structure assignments; and (2) structure against sequence with predicted secondary structures. The conservation of SSEs at each alignment position was defined as the deviation of observed SSE frequencies from the uniform distribution. This offers a useful resource to define and examine the core of superfamily folds. Even when the structure of only a single member of a superfamily is known, the extended method can be used to predict the conservation of SSEs. Such information will be useful when modelling the structure of other members of a superfamily or identifying structurally and functionally important positions in the fold.     

Isolation and characterization of novel glycolipids with blood group A-related structures: galactosyl-A and sialosylgalactosyl-A

Two glycosphingolipids with the following novel structures have been isolated from human blood cells and characterized by NMR, direct probe mass spectrometry, fast atom bombardment-mass spectrometry, and methylation analysis: (Formula: see text). Both structure i and structure ii are characterized by substitution of beta-galactosyl or sialosyl-beta-galactosyl residue at the terminal alpha-GalNAc residue of blood group A determinant and are therefore specific products associated with the blood group A phenotype.     

STARS: statistics on inter-atomic distances and torsion angles in protein secondary structures

SUMMARY: A graphics package has been developed for performing statistics on interatomic distances and torsion angles in protein secondary structures (STARS) from a protein crystal structure database. It allows one to obtain both the graphical view and the text format of distributions of the distances and angles for atoms located in 10 types of protein secondary structures. STARS will facilitate assignment of ambiguous NOESY peaks, structure determination by nuclear magnetic resonance, structure validation and comparison of protein folds. AVAILABILITY: All data, documents and execute files are freely downloadable at http://stars.zhengyuhome.com. The software works appropriately on Windows system, without any compilation or installation. CONTACT: dbsydw@nus.edu.sg.     

鼻腔结构异常与慢性泪囊炎的关系及对手术预后的影响

摘要 目的：研究鼻腔结构异常与慢性泪囊炎（CD）的关系及对手术预后的影响。方法：将从2017年2月～2019年2月青岛大学附属青岛市市立医院收治的200例CD患者纳入研究,分析其鼻腔结构异常发生情况。将患者按照是否发生鼻腔结构异常分成异常组（n=132）及无异常组（n=68）,比较两组各项基线资料,并分析CD患者鼻腔结构异常发生的影响因素。将所有患者按照术后疗效的差异分成治愈组（n=152）及未治愈组（n=48）,并以多因素Logistic回归分析CD患者预后的影响因素。结果：200例患者共检出鼻腔结构异常132例,占比66.00%。异常组年龄＜60岁、职业状态为待业以及有吸烟史人数占比均高于无异常组（均P＜0.05）。经多因素Logistic回归分析发现：年龄＜60岁、职业状态为待业以及有吸烟史均是CD患者鼻腔结构异常的危险因素（均P＜0.05）。经单因素分析可得：年龄、鼻泪管引流管拔除时间以及鼻腔结构异常均和CD患者预后有关（均P＜0.05）。经多因素Logistic回归分析发现：年龄≥60岁、鼻泪管引流管拔除时间＞术后3个月以及鼻腔结构异常均是CD患者预后的危险因素（均P＜0.05）。结论：鼻腔结构异常与CD发生、发展密切相关,且多见于年龄＜60岁,有吸烟史以及待业人群中。此外,年龄≥60岁、鼻泪管引流管拔除时间在术后3个月以上以及鼻腔结构异常均是CD患者手术预后的独立危险因素,应予以重点关注。     

Significant demographic and fine-scale genetic structure in expanding and senescing populations of the terrestrial orchid Cymbidium goeringii (Orchidaceae)

? Premise of the study: Fine-scale genetic structure (FSGS) in plants is influenced by variation in spatial and temporal demographic processes. To determine how demographic structure and FSGS change with stages of population succession, we studied replicate expanding and senescing populations of the Asian terrestrial orchid Cymbidium goeringii. ? Methods: We used spatial autocorrelation methods (O-ring and kinship statistics) to quantify spatial demographic structure and FSGS in two expanding and two senescing populations, also measuring genetic diversity and inbreeding in each. ? Key results: All populations exhibited significant aggregation of individuals and FSGS at short spatial scales. In expanding populations, this finding was associated with high recruitment rates, suggesting restricted seed dispersal. In senescing populations, recruitment was minimal, suggesting alternative mechanisms of aggregation, perhaps including spatial associations with mycorrhizal fungi. All populations had significant evidence of genetic bottlenecks, and inbreeding levels were consistently high. ? Conclusions: Our results indicate that different successional stages can generate similar patterns of spatial demographic and genetic structure, but as a consequence of different processes. These results contrast with the only other study of senescence effects on population genetic structure in an herbaceous perennial, which found little to no FSGS in senescing populations. With the exception of populations subject to mass collection by orchid sellers, significant FSGS is characteristic of the 16 terrestrial orchid species examined to date. From a conservation perspective, this result suggests that inference of orchid population history will benefit from analyses of both FSGS and demographic structure in combination with other ecological field data.     

小鼠富亮氨酸重复结构蛋白Lrig2 基因、蛋白结构及组织定位分析

目的:分析小鼠富亮氨酸重复结构蛋白家族成员Lrig2的基因与蛋白的结构,明确其组织分布和定位,并对其功能进行初步预测。方法:利用生物信息学分析技术对小鼠Lrig2基因的染色体定位、蛋白结构进行分析预测;通过RT-PCR、mRNA原位杂交技术检测Lrig2基因在小鼠不同组织中的表达定位;通过系统进化树分析Lrig2与其他Lrrs蛋白家族成员的同源性。结果:生物信息学分析显示,Lrig2是一种跨膜蛋白受体,是Lrrs蛋白超家族成员之一,胞外区含有15个Lrr模序、3个免疫球蛋白样结构域,存在单一的跨膜结构域;Lrig2在小鼠的多个组织中表达,其中在胸腺、脾脏等组织中表达较强;系统树分析显示,Lrigs蛋白是sLrPs超家族成员,是一种跨膜蛋白受体。结论:Lrig2在免疫组织中表达较强,推测其可能在肿瘤免疫应答进程中发挥重要的效能。     

Structure and properties of totally synthetic galacto- and gluco-cerebrosides

The structural and thermal properties of aqueous dispersions of the totally synthetic cerebrosides, D-erythro-N-palmitoyl galactosyl- and glucosyl-C18-sphingosine (C16:0-GalCer and C16:0-GluCer, respectively) have been studied using differential scanning calorimetry (DSC) and X-ray diffraction. Over the temperature range 0-100 degrees C, both C16:0-GalCer and C16:0-GluCer show complex thermal transitions characteristic of polymorphic behavior of exclusively bilayer phases. On heating, hydrated C16:0-GalCer undergoes an exothermic bilayer-bilayer transition at 59 degrees C to produce a stable bilayer crystal form. X-ray diffraction at 70 degrees C reveals a bilayer structure with an ordered hydrocarbon chain-packing arrangement. This ordered bilayer phase undergoes an endothermic chain-melting transition at 85 degrees C to the bilayer liquid crystalline state. Similar behavior is exhibited by hydrated C16:0-GluCer which undergoes the exothermic transition at 49 degrees C and a chain-melting transition at 87 degrees C. The exothermic transitions observed on heating hydrated C16:0-GalCer and C16:0-GluCer are irreversible and dependent upon previous chain melting, prior cooling rate, and time of incubation at low temperatures. Thus, the structure and properties of totally synthetic C16:0-GalCer and C16:0-GluCer with identical sphingosine (C18:1) and fatty acid (C16:0) chains are quite similar, suggesting that the precise isomeric structure of the linked sugar plays only a minor role in regulating the properties of hydrated cerebrosides. Further, these studies indicate that the complex thermal behavior and bilayer phase formation exhibited by these single-sugar cerebrosides are intrinsic properties and not due to the heterogeneity of the sphingosine base found in natural and partially synthetic cerebrosides.