DSSPcont: continuous secondary structure assignments for proteins

PubMed Central

Carter, Phil; Andersen, Claus A. F.; Rost, Burkhard

2003-01-01

The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces ‘static’ by ‘dynamic’ states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure. PMID:12824310

Prediction of protein secondary structure content for the twilight zone sequences.

PubMed

Homaeian, Leila; Kurgan, Lukasz A; Ruan, Jishou; Cios, Krzysztof J; Chen, Ke

2007-11-15

Secondary protein structure carries information about local structural arrangements, which include three major conformations: alpha-helices, beta-strands, and coils. Significant majority of successful methods for prediction of the secondary structure is based on multiple sequence alignment. However, multiple alignment fails to provide accurate results when a sequence comes from the twilight zone, that is, it is characterized by low (<30%) homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive sequence representation, called PSSC-core. The method uses a multiple linear regression model and introduces a comprehensive feature-based sequence representation to predict amount of helices and strands for sequences from the twilight zone. The PSSC-core method was tested and compared with two other state-of-the-art prediction methods on a set of 2187 twilight zone sequences. The results indicate that our method provides better predictions for both helix and strand content. The PSSC-core is shown to provide statistically significantly better results when compared with the competing methods, reducing the prediction error by 5-7% for helix and 7-9% for strand content predictions. The proposed feature-based sequence representation uses a comprehensive set of physicochemical properties that are custom-designed for each of the helix and strand content predictions. It includes composition and composition moment vectors, frequency of tetra-peptides associated with helical and strand conformations, various property-based groups like exchange groups, chemical groups of the side chains and hydrophobic group, auto-correlations based on hydrophobicity, side-chain masses, hydropathy, and conformational patterns for beta-sheets. The PSSC-core method provides an alternative for predicting the secondary structure content that can be used to validate and constrain results of other structure prediction methods. At the same time, it also provides useful insight into design of successful protein sequence representations that can be used in developing new methods related to prediction of different aspects of the secondary protein structure. (c) 2007 Wiley-Liss, Inc.

Modeling repetitive, non‐globular proteins

PubMed Central

Basu, Koli; Campbell, Robert L.; Guo, Shuaiqi; Sun, Tianjun

2016-01-01

Abstract While ab initio modeling of protein structures is not routine, certain types of proteins are more straightforward to model than others. Proteins with short repetitive sequences typically exhibit repetitive structures. These repetitive sequences can be more amenable to modeling if some information is known about the predominant secondary structure or other key features of the protein sequence. We have successfully built models of a number of repetitive structures with novel folds using knowledge of the consensus sequence within the sequence repeat and an understanding of the likely secondary structures that these may adopt. Our methods for achieving this success are reviewed here. PMID:26914323

Isotropic and Anisotropic Growth of Metal-Organic Framework (MOF) on MOF: Logical Inference on MOF Structure Based on Growth Behavior and Morphological Feature.

PubMed

Choi, Sora; Kim, Taeho; Ji, Hoyeon; Lee, Hee Jung; Oh, Moonhyun

2016-11-02

The growth of one metal-organic framework (MOF) on another MOF for constructing a heterocompositional hybrid MOF is an interesting research topic because of the curiosity regarding the occurrence of this phenomenon and the value of hybrid MOFs as multifunctional materials or routes for fine-tuning MOF properties. In particular, the anisotropic growth of MOF on MOF is fascinating for the development of MOFs possessing atypical shapes and heterostructures or abnormal properties. Herein, we clarify the understanding of growth behavior of a secondary MOF on an initial MOF template, such as isotropic or anisotropic ways associated with their cell parameters. The isotropic growth of MIL-68-Br on the MIL-68 template results in the formation of core-shell-type MIL-68@MIL-68-Br. However, the unique anisotropic growth of a secondary MOF (MOF-NDC) on the MIL-68 template results in semitubular particles, and structural features of this unknown secondary MOF are successfully speculated for the first time on the basis of its unique growth behavior and morphological characteristics. Finally, the validation of this structural speculation is verified by the powder X-ray diffraction and the selected area electron diffraction studies. The results suggests that the growth behavior and morphological features of MOFs should be considered to be important factors for understanding the MOFs' structures.

Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations.

PubMed

Hu, Xihao; Wu, Yang; Lu, Zhi John; Yip, Kevin Y

2016-11-01

High-throughput sequencing has been used to study posttranscriptional regulations, where the identification of protein-RNA binding is a major and fast-developing sub-area, which is in turn benefited by the sequencing methods for whole-transcriptome probing of RNA secondary structures. In the study of RNA secondary structures using high-throughput sequencing, bases are modified or cleaved according to their structural features, which alter the resulting composition of sequencing reads. In the study of protein-RNA binding, methods have been proposed to immuno-precipitate (IP) protein-bound RNA transcripts in vitro or in vivo By sequencing these transcripts, the protein-RNA interactions and the binding locations can be identified. For both types of data, read counts are affected by a combination of confounding factors, including expression levels of transcripts, sequence biases, mapping errors and the probing or IP efficiency of the experimental protocols. Careful processing of the sequencing data and proper extraction of important features are fundamentally important to a successful analysis. Here we review and compare different experimental methods for probing RNA secondary structures and binding sites of RNA-binding proteins (RBPs), and the computational methods proposed for analyzing the corresponding sequencing data. We suggest how these two types of data should be integrated to study the structural properties of RBP binding sites as a systematic way to better understand posttranscriptional regulations. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Effective Moment Feature Vectors for Protein Domain Structures

PubMed Central

Shi, Jian-Yu; Yiu, Siu-Ming; Zhang, Yan-Ning; Chin, Francis Yuk-Lun

2013-01-01

Imaging processing techniques have been shown to be useful in studying protein domain structures. The idea is to represent the pairwise distances of any two residues of the structure in a 2D distance matrix (DM). Features and/or submatrices are extracted from this DM to represent a domain. Existing approaches, however, may involve a large number of features (100–400) or complicated mathematical operations. Finding fewer but more effective features is always desirable. In this paper, based on some key observations on DMs, we are able to decompose a DM image into four basic binary images, each representing the structural characteristics of a fundamental secondary structure element (SSE) or a motif in the domain. Using the concept of moments in image processing, we further derive 45 structural features based on the four binary images. Together with 4 features extracted from the basic images, we represent the structure of a domain using 49 features. We show that our feature vectors can represent domain structures effectively in terms of the following. (1) We show a higher accuracy for domain classification. (2) We show a clear and consistent distribution of domains using our proposed structural vector space. (3) We are able to cluster the domains according to our moment features and demonstrate a relationship between structural variation and functional diversity. PMID:24391828

Bioactive natural compounds from the plant endophytic fungi Pestalotiopsis spp.

PubMed

Wang, Kuiwu; Lei, Jinxiu; Wei, Jiguang; Yao, Nan

2012-11-01

The plant-endophytic strains of the fungus Pestalotiopsis (Amphisphaeriaceae) are distributed throughout the world. Previous chemical investigation of members of the genus resulted in the discovery of various bioactive secondary metabolites including chromones, cytosporones, polyketides, terpenoids and coumarins with diverse structural features. The present report reviews the papers, which have appeared in the literature till now, concerning the isolation, structural elucidation, and biological activities of the secondary metabolites from Pestalotiopsis species.

Secondary structure of the 3'-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities.

PubMed

Rauscher, S; Flamm, C; Mandl, C W; Heinz, F X; Stadler, P F

1997-07-01

The prediction of the complete matrix of base pairing probabilities was applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only well-defined secondary structure elements, but also regions of high structural flexibility. Flaviviruses, many of which are important human pathogens, have a common genomic organization, but exhibit a significant degree of RNA sequence diversity in the functionally important 3'-NCR. We demonstrate the presence of secondary structures shared by all flaviviruses, as well as structural features that are characteristic for groups of viruses within the genus reflecting the established classification scheme. The significance of most of the predicted structures is corroborated by compensatory mutations. The availability of infectious clones for several flaviviruses will allow the assessment of these structural elements in processes of the viral life cycle, such as replication and assembly.

A Method for WD40 Repeat Detection and Secondary Structure Prediction

PubMed Central

Wang, Yang; Jiang, Fan; Zhuo, Zhu; Wu, Xian-Hui; Wu, Yun-Dong

2013-01-01

WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction. PMID:23776530

Hot spot of structural ambivalence in prion protein revealed by secondary structure principal component analysis.

PubMed

Yamamoto, Norifumi

2014-08-21

The conformational conversion of proteins into an aggregation-prone form is a common feature of various neurodegenerative disorders including Alzheimer's, Huntington's, Parkinson's, and prion diseases. In the early stage of prion diseases, secondary structure conversion in prion protein (PrP) causing β-sheet expansion facilitates the formation of a pathogenic isoform with a high content of β-sheets and strong aggregation tendency to form amyloid fibrils. Herein, we propose a straightforward method to extract essential information regarding the secondary structure conversion of proteins from molecular simulations, named secondary structure principal component analysis (SSPCA). The definite existence of a PrP isoform with an increased β-sheet structure was confirmed in a free-energy landscape constructed by mapping protein structural data into a reduced space according to the principal components determined by the SSPCA. We suggest a "spot" of structural ambivalence in PrP-the C-terminal part of helix 2-that lacks a strong intrinsic secondary structure, thus promoting a partial α-helix-to-β-sheet conversion. This result is important to understand how the pathogenic conformational conversion of PrP is initiated in prion diseases. The SSPCA has great potential to solve various challenges in studying highly flexible molecular systems, such as intrinsically disordered proteins, structurally ambivalent peptides, and chameleon sequences.

Transformations of dislocation martensite in tempering secondary-hardening steel

NASA Astrophysics Data System (ADS)

Gorynin, I. V.; Rybin, V. V.; Malyshevskii, V. A.; Semicheva, T. G.; Sherokhina, L. G.

1999-09-01

Analysis of the evolution of the fine structure of secondary-hardening steel in tempering makes it possible to understand the nature of processes that cause changes in the strength and ductility. They are connected with the changes that occur in the solid solution, the ensemble of disperse segregations of the carbide phase, and the dislocation structure of martensite. These transformations are interrelated, and their specific features are determined by the chemical composition of the steel.

[Developmental anatomy of anomalous structure and investigation of medicinal parts Sophora flavescens].

PubMed

Wang, Jun; Xie, Xiaomei; Peng, Huasheng

2012-06-01

To elucidate the composition structure of "annual rings" and the formation process of anomalous structures in Sophora flavescens, and further discuss the medicinal parts of S. flavescens. Based on investigation on S. flavescens in its producing areas, the morphology of root systems was observed, and the developmental anatomy of roots was researched. Creeping underground rhizomes of S. flavescen existed in some parts of the north place, there were many differences in appearance characters and microscopic features between these roots and rhizomes. Parenchyma cells in secondary xylem regained meristematic ability, became into anomalous cambia, and then developed into anomalous structures. "Annual rings" in transverse section of S. flavescens were not actually growth rings, they were made up of anomalous parenchyma girdle in secondary xylem and normal secondary structure. Roots are the medicinal parts of S. flavescens. This paper suggests that "annual rings" in the decoction pieces of S. flavescens should be called "annular structure".

SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

PubMed

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-05-01

Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods.

SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences

PubMed Central

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-01-01

Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods. PMID:18452616

Critical Features of Fragment Libraries for Protein Structure Prediction

PubMed Central

dos Santos, Karina Baptista

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction. PMID:28085928

Critical Features of Fragment Libraries for Protein Structure Prediction.

PubMed

Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.

Designer biomass for next-generation biorefineries: leveraging recent insights into xylan structure and biosynthesis.

PubMed

Smith, Peter J; Wang, Hsin-Tzu; York, William S; Peña, Maria J; Urbanowicz, Breeanna R

2017-01-01

Xylans are the most abundant noncellulosic polysaccharides in lignified secondary cell walls of woody dicots and in both primary and secondary cell walls of grasses. These polysaccharides, which comprise 20-35% of terrestrial biomass, present major challenges for the efficient microbial bioconversion of lignocellulosic feedstocks to fuels and other value-added products. Xylans play a significant role in the recalcitrance of biomass to degradation, and their bioconversion requires metabolic pathways that are distinct from those used to metabolize cellulose. In this review, we discuss the key differences in the structural features of xylans across diverse plant species, how these features affect their interactions with cellulose and lignin, and recent developments in understanding their biosynthesis. In particular, we focus on how the combined structural and biosynthetic knowledge can be used as a basis for biomass engineering aimed at developing crops that are better suited as feedstocks for the bioconversion industry.

Protein functional features are reflected in the patterns of mRNA translation speed.

PubMed

López, Daniel; Pazos, Florencio

2015-07-09

The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins. We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features. This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.

The Crystal Structures of Potentially Tautomeric Compounds

NASA Astrophysics Data System (ADS)

Furmanova, Nina G.

1981-08-01

Data on the structures of potentially proto-, metallo-, and carbono-tropic compounds, obtained mainly by X-ray diffraction, are surveyed. The results of neutron and electron diffraction studies have also been partly used. It is shown that a characteristic feature of all the systems considered is the formation of hydrogen or secondary bonds ensuring the contribution of both possible tautomeric forms to the structure. Systematic consideration of the experimental data leads to the conclusion that there is a close relation between the crystal structure and the dynamic behaviour of the molecules in solution and that secondary and hydrogen bonds play a significant role in the tautomeric transition. The bibliography includes 152 references.

The Cognitive Dimensions of Information Structures.

ERIC Educational Resources Information Center

Green, T. R. G.

1994-01-01

Describes a set of terms (viscosity, hidden dependencies, imposes guess-ahead, abstraction level, and secondary notation) intended as a set of discussion tools for nonspecialists to converse about the structural features of a range of information artifacts. Explains the terms using spreadsheets as an example. (SR)

Common structural features of cholesterol binding sites in crystallized soluble proteins

PubMed Central

Bukiya, Anna N.; Dopico, Alejandro M.

2017-01-01

Cholesterol-protein interactions are essential for the architectural organization of cell membranes and for lipid metabolism. While cholesterol-sensing motifs in transmembrane proteins have been identified, little is known about cholesterol recognition by soluble proteins. We reviewed the structural characteristics of binding sites for cholesterol and cholesterol sulfate from crystallographic structures available in the Protein Data Bank. This analysis unveiled key features of cholesterol-binding sites that are present in either all or the majority of sites: i) the cholesterol molecule is generally positioned between protein domains that have an organized secondary structure; ii) the cholesterol hydroxyl/sulfo group is often partnered by Asn, Gln, and/or Tyr, while the hydrophobic part of cholesterol interacts with Leu, Ile, Val, and/or Phe; iii) cholesterol hydrogen-bonding partners are often found on α-helices, while amino acids that interact with cholesterol’s hydrophobic core have a slight preference for β-strands and secondary structure-lacking protein areas; iv) the steroid’s C21 and C26 constitute the “hot spots” most often seen for steroid-protein hydrophobic interactions; v) common “cold spots” are C8–C10, C13, and C17, at which contacts with the proteins were not detected. Several common features we identified for soluble protein-steroid interaction appear evolutionarily conserved. PMID:28420706

Determination of secondary flow morphologies by wavelet analysis in a curved artery model with physiological inflow

NASA Astrophysics Data System (ADS)

Bulusu, Kartik V.; Hussain, Shadman; Plesniak, Michael W.

2014-11-01

Secondary flow vortical patterns in arterial curvatures have the potential to affect several cardiovascular phenomena, e.g., progression of atherosclerosis by altering wall shear stresses, carotid atheromatous disease, thoracic aortic aneurysms and Marfan's syndrome. Temporal characteristics of secondary flow structures vis-à-vis physiological (pulsatile) inflow waveform were explored by continuous wavelet transform (CWT) analysis of phase-locked, two-component, two-dimensional particle image velocimeter data. Measurements were made in a 180° curved artery test section upstream of the curvature and at the 90° cross-sectional plane. Streamwise, upstream flow rate measurements were analyzed using a one-dimensional antisymmetric wavelet. Cross-stream measurements at the 90° location of the curved artery revealed interesting multi-scale, multi-strength coherent secondary flow structures. An automated process for coherent structure detection and vortical feature quantification was applied to large ensembles of PIV data. Metrics such as the number of secondary flow structures, their sizes and strengths were generated at every discrete time instance of the physiological inflow waveform. An autonomous data post-processing method incorporating two-dimensional CWT for coherent structure detection was implemented. Loss of coherence in secondary flow structures during the systolic deceleration phase is observed in accordance with previous research. The algorithmic approach presented herein further elucidated the sensitivity and dependence of morphological changes in secondary flow structures on quasiperiodicity and magnitude of temporal gradients in physiological inflow conditions.

RiboSketch: Versatile Visualization of Multi-stranded RNA and DNA Secondary Structure.

PubMed

Lu, Jacob S; Bindewald, Eckart; Kasprzak, Wojciech; Shapiro, Bruce A

2018-06-15

Creating clear, visually pleasing 2D depictions of RNA and DNA strands and their interactions is important to facilitate and communicate insights related to nucleic acid structure. Here we present RiboSketch, a secondary structure image production application that enables the visualization of multistranded structures via layout algorithms, comprehensive editing capabilities, and a multitude of simulation modes. These interactive features allow RiboSketch to create publication quality diagrams for structures with a wide range of composition, size, and complexity. The program may be run in any web browser without the need for installation, or as a standalone Java application. https://binkley2.ncifcrf.gov/users/bindewae/ribosketch_web.

Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.

PubMed

Hsing, Michael; Cherkasov, Artem

2008-06-25

Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites.

Composición y estructura de un bosque tropical urbano en el karso norteno de Puerto Rico

Treesearch

E. López Machado; K. Soto Hidalgo; T. Heartsill-Scalley

2012-01-01

Tropical secondary forests provide many products, environmental services, and recreation. These forests have a set of biological features, such as their high productivity and a uniform composition of dominant tree species. To understand the composition and structure of a secondary forest in the northern karst zone, we selected the Santa Ana Environmental Center (CASA...

Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure.

PubMed

Song, Jiangning; Yuan, Zheng; Tan, Hao; Huber, Thomas; Burrage, Kevin

2007-12-01

Disulfide bonds are primary covalent crosslinks between two cysteine residues in proteins that play critical roles in stabilizing the protein structures and are commonly found in extracy-toplasmatic or secreted proteins. In protein folding prediction, the localization of disulfide bonds can greatly reduce the search in conformational space. Therefore, there is a great need to develop computational methods capable of accurately predicting disulfide connectivity patterns in proteins that could have potentially important applications. We have developed a novel method to predict disulfide connectivity patterns from protein primary sequence, using a support vector regression (SVR) approach based on multiple sequence feature vectors and predicted secondary structure by the PSIPRED program. The results indicate that our method could achieve a prediction accuracy of 74.4% and 77.9%, respectively, when averaged on proteins with two to five disulfide bridges using 4-fold cross-validation, measured on the protein and cysteine pair on a well-defined non-homologous dataset. We assessed the effects of different sequence encoding schemes on the prediction performance of disulfide connectivity. It has been shown that the sequence encoding scheme based on multiple sequence feature vectors coupled with predicted secondary structure can significantly improve the prediction accuracy, thus enabling our method to outperform most of other currently available predictors. Our work provides a complementary approach to the current algorithms that should be useful in computationally assigning disulfide connectivity patterns and helps in the annotation of protein sequences generated by large-scale whole-genome projects. The prediction web server and Supplementary Material are accessible at http://foo.maths.uq.edu.au/~huber/disulfide

Secondary signal imaging (SSI) electron tomography (SSI-ET): A new three-dimensional metrology for mesoscale specimens in transmission electron microscope.

PubMed

Han, Chang Wan; Ortalan, Volkan

2015-09-01

We have demonstrated a new electron tomography technique utilizing the secondary signals (secondary electrons and backscattered electrons) for ultra thick (a few μm) specimens. The Monte Carlo electron scattering simulations reveal that the amount of backscattered electrons generated by 200 and 300keV incident electrons is a monotonic function of the sample thickness and this causes the thickness contrast satisfying the projection requirement for the tomographic reconstruction. Additional contribution of the secondary electrons emitted from the edges of the specimens enhances the visibility of the surface features. The acquired SSI tilt series of the specimen having mesoscopic dimensions are successfully reconstructed verifying that this new technique, so called the secondary signal imaging electron tomography (SSI-ET), can directly be utilized for 3D structural analysis of mesoscale structures. Published by Elsevier Ltd.

Two-dimensional sup 1 H NMR studies on HPr protein from Staphylococcus aureus: Complete sequential assignments and secondary structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalbitzer, H.R.; Neidig, K.P.; Hengstenberg, W.

1991-11-19

Complete sequence-specific assignments of the {sup 1}H NMR spectrum of HPr protein from Staphylococcus aureus were obtained by two-dimensional NMR methods. Important secondary structure elements that can be derived from the observed nuclear Overhauser effects are a large antiparallel {beta}-pleated sheet consisting of four strands, A, B, C, D, a segment S{sub AB} consisting of an extended region around the active-center histidine (His-15) and an {alpha}-helix, a half-turn between strands B and C, a segment S{sub CD} which shows no typical secondary structure, and the {alpha}-helical, C-terminal segment S{sub term}. These general structural features are similar to those found earliermore » in HPr proteins from different microorganisms such as Escherichia coli, Bacillus subtilis, and Streptococcus faecalis.« less

Linking hydro-morphology with invertebrate ecology in diverse morphological units of a large river-floodplain system

NASA Astrophysics Data System (ADS)

Blettler, Martín. C. M.; Amsler, Mario L.; Eberle, Eliana G.; Szupiany, Ricardo; Latosinski, Francisco G.; Abrial, Elie; Oberholster, Paul J.; Espinola, Luis A.; Paira, Aldo; Poza, Ailen; Rodrigues Capítulo, Alberto

2016-12-01

Interdisciplinary research in the fields of ecohydrology and ecogeomorphology is becoming increasingly important as a way to understand how biological and physical processes interact with each other in river systems. The objectives of the current study were 1) to determine changes in invertebrate community due to hydrological stages, 2) to link local physical features [flow configuration, sediment composition and morphological feature) with the ecological structure between and within dissimilar morphological units (meander and confluence), and 3) to determine the existence and the origin of bed hydro-geomorphic patches, determining their ecological structure. Results were discussed in the frame of prevailing ecological models and concepts. The study site extends over a floodplain area of the large Paraná River (Argentina), including minor and major secondary channels as well as the main channel. Overall results suggested that hydrodynamics was the driving force determining distribution patterns of benthic assemblages in the floodplain. However, while the invertebrates living in minor secondary channels seem to benefit from flooding, this hydrological phase had the opposite effect on organisms from the main and major secondary channels. We also found a clear linkage between physical features and invertebrate ecology, which caused a dissimilar fauna structure between and within the meander and the confluence. Furthermore, several sandy-patches were recorded in the confluence. These patches were colonized by the particular benthic assemblage recorded in the main channel, supported the view of rivers as patchy discontinua, under uncertain ecological equilibrium.

Information-Theoretic Uncertainty of SCFG-Modeled Folding Space of The Non-coding RNA

PubMed Central

Manzourolajdad, Amirhossein; Wang, Yingfeng; Shaw, Timothy I.; Malmberg, Russell L.

2012-01-01

RNA secondary structure ensembles define probability distributions for alternative equilibrium secondary structures of an RNA sequence. Shannon’s Entropy is a measure for the amount of diversity present in any ensemble. In this work, Shannon’s entropy of the SCFG ensemble on an RNA sequence is derived and implemented in polynomial time for both structurally ambiguous and unambiguous grammars. Micro RNA sequences generally have low folding entropy, as previously discovered. Surprisingly, signs of significantly high folding entropy were observed in certain ncRNA families. More effective models coupled with targeted randomization tests can lead to a better insight into folding features of these families. PMID:23160142

In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.

PubMed

Meyer, Irmtraud M

2017-05-01

RNA transcripts are the primary products of active genes in any living organism, including many viruses. Their cellular destiny not only depends on primary sequence signals, but can also be determined by RNA structure. Recent experimental evidence shows that many transcripts can be assigned more than a single functional RNA structure throughout their cellular life and that structure formation happens co-transcriptionally, i.e. as the transcript is synthesised in the cell. Moreover, functional RNA structures are not limited to non-coding transcripts, but can also feature in coding transcripts. The picture that now emerges is that RNA structures constitute an additional layer of information that can be encoded in any RNA transcript (and on top of other layers of information such as protein-context) in order to exert a wide range of functional roles. Moreover, different encoded RNA structures can be expressed at different stages of a transcript's life in order to alter the transcript's behaviour depending on its actual cellular context. Similar to the concept of alternative splicing for protein-coding genes, where a single transcript can yield different proteins depending on cellular context, it is thus appropriate to propose the notion of alternative RNA structure expression for any given transcript. This review introduces several computational strategies that my group developed to detect different aspects of RNA structure expression in vivo. Two aspects are of particular interest to us: (1) RNA secondary structure features that emerge during co-transcriptional folding and (2) functional RNA structure features that are expressed at different times of a transcript's life and potentially mutually exclusive. Copyright © 2017. Published by Elsevier Inc.

Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs.

PubMed

Shamim, Mohammad Tabrez Anwar; Anwaruddin, Mohammad; Nagarajaram, H A

2007-12-15

Fold recognition is a key step in the protein structure discovery process, especially when traditional sequence comparison methods fail to yield convincing structural homologies. Although many methods have been developed for protein fold recognition, their accuracies remain low. This can be attributed to insufficient exploitation of fold discriminatory features. We have developed a new method for protein fold recognition using structural information of amino acid residues and amino acid residue pairs. Since protein fold recognition can be treated as a protein fold classification problem, we have developed a Support Vector Machine (SVM) based classifier approach that uses secondary structural state and solvent accessibility state frequencies of amino acids and amino acid pairs as feature vectors. Among the individual properties examined secondary structural state frequencies of amino acids gave an overall accuracy of 65.2% for fold discrimination, which is better than the accuracy by any method reported so far in the literature. Combination of secondary structural state frequencies with solvent accessibility state frequencies of amino acids and amino acid pairs further improved the fold discrimination accuracy to more than 70%, which is approximately 8% higher than the best available method. In this study we have also tested, for the first time, an all-together multi-class method known as Crammer and Singer method for protein fold classification. Our studies reveal that the three multi-class classification methods, namely one versus all, one versus one and Crammer and Singer method, yield similar predictions. Dataset and stand-alone program are available upon request.

Predicting turns in proteins with a unified model.

PubMed

Song, Qi; Li, Tonghua; Cong, Peisheng; Sun, Jiangming; Li, Dapeng; Tang, Shengnan

2012-01-01

Turns are a critical element of the structure of a protein; turns play a crucial role in loops, folds, and interactions. Current prediction methods are well developed for the prediction of individual turn types, including α-turn, β-turn, and γ-turn, etc. However, for further protein structure and function prediction it is necessary to develop a uniform model that can accurately predict all types of turns simultaneously. In this study, we present a novel approach, TurnP, which offers the ability to investigate all the turns in a protein based on a unified model. The main characteristics of TurnP are: (i) using newly exploited features of structural evolution information (secondary structure and shape string of protein) based on structure homologies, (ii) considering all types of turns in a unified model, and (iii) practical capability of accurate prediction of all turns simultaneously for a query. TurnP utilizes predicted secondary structures and predicted shape strings, both of which have greater accuracy, based on innovative technologies which were both developed by our group. Then, sequence and structural evolution features, which are profile of sequence, profile of secondary structures and profile of shape strings are generated by sequence and structure alignment. When TurnP was validated on a non-redundant dataset (4,107 entries) by five-fold cross-validation, we achieved an accuracy of 88.8% and a sensitivity of 71.8%, which exceeded the most state-of-the-art predictors of certain type of turn. Newly determined sequences, the EVA and CASP9 datasets were used as independent tests and the results we achieved were outstanding for turn predictions and confirmed the good performance of TurnP for practical applications.

Predicting Turns in Proteins with a Unified Model

PubMed Central

Song, Qi; Li, Tonghua; Cong, Peisheng; Sun, Jiangming; Li, Dapeng; Tang, Shengnan

2012-01-01

Motivation Turns are a critical element of the structure of a protein; turns play a crucial role in loops, folds, and interactions. Current prediction methods are well developed for the prediction of individual turn types, including α-turn, β-turn, and γ-turn, etc. However, for further protein structure and function prediction it is necessary to develop a uniform model that can accurately predict all types of turns simultaneously. Results In this study, we present a novel approach, TurnP, which offers the ability to investigate all the turns in a protein based on a unified model. The main characteristics of TurnP are: (i) using newly exploited features of structural evolution information (secondary structure and shape string of protein) based on structure homologies, (ii) considering all types of turns in a unified model, and (iii) practical capability of accurate prediction of all turns simultaneously for a query. TurnP utilizes predicted secondary structures and predicted shape strings, both of which have greater accuracy, based on innovative technologies which were both developed by our group. Then, sequence and structural evolution features, which are profile of sequence, profile of secondary structures and profile of shape strings are generated by sequence and structure alignment. When TurnP was validated on a non-redundant dataset (4,107 entries) by five-fold cross-validation, we achieved an accuracy of 88.8% and a sensitivity of 71.8%, which exceeded the most state-of-the-art predictors of certain type of turn. Newly determined sequences, the EVA and CASP9 datasets were used as independent tests and the results we achieved were outstanding for turn predictions and confirmed the good performance of TurnP for practical applications. PMID:23144872

Predicting beta-turns in proteins using support vector machines with fractional polynomials

PubMed Central

2013-01-01

Background β-turns are secondary structure type that have essential role in molecular recognition, protein folding, and stability. They are found to be the most common type of non-repetitive structures since 25% of amino acids in protein structures are situated on them. Their prediction is considered to be one of the crucial problems in bioinformatics and molecular biology, which can provide valuable insights and inputs for the fold recognition and drug design. Results We propose an approach that combines support vector machines (SVMs) and logistic regression (LR) in a hybrid prediction method, which we call (H-SVM-LR) to predict β-turns in proteins. Fractional polynomials are used for LR modeling. We utilize position specific scoring matrices (PSSMs) and predicted secondary structure (PSS) as features. Our simulation studies show that H-SVM-LR achieves Qtotal of 82.87%, 82.84%, and 82.32% on the BT426, BT547, and BT823 datasets respectively. These values are the highest among other β-turns prediction methods that are based on PSSMs and secondary structure information. H-SVM-LR also achieves favorable performance in predicting β-turns as measured by the Matthew's correlation coefficient (MCC) on these datasets. Furthermore, H-SVM-LR shows good performance when considering shape strings as additional features. Conclusions In this paper, we present a comprehensive approach for β-turns prediction. Experiments show that our proposed approach achieves better performance compared to other competing prediction methods. PMID:24565438

Predicting beta-turns in proteins using support vector machines with fractional polynomials.

PubMed

Elbashir, Murtada; Wang, Jianxin; Wu, Fang-Xiang; Wang, Lusheng

2013-11-07

β-turns are secondary structure type that have essential role in molecular recognition, protein folding, and stability. They are found to be the most common type of non-repetitive structures since 25% of amino acids in protein structures are situated on them. Their prediction is considered to be one of the crucial problems in bioinformatics and molecular biology, which can provide valuable insights and inputs for the fold recognition and drug design. We propose an approach that combines support vector machines (SVMs) and logistic regression (LR) in a hybrid prediction method, which we call (H-SVM-LR) to predict β-turns in proteins. Fractional polynomials are used for LR modeling. We utilize position specific scoring matrices (PSSMs) and predicted secondary structure (PSS) as features. Our simulation studies show that H-SVM-LR achieves Qtotal of 82.87%, 82.84%, and 82.32% on the BT426, BT547, and BT823 datasets respectively. These values are the highest among other β-turns prediction methods that are based on PSSMs and secondary structure information. H-SVM-LR also achieves favorable performance in predicting β-turns as measured by the Matthew's correlation coefficient (MCC) on these datasets. Furthermore, H-SVM-LR shows good performance when considering shape strings as additional features. In this paper, we present a comprehensive approach for β-turns prediction. Experiments show that our proposed approach achieves better performance compared to other competing prediction methods.

Secondary Electron Emission Spectroscopy of Diamond Surfaces

NASA Technical Reports Server (NTRS)

Krainsky, Isay L.; Asnin, Vladimir M.; Petukhov, Andre G.

1999-01-01

This report presents the results of the secondary electron emission spectroscopy study of hydrogenated diamond surfaces for single crystals and chemical vapor-deposited polycrystalline films. One-electron calculations of Auger spectra of diamond surfaces having various hydrogen coverages are presented, the major features of the experimental spectra are explained, and a theoretical model for Auger spectra of hydrogenated diamond surfaces is proposed. An energy shift and a change in the line shape of the carbon core-valence-valence (KVV) Auger spectra were observed for diamond surfaces after exposure to an electron beam or by annealing at temperatures higher than 950 C. This change is related to the redistribution of the valence-band local density of states caused by hydrogen desorption from the surface. A strong negative electron affinity (NEA) effect, which appeared as a large, narrow peak in the low-energy portion of the spectrum of the secondary electron energy distribution, was also observed on the diamond surfaces. A fine structure in this peak, which was found for the first time, reflected the energy structure of the bottom of the conduction band. Further, the breakup of the bulk excitons at the surface during secondary electron emission was attributed to one of the features of this structure. The study demonstrated that the NEA type depends on the extent of hydrogen coverage of the diamond surface, changing from the true type for the completely hydrogenated surface to the effective type for the partially hydrogenated surface.

RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.

PubMed

Antczak, Maciej; Zok, Tomasz; Popenda, Mariusz; Lukasiak, Piotr; Adamiak, Ryszard W; Blazewicz, Jacek; Szachniuk, Marta

2014-07-01

In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee-a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Learning and Improving in Quality Improvement Collaboratives: Which Collaborative Features Do Participants Value Most?

PubMed Central

Nembhard, Ingrid M

2009-01-01

Objective To understand participants' views on the relative helpfulness of various features of collaboratives, why each feature was helpful and which features the most successful participants viewed as most central to their success. Data Sources Primary data collected from 53 teams in four 2004–2005 Institute for Healthcare Improvement (IHI) Breakthrough Series collaboratives; secondary data from IHI and demographic sources. Study Design Cross-sectional analyses were conducted to assess participants' views of 12 features, and the relationship between their views and performance improvement. Data Collection Methods Participants' views on features were obtained via self-administered surveys and semi-structured telephone interviews. Performance improvement data were obtained from IHI and demographic data from secondary sources. Principal Findings Participants viewed six features as most helpful for advancing their improvement efforts overall and knowledge acquisition in particular: collaborative faculty, solicitation of their staff's ideas, change package, Plan-Do-Study-Act cycles, Learning Session interactions, and collaborative extranet. These features also provided participants with motivation, social support, and project management skills. Features enabling interorganizational learning were rated higher by teams whose organizations improved significantly than by other teams. Conclusions Findings identify features of collaborative design and implementation that participants view as most helpful and highlight the importance of interorganizational features, at least for those organizations that most improve. PMID:19040423

PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates.

PubMed

Mavridis, Lazaros; Janes, Robert W

2017-01-01

Circular dichroism (CD) spectroscopy is extensively utilized for determining the percentages of secondary structure content present in proteins. However, although a large contributor, secondary structure is not the only factor that influences the shape and magnitude of the CD spectrum produced. Other structural features can make contributions so an entire protein structural conformation can give rise to a CD spectrum. There is a need for an application capable of generating protein CD spectra from atomic coordinates. However, no empirically derived method to do this currently exists. PDB2CD has been created as an empirical-based approach to the generation of protein CD spectra from atomic coordinates. The method utilizes a combination of structural features within the conformation of a protein; not only its percentage secondary structure content, but also the juxtaposition of these structural components relative to one another, and the overall structure similarity of the query protein to proteins in our dataset, the SP175 dataset, the 'gold standard' set obtained from the Protein Circular Dichroism Data Bank (PCDDB). A significant number of the CD spectra associated with the 71 proteins in this dataset have been produced with excellent accuracy using a leave-one-out cross-validation process. The method also creates spectra in good agreement with those of a test set of 14 proteins from the PCDDB. The PDB2CD package provides a web-based, user friendly approach to enable researchers to produce CD spectra from protein atomic coordinates. http://pdb2cd.cryst.bbk.ac.uk CONTACT: r.w.janes@qmul.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Methods for isolation of marine-derived endophytic fungi and their bioactive secondary products.

PubMed

Kjer, Julia; Debbab, Abdessamad; Aly, Amal H; Proksch, Peter

2010-03-01

Marine-derived fungi have been shown in recent years to produce a plethora of new bioactive secondary metabolites, some of them featuring new carbon frameworks hitherto unprecedented in nature. These compounds are of interest as new lead structures for medicine as well as for plant protection. The aim of this protocol is to give a detailed description of methods useful for the isolation and cultivation of fungi associated with various marine organisms (sponges, algae and mangrove plants) for the extraction, characterization and structure elucidation of biologically active secondary metabolites produced by these marine-derived endophytic fungi, and for the preliminary evaluation of their pharmacological properties based on rapid 'in house' screening systems. Some results exemplifying the positive outcomes of the protocol are given at the end. From sampling in marine environment to completion of the structure elucidation and bioactivity screening, a period of at least 3 months has to be scheduled.

ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)

PubMed Central

2008-01-01

Background Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment. Results The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae. Conclusion In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics. PMID:18655698

How Structure Defines Affinity in Protein-Protein Interactions

PubMed Central

Erijman, Ariel; Rosenthal, Eran; Shifman, Julia M.

2014-01-01

Protein-protein interactions (PPI) in nature are conveyed by a multitude of binding modes involving various surfaces, secondary structure elements and intermolecular interactions. This diversity results in PPI binding affinities that span more than nine orders of magnitude. Several early studies attempted to correlate PPI binding affinities to various structure-derived features with limited success. The growing number of high-resolution structures, the appearance of more precise methods for measuring binding affinities and the development of new computational algorithms enable more thorough investigations in this direction. Here, we use a large dataset of PPI structures with the documented binding affinities to calculate a number of structure-based features that could potentially define binding energetics. We explore how well each calculated biophysical feature alone correlates with binding affinity and determine the features that could be used to distinguish between high-, medium- and low- affinity PPIs. Furthermore, we test how various combinations of features could be applied to predict binding affinity and observe a slow improvement in correlation as more features are incorporated into the equation. In addition, we observe a considerable improvement in predictions if we exclude from our analysis low-resolution and NMR structures, revealing the importance of capturing exact intermolecular interactions in our calculations. Our analysis should facilitate prediction of new interactions on the genome scale, better characterization of signaling networks and design of novel binding partners for various target proteins. PMID:25329579

regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution.

PubMed

Zhang, Xinjun; Li, Meng; Lin, Hai; Rao, Xi; Feng, Weixing; Yang, Yuedong; Mort, Matthew; Cooper, David N; Wang, Yue; Wang, Yadong; Wells, Clark; Zhou, Yaoqi; Liu, Yunlong

2017-09-01

While synonymous single-nucleotide variants (sSNVs) have largely been unstudied, since they do not alter protein sequence, mounting evidence suggests that they may affect RNA conformation, splicing, and the stability of nascent-mRNAs to promote various diseases. Accurately prioritizing deleterious sSNVs from a pool of neutral ones can significantly improve our ability of selecting functional genetic variants identified from various genome-sequencing projects, and, therefore, advance our understanding of disease etiology. In this study, we develop a computational algorithm to prioritize sSNVs based on their impact on mRNA splicing and protein function. In addition to genomic features that potentially affect splicing regulation, our proposed algorithm also includes dozens structural features that characterize the functions of alternatively spliced exons on protein function. Our systematical evaluation on thousands of sSNVs suggests that several structural features, including intrinsic disorder protein scores, solvent accessible surface areas, protein secondary structures, and known and predicted protein family domains, show significant differences between disease-causing and neutral sSNVs. Our result suggests that the protein structure features offer an added dimension of information while distinguishing disease-causing and neutral synonymous variants. The inclusion of structural features increases the predictive accuracy for functional sSNV prioritization.

Growth-dissolution-regrowth transitions of Fe3O4 nanoparticles as building blocks for 3D magnetic nanoparticle clusters under hydrothermal conditions.

PubMed

Lin, Mouhong; Huang, Haoliang; Liu, Zuotao; Liu, Yingju; Ge, Junbin; Fang, Yueping

2013-12-10

Magnetic nanoparticle clusters (MNCs) are a class of secondary structural materials that comprise chemically defined nanoparticles assembled into clusters of defined size. Herein, MNCs are fabricated through a one-pot solvothermal reaction featuring self-limiting assembly of building blocks and the controlled reorganization process. Such growth-dissolution-regrowth fabrication mechanism overcomes some limitations of conventional solvothermal fabrication methods with regard to restricted available feature size and structural complexity, which can be extended to other oxides (as long as one can be chelated by EDTA-2Na). Based on this method, the nanoparticle size of MNCs is tuned between 6.8 and 31.2 nm at a fixed cluster diameter of 120 nm, wherein the critical size for superparamagnetic-ferromagnetic transition is estimated from 13.5 to 15.7 nm. Control over the nature and secondary structure of MNCs gives an excellent model system to understand the nanoparticle size-dependent magnetic properties of MNCs. MNCs have potential applications in many different areas, while this work evaluates their cytotoxicity and Pb(2+) adsorption capacity as initial application study.

A sampling-based method for ranking protein structural models by integrating multiple scores and features.

PubMed

Shi, Xiaohu; Zhang, Jingfen; He, Zhiquan; Shang, Yi; Xu, Dong

2011-09-01

One of the major challenges in protein tertiary structure prediction is structure quality assessment. In many cases, protein structure prediction tools generate good structural models, but fail to select the best models from a huge number of candidates as the final output. In this study, we developed a sampling-based machine-learning method to rank protein structural models by integrating multiple scores and features. First, features such as predicted secondary structure, solvent accessibility and residue-residue contact information are integrated by two Radial Basis Function (RBF) models trained from different datasets. Then, the two RBF scores and five selected scoring functions developed by others, i.e., Opus-CA, Opus-PSP, DFIRE, RAPDF, and Cheng Score are synthesized by a sampling method. At last, another integrated RBF model ranks the structural models according to the features of sampling distribution. We tested the proposed method by using two different datasets, including the CASP server prediction models of all CASP8 targets and a set of models generated by our in-house software MUFOLD. The test result shows that our method outperforms any individual scoring function on both best model selection, and overall correlation between the predicted ranking and the actual ranking of structural quality.

An in-silico method for identifying aggregation rate enhancer and mitigator mutations in proteins.

PubMed

Rawat, Puneet; Kumar, Sandeep; Michael Gromiha, M

2018-06-24

Newly synthesized polypeptides must pass stringent quality controls in cells to ensure appropriate folding and function. However, mutations, environmental stresses and aging can reduce efficiencies of these controls, leading to accumulation of protein aggregates, amyloid fibrils and plaques. In-vitro experiments have shown that even single amino acid substitutions can drastically enhance or mitigate protein aggregation kinetics. In this work, we have collected a dataset of 220 unique mutations in 25 proteins and classified them as enhancers or mitigators on the basis of their effect on protein aggregation rate. The data were analyzed via machine learning to identify features capable of distinguishing between aggregation rate enhancers and mitigators. Our initial Support Vector Machine (SVM) model separated such mutations with an overall accuracy of 69%. When local secondary structures at the mutation sites were considered, the accuracies further improved by 13-15%. The machine-learnt features are distinct for each secondary structure class at mutation sites. Protein stability and flexibility changes are important features for mutations in α-helices. β-strand propensity, polarity and charge become important when mutations occur in β-strands and ability to form secondary structure, helical tendency and aggregation propensity are important for mutations lying in coils. These results have been incorporated into a sequence-based algorithm (available at http://www.iitm.ac.in/bioinfo/aggrerate-disc/) capable of predicting whether a mutation will enhance or mitigate a protein's aggregation rate. This algorithm will find several applications towards understanding protein aggregation in human diseases, enable in-silico optimization of biopharmaceuticals and enzymes for improved biophysical attributes and de novo design of bio-nanomaterials. Copyright © 2018. Published by Elsevier B.V.

Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

PubMed Central

Li, Bi-Qing; Feng, Kai-Yan; Chen, Lei; Huang, Tao; Cai, Yu-Dong

2012-01-01

Prediction of protein-protein interaction (PPI) sites is one of the most challenging problems in computational biology. Although great progress has been made by employing various machine learning approaches with numerous characteristic features, the problem is still far from being solved. In this study, we developed a novel predictor based on Random Forest (RF) algorithm with the Minimum Redundancy Maximal Relevance (mRMR) method followed by incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility. We also included five 3D structural features to predict protein-protein interaction sites and achieved an overall accuracy of 0.672997 and MCC of 0.347977. Feature analysis showed that 3D structural features such as Depth Index (DPX) and surface curvature (SC) contributed most to the prediction of protein-protein interaction sites. It was also shown via site-specific feature analysis that the features of individual residues from PPI sites contribute most to the determination of protein-protein interaction sites. It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction. PMID:22937126

New Era of Studying RNA Secondary Structure and Its Influence on Gene Regulation in Plants.

PubMed

Yang, Xiaofei; Yang, Minglei; Deng, Hongjing; Ding, Yiliang

2018-01-01

The dynamic structure of RNA plays a central role in post-transcriptional regulation of gene expression such as RNA maturation, degradation, and translation. With the rise of next-generation sequencing, the study of RNA structure has been transformed from in vitro low-throughput RNA structure probing methods to in vivo high-throughput RNA structure profiling. The development of these methods enables incremental studies on the function of RNA structure to be performed, revealing new insights of novel regulatory mechanisms of RNA structure in plants. Genome-wide scale RNA structure profiling allows us to investigate general RNA structural features over 10s of 1000s of mRNAs and to compare RNA structuromes between plant species. Here, we provide a comprehensive and up-to-date overview of: (i) RNA structure probing methods; (ii) the biological functions of RNA structure; (iii) genome-wide RNA structural features corresponding to their regulatory mechanisms; and (iv) RNA structurome evolution in plants.

Protein sectors: evolutionary units of three-dimensional structure

PubMed Central

Halabi, Najeeb; Rivoire, Olivier; Leibler, Stanislas; Ranganathan, Rama

2011-01-01

Proteins display a hierarchy of structural features at primary, secondary, tertiary, and higher-order levels, an organization that guides our current understanding of their biological properties and evolutionary origins. Here, we reveal a structural organization distinct from this traditional hierarchy by statistical analysis of correlated evolution between amino acids. Applied to the S1A serine proteases, the analysis indicates a decomposition of the protein into three quasi-independent groups of correlated amino acids that we term “protein sectors”. Each sector is physically connected in the tertiary structure, has a distinct functional role, and constitutes an independent mode of sequence divergence in the protein family. Functionally relevant sectors are evident in other protein families as well, suggesting that they may be general features of proteins. We propose that sectors represent a structural organization of proteins that reflects their evolutionary histories. PMID:19703402

The Visual Syntax of Algebra.

ERIC Educational Resources Information Center

Kirshner, David

1989-01-01

A structured system of visual features is seen to parallel the propositional hierarchy of operations usually associated with the parsing of algebraic expressions. Women more than men were found to depend on these visual cues. Possible causes and consequences are discussed. Subjects were secondary and college students. (Author/DC)

Prediction of beta-turns and beta-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN).

PubMed

Kirschner, Andreas; Frishman, Dmitrij

2008-10-01

Prediction of beta-turns from amino acid sequences has long been recognized as an important problem in structural bioinformatics due to their frequent occurrence as well as their structural and functional significance. Because various structural features of proteins are intercorrelated, secondary structure information has been often employed as an additional input for machine learning algorithms while predicting beta-turns. Here we present a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN) capable of predicting multiple mutually dependent structural motifs and demonstrate its efficiency in recognizing three aspects of protein structure: beta-turns, beta-turn types, and secondary structure. The advantage of our method compared to other predictors is that it does not require any external input except for sequence profiles because interdependencies between different structural features are taken into account implicitly during the learning process. In a sevenfold cross-validation experiment on a standard test dataset our method exhibits the total prediction accuracy of 77.9% and the Mathew's Correlation Coefficient of 0.45, the highest performance reported so far. It also outperforms other known methods in delineating individual turn types. We demonstrate how simultaneous prediction of multiple targets influences prediction performance on single targets. The MOLEBRNN presented here is a generic method applicable in a variety of research fields where multiple mutually depending target classes need to be predicted. http://webclu.bio.wzw.tum.de/predator-web/.

Using secondary structure to identify ribosomal numts: cautionary examples from the human genome.

PubMed

Olson, Link E; Yoder, Anne D

2002-01-01

The identification of inadvertently sequenced mitochondrial pseudogenes (numts) is critical to any study employing mitochondrial DNA sequence data. Failure to discriminate numts correctly can confound phylogenetic reconstruction and studies of molecular evolution. This is especially problematic for ribosomal mtDNA genes. Unlike protein-coding loci, whose pseudogenes tend to accumulate diagnostic frameshift or premature stop mutations, functional ribosomal genes are not constrained to maintain a reading frame and can accumulate insertion-deletion events of varying length, particularly in nonpairing regions. Several authors have advocated using structural features of the transcribed rRNA molecule to differentiate functional mitochondrial rRNA genes from their nuclear paralogs. We explored this approach using the mitochondrial 12S rRNA gene and three known 12S numts from the human genome in the context of anthropoid phylogeny and the inferred secondary structure of primate 12S rRNA. Contrary to expectation, each of the three human numts exhibits striking concordance with secondary structure models, with little, if any, indication of their pseudogene status, and would likely escape detection based on structural criteria alone. Furthermore, we show that the unwitting inclusion of a particularly ancient (18-25 Myr old) and surprisingly cryptic human numt in a phylogenetic analysis would yield a well-supported but dramatically incorrect conclusion regarding anthropoid relationships. Though we endorse the use of secondary structure models for inferring positional homology wholeheartedly, we caution against reliance on structural criteria for the discrimination of rRNA numts, given the potential fallibility of this approach.

Automated Extraction of Secondary Flow Features

NASA Technical Reports Server (NTRS)

Dorney, Suzanne M.; Haimes, Robert

2005-01-01

The use of Computational Fluid Dynamics (CFD) has become standard practice in the design and development of the major components used for air and space propulsion. To aid in the post-processing and analysis phase of CFD many researchers now use automated feature extraction utilities. These tools can be used to detect the existence of such features as shocks, vortex cores and separation and re-attachment lines. The existence of secondary flow is another feature of significant importance to CFD engineers. Although the concept of secondary flow is relatively understood there is no commonly accepted mathematical definition for secondary flow. This paper will present a definition for secondary flow and one approach for automatically detecting and visualizing secondary flow.

Astronomy textbook images: do they really help students?

NASA Astrophysics Data System (ADS)

Testa, Italo; Leccia, Silvio; Puddu, Emanuella

2014-05-01

In this paper we present a study on the difficulties secondary school students experience in interpreting textbook images of elementary astronomical phenomena, namely, the changing of the seasons, Sun and lunar eclipses and Moon phases. Six images from a commonly used textbook in Italian secondary schools were selected. Interviews of 45 min about the astronomical concepts related to the images were carried out with eighteen students attending the last year of secondary school (aged 17-18). Students’ responses were analyzed through a semiotic framework based on the different types of visual representation structures. We found that the wide range of difficulties shown by students come from naïve or alternative ideas due to incorrect or inadequate geometric models of the addressed phenomena. As a primary implication of this study, we suggest that teachers should pay attention to specific iconic features of the discussed images, e.g., the compositional structure and the presence of real/symbolic elements.

Persistence of urban organic aerosols composition: Decoding their structural complexity and seasonal variability.

PubMed

Matos, João T V; Duarte, Regina M B O; Lopes, Sónia P; Silva, Artur M S; Duarte, Armando C

2017-12-01

Organic Aerosols (OAs) are typically defined as highly complex matrices whose composition changes in time and space. Focusing on time vector, this work uses two-dimensional nuclear magnetic resonance (2D NMR) techniques to examine the structural features of water-soluble (WSOM) and alkaline-soluble organic matter (ASOM) sequentially extracted from fine atmospheric aerosols collected in an urban setting during cold and warm seasons. This study reveals molecular signatures not previously decoded in NMR-related studies of OAs as meaningful source markers. Although the ASOM is less hydrophilic and structurally diverse than its WSOM counterpart, both fractions feature a core with heteroatom-rich branched aliphatics from both primary (natural and anthropogenic) and secondary origin, aromatic secondary organics originated from anthropogenic aromatic precursors, as well as primary saccharides and amino sugar derivatives from biogenic emissions. These common structures represent those 2D NMR spectral signatures that are present in both seasons and can thus be seen as an "annual background" profile of the structural composition of OAs at the urban location. Lignin-derived structures, nitroaromatics, disaccharides, and anhydrosaccharides signatures were also identified in the WSOM samples only from periods identified as smoke impacted, which reflects the influence of biomass-burning sources. The NMR dataset on the H-C molecules backbone was also used to propose a semi-quantitative structural model of urban WSOM, which will aid efforts for more realistic studies relating the chemical properties of OAs with their atmospheric behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions

PubMed Central

2017-01-01

Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions. PMID:28922400

Role of the Substrate Specificity-Defining Residues of Human SIRT5 in Modulating the Structural Stability and Inhibitory Features of the Enzyme.

PubMed

Yu, Junru; Haldar, Manas; Mallik, Sanku; Srivastava, D K

2016-01-01

Sirtuins are emerging as the key regulators of metabolism and aging, and their potential activators and inhibitors are being explored as therapeutics for improving health and treating associated diseases. Despite the global structural similarity among all seven isoforms of sirtuins (of which most of them catalyze the deacetylation reaction), SIRT5 is the only isoform that catalyzes the cleavage of negatively charged acylated substrates, and the latter feature appears to be encoded by the presence of Tyr102 and Arg105 residues at the active site pocket of the enzyme. To determine the contributions of the above residues in SIRT5 (vis a vis the corresponding residues of SIRT1) on substrate selectivity, inhibition by EX527 and nicotinamide, secondary structural features and thermal stability of the enzymes, we created single and double mutations (viz. Y102A, R105l, and Y102A/R105I) in SIRT5. The kinetic data revealed that while Y102A mutant enzyme catalyzed both deacetylation and desuccinylation reactions with comparable efficiencies, R105I and Y102A/R105I mutant enzymes favored the deacetylase reaction. Like SIRT1, the nicotinamide inhibition of SIRT5 double mutant (Y102A/R105I) exhibited the mixed non-competitive behavior. On the other hand, the desuccinylation reaction of both wild-type and Y102A mutant enzymes conformed to the competitive inhibition model. The inhibitory potency of EX527 progressively increased from Y102A, R105I, to Y102A/R105 mutant enzymes in SIRT5, but it did not reach to the level obtained with SIRT1. The CD spectroscopic data for the wild-type and mutant enzymes revealed changes in the secondary structural features of the enzymes, and such changes were more pronounced on examining their thermal denaturation patterns. A cumulative account of our experimental data reveal mutual cooperation between Y102 and R105 residues in promoting the desuccinylation versus deacetylation reaction in SIRT5, and the overall catalytic feature of the enzyme is manifested via the mutation induced modulation in the protein structure.

Role of the Substrate Specificity-Defining Residues of Human SIRT5 in Modulating the Structural Stability and Inhibitory Features of the Enzyme

PubMed Central

Yu, Junru; Haldar, Manas; Mallik, Sanku; Srivastava, D. K.

2016-01-01

Sirtuins are emerging as the key regulators of metabolism and aging, and their potential activators and inhibitors are being explored as therapeutics for improving health and treating associated diseases. Despite the global structural similarity among all seven isoforms of sirtuins (of which most of them catalyze the deacetylation reaction), SIRT5 is the only isoform that catalyzes the cleavage of negatively charged acylated substrates, and the latter feature appears to be encoded by the presence of Tyr102 and Arg105 residues at the active site pocket of the enzyme. To determine the contributions of the above residues in SIRT5 (vis a vis the corresponding residues of SIRT1) on substrate selectivity, inhibition by EX527 and nicotinamide, secondary structural features and thermal stability of the enzymes, we created single and double mutations (viz. Y102A, R105l, and Y102A/R105I) in SIRT5. The kinetic data revealed that while Y102A mutant enzyme catalyzed both deacetylation and desuccinylation reactions with comparable efficiencies, R105I and Y102A/R105I mutant enzymes favored the deacetylase reaction. Like SIRT1, the nicotinamide inhibition of SIRT5 double mutant (Y102A/R105I) exhibited the mixed non-competitive behavior. On the other hand, the desuccinylation reaction of both wild-type and Y102A mutant enzymes conformed to the competitive inhibition model. The inhibitory potency of EX527 progressively increased from Y102A, R105I, to Y102A/R105 mutant enzymes in SIRT5, but it did not reach to the level obtained with SIRT1. The CD spectroscopic data for the wild-type and mutant enzymes revealed changes in the secondary structural features of the enzymes, and such changes were more pronounced on examining their thermal denaturation patterns. A cumulative account of our experimental data reveal mutual cooperation between Y102 and R105 residues in promoting the desuccinylation versus deacetylation reaction in SIRT5, and the overall catalytic feature of the enzyme is manifested via the mutation induced modulation in the protein structure. PMID:27023330

Secondary structural entropy in RNA switch (Riboswitch) identification.

PubMed

Manzourolajdad, Amirhossein; Arnold, Jonathan

2015-04-28

RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. A typical class of riboswitch has its own unique structural and biological complexity, making de novo riboswitch identification a formidable task. Traditionally, riboswitches have been identified through comparative genomics based on sequence and structural homology. The limitations of structural-homology-based approaches, coupled with the assumption that there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods for riboswitch identification, possibly based on features intrinsic to their structure. As of yet, no such reliable method has been proposed. We used structural entropy of riboswitch sequences as a measure of their secondary structural dynamics. Entropy values of a diverse set of riboswitches were compared to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under different stochastic context-free grammar folding models. Significance of our results was evaluated by comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics. Classifiers based on structural entropy optimized via sequence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis, Escherichia coli, and Synechococcus elongatus as an exploration of structural entropy based approaches. The unusually long untranslated region of the cotH in Bacillus subtilis, as well as upstream regions of certain genes, such as the sucC genes were associated with significant structural entropy values in genome-wide examinations. Various tests show that there is in fact a relationship between higher structural entropy and the potential for the RNA sequence to have alternative structures, within the limitations of our methodology. This relationship, though modest, is consistent across various tests. Understanding the behavior of structural entropy as a fairly new feature for RNA conformational dynamics, however, may require extensive exploratory investigation both across RNA sequences and folding models.

Seals/Secondary Fluid Flows Workshop 1997; Volume I

NASA Technical Reports Server (NTRS)

Hendricks, Robert C. (Editor)

2006-01-01

The 1997 Conference provided discussions and data on (a) program overviews, (b) developments in seals and secondary air management systems, (c) interactive seals flows with secondary air or fluid flows and powerstream flows, (d) views of engine externals and limitations, (e) high speed engine research sealing needs and demands, and (f) a short course on engine design development margins. Sealing concepts discussed include, mechanical rim and cavity seals, leaf, finger, air/oil, rope, floating-brush, floating-T-buffer, and brush seals. Engine externals include all components of engine fluid systems, sensors and their support structures that lie within or project through the nacelle. The clean features of the nacelle belie the minefield of challenges and opportunities that lie within. Seals; Secondary air flows; Rotordynamics; Gas turbine; Aircraft; CFD; Testing; Turbomachinery

nRC: non-coding RNA Classifier based on structural features.

PubMed

Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

2017-01-01

Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

Rotor systems research aircraft predesign study. Volume 4: Preliminary draft detail specification

NASA Technical Reports Server (NTRS)

Miller, A. N.; Linden, A. W.

1972-01-01

The RSRA requirements are presented in a detail specification format. Coverage of the requirements includes the following headings: (1) aircraft characteristics, (2) general features of design and construction, (3) aerodynamics, (4) structural design criteria, (5) flight control system, (6) propulsion subsystem, and (7) secondary power and distribution subsystem.

The Narrative Process of Improving Vocational Classroom Practice

ERIC Educational Resources Information Center

Sharman, Kathleen Y.

2011-01-01

This research inquires into the use of stories by vocational teachers. These stories are of interest because they are a fundamental feature of both the subject content and the social structures of vocational classrooms. The trade experiences of vocational teachers are brought to the classroom through stories. These stories have a secondary effect…

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.

PubMed

Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

2016-01-11

Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

Riboswitches: emerging themes in RNA structure and function.

PubMed

Montange, Rebecca K; Batey, Robert T

2008-01-01

Riboswitches are RNAs capable of binding cellular metabolites using a diverse array of secondary and tertiary structures to modulate gene expression. The recent determination of the three-dimensional structures of parts of six different riboswitches illuminates common features that allow riboswitches to be grouped into one of two types. Type I riboswitches, as exemplified by the purine riboswitch, are characterized by a single, localized binding pocket supported by a largely pre-established global fold. This arrangement limits ligand-induced conformational changes in the RNA to a small region. In contrast, Type II riboswitches, such as the thiamine pyrophosphate riboswitch, contain binding pockets split into at least two spatially distinct sites. As a result, binding induces both local changes to the binding pocket and global architecture. Similar organizational themes are found in other noncoding RNAs, making it possible to begin to build a hierarchical classification of RNA structure based on the spatial organization of their active sites and associated secondary structural elements.

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

NASA Astrophysics Data System (ADS)

Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

2016-01-01

Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

Global Organization of a Positive-strand RNA Virus Genome

PubMed Central

Wu, Baodong; Grigull, Jörg; Ore, Moriam O.; Morin, Sylvie; White, K. Andrew

2013-01-01

The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV) contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2′-hydroxyl acylation analysed by primer extension (i.e. SHAPE), which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context. PMID:23717202

Hepatitis Delta Antigen Requires a Flexible Quasi-Double-Stranded RNA Structure To Bind and Condense Hepatitis Delta Virus RNA in a Ribonucleoprotein Complex

PubMed Central

Griffin, Brittany L.; Chasovskikh, Sergey; Dritschilo, Anatoly

2014-01-01

ABSTRACT The circular genome and antigenome RNAs of hepatitis delta virus (HDV) form characteristic unbranched, quasi-double-stranded RNA secondary structures in which short double-stranded helical segments are interspersed with internal loops and bulges. The ribonucleoprotein complexes (RNPs) formed by these RNAs with the virus-encoded protein hepatitis delta antigen (HDAg) perform essential roles in the viral life cycle, including viral replication and virion formation. Little is understood about the formation and structure of these complexes and how they function in these key processes. Here, the specific RNA features required for HDAg binding and the topology of the complexes formed were investigated. Selective 2′OH acylation analyzed by primer extension (SHAPE) applied to free and HDAg-bound HDV RNAs indicated that the characteristic secondary structure of the RNA is preserved when bound to HDAg. Notably, the analysis indicated that predicted unpaired positions in the RNA remained dynamic in the RNP. Analysis of the in vitro binding activity of RNAs in which internal loops and bulges were mutated and of synthetically designed RNAs demonstrated that the distinctive secondary structure, not the primary RNA sequence, is the major determinant of HDAg RNA binding specificity. Atomic force microscopy analysis of RNPs formed in vitro revealed complexes in which the HDV RNA is substantially condensed by bending or wrapping. Our results support a model in which the internal loops and bulges in HDV RNA contribute flexibility to the quasi-double-stranded structure that allows RNA bending and condensing by HDAg. IMPORTANCE RNA-protein complexes (RNPs) formed by the hepatitis delta virus RNAs and protein, HDAg, perform critical roles in virus replication. Neither the structures of these RNPs nor the RNA features required to form them have been characterized. HDV RNA is unusual in that it forms an unbranched quasi-double-stranded structure in which short base-paired segments are interspersed with internal loops and bulges. We analyzed the role of the HDV RNA sequence and secondary structure in the formation of a minimal RNP and visualized the structure of this RNP using atomic force microscopy. Our results indicate that HDAg does not recognize the primary sequence of the RNA; rather, the principle contribution of unpaired bases in HDV RNA to HDAg binding is to allow flexibility in the unbranched quasi-double-stranded RNA structure. Visualization of RNPs by atomic force microscopy indicated that the RNA is significantly bent or condensed in the complex. PMID:24741096

Profiling of acarviostatin family secondary metabolites secreted by Streptomyces coelicoflavus ZG0656 using ultraperformance liquid chromatography coupled with electrospray ionization mass spectrometry.

PubMed

Geng, Peng; Meng, Xiansheng; Bai, Gang; Luo, Guoan

2008-10-01

Profiling of acarviostatin family secondary metabolites secreted by Streptomyces coelicoflavus ZG0656 was performed by means of a rapid and facile procedure using ultraperformance liquid chromatography coupled with electrospray ionization mass spectrometry (UPLC/ESI-MS). The acarviostatins were separated on a C18 UPLC column with a series of acetonitrile-aqueous ammonia gradients. The target homologues were detected using the multiple reaction monitoring mode, and the chemical structures were confirmed by analyzing the diagnostic fragment ions in their MS/MS spectra. All six known reference acarviostatins (I03, II03, II13, II23, III03, IV03) were thus identified. In addition, at least 74 acarviostatin homologues, including 65 novel compounds, were characterized. Some of the features of the novel structures included having up to five acarviosine moieties, an acarviosine moiety at the reducing terminus, or an incomplete acarviosine moiety at the nonreducing terminus. This type of investigation may be useful for researchers who study secondary metabolomics in microorganisms and plants, especially those who perform metabolic profiling of aminooligosaccharides and other natural products with similar structures.

DSSR-enhanced visualization of nucleic acid structures in Jmol

PubMed Central

Hanson, Robert M.

2017-01-01

Abstract Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). PMID:28472503

A cross-site comparison of methods used for hydrogeologic characterization of the Galena-Platteville aquifer in Illinois and Wisconsin, with examples from selected Superfund sites

USGS Publications Warehouse

Kay, Robert T.; Mills, Patrick C.; Dunning, Charles P.; Yeskis, Douglas J.; Ursic, James R.; Vendl, Mark

2004-01-01

The effectiveness of 28 methods used to characterize the fractured Galena-Platteville aquifer at eight sites in northern Illinois and Wisconsin is evaluated. Analysis of government databases, previous investigations, topographic maps, aerial photographs, and outcrops was essential to understanding the hydrogeology in the area to be investigated. The effectiveness of surface-geophysical methods depended on site geology. Lithologic logging provided essential information for site characterization. Cores were used for stratigraphy and geotechnical analysis. Natural-gamma logging helped identify the effect of lithology on the location of secondary- permeability features. Caliper logging identified large secondary-permeability features. Neutron logs identified trends in matrix porosity. Acoustic-televiewer logs identified numerous secondary-permeability features and their orientation. Borehole-camera logs also identified a number of secondary-permeability features. Borehole ground-penetrating radar identified lithologic and secondary-permeability features. However, the accuracy and completeness of this method is uncertain. Single-point-resistance, density, and normal resistivity logs were of limited use. Water-level and water-quality data identified flow directions and indicated the horizontal and vertical distribution of aquifer permeability and the depth of the permeable features. Temperature, spontaneous potential, and fluid-resistivity logging identified few secondary-permeability features at some sites and several features at others. Flowmeter logging was the most effective geophysical method for characterizing secondary-permeability features. Aquifer tests provided insight into the permeability distribution, identified hydraulically interconnected features, the presence of heterogeneity and anisotropy, and determined effective porosity. Aquifer heterogeneity prevented calculation of accurate hydraulic properties from some tests. Different methods, such as flowmeter logging and slug testing, occasionally produced different interpretations. Aquifer characterization improved with an increase in the number of data points, the period of data collection, and the number of methods used.

Controlling silk fibroin particle features for drug delivery

PubMed Central

Lammel, Andreas; Hu, Xiao; Park, Sang-Hyug; Kaplan, David L.; Scheibel, Thomas

2010-01-01

Silk proteins are a promising material for drug delivery due to their aqueous processability, biocompatibility, and biodegradability. A simple aqueous preparation method for silk fibroin particles with controllable size, secondary structure and zeta potential is reported. The particles were produced by salting out a silk fibroin solution with potassium phosphate. The effect of ionic strength and pH of potassium phosphate solution on the yield and morphology of the particles was determined. Secondary structure and zeta potential of the silk particles could be controlled by pH. Particles produced by salting out with 1.25 M potassium phosphate pH 6 showed a dominating silk II (crystalline) structure whereas particles produced at pH 9 were mainly composed of silk I (less crystalline). The results show that silk I rich particles possess chemical and physical stability and secondary structure which remained unchanged during post treatments even upon exposure to 100% ethanol or methanol. A model is presented to explain the process of particle formation based on intra- and intermolecular interactions of the silk domains, influenced by pH and kosmotrope salts. The reported silk fibroin particles can be loaded with small molecule model drugs, such as alcian blue, rhodamine B, and crystal violet, by simple absorption based on electrostatic interactions. In vitro release of these compounds from the silk particles depends on charge – charge interactions between the compounds and the silk. With crystal violet we demonstrated that the release kinetics are dependent on the secondary structure of the particles. PMID:20219241

The effects of two secondary science teacher education program structures on teachers' habits of mind and action

NASA Astrophysics Data System (ADS)

Bergman, Daniel Jay

2007-12-01

This study investigated the effects of the Iowa State University Secondary Science Teacher Education Program (ISU SSTEP) on the educational goals and habits of mind exhibited by its graduates. Ten teachers from ISU SSTEP participated in the study---five from the former program featuring one semester of science teaching methods, five from the current program featuring three semesters of science teaching methods (four for the graduate certification consortium). A naturalistic inquiry research approach included the following methods used with each teacher: three classroom observations, classroom artifact analysis, teacher questionnaires and semi-structured interviews, and questionnaires for students about perceived emphasis of educational goals. Evidence exists that graduates from the current ISU SSTEP format exhibited a closer match to the educational goals promoted, modeled, and advocated by the science teaching methods faculty. Graduates from the current ISU SSTEP also exhibited a closer match to the habits of mind---understanding, action, reflection, action plan for improvement---promoted and modeled by the program. This study has implications for other secondary science teacher education programs, particularly increasing the number of science teaching methods courses; teaching meaningful content of both concepts and skills through a research-based framework; modeling the appropriate teacher behaviors, strategies, habits, and goal promotion by methods instructors; and addressing issues of institutional constraints experienced by future teachers.

New Protein Mimetics: The Zinc Finger Motif as a Locked-In Tertiary Fold.

PubMed

Tuchscherer, Gabriele; Lehmann, Christian; Mathieu, Marc

1998-11-16

The principle of a molecular kit is used for the covalent assembly of secondary structure forming peptide blocks to predetermined packing topologies. The resulting locked-in folds (LIFs; depicted schematically) are readily accessible and bypass the intriguing folding problem of linear peptide chains. This strategy allows, for example, mimicking of the essential structural and functional features of zinc finger proteins. © 1998 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases

PubMed Central

Laskar, Aparna; Chatterjee, Aniruddha; Chatterjee, Somnath; Rodger, Euan J.

2012-01-01

Serine proteases are involved in a variety of biological processes and are classified into clans sharing structural homology. Although various three-dimensional structures of SC clan proteases have been experimentally determined, they are mostly bacterial and animal proteases, with some from archaea, plants, and fungi, and as yet no structures have been determined for protozoa. To bridge this gap, we have used molecular modeling techniques to investigate the structural properties of different SC clan serine proteases from a diverse range of taxa. Either SWISS-MODEL was used for homology-based structure prediction or the LOOPP server was used for threading-based structure prediction. The predicted models were refined using Insight II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on SC clan serine proteases. PMID:23213528

Prediction of protein structural classes by Chou's pseudo amino acid composition: approached using continuous wavelet transform and principal component analysis.

PubMed

Li, Zhan-Chao; Zhou, Xi-Bin; Dai, Zong; Zou, Xiao-Yong

2009-07-01

A prior knowledge of protein structural classes can provide useful information about its overall structure, so it is very important for quick and accurate determination of protein structural class with computation method in protein science. One of the key for computation method is accurate protein sample representation. Here, based on the concept of Chou's pseudo-amino acid composition (AAC, Chou, Proteins: structure, function, and genetics, 43:246-255, 2001), a novel method of feature extraction that combined continuous wavelet transform (CWT) with principal component analysis (PCA) was introduced for the prediction of protein structural classes. Firstly, the digital signal was obtained by mapping each amino acid according to various physicochemical properties. Secondly, CWT was utilized to extract new feature vector based on wavelet power spectrum (WPS), which contains more abundant information of sequence order in frequency domain and time domain, and PCA was then used to reorganize the feature vector to decrease information redundancy and computational complexity. Finally, a pseudo-amino acid composition feature vector was further formed to represent primary sequence by coupling AAC vector with a set of new feature vector of WPS in an orthogonal space by PCA. As a showcase, the rigorous jackknife cross-validation test was performed on the working datasets. The results indicated that prediction quality has been improved, and the current approach of protein representation may serve as a useful complementary vehicle in classifying other attributes of proteins, such as enzyme family class, subcellular localization, membrane protein types and protein secondary structure, etc.

Meteoroid and debris special investigation group data acquisition procedures

NASA Technical Reports Server (NTRS)

See, Thomas H.; Allbrooks, Martha K.; Atkinson, Dale R.; Sapp, Clyde A.; Simon, Charles G.; Zolensky, Mike E.

1992-01-01

The entire LDEF spacecraft was examined by M&D SIG for impact (i.e., craters greater than or = 0.5 mm and penetrations greater than or = 0.3 mm in diameter) and related features (e.g., debris, secondaries). During the various detailed surveys conducted at NASA Kennedy, approx. 5,000 impact related features were photodocumented, and their locations measured and recorded; an additional approx. 30,000 smaller features were counted. The equipment and techniques used by the M&D SIG permitted the determination and recording of the locations and diameters of the 5,000 imaged features. A variety of experimental and LDEF structural hardware was acquired by the M&D SIG and is presently being examined and curated at NASA Johnson.

Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

PubMed

Koch, Oliver; Cole, Jason; Block, Peter; Klebe, Gerhard

2009-10-01

Secbase is presented as a novel extension module of Relibase. It integrates the information about secondary structure elements into the retrieval facilities of Relibase. The data are accessible via the extended Relibase user interface, and integrated retrieval queries can be addressed using an extended version of Reliscript. The primary information about alpha-helices and beta-sheets is used as provided by the PDB. Furthermore, a uniform classification of all turn families, based on recent clustering methods, and a new helix assignment that is based on this turn classification has been included. Algorithms to analyze the geometric features of helices and beta-strands were also implemented. To demonstrate the performance of the Secbase implementation, some application examples are given. They provide new insights into the involvement of secondary structure elements in ligand binding. A survey of water molecules detected next to the N-terminus of helices is analyzed to show their involvement in ligand binding. Additionally, the parallel oriented NH groups at the alpha-helix N-termini provide special binding motifs to bind particular ligand functional groups with two adjacent oxygen atoms, e.g., as found in negatively charged carboxylate or phosphate groups, respectively. The present study also shows that the specific structure of the first turn of alpha-helices provides a suitable explanation for stabilizing charged structures. The magnitude of the overall helix macrodipole seems to have no or only a minor influence on binding. Furthermore, an overview of the involvement of secondary structure elements with the recognition of some important endogenous ligands such as cofactors shows some distinct preference for particular binding motifs and amino acids.

Two Types of 2D Layered Iodoargentates Based on Trimeric [Ag3I7] Secondary Building Units and Hexameric [Ag6I12] Ternary Building Units: Syntheses, Crystal Structures, and Efficient Visible Light Responding Photocatalytic Properties.

PubMed

Lei, Xiao-Wu; Yue, Cheng-Yang; Zhao, Jian-Qiang; Han, Yong-Fang; Yang, Jiang-Tao; Meng, Rong-Rong; Gao, Chuan-Sheng; Ding, Hao; Wang, Chun-Yan; Chen, Wan-Dong; Hong, Mao-Chun

2015-11-16

With mixed transition-metal-complex, alkali-metal, or organic cations as structure-directing agents, a series of novel two-dimensional (2D) layered inorganic-organic hybrid iodoargentates, namely, Kx[TM(2,2-bipy)3]2Ag6I11 (TM = Mn (1), Fe (2), Co (3), Ni (4), Zn (5); x = 0.89-1) and [(Ni(2,2-bipy)3][H-2,2-bipy]Ag3I6 (6), have been solvothermally synthesized and structurally characterized. All the title compounds feature 2D microporous layers composed by [Ag3I7] secondary building units based on AgI4 tetrahedra. Differently, the [Ag3I7] trimers are directly interconnected via corner-sharing to form the 2D [Ag6I11](5-) layer in compounds 1-5, whereas two neighboring [Ag3I7] trimers are initially condensed into a hexameric [Ag6I12] ternary building unit as a new node, which further self-assembles, leading to the 2D [Ag6I10](4-) layer in compound 6. The UV-vis diffuse-reflectance measurements reveal that all the compounds possess proper semiconductor behaviors with tunable band gaps of 1.66-2.75 eV, which lead to highly efficient photocatalytic degradation activities over organic pollutants under visible light irradiation compared to that of N-dotted P25. Interestingly, all the samples feature distinct photodegradative speeds at the same reaction conditions, and compound 1 features the highest photocatalytic activity among the title phases. The luminescence properties, band structures, and thermal stabilities were also studied.

Improving Decision Making in Schools through Teacher Participation

ERIC Educational Resources Information Center

Mualuko, Ndiku J.; Mukasa, Simiyu A.; Achoka, Judy S. K.

2009-01-01

The hierarchical structure that places head teachers at the apex of a pyramid of staff is a common feature in secondary schools in Kenya. In this arrangement, school heads are poised to use their superior knowledge and experience to direct and control the working of the entire school. This negatively affects efficiency and productivity of the…

Heterotopias in Physical Education: Towards a Queer Pedagogy?

ERIC Educational Resources Information Center

Larsson, Håkan; Quennerstedt, Mikael; Öhman, Marie

2014-01-01

This article sets out to outline how prevailing gender structures can be challenged in physical education (PE) by exploring queer potentials in an event that took place during a dancing lesson in an upper secondary PE class. The event and its features were documented through video recording and post-lesson interviews with the teacher and some of…

Transcriptional control by G-quadruplexes: In vivo roles and perspectives for specific intervention.

PubMed

Armas, Pablo; David, Aldana; Calcaterra, Nora B

2017-01-01

G-quadruplexes are non-canonical DNA secondary structures involved in several genomic and molecular processes. Here, we summarize the main G-quadruplex features and evidences proving the in vivo role on the transcriptional regulation of genes required for zebrafish embryonic development. We also discuss alternative strategies for specifically interfering G-quadruplex in vivo.

Educational Experiences and Needs of Higher Education Students with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Cai, Ru Ying; Richdale, Amanda L.

2016-01-01

Little research directly examines the needs of post-secondary students with ASD. The experiences and support needs of 23 students with ASD enrolled in two universities and four colleges, and 15 family members were explored in 15 semi-structured focus groups. Thematic analysis identified five themes: core ASD features, co-morbid conditions,…

Adolescent Weak Decoders Writing in a Shallow Orthography: Process and Product

ERIC Educational Resources Information Center

Torrance, Mark; Rønneberg, Vibeke; Johansson, Christer; Uppstad, Per Henning

2016-01-01

It has been hypothesized that students with dyslexia struggle with writing because of a word-level focus that reduces attention to higher level textual features (structure, theme development). This may result from difficulties with spelling and/or difficulties with reading. Twenty-six Norwegian upper secondary students (M = 16.9 years) with weak…

Curriculum Choices and School-To-Work Transitions among Upper-Secondary School Leavers in Scotland and Ireland

ERIC Educational Resources Information Center

Iannelli, Cristina; Smyth, Emer

2017-01-01

David Raffe was a highly influential figure in the field of transitions research. His work carefully delineated how national institutional policies shape transition processes and outcomes. Curriculum structure and organisation were seen as key features of these transition systems, his work tracing the relative impact of vocational and academic…

Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS)☟

PubMed Central

Xin, Dongyue; Ko, Eunhwa; Perez, Lisa M.; Ioerger, Thomas R.; Burgess, Kevin

2013-01-01

Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, “minimalist helical mimics”. It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i+4, i+7 side-chains in orientations that best resemble an ideal α-helix, and is a different mimic required for a i, i+3, i+7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds;(iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay Cα and Cβ coordinates of all the conformers on all the sets of side-chain “triads” in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the “side-chain correspondences” (eg i, i+4, i+7 or i, i+3, i+4) of those overlays, and the energy of this state relative to the minimum located. This protocol was tested on some of the most widely cited minimalist α-helical mimics (1 – 8 in the text). The data obtained indicates several of these compounds preferentially exist in conformations that resemble other secondary structures as well as α-helices, and many of the α-helical conformations have unexpected side-chain correspondences. These observations imply the featured minimalist mimics have more scope for disrupting PPI interfaces than previously anticipated. Finally, the same simulation method was used to match preferred conformations of minimalist mimics with actual protein/peptide structures at interfaces providing quantitative comparisons of predicted fits of the test mimics at protein-protein interaction sites. PMID:24121516

Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS).

PubMed

Xin, Dongyue; Ko, Eunhwa; Perez, Lisa M; Ioerger, Thomas R; Burgess, Kevin

2013-11-28

Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, "minimalist helical mimics". It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i + 4, i + 7 side-chains in orientations that best resemble an ideal α-helix, and is a different mimic required for a i, i + 3, i + 7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; (iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay Cα and Cβ coordinates of all the conformers on all the sets of side-chain "triads" in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the "side-chain correspondences" (e.g. i, i + 4, i + 7 or i, i + 3, i + 4) of those overlays, and the energy of this state relative to the minimum located. This protocol was tested on some of the most widely cited minimalist α-helical mimics (1-8 in the text). The data obtained indicates several of these compounds preferentially exist in conformations that resemble other secondary structures as well as α-helices, and many of the α-helical conformations have unexpected side-chain correspondences. These observations imply the featured minimalist mimics have more scope for disrupting PPI interfaces than previously anticipated. Finally, the same simulation method was used to match preferred conformations of minimalist mimics with actual protein/peptide structures at interfaces providing quantitative comparisons of predicted fits of the test mimics at protein-protein interaction sites.

Infiltrative cervical lesions causing symptomatic occipital neuralgia.

PubMed

Sierra-Hidalgo, F; Ruíz, J; Morales-Cartagena, A; Martínez-Salio, A; Serna, J de la; Hernández-Gallego, J

2011-10-01

Occipital neuralgia is a well-recognized cause of posterior head and neck pain that may associate mild sensory changes in the cutaneous distribution of the occipital nerves, lacking a recognizable local structural aetiology in most cases. Atypical clinical features or an abnormal neurological examination are alerts for a potential underlying cause of pain, although cases of clinically typical occipital neuralgia as isolated manifestation of lesions of the cervical spinal cord, cervical roots, or occipital nerves have been increasingly reported. We describe two cases (one with typical and another one with atypical clinical features) of occipital neuralgia secondary to paravertebral pyomyositis and vertebral relapse of multiple myeloma in patients with relevant medical history that aroused the possibility of an underlying structural lesion. We discuss the need for cranio-cervical magnetic resonance imaging in all patients with occipital neuralgia, even when typical clinical features are present and neurological examination is completely normal.

Unique Structural Features and Sequence Motifs of Proline Utilization A (PutA)

PubMed Central

Singh, Ranjan K.; Tanner, John J.

2013-01-01

Proline utilization A proteins (PutAs) are bifunctional enzymes that catalyze the oxidation of proline to glutamate using spatially separated proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase active sites. Here we use the crystal structure of the minimalist PutA from Bradyrhizobium japonicum (BjPutA) along with sequence analysis to identify unique structural features of PutAs. This analysis shows that PutAs have secondary structural elements and domains not found in the related monofunctional enzymes. Some of these extra features are predicted to be important for substrate channeling in BjPutA. Multiple sequence alignment analysis shows that some PutAs have a 17-residue conserved motif in the C-terminal 20–30 residues of the polypeptide chain. The BjPutA structure shows that this motif helps seal the internal substrate-channeling cavity from the bulk medium. Finally, it is shown that some PutAs have a 100–200 residue domain of unknown function in the C-terminus that is not found in minimalist PutAs. Remote homology detection suggests that this domain is homologous to the oligomerization beta-hairpin and Rossmann fold domain of BjPutA. PMID:22201760

nextPARS: parallel probing of RNA structures in Illumina

PubMed Central

Saus, Ester; Willis, Jesse R.; Pryszcz, Leszek P.; Hafez, Ahmed; Llorens, Carlos; Himmelbauer, Heinz

2018-01-01

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing. PMID:29358234

Diagnosis of secondary pulmonary lymphangiectasia in congenital heart disease: a novel role for chest ultrasound and prognostic implications.

PubMed

Lam, Christopher Z; Bhamare, Tanmay Anant; Gazzaz, Tamadhir; Manson, David; Humpl, Tilman; Seed, Mike

2017-10-01

Secondary pulmonary lymphangiectasia is a complication of congenital heart disease that results from chronic pulmonary venous obstruction. We aimed to evaluate the performance of chest ultrasound (US) in diagnosing secondary pulmonary lymphangiectasia and to review the clinical course of children with secondary pulmonary lymphangiectasia. Chest US was performed on 26 children with hypoplastic left heart syndrome, total anomalous pulmonary venous connection or cor triatriatum in a prospective observational study. Thirteen children had pulmonary venous obstruction (62% male; median age: 17 days old, range: 1-430 days old) and 13 children did not have obstruction (62% male; median age: 72 days old, range: 4-333 days old). US features of secondary pulmonary lymphangiectasia were documented and diagnostic performance was determined. Clinical course of patients with secondary pulmonary lymphangiectasia was reviewed. Eleven of 13 (84.6%) patients in the obstructed group had a clinical and/or biopsy diagnosis of secondary pulmonary lymphangiectasia. Statistically significant chest US criteria for diagnosis were presence of irregular lung surface (likelihood ratio [LR] 6.8, 95% confidence interval [CI] 1.9-25.1), subpleural cystic appearing structures (LR 3.6, 95% CI 1.2-10.7), and combination of subpleural cystic appearing structures and surface irregularity together (LR 10.9, 95% CI 1.6-75.0). Seven of 11 (63.6%) patients with secondary pulmonary lymphangiectasia died during follow-up, the majority due to cardiopulmonary failure or complications. Chest US is an accurate and reproducible bedside method for diagnosing secondary pulmonary lymphangiectasia in patients with pulmonary venous obstruction. These patients may have worse prognoses.

A novel diamond micro-/nano-machining process for the generation of hierarchical micro-/nano-structures

NASA Astrophysics Data System (ADS)

Zhu, Zhiwei; To, Suet; Ehmann, Kornel F.; Xiao, Gaobo; Zhu, Wule

2016-03-01

A new mechanical micro-/nano-machining process that combines rotary spatial vibrations (RSV) of a diamond tool and the servo motions of the workpiece is proposed and applied for the generation of multi-tier hierarchical micro-/nano-structures. In the proposed micro-/nano-machining system, the servo motion, as the primary cutting motion generated by a slow-tool-servo, is adopted for the fine generation of the primary surfaces with complex shapes. The RSV, as the tertiary cutting operation, is superimposed on the secondary fundamental rotary cutting motion to construct secondary nano-structures on the primary surface. Since the RSV system generally works at much higher frequencies and motion resolution than the primary and secondary motions, it leads to an inherent hierarchical cutting architecture. To investigate the machining performance, complex micro-/nano-structures were generated and explored by both numerical simulations and actual cutting tests. Rotary vibrations of the diamond tool at a constant rotational distance offer an inherent constant cutting velocity, leading to the ability for the generation of homogeneous micro-/nano-structures with fixed amplitudes and frequencies of the vibrations, even over large-scale surfaces. Furthermore, by deliberately combining the non-resonant three-axial vibrations and the servo motion, the generation of a variety of micro-/nano-structures with complex shapes and with flexibly tunable feature sizes can be achieved.

Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na+ coupling

NASA Astrophysics Data System (ADS)

Perez, Camilo; Faust, Belinda; Mehdipour, Ahmad Reza; Francesconi, Kevin A.; Forrest, Lucy R.; Ziegler, Christine

2014-07-01

The Na+-coupled betaine symporter BetP shares a highly conserved fold with other sequence unrelated secondary transporters, for example, with neurotransmitter symporters. Recently, we obtained atomic structures of BetP in distinct conformational states, which elucidated parts of its alternating-access mechanism. Here, we report a structure of BetP in a new outward-open state in complex with an anomalous scattering substrate, adding a fundamental piece to an unprecedented set of structural snapshots for a secondary transporter. In combination with molecular dynamics simulations these structural data highlight important features of the sequential formation of the substrate and sodium-binding sites, in which coordinating water molecules play a crucial role. We observe a strictly interdependent binding of betaine and sodium ions during the coupling process. All three sites undergo progressive reshaping and dehydration during the alternating-access cycle, with the most optimal coordination of all substrates found in the closed state.

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

PubMed Central

Novikova, Irina V.; Hennelly, Scott P.; Sanbonmatsu, Karissa Y.

2012-01-01

While functional roles of several long non-coding RNAs (lncRNAs) have been determined, the molecular mechanisms are not well understood. Here, we report the first experimentally derived secondary structure of a human lncRNA, the steroid receptor RNA activator (SRA), 0.87 kB in size. The SRA RNA is a non-coding RNA that coactivates several human sex hormone receptors and is strongly associated with breast cancer. Coding isoforms of SRA are also expressed to produce proteins, making the SRA gene a unique bifunctional system. Our experimental findings (SHAPE, in-line, DMS and RNase V1 probing) reveal that this lncRNA has a complex structural organization, consisting of four domains, with a variety of secondary structure elements. We examine the coevolution of the SRA gene at the RNA structure and protein structure levels using comparative sequence analysis across vertebrates. Rapid evolutionary stabilization of RNA structure, combined with frame-disrupting mutations in conserved regions, suggests that evolutionary pressure preserves the RNA structural core rather than its translational product. We perform similar experiments on alternatively spliced SRA isoforms to assess their structural features. PMID:22362738

DSSR-enhanced visualization of nucleic acid structures in Jmol.

PubMed

Hanson, Robert M; Lu, Xiang-Jun

2017-07-03

Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Petrosal anatomy and inner ear structures of the Late Jurassic Henkelotherium (Mammalia, Cladotheria, Dryolestoidea): insight into the early evolution of the ear region in cladotherian mammals

PubMed Central

Ruf, Irina; Luo, Zhe-Xi; Wible, John R; Martin, Thomas

2009-01-01

The petrosal anatomy and inner ear structure of Jurassic cladotherian mammals represent the ancestral morphological conditions (groundplan) from which modern therian mammals (marsupials and placentals) have evolved. We present the reconstruction of the petrosal and inner ear features of the Late Jurassic dryolestoid mammal Henkelotherium guimarotae from high-resolution computed tomography and three-dimensional imaging analysis. This study of Henkelotherium revealed a combination of derived and primitive features, including: cladotherian apomorphies, such as the promontorial sulcus for the internal carotid artery and reduced lateral trough; trechnotherian characters, such as an enclosed cochlear canaliculus for the perilymphatic duct, post-promontorial tympanic sinus and caudal tympanic process; in addition to plesiomorphic mammalian features, such as the cavum supracochleare and prootic canal. The inner ear of Henkelotherium shows a division between the utricle and saccule, a cochlear canal coiled through at least 270°, a distinctive primary bony lamina for the basilar membrane, and a secondary bony lamina. The development of the primary and secondary bony laminae in the cochlear canal is suggested here to be correlated with the concurrent coiling of the bony canal and membranous duct of the inner ear cochlea, apomorphies of the more inclusive cladotherian clade that also represent the ancestral morphotype of modern therian mammals. Because these features are crucial for high-frequency hearing in extant therian mammals, their early appearance in Late Jurassic cladotherians suggests a more ancient origination for high-frequency hearing in mammalian history than previously thought. PMID:19438763

Computational study of RNA folding kinetics and thermodynamics

NASA Astrophysics Data System (ADS)

Morgan, Steven Robert

RNA in its many forms is involved in the processes of protein manufacture, gene splicing, catalysis and gene regulation. It is also the store of genetic information in some viruses. The function of the RNA is determined by its structure, and it is the purpose of this thesis to investigate kinetic and thermodynamic properties of RNA secondary structures in order to obtain a better understanding of their formation and function. Our main tenet is that kinetic formation of RNA structure is necessary to explain features found in natural RNA structures, as well as aspects of the biological function of RNA. Firstly we show that examination of the energies of fragments of RNA secondary structure provides evidence for kinetic formation of structure. Local regions of RNA of length less than about 100 nucleotides adopt a conformation with energy near or equal to the minimum possible for those regions, whilst the energies of larger domains are much further from the their respective minima. This is consistent with the patterns that would be expected if RNA structure is folded Idneticatic during transcription. A Monte-Carlo algorithm is then used to model the kinetic folding of RNA during transcriptional growth. The algorithm is capable of finding the correct structure of a natural RNA for which the minimum free energy approach is unsuccessful. In the viral phage MS2 Idneticatic formed RNA structure plays an important role in the regulation of gene expression. The folding algorithm can accurately model this by IdneticaUy controlling access to the gene initiation region. The algorithm is also successfully used to model the control of replication in the ColEl plasmid. Taking a different approach, we then use a simplified model of RNA secondary structure to investigate the size of energy barriers between degenerate minimum energy structures. This model has much in common with physical systems such as spin glasses, and in fact shows similar behaviour to these systems in that energy barriers between structures grow quickly with the length of the RNA sequence. These barriers will serve to trap RNA in non-optimal structures. Together these studies demonstrate the necessity of studying RNA secondary structure from a kinetic point of view, and provide clear directions in which further work may be taken. Kinetic models of RNA secondary structure should continue to prove useful in modelling the structure and function of RNA.

Artificial engineering of secondary lymphoid organs.

PubMed

Tan, Jonathan K H; Watanabe, Takeshi

2010-01-01

Secondary lymphoid organs such as spleen and lymph nodes are highly organized immune structures essential for the initiation of immune responses. They display distinct B cell and T cell compartments associated with specific stromal follicular dendritic cells and fibroblastic reticular cells, respectively. Interweaved through the parenchyma is a conduit system that distributes small antigens and chemokines directly to B and T cell zones. While most structural aspects between lymph nodes and spleen are common, the entry of lymphocytes, antigen-presenting cells, and antigen into lymphoid tissues is regulated differently, reflecting the specialized functions of each organ in filtering either lymph or blood. The overall organization of lymphoid tissue is vital for effective antigen screening and recognition, and is a feature which artificially constructed lymphoid organoids endeavor to replicate. Synthesis of artificial lymphoid tissues is an emerging field that aims to provide therapeutic application for the treatment of severe infection, cancer, and age-related involution of secondary lymphoid tissues. The development of murine artificial lymphoid tissues has benefited greatly from an understanding of organogenesis of lymphoid organs, which has delineated cellular and molecular elements essential for the recruitment and organization of lymphocytes into lymphoid structures. Here, the field of artificial lymphoid tissue engineering is considered including elements of lymphoid structure and development relevant to organoid synthesis. (c) 2010 Elsevier Inc. All rights reserved.

White light emission and second harmonic generation from secondary group participation (SGP) in a coordination network.

PubMed

He, Jun; Zeller, Matthias; Hunter, Allen D; Xu, Zhengtao

2012-01-25

We describe a white emitting coordination network solid that can be conveniently applied as a thin film onto a commercial UV-LED lamp for practical white lighting applications. The solid state material was discovered in an exercise of exploring molecular building blocks equipped with secondary groups for fine-tuning the structures and properties of coordination nets. Specifically, CH(3)SCH(2)CH(2)S- and (S)-CH(3)(OH)CHCH(2)S- (2-hydroxylpropyl) were each attached as secondary groups to the 2,5- positions of 1,4-benzenedicarboxylic acid (bdc), and the resultant molecules (L1 and L2, respectively) were crystallized with Pb(II) into the topologically similar 3D nets of PbL1 and PbL2, both consisting of interlinked Pb-carboxyl chains. While the CH(3)S- groups in PbL1 are not bonded to the Pb(II) centers, the hydroxy groups in PbL2 participate in coordinating to Pb(II) and thus modify the bonding features around the Pb(II), but only to a slight and subtle degree (e.g., Pb-O distances 2.941-3.116 Å). Interestingly, the subtle change in structure significantly impacts the properties, i.e., while the photoluminescence of PbL1 is yellowish green, PbL2 features bright white emission. Also, the homochiral side group in PbL2 imparts significant second harmonic generation, in spite of its seemingly weak association with the main framework (the NLO-phore). In a broad perspective, this work showcases the idea of secondary group participation (SGP) in the construction of coordination networks, an idea that parallels that of hemilabile ligands in organometallics and points to an effective strategy in developing advanced functions in solid state framework materials. © 2011 American Chemical Society

Transcriptional control by G-quadruplexes: In vivo roles and perspectives for specific intervention

PubMed Central

Armas, Pablo; David, Aldana; Calcaterra, Nora B.

2017-01-01

ABSTRACT G-quadruplexes are non-canonical DNA secondary structures involved in several genomic and molecular processes. Here, we summarize the main G-quadruplex features and evidences proving the in vivo role on the transcriptional regulation of genes required for zebrafish embryonic development. We also discuss alternative strategies for specifically interfering G-quadruplex in vivo. PMID:27696937

Comment on "Athabasca Valles, Mars: a lava-draped channel system".

PubMed

Page, David P

2008-06-20

Jaeger et al. (Reports, 21 September 2007, p. 1709) presented images of the Athabasca Valles channel system on Mars and asserted that the observed deposits are composed of thin, fluid lavas. However, all the features they described are secondary and postdate the surface by many millions of years, as documented by structural relationships with small, young impact craters.

Computer Simulation of Fracture in Aerogels

NASA Technical Reports Server (NTRS)

Good, Brian S.

2006-01-01

Aerogels are of interest to the aerospace community primarily for their thermal properties, notably their low thermal conductivities. While the gels are typically fragile, recent advances in the application of conformal polymer layers to these gels has made them potentially useful as lightweight structural materials as well. In this work, we investigate the strength and fracture behavior of silica aerogels using a molecular statics-based computer simulation technique. The gels' structure is simulated via a Diffusion Limited Cluster Aggregation (DLCA) algorithm, which produces fractal structures representing experimentally observed aggregates of so-called secondary particles, themselves composed of amorphous silica primary particles an order of magnitude smaller. We have performed multi-length-scale simulations of fracture in silica aerogels, in which the interaction b e e n two secondary particles is assumed to be described by a Morse pair potential parameterized such that the potential range is much smaller than the secondary particle size. These Morse parameters are obtained by atomistic simulation of models of the experimentally-observed amorphous silica "bridges," with the fracture behavior of these bridges modeled via molecular statics using a Morse/Coulomb potential for silica. We consider the energetics of the fracture, and compare qualitative features of low-and high-density gel fracture.

Structure and formation of convection of secondary rainbands in a simulated typhoon Jangmi (2008)

NASA Astrophysics Data System (ADS)

Xiao, Jing; Tan, Zhe-Min; Chow, Kim-Chiu

2018-04-01

Secondary rainbands in tropical cyclone are relatively transient compared with the quasi-stationary principle rainbands. To have a better understanding on their convective structure, a cloud-resolving scale numerical simulation of the super typhoon Jangmi (2008) was performed. The results suggest that the convections in secondary rainbands have some distinctive features that may not be seen in other types of rainbands in tropical cyclone. First, they have a front-like structure and are triggered to form above the boundary layer by the convergence of the above-boundary outflow from the inner side (warmer) and the descending inflow (colder) from the outer side. These elevated convections can be further confirmed by the three-dimensional backward trajectory calculations. Second, due to the release in baroclinic energy, the lower portion of the mid-level inflow from outside may penetrate into the bottom of the convection tower and may help accelerate the boundary layer inflow in the inner side. Third, the local maximum tangential wind is concentrated in the updraft region, with a lower portion which is dipping inward. Tangential wind budget analysis also suggests that the maxima are mainly contributed by the updraft advection, and can be advected cyclonically downstream by the tangential advection.

Small-scale structural heterogeneity and well-communication problems in the Granny Creek oil field of West Virginia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, L.; Wilson, T.H.; Shumaker, R.C.

1993-08-01

Seismic interpretations of the Granny Creek oil field in West Virginia suggest the presence of numerous small-scale fracture zones and faults. Seismic disruptions interpreted as faults and/or fracture zones are represented by abrupt reflection offsets, local amplitude reductions, and waveform changes. These features are enhanced through reprocessing, and the majority of the improvements to the data result from the surface consistent application of zero-phase deconvolution. Reprocessing yields a 20% improvement of resolution. Seismic interpretations of these features as small faults and fracture zones are supported by nearby offset vertical seismic profiles and by their proximity to wells between which directmore » communication occurs during waterflooding. Four sets of faults are interpreted based on subsurface and seismic data. Direct interwell communication is interpreted to be associated only with a northeast-trending set of faults, which are believed to have detached structural origins. Subsequent reactivation of deeper basement faults may have opened fractures along this trend. These faults have a limited effect on primary production, but cause many well-communication problems and reduce secondary production. Seismic detection of these zones is important to the economic and effective design of secondary recovery operations, because direct well communication often results in significant reduction of sweep efficiency during waterflooding. Prior information about the location of these zones would allow secondary recovery operations to avoid potential problem areas and increase oil recovery.« less

Computational identification of structural factors affecting the mutagenic potential of aromatic amines: study design and experimental validation.

PubMed

Slavov, Svetoslav H; Stoyanova-Slavova, Iva; Mattes, William; Beger, Richard D; Brüschweiler, Beat J

2018-07-01

A grid-based, alignment-independent 3D-SDAR (three-dimensional spectral data-activity relationship) approach based on simulated 13 C and 15 N NMR chemical shifts augmented with through-space interatomic distances was used to model the mutagenicity of 554 primary and 419 secondary aromatic amines. A robust modeling strategy supported by extensive validation including randomized training/hold-out test set pairs, validation sets, "blind" external test sets as well as experimental validation was applied to avoid over-parameterization and build Organization for Economic Cooperation and Development (OECD 2004) compliant models. Based on an experimental validation set of 23 chemicals tested in a two-strain Salmonella typhimurium Ames assay, 3D-SDAR was able to achieve performance comparable to 5-strain (Ames) predictions by Lhasa Limited's Derek and Sarah Nexus for the same set. Furthermore, mapping of the most frequently occurring bins on the primary and secondary aromatic amine structures allowed the identification of molecular features that were associated either positively or negatively with mutagenicity. Prominent structural features found to enhance the mutagenic potential included: nitrobenzene moieties, conjugated π-systems, nitrothiophene groups, and aromatic hydroxylamine moieties. 3D-SDAR was also able to capture "true" negative contributions that are particularly difficult to detect through alternative methods. These include sulphonamide, acetamide, and other functional groups, which not only lack contributions to the overall mutagenic potential, but are known to actively lower it, if present in the chemical structures of what otherwise would be potential mutagens.

Terrestrial Analogs for Surface Properties Associated with Impact Cratering on the Moon - Self-secondary Impact Features at Kings Bowl, Idaho

NASA Astrophysics Data System (ADS)

Matiella Novak, M. A.; Zanetti, M.; Neish, C.; Kukko, A.; Fan, K.; Heldmann, J.; Hughes, S. S.

2017-12-01

The Kings Bowl (KB) eruptive fissure and lava field, located in the southern end of Craters of the Moon National Monument, Idaho, is an ideal location for planetary analogue field studies of surface properties related to volcanic and impact processes. Here we look at possible impact features present in the KB lava field near the main vent that resulted in squeeze-ups of molten lava from beneath a semi-solid lava lake crust. These may have been caused by the ejection of blocks during the phreatic eruption that formed the Kings Bowl pit, and their subsequent impact into a partially solidified lava pond. We compare and contrast these features with analogous self-secondary impact features, such as irregular, rimless secondary craters ("splash craters") observed in lunar impact melt deposits, to better understand how self-secondary impacts determine the surface properties of volcanic and impact crater terrains. We do this by analyzing field measurements of these features, as well as high-resolution DEM data collected through the Kinematic LiDAR System (KLS), both of which give us feature dimensions and distributions. We then compare these data with self-secondary impact features on the Moon and related surface roughness constrained through Lunar Reconnaissance Orbiter observations (Mini-RF and LROC NACs). Possible self-secondary impact features can be found in association with many lunar impact craters. These are formed when ballistic ejecta from the crater falls onto the ejecta blanket and melt surrounding the newly formed crater. Self-secondary impact features involving impact melt deposits are particularly useful to study because the visibly smooth melt texture serves to highlight the impact points in spacecraft imagery. The unusual morphology of some of these features imply that they formed when the melt had not yet completely solidified, strongly suggesting a source of impactors from the primary crater itself. We will also discuss ongoing efforts to integrate field and LiDAR data collected at KB with virtual reality environments as another technique for advancing exploration efforts through analogue field studies of impact features.

Looking on the bright side: The story of AA Doradus as revealed by its cool companion

NASA Astrophysics Data System (ADS)

Vučković, M.; Østensen, R. H.; Németh, P.; Bloemen, S.; Pápics, P. I.

2016-02-01

The effects of irradiation on the secondary stars of close binary systems are crucial for reliably determining the system parameters and for understanding the close binary evolution. They affect the stellar structure of the irradiated star and are reflected in the appearance of characteristic features in the spectroscopic and photometric data of these systems. We aim to study the light that originates from the irradiated side of the low-mass component of a close binary eclipsing system, which comprises a hot subdwarf primary and a low mass companion, to precisely interpret their high precision photometric and spectroscopic data, and accurately determine their system and surface parameters. We reanalyse the archival high-resolution time-resolved VLT/UVES spectra of AA Dor system, where irradiation features have already been detected. After removing the predominant contribution of the hot subdwarf primary, the residual spectra reveal more than 100 emission lines from the heated side of the secondary, which show maximum intensity close to the phases around the secondary eclipse. We analyse the residual spectrum to model the irradiation of the low-mass secondary. We perform a detailed analysis of 22 narrow emission lines of the irradiated secondary, mainly of O II, with a few significant C II lines. Their phase profiles constrain the emission region of the heated side to a radius ≥95% of the radius of the secondary, while the shape of their velocity profiles reveals two distinct asymmetry features, one at the quadrature and the other at the secondary eclipse. In addition, we identify weaker emission signatures originating from more than 70 lines, including lines from He I, N II, Si III, Ca II, and Mg II. From the emission lines of the heated side of the secondary star, we determine the radial velocity semi-amplitude of the centre-of-light and correct it to the centre-of-mass of the secondary which, in turn, gives accurate masses of both components of the AA Dor system. The resulting masses M1 = 0.46 ± 0.01 M⊙ and M2 = 0.079 ± 0.002 M⊙ are in perfect accordance with those of a canonical hot subdwarf primary and a low mass that is just at the substellar limit for the companion. We also compute a first generation atmosphere model of the low mass secondary, which includes irradiation effects and matches the observed spectrum well. We find an indication of an extended atmosphere of the irradiated secondary star. Based on observations collected at the European Southern Observatory, Chile. Program ID: 066.D-1800.

Extant fold-switching proteins are widespread.

PubMed

Porter, Lauren L; Looger, Loren L

2018-06-05

A central tenet of biology is that globular proteins have a unique 3D structure under physiological conditions. Recent work has challenged this notion by demonstrating that some proteins switch folds, a process that involves remodeling of secondary structure in response to a few mutations (evolved fold switchers) or cellular stimuli (extant fold switchers). To date, extant fold switchers have been viewed as rare byproducts of evolution, but their frequency has been neither quantified nor estimated. By systematically and exhaustively searching the Protein Data Bank (PDB), we found ∼100 extant fold-switching proteins. Furthermore, we gathered multiple lines of evidence suggesting that these proteins are widespread in nature. Based on these lines of evidence, we hypothesized that the frequency of extant fold-switching proteins may be underrepresented by the structures in the PDB. Thus, we sought to identify other putative extant fold switchers with only one solved conformation. To do this, we identified two characteristic features of our ∼100 extant fold-switching proteins, incorrect secondary structure predictions and likely independent folding cooperativity, and searched the PDB for other proteins with similar features. Reassuringly, this method identified dozens of other proteins in the literature with indication of a structural change but only one solved conformation in the PDB. Thus, we used it to estimate that 0.5-4% of PDB proteins switch folds. These results demonstrate that extant fold-switching proteins are likely more common than the PDB reflects, which has implications for cell biology, genomics, and human health. Copyright © 2018 the Author(s). Published by PNAS.

Evolutionary diversification of secondary mechanoreceptor cells in tunicata.

PubMed

Rigon, Francesca; Stach, Thomas; Caicci, Federico; Gasparini, Fabio; Burighel, Paolo; Manni, Lucia

2013-06-04

Hair cells are vertebrate secondary sensory cells located in the ear and in the lateral line organ. Until recently, these cells were considered to be mechanoreceptors exclusively found in vertebrates that evolved within this group. Evidence of secondary mechanoreceptors in some tunicates, the proposed sister group of vertebrates, has recently led to the hypothesis that vertebrate and tunicate secondary sensory cells share a common origin. Secondary sensory cells were described in detail in two tunicate groups, ascidians and thaliaceans, in which they constitute an oral sensory structure called the coronal organ. Among thaliaceans, the organ is absent in salps and it has been hypothesised that this condition is due to a different feeding system adopted by this group of animals. No information is available as to whether a comparable structure exists in the third group of tunicates, the appendicularians, although different sensory structures are known to be present in these animals. We studied the detailed morphology of appendicularian oral mechanoreceptors. Using light and electron microscopy we could demonstrate that the mechanosensory organ called the circumoral ring is composed of secondary sensory cells. We described the ultrastructure of the circumoral organ in two appendicularian species, Oikopleura dioica and Oikopleura albicans, and thus taxonomically completed the data collection of tunicate secondary sensory cells. To understand the evolution of secondary sensory cells in tunicates, we performed a cladistic analysis using morphological data. We constructed a matrix consisting of 19 characters derived from detailed ultrastructural studies in 16 tunicate species and used a cephalochordate and three vertebrate species as outgroups. Our study clearly shows that the circumoral ring is the appendicularian homologue of the coronal organ of other tunicate taxa. The cladistic analysis enabled us to reconstruct the features of the putative ancestral hair cell in tunicates, represented by a simple monociliated cell. This cell successively differentiated into the current variety of oral mechanoreceptors in the various tunicate lineages. Finally, we demonstrated that the inferred evolutionary changes coincide with major transitions in the feeding strategies in each respective lineage.

The sonographic features of malignant mediastinal lymph nodes and a proposal for an algorithmic approach for sampling during endobronchial ultrasound.

PubMed

Alici, Ibrahim Onur; Yılmaz Demirci, Nilgün; Yılmaz, Aydın; Karakaya, Jale; Özaydın, Esra

2016-09-01

There are several papers on the sonographic features of mediastinal lymph nodes affected by several diseases, but none gives the importance and clinical utility of the features. In order to find out which lymph node should be sampled in a particular nodal station during endobronchial ultrasound, we investigated the diagnostic performances of certain sonographic features and proposed an algorithmic approach. We retrospectively analyzed 1051 lymph nodes and randomly assigned them into a preliminary experimental and a secondary study group. The diagnostic performances of the sonographic features (gray scale, echogeneity, shape, size, margin, presence of necrosis, presence of calcification and absence of central hilar structure) were calculated, and an algorithm for lymph node sampling was obtained with decision tree analysis in the experimental group. Later, a modified algorithm was applied to the patients in the study group to give the accuracy. The demographic characteristics of the patients were not statistically significant between the primary and the secondary groups. All of the features were discriminative between malignant and benign diseases. The modified algorithm sensitivity, specificity, and positive and negative predictive values and diagnostic accuracy for detecting metastatic lymph nodes were 100%, 51.2%, 50.6%, 100% and 67.5%, respectively. In this retrospective analysis, the standardized sonographic classification system and the proposed algorithm performed well in choosing the node that should be sampled in a particular station during endobronchial ultrasound. © 2015 John Wiley & Sons Ltd.

Elasticity and Inverse Temperature Transition in Elastin

DOE PAGES

Perticaroli, Stefania; Ehlers, Georg; Jalarvo, Niina; ...

2015-09-22

Structurally, elastin is protein and biomaterial that provides elasticity and resilience to a range of tissues. This work provides insights into the elastic properties of elastin and its peculiar inverse temperature transition (ITT). These features are dependent on hydration of elastin and are driven by a similar mechanism of hydrophobic collapse to an entropically favorable state. Moreover, when using neutron scattering, we quantify the changes in the geometry of molecular motions above and below the transition temperature, showing a reduction in the displacement of water-induced motions upon hydrophobic collapse at the ITT. Finally, we measured the collective vibrations of elastinmore » gels as a function of elongation, revealing no changes in the spectral features associated with local rigidity and secondary structure, in agreement with the entropic origin of elasticity.« less

X-Ray Crystal Structure of the passenger domain of Plasmid encoded toxin(Pet), an Autotransporter Enterotoxin from enteroaggregative Escherichia coli (EAEC)

PubMed Central

Meza-Aguilar, J. Domingo; Fromme, Petra; Torres-Larios, Alfredo; Mendoza-Hernández, Guillermo; Hernandez-Chiñas, Ulises; Monteros, Roberto A. Arreguin-Espinosa de los; Campos, Carlos A. Eslava; Fromme, Raimund

2014-01-01

Autotransporters (ATs) represent a superfamily of proteins produced by a variety of pathogenic bacteria, which include the pathogenic groups of Escherichia coli (E. coli) associated with gastrointestinal and urinary tract infections. We present the first X-ray structure of the passenger domain from the Plasmid-encoded toxin (Pet) a 100 kDa protein at 2.3 Å resolution which is a cause of acute diarrhea in both developing and industrialized countries. Pet is a cytoskeleton-altering toxin that induces loss of actin stress fibers. While Pet (pdb code: 4OM9) shows only a sequence identity of 50 % compared to the closest related protein sequence, extracellular serine protease plasmid (EspP) the structural features of both proteins are conserved. A closer structural look reveals that Pet contains a β-pleaded sheet at the sequence region of residues 181-190, the corresponding structural domain in EspP consists of a coiled loop. Secondary, the Pet passenger domain features a more pronounced beta sheet between residues 135-143 compared to the structure of EspP. PMID:24530907

[Fe II] emissions associated with the young interacting binary UY Aurigae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pyo, Tae-Soo; Hayashi, Masahiko; Beck, Tracy L.

We present high-resolution 1.06-1.28 μm spectra toward the interacting binary UY Aur obtained with GEMINI/NIFS and the adaptive optics system Altair. We have detected [Fe II] λ1.257 μm and He I λ1.083 μm lines from both UY Aur A (the primary source) and UY Aur B (the secondary). In [Fe II] UY Aur A drives fast and widely opening outflows with an opening angle of ∼90° along a position angle of ∼40°, while UY Aur B is associated with a redshifted knot. The blueshifted and redshifted emissions show a complicated structure between the primary and secondary. The radial velocities ofmore » the [Fe II] emission features are similar for UY Aur A and B: ∼ –100 km s{sup –1} for the blueshifted emission and ∼ +130 km s{sup –1} for the redshifted component. The He I line profile observed toward UY Aur A comprises a central emission feature with deep absorptions at both blueshifted and redshifted velocities. These absorption features may be explained by stellar wind models. The He I line profile of UY Aur B shows only an emission feature.« less

PredictProtein—an open resource for online prediction of protein structural and functional features

PubMed Central

Yachdav, Guy; Kloppmann, Edda; Kajan, Laszlo; Hecht, Maximilian; Goldberg, Tatyana; Hamp, Tobias; Hönigschmid, Peter; Schafferhans, Andrea; Roos, Manfred; Bernhofer, Michael; Richter, Lothar; Ashkenazy, Haim; Punta, Marco; Schlessinger, Avner; Bromberg, Yana; Schneider, Reinhard; Vriend, Gerrit; Sander, Chris; Ben-Tal, Nir; Rost, Burkhard

2014-01-01

PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein–protein binding sites (ISIS2), protein–polynucleotide binding sites (SomeNA) and predictions of the effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics. To this end, the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures. The web server and sources are available at http://ppopen.rostlab.org. PMID:24799431

Improved measurements of RNA structure conservation with generalized centroid estimators.

PubMed

Okada, Yohei; Saito, Yutaka; Sato, Kengo; Sakakibara, Yasubumi

2011-01-01

Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also bioinformatics. Secondary structures of ncRNAs are employed as a key feature of ncRNA analysis since biological functions of ncRNAs are deeply related to their secondary structures. Although the minimum free energy (MFE) structure of an RNA sequence is regarded as the most stable structure, MFE alone could not be an appropriate measure for identifying ncRNAs since the free energy is heavily biased by the nucleotide composition. Therefore, instead of MFE itself, several alternative measures for identifying ncRNAs have been proposed such as the structure conservation index (SCI) and the base pair distance (BPD), both of which employ MFE structures. However, these measurements are unfortunately not suitable for identifying ncRNAs in some cases including the genome-wide search and incur high false discovery rate. In this study, we propose improved measurements based on SCI and BPD, applying generalized centroid estimators to incorporate the robustness against low quality multiple alignments. Our experiments show that our proposed methods achieve higher accuracy than the original SCI and BPD for not only human-curated structural alignments but also low quality alignments produced by CLUSTAL W. Furthermore, the centroid-based SCI on CLUSTAL W alignments is more accurate than or comparable with that of the original SCI on structural alignments generated with RAF, a high quality structural aligner, for which twofold expensive computational time is required on average. We conclude that our methods are more suitable for genome-wide alignments which are of low quality from the point of view on secondary structures than the original SCI and BPD.

Structural protein descriptors in 1-dimension and their sequence-based predictions.

PubMed

Kurgan, Lukasz; Disfani, Fatemeh Miri

2011-09-01

The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods.

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

PubMed Central

Kumar, Yadhu; Westram, Ralf; Kipfer, Peter; Meier, Harald; Ludwig, Wolfgang

2006-01-01

Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via . PMID:16672074

Protein 8-class secondary structure prediction using conditional neural fields.

PubMed

Wang, Zhiyong; Zhao, Feng; Peng, Jian; Xu, Jinbo

2011-10-01

Compared with the protein 3-class secondary structure (SS) prediction, the 8-class prediction gains less attention and is also much more challenging, especially for proteins with few sequence homologs. This paper presents a new probabilistic method for 8-class SS prediction using conditional neural fields (CNFs), a recently invented probabilistic graphical model. This CNF method not only models the complex relationship between sequence features and SS, but also exploits the interdependency among SS types of adjacent residues. In addition to sequence profiles, our method also makes use of non-evolutionary information for SS prediction. Tested on the CB513 and RS126 data sets, our method achieves Q8 accuracy of 64.9 and 64.7%, respectively, which are much better than the SSpro8 web server (51.0 and 48.0%, respectively). Our method can also be used to predict other structure properties (e.g. solvent accessibility) of a protein or the SS of RNA. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural Interplay - Tuning Mechanics in Peptide-Polyurea Hybrids

NASA Astrophysics Data System (ADS)

Korley, Lashanda

Utilizing cues from natural materials, we have been inspired to explore the hierarchical arrangement critical to energy absorption and mechanical enhancement in synthetic systems. Of particular interest is the soft domain ordering proposed as a contributing element to the observed toughness in spider silk. Multiblock copolymers, are ideal and dynamic systems in which to explore this approach via variations in secondary structure of nature's building blocks - peptides. We have designed a new class of polyurea hybrids that incorporate peptidic copolymers as the soft segment. The impact of hierarchical ordering on the thermal, mechanical, and morphological behavior of these bio-inspired polyurethanes with a siloxane-based, peptide soft segment was investigated. These peptide-polyurethane/urea hybrids were microphase segregated, and the beta-sheet secondary structure of the soft segment was preserved during polymerization and film casting. Toughness enhancement at low strains was achieved, but the overall extensibility of the peptide-incorporated systems was reduced due to the unique hard domain organization. To decouple the secondary structure influence in the siloxane-peptide soft segment from mechanics dominated by the hard domain, we also developed non-chain extended peptide-polyurea hybrids in which the secondary structure (beta sheet vs. alpha helix) was tuned via choice of peptide and peptide length. It was shown that this structural approach allowed tailoring of extensibility, toughness, and modulus. The sheet-dominant hybrid materials were typically tougher and more elastic due to intermolecular H-bonding facilitating load distribution, while the helical-prevalent systems generally exhibited higher stiffness. Recently, we have explored the impact of a molecular design strategy that overlays a covalent and physically crosslinked architecture in these peptide-polyurea hybrids, demonstrating that physical constraints in the network hybrids influences peptide hydrogen bonding and morphology. These structural features correlated well with systematic changes in modulus, extensibility, and hysteresis. Complementary to this effort is the design of PEG-based peptide-polyurea hybrids with tunable and responsive as structural and injectable hydrogels. The authors acknowledge funding support from the National Science Foundation (CAREER DMR-0953236).

Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors.

PubMed

Batkhishig, Dashdavaa; Bilguun, Khurelbaatar; Enkhbayar, Purevjav; Miyashita, Hiroki; Kretsinger, Robert H; Matsushima, Norio

2018-06-01

Leucine rich repeats (LRRs) are present in over 100,000 proteins from viruses to eukaryotes. The LRRs are 20-30 residues long and occur in tandem. LRRs form parallel stacks of short β-strands and then assume a super helical arrangement called a solenoid structure. Individual LRRs are separated into highly conserved segment (HCS) with the consensus of LxxLxLxxNxL and variable segment (VS). Eight classes have been recognized. Bacterial LRRs are short and characterized by two prolines in the VS; the consensus is xxLPxLPxx with Nine residues (N-subtype) and xxLPxxLPxx with Ten residues (T-subtype). Bacterial LRRs are contained in type III secretion system effectors such as YopM, IpaH3/9.8, SspH1/2, and SlrP from bacteria. Some LRRs in decorin, fribromodulin, TLR8/9, and FLRT2/3 from vertebrate also contain the motifs. In order to understand structural features of bacterial LRRs, we performed both secondary structures assignments using four programs-DSSP-PPII, PROSS, SEGNO, and XTLSSTR-and HELFIT analyses (calculating helix axis, pitch, radius, residues per turn, and handedness), based on the atomic coordinates of their crystal structures. The N-subtype VS adopts a left handed polyproline II helix (PPII) with four, five or six residues and a type I β-turn at the C-terminal side. Thus, the N-subtype is characterized by a super secondary structure consisting of a PPII and a β-turn. In contrast, the T-subtype VS prefers two separate PPIIs with two or three and two residues. The HELFIT analysis indicates that the type I β-turn is a right handed helix. The HELFIT analysis determines three unit vectors of the helix axes of PPII (P), β-turn (B), and LRR domain (A). Three structural parameters using these three helix axes are suggested to characterize the super secondary structure and the LRR domain.

Improve the prediction of RNA-binding residues using structural neighbours.

PubMed

Li, Quan; Cao, Zanxia; Liu, Haiyan

2010-03-01

The interactions between RNA-binding proteins (RBPs) with RNA play key roles in managing some of the cell's basic functions. The identification and prediction of RNA binding sites is important for understanding the RNA-binding mechanism. Computational approaches are being developed to predict RNA-binding residues based on the sequence- or structure-derived features. To achieve higher prediction accuracy, improvements on current prediction methods are necessary. We identified that the structural neighbors of RNA-binding and non-RNA-binding residues have different amino acid compositions. Combining this structure-derived feature with evolutionary (PSSM) and other structural information (secondary structure and solvent accessibility) significantly improves the predictions over existing methods. Using a multiple linear regression approach and 6-fold cross validation, our best model can achieve an overall correct rate of 87.8% and MCC of 0.47, with a specificity of 93.4%, correctly predict 52.4% of the RNA-binding residues for a dataset containing 107 non-homologous RNA-binding proteins. Compared with existing methods, including the amino acid compositions of structure neighbors lead to clearly improvement. A web server was developed for predicting RNA binding residues in a protein sequence (or structure),which is available at http://mcgill.3322.org/RNA/.

Stardust Interstellar Preliminary Examination V: XRF Analyses of Interstellar Dust Candidates at ESRF ID13

NASA Technical Reports Server (NTRS)

Brenker, Frank E.; Westphal, Andrew J.; Simionovici, Alexandre S.; Flynn, George J.; Gainsforth, Zack; Allen, Carlton C.; Sanford, Scott; Zolensky, Michael E.; Bastien, Ron K.; Frank, David R.

2014-01-01

Here, we report analyses by synchrotron X-ray fluorescence microscopy of the elemental composition of eight candidate impact features extracted from the Stardust Interstellar Dust Collector (SIDC). Six of the features were unambiguous tracks, and two were crater-like features. Five of the tracks are so-called midnight tracks that is, they had trajectories consistent with an origin either in the interstellar dust stream or as secondaries from impacts on the Sample Return Capsule (SRC). In a companion paper reporting synchrotron X-ray diffraction analyses of ISPE candidates, we show that two of these particles contain natural crystalline materials: the terminal particle of track 30contains olivine and spinel, and the terminal particle of track 34 contains olivine. Here, we show that the terminal particle of track 30, Orion, shows elemental abundances, normalized to Fe, that are close to CI values, and a complex, fine-grained structure. The terminal particle of track 34, Hylabrook, shows abundances that deviate strongly from CI, but shows little fine structure and is nearly homogenous. The terminal particles of other midnight tracks, 29 and 37, had heavy element abundances below detection threshold. A third, track28, showed a composition inconsistent with an extraterrestrial origin, but also inconsistent with known spacecraft materials. A sixth track, with a trajectory consistent with secondary ejecta from an impact on one of the spacecraft solar panels, contains abundant Ce and Zn. This is consistent with the known composition of the glass covering the solar panel. Neither crater-like feature is likely to be associated with extraterrestrial materials. We also analyzed blank aerogel samples to characterize background and variability between aerogel tiles. We found significant differences in contamination levels and compositions, emphasizing the need for local background subtraction for accurate quantification.

First-principles investigation of the structural characteristics of LiMO2 cathode materials for lithium secondary batteries

NASA Astrophysics Data System (ADS)

Kim, Yongseon

2015-11-01

The structural features related to the defects of LiMO2 (M = Ni, Co, Mn) cathode materials for lithium secondary batteries were investigated by a simulation of phase diagrams based on first-principle calculations. Crystal models with various types of point defects were designed and dealt with as independent phases, which enabled an examination of the thermodynamic stability of the defects. A perfect phase without defects appeared to be the most stable for LiCoO2, whereas the formation of Li vacancies, O vacancies, and antisites between Li and Ni was thermodynamically unavoidable for LiNiO2. The introduction of both Co and Mn in LiNiO2 was effective in reducing the formation of point defects, but increasing the relative amount of Mn was undesirable because the antisite defect remained stable with Mn doping. The simulation showed good agreement with the experimental data and previous reports. Therefore, the method and the results of this study are expected to be useful for examining the synthesis, structure and related properties of layer-structured cathode materials.

Molecular engineering of phosphole-based conjugated materials

NASA Astrophysics Data System (ADS)

Ren, Yi

The work in this thesis focuses on the molecular engineering of phosphorus-based conjugated materials. In the first part (Chapters Two and Three), new phosphorus-based conjugated systems were designed and synthesized to study the effect of the heteroelement on the electronic properties of the π-conjugated systems. The second part (Chapters Four and Five) deals with the self-assembly features of specifically designed phosphorus-based conjugated systems. In Chapter Two, electron-poor and electron-rich aromatic substituents were introduced to the dithienophosphole core in order to balance the electron-accepting and electron-donating character of the systems. Furthermore, an intriguing intramolecular charge transfer process could be observed between two dithienophosphole cores in a bridged bisphosphole-system. In Chapter Three, a secondary heteroelement (Si, P, S) was incorporated in the phosphorus-based conjugated systems. Extensive structure-property studies revealed that the secondary heteroelement can effectively manipulate the communication in phosphinine-based systems. The study of a heterotetracene system allowed for selectively applying distinct heteroatom (S/P) chemistries, which offers a powerful tool for the modification of the electronic structure of the system. More importantly, the heteroatom-specific electronic nature (S/P) can be utilized to selectively control different photophysical aspects (energy gap and fluorescence quantum yield). Furthermore, additional molecular engineering of the heterotetracene provided access to well-defined 1D microstructures, which opened the door for designing multi-functional self-assembled phosphorus-based materials. In Chapter Four, the self-organizing phosphole-lipid system is introduced, which combines the features of phospholipids with the electronics of phospholes. Its amphiphilic nature induces intriguing self-assembly features - liquid crystal and soft crystal architectures, both exhibiting well-organized lamellar structure at a wide range of temperatures. Importantly, its dynamic structure endows the phosphole-lipid system with intriguing external stimuli-responsive features allowing for the modification of the emission of the system without further chemical modification. Chapter Five describes how further molecular engineering allowed for access to a series of new highly fluorescent phosphole-lipid organogels. Remarkably, the external-stimuli responsive features of the system can be amplified in a donor-acceptor system accessible through changes in long distance fluorescence resonance energy transfer processes. In addition, the first fluorescent liquid phospholes could also be accessed in the context of the work on the new phosphole-lipid system.

RAG-3D: A search tool for RNA 3D substructures

DOE PAGES

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

2015-08-24

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

RAG-3D: a search tool for RNA 3D substructures

PubMed Central

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

2015-01-01

To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

RAG-3D: A search tool for RNA 3D substructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.

PubMed

Manrubia, Susanna; Cuesta, José A

2017-04-01

An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype-phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes. © 2017 The Author(s).

Exploration of electrostatic interaction in the hydrophobic pocket of lysozyme: Importance of ligand-induced perturbation of the secondary structure on the mode of binding of exogenous ligand and possible consequences.

PubMed

Panja, Sudipta; Halder, Mintu

2016-08-01

Exogenous ligand binding can be adequate to alter the secondary structure of biomolecules besides other external stimuli. In such cases, structural alterations can complicate on the nature of interaction with the exogenous molecules. In order to accommodate the exogenous ligand, the biomolecule has to unfold resulting in a considerable change to its properties. If the bound ligand can be unbound, the biomolecule gets the opportunity to refold back and return to its native state. Keeping this in mind, we have purposely investigated the interaction of tartrazine (TZ), a well abundant azo food colorant, with two homologous lysozymes, namely, human lysozyme (HLZ) and chicken egg white lysozyme (CEWLZ) in physiological pH condition. The binding of TZ with lysozymes has been identified to accompany a ligand-induced secondary structure alteration as indicated by the circular dichroism spectra, and the reduction of α-helical content is more with HLZ than CEWLZ. Interestingly, the binding is identified to occur in the electronic ground state of TZ with lysozyme in its hydrophobic cavity, containing excess of positive charge, predominantly via electrostatic interaction. With increase of salinity of the medium the protein tends to refold back due to wakening of electrostatic forces and consequent reduction of strength of ligand interaction and unbinding. The entropy enthalpy compensation (EEC) has been probed to understand the binding features and it is found that CEWLZ-TZ shows better compensation than HLZ-TZ complex. This is presumably due to the fact that with CEWLZ the binding does not accompany substantial change in the protein secondary structure and hence ineffective to scramble the EEC. The present study initiates the importance of ligand-perturbed structural alteration of biomolecule in controlling the thermodynamics of binding. If there is a considerable alteration of the protein secondary structure due to binding, it is indicative that such changes should bring in the overall loss of activity of protein. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular modeling of the human sperm associated antigen 11 B (SPAG11B) proteins.

PubMed

Narmadha, Ganapathy; Yenugu, Suresh

2015-04-01

Antimicrobial proteins and peptides are ubiquitous in nature with diverse structural and biological properties. Among them, the human beta-defensins are known to contribute to the innate immune response. Besides the defensins, a number of defensin-like proteins and peptides are expressed in many organ systems including the male reproductive system. Some of the protein isoforms encoded by the sperm associated antigen 11B (SPAG11) gene in humans are beta-defensin-like and exhibit structure dependent and salt tolerant antimicrobial activity, besides contributing to sperm maturation. Though some of the functional roles of these proteins are reported, the structural and molecular features that contribute to their antimicrobial activity is not yet reported. In this study, using in silico tools, we report the three dimensional structure of the human SPAG11B proteins and their C-terminal peptides. web-based hydropathy, amphipathicity, and topology (WHAT) analyses and grand average of hydropathy (GRAVY) indices show that these proteins and peptides are amphipathic and highly hydrophilic. Self-optimized prediction method with alignment (SOPMA) analyses and circular dichroism data suggest that the secondary structure of these proteins and peptides primarily contain beta-sheet and random coil structure and alpha-helix to a lesser extent. Ramachandran plots show that majority of the amino acids in these proteins and peptides fall in the permissible regions, thus indicating stable structures. The secondary structure of SPAG11B isoforms and their peptides were not perturbed with increasing NaCl concentration (0-300 mM) and at different pH (3, 7, and 10), thus reinforcing our previously reported observation that their antimicrobial activity is salt tolerant. To the best of our knowledge, for the first time, results of our study provide vital information on the structural features of SPAG11B protein isoforms and their contribution to antimicrobial activity.

The separation between the 5'-3' ends in long RNA molecules is short and nearly constant.

PubMed

Leija-Martínez, Nehemías; Casas-Flores, Sergio; Cadena-Nava, Rubén D; Roca, Joan A; Mendez-Cabañas, José A; Gomez, Eduardo; Ruiz-Garcia, Jaime

2014-12-16

RNA molecules play different roles in coding, decoding and gene expression regulation. Such roles are often associated to the RNA secondary or tertiary structures. The folding dynamics lead to multiple secondary structures of long RNA molecules, since an RNA molecule might fold into multiple distinct native states. Despite an ensemble of different structures, it has been theoretically proposed that the separation between the 5' and 3' ends of long single-stranded RNA molecules (ssRNA) remains constant, independent of their base content and length. Here, we present the first experimental measurements of the end-to-end separation in long ssRNA molecules. To determine this separation, we use single molecule Fluorescence Resonance Energy Transfer of fluorescently end-labeled ssRNA molecules ranging from 500 to 5500 nucleotides in length, obtained from two viruses and a fungus. We found that the end-to-end separation is indeed short, within 5-9 nm. It is remarkable that the separation of the ends of all RNA molecules studied remains small and similar, despite the origin, length and differences in their secondary structure. This implies that the ssRNA molecules are 'effectively circularized' something that might be a general feature of RNAs, and could result in fine-tuning for translation and gene expression regulation. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

An Experimental and Numerical Investigation of Endwall Aerodynamics and Heat Transfer in a Gas Turbine Nozzle Guide Vane with Slot Film Cooling

NASA Astrophysics Data System (ADS)

Alqefl, Mahmood Hasan

In many regions of the high-pressure gas turbine, film cooling flows are used to protect the turbine components from the combustor exit hot gases. Endwalls are challenging to cool because of the complex system of secondary flows that disturb surface film coolant coverage. The secondary flow vortices wash the film coolant from the surface into the mainstream significantly decreasing cooling effectiveness. In addition to being effected by secondary flow structures, film cooling flow can also affect these structures by virtue of their momentum exchange. In addition, many studies in the literature have shown that endwall contouring affects the strength of passage secondary flows. Therefore, to develop better endwall cooling schemes, a good understanding of passage aerodynamics and heat transfer as affected by interactions of film cooling flows with secondary flows is required. This experimental and computational study presents results from a linear, stationary, two-passage cascade representing the first stage nozzle guide vane of a high-pressure gas turbine with an axisymmetrically contoured endwall. The sources of film cooling flows are upstream combustor liner coolant and endwall slot film coolant injected immediately upstream of the cascade passage inlet. The operating conditions simulate combustor exit flow features, with a high Reynolds number of 390,000 and approach flow turbulence intensity of 11% with an integral length scale of 21% of the chord length. Measurements are performed with varying slot film cooling mass flow to mainstream flow rate ratios (MFR). Aerodynamic effects are documented with five-hole probe measurements at the exit plane. Heat transfer is documented through recovery temperature measurements with a thermocouple. General secondary flow features are observed. Total pressure loss measurements show that varying the slot film cooling MFR has some effects on passage loss. Velocity vectors and vorticity distributions show a very thin, yet intense, cross-pitch flow on the contoured endwall side. Endwall adiabatic effectiveness values and coolant distribution thermal fields show minimal effects of varying slot film coolant MFR. This suggests the dominant effects of combustor liner coolant. show dominant effects of combustor liner coolant on cooling the endwall. A coolant vorticity correlation presenting the advective mixing of the coolant due to secondary flow vorticity at the exit plane is also discussed.

Modularity in protein structures: study on all-alpha proteins.

PubMed

Khan, Taushif; Ghosh, Indira

2015-01-01

Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

Nurture Groups in a Scottish Secondary School: Purpose, Features, Value and Areas for Development

ERIC Educational Resources Information Center

Kourmoulaki, Athina

2013-01-01

Nurture groups (NGs) are increasingly being established in Scottish secondary schools yet research in this context is limited. The current study explores the purpose, features and value of two NGs in a Scottish secondary school through interviewing current and former NG members, parents/carers, NG staff and other school staff. A thematic analysis…

Preprocessing Structured Clinical Data for Predictive Modeling and Decision Support

PubMed Central

Oliveira, Mónica Duarte; Janela, Filipe; Martins, Henrique M. G.

2016-01-01

Summary Background EHR systems have high potential to improve healthcare delivery and management. Although structured EHR data generates information in machine-readable formats, their use for decision support still poses technical challenges for researchers due to the need to preprocess and convert data into a matrix format. During our research, we observed that clinical informatics literature does not provide guidance for researchers on how to build this matrix while avoiding potential pitfalls. Objectives This article aims to provide researchers a roadmap of the main technical challenges of preprocessing structured EHR data and possible strategies to overcome them. Methods Along standard data processing stages – extracting database entries, defining features, processing data, assessing feature values and integrating data elements, within an EDPAI framework –, we identified the main challenges faced by researchers and reflect on how to address those challenges based on lessons learned from our research experience and on best practices from related literature. We highlight the main potential sources of error, present strategies to approach those challenges and discuss implications of these strategies. Results Following the EDPAI framework, researchers face five key challenges: (1) gathering and integrating data, (2) identifying and handling different feature types, (3) combining features to handle redundancy and granularity, (4) addressing data missingness, and (5) handling multiple feature values. Strategies to address these challenges include: cross-checking identifiers for robust data retrieval and integration; applying clinical knowledge in identifying feature types, in addressing redundancy and granularity, and in accommodating multiple feature values; and investigating missing patterns adequately. Conclusions This article contributes to literature by providing a roadmap to inform structured EHR data preprocessing. It may advise researchers on potential pitfalls and implications of methodological decisions in handling structured data, so as to avoid biases and help realize the benefits of the secondary use of EHR data. PMID:27924347

The mitochondrial genomes of Campodea fragilis and C. lubbocki(Hexapoda: Diplura): high genetic divergence in a morphologically uniformtaxon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podsiadlowski, L.; Carapelli, A.; Nardi, F.

2005-12-01

Mitochondrial genomes from two dipluran hexapods of the genus Campodea have been sequenced. Gene order is the same as in most other hexapods and crustaceans. Secondary structures of tRNAs reveal specific structural changes in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2. Comparative analyses of nucleotide and amino acid composition, as well as structural features of both ribosomal RNA subunits, reveal substantial differences among the analyzed taxa. Although the two Campodea species are morphologically highly uniform, genetic divergence is larger than expected, suggesting a long evolutionary history under stable ecological conditions.

A systematic review on popularity, application and characteristics of protein secondary structure prediction tools.

PubMed

Kashani-Amin, Elaheh; Tabatabaei-Malazy, Ozra; Sakhteman, Amirhossein; Larijani, Bagher; Ebrahim-Habibi, Azadeh

2018-02-27

Prediction of proteins' secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple secondary structure prediction (SSP) options is challenging. The current study is an insight onto currently favored methods and tools, within various contexts. A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of 209 studies were finally found eligible to extract data. Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating a SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. This study provides a comprehensive insight about the recent usage of SSP tools which could be helpful for selecting a proper tool's choice. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Prediction of active sites of enzymes by maximum relevance minimum redundancy (mRMR) feature selection.

PubMed

Gao, Yu-Fei; Li, Bi-Qing; Cai, Yu-Dong; Feng, Kai-Yan; Li, Zhan-Dong; Jiang, Yang

2013-01-27

Identification of catalytic residues plays a key role in understanding how enzymes work. Although numerous computational methods have been developed to predict catalytic residues and active sites, the prediction accuracy remains relatively low with high false positives. In this work, we developed a novel predictor based on the Random Forest algorithm (RF) aided by the maximum relevance minimum redundancy (mRMR) method and incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility to predict active sites of enzymes and achieved an overall accuracy of 0.885687 and MCC of 0.689226 on an independent test dataset. Feature analysis showed that every category of the features except disorder contributed to the identification of active sites. It was also shown via the site-specific feature analysis that the features derived from the active site itself contributed most to the active site determination. Our prediction method may become a useful tool for identifying the active sites and the key features identified by the paper may provide valuable insights into the mechanism of catalysis.

In Situ FTIR Microspectroscopy of Brain Tissue from a Transgenic Mouse Model of Alzheimer Disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rak,M.; Del Bigio, M.; Mai, S.

2007-01-01

Plaques composed of the A{beta} peptide are the main pathological feature of Alzheimer's disease. Dense-core plaques are fibrillar deposits of A{beta}, showing all the classical properties of amyloid including {beta}-sheet secondary structure, while diffuse plaques are amorphous deposits. We studied both plaque types, using synchrotron infrared (IR) microspectroscopy, a technique that allows the chemical composition and average protein secondary structure to be investigated in situ. We examined plaques in hippocampal, cortical and caudal tissue from 5- to 21-month-old TgCRND8 mice, a transgenic model expressing doubly mutant amyloid precursor protein, and displaying impaired hippocampal function and robust pathology from an earlymore » age. Spectral analysis confirmed that the congophilic plaque cores were composed of protein in a {beta}-sheet conformation. The amide I maximum of plaque cores was at 1623 cm-1, and unlike for in vitro A{beta} fibrils, the high-frequency (1680-1690 cm-1) component attributed to antiparallel {beta}-sheet was not observed. A significant elevation in phospholipids was found around dense-core plaques in TgCRND8 mice ranging in age from 5 to 21 months. In contrast, diffuse plaques were not associated with IR detectable changes in protein secondary structure or relative concentrations of any other tissue components.« less

Acoustic Features Influence Musical Choices Across Multiple Genres.

PubMed

Barone, Michael D; Bansal, Jotthi; Woolhouse, Matthew H

2017-01-01

Based on a large behavioral dataset of music downloads, two analyses investigate whether the acoustic features of listeners' preferred musical genres influence their choice of tracks within non-preferred, secondary musical styles. Analysis 1 identifies feature distributions for pairs of genre-defined subgroups that are distinct. Using correlation analysis, these distributions are used to test the degree of similarity between subgroups' main genres and the other music within their download collections. Analysis 2 explores the issue of main-to-secondary genre influence through the production of 10 feature-influence matrices, one per acoustic feature, in which cell values indicate the percentage change in features for genres and subgroups compared to overall population averages. In total, 10 acoustic features and 10 genre-defined subgroups are explored within the two analyses. Results strongly indicate that the acoustic features of people's main genres influence the tracks they download within non-preferred, secondary musical styles. The nature of this influence and its possible actuating mechanisms are discussed with respect to research on musical preference, personality, and statistical learning.

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.

PubMed

Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

2003-06-06

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.

Diterpenes from the Marine Algae of the Genus Dictyota.

PubMed

Chen, Jiayun; Li, Hong; Zhao, Zishuo; Xia, Xue; Li, Bo; Zhang, Jinrong; Yan, Xiaojun

2018-05-11

Species of the brown algae of the genus Dictyota are rich sources of bioactive secondary metabolites with diverse structural features. Excellent progress has been made in the discovery of diterpenes possessing broad chemical defensive activities from this genus. Most of these diterpenes exhibit significant biological activities, such as antiviral, cytotoxic and chemical defensive activities. In the present review, we summarized diterpenes isolated from the brown algae of the genus.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhong,Z.; Bennett, D.; Chapman, D.

We explored diffraction enhanced imaging (DEI) in both planar and computed tomography (CT) modes for early detection of beta amyloid deposition, a hallmark feature in Alzheimer's disease (AD). Since amyloid plaques precede clinical symptoms by years, their early detection is of great interest. These findings were correlated with results from synchrotron infrared microspectroscopic imaging and X-ray fluorescence microscopy, to determine the secondary structure of the amyloid beta protein and metal concentration in the amyloid plaques, respectively.

Beyond Academic Tracking: Using Cluster Analysis and Self-Organizing Maps to Investigate Secondary Students' Chemistry Self-Concept

ERIC Educational Resources Information Center

Nielsen, Sara E.; Yezierski, Ellen J.

2016-01-01

Academic tracking, placing students in different classes based on past performance, is a common feature of the American secondary school system. A longitudinal study of secondary students' chemistry self-concept scores was conducted, and one feature of the study was the presence of academic tracking. Though academic tracking is one way to group…

Computational modeling of membrane proteins

PubMed Central

Leman, Julia Koehler; Ulmschneider, Martin B.; Gray, Jeffrey J.

2014-01-01

The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefitted from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade. PMID:25355688

[Skeletal manifestations of primary and secondary hyperparathyroiditis. Differential radiological diagnostic problems].

PubMed

Melella, A; Basilico, L; Lupini, A; Renda, F

1978-10-31

Primary and secondary hyperparathyroidism are both marked by widespread skeletal demineralisation, subperiosteal erosion of the cortex, brown tumours, osteosclerosis, and extraosseous calcification. Differential diagnosis is guided by the different association of these findings. Brown tumours and more extensive erosion are marks of the primary form, whereas osteosclerosis and extra-osseous calcification are a prominent feature of secondary hyperparathyroidism. Radiologists, therefore, should direct their attention to features suggesting the presence of secondary forms in addition to looking for bone alterations associated with hyperparathyroidism.

Crystallographic characterizations of eutectic and secondary carbides in a Fe-12Cr-2.5Mo-1.5W-3V-1.25C alloy

NASA Astrophysics Data System (ADS)

Guo, Jing; Liu, Ligang; Feng, Yunli; Liu, Sha; Ren, Xuejun; Yang, Qingxiang

2017-03-01

In this work, the morphology and structures of the eutectic and secondary carbides in a new high chromium Fe-12Cr-2.5Mo-1.5W-3V-1.25C designed for cold-rolling work roll were systematically studied. The precipitated carbides inside the grains and along the grain boundaries were investigated with optical microscope, scanning electron microscopy with energy dispersive spectroscopy, transmission electron microscopy and X-Ray diffraction. Selected area diffraction patterns have been successfully used to identify the crystal formation and lattice constants of the carbides with different alloying elements. The results show that the eutectic carbides precipitated contain MC and M2C distributed along the grain boundaries with dendrite feature. The composition and crystal structure analysis shows that the eutectic MC carbides contain VC and WC with a cubic and hexagonal crystal lattice structures respectively, while the eutectic M2C carbides predominantly contain V2C and Mo2C with orthorhombic and hexagonal crystal lattices respectively. The secondary carbides contain MC, M2C, M7C3 formed along the grain boundaries and their sizes are much larger than the eutectic carbides ones. The secondary M23C6 is much small (0.3-0.5μm) and is distributed dispersively inside the grain. Similar to the eutectic carbides, the secondary carbides also contain VC, WC, V2C, and Mo2C. M7C3 is hexagonal (Fe,Cr)7C3, while M23C6 is indexed to be in a cubic crystal form.

Visualization of protein sequence features using JavaScript and SVG with pViz.js.

PubMed

Mukhyala, Kiran; Masselot, Alexandre

2014-12-01

pViz.js is a visualization library for displaying protein sequence features in a Web browser. By simply providing a sequence and the locations of its features, this lightweight, yet versatile, JavaScript library renders an interactive view of the protein features. Interactive exploration of protein sequence features over the Web is a common need in Bioinformatics. Although many Web sites have developed viewers to display these features, their implementations are usually focused on data from a specific source or use case. Some of these viewers can be adapted to fit other use cases but are not designed to be reusable. pViz makes it easy to display features as boxes aligned to a protein sequence with zooming functionality but also includes predefined renderings for secondary structure and post-translational modifications. The library is designed to further customize this view. We demonstrate such applications of pViz using two examples: a proteomic data visualization tool with an embedded viewer for displaying features on protein structure, and a tool to visualize the results of the variant_effect_predictor tool from Ensembl. pViz.js is a JavaScript library, available on github at https://github.com/Genentech/pviz. This site includes examples and functional applications, installation instructions and usage documentation. A Readme file, which explains how to use pViz with examples, is available as Supplementary Material A. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Low-Altitude Satellite Measurements of Pulsating Auroral Electrons

NASA Technical Reports Server (NTRS)

Samara, M.; Michell, R. G.; Redmon, R. J.

2015-01-01

We present observations from the Defense Meteorological Satellite Program and Reimei satellites, where common-volume high-resolution ground-based auroral imaging data are available. These satellite overpasses of ground-based all-sky imagers reveal the specific features of the electron populations responsible for different types of pulsating aurora modulations. The energies causing the pulsating aurora mostly range from 3 keV to 20 keV but can at times extend up to 30 keV. The secondary, low-energy electrons (<1 keV) are diminished from the precipitating distribution when there are strong temporal variations in auroral intensity. There are often persistent spatial structures present inside regions of pulsating aurora, and in these regions there are secondary electrons in the precipitating populations. The reduction of secondary electrons is consistent with the strongly temporally varying pulsating aurora being associated with field-aligned currents and hence parallel potential drops of up to 1 kV.

Identification of the feature that causes the I-band secondary maximum of a Type Ia supernova

NASA Astrophysics Data System (ADS)

Jack, D.; Baron, E.; Hauschildt, P. H.

2015-06-01

We obtained a time series of spectra covering the secondary maximum in the I band of the bright Type Ia supernova 2014J in M82 with the TIGRE telescope. Comparing the observations with theoretical models calculated with the time dependent extension of the PHOENIX code, we identify the feature that causes the secondary maximum in the I-band light curve. Fe II 3d6(3D)4s-3d6(5D)4p and similar high-excitation transitions produce a blended feature at ˜7500 Å, which causes the rise of the light curve towards the secondary maximum. The series of observed spectra of SN 2014J and archival data of SN 2011fe confirm this conclusion. We further studied the plateau phase of the R-band light curve of SN 2014J and searched for features which contribute to the flux. The theoretical models do not clearly indicate a new feature that may cause the R-band plateau phase. However, Co II features in the range of 6500-7000 Å and the Fe II feature of the I band are clearly seen in the theoretical spectra, but do not appear to provide all of the flux necessary for the R-band plateau.

Molecular Characterization and Antimicrobial Activity of an Endolichenic Fungus, Aspergillus sp. Isolated from Parmelia caperata of Similipal Biosphere Reserve, India.

PubMed

Padhi, Srichandan; Das, Devaranjan; Panja, Suraj; Tayung, Kumananda

2017-06-01

Endolichenic fungi are microbes that inhabit healthy inner lichen tissues without any disease symptoms. They have been reported to produce new and interesting bioactive metabolites. In the present study, an endolichenic fungus frequently isolated from surface-sterilized lichen thallus of Parmelia caperata has been described. The fungus was identified as Aspergillus tubingensis based on morphological traits and ITS rDNA sequence. Crude metabolites extracted from the culture broth exhibited considerable antimicrobial activity against a panel of clinically significant human pathogens. The fungus showed optimum antimicrobial activity in PDB medium in day 7 of incubation period. PDB medium amended with 1 % NaCl and at alkaline pH was found to be optimal for antimicrobial metabolites production. Enhanced activity was observed when the fungus was exposed briefly to a heat shock of 60 °C during incubation. The metabolites showed optimum λ-max at 214 nm with an absorbance value of 1.589. Molecular characterization of the isolate was carried out by ITS phylogeny and ITS2 secondary structure analyses. The phylogenetic trees based on both ITS rDNA and ITS2 sequences showed the isolate within the clade A. tubingensis. Considering the ubiquity and ambiguity in identifying Aspergillus species of different lifestyles, a method to differentiate pathogenic and endophytic Aspergillus at species level was developed using ITS2 secondary structure analysis. The results showed common folding pattern in the secondary structures with a helix and a 5' dangling end found to be highly conserved. Certain features in the secondary structure like multi-bulges and a symmetric interior loop were observed to be unique which distinguish our isolate from other A. tubingensis.

Sensory Hair Cells: An Introduction to Structure and Physiology.

PubMed

McPherson, Duane R

2018-06-18

Sensory hair cells are specialized secondary sensory cells that mediate our senses of hearing, balance, linear acceleration, and angular acceleration (head rotation). In addition, hair cells in fish and amphibians mediate sensitivity to water movement through the lateral line system, and closely related electroreceptive cells mediate sensitivity to low-voltage electric fields in the aquatic environment of many fish species and several species of amphibian.Sensory hair cells share many structural and functional features across all vertebrate groups, while at the same time they are specialized for employment in a wide variety of sensory tasks. The complexity of hair cell structure is large, and the diversity of hair cell applications in sensory systems exceeds that seen for most, if not all, sensory cell types. The intent of this review is to summarize the more significant structural features and some of the more interesting and important physiological mechanisms that have been elucidated thus far. Outside vertebrates, hair cells are only known to exist in the coronal organ of tunicates. Electrical resonance, electromotility, and their exquisite mechanical sensitivity all contribute to the attractiveness of hair cells as a research subject.

Structural investigation of the Grenville Province by radar and other imaging and nonimaging sensors

NASA Technical Reports Server (NTRS)

Lowman, P. D., Jr.; Blodget, H. W.; Webster, W. J., Jr.; Paia, S.; Singhroy, V. H.; Slaney, V. R.

1984-01-01

The structural investigation of the Canadian Shield by orbital radar and LANDSAT, is outlined. The area includes parts of the central metasedimentary belt and the Ontario gneiss belt, and major structures as well-expressed topographically. The primary objective is to apply SIR-B data to the mapping of this key part of the Grenville orogen, specifically ductile fold structures and associated features, and igneous, metamorphic, and sedimentary rock (including glacial and recent sediments). Secondary objectives are to support the Canadian RADARSAT project by evaluating the baseline parameters of a Canadian imaging radar satellite planned for late in the decade. The baseline parameters include optimum incidence and azimuth angles. The experiment is to develop techniques for the use of multiple data sets.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

NASA Astrophysics Data System (ADS)

Samanta, Sudipta; Mukherjee, Sanchita

2018-01-01

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade.

PubMed

Samanta, Sudipta; Mukherjee, Sanchita

2018-01-28

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

The synthesis of monomers with pendent ethynyl groups for modified high performance thermoplastics

NASA Technical Reports Server (NTRS)

Nwokogu, Godson C.; Antoine, Miquel D.; Ansong, Omari

1994-01-01

Synthetic schemes were developed and optimized for twelve new monomers possessing unique structural features and one aspartimide. Two synthetic pathways were compared for preparation of the triarylethane monomers with pendent ethynyl groups. The results show that one of these pathways can be generally applied. The alternative pathway was applicable to the preparation of only one of the twelve compounds, the problem being secondary reactions of the initially formed desired product.

Imagine the Universe! The Anatomy of Black Holes. Probing the Structure & Evolution of the Cosmos. An Information and Activity Booklet. Grades 9-12, 1998-1999.

ERIC Educational Resources Information Center

Whitlock, Laura A.; Granger, Kara C.; Mahon, Jane D.

The information provided in this booklet is meant to give the necessary background information so that the science of black holes can be taught confidently to secondary students. The featured activities can be used to engage and excite students about the topic of black holes in different disciplines and in a number of ways. Activities include: (1)…

Acoustic Features Influence Musical Choices Across Multiple Genres

PubMed Central

Barone, Michael D.; Bansal, Jotthi; Woolhouse, Matthew H.

2017-01-01

Based on a large behavioral dataset of music downloads, two analyses investigate whether the acoustic features of listeners' preferred musical genres influence their choice of tracks within non-preferred, secondary musical styles. Analysis 1 identifies feature distributions for pairs of genre-defined subgroups that are distinct. Using correlation analysis, these distributions are used to test the degree of similarity between subgroups' main genres and the other music within their download collections. Analysis 2 explores the issue of main-to-secondary genre influence through the production of 10 feature-influence matrices, one per acoustic feature, in which cell values indicate the percentage change in features for genres and subgroups compared to overall population averages. In total, 10 acoustic features and 10 genre-defined subgroups are explored within the two analyses. Results strongly indicate that the acoustic features of people's main genres influence the tracks they download within non-preferred, secondary musical styles. The nature of this influence and its possible actuating mechanisms are discussed with respect to research on musical preference, personality, and statistical learning. PMID:28725200

Moving beyond Watson-Crick models of coarse grained DNA dynamics.

PubMed

Linak, Margaret C; Tourdot, Richard; Dorfman, Kevin D

2011-11-28

DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

The structural analysis of the mitochondrial SSUrRNA implies a close phylogenetic relationship between mitochondria from plants and from the heterotrophic alga Prototheca wickerhamii.

PubMed

Wolff, G; Kück, U

1990-04-01

The gene for the mitochondrial small subunit rRNA (SSUrRNA) from the heterotrophic alga Prototheca wickerhamii has been isolated from a gene library of extranuclear DNA. Sequence and structural analyses allow the determination of a secondary structure model for this rRNA. In addition, several sequence motifs are present which are typically found in SSUrRNAs of various mitochondrial origins. Unexpectedly, the Prototheca RNA sequence has more features in common with mitochondrial SSUrRNAs from plants than with that from the green alga Chlamydomonas reinhardtii. The phylogenetic relationship between mitochondria from plants and algae is discussed.

An Environmentally Sensitive Fluorescent Dye as a Multidimensional Probe of Amyloid Formation

PubMed Central

2016-01-01

We have explored amyloid formation using poly(amino acid) model systems in which differences in peptide secondary structure and hydrophobicity can be introduced in a controlled manner. We show that an environmentally sensitive fluorescent dye, dapoxyl, is able to identify β-sheet structure and hydrophobic surfaces, structural features likely to be related to toxicity, as a result of changes in its excitation and emission profiles and its relative quantum yield. These results show that dapoxyl is a multidimensional probe of the time dependence of amyloid aggregation, which provides information about the presence and nature of metastable aggregation intermediates that is inaccessible to the conventional probes that rely on changes in quantum yield alone. PMID:26865546

StruLocPred: structure-based protein subcellular localisation prediction using multi-class support vector machine.

PubMed

Zhou, Wengang; Dickerson, Julie A

2012-01-01

Knowledge of protein subcellular locations can help decipher a protein's biological function. This work proposes new features: sequence-based: Hybrid Amino Acid Pair (HAAP) and two structure-based: Secondary Structural Element Composition (SSEC) and solvent accessibility state frequency. A multi-class Support Vector Machine is developed to predict the locations. Testing on two established data sets yields better prediction accuracies than the best available systems. Comparisons with existing methods show comparable results to ESLPred2. When StruLocPred is applied to the entire Arabidopsis proteome, over 77% of proteins with known locations match the prediction results. An implementation of this system is at http://wgzhou.ece. iastate.edu/StruLocPred/.

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

PubMed Central

Knudsen, Vegeir; Caetano-Anollés, Gustavo

2008-01-01

The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at ‘http://www.manet.uiuc.edu/nobai/nobai.php’. This web site is free and open to all users and there is no login requirement. PMID:18448469

Energetic rationale for an unexpected and abrupt reversal of guanidinium chloride-induced unfolding of peptide deformylase.

PubMed

Berg, Alexander K; Manokaran, Sumathra; Eiler, Daniel; Kooren, Joel; Mallik, Sanku; Srivastava, D K

2008-01-01

Peptide deformylase (PDF) catalyzes the removal of formyl group from the N-terminal methionine residues of nascent proteins in prokaryotes, and this enzyme is a high priority target for antibiotic design. In pursuit of delineating the structural-functional features of Escherichia coli PDF (EcPDF), we investigated the mechanistic pathway for the guanidinium chloride (GdmCl)-induced unfolding of the enzyme by monitoring the secondary structural changes via CD spectroscopy. The experimental data revealed that EcPDF is a highly stable enzyme, and it undergoes slow denaturation in the presence of varying concentrations of GdmCl. The most interesting aspect of these studies has been the abrupt reversal of the unfolding pathway at low to moderate concentrations of the denaturant, but not at high concentration. An energetic rationale for such an unprecedented feature in protein chemistry is offered.

A semi-supervised learning approach for RNA secondary structure prediction.

PubMed

Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

2015-08-01

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

Maintenance of headland-associated linear sandbanks: modelling the secondary flows and sediment transport

NASA Astrophysics Data System (ADS)

Berthot, Alexis; Pattiaratchi, Charitha

2005-12-01

Linear sandbanks are located globally in areas where there are strong currents and an abundance of sand. In the recent years, these sandbanks have become of strategic interest as a potential source of marine aggregates (sand and gravel) and mineral deposits. They form the seaward boundary of the nearshore zone and therefore are important for the stability of the coastal system. They also commonly reach the sea surface and thus pose a threat to navigation. Headland-associated linear sandbanks are a specific type of sandbanks which are located in the lee of coastal topographic features such as headlands and islands. Interaction between tidal currents and topographic features generate complex three-dimensional circulation patterns that significantly influence the distribution of sediments in the vicinity of the feature. Field and numerical model investigations of the three-dimensional flow structure have been undertaken on the Levillain Shoal, a headland-associated linear sandbank present in the lee of Cape Levillain (Shark Bay, Western Australia). The field data indicated the presence of secondary flows near the tip of the cape and around the bank which were re-produced in the numerical simulations. Numerical results have shown that residual eddies are not representative of the sediment transport and that secondary currents enhance the convergence of sediment towards the sandbank. Maintenance processes have been investigated. Sediment transport paths near the cape and the bank indicate that the sandbank is part of a sand circulation cell where the sand is circulating around the bank with exchanges between the sandbank and the headland.

Predicting β-Turns in Protein Using Kernel Logistic Regression

PubMed Central

Elbashir, Murtada Khalafallah; Sheng, Yu; Wang, Jianxin; Wu, FangXiang; Li, Min

2013-01-01

A β-turn is a secondary protein structure type that plays a significant role in protein configuration and function. On average 25% of amino acids in protein structures are located in β-turns. It is very important to develope an accurate and efficient method for β-turns prediction. Most of the current successful β-turns prediction methods use support vector machines (SVMs) or neural networks (NNs). The kernel logistic regression (KLR) is a powerful classification technique that has been applied successfully in many classification problems. However, it is often not found in β-turns classification, mainly because it is computationally expensive. In this paper, we used KLR to obtain sparse β-turns prediction in short evolution time. Secondary structure information and position-specific scoring matrices (PSSMs) are utilized as input features. We achieved Q total of 80.7% and MCC of 50% on BT426 dataset. These results show that KLR method with the right algorithm can yield performance equivalent to or even better than NNs and SVMs in β-turns prediction. In addition, KLR yields probabilistic outcome and has a well-defined extension to multiclass case. PMID:23509793

Predicting β-turns in protein using kernel logistic regression.

PubMed

Elbashir, Murtada Khalafallah; Sheng, Yu; Wang, Jianxin; Wu, Fangxiang; Li, Min

2013-01-01

A β-turn is a secondary protein structure type that plays a significant role in protein configuration and function. On average 25% of amino acids in protein structures are located in β-turns. It is very important to develope an accurate and efficient method for β-turns prediction. Most of the current successful β-turns prediction methods use support vector machines (SVMs) or neural networks (NNs). The kernel logistic regression (KLR) is a powerful classification technique that has been applied successfully in many classification problems. However, it is often not found in β-turns classification, mainly because it is computationally expensive. In this paper, we used KLR to obtain sparse β-turns prediction in short evolution time. Secondary structure information and position-specific scoring matrices (PSSMs) are utilized as input features. We achieved Q total of 80.7% and MCC of 50% on BT426 dataset. These results show that KLR method with the right algorithm can yield performance equivalent to or even better than NNs and SVMs in β-turns prediction. In addition, KLR yields probabilistic outcome and has a well-defined extension to multiclass case.

The new protein topology graph library web server.

PubMed

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

1H and 15N NMR resonance assignments and secondary structure of titin type I domains.

PubMed

Muhle-Goll, C; Nilges, M; Pastore, A

1997-01-01

Titin/connectin is a giant muscle protein with a highly modular architecture consisting of multiple repeats of two sequence motifs, named type I and type II. Type I modules have been suggested to be intracellular members of the fibronectin type III (Fn3) domain family. Along the titin sequence they are exclusively present in the region of the molecule located in the sarcomere A-band. This region has been shown to interact with myosin and C-protein. One of the most noticeable features of type I modules is that they are particularly rich in semiconserved prolines, since these residues account for about 8% of their sequence. We have determined the secondary structure of a representative type I domain (A71) by 15N and 1H NMR. We show that the type I domains of titin have the Fn3 fold as proposed, consisting of a three- and a four-stranded beta-sheet. When the two sheets are placed on top of each other to form the beta-sandwich characteristic of the Fn3 fold, 8 out of 10 prolines are found on the same side of the molecule and form an exposed hydrophobic patch. This suggests that the semiconserved prolines might be relevant for the function of type I modules, providing a surface for binding to other A-band proteins. The secondary structure of A71 was structurally aligned to other extracellular Fn3 modules of known 3D structure. The alignment shows that titin type I modules have closest similarity to the first Fn3 domain of Drosophila neuroglian.

Prediction of redox-sensitive cysteines using sequential distance and other sequence-based features.

PubMed

Sun, Ming-An; Zhang, Qing; Wang, Yejun; Ge, Wei; Guo, Dianjing

2016-08-24

Reactive oxygen species can modify the structure and function of proteins and may also act as important signaling molecules in various cellular processes. Cysteine thiol groups of proteins are particularly susceptible to oxidation. Meanwhile, their reversible oxidation is of critical roles for redox regulation and signaling. Recently, several computational tools have been developed for predicting redox-sensitive cysteines; however, those methods either only focus on catalytic redox-sensitive cysteines in thiol oxidoreductases, or heavily depend on protein structural data, thus cannot be widely used. In this study, we analyzed various sequence-based features potentially related to cysteine redox-sensitivity, and identified three types of features for efficient computational prediction of redox-sensitive cysteines. These features are: sequential distance to the nearby cysteines, PSSM profile and predicted secondary structure of flanking residues. After further feature selection using SVM-RFE, we developed Redox-Sensitive Cysteine Predictor (RSCP), a SVM based classifier for redox-sensitive cysteine prediction using primary sequence only. Using 10-fold cross-validation on RSC758 dataset, the accuracy, sensitivity, specificity, MCC and AUC were estimated as 0.679, 0.602, 0.756, 0.362 and 0.727, respectively. When evaluated using 10-fold cross-validation with BALOSCTdb dataset which has structure information, the model achieved performance comparable to current structure-based method. Further validation using an independent dataset indicates it is robust and of relatively better accuracy for predicting redox-sensitive cysteines from non-enzyme proteins. In this study, we developed a sequence-based classifier for predicting redox-sensitive cysteines. The major advantage of this method is that it does not rely on protein structure data, which ensures more extensive application compared to other current implementations. Accurate prediction of redox-sensitive cysteines not only enhances our understanding about the redox sensitivity of cysteine, it may also complement the proteomics approach and facilitate further experimental investigation of important redox-sensitive cysteines.

CCProf: exploring conformational change profile of proteins

PubMed Central

Chang, Che-Wei; Chou, Chai-Wei; Chang, Darby Tien-Hao

2016-01-01

In many biological processes, proteins have important interactions with various molecules such as proteins, ions or ligands. Many proteins undergo conformational changes upon these interactions, where regions with large conformational changes are critical to the interactions. This work presents the CCProf platform, which provides conformational changes of entire proteins, named conformational change profile (CCP) in the context. CCProf aims to be a platform where users can study potential causes of novel conformational changes. It provides 10 biological features, including conformational change, potential binding target site, secondary structure, conservation, disorder propensity, hydropathy propensity, sequence domain, structural domain, phosphorylation site and catalytic site. All these information are integrated into a well-aligned view, so that researchers can capture important relevance between different biological features visually. The CCProf contains 986 187 protein structure pairs for 3123 proteins. In addition, CCProf provides a 3D view in which users can see the protein structures before and after conformational changes as well as binding targets that induce conformational changes. All information (e.g. CCP, binding targets and protein structures) shown in CCProf, including intermediate data are available for download to expedite further analyses. Database URL: http://zoro.ee.ncku.edu.tw/ccprof/ PMID:27016699

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaminski, K.; Adrjanowicz, K.; Paluch, M.

Time-dependent isothermal dielectric measurements were carried out deeply in the glassy state on two very important saccharides: sucrose and trehalose. In both compounds two prominent secondary relaxation processes were identified. The faster one is an inherent feature of the whole family of carbohydrates. The slower one can also be detected in oligo- and polysaccharides. It was shown earlier that the {beta} process is the Johari-Goldstein (JG) relaxation coupled to motions of the glycosidic linkage, while the {gamma} relaxation originates from motions of the exocyclic hydroxymethyl unit. Recently, it was shown that the JG relaxation process can be used to determinemore » structural relaxation times in the glassy state [R. Casalini and C. M. Roland, Phys. Rev. Lett. 102, 035701 (2009)]. In this paper we present the results of an analysis of the data obtained during aging using two independent approaches. The first was proposed by Casalini and Roland, and the second one is based on the variation of the dielectric strength of the secondary relaxation process during aging [J. K. Vij and G. Power, J. Non-Cryst. Solids 357, 783 (2011)]. Surprisingly, we found that the estimated structural relaxation times in the glassy state of both saccharides are almost the same, independent of the type of secondary mode. This finding calls into question the common view that secondary modes of intramolecular origin do not provide information about the dynamics of the glassy state.« less

Educational Experiences and Needs of Higher Education Students with Autism Spectrum Disorder.

PubMed

Cai, Ru Ying; Richdale, Amanda L

2016-01-01

Little research directly examines the needs of post-secondary students with ASD. The experiences and support needs of 23 students with ASD enrolled in two universities and four colleges, and 15 family members were explored in 15 semi-structured focus groups. Thematic analysis identified five themes: core ASD features, co-morbid conditions, transition, disclosure, and services and support. Most students felt educationally but not socially supported; most families felt support was poor in both areas. Transition from secondary school was often unplanned, and disclosure of diagnosis usually occurred after enrolment, often following a significant problem. Many parents provided substantial student support. Thus disclosure of ASD diagnosis and meeting the individual needs of these students are important considerations as higher education enrolments increase.

Secondary motion in three-dimensional branching networks

NASA Astrophysics Data System (ADS)

Guha, Abhijit; Pradhan, Kaustav

2017-06-01

A major aim of the present work is to understand and thoroughly document the generation, the three-dimensional distribution, and the evolution of the secondary motion as the fluid progresses downstream through a branched network. Six generations (G0-G5) of branches (involving 63 straight portions and 31 bifurcation modules) are computed in one go; such computational challenges are rarely taken in the literature. More than 30 × 106 computational elements are employed for high precision of computed results and fine quality of the flow visualization diagrams. The study of co-planar vis-à-vis non-planar space-filling configurations establishes a quantitative evaluation of the dependence of the fluid dynamics on the three-dimensional arrangement of the same individual branches. As compared to the secondary motion in a simple curved pipe, three distinctive features, viz., the change of shape and size of the flow-cross-section, the division of non-uniform primary flow in a bifurcation module, and repeated switchover from clockwise to anticlockwise curvature and vice versa in the flow path, make the present situation more complex. It is shown that the straight portions in the network, in general, attenuate the secondary motion, while the three-dimensionally complex bifurcation modules generate secondary motion and may alter the number, arrangement, and structure of vortices. A comprehensive picture of the evolution of quantitative flow visualizations of the secondary motion is achieved by constructing contours of secondary velocity | v → S | , streamwise vorticity ω S , and λ 2 iso-surfaces. It is demonstrated, for example, that for in-plane configuration, the vortices on any plane appear in pair (i.e., for each clockwise rotating vortex, there is an otherwise identical anticlockwise vortex), whereas the vortices on a plane for the out-of-plane configuration may be dissimilar, and there may even be an odd number of vortices. We have formulated three new parameters (ES/P, δ S F , and δ G n ) for a quantitative description of the overall features of the secondary flow field. δ S F represents a non-uniformity index of the secondary flow in an individual branch, ES/P represents the mass-flow-averaged relative kinetic energy of the secondary motion in an individual branch, and δ G n provides a measure of the non-uniformity of the secondary flow between various branches of the same generation Gn. The repeated enhancement of the secondary kinetic energy in the bifurcation modules is responsible for the occurrence of significant values of ES/P even in generation G5. For both configurations, it is found that for any bifurcation module, the value of ES/P is greater in that daughter branch in which the mass-flow rate is greater. Even though the various contour plots of the complex secondary flow structure appear visually very different from one another, the values of δ S F are found to lie within a small range ( 0.37 ≤ δ S F ≤ 0.66 ) for the six-generation networks studied. It is shown that δ G n grows as the generation number Gn increases. It is established that the out-of-plane configuration, in general, creates more secondary kinetic energy (higher ES/P), a similar level of non-uniformity in the secondary flow in an individual branch (similar δ S F ), and a significantly lower level of non-uniformity in the distribution of secondary motion among various branches of the same generation (much lower δ G n ), as compared to the in-plane arrangement of the same branches.

Secondary motion in three-dimensional branching networks

PubMed Central

Guha, Abhijit; Pradhan, Kaustav

2017-01-01

A major aim of the present work is to understand and thoroughly document the generation, the three-dimensional distribution, and the evolution of the secondary motion as the fluid progresses downstream through a branched network. Six generations (G0-G5) of branches (involving 63 straight portions and 31 bifurcation modules) are computed in one go; such computational challenges are rarely taken in the literature. More than 30 × 106 computational elements are employed for high precision of computed results and fine quality of the flow visualization diagrams. The study of co-planar vis-à-vis non-planar space-filling configurations establishes a quantitative evaluation of the dependence of the fluid dynamics on the three-dimensional arrangement of the same individual branches. As compared to the secondary motion in a simple curved pipe, three distinctive features, viz., the change of shape and size of the flow-cross-section, the division of non-uniform primary flow in a bifurcation module, and repeated switchover from clockwise to anticlockwise curvature and vice versa in the flow path, make the present situation more complex. It is shown that the straight portions in the network, in general, attenuate the secondary motion, while the three-dimensionally complex bifurcation modules generate secondary motion and may alter the number, arrangement, and structure of vortices. A comprehensive picture of the evolution of quantitative flow visualizations of the secondary motion is achieved by constructing contours of secondary velocity v→S, streamwise vorticity ωS, and λ2 iso-surfaces. It is demonstrated, for example, that for in-plane configuration, the vortices on any plane appear in pair (i.e., for each clockwise rotating vortex, there is an otherwise identical anticlockwise vortex), whereas the vortices on a plane for the out-of-plane configuration may be dissimilar, and there may even be an odd number of vortices. We have formulated three new parameters (ES/P, δSF, and δGn) for a quantitative description of the overall features of the secondary flow field. δSF represents a non-uniformity index of the secondary flow in an individual branch, ES/P represents the mass-flow-averaged relative kinetic energy of the secondary motion in an individual branch, and δGn provides a measure of the non-uniformity of the secondary flow between various branches of the same generation Gn. The repeated enhancement of the secondary kinetic energy in the bifurcation modules is responsible for the occurrence of significant values of ES/P even in generation G5. For both configurations, it is found that for any bifurcation module, the value of ES/P is greater in that daughter branch in which the mass-flow rate is greater. Even though the various contour plots of the complex secondary flow structure appear visually very different from one another, the values of δSF are found to lie within a small range (0.37≤δSF≤0.66) for the six-generation networks studied. It is shown that δGn grows as the generation number Gn increases. It is established that the out-of-plane configuration, in general, creates more secondary kinetic energy (higher ES/P), a similar level of non-uniformity in the secondary flow in an individual branch (similar δSF), and a significantly lower level of non-uniformity in the distribution of secondary motion among various branches of the same generation (much lower δGn), as compared to the in-plane arrangement of the same branches. PMID:28713213

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.

PubMed

Bhattacharya, Debswapna; Adhikari, Badri; Li, Jilong; Cheng, Jianlin

2016-07-01

Speed, accuracy and robustness of building protein fragment library have important implications in de novo protein structure prediction since fragment-based methods are one of the most successful approaches in template-free modeling (FM). Majority of the existing fragment detection methods rely on database-driven search strategies to identify candidate fragments, which are inherently time-consuming and often hinder the possibility to locate longer fragments due to the limited sizes of databases. Also, it is difficult to alleviate the effect of noisy sequence-based predicted features such as secondary structures on the quality of fragment. Here, we present FRAGSION, a database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model. FRAGSION offers some unique features compared to existing approaches in that it (i) is lightning-fast, consuming only few seconds of CPU time to generate fragment library for a protein of typical length (300 residues); (ii) can generate dynamic-size fragments of any length (even for the whole protein sequence) and (iii) offers ways to handle noise in predicted secondary structure during fragment sampling. On a FM dataset from the most recent Critical Assessment of Structure Prediction, we demonstrate that FGRAGSION provides advantages over the state-of-the-art fragment picking protocol of ROSETTA suite by speeding up computation by several orders of magnitude while achieving comparable performance in fragment quality. Source code and executable versions of FRAGSION for Linux and MacOS is freely available to non-commercial users at http://sysbio.rnet.missouri.edu/FRAGSION/ It is bundled with a manual and example data. chengji@missouri.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Prediction of Protein Modification Sites of Pyrrolidone Carboxylic Acid Using mRMR Feature Selection and Analysis

PubMed Central

Zheng, Lu-Lu; Niu, Shen; Hao, Pei; Feng, KaiYan; Cai, Yu-Dong; Li, Yixue

2011-01-01

Pyrrolidone carboxylic acid (PCA) is formed during a common post-translational modification (PTM) of extracellular and multi-pass membrane proteins. In this study, we developed a new predictor to predict the modification sites of PCA based on maximum relevance minimum redundancy (mRMR) and incremental feature selection (IFS). We incorporated 727 features that belonged to 7 kinds of protein properties to predict the modification sites, including sequence conservation, residual disorder, amino acid factor, secondary structure and solvent accessibility, gain/loss of amino acid during evolution, propensity of amino acid to be conserved at protein-protein interface and protein surface, and deviation of side chain carbon atom number. Among these 727 features, 244 features were selected by mRMR and IFS as the optimized features for the prediction, with which the prediction model achieved a maximum of MCC of 0.7812. Feature analysis showed that all feature types contributed to the modification process. Further site-specific feature analysis showed that the features derived from PCA's surrounding sites contributed more to the determination of PCA sites than other sites. The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations. PMID:22174779

Odorant Sensory Input Modulates DNA Secondary Structure Formation and Heterogeneous Ribonucleoprotein Recruitment on the Tyrosine Hydroxylase and Glutamic Acid Decarboxylase 1 Promoters in the Olfactory Bulb.

PubMed

Wang, Meng; Cai, Elizabeth; Fujiwara, Nana; Fones, Lilah; Brown, Elizabeth; Yanagawa, Yuchio; Cave, John W

2017-05-03

Adaptation of neural circuits to changes in sensory input can modify several cellular processes within neurons, including neurotransmitter biosynthesis levels. For a subset of olfactory bulb interneurons, activity-dependent changes in GABA are reflected by corresponding changes in Glutamate decarboxylase 1 ( Gad1 ) expression levels. Mechanisms regulating Gad1 promoter activity are poorly understood, but here we show that a conserved G:C-rich region in the mouse Gad1 proximal promoter region both recruits heterogeneous nuclear ribonucleoproteins (hnRNPs) that facilitate transcription and forms single-stranded DNA secondary structures associated with transcriptional repression. This promoter architecture and function is shared with Tyrosine hydroxylase ( Th ), which is also modulated by odorant-dependent activity in the olfactory bulb. This study shows that the balance between DNA secondary structure formation and hnRNP binding on the mouse Th and Gad1 promoters in the olfactory bulb is responsive to changes in odorant-dependent sensory input. These findings reveal that Th and Gad1 share a novel transcription regulatory mechanism that facilitates sensory input-dependent regulation of dopamine and GABA expression. SIGNIFICANCE STATEMENT Adaptation of neural circuits to changes in sensory input can modify several cellular processes within neurons, including neurotransmitter biosynthesis levels. This study shows that transcription of genes encoding rate-limiting enzymes for GABA and dopamine biosynthesis ( Gad1 and Th , respectively) in the mammalian olfactory bulb is regulated by G:C-rich regions that both recruit heterogeneous nuclear ribonucleoproteins (hnRNPs) to facilitate transcription and form single-stranded DNA secondary structures associated with repression. hnRNP binding and formation of DNA secondary structure on the Th and Gad1 promoters are mutually exclusive, and odorant sensory input levels regulate the balance between these regulatory features. These findings reveal that Th and Gad1 share a transcription regulatory mechanism that facilitates odorant-dependent regulation of dopamine and GABA expression levels. Copyright © 2017 the authors 0270-6474/17/374778-12$15.00/0.

Structural and Sequence Stratigraphic Analysis of the Onshore Nile Delta, Egypt.

NASA Astrophysics Data System (ADS)

Barakat, Moataz; Dominik, Wilhelm

2010-05-01

The Nile Delta is considered the earliest known delta in the world. It was already described by Herodotus in the 5th Century AC. Nowadays; the Nile Delta is an emerging giant gas province in the Middle East with proven gas reserves which have more than doubled in size in the last years. The Nile Delta basin contains a thick sedimentary sequence inferred to extend from Jurassic to recent time. Structural styles and depositional environments varied during this period. Facies architecture and sequence stratigraphy of the Nile Delta are resolved using seismic stratigraphy based on (2D seismic lines) including synthetic seismograms and tying in well log data. Synthetic seismograms were constructed using sonic and density logs. The combination of structural interpretation and sequence stratigraphy of the development of the basin was resolved. Seven chrono-stratigraphic boundaries have been identified and correlated on seismic and well log data. Several unconformity boundaries also identified on seismic lines range from angular to disconformity type. Furthermore, time structure maps, velocity maps, depth structure maps as well as Isopach maps were constructed using seismic lines and log data. Several structural features were identified: normal faults, growth faults, listric faults, secondary antithetic faults and large rotated fault blocks of manly Miocene age. In some cases minor rollover structures could be identified. Sedimentary features such as paleo-channels were distinctively recognized. Typical Sequence stratigraphic features such as incised valley, clinoforms, topsets, offlaps and onlaps are identified and traced on the seismic lines allowing a good insight into sequence stratigraphic history of the Nile Delta most especially in the Miocene to Pliocene clastic sedimentary succession.

RNA-SSPT: RNA Secondary Structure Prediction Tools.

PubMed

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

RNA-SSPT: RNA Secondary Structure Prediction Tools

PubMed Central

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

Antimicrobial peptides: a new class of antimalarial drugs?

PubMed Central

Vale, Nuno; Aguiar, Luísa; Gomes, Paula

2014-01-01

A range of antimicrobial peptides (AMP) exhibit activity on malaria parasites, Plasmodium spp., in their blood or mosquito stages, or both. These peptides include a diverse array of both natural and synthetic molecules varying greatly in size, charge, hydrophobicity, and secondary structure features. Along with an overview of relevant literature reports regarding AMP that display antiplasmodial activity, this review makes a few considerations about those molecules as a potential new class of antimalarial drugs. PMID:25566072

Stochastic Modeling as a Means of Automatic Speech Recognition

DTIC Science & Technology

1975-04-01

companng ihc features of different speech recognition systems, attention is often focused on thc control structures and the methods o’ communication...with no need to use secondary storage . Note that we go from a group of separate knowledge sources to an integrated network representation in...exhaust the available lime or storage . - - - . . 1- .-.-.. mmm^~ i — ■ ■ ’ ■ C haplcr I - IN I ROÜliCl ION Page 13 On the other hand

Skin friction fields on delta wings

NASA Astrophysics Data System (ADS)

Woodiga, S. A.; Liu, Tianshu

2009-12-01

The normalized skin friction fields on a 65° delta wing and a 76°/40° double-delta wing are measured by using a global luminescent oil-film skin friction meter. The detailed topological structures of skin friction fields on the wings are revealed for different angles of attack and the important features are detected such as reattachment lines, secondary separation lines, vortex bursting and vortex interaction. The comparisons with the existing flow visualization results are discussed.

Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility.

PubMed

Zhang, Hua; Zhang, Tuo; Gao, Jianzhao; Ruan, Jishou; Shen, Shiyi; Kurgan, Lukasz

2012-01-01

Proteins fold through a two-state (TS), with no visible intermediates, or a multi-state (MS), via at least one intermediate, process. We analyze sequence-derived factors that determine folding types by introducing a novel sequence-based folding type predictor called FOKIT. This method implements a logistic regression model with six input features which hybridize information concerning amino acid composition and predicted secondary structure and solvent accessibility. FOKIT provides predictions with average Matthews correlation coefficient (MCC) between 0.58 and 0.91 measured using out-of-sample tests on four benchmark datasets. These results are shown to be competitive or better than results of four modern predictors. We also show that FOKIT outperforms these methods when predicting chains that share low similarity with the chains used to build the model, which is an important advantage given the limited number of annotated chains. We demonstrate that inclusion of solvent accessibility helps in discrimination of the folding kinetic types and that three of the features constitute statistically significant markers that differentiate TS and MS folders. We found that the increased content of exposed Trp and buried Leu are indicative of the MS folding, which implies that the exposure/burial of certain hydrophobic residues may play important role in the formation of the folding intermediates. Our conclusions are supported by two case studies.

Prokaryotic and eukaryotic features observed on the secondary structures of Giardia SSU rRNAs and its phylogenetic implications.

PubMed

Hwang, Ui Wook

2007-04-01

Phylogenetic position of a diplomonad protist Giardia, a principle cause of diarrhea, among eukaryotes has been vigorously debated so far. Through the comparisons of primary and secondary structures of SSU rRNAs of G. intestinalis, G. microti, G. ardeae, and G. muris, I found two major indel regions (a 6-nt indel and a 22-26-nt indel), which correspond to the helix 10 of the V2 region and helices E23-8 to E23-9 of the V4 region, respectively. As generally shown in eukaryotes, G. intestinalis and G. microti have commonly a relatively longer helix 10 (a 7-bp stem and a 4-nt loop), and also the eukaryote-specific helices E23-6 to E23-9. On the other hand, G. muris and G. ardeae have a shorter helix 10: a 2-bp stem and a 6-nt loop in G. ardeae and a 3-bp stem and a 6-nt loop in G. muris. In the V4, they have a single long helix (like the P23-1 helix in prokaryotes) instead of the helices E23-6 to E23-9. Among the four Giardia species, co-appearance of prokaryote- and eukaryote-typical features might be significant evidence to suggest that Giardia (Archezoa) is a living fossil showing an "intermediate stage" during the evolution from prokaryotes to eukaryotes.

Effect of incubation temperature on the self-assembly of regenerated silk fibroin: a study using AFM.

PubMed

Zhong, Jian; Liu, Xunwei; Wei, Daixu; Yan, Juan; Wang, Ping; Sun, Gang; He, Dannong

2015-05-01

Understanding effect of temperature on the molecular self-assembly process will be helpful to unravel the structure-function relationship of biomolecule and to provide important information for the bottom-up approach to nanotechnology. In this work, the effect of incubation temperature on the secondary structures and morphological structures of regenerated silk fibroin (RSF) was systematically studied using atomic force microscopy and Fourier Transform infrared spectroscopy. The effect of incubation temperature on RSF self-assembly was dependent on RSF concentration. For the RSF solution with relatively low concentrations (15 μg/mL and 60 μg/mL), the increase of the incubation temperature mainly accelerated the formation and aggregation of antiparallel β-sheet protofibrils and decreased the formation of random coil protofilaments/globule-like molecules. For the RSF solution with relatively high concentrations (300 μg/mL and 1.5mg/mL), the increase of the incubation temperature mainly accelerated the formation and aggregation of antiparallel β-sheet RSF features (protofibrils and globule-like features) and decreased the formation of random coil bead-like features. This work implies that the morphology and conformation of biomacromolecules could be tuned by controlling the incubation temperature. Further, it will be beneficial to basic understanding of the nanoscale structure formation in different silk-based biomaterials. Copyright © 2015 Elsevier B.V. All rights reserved.

Interpreting U-Pb data from primary and secondary features in lunar zircon

NASA Astrophysics Data System (ADS)

Grange, M. L.; Pidgeon, R. T.; Nemchin, A. A.; Timms, N. E.; Meyer, C.

2013-01-01

In this paper, we describe primary and secondary microstructures and textural characteristics found in lunar zircon and discuss the relationships between these features and the zircon U-Pb isotopic systems and the significance of these features for understanding lunar processes. Lunar zircons can be classified according to: (i) textural relationships between zircon and surrounding minerals in the host breccias, (ii) the internal microstructures of the zircon grains as identified by optical microscopy, cathodoluminescence (CL) imaging and electron backscattered diffraction (EBSD) mapping and (iii) results of in situ ion microprobe analyses of the Th-U-Pb isotopic systems. Primary zircon can occur as part of a cogenetic mineral assemblage (lithic clast) or as an individual mineral clast and is unzoned, or has sector and/or oscillatory zoning. The age of primary zircon is obtained when multiple ion microprobe analyses across the polished surface of the grain give reproducible and essentially concordant data. A secondary set of microstructures, superimposed on primary zircon, include localised recrystallised domains, localised amorphous domains, crystal-plastic deformation, planar deformation features and fractures, and are associated with impact processes. The first two secondary microstructures often yield internally consistent and close to concordant U-Pb ages that we interpret as dating impact events. Others secondary microstructures such as planar deformation features, crystal-plastic deformation and micro-fractures can provide channels for Pb diffusion and result in partial resetting of the U-Pb isotopic systems.

IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.

PubMed

Hadjithomas, Michalis; Chen, I-Min Amy; Chu, Ken; Ratner, Anna; Palaniappan, Krishna; Szeto, Ernest; Huang, Jinghua; Reddy, T B K; Cimermančič, Peter; Fischbach, Michael A; Ivanova, Natalia N; Markowitz, Victor M; Kyrpides, Nikos C; Pati, Amrita

2015-07-14

In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In this work, we present IMG-ABC (https://img.jgi.doe.gov/abc), an atlas of biosynthetic gene clusters within the Integrated Microbial Genomes (IMG) system, which is aimed at harnessing the power of "big" genomic data for discovering small molecules. IMG-ABC relies on IMG's comprehensive integrated structural and functional genomic data for the analysis of biosynthetic gene clusters (BCs) and associated secondary metabolites (SMs). SMs and BCs serve as the two main classes of objects in IMG-ABC, each with a rich collection of attributes. A unique feature of IMG-ABC is the incorporation of both experimentally validated and computationally predicted BCs in genomes as well as metagenomes, thus identifying BCs in uncultured populations and rare taxa. We demonstrate the strength of IMG-ABC's focused integrated analysis tools in enabling the exploration of microbial secondary metabolism on a global scale, through the discovery of phenazine-producing clusters for the first time in Alphaproteobacteria. IMG-ABC strives to fill the long-existent void of resources for computational exploration of the secondary metabolism universe; its underlying scalable framework enables traversal of uncovered phylogenetic and chemical structure space, serving as a doorway to a new era in the discovery of novel molecules. IMG-ABC is the largest publicly available database of predicted and experimental biosynthetic gene clusters and the secondary metabolites they produce. The system also includes powerful search and analysis tools that are integrated with IMG's extensive genomic/metagenomic data and analysis tool kits. As new research on biosynthetic gene clusters and secondary metabolites is published and more genomes are sequenced, IMG-ABC will continue to expand, with the goal of becoming an essential component of any bioinformatic exploration of the secondary metabolism world. Copyright © 2015 Hadjithomas et al.

Primary vs. Secondary Antibody Deficiency: Clinical Features and Infection Outcomes of Immunoglobulin Replacement

PubMed Central

Duraisingham, Sai S.; Buckland, Matthew; Dempster, John; Lorenzo, Lorena; Grigoriadou, Sofia; Longhurst, Hilary J.

2014-01-01

Secondary antibody deficiency can occur as a result of haematological malignancies or certain medications, but not much is known about the clinical and immunological features of this group of patients as a whole. Here we describe a cohort of 167 patients with primary or secondary antibody deficiencies on immunoglobulin (Ig)-replacement treatment. The demographics, causes of immunodeficiency, diagnostic delay, clinical and laboratory features, and infection frequency were analysed retrospectively. Chemotherapy for B cell lymphoma and the use of Rituximab, corticosteroids or immunosuppressive medications were the most common causes of secondary antibody deficiency in this cohort. There was no difference in diagnostic delay or bronchiectasis between primary and secondary antibody deficiency patients, and both groups experienced disorders associated with immune dysregulation. Secondary antibody deficiency patients had similar baseline levels of serum IgG, but higher IgM and IgA, and a higher frequency of switched memory B cells than primary antibody deficiency patients. Serious and non-serious infections before and after Ig-replacement were also compared in both groups. Although secondary antibody deficiency patients had more serious infections before initiation of Ig-replacement, treatment resulted in a significant reduction of serious and non-serious infections in both primary and secondary antibody deficiency patients. Patients with secondary antibody deficiency experience similar delays in diagnosis as primary antibody deficiency patients and can also benefit from immunoglobulin-replacement treatment. PMID:24971644

Mapping the Sedna-Lavinia Region of Venus

NASA Technical Reports Server (NTRS)

Campbell, Bruce A.; Anderson, Ross F.

2008-01-01

Geologic mapping of Venus at 1:5 M scale has shown in great detail the flow complexes of volcanoes, coronae, and shield fields, and the varying structural patterns that differentiate tesserae from corona rims and isolated patches of densely lineated terrain. In most cases, however, the lower-elevation plains between the higher-standing landforms are discriminated only on the basis of potentially secondary features such as late-stage lava flooding or tectonic overprinting. This result, in which volcanoes and tesserae appear as "islands in the sea," places weak constraints on the relative age of large upland regions and the nature of the basement terrain. In this work, we focus on the spatial distribution and topography of densely lineated and tessera units over a large region of Venus, and their relationship to apparently later corona and shield flow complexes. The goal is to identify likely connections between patches of deformed terrain that suggest earlier features of regional extent, and to compare the topography of linked patches with other such clusters as a guide to whether they form larger tracts beneath the plains. Mapping Approach. We are mapping the region from 57S to 57N, 300E-60E. Since the 1:5 M quadrangles emphasize detail of tessera structure and corona/edifice flows, we simply adopt the outlines of these features as they relate to the outcrops of either "densely lineated terrain" or tessera (Fig. 1). The densely lineated material is mapped in many quadrangles based on pervasive structural deformation, typically with a single major axis (in contrast to the overlapping orthogonal patterns on tesserae). This unit definition is often extended to include material of corona rims. We do not at present differentiate between plains units, since earlier efforts show that their most defining attributes may be secondary to the original emplacement (e.g., lobate or sheet-like flooding by thin flow units, tectonic patterns related to regional and localized stress regimes) [1].

Doppler tomography of XTE J1118+480 revealing chromospheric emission from the secondary star

NASA Astrophysics Data System (ADS)

Zurita, C.; González Hernández, J. I.; Escorza, A.; Casares, J.

2016-08-01

Doppler tomography of emission lines in low-mass X-ray binaries allows us to investigate the structure and variability of the accretion discs as well as possible activity arising from the secondary stars. We present Doppler maps of the black hole binary XTE J1118+480 from spectra obtained using OSIRIS@GTC during quiescence on four different nights in 2011 and 2012. Doppler imaging of the Hα line shows, for the first time, a narrow component from the secondary star with observed equivalent widths varying in the range 1.2-2.9 Å but not correlated with the veiling of the accretion disc. The Hα flux of the secondary star is too large to be powered by X-ray irradiation, supporting chromospheric activity, possibly induced by rapid rotation, as the most likely origin of this feature in the black hole X-ray binary XTE J1118+480. In addition, we detect variations in the centroid of the Hα line on nightly basis. These are likely caused by a precessing accretion disc, although with a much lower amplitude (˜50 km s-1) than previously observed.

Validating Female Psychopathy Subtypes: Differences in Personality, Antisocial and Violent Behavior, Substance Abuse, Trauma, and Mental Health

PubMed Central

Hicks, Brian M.; Vaidyanathan, Uma; Patrick, Christopher J.

2010-01-01

Recent empirical investigations utilizing male prisoners have begun to validate clinical conceptualizations of primary and secondary psychopathy subtypes. We extended this literature by identifying similar psychopathic subtypes in female prisoners on the basis of personality structure using model-based cluster analysis. Secondary psychopaths (n = 39) were characterized by personality traits of negative emotionality and low behavioral constraint, an early onset of antisocial and criminal behavior, greater substance use and abuse, more violent behavior and institutional misconduct, and more mental health problems including symptoms of post-traumatic stress disorder and suicide attempts. Primary psychopaths (n = 31) exhibited few distinguishing personality features but were prolific criminals especially in regards to non-violent crime, and exhibited relatively few mental health problems despite substantial exposure to traumatic events. The results support alternative etiological pathways to antisocial and criminal behavior that are evident in personality structure as well as gender similarities and differences in the manifestation of psychopathic personalities. PMID:20582155

3D Flow in the Venom Channel of a Spitting Cobra: Do the Ridges in the Fangs Act as Fluid Guide Vanes?

PubMed Central

Triep, Michael; Hess, David; Chaves, Humberto; Brücker, Christoph; Balmert, Alexander; Westhoff, Guido; Bleckmann, Horst

2013-01-01

The spitting cobra Naja pallida can eject its venom towards an offender from a distance of up to two meters. The aim of this study was to understand the mechanisms responsible for the relatively large distance covered by the venom jet although the venom channel is only of micro-scale. Therefore, we analysed factors that influence secondary flow and pressure drop in the venom channel, which include the physical-chemical properties of venom liquid and the morphology of the venom channel. The cobra venom showed shear-reducing properties and the venom channel had paired ridges that span from the last third of the channel to its distal end, terminating laterally and in close proximity to the discharge orifice. To analyze the functional significance of these ridges we generated a numerical and an experimental model of the venom channel. Computational fluid dynamics (CFD) and Particle-Image Velocimetry (PIV) revealed that the paired interior ridges shape the flow structure upstream of the sharp 90° bend at the distal end. The occurrence of secondary flow structures resembling Dean-type vortical structures in the venom channel can be observed, which induce additional pressure loss. Comparing a venom channel featuring ridges with an identical channel featuring no ridges, one can observe a reduction of pressure loss of about 30%. Therefore it is concluded that the function of the ridges is similar to guide vanes used by engineers to reduce pressure loss in curved flow channels. PMID:23671569

Identification of DNA-Binding Proteins Using Structural, Electrostatic and Evolutionary Features

PubMed Central

Nimrod, Guy; Szilágyi, András; Leslie, Christina; Ben-Tal, Nir

2009-01-01

Summary DNA binding proteins (DBPs) often take part in various crucial processes of the cell's life cycle. Therefore, the identification and characterization of these proteins are of great importance. We present here a random forests classifier for identifying DBPs among proteins with known three-dimensional structures. First, clusters of evolutionarily conserved regions (patches) on the protein's surface are detected using the PatchFinder algorithm; previous studies showed that these regions are typically the proteins' functionally important regions. Next, we train a classifier using features like the electrostatic potential, cluster-based amino acid conservation patterns and the secondary structure content of the patches, as well as features of the whole protein including its dipole moment. Using 10-fold cross validation on a dataset of 138 DNA-binding proteins and 110 proteins which do not bind DNA, the classifier achieved a sensitivity and a specificity of 0.90, which is overall better than the performance of previously published methods. Furthermore, when we tested 5 different methods on 11 new DBPs which did not appear in the original dataset, only our method annotated all correctly. The resulting classifier was applied to a collection of 757 proteins of known structure and unknown function. Of these proteins, 218 were predicted to bind DNA, and we anticipate that some of them interact with DNA using new structural motifs. The use of complementary computational tools supports the notion that at least some of them do bind DNA. PMID:19233205

Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.

PubMed

Nimrod, Guy; Szilágyi, András; Leslie, Christina; Ben-Tal, Nir

2009-04-10

DNA-binding proteins (DBPs) participate in various crucial processes in the life-cycle of the cells, and the identification and characterization of these proteins is of great importance. We present here a random forests classifier for identifying DBPs among proteins with known 3D structures. First, clusters of evolutionarily conserved regions (patches) on the surface of proteins were detected using the PatchFinder algorithm; earlier studies showed that these regions are typically the functionally important regions of proteins. Next, we trained a classifier using features like the electrostatic potential, cluster-based amino acid conservation patterns and the secondary structure content of the patches, as well as features of the whole protein, including its dipole moment. Using 10-fold cross-validation on a dataset of 138 DBPs and 110 proteins that do not bind DNA, the classifier achieved a sensitivity and a specificity of 0.90, which is overall better than the performance of published methods. Furthermore, when we tested five different methods on 11 new DBPs that did not appear in the original dataset, only our method annotated all correctly. The resulting classifier was applied to a collection of 757 proteins of known structure and unknown function. Of these proteins, 218 were predicted to bind DNA, and we anticipate that some of them interact with DNA using new structural motifs. The use of complementary computational tools supports the notion that at least some of them do bind DNA.

Using a Digital Pen to Support Secondary Students with Learning Disabilities

ERIC Educational Resources Information Center

Ok, Min Wook; Rao, Kavita

2017-01-01

Secondary students with learning disabilities (LD) can benefit from using assistive and instructional technologies to support content and skill acquisition. Digital pens have features that can be beneficial for students who struggle with comprehension, note taking, and organization. Livescribe pens, in particular, provide a variety features that…

Weaving Contexts of Participation Online: The Digital Tapestry of Secondary English Teachers

ERIC Educational Resources Information Center

Rodesiler, Luke

2014-01-01

This article presents research from a qualitative study exploring five secondary English teachers' professionally oriented participation online. Drawing upon Cole's (1996) "surround" and "weaving" views of context, the specific line of research featured here was guided by the following question: What are the features of the…

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines

PubMed Central

2014-01-01

Background It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models. Results We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to make predictions. We also trained a SVM model with two new additional features (profiles and SOV scores) on 20 CASP8 targets and found that including them can only improve the performance when real deviations between native and model are higher than 5Å. The SMOQ tool finally released uses the basic feature set trained on 85 CASP8 targets. Moreover, SMOQ implemented a way to convert predicted local quality scores into a global quality score. SMOQ was tested on the 84 CASP9 single-domain targets. The average difference between the residue-specific distance deviation predicted by our method and the actual distance deviation on the test data is 2.637Å. The global quality prediction accuracy of the tool is comparable to other good tools on the same benchmark. Conclusion SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/. PMID:24776231

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.

PubMed

Cao, Renzhi; Wang, Zheng; Wang, Yiheng; Cheng, Jianlin

2014-04-28

It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models. We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to make predictions. We also trained a SVM model with two new additional features (profiles and SOV scores) on 20 CASP8 targets and found that including them can only improve the performance when real deviations between native and model are higher than 5Å. The SMOQ tool finally released uses the basic feature set trained on 85 CASP8 targets. Moreover, SMOQ implemented a way to convert predicted local quality scores into a global quality score. SMOQ was tested on the 84 CASP9 single-domain targets. The average difference between the residue-specific distance deviation predicted by our method and the actual distance deviation on the test data is 2.637Å. The global quality prediction accuracy of the tool is comparable to other good tools on the same benchmark. SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/.

X-ray crystal structure of the passenger domain of plasmid encoded toxin(Pet), an autotransporter enterotoxin from enteroaggregative Escherichia coli (EAEC)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Domingo Meza-Aguilar, J.; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato Oncología e Investigación, Hospital Infantil de México Federico Gómez 06720, D.F.; Fromme, Petra

Highlights: • X-ray crystal structure of the passenger domain of Plasmid encoded toxin at 2.3 Å. • Structural differences between Pet passenger domain and EspP protein are described. • High flexibility of the C-terminal beta helix is structurally assigned. - Abstract: Autotransporters (ATs) represent a superfamily of proteins produced by a variety of pathogenic bacteria, which include the pathogenic groups of Escherichia coli (E. coli) associated with gastrointestinal and urinary tract infections. We present the first X-ray structure of the passenger domain from the Plasmid-encoded toxin (Pet) a 100 kDa protein at 2.3 Å resolution which is a cause ofmore » acute diarrhea in both developing and industrialized countries. Pet is a cytoskeleton-altering toxin that induces loss of actin stress fibers. While Pet (pdb code: 4OM9) shows only a sequence identity of 50% compared to the closest related protein sequence, extracellular serine protease plasmid (EspP) the structural features of both proteins are conserved. A closer structural look reveals that Pet contains a β-pleaded sheet at the sequence region of residues 181–190, the corresponding structural domain in EspP consists of a coiled loop. Secondary, the Pet passenger domain features a more pronounced beta sheet between residues 135 and 143 compared to the structure of EspP.« less

A Cretaceous eutriconodont and integument evolution in early mammals.

PubMed

Martin, Thomas; Marugán-Lobón, Jesús; Vullo, Romain; Martín-Abad, Hugo; Luo, Zhe-Xi; Buscalioni, Angela D

2015-10-15

The Mesozoic era (252-66 million years ago), known as the domain of dinosaurs, witnessed a remarkable ecomorphological diversity of early mammals. The key mammalian characteristics originated during this period and were prerequisite for their evolutionary success after extinction of the non-avian dinosaurs 66 million years ago. Many ecomorphotypes familiar to modern mammal fauna evolved independently early in mammalian evolutionary history. Here we report a 125-million-year-old eutriconodontan mammal from Spain with extraordinary preservation of skin and pelage that extends the record of key mammalian integumentary features into the Mesozoic era. The new mammalian specimen exhibits such typical mammalian features as pelage, mane, pinna, and a variety of skin structures: keratinous dermal scutes, protospines composed of hair-like tubules, and compound follicles with primary and secondary hairs. The skin structures of this new Mesozoic mammal encompass the same combination of integumentary features as those evolved independently in other crown Mammalia, with similarly broad structural variations as in extant mammals. Soft tissues in the thorax and abdomen (alveolar lungs and liver) suggest the presence of a muscular diaphragm. The eutriconodont has molariform tooth replacement, ossified Meckel's cartilage of the middle ear, and specialized xenarthrous articulations of posterior dorsal vertebrae, convergent with extant xenarthran mammals, which strengthened the vertebral column for locomotion.

Detailed Mapping of the Alu Volcano, Ethiopia

NASA Astrophysics Data System (ADS)

Agrain, Guillaume; Buso, Roxane; Carlier, Jean; van Wyk de Vries, Benjamin

2017-04-01

The Alu volcano in the Danakil Depression is interpreted as a forced-fold related uplift, related to progressive intrusions of sills, or similar tabular intrusions. Alu is in a very isolated and difficult to access area, but Google Earth provides high resolution images that can be used for mapping the structure and volcanic features. We use the imagery to map in as much detail as possible all the morphological features of Alu, which we separate into primary volcanic features and secondary structural features. The mapping has been undertaken by a group undergraduates, graduates and researchers. The group has checked and validated the interpretation of each feature mapped. The data set is available as a kmz, and has been imported into QGIS. The detailed mapping reveals a complex history of multiple lava fields and fissure eruptions, some which pre-date uplift, while others have occurred during uplift, but are subsequently deformed. Similarly, there are cross-cutting structures, and we are able to set up a chronology of events. This shows that uplift grew in an area which was already covered by lavas, that some lava has been probably erupted from Alu's flanks, while most eruptions have been from around the base of Alu. Early in the deformation, thrust faults developed on the lower flanks, similar to those described near the Grosmanaux uplift (van Wyk de Vries et al 2014). These are cut by the larger faults, and by minor fissures. The mapping provides an accessible way of preparing for dedicated fieldwork in preparation of an eventual field expedition to Alu, while extracting the most from remote sensing data.

Bend sweep angle and Reynolds number effects on hemodynamics of s-shaped arteries.

PubMed

Niazmand, H; Rajabi Jaghargh, E

2010-09-01

The purpose of this study is to investigate the effects of the Reynolds number and the bend sweep angle on the blood flow patterns of S-shaped bends. The numerical simulations of steady flows in S-shaped bends with sweep angles of 45 degrees , 90 degrees , and 135 degrees are performed at Reynolds numbers of 125, 500, and 960. Hemodynamic characteristics such as secondary flows, vorticity, and axial velocity profiles are analyzed in detail. Flow patterns in S-shaped bends are strongly dependent on both Reynolds number and bend sweep angle, which can be categorized into three groups based on the first bend secondary flow effects on the transverse flow of the second bend. For low Reynolds numbers and any sweep angles, secondary flows in the second bend eliminate the first bend effects in the early sections of the second bend and therefore the axial velocity profile is consistent with the bend curvature, while for high Reynolds numbers depending on the bend sweep angles the secondary vortex pattern of the first bend may persist partially or totally throughout the second bend leading to a four-vortex secondary structure. Moreover, an interesting flow feature observed at the Reynolds number of 960 is that the secondary flow asymmetrical behavior occurred around the second bend exit and along the outflow straight section. This symmetry-breaking phenomenon which has not been reported in the previous studies is shown to be more pronounced in the 90 degrees S-shaped bend as compared to other models considered here. The probability of flow separation as one of the important flow features contributing to the onset and development of arterial wall diseases is also studied. It is observed that the second bend outer wall of gentle bends with sweep angles from 20 degrees to 30 degrees at high enough Reynolds numbers are prone to flow separation.

K-Partite RNA Secondary Structures

NASA Astrophysics Data System (ADS)

Jiang, Minghui; Tejada, Pedro J.; Lasisi, Ramoni O.; Cheng, Shanhong; Fechser, D. Scott

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k pseudoknot-free sub-structures. Most known RNA secondary structures are either bipartite or tripartite. We show that there exists a constant number k such that any secondary structure can be modified into a k-partite secondary structure with approximately the same free energy. This offers a partial explanation of the prevalence of k-partite secondary structures with small k. We give a complete characterization of the computational complexities of recognizing k-partite secondary structures for all k ≥ 2, and show that this recognition problem is essentially the same as the k-colorability problem on circle graphs. We present two simple heuristics, iterated peeling and first-fit packing, for finding k-partite RNA secondary structures. For maximizing the number of base pair stackings, our iterated peeling heuristic achieves a constant approximation ratio of at most k for 2 ≤ k ≤ 5, and at most frac6{1-(1-6/k)^k} le frac6{1-e^{-6}} < 6.01491 for k ≥ 6. Experiment on sequences from PseudoBase shows that our first-fit packing heuristic outperforms the leading method HotKnots in predicting RNA secondary structures with pseudoknots. Source code, data set, and experimental results are available at http://www.cs.usu.edu/ mjiang/rna/kpartite/.

A computational method for predicting regulation of human microRNAs on the influenza virus genome

PubMed Central

2013-01-01

Background While it has been suggested that host microRNAs (miRNAs) may downregulate viral gene expression as an antiviral defense mechanism, such a mechanism has not been explored in the influenza virus for human flu studies. As it is difficult to conduct related experiments on humans, computational studies can provide some insight. Although many computational tools have been designed for miRNA target prediction, there is a need for cross-species prediction, especially for predicting viral targets of human miRNAs. However, finding putative human miRNAs targeting influenza virus genome is still challenging. Results We developed machine-learning features and conducted comprehensive data training for predicting interactions between H1N1 genome segments and host miRNA. We defined our seed region as the first ten nucleotides from the 5' end of the miRNA to the 3' end of the miRNA and integrated various features including the number of consecutive matching bases in the seed region of 10 bases, a triplet feature in seed regions, thermodynamic energy, penalty of bulges and wobbles at binding sites, and the secondary structure of viral RNA for the prediction. Conclusions Compared to general predictive models, our model fully takes into account the conservation patterns and features of viral RNA secondary structures, and greatly improves the prediction accuracy. Our model identified some key miRNAs including hsa-miR-489, hsa-miR-325, hsa-miR-876-3p and hsa-miR-2117, which target HA, PB2, MP and NS of H1N1, respectively. Our study provided an interesting hypothesis concerning the miRNA-based antiviral defense mechanism against influenza virus in human, i.e., the binding between human miRNA and viral RNAs may not result in gene silencing but rather may block the viral RNA replication. PMID:24565017

Climate change and adaptational impacts in coastal systems: the case of sea defences.

PubMed

Firth, Louise B; Mieszkowska, Nova; Thompson, Richard C; Hawkins, Stephen J

2013-09-01

We briefly review how coastal ecosystems are responding to and being impacted by climate change, one of the greatest challenges facing society today. In adapting to rising and stormier seas associated with climate change, coastal defence structures are proliferating and becoming dominant coastal features, particularly in urbanised areas. Whilst the primary function of these structures is to protect coastal property and infrastructure, they inevitably have a significant secondary impact on the local environment and ecosystems. In this review we outline some of the negative and positive effects of these structures on physical processes, impacts on marine species, and the novel engineering approaches that have been employed to improve the ecological value of these structures in recent years. Finally we outline guidelines for an environmentally sensitive approach to design of such structures in the marine environment.

Identification of possible non-stationary effects in a new type of vortex furnace

NASA Astrophysics Data System (ADS)

Shadrin, Evgeniy Yu.; Anufriev, Igor S.; Papulov, Anatoly P.

2017-10-01

The article presents the results of an experimental study of pressure and velocity pulsations in the model of improved vortex furnace with distributed air supply and vertically oriented nozzles of the secondary blast. Investigation of aerodynamic characteristics of a swirling flow with different regime parameters was conducted in an isothermal laboratory model (in 1:25 scale) of vortex furnace using laser Doppler measuring system and pressure pulsations analyzer. The obtained results have revealed a number of features of the flow structure, and the spectral analysis of pressure and velocity pulsations allows to speak about the absence of large-scale unsteady vortical structures in the studied design.

Nicked apomyoglobin: a noncovalent complex of two polypeptide fragments comprising the entire protein chain.

PubMed

Musi, Valeria; Spolaore, Barbara; Picotti, Paola; Zambonin, Marcello; De Filippis, Vincenzo; Fontana, Angelo

2004-05-25

Limited proteolysis of the 153-residue chain of horse apomyoglobin (apoMb) by thermolysin results in the selective cleavage of the peptide bond Pro88-Leu89. The N-terminal (residues 1-88) and C-terminal (residues 89-153) fragments of apoMb were isolated to homogeneity and their conformational and association properties investigated in detail. Far-UV circular dichroism (CD) measurements revealed that both fragments in isolation acquire a high content of helical secondary structure, while near-UV CD indicated the absence of tertiary structure. A 1:1 mixture of the fragments leads to a tight noncovalent protein complex (1-88/89-153, nicked apoMb), characterized by secondary and tertiary structures similar to those of intact apoMb. The apoMb complex binds heme in a nativelike manner, as given by CD measurements in the Soret region. Second-derivative absorption spectra in the 250-300 nm region provided evidence that the degree of exposure of Tyr residues in the nicked species is similar to that of the intact protein at neutral pH. Also, the microenvironment of Trp residues, located in positions 7 and 14 of the 153-residue chain of the protein, is similar in both protein species, as given by fluorescence emission data. Moreover, in analogy to intact apoMb, the nicked protein binds the hydrophobic dye 1-anilinonaphthalene-8-sulfonate (ANS). Taken together, our results indicate that the two proteolytic fragments 1-88 and 89-153 of apoMb adopt partly folded states characterized by sufficiently nativelike conformational features that promote their specific association and mutual stabilization into a nicked protein species much resembling in its structural features intact apoMb. It is suggested that the formation of a noncovalent complex upon fragment complementation can mimic the protein folding process of the entire protein chain, with the difference that the folding of the complementary fragments is an intermolecular process. In particular, this study emphasizes the importance of interactions between marginally stable elements of secondary structure in promoting the tertiary contacts of a native protein. Considering that apoMb has been extensively used as a paradigm in protein folding studies for the past few decades, the novel fragment complementing system of apoMb here described appears to be very useful for investigating the initial as well as late events in protein folding.

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

PubMed

Jossinet, Fabrice; Ludwig, Thomas E; Westhof, Eric

2010-08-15

Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research. Assemble is released under an open-source license (MIT license) and is freely available at http://bioinformatics.org/assemble. It is implemented in the Java language and runs on MacOSX, Linux and Windows operating systems.

Predicting residue-wise contact orders in proteins by support vector regression.

PubMed

Song, Jiangning; Burrage, Kevin

2006-10-03

The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

Lattice-free prediction of three-dimensional structure of programmed DNA assemblies

PubMed Central

Pan, Keyao; Kim, Do-Nyun; Zhang, Fei; Adendorff, Matthew R.; Yan, Hao; Bathe, Mark

2014-01-01

DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science. PMID:25470497

Secondary eyewall formation as a progressive boundary layer response

NASA Astrophysics Data System (ADS)

Abarca, S. F.; Montgomery, M. T.; Bell, M. M.

2012-12-01

The robust observational (satellite based) evidence that secondary eyewalls are common features in major hurricanes contrasts with the scarce in situ observations of the phenomena and its life cycle. This lack of observations has resulted in an incomplete understanding of the dynamics of secondary eyewall formation (SEF). A wide variety of physical processes have been invoked to explain SEF, but only the recently proposed theory of a progressive boundary layer control in SEF has been supported by a variety of full physics mesoscale numerical integrations. The RAINEX field project provided unique observations of the secondary eyewall of Hurricane Rita (2005) both before and during the time Rita exhibited a clear secondary eyewall structure. These observations have contributed to the advancement of the understanding of the secondary eyewall phenomenon. However, in the RAINEX experiment, there was limited data sampling during the development of the secondary wind maxima, thereby precluding a complete observational investigation of the dynamics of SEF. In this presentation we adopt an azimuthally-averaged perspective of the flow dynamics and we test the newly proposed theory of a progressive boundary layer control on SEF. Specifically, we use both RAINEX data as well as data from high resolution, full physics mesoscale numerical simulations to initialize and force an axisymmetric slab boundary layer model with radial diffusion included. The objective is to investigate whether such a reduced boundary layer model can generate secondary wind maxima as a response to environments like those that result in SEF in nature and in full physics simulations.

Algorithm, applications and evaluation for protein comparison by Ramanujan Fourier transform.

PubMed

Zhao, Jian; Wang, Jiasong; Hua, Wei; Ouyang, Pingkai

2015-12-01

The amino acid sequence of a protein determines its chemical properties, chain conformation and biological functions. Protein sequence comparison is of great importance to identify similarities of protein structures and infer their functions. Many properties of a protein correspond to the low-frequency signals within the sequence. Low frequency modes in protein sequences are linked to the secondary structures, membrane protein types, and sub-cellular localizations of the proteins. In this paper, we present Ramanujan Fourier transform (RFT) with a fast algorithm to analyze the low-frequency signals of protein sequences. The RFT method is applied to similarity analysis of protein sequences with the Resonant Recognition Model (RRM). The results show that the proposed fast RFT method on protein comparison is more efficient than commonly used discrete Fourier transform (DFT). RFT can detect common frequencies as significant feature for specific protein families, and the RFT spectrum heat-map of protein sequences demonstrates the information conservation in the sequence comparison. The proposed method offers a new tool for pattern recognition, feature extraction and structural analysis on protein sequences. Copyright © 2015 Elsevier Ltd. All rights reserved.

Force field-dependent structural divergence revealed during long time simulations of Calbindin d9k.

PubMed

Project, Elad; Nachliel, Esther; Gutman, Menachem

2010-07-15

The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S(2) order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison with experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data. Copyright 2009 Wiley Periodicals, Inc.

Orientale and Caloris. [lunar basins with similar structural features

NASA Technical Reports Server (NTRS)

Mccauley, J. F.

1977-01-01

Based on revised stratigraphy, structural interpretation, explosion-crater data, and a genetic model for Orientale, it is suggested that Orientale and Caloris have much in common. It is noted that: (1) although the basin fill in Caloris is different from that seen in Orientale, the materials between the most prominent scarp and the weakly-developed outer scarp may be degraded equivalents of the massifs and knobs associated with the Montes Rook, (2) the Montes Rook and the main Caloris scarp have similar stratigraphic and structural features, (3) the lineated ejecta derived from shallower horizons are found near and beyond the weakly-developed outer Caloris scarp which is the counterpart of the Orientale scarp, (4) a well developed field of secondary craters is observed beyond 1 basin diameter at Caloris, (5) the observed textural differences between the material around the main Caloris scarp and the lineated material beyond suggest that Mercury is layered and that Caloris crater excavated coherent materials from one or more of these layers at depth, and (6) the difference in spacing between the Caloris rings is not related to internal layering effects.

Neuropathy secondary to drugs

MedlinePlus

... drugs URL of this page: //medlineplus.gov/ency/article/000700.htm Neuropathy secondary to drugs To use the sharing features on this page, please enable JavaScript. Neuropathy secondary to drugs is a loss of ...

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.

PubMed

Bosi, Emanuele; Fondi, Marco; Orlandini, Valerio; Perrin, Elena; Maida, Isabel; de Pascale, Donatella; Tutino, Maria Luisa; Parrilli, Ermenegilda; Lo Giudice, Angelina; Filloux, Alain; Fani, Renato

2017-01-17

Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.

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Science.gov Websites

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Structural control on geothermal circulation in the Cerro Tuzgle-Tocomar geothermal volcanic area (Puna plateau, Argentina)

NASA Astrophysics Data System (ADS)

Giordano, Guido; Pinton, Annamaria; Cianfarra, Paola; Baez, Walter; Chiodi, Agostina; Viramonte, José; Norini, Gianluca; Groppelli, Gianluca

2013-01-01

The reconstruction of the stratigraphical-structural framework and the hydrogeology of geothermal areas is fundamental for understanding the relationships between cap rocks, reservoir and circulation of geothermal fluids and for planning the exploitation of the field. The Cerro Tuzgle-Tocomar geothermal volcanic area (Puna plateau, Central Andes, NW Argentina) has a high geothermal potential. It is crossed by the active NW-SE trans-Andean tectonic lineament known as the Calama-Olacapato-Toro (COT) fault system, which favours a high secondary permeability testified by the presence of numerous springs. This study presents new stratigraphic and hydrogeological data on the geothermal field, together with the analysis from remote sensed image analysis of morphostructural evidences associated with the structural framework and active tectonics. Our data suggest that the main geothermal reservoir is located within or below the Pre-Palaeozoic-Ordovician basement units, characterised by unevenly distributed secondary permeability. The reservoir is recharged by infiltration in the ridges above 4500 m a.s.l., where basement rocks are in outcrop. Below 4500 m a.s.l., the reservoir is covered by the low permeable Miocene-Quaternary units that allow a poor circulation of shallow groundwater. Geothermal fluids upwell in areas with more intense fracturing, especially where main regional structures, particularly NW-SE COT-parallel lineaments, intersect with secondary structures, such as at the Tocomar field. Away from the main tectonic features, such as at the Cerro Tuzgle field, the less developed network of faults and fractures allows only a moderate upwelling of geothermal fluids and a mixing between hot and shallow cold waters. The integration of field-based and remote-sensing analyses at the Cerro Tuzgle-Tocomar area proved to be effective in approaching the prospection of remote geothermal fields, and in defining the conceptual model for geothermal circulation.

Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks

PubMed Central

Aguirre, Jacobo; Buldú, Javier M.; Stich, Michael; Manrubia, Susanna C.

2011-01-01

The evolution and adaptation of molecular populations is constrained by the diversity accessible through mutational processes. RNA is a paradigmatic example of biopolymer where genotype (sequence) and phenotype (approximated by the secondary structure fold) are identified in a single molecule. The extreme redundancy of the genotype-phenotype map leads to large ensembles of RNA sequences that fold into the same secondary structure and can be connected through single-point mutations. These ensembles define neutral networks of phenotypes in sequence space. Here we analyze the topological properties of neutral networks formed by 12-nucleotides RNA sequences, obtained through the exhaustive folding of sequence space. A total of 412 sequences fragments into 645 subnetworks that correspond to 57 different secondary structures. The topological analysis reveals that each subnetwork is far from being random: it has a degree distribution with a well-defined average and a small dispersion, a high clustering coefficient, and an average shortest path between nodes close to its minimum possible value, i.e. the Hamming distance between sequences. RNA neutral networks are assortative due to the correlation in the composition of neighboring sequences, a feature that together with the symmetries inherent to the folding process explains the existence of communities. Several topological relationships can be analytically derived attending to structural restrictions and generic properties of the folding process. The average degree of these phenotypic networks grows logarithmically with their size, such that abundant phenotypes have the additional advantage of being more robust to mutations. This property prevents fragmentation of neutral networks and thus enhances the navigability of sequence space. In summary, RNA neutral networks show unique topological properties, unknown to other networks previously described. PMID:22028856

Design and commission of an experimental test rig to apply a full-scale pressure load on composite sandwich panels representative of an aircraft secondary structure

NASA Astrophysics Data System (ADS)

Crump, D. A.; Dulieu-Barton, J. M.; Savage, J.

2010-01-01

This paper describes the design of a test rig, which is used to apply a representative pressure load to a full-scale composite sandwich secondary aircraft structure. A generic panel was designed with features to represent those in the composite sandwich secondary aircraft structure. To provide full-field strain data from the panels, the test rig was designed for use with optical measurement techniques such as thermoelastic stress analysis (TSA) and digital image correlation (DIC). TSA requires a cyclic load to be applied to a structure for the measurement of the strain state; therefore, the test rig has been designed to be mounted on a standard servo-hydraulic test machine. As both TSA and DIC require an uninterrupted view of the surface of the test panel, an important consideration in the design is facilitating the optical access for the two techniques. To aid the test rig design a finite element (FE) model was produced. The model provides information on the deflections that must be accommodated by the test rig, and ensures that the stress and strain levels developed in the panel when loaded in the test rig would be sufficient for measurement using TSA and DIC. Finally, initial tests using the test rig have shown it to be capable of achieving the required pressure and maintaining a cyclic load. It was also demonstrated that both TSA and DIC data can be collected from the panels under load, which are used to validate the stress and deflection derived from the FE model.

Infrared spectroscopy of dense clouds in the C-H stretch region - Methanol and 'diamonds'

NASA Technical Reports Server (NTRS)

Allamandola, L. J.; Sandford, S. A.; Tielens, A. G. G. M.; Herbst, T. M.

1992-01-01

The paper presents high spectral resolution studies in the 3100-2600/cm range of the protostars NGC 7538 IRS9, W33A, W3 IRS 5, and S140 IRS 1. Well-resolved absorption bands at about 2825/cm and 2880/cm were found superposed on the LF wing of the strong O-H stretch feature. The 2880/cm band, previously detected toward W33A, is also in the spectrum of NGC 7538 IRS 9. The relative strength of these two bands varies, showing that they are associated with two different carriers. The new band at about 2880/cm falls near the position of C-H stretching vibrations in tertiary carbon atoms. The strength of this feature, in combination with the lack of strong features associated with primary and secondary carbon atoms, suggests that the carrier of the new feature has a diamondlike structure. This new feature is tentatively attributed to interstellar 'diamonds'. The detection of this band in the spectra of all four dense molecular clouds suggests that the carrier is ubiquitous in dense clouds.

Search for Past Life on Mars: Possible Relict Biogenic Activity in Martian Meteorite ALH84001

NASA Technical Reports Server (NTRS)

McKay, David S.; Gibson, Everett K., Jr.; Thomas-Keprta, Kathie L.; Vali, Hojatollah; Romanek, Christopher S.; Clemett, Simon J.; Chillier, Xavier D. F.; Maechling, Claude R.; Zare, Richard N.

1996-01-01

Fresh fracture surfaces of the martian meteorite ALH84001 contain abundant polycyclic aromatic hydrocarbons (PAHs). These fresh fracture surfaces also display carbonate globules. Contamination studies suggest the PAHs are indigenous to the meteorite. High resolution scanning and transmission electron microscopy study of surface textures and internal structures of selected carbonate globules show that the globules contain fine-grained, secondary phases of single-domain magnetite and Fe-monosulfides. The carbonate globules are similar in texture and size to some terrestrial bacterially induced carbonate precipitates. Although inorganic formation is possible, formation of the globules by biogenic processes could explain many of the observed features including the PAHs. The PAHs, the carbonate globules, and their associated secondary mineral phases and textures could thus be fossil remains of a past martian biota.

SOV_refine: A further refined definition of segment overlap score and its significance for protein structure similarity.

PubMed

Liu, Tong; Wang, Zheng

2018-01-01

The segment overlap score (SOV) has been used to evaluate the predicted protein secondary structures, a sequence composed of helix (H), strand (E), and coil (C), by comparing it with the native or reference secondary structures, another sequence of H, E, and C. SOV's advantage is that it can consider the size of continuous overlapping segments and assign extra allowance to longer continuous overlapping segments instead of only judging from the percentage of overlapping individual positions as Q3 score does. However, we have found a drawback from its previous definition, that is, it cannot ensure increasing allowance assignment when more residues in a segment are further predicted accurately. A new way of assigning allowance has been designed, which keeps all the advantages of the previous SOV score definitions and ensures that the amount of allowance assigned is incremental when more elements in a segment are predicted accurately. Furthermore, our improved SOV has achieved a higher correlation with the quality of protein models measured by GDT-TS score and TM-score, indicating its better abilities to evaluate tertiary structure quality at the secondary structure level. We analyzed the statistical significance of SOV scores and found the threshold values for distinguishing two protein structures (SOV_refine  > 0.19) and indicating whether two proteins are under the same CATH fold (SOV_refine > 0.94 and > 0.90 for three- and eight-state secondary structures respectively). We provided another two example applications, which are when used as a machine learning feature for protein model quality assessment and comparing different definitions of topologically associating domains. We proved that our newly defined SOV score resulted in better performance. The SOV score can be widely used in bioinformatics research and other fields that need to compare two sequences of letters in which continuous segments have important meanings. We also generalized the previous SOV definitions so that it can work for sequences composed of more than three states (e.g., it can work for the eight-state definition of protein secondary structures). A standalone software package has been implemented in Perl with source code released. The software can be downloaded from http://dna.cs.miami.edu/SOV/.

Insight on the Peruvian Amazon River: A Planform Metric Characterization of its Morphodynamics

NASA Astrophysics Data System (ADS)

Garcia, A. M. P.; Ortals, C.; Frias, C. E.; Abad, J. D.; Vizcarra, J.

2014-12-01

Starting in Peru, the Amazon River flows through Colombia and Brazil; additionally, tributaries from Bolivia, Venezuela, and Ecuador contribute to the massive river and its unique geomorphic features. Accordingly, the Amazon Basin has become an important aspect of South America; it is an area of extraordinary biodiversity, rich resources, and unique cultures. However, due to the sheer magnitude and exceptionality of the Amazon River, research regarding the morphodynamic processes that shape and define the river has been difficult. Consequently, current research has not completely understood the planform dynamics of some portions of this river that present a main channel and secondary channels known as "anabranching structures". The purpose of this research was to gain an understanding of the geomorphology of the upper Amazon, the Peruvian section, by obtaining migration rates and planform metrics, including channel count, length, width, and sinuosity, as well as island count, area, and shape. With this data, the morphodynamics of the Peruvian Amazon, especially the relationship between the main channel and its secondary channels in each "anabranching structure" along the river, could be analyzed according to correlations found between various metrics. This analysis was carried out for 5-year time spans over a period of 25 years. Preliminary results showed that the average migration rate versus channel bend radius envelope peak is lower for the secondary channels than for the main channel. However, the maximum migration rate was not always found in the main channel; for several structures, the most dynamic channels were the secondary ones. This implies a certain periodicity to the river's migratory patterns that could be related to the valley boundaries, the local channel sinuosity or geological formations in the study area.

The Crab pulsar light curve in the soft gamma ray range: FIGARO II results

NASA Technical Reports Server (NTRS)

Massaro, E.; Agrinier, B.; Barouch, E.; Comte, R.; Costa, E.; Cusumano, G. C.; Gerardi, G.; Lemoine, D.; Mandrou, P.; Masnou, J. L.

1992-01-01

The FIGARO II experiment (a large area, balloon borne, crystal scintillator detector working from 0.15 to 4.3 MeV) observed the Crab pulsar on 1990 Jul. 9 for about seven hours. The study of the pulse profile confirms some structures detected with a low significance during the shorter observation of 1986, and adds new important elements to the picture. In particular, between the two main peaks, two secondary peaks appear centered at phase values 0.1 and 0.3, in the energy range 0.38 to 0.49 MeV; in the same energy range, a spectral feature at 0.44 MeV, interpreted as a redshifted positron annihilation line, was observed during the same balloon flight in the phase interval including the second main peak and the neighboring secondary peak. If the phase interval considered is extended to include also the other secondary peak, the significance of the spectral line appears to increase.

Hallerman-Streiff-like syndrome presenting with laterality and cardiac defects.

PubMed

Morice-Picard, Fanny; Marlin, Sandrine; Rooryck, Caroline; Fayon, Mickael; Thambo, Jeao-Benoît; Demarquez, Jean-Louis; Fauroux, Brigitte; Denoyelle, Francoise; Lacombe, Didier

2009-04-01

We report two patients considered to have an atypical presentation of Hallerman-Streiff syndrome (HSS) associated with laterality and cardiac defects. Clinical features include typical facial gestalt, atrophy of the skin, and hypotrichosis. Ophthalmologic abnormalities, normally present in HSS, are only found in one of the two patients. Both of them have respiratory problems secondary to the classical narrow upper airway described in this syndrome. Both these patients have laterality defects and one has additional structural cardiac malformations. Cardiac defects have occasionally been reported in the HSS literature, but are not considered as a classical feature of the syndrome. Situs inversus has never been reported in this syndrome. Almost all HSS cases have been sporadic and their origin and inheritance pattern remain unknown.

A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc03464d

PubMed Central

Zheng, Xueyun; Aly, Noor A.; Zhou, Yuxuan; Dupuis, Kevin T.; Bilbao, Aivett; Paurus, Vanessa L.; Orton, Daniel J.; Wilson, Ryan; Payne, Samuel H.; Smith, Richard D.

2017-01-01

The confident identification of metabolites and xenobiotics in biological and environmental studies is an analytical challenge due to their immense dynamic range, vast chemical space and structural diversity. Ion mobility spectrometry (IMS) is widely used for small molecule analyses since it can separate isomeric species and be easily coupled with front end separations and mass spectrometry for multidimensional characterizations. However, to date IMS metabolomic and exposomic studies have been limited by an inadequate number of accurate collision cross section (CCS) values for small molecules, causing features to be detected but not confidently identified. In this work, we utilized drift tube IMS (DTIMS) to directly measure CCS values for over 500 small molecules including primary metabolites, secondary metabolites and xenobiotics. Since DTIMS measurements do not need calibrant ions or calibration like some other IMS techniques, they avoid calibration errors which can cause problems in distinguishing structurally similar molecules. All measurements were performed in triplicate in both positive and negative polarities with nitrogen gas and seven different electric fields, so that relative standard deviations (RSD) could be assessed for each molecule and structural differences studied. The primary metabolites analyzed to date have come from key metabolism pathways such as glycolysis, the pentose phosphate pathway and the tricarboxylic acid cycle, while the secondary metabolites consisted of classes such as terpenes and flavonoids, and the xenobiotics represented a range of molecules from antibiotics to polycyclic aromatic hydrocarbons. Different CCS trends were observed for several of the diverse small molecule classes and when urine features were matched to the database, the addition of the IMS dimension greatly reduced the possible number of candidate molecules. This CCS database and structural information are freely available for download at http://panomics.pnnl.gov/metabolites/ with new molecules being added frequently. PMID:29568436

Cellulose synthase complexes act in a concerted fashion to synthesize highly aggregated cellulose in secondary cell walls of plants

PubMed Central

Li, Shundai; Bashline, Logan; Zheng, Yunzhen; Xin, Xiaoran; Huang, Shixin; Kong, Zhaosheng; Kim, Seong H.; Cosgrove, Daniel J.; Gu, Ying

2016-01-01

Cellulose, often touted as the most abundant biopolymer on Earth, is a critical component of the plant cell wall and is synthesized by plasma membrane-spanning cellulose synthase (CESA) enzymes, which in plants are organized into rosette-like CESA complexes (CSCs). Plants construct two types of cell walls, primary cell walls (PCWs) and secondary cell walls (SCWs), which differ in composition, structure, and purpose. Cellulose in PCWs and SCWs is chemically identical but has different physical characteristics. During PCW synthesis, multiple dispersed CSCs move along a shared linear track in opposing directions while synthesizing cellulose microfibrils with low aggregation. In contrast, during SCW synthesis, we observed swaths of densely arranged CSCs that moved in the same direction along tracks while synthesizing cellulose microfibrils that became highly aggregated. Our data support a model in which distinct spatiotemporal features of active CSCs during PCW and SCW synthesis contribute to the formation of cellulose with distinct structure and organization in PCWs and SCWs of Arabidopsis thaliana. This study provides a foundation for understanding differences in the formation, structure, and organization of cellulose in PCWs and SCWs. PMID:27647923

Cellulose synthase complexes act in a concerted fashion to synthesize highly aggregated cellulose in secondary cell walls of plants.

PubMed

Li, Shundai; Bashline, Logan; Zheng, Yunzhen; Xin, Xiaoran; Huang, Shixin; Kong, Zhaosheng; Kim, Seong H; Cosgrove, Daniel J; Gu, Ying

2016-10-04

Cellulose, often touted as the most abundant biopolymer on Earth, is a critical component of the plant cell wall and is synthesized by plasma membrane-spanning cellulose synthase (CESA) enzymes, which in plants are organized into rosette-like CESA complexes (CSCs). Plants construct two types of cell walls, primary cell walls (PCWs) and secondary cell walls (SCWs), which differ in composition, structure, and purpose. Cellulose in PCWs and SCWs is chemically identical but has different physical characteristics. During PCW synthesis, multiple dispersed CSCs move along a shared linear track in opposing directions while synthesizing cellulose microfibrils with low aggregation. In contrast, during SCW synthesis, we observed swaths of densely arranged CSCs that moved in the same direction along tracks while synthesizing cellulose microfibrils that became highly aggregated. Our data support a model in which distinct spatiotemporal features of active CSCs during PCW and SCW synthesis contribute to the formation of cellulose with distinct structure and organization in PCWs and SCWs of Arabidopsis thaliana This study provides a foundation for understanding differences in the formation, structure, and organization of cellulose in PCWs and SCWs.

Seismic constraints and coulomb stress changes of a blind thrust fault system, 2: Northridge, California

USGS Publications Warehouse

Stein, Ross S.; Lin, Jian

2006-01-01

We review seismicity, surface faulting, and Coulomb stress changes associated with the 1994 Northridge, California, earthquake. All of the observed surface faulting is shallow, extending meters to tens of meters below the surface. Relocated aftershocks reveal no seismicity shallower than 2 km depth. Although many of the aftershocks lie along the thrust fault and its up-dip extension, there are also a significant number of aftershocks in the core of the gentle anticline above the thrust, and elsewhere on the up-thrown block. These aftershocks may be associated with secondary ramp thrusts or flexural slip faults at a depth of 2-4 km. The geological structures typically associated with a blind thrust fault, such as anticlinal uplift and an associated syncline, are obscured and complicated by surface thrust faults associated with the San Fernando fault that overly the Northridge structures. Thus the relationship of the geological structure and topography to the underlying thrust fault is much more complex for Northridge than it is for the 1983 Coalinga, California, earthquake. We show from a Coulomb stress analysis that secondary surface faulting, diffuse aftershocks, and triggered sequences of moderate-sized mainshocks, are expected features of moderate-sized blind thrust earthquakes.

Influence of the microstructure on the physicomechanical properties of the aluminum alloy Al-Mg-Si nanostructured under severe plastic deformation

NASA Astrophysics Data System (ADS)

Mavlyutov, A. M.; Kasatkin, I. A.; Murashkin, M. Yu.; Valiev, R. Z.; Orlova, T. S.

2015-10-01

The microstructural features, strength, and electrical conductivity of the electrotechnical aluminum alloy 6201 of the Al-Mg-Si system was investigated. The alloy was nanostructured using severe plastic deformation by high pressure torsion at different temperatures and in different deformation regimes. As a result, the samples had an ultrafine-grain structure with nanoinclusions of secondary phases, which provided an excellent combination of high strength (conventional yield strength σ0.2 = 325-410 MPa) and electrical conductivity (55-52% IACS). The contributions from different mechanisms to the strengthening were analyzed. It was experimentally found that the introduction of an additional dislocation density (an increase from 2 × 1013 to 5 × 1013 m-2) with the same basic parameters of the ultrafine-grain structure (grain size, size and distribution of particles of secondary strengthening phases) leads to an increase in the strength of the alloy by ~15%, while the electrical conductivity of the material changes insignificantly. The contribution from grain boundaries to the electrical resistivity of the alloy with an ultrafine-grain structure upon the change in their state, most likely, due to a change in the degree of nonequilibrium was estimated.

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo.

PubMed

Zubradt, Meghan; Gupta, Paromita; Persad, Sitara; Lambowitz, Alan M; Weissman, Jonathan S; Rouskin, Silvi

2017-01-01

Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase. DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low-abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in noncanonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs with their mature isoforms. These applications illustrate DMS-MaPseq's capacity to dramatically expand in vivo analysis of RNA structure.

Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM.

PubMed

Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

2015-01-01

Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM). Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS), segmented PsePSSM, and segmented autocovariance transformation (ACT) based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640) are adopted in this paper. Then a 700-dimensional (700D) feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA). To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences.

Fine structural features of nanoscale zero-valent iron characterized by spherical aberration corrected scanning transmission electron microscopy (Cs-STEM).

PubMed

Liu, Airong; Zhang, Wei-xian

2014-09-21

An angstrom-resolution physical model of nanoscale zero-valent iron (nZVI) is generated with a combination of spherical aberration corrected scanning transmission electron microscopy (Cs-STEM), selected area electron diffraction (SAED), energy-dispersive X-ray spectroscopy (EDS) and electron energy-loss spectroscopy (EELS) on the Fe L-edge. Bright-field (BF), high-angle annular dark-field (HAADF) and secondary electron (SE) imaging of nZVI acquired by a Hitachi HD-2700 STEM show near atomic resolution images and detailed morphological and structural information of nZVI. The STEM-EDS technique confirms that the fresh nZVI comprises of a metallic iron core encapsulated with a thin layer of iron oxides or oxyhydroxides. SAED patterns of the Fe core suggest the polycrystalline structure in the metallic core and amorphous nature of the oxide layer. Furthermore, Fe L-edge of EELS shows varied structural features from the innermost Fe core to the outer oxide shell. A qualitative analysis of the Fe L(2,3) edge fine structures reveals that the shell of nZVI consists of a mixed Fe(II)/Fe(III) phase close to the Fe (0) interface and a predominantly Fe(III) at the outer surface of nZVI.

The Inclusion of Chitosan in Poly-ε-caprolactone Nanoparticles: Impact on the Delivery System Characteristics and on the Adsorbed Ovalbumin Secondary Structure.

PubMed

Jesus, Sandra; Fragal, Elizangela H; Rubira, Adley F; Muniz, Edvani C; Valente, Artur J M; Borges, Olga

2018-01-01

This report extensively explores the benefits of including chitosan into poly-ε-caprolactone (PCL) nanoparticles (NPs) to obtain an improved protein/antigen delivery system. Blend NPs (PCL/chitosan NPs) showed improved protein adsorption efficacy (84%) in low shear stress and aqueous environment, suggesting that a synergistic effect between PCL hydrophobic nature and the positive charges of chitosan present at the particle surface was responsible for protein interaction. Additionally, thermal analysis suggested the blend NPs were more stable than the isolated polymers and cytotoxicity assays in a primary cell culture revealed chitosan inclusion in PCL NPs reduced the toxicity of the delivery system. A quantitative 6-month stability study showed that the inclusion of chitosan in PCL NPs did not induce a change in adsorbed ovalbumin (OVA) secondary structure characterized by the increase in the unordered conformation (random coil), as it was observed for OVA adsorbed to chitosan NPs. Additionally, the slight conformational changes occurred, are not expected to compromise ovalbumin secondary structure and activity, during a 6-month storage even at high temperatures (45°C). In simulated biological fluids, PCL/chitosan NPs showed an advantageous release profile for oral delivery. Overall, the combination of PCL and chitosan characteristics provide PCL/chitosan NPs valuable features particularly important to the development of vaccines for developing countries, where it is difficult to ensure cold chain transportation and non-parenteral formulations would be preferred.

Root development and structure in seedlings of Ginkgo biloba.

PubMed

Bonacorsi, Nikole K; Seago, James L

2016-02-01

The popular, highly recognizable, well-known gymnosperm, Ginkgo biloba, was studied to document selected developmental features, which are little known in its primary root system from root tips to cotyledonary node following seed germination. Using seedlings grown in soil, vermiculite, or a mixture, we examined sections at various distances from the root cap to capture a developmental sequence of anatomical structures by using standard brightfield, epifluorescence, and confocal microscopic techniques. The vascular cylinder is usually a diarch stele, although modified diarchy and triarchy are found. Between exarch protoxylem poles, metaxylem usually develops into a complete disc, except near the transition region, which has irregularly arranged tracheary cells. The disc of primary xylem undergoes secondary growth on its metaxylem flanks with many tracheids added radially within a few weeks. Production of fibers in secondary phloem also accompanies secondary growth. In the cortex, endodermis produces Casparian bands early in development and continues into the upper transition region. Phi cells with phi-thickenings (bands of lignified walls) of a layer of inner cortex are often evident before endodermis, and then adjoining, additional layers of cortex develop phi cells; phi cells do not occur in the upper transition region or stem. An exodermis is produced early in root development and is continuous into the transition region and cotyledonary node. Seedling root axes of Ginkgo biloba are more complex than the literature suggests, and our findings contribute to our knowledge of root structure of this ancient gymnosperm. © 2016 Botanical Society of America.

Rose spring dwarf-associated virus has RNA structural and gene-expression features like those of Barley yellow dwarf virus

PubMed Central

Salem, Nida’ M.; Miller, W. Allen; Rowhani, Adib; Golino, Deborah A.; Moyne, Anne-Laure; Falk, Bryce W.

2015-01-01

We determined the complete nucleotide sequence of the Rose spring dwarf-associated virus (RSDaV) genomic RNA (GenBank accession no. EU024678) and compared its predicted RNA structural characteristics affecting gene expression. A cDNA library was derived from RSDaV double-stranded RNAs (dsRNAs) purified from infected tissue. Nucleotide sequence analysis of the cloned cDNAs, plus for clones generated by 5′- and 3′-RACE showed the RSDaV genomic RNA to be 5,808 nucleotides. The genomic RNA contains five major open reading frames (ORFs), and three small ORFs in the 3′-terminal 800 nucleotides, typical for viruses of genus Luteovirus in the family Luteoviridae. Northern blot hybridization analysis revealed the genomic RNA and two prominent subgenomic RNAs of approximately 3 kb and 1 kb. Putative 5′ ends of the sgRNAs were predicted by identification of conserved sequences and secondary structures which resembled the Barley yellow dwarf virus (BYDV) genomic RNA 5′ end and subgenomic RNA promoter sequences. Secondary structures of the BYDV-like ribosomal frameshift elements and cap-independent translation elements, including long-distance base pairing spanning four kb were identified. These contain similarities but also informative differences with the BYDV structures, including a strikingly different structure predicted for the 3′ cap-independent translation element. These analyses of the RSDaV genomic RNA show more complexity for the RNA structural elements for members of the Luteoviridae. PMID:18329064

Rose spring dwarf-associated virus has RNA structural and gene-expression features like those of Barley yellow dwarf virus.

PubMed

Salem, Nida' M; Miller, W Allen; Rowhani, Adib; Golino, Deborah A; Moyne, Anne-Laure; Falk, Bryce W

2008-06-05

We determined the complete nucleotide sequence of the Rose spring dwarf-associated virus (RSDaV) genomic RNA (GenBank accession no. EU024678) and compared its predicted RNA structural characteristics affecting gene expression. A cDNA library was derived from RSDaV double-stranded RNAs (dsRNAs) purified from infected tissue. Nucleotide sequence analysis of the cloned cDNAs, plus for clones generated by 5'- and 3'-RACE showed the RSDaV genomic RNA to be 5808 nucleotides. The genomic RNA contains five major open reading frames (ORFs), and three small ORFs in the 3'-terminal 800 nucleotides, typical for viruses of genus Luteovirus in the family Luteoviridae. Northern blot hybridization analysis revealed the genomic RNA and two prominent subgenomic RNAs of approximately 3 kb and 1 kb. Putative 5' ends of the sgRNAs were predicted by identification of conserved sequences and secondary structures which resembled the Barley yellow dwarf virus (BYDV) genomic RNA 5' end and subgenomic RNA promoter sequences. Secondary structures of the BYDV-like ribosomal frameshift elements and cap-independent translation elements, including long-distance base pairing spanning four kb were identified. These contain similarities but also informative differences with the BYDV structures, including a strikingly different structure predicted for the 3' cap-independent translation element. These analyses of the RSDaV genomic RNA show more complexity for the RNA structural elements for members of the Luteoviridae.

Structure of a fungal form of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans

PubMed Central

Dahal, Gopal; Viola, Ronald E.

2015-01-01

Aspartate semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate-biosynthetic pathway and represents a valid target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β-aspartyl phosphate to produce the key intermediate aspartate semialdehyde. Production of this intermediate represents the first committed step in the biosynthesis of the essential amino acids methionine, isoleucine and threonine in fungi, and also the amino acid lysine in bacteria. The structure of a new fungal form of ASADH from Cryptococcus neoformans has been determined to 2.6 Å resolution. The overall structure of CnASADH is similar to those of its bacterial orthologs, but with some critical differences both in biological assembly and in secondary-structural features that can potentially be exploited for the development of species-selective drugs. PMID:26527262

Propriospinal myoclonus

PubMed Central

van der Salm, Sandra M.A.; Erro, Roberto; Cordivari, Carla; Edwards, Mark J.; Koelman, Johannes H.T.M.; van den Ende, Tom; Bhatia, Kailash P.; van Rootselaar, Anne-Fleur; Brown, Peter

2014-01-01

Objective: Propriospinal myoclonus (PSM) is a rare disorder with repetitive, usually flexor arrhythmic brief jerks of the trunk, hips, and knees in a fixed pattern. It has a presumed generation in the spinal cord and diagnosis depends on characteristic features at polymyography. Recently, a historical paradigm shift took place as PSM has been reported to be a functional (or psychogenic) movement disorder (FMD) in most patients. This review aims to characterize the clinical features, etiology, electrophysiologic features, and treatment outcomes of PSM. Methods: Re-evaluation of all published PSM cases and systematic scoring of clinical and electrophysiologic characteristics in all published cases since 1991. Results: Of the 179 identified patients with PSM (55% male), the mean age at onset was 43 years (range 6–88 years). FMD was diagnosed in 104 (58%) cases. In 12 cases (26% of reported secondary cases, 7% of total cases), a structural spinal cord lesion was found. Clonazepam and botulinum toxin may be effective in reducing jerks. Conclusions: FMD is more frequent than previously assumed. Structural lesions reported to underlie PSM are scarce. Based on our clinical experience and the reviewed literature, we recommend polymyography to assess recruitment variability combined with a Bereitschaftspotential recording in all cases. PMID:25305154

MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation.

PubMed

Falconi, M; Oteri, F; Eliseo, T; Cicero, D O; Desideri, A

2008-08-01

The structural dynamics of the DNA binding domains of the human papillomavirus strain 16 and the bovine papillomavirus strain 1, complexed with their DNA targets, has been investigated by modeling, molecular dynamics simulations, and nuclear magnetic resonance analysis. The simulations underline different dynamical features of the protein scaffolds and a different mechanical interaction of the two proteins with DNA. The two protein structures, although very similar, show differences in the relative mobility of secondary structure elements. Protein structural analyses, principal component analysis, and geometrical and energetic DNA analyses indicate that the two transcription factors utilize a different strategy in DNA recognition and deformation. Results show that the protein indirect DNA readout is not only addressable to the DNA molecule flexibility but it is finely tuned by the mechanical and dynamical properties of the protein scaffold involved in the interaction.

Effect of Secondary Doping Using Sorbitol on Structure and Transport Properties of PEDOT-PSS Thin Films

NASA Astrophysics Data System (ADS)

Khasim, Syed; Pasha, Apsar; Roy, Aashish S.; Parveen, Ameena; Badi, Nacer

2017-07-01

Poly(3,4-ethylene dioxythiophene):poly(styrenesulphonate) (PEDOT-PSS) in the recent past has emerged as one of the most fascinating conducting polymers for many device applications. The unique feature of PEDOT-PSS is its transparency in the entire visible spectrum with excellent thermal stability. The PEDOT-PSS as prepared as an aqueous dispersion has very low conductivity, and it hinders the performance of a device. In this work we report the conductivity enhancement of PEDOT-PSS thin films through secondary doping using a polar organic solvent such as sorbitol. The mechanism of conductivity enhancement was studied through various physical and chemical characterizations. The effect of sorbitol concentration on structure and transport properties of PEDOT-PSS thin films was investigated in detail. The structural and morphological modifications in PEDOT-PSS due to the addition of sorbitol was studied through Fourier transform spectroscopy, Ultra Violet-visible spectroscopy, theromogravimetric analysis, scanning electron microscopy and atomic force microscopy. The interactions resulting from conformational changes of PEDOT chains that changes from coiled to linear structure due to the sorbitol treatment significantly improves the conductivity of PEDOT-PSS films. The secondary doping of sorbitol reduces the energy barrier that facilitates the charge carrier hopping leading to enhanced conductivity. We have observed that the conductivity of PEDOT-PSS thin films was increased by two fold due to sorbitol treatment when compared to conductivity of pure PEDOT-PSS. We have carried out detailed analysis of dielectric parameters of sorbitol-treated PEDOT-PSS films and found that sorbitol treatment has a significant effect on various dielectric attributes of PEDOT-PSS films. Hence, secondary doping using sorbitol could be a useful way to effectively tailor the conductivity and dielectric properties of PEDOT-PSS thin films that can be used as flexible electrodes in optoelectronic devices.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

PubMed Central

Hafsa, Noor E.; Arndt, David; Wishart, David S.

2015-01-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

Experimental and computational study of complex shockwave dynamics in laser ablation plumes in argon atmosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harilal, S. S.; Miloshevsky, G. V.; Diwakar, P. K.

2012-08-15

We investigated spatio-temporal evolution of ns laser ablation plumes at atmospheric pressure, a favored condition for laser-induced breakdown spectroscopy and laser-ablation inductively coupled plasma mass-spectrometry. The 1064 nm, 6 ns pulses from a Nd:YAG laser were focused on to an Al target and the generated plasma was allowed to expand in 1 atm Ar. The hydrodynamic expansion features were studied using focused shadowgraphy and gated 2 ns self-emission visible imaging. Shadowgram images showed material ejection and generation of shock fronts. A secondary shock is observed behind the primary shock during the time window of 100-500 ns with instabilities near themore » laser cone angle. By comparing the self-emission images obtained using fast photography, it is concluded that the secondary shocks observed in the shadowgraphy were generated by fast moving target material. The plume front estimates using fast photography exhibited reasonable agreement with data obtained from shadowgraphy at early times {<=}400 ns. However, at later times, fast photography images showed plume confinement while the shadowgraphic images showed propagation of the plume front even at greater times. The structure and dynamics of the plume obtained from optical diagnostic tools were compared to numerical simulations. We have shown that the main features of plume expansion in ambient Ar observed in the experiments can be reproduced using a continuum hydrodynamics model which provided valuable insight into the expansion dynamics and shock structure of the plasma plume.« less

The characterization of Cr secondary oxide phases in ZnO films studied by X-ray spectroscopy and photoemission spectroscopy

NASA Astrophysics Data System (ADS)

Chiou, J. W.; Chang, S. Y.; Huang, W. H.; Chen, Y. T.; Hsu, C. W.; Hu, Y. M.; Chen, J. M.; Chen, C.-H.; Kumar, K.; Guo, J.-H.

2011-03-01

X-ray absorption near-edge structure (XANES), X-ray emission spectroscopy (XES), and X-ray photoemission spectroscopy (XPS) were used to characterize the Cr secondary oxide phases in ZnO films that had been prepared using a co-sputtering method. Analysis of the Cr L3,2-edge XANES spectra reveals that the intensity of white-line features decreases subtly as the sputtering power increases, indicating that the occupation of Cr 3 d orbitals increases with Cr concentration in (Zn, Cr)O films. The O K-edge spectra show that the intensity of XANES features of (Zn, Cr)O films is lower than those of ZnO film, suggesting enhanced occupation of O 2 p-derived states through O 2 p-Cr 3 d hybridization. The XES and XPS spectra indicate that the line shapes in the valence band of (Zn, Cr)O films are quite different from those of ZnO and that the Cr 2O 3 phase dominates the spinel structure of (Zn, Cr)O films increasingly as the Cr sputtering power is increased. Over all results suggest that the non-ferromagnetic behavior of (Zn, Cr)O films can be attributed to the dominant presence of Cr 2O 3, whereas the bulk comprise phase segregations of Cr 2O 3 and/or ZnCr 2O 4, which results them the most stable TM-doped ZnO material against etching.

Secondary psychoses: an update

PubMed Central

Keshavan, Matcheri S; Kaneko, Yoshio

2013-01-01

Psychotic disorders due to a known medical illness or substance use are collectively termed secondary psychoses. In this paper, we first review the historic evolution of the concept of secondary versus primary psychosis and how this distinction supplanted the earlier misleading classification of psychoses into organic and functional. We then outline the clinical features and approach to the diagnosis of secondary psychotic disorders. Features such as atypical presentation, temporal relation to detectable medical cause, evidence of direct physiological causal relationship to the etiological agent, and the absence of evidence of a primary psychotic illness that may better explain the presentation suggest consideration of a secondary psychosis. Finally, we discuss how careful studies of secondary psychotic disorders can help elucidate the pathophysiology of primary, or idiopathic, psychotic disorders such as schizophrenia. We illustrate this issue through a discussion of three secondary psychotic disorders — psychoses associated with temporal lobe epilepsy, velocardiofacial syndrome, and N-methyl D-aspartate (NMDA) receptor encephalitis — that can, respectively, provide neuroanatomical, genetic, and neurochemical models of schizophrenia pathogenesis. PMID:23471787

Marine Microbial Secondary Metabolites: Pathways, Evolution and Physiological Roles.

PubMed

Giordano, Daniela; Coppola, Daniela; Russo, Roberta; Denaro, Renata; Giuliano, Laura; Lauro, Federico M; di Prisco, Guido; Verde, Cinzia

2015-01-01

Microbes produce a huge array of secondary metabolites endowed with important ecological functions. These molecules, which can be catalogued as natural products, have long been exploited in medical fields as antibiotics, anticancer and anti-infective agents. Recent years have seen considerable advances in elucidating natural-product biosynthesis and many drugs used today are natural products or natural-product derivatives. The major contribution to recent knowledge came from application of genomics to secondary metabolism and was facilitated by all relevant genes being organised in a contiguous DNA segment known as gene cluster. Clustering of genes regulating biosynthesis in bacteria is virtually universal. Modular gene clusters can be mixed and matched during evolution to generate structural diversity in natural products. Biosynthesis of many natural products requires the participation of complex molecular machines known as polyketide synthases and non-ribosomal peptide synthetases. Discovery of new evolutionary links between the polyketide synthase and fatty acid synthase pathways may help to understand the selective advantages that led to evolution of secondary-metabolite biosynthesis within bacteria. Secondary metabolites confer selective advantages, either as antibiotics or by providing a chemical language that allows communication among species, with other organisms and their environment. Herewith, we discuss these aspects focusing on the most clinically relevant bioactive molecules, the thiotemplated modular systems that include polyketide synthases, non-ribosomal peptide synthetases and fatty acid synthases. We begin by describing the evolutionary and physiological role of marine natural products, their structural/functional features, mechanisms of action and biosynthesis, then turn to genomic and metagenomic approaches, highlighting how the growing body of information on microbial natural products can be used to address fundamental problems in environmental evolution and biotechnology. © 2015 Elsevier Ltd. All rights reserved.

Learner Background and the Acquisition of Discourse Features of Korean in the Australian Secondary School Context

ERIC Educational Resources Information Center

Kim, Sun Hee Ok

2012-01-01

This paper explores how learner background shapes learner performance on discourse features in writing by analysing data produced as part of the Student Achievement in Asian Languages Education project (Scarino et al., 2011) by Year 10 (mid-secondary school) students learning Korean as a foreign or heritage language. Five participants were in…

Determination of Secondary Students' Preferences Regarding Design Features Used in Digital Textbooks

ERIC Educational Resources Information Center

Öngöz, Sakine; Mollamehmetoglu, Mehmet Zülküf

2017-01-01

The aim of this study was to determine secondary school students' choice of design features for digital textbooks. As a part of the research--which was conducted using a mixed technique--a literature review was carried out to source points to consider in the designing of digital textbooks and experts' opinions were obtained. Based on the results,…

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

DOE PAGES

Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken; ...

2016-11-29

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic genemore » clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.« less

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic genemore » clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.« less

Monte Carlo modeling of single-molecule cytoplasmic dynein.

PubMed

Singh, Manoranjan P; Mallik, Roop; Gross, Steven P; Yu, Clare C

2005-08-23

Molecular motors are responsible for active transport and organization in the cell, underlying an enormous number of crucial biological processes. Dynein is more complicated in its structure and function than other motors. Recent experiments have found that, unlike other motors, dynein can take different size steps along microtubules depending on load and ATP concentration. We use Monte Carlo simulations to model the molecular motor function of cytoplasmic dynein at the single-molecule level. The theory relates dynein's enzymatic properties to its mechanical force production. Our simulations reproduce the main features of recent single-molecule experiments that found a discrete distribution of dynein step sizes, depending on load and ATP concentration. The model reproduces the large steps found experimentally under high ATP and no load by assuming that the ATP binding affinities at the secondary sites decrease as the number of ATP bound to these sites increases. Additionally, to capture the essential features of the step-size distribution at very low ATP concentration and no load, the ATP hydrolysis of the primary site must be dramatically reduced when none of the secondary sites have ATP bound to them. We make testable predictions that should guide future experiments related to dynein function.

Hard x ray observations of Vela X-1 and A0535+26 with HEXE: Discovery of cyclotron lines

NASA Technical Reports Server (NTRS)

Kendziorra, E.; Mony, B.; Kretschmar, P.; Maisack, M.; Staubert, R.; Doebereiner, S.; Englhauser, J.; Pietsch, W.; Reppin, C.; Truemper, J.

1992-01-01

The X ray pulsars Vela X-1 (4U 0900-40) and A0535+26) were observed with the High Energy X ray Experiment (HEXE) onboard the Mir space station at energies above 20 keV. The pulse profiles of Vela X-1 (P = 283.22 s for JD 244 7486) and A0535+26 (P = 103.27 s for JD 244 7626) were measured up to at least 100 keV. The time averaged pulse profiles of the two sources both show a clear double peak structure with an asymmetric main pulse and a more symmetric secondary pulse. The spectrum of the main pulse is significantly harder than that of the secondary. Pulse phase resolved spectra show absorption features at 54 keV and possibly 27 keV for Vela X-1 and around 100 keV for A0535+26. If these features are interpreted as second and first harmonic (fundamental) cyclotron absorption lines, lower limits are derived of 2.6 x 10(exp 12) and 4.3 x 10(exp 12) Gauss for the magnetic fields of the neutron stars in Vela X-1 and A0535+26, respectively.

COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features.

PubMed

Hu, Long; Xu, Zhiyu; Hu, Boqin; Lu, Zhi John

2017-01-09

Recent genomic studies suggest that novel long non-coding RNAs (lncRNAs) are specifically expressed and far outnumber annotated lncRNA sequences. To identify and characterize novel lncRNAs in RNA sequencing data from new samples, we have developed COME, a coding potential calculation tool based on multiple features. It integrates multiple sequence-derived and experiment-based features using a decompose-compose method, which makes it more accurate and robust than other well-known tools. We also showed that COME was able to substantially improve the consistency of predication results from other coding potential calculators. Moreover, COME annotates and characterizes each predicted lncRNA transcript with multiple lines of supporting evidence, which are not provided by other tools. Remarkably, we found that one subgroup of lncRNAs classified by such supporting features (i.e. conserved local RNA secondary structure) was highly enriched in a well-validated database (lncRNAdb). We further found that the conserved structural domains on lncRNAs had better chance than other RNA regions to interact with RNA binding proteins, based on the recent eCLIP-seq data in human, indicating their potential regulatory roles. Overall, we present COME as an accurate, robust and multiple-feature supported method for the identification and characterization of novel lncRNAs. The software implementation is available at https://github.com/lulab/COME. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Characterization of protein and carbohydrate mid-IR spectral features in crop residues

NASA Astrophysics Data System (ADS)

Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

2014-08-01

To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals.

Characterization of protein and carbohydrate mid-IR spectral features in crop residues.

PubMed

Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

2014-08-14

To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals. Copyright © 2014 Elsevier B.V. All rights reserved.

The structure of people's hair.

PubMed

Yang, Fei-Chi; Zhang, Yuchen; Rheinstädter, Maikel C

2014-01-01

Hair is a filamentous biomaterial consisting mainly of proteins in particular keratin. The structure of human hair is well known: the medulla is a loosely packed, disordered region near the centre of the hair surrounded by the cortex, which contains the major part of the fibre mass, mainly consisting of keratin proteins and structural lipids. The cortex is surrounded by the cuticle, a layer of dead, overlapping cells forming a protective layer around the hair. The corresponding structures have been studied extensively using a variety of different techniques, such as light, electron and atomic force microscopes, and also X-ray diffraction. We were interested in the question how much the molecular hair structure differs from person to person, between male and female hair, hair of different appearances such as colour and waviness. We included hair from parent and child, identical and fraternal twins in the study to see if genetically similar hair would show similar structural features. The molecular structure of the hair samples was studied using high-resolution X-ray diffraction, which covers length scales from molecules up to the organization of secondary structures. Signals due to the coiled-coil phase of α-helical keratin proteins, intermediate keratin filaments in the cortex and from the lipid layers in the cell membrane complex were observed in the specimen of all individuals, with very small deviations. Despite the relatively small number of individuals (12) included in this study, some conclusions can be drawn. While the general features were observed in all individuals and the corresponding molecular structures were almost identical, additional signals were observed in some specimen and assigned to different types of lipids in the cell membrane complex. Genetics seem to play a role in this composition as identical patterns were observed in hair from father and daughter and identical twins, however, not for fraternal twins. Identification and characterization of these features is an important step towards the detection of abnormalities in the molecular structure of hair as a potential diagnostic tool for certain diseases.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

PubMed

Hafsa, Noor E; Arndt, David; Wishart, David S

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The conservation and function of RNA secondary structure in plants

PubMed Central

Vandivier, Lee E.; Anderson, Stephen J.; Foley, Shawn W.; Gregory, Brian D.

2016-01-01

RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts. Here, we review the origins, form, and function of RNA secondary structure, focusing on plants. We then provide an overview of methods for probing secondary structure, from physical methods such as X-ray crystallography and nuclear magnetic resonance imaging (NMR) to chemical and nuclease probing methods. Marriage with high-throughput sequencing has enabled these latter methods to scale across whole transcriptomes, yielding tremendous new insights into the form and function of RNA secondary structure. PMID:26865341

Numerical Simulation of Coronal Waves Interacting with Coronal Holes. III. Dependence on Initial Amplitude of the Incoming Wave

NASA Astrophysics Data System (ADS)

Piantschitsch, Isabell; Vršnak, Bojan; Hanslmeier, Arnold; Lemmerer, Birgit; Veronig, Astrid; Hernandez-Perez, Aaron; Čalogović, Jaša

2018-06-01

We performed 2.5D magnetohydrodynamic (MHD) simulations showing the propagation of fast-mode MHD waves of different initial amplitudes and their interaction with a coronal hole (CH), using our newly developed numerical code. We find that this interaction results in, first, the formation of reflected, traversing, and transmitted waves (collectively, secondary waves) and, second, in the appearance of stationary features at the CH boundary. Moreover, we observe a density depletion that is moving in the opposite direction of the incoming wave. We find a correlation between the initial amplitude of the incoming wave and the amplitudes of the secondary waves as well as the peak values of the stationary features. Additionally, we compare the phase speed of the secondary waves and the lifetime of the stationary features to observations. Both effects obtained in the simulation, the evolution of secondary waves, as well as the formation of stationary fronts at the CH boundary, strongly support the theory that coronal waves are fast-mode MHD waves.

Understanding and Mitigating Tip Leakage and Endwall Losses in High Pressure Ratio Cores

NASA Technical Reports Server (NTRS)

Christophel, Jesse

2015-01-01

Reducing endwall and tip secondary flow losses will be a key enabler for the next generation of commercial and military air transport and will be an improvement on the state-of-the-art in turbine loss reduction strategies. The objective of this research is three-fold: 1) To improve understanding of endwall secondary flow and tip clearance losses 2) To develop novel technologies to mitigate these losses and test them in low-speed cascade and rig environments 3) To validate predictive tools To accomplish these objectives, Pratt & Whitney (P&W) has teamed with Pennsylvania State University (PSU) to experimentally test new features designed by P&W. P&W will create new rim-cavity features to reduce secondary flow loss and improve purge flow cooling effectiveness and new blade tip features to manage leakage flows and reduce tip leakage secondary flow loss. P&W is currently developing technologies in these two areas that expect to be assimilated in the N+2/N+3 generation of commercial engines.

Acute headache diagnosis in pregnant women

PubMed Central

Farmakidis, Constantine; Dayal, Ashlesha K.; Lipton, Richard B.

2015-01-01

Objective: To characterize demographic and clinical features in pregnant women presenting with acute headache, and to identify clinical features associated with secondary headache. Methods: We conducted a 5-year, single-center, retrospective study of consecutive pregnant women presenting to acute care with headache receiving neurologic consultation. Results: The 140 women had a mean age of 29 ± 6.4 years and often presented in the third trimester (56.4%). Diagnoses were divided into primary (65.0%) and secondary (35.0%) disorders. The most common primary headache disorder was migraine (91.2%) and secondary headache disorders were hypertensive disorders (51.0%). The groups were similar in demographics, gestational ages, and most headache features. In univariate analysis, secondary headaches were associated with a lack of headache history (36.7% vs 13.2%, p = 0.0012), seizures (12.2% vs 0.0%, p = 0.0015), elevated blood pressure (55.1% vs 8.8%, p < 0.0001), fever (8.2% vs 0.0%, p = 0.014), and an abnormal neurologic examination (34.7% vs 16.5%, p = 0.014). In multivariate logistic regression, elevated blood pressure (odds ratio [OR] 17.0, 95% confidence interval [CI] 4.2–56.0) and a lack of headache history (OR 4.9, 95% CI 1.7–14.5) had an increased association with secondary headache, while psychiatric comorbidity (OR 0.13, 95% CI 0.021–0.78) and phonophobia (OR 0.29, 95% CI 0.09–0.91) had a reduced association with secondary headache. Conclusions: Among pregnant women receiving inpatient neurologic consultation, more than one-third have secondary headache. Diagnostic vigilance should be heightened in the absence of a headache history and if seizures, hypertension, or fever are present. Attack features may not adequately distinguish primary vs secondary disorders, and low thresholds for neuroimaging and monitoring for preeclampsia are justified. PMID:26291282

Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences

PubMed Central

2016-01-01

X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H–1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions. PMID:28029251

Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains.

PubMed

Bortoluzzi, Alessio; Amato, Anastasia; Lucas, Xavier; Blank, Manuel; Ciulli, Alessio

2017-05-04

The plant homeodomain (PHD) fingers are among the largest family of epigenetic domains, first characterized as readers of methylated H3K4. Readout of histone post-translational modifications by PHDs has been the subject of intense investigation; however, less is known about the recognition of secondary structure features within the histone tail itself. We solved the crystal structure of the PHD finger of the bromodomain adjacent to zinc finger 2A [BAZ2A, also known as TIP5 (TTF-I/interacting protein 5)] in complex with unmodified N-terminal histone H3 tail. The peptide is bound in a helical folded-back conformation after K4, induced by an acidic patch on the protein surface that prevents peptide binding in an extended conformation. Structural bioinformatics analyses identify a conserved Asp/Glu residue that we name 'acidic wall', found to be mutually exclusive with the conserved Trp for K4Me recognition. Neutralization or inversion of the charges at the acidic wall patch in BAZ2A, and homologous BAZ2B, weakened H3 binding. We identify simple mutations on H3 that strikingly enhance or reduce binding, as a result of their stabilization or destabilization of H3 helicity. Our work unravels the structural basis for binding of the helical H3 tail by PHD fingers and suggests that molecular recognition of secondary structure motifs within histone tails could represent an additional layer of regulation in epigenetic processes. © 2017 The Author(s).

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

IMG-ABC. A knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites

DOE PAGES

Hadjithomas, Michalis; Chen, I-Min Amy; Chu, Ken; ...

2015-07-14

In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In this work, we present IMG-ABC (https://img.jgi.doe.gov/abc), an atlas of biosynthetic gene clusters within the Integrated Microbial Genomes (IMG) system, which is aimed at harnessing the power of “big” genomic data for discovering small molecules. IMG-ABC relies on IMG’s comprehensive integrated structural and functional genomic data for the analysis of biosynthetic gene clusters (BCs) and associated secondary metabolites (SMs). SMs and BCs serve asmore » the two main classes of objects in IMG-ABC, each with a rich collection of attributes. A unique feature of IMG-ABC is the incorporation of both experimentally validated and computationally predicted BCs in genomes as well as metagenomes, thus identifying BCs in uncultured populations and rare taxa. We demonstrate the strength of IMG-ABC’s focused integrated analysis tools in enabling the exploration of microbial secondary metabolism on a global scale, through the discovery of phenazine-producing clusters for the first time in lphaproteobacteria. IMG-ABC strives to fill the long-existent void of resources for computational exploration of the secondary metabolism universe; its underlying scalable framework enables traversal of uncovered phylogenetic and chemical structure space, serving as a doorway to a new era in the discovery of novel molecules. IMG-ABC is the largest publicly available database of predicted and experimental biosynthetic gene clusters and the secondary metabolites they produce. The system also includes powerful search and analysis tools that are integrated with IMG’s extensive genomic/metagenomic data and analysis tool kits. As new research on biosynthetic gene clusters and secondary metabolites is published and more genomes are sequenced, IMG-ABC will continue to expand, with the goal of becoming an essential component of any bioinformatic exploration of the secondary metabolism world.« less

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.

PubMed

Utturkar, Sagar M; Klingeman, Dawn M; Hurt, Richard A; Brown, Steven D

2017-01-01

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

Absolute comparison of simulated and experimental protein-folding dynamics

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Nguyen, Houbi; Pande, Vijay S.; Gruebele, Martin

2002-11-01

Protein folding is difficult to simulate with classical molecular dynamics. Secondary structure motifs such as α-helices and β-hairpins can form in 0.1-10µs (ref. 1), whereas small proteins have been shown to fold completely in tens of microseconds. The longest folding simulation to date is a single 1-µs simulation of the villin headpiece; however, such single runs may miss many features of the folding process as it is a heterogeneous reaction involving an ensemble of transition states. Here, we have used a distributed computing implementation to produce tens of thousands of 5-20-ns trajectories (700µs) to simulate mutants of the designed mini-protein BBA5. The fast relaxation dynamics these predict were compared with the results of laser temperature-jump experiments. Our computational predictions are in excellent agreement with the experimentally determined mean folding times and equilibrium constants. The rapid folding of BBA5 is due to the swift formation of secondary structure. The convergence of experimentally and computationally accessible timescales will allow the comparison of absolute quantities characterizing in vitro and in silico (computed) protein folding.

Protein Aggregation/Folding: The Role of Deterministic Singularities of Sequence Hydrophobicity as Determined by Nonlinear Signal Analysis of Acylphosphatase and Aβ(1–40)

PubMed Central

Zbilut, Joseph P.; Colosimo, Alfredo; Conti, Filippo; Colafranceschi, Mauro; Manetti, Cesare; Valerio, MariaCristina; Webber, Charles L.; Giuliani, Alessandro

2003-01-01

The problem of protein folding vs. aggregation was investigated in acylphosphatase and the amyloid protein Aβ(1–40) by means of nonlinear signal analysis of their chain hydrophobicity. Numerical descriptors of recurrence patterns provided the basis for statistical evaluation of folding/aggregation distinctive features. Static and dynamic approaches were used to elucidate conditions coincident with folding vs. aggregation using comparisons with known protein secondary structure classifications, site-directed mutagenesis studies of acylphosphatase, and molecular dynamics simulations of amyloid protein, Aβ(1–40). The results suggest that a feature derived from principal component space characterized by the smoothness of singular, deterministic hydrophobicity patches plays a significant role in the conditions governing protein aggregation. PMID:14645049

Vortices at the magnetic equator generated by hybrid Alfvén resonant waves

NASA Astrophysics Data System (ADS)

Hiraki, Yasutaka

2015-01-01

We performed three-dimensional magnetohydrodynamic simulations of shear Alfvén waves in a full field line system with magnetosphere-ionosphere coupling and plasma non-uniformities. Feedback instability of the Alfvén resonant modes showed various nonlinear features under the field line cavities: (i) a secondary flow shear instability occurs at the magnetic equator, (ii) trapping of the ionospheric Alfvén resonant modes facilitates deformation of field-aligned current structures, and (iii) hybrid Alfvén resonant modes grow to cause vortices and magnetic oscillations around the magnetic equator. Essential features in the initial brightening of auroral arc at substorm onsets could be explained by the dynamics of Alfvén resonant modes, which are the nature of the field line system responding to a background rapid change.

Croup

MedlinePlus

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Rickets

MedlinePlus

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Structural and functional characterization of the protein kinase Mps1 in Arabidopsis thaliana.

PubMed

de Oliveira, Eduardo Alves Gamosa; Romeiro, Nelilma Correia; Ribeiro, Elane da Silva; Santa-Catarina, Claudete; Oliveira, Antônia Elenir Amâncio; Silveira, Vanildo; de Souza Filho, Gonçalo Apolinário; Venancio, Thiago Motta; Cruz, Marco Antônio Lopes

2012-01-01

In eukaryotes, protein kinases catalyze the transfer of a gamma-phosphate from ATP (or GTP) to specific amino acids in protein targets. In plants, protein kinases have been shown to participate in signaling cascades driving responses to environmental stimuli and developmental processes. Plant meristems are undifferentiated tissues that provide the major source of cells that will form organs throughout development. However, non-dividing specialized cells can also dedifferentiate and re-initiate cell division if exposed to appropriate conditions. Mps1 (Monopolar spindle) is a dual-specificity protein kinase that plays a critical role in monitoring the accuracy of chromosome segregation in the mitotic checkpoint mechanism. Although Mps1 functions have been clearly demonstrated in animals and fungi, its role in plants is so far unclear. Here, using structural and biochemical analyses here we show that Mps1 has highly similar homologs in many plant genomes across distinct lineages (e.g. AtMps1 in Arabidopsis thaliana). Several structural features (i.e. catalytic site, DFG motif and threonine triad) are clearly conserved in plant Mps1 kinases. Structural and sequence analysis also suggest that AtMps1 interact with other cell cycle proteins, such as Mad2 and MAPK1. By using a very specific Mps1 inhibitor (SP600125) we show that compromised AtMps1 activity hampers the development of A. thaliana seedlings in a dose-dependent manner, especially in secondary roots. Moreover, concomitant administration of the auxin IAA neutralizes the AtMps1 inhibition phenotype, allowing secondary root development. These observations let us to hypothesize that AtMps1 might be a downstream regulator of IAA signaling in the formation of secondary roots. Our results indicate that Mps1 might be a universal component of the Spindle Assembly Checkpoint machinery across very distant lineages of eukaryotes.

Adaptive expansion of the maize maternally expressed gene (Meg) family involves changes in expression patterns and protein secondary structures of its members

PubMed Central

2014-01-01

Background The Maternally expressed gene (Meg) family is a locally-duplicated gene family of maize which encodes cysteine-rich proteins (CRPs). The founding member of the family, Meg1, is required for normal development of the basal endosperm transfer cell layer (BETL) and is involved in the allocation of maternal nutrients to growing seeds. Despite the important roles of Meg1 in maize seed development, the evolutionary history of the Meg cluster and the activities of the duplicate genes are not understood. Results In maize, the Meg gene cluster resides in a 2.3 Mb-long genomic region that exhibits many features of non-centromeric heterochromatin. Using phylogenetic reconstruction and syntenic alignments, we identified the pedigree of the Meg family, in which 11 of its 13 members arose in maize after allotetraploidization ~4.8 mya. Phylogenetic and population-genetic analyses identified possible signatures suggesting recent positive selection in Meg homologs. Structural analyses of the Meg proteins indicated potentially adaptive changes in secondary structure from α-helix to β-strand during the expansion. Transcriptomic analysis of the maize endosperm indicated that 6 Meg genes are selectively activated in the BETL, and younger Meg genes are more active than older ones. In endosperms from B73 by Mo17 reciprocal crosses, most Meg genes did not display parent-specific expression patterns. Conclusions Recently-duplicated Meg genes have different protein secondary structures, and their expressions in the BETL dominate over those of older members. Together with the signs of positive selections in the young Meg genes, these results suggest that the expansion of the Meg family involves potentially adaptive transitions in which new members with novel functions prevailed over older members. PMID:25084677

Diaper Rash

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Infant Jaundice

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Meckel's Diverticulum

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Provenance and diagenesis of the evaporite-bearing Burns formation, Meridiani Planum, Mars

USGS Publications Warehouse

McLennan, S.M.; Bell, J.F.; Calvin, W.M.; Christensen, P.R.; Clark, B. C.; de Souza, P.A.; Farmer, J.; Farrand, W. H.; Fike, D.A.; Gellert, Ralf; Ghosh, A.; Glotch, T.D.; Grotzinger, J.P.; Hahn, B.; Herkenhoff, K. E.; Hurowitz, J.A.; Johnson, J. R.; Johnson, S.S.; Jolliff, B.; Klingelhofer, G.; Knoll, A.H.; Learner, Z.; Malin, M.C.; McSween, H.Y.; Pocock, J.; Ruff, S.W.; Soderblom, L.A.; Squyres, S. W.; Tosca, N.J.; Watters, W.A.; Wyatt, M.B.; Yen, A.

2005-01-01

Impure reworked evaporitic sandstones, preserved on Meridiani Planum, Mars, are mixtures of roughly equal amounts of altered siliciclastic debris, of basaltic provenance (40 ?? 10% by mass), and chemical constituents, dominated by evaporitic minerals (jarosite, Mg-, Ca-sulfates ?? chlorides ?? Fe-, Na-sulfates), hematite and possibly secondary silica (60 ?? 10%). These chemical constituents and their relative abundances are not an equilibrium evaporite assemblage and to a substantial degree have been reworked by aeolian and subaqueous transport. Ultimately they formed by evaporation of acidic waters derived from interaction with olivine-bearing basalts and subsequent diagenetic alteration. The rocks experienced an extended diagenetic history, with at least two and up to four distinct episodes of cementation, including stratigraphically restricted zones of recrystallization and secondary porosity, non-randomly distributed, highly spherical millimeter-scale hematitic concretions, millimeter-scale crystal molds, interpreted to have resulted from dissolution of a highly soluble evaporite mineral, elongate to sheet-like vugs and evidence for minor synsedimentary deformation (convolute and contorted bedding, possible teepee structures or salt ridge features). Other features that may be diagenetic, but more likely are associated with relatively recent meteorite impact, are meter-scale fracture patterns, veins and polygonal fractures on rock surfaces that cut across bedding. Crystallization of minerals that originally filled the molds, early cement and sediment deformation occurred syndepositionally or during early diagenesis. All other diagenetic features are consistent with formation during later diagenesis in the phreatic (fluid saturated) zone or capillary fringe of a groundwater table under near isotropic hydrological conditions such as those expected during periodic groundwater recharge. Textural evidence suggests that rapidly formed hematitic concretions post-date the primary mineral now represented by crystal molds and early pore-filling cements but pre-date secondary moldic and vug porosity. The second generation of cements followed formation of secondary porosity. This paragenetic sequence is consistent with an extended history of syndepositional through post-depositional diagenesis in the presence of a slowly fluctuating, chemically evolving, but persistently high ionic strength groundwater system. ?? 2005 Elsevier B.V. All rights reserved.

Provenance and diagenesis of the evaporite-bearing Burns formation, Meridiani Planum, Mars

NASA Astrophysics Data System (ADS)

McLennan, S. M.; Bell, J. F.; Calvin, W. M.; Christensen, P. R.; Clark, B. C.; de Souza, P. A.; Farmer, J.; Farrand, W. H.; Fike, D. A.; Gellert, R.; Ghosh, A.; Glotch, T. D.; Grotzinger, J. P.; Hahn, B.; Herkenhoff, K. E.; Hurowitz, J. A.; Johnson, J. R.; Johnson, S. S.; Jolliff, B.; Klingelhöfer, G.; Knoll, A. H.; Learner, Z.; Malin, M. C.; McSween, H. Y.; Pocock, J.; Ruff, S. W.; Soderblom, L. A.; Squyres, S. W.; Tosca, N. J.; Watters, W. A.; Wyatt, M. B.; Yen, A.

2005-11-01

Impure reworked evaporitic sandstones, preserved on Meridiani Planum, Mars, are mixtures of roughly equal amounts of altered siliciclastic debris, of basaltic provenance (40 ± 10% by mass), and chemical constituents, dominated by evaporitic minerals (jarosite, Mg-, Ca-sulfates ± chlorides ± Fe-, Na-sulfates), hematite and possibly secondary silica (60 ± 10%). These chemical constituents and their relative abundances are not an equilibrium evaporite assemblage and to a substantial degree have been reworked by aeolian and subaqueous transport. Ultimately they formed by evaporation of acidic waters derived from interaction with olivine-bearing basalts and subsequent diagenetic alteration. The rocks experienced an extended diagenetic history, with at least two and up to four distinct episodes of cementation, including stratigraphically restricted zones of recrystallization and secondary porosity, non-randomly distributed, highly spherical millimeter-scale hematitic concretions, millimeter-scale crystal molds, interpreted to have resulted from dissolution of a highly soluble evaporite mineral, elongate to sheet-like vugs and evidence for minor synsedimentary deformation (convolute and contorted bedding, possible teepee structures or salt ridge features). Other features that may be diagenetic, but more likely are associated with relatively recent meteorite impact, are meter-scale fracture patterns, veins and polygonal fractures on rock surfaces that cut across bedding. Crystallization of minerals that originally filled the molds, early cement and sediment deformation occurred syndepositionally or during early diagenesis. All other diagenetic features are consistent with formation during later diagenesis in the phreatic (fluid saturated) zone or capillary fringe of a groundwater table under near isotropic hydrological conditions such as those expected during periodic groundwater recharge. Textural evidence suggests that rapidly formed hematitic concretions post-date the primary mineral now represented by crystal molds and early pore-filling cements but pre-date secondary moldic and vug porosity. The second generation of cements followed formation of secondary porosity. This paragenetic sequence is consistent with an extended history of syndepositional through post-depositional diagenesis in the presence of a slowly fluctuating, chemically evolving, but persistently high ionic strength groundwater system.

Solution structure of Syrian hamster prion protein rPrP(90-231).

PubMed

Liu, H; Farr-Jones, S; Ulyanov, N B; Llinas, M; Marqusee, S; Groth, D; Cohen, F E; Prusiner, S B; James, T L

1999-04-27

NMR has been used to refine the structure of Syrian hamster (SHa) prion protein rPrP(90-231), which is commensurate with the infectious protease-resistant core of the scrapie prion protein PrPSc. The structure of rPrP(90-231), refolded to resemble the normal cellular isoform PrPC spectroscopically and immunologically, has been studied using multidimensional NMR; initial results were published [James et al. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 10086-10091]. We now report refinement with better definition revealing important structural and dynamic features which can be related to biological observations pertinent to prion diseases. Structure refinement was based on 2778 unambiguously assigned nuclear Overhauser effect (NOE) connectivities, 297 ambiguous NOE restraints, and 63 scalar coupling constants (3JHNHa). The structure is represented by an ensemble of 25 best-scoring structures from 100 structures calculated using ARIA/X-PLOR and further refined with restrained molecular dynamics using the AMBER 4.1 force field with an explicit shell of water molecules. The rPrP(90-231) structure features a core domain (residues 125-228), with a backbone atomic root-mean-square deviation (RMSD) of 0.67 A, consisting of three alpha-helices (residues 144-154, 172-193, and 200-227) and two short antiparallel beta-strands (residues 129-131 and 161-163). The N-terminus (residues 90-119) is largely unstructured despite some sparse and weak medium-range NOEs implying the existence of bends or turns. The transition region between the core domain and flexible N-terminus, i.e., residues 113-128, consists of hydrophobic residues or glycines and does not adopt any regular secondary structure in aqueous solution. There are about 30 medium- and long-range NOEs within this hydrophobic cluster, so it clearly manifests structure. Multiple discrete conformations are evident, implying the possible existence of one or more metastable states, which may feature in conversion of PrPC to PrPSc. To obtain a more comprehensive picture of rPrP(90-231), dynamics have been studied using amide hydrogen-deuterium exchange and 15N NMR relaxation times (T1 and T2) and 15N{1H} NOE measurements. Comparison of the structure with previous reports suggests sequence-dependent features that may be reflected in a species barrier to prion disease transmission.

Trilobite spines and beetle horns: sexual selection in the Palaeozoic?

PubMed Central

Knell, Robert J; Fortey, Richard A

2005-01-01

Raphiophorid trilobites commonly bore median cephalic protuberances such as spines or bulbs, showing a remarkable variety of form. It is unlikely that their primary function was for protection or in hydrodynamics. A case is made that they were secondary sexual features, by comparison with similar morphological structures developed on rhinoceros beetles and other arthropods. This interpretation is supported by four lines of evidence: their ontogeny, their diversity, the existence of plausible examples of sexual dimorphs in some cases and the fact that they show positive allometry. PMID:17148165

Trilobite spines and beetle horns: sexual selection in the Palaeozoic?

PubMed

Knell, Robert J; Fortey, Richard A

2005-06-22

Raphiophorid trilobites commonly bore median cephalic protuberances such as spines or bulbs, showing a remarkable variety of form. It is unlikely that their primary function was for protection or in hydrodynamics. A case is made that they were secondary sexual features, by comparison with similar morphological structures developed on rhinoceros beetles and other arthropods. This interpretation is supported by four lines of evidence: their ontogeny, their diversity, the existence of plausible examples of sexual dimorphs in some cases and the fact that they show positive allometry.

X-ray diffraction and X-ray standing-wave study of the lead stearate film structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blagov, A. E.; Dyakova, Yu. A.; Kovalchuk, M. V.

2016-05-15

A new approach to the study of the structural quality of crystals is proposed. It is based on the use of X-ray standing-wave method without measuring secondary processes and considers the multiwave interaction of diffraction reflections corresponding to different harmonics of the same crystallographic reflection. A theory of multiwave X-ray diffraction is developed to calculate the rocking curves in the X-ray diffraction scheme under consideration for a long-period quasi-one-dimensional crystal. This phase-sensitive method is used to study the structure of a multilayer lead stearate film on a silicon substrate. Some specific structural features are revealed for the surface layer ofmore » the thin film, which are most likely due to the tilt of the upper layer molecules with respect to the external normal to the film surface.« less

Ceramic Nanocomposites from Tailor-Made Preceramic Polymers

PubMed Central

Mera, Gabriela; Gallei, Markus; Bernard, Samuel; Ionescu, Emanuel

2015-01-01

The present Review addresses current developments related to polymer-derived ceramic nanocomposites (PDC-NCs). Different classes of preceramic polymers are briefly introduced and their conversion into ceramic materials with adjustable phase compositions and microstructures is presented. Emphasis is set on discussing the intimate relationship between the chemistry and structural architecture of the precursor and the structural features and properties of the resulting ceramic nanocomposites. Various structural and functional properties of silicon-containing ceramic nanocomposites as well as different preparative strategies to achieve nano-scaled PDC-NC-based ordered structures are highlighted, based on selected ceramic nanocomposite systems. Furthermore, prospective applications of the PDC-NCs such as high-temperature stable materials for thermal protection systems, membranes for hot gas separation purposes, materials for heterogeneous catalysis, nano-confinement materials for hydrogen storage applications as well as anode materials for secondary ion batteries are introduced and discussed in detail. PMID:28347023

Molecular properties of food allergens.

PubMed

Breiteneder, Heimo; Mills, E N Clare

2005-01-01

Plant food allergens belong to a rather limited number of protein families and are also characterized by a number of biochemical and physicochemical properties, many of which are also shared by food allergens of animal origin. These include thermal stability and resistance to proteolysis, which are enhanced by an ability to bind ligands, such as metal ions, lipids, or steroids. Other types of lipid interaction, including membranes or other lipid structures, represent another feature that might promote the allergenic properties of certain food proteins. A structural feature clearly related to stability is intramolecular disulfide bonds alongside posttranslational modifications, such as N-glycosylation. Some plant food allergens, such as the cereal seed storage prolamins, are rheomorphic proteins with polypeptide chains that adopt an ensemble of secondary structures resembling unfolded or partially folded proteins. Other plant food allergens are characterized by the presence of repetitive structures, the ability to form oligomers, and the tendency to aggregate. A summary of our current knowledge regarding the molecular properties of food allergens is presented. Although we cannot as yet predict the allergenicity of a given food protein, understanding of the molecular properties that might predispose them to becoming allergens is an important first step and will undoubtedly contribute to the integrative allergenic risk assessment process being adopted by regulators.

The persuasion network is modulated by drug-use risk and predicts anti-drug message effectiveness

PubMed Central

Mangus, J Michael; Turner, Benjamin O

2017-01-01

Abstract While a persuasion network has been proposed, little is known about how network connections between brain regions contribute to attitude change. Two possible mechanisms have been advanced. One hypothesis predicts that attitude change results from increased connectivity between structures implicated in affective and executive processing in response to increases in argument strength. A second functional perspective suggests that highly arousing messages reduce connectivity between structures implicated in the encoding of sensory information, which disrupts message processing and thereby inhibits attitude change. However, persuasion is a multi-determined construct that results from both message features and audience characteristics. Therefore, persuasive messages should lead to specific functional connectivity patterns among a priori defined structures within the persuasion network. The present study exposed 28 subjects to anti-drug public service announcements where arousal, argument strength, and subject drug-use risk were systematically varied. Psychophysiological interaction analyses provide support for the affective-executive hypothesis but not for the encoding-disruption hypothesis. Secondary analyses show that video-level connectivity patterns among structures within the persuasion network predict audience responses in independent samples (one college-aged, one nationally representative). We propose that persuasion neuroscience research is best advanced by considering network-level effects while accounting for interactions between message features and target audience characteristics. PMID:29140500

Elementary teachers' perceptions about the effective features of explicit-reflective nature of science instruction

NASA Astrophysics Data System (ADS)

Adibelli-Sahin, Elif; Deniz, Hasan

2017-04-01

This qualitative study explored elementary teachers' perceptions about the effective features of explicit-reflective nature of science (NOS) instruction. Our participants were four elementary teachers from a public charter school located in the Southwestern U.S.A. The four elementary teachers participated in an academic year-long professional development about NOS which consisted of NOS training and NOS teaching phases. After each phase of the professional development, we specifically asked our participants which features of the explicit-reflective NOS instruction they found effective in improving their NOS conceptions by presenting pre- and post-profiles of their NOS conceptions. We identified nine features perceived by the participants as effective components of explicit-reflective NOS instruction: (1) specific focus on NOS content, (2) participation in hands-on NOS activities, (3) introductory NOS readings, (4) multiple types/forms of reflection, (5) multiple exposure to NOS content, (6) structural consistency in the presentation of NOS content, (7) the evaluation of secondary NOS data from elementary students, (8) the analysis of national and state science standards in terms of NOS content, and (9) NOS teaching experience.

Shortness of Breath

MedlinePlus

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Comparison of clinicopathologic characteristics of gastric follicular lymphomas and duodenal follicular lymphomas.

PubMed

Maeshima, Akiko Miyagi; Taniguchi, Hirokazu; Suzuki, Tomotaka; Yuda, Sayako; Toyoda, Kosuke; Yamauchi, Nobuhiko; Makita, Shinichi; Fukuhara, Suguru; Munakata, Wataru; Maruyama, Dai; Kobayashi, Yukio; Saito, Yutaka; Tobinai, Kensei

2017-07-01

We compared the incidence, esophagogastroduodenoscopy (EGD) findings, and histopathologic characteristics of gastric and duodenal follicular lymphomas (FL). Of 626 FL cases, primary gastric FL and secondary gastric involvement of FL were observed in 1% and 5% of the cases, respectively, which were lower incidences than duodenal FL (10% and 9%, respectively). Gastric FL usually appeared as submucosal tumors (primary, 71%; secondary, 79%), whereas duodenal FL, as granular lesions (primary, 92%: secondary, 87%). In the granular duodenal lesions, the neoplastic follicles were located sparsely on the muscularis mucosa and could be found between villi, whereas in the stomach, similar lesions were hidden within the lamina propria, and only larger lesions such as submucosal tumors could be detected on the mucosal surface. The differences in the incidences and EGD findings were considered to be associated with structural differences of the lamina propria. Typical FL features: grades 1-2 histology, follicularity, and CD10 + and/or BCL6 + and BCL2 + were usually observed in all primary and secondary gastric and duodenal FL. Gastroduodenal and bone marrow involvement were found in 12% and 33% of the cases, respectively, and there was no significant correlation between them (P=.095). Twenty-nine cases (5%) were up-staged by gastroduodenal-positive results. In conclusion, the histopathology of gastric FL was similar to that of duodenal and nodal FL; the differences in the incidence and EGD findings between gastric and duodenal FL were considered to be associated with structural difference of the lamina propria, and EGD was useful as a staging procedure. Copyright © 2017 Elsevier Inc. All rights reserved.

repRNA: a web server for generating various feature vectors of RNA sequences.

PubMed

Liu, Bin; Liu, Fule; Fang, Longyun; Wang, Xiaolong; Chou, Kuo-Chen

2016-02-01

With the rapid growth of RNA sequences generated in the postgenomic age, it is highly desired to develop a flexible method that can generate various kinds of vectors to represent these sequences by focusing on their different features. This is because nearly all the existing machine-learning methods, such as SVM (support vector machine) and KNN (k-nearest neighbor), can only handle vectors but not sequences. To meet the increasing demands and speed up the genome analyses, we have developed a new web server, called "representations of RNA sequences" (repRNA). Compared with the existing methods, repRNA is much more comprehensive, flexible and powerful, as reflected by the following facts: (1) it can generate 11 different modes of feature vectors for users to choose according to their investigation purposes; (2) it allows users to select the features from 22 built-in physicochemical properties and even those defined by users' own; (3) the resultant feature vectors and the secondary structures of the corresponding RNA sequences can be visualized. The repRNA web server is freely accessible to the public at http://bioinformatics.hitsz.edu.cn/repRNA/ .

First-principles surface interaction studies of aluminum-copper and aluminum-copper-magnesium secondary phases in aluminum alloys

NASA Astrophysics Data System (ADS)

da Silva, Thiago H.; Nelson, Eric B.; Williamson, Izaak; Efaw, Corey M.; Sapper, Erik; Hurley, Michael F.; Li, Lan

2018-05-01

First-principles density functional theory-based calculations were performed to study θ-phase Al2Cu, S-phase Al2CuMg surface stability, as well as their interactions with water molecules and chloride (Cl-) ions. These secondary phases are commonly found in aluminum-based alloys and are initiation points for localized corrosion. Density functional theory (DFT)-based simulations provide insight into the origins of localized (pitting) corrosion processes of aluminum-based alloys. For both phases studied, Cl- ions cause atomic distortions on the surface layers. The nature of the distortions could be a factor to weaken the interlayer bonds in the Al2Cu and Al2CuMg secondary phases, facilitating the corrosion process. Electronic structure calculations revealed not only electron charge transfer from Cl- ions to alloy surface but also electron sharing, suggesting ionic and covalent bonding features, respectively. The S-phase Al2CuMg structure has a more active surface than the θ-phase Al2Cu. We also found a higher tendency of formation of new species, such as Al3+, Al(OH)2+, HCl, AlCl2+, Al(OH)Cl+, and Cl2 on the S-phase Al2CuMg surface. Surface chemical reactions and resultant species present contribute to establishment of local surface chemistry that influences the corrosion behavior of aluminum alloys.

Spitting Up in Babies

MedlinePlus

... information applies to you and to get more information on this subject. Featured ContentSecondary DrowningRead Article >>Secondary DrowningSensory Processing Disorder (SPD)Read Article >>Sensory Processing Disorder (SPD) ...

Structure and function of echinoderm telomerase RNA

PubMed Central

Podlevsky, Joshua D.; Li, Yang; Chen, Julian J.-L.

2016-01-01

Telomerase is a ribonucleoprotein (RNP) enzyme that requires an integral telomerase RNA (TR) subunit, in addition to the catalytic telomerase reverse transcriptase (TERT), for enzymatic function. The secondary structures of TRs from the three major groups of species, ciliates, fungi, and vertebrates, have been studied extensively and demonstrate dramatic diversity. Herein, we report the first comprehensive secondary structure of TR from echinoderms—marine invertebrates closely related to vertebrates—determined by phylogenetic comparative analysis of 16 TR sequences from three separate echinoderm classes. Similar to vertebrate TR, echinoderm TR contains the highly conserved template/pseudoknot and H/ACA domains. However, echinoderm TR lacks the ancestral CR4/5 structural domain found throughout vertebrate and fungal TRs. Instead, echinoderm TR contains a distinct simple helical region, termed eCR4/5, that is functionally equivalent to the CR4/5 domain. The urchin and brittle star eCR4/5 domains bind specifically to their respective TERT proteins and stimulate telomerase activity. Distinct from vertebrate telomerase, the echinoderm TR template/pseudoknot domain with the TERT protein is sufficient to reconstitute significant telomerase activity. This gain-of-function of the echinoderm template/pseudoknot domain for conferring telomerase activity presumably facilitated the rapid structural evolution of the eCR4/5 domain throughout the echinoderm lineage. Additionally, echinoderm TR utilizes the template-adjacent P1.1 helix as a physical template boundary element to prevent nontelomeric DNA synthesis, a mechanism used by ciliate and fungal TRs. Thus, the chimeric and eccentric structural features of echinoderm TR provide unparalleled insights into the rapid evolution of telomerase RNP structure and function. PMID:26598712

RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

ERIC Educational Resources Information Center

Ellington, Roni; Wachira, James; Nkwanta, Asamoah

2010-01-01

The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses…

Fourier-based classification of protein secondary structures.

PubMed

Shu, Jian-Jun; Yong, Kian Yan

2017-04-15

The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications. The paper presents a technique for the classification of protein secondary structures based on protein "signal-plotting" and the use of the Fourier technique for digital signal processing. New indices are proposed to classify protein secondary structures by analyzing hydrophobicity profiles. The approach is simple and straightforward. Results show that the more types of protein secondary structures can be classified by means of these newly-proposed indices. Copyright © 2017 Elsevier Inc. All rights reserved.

Which features of primary care affect unscheduled secondary care use? A systematic review

PubMed Central

Huntley, Alyson; Lasserson, Daniel; Wye, Lesley; Morris, Richard; Checkland, Kath; England, Helen; Salisbury, Chris; Purdy, Sarah

2014-01-01

Objectives To conduct a systematic review to identify studies that describe factors and interventions at primary care practice level that impact on levels of utilisation of unscheduled secondary care. Setting Observational studies at primary care practice level. Participants Studies included people of any age of either sex living in Organisation for Economic Co-operation and Development (OECD) countries with any health condition. Primary and secondary outcome measures The primary outcome measure was unscheduled secondary care as measured by emergency department attendance and emergency hospital admissions. Results 48 papers were identified describing potential influencing features on emergency department visits (n=24 studies) and emergency admissions (n=22 studies). Patient factors associated with both outcomes were increased age, reduced socioeconomic status, lower educational attainment, chronic disease and multimorbidity. Features of primary care affecting unscheduled secondary care were more complex. Being able to see the same healthcare professional reduced unscheduled secondary care. Generally, better access was associated with reduced unscheduled care in the USA. Proximity to healthcare provision influenced patterns of use. Evidence relating to quality of care was limited and mixed. Conclusions The majority of research was from different healthcare systems and limited in the extent to which it can inform policy. However, there is evidence that continuity of care is associated with reduced emergency department attendance and emergency hospital admissions. PMID:24860000

Molecular, mesoscopic and microscopic structure evolution during amylase digestion of extruded maize and high amylose maize starches.

PubMed

Shrestha, Ashok K; Blazek, Jaroslav; Flanagan, Bernadine M; Dhital, Sushil; Larroque, Oscar; Morell, Matthew K; Gilbert, Elliot P; Gidley, Michael J

2015-03-15

Extrusion processing of cereal starch granules with high (>50%) amylose content is a promising approach to create nutritionally desirable resistant starch, i.e. starch that escapes digestion in the small intestine. Whilst high amylose content seems to be required, the structural features responsible for the slow digestion of extrudates are not fully understood. We report the effects of partial enzyme digestion of extruded maize starches on amylopectin branch length profiles, double and single helix contents, crystallinity and lamellar periodicity. Comparing results for three extruded maize starches (27, 57, and 84% apparent amylose) that differ in amylase-sensitivity allows conclusions to be drawn concerning the rate-determining features operating under the digestion conditions used. Enzyme resistance is shown to originate from a combination of molecular and mesoscopic factors, including both recrystallization and an increase in very short branches during the digestion process. This is in contrast to the behaviour of the same starches in the granular form (Shrestha et al., 2012) where molecular and mesoscopic factors are secondary to microscopic structures in determining enzyme susceptibility. Based on the structure of residual material after long-time digestion (>8h), a model for resistant starch from processed high amylose maize starches is proposed based on a fringed micelle structure with lateral aggregation and enzyme susceptibility both limited by attached clusters of branch points. Copyright © 2014 Elsevier Ltd. All rights reserved.

Features of the Jordanian Cultural Identity in the Islamic Education Books for the Two Phases of Primary and Secondary Education in Jordan

ERIC Educational Resources Information Center

Alsoudi, Khalid A.

2017-01-01

The study aimed to investigate the subjects relating to the features of Jordanian cultural identity in Islamic education books for secondary and basic stages in Jordan which are (23) books through analyzing their content. For achieving the goals of the study, the researcher prepared an analysis list included a number of sub-elements distributed on…

Deciphering the shape and deformation of secondary structures through local conformation analysis

PubMed Central

2011-01-01

Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

Deciphering the shape and deformation of secondary structures through local conformation analysis.

PubMed

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes.

PubMed

Hadjithomas, Michalis; Chen, I-Min A; Chu, Ken; Huang, Jinghua; Ratner, Anna; Palaniappan, Krishna; Andersen, Evan; Markowitz, Victor; Kyrpides, Nikos C; Ivanova, Natalia N

2017-01-04

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Clinical features of major depressive disorders treated in secondary health care facilities in Chile].

PubMed

Salvo, Lilian; Saldivia, Sandra; Parra, Carlos; Rodríguez, Román; Cifuentes, Manuel; Acevedo, Paola; Díaz, Marcela; Ormazabal, Mitza; Guerra, Ivonne; Navarrete, Nicol; Bravo, Verónica; Castro, Andrea

2017-03-01

Depression is considered the second leading cause of disability worldwide. To describe the clinical characteristics and the evolution of major depressive disorder (MDD) in secondary care. To evaluate the association between socio-demographic and clinic variables with the first or recurrent major depressive events (MDE). Clinical features, treatment, remission and duration of MDE were evaluated during a follow up lasting 12 months in 112 participants aged 44 ± 15 years (79% women). Patients were assessed as outpatients every three months at three psychiatric care centers of Chile. Clinical interviews were carried out using DSM-IV diagnostic criteria checklists and the Hamilton Depression Scale was applied. Most patients were referred from primary care. The mean time lapse for referral to the secondary level was 10.8 months. Most patients had episodes that were recurrent, severe, with a high rate of psychosis, with suicide attempts and melancholic features and with psychiatric and medical comorbidities. Remission rate was 27.5%. In only 16 % of patients, the episode lasted six months or less. The group with recurrent episodes had different age, sex and clinical features. MDD treated at the secondary care level is severe and its symptoms are intense. The time lapse prior to referral was prolonged. Primary care management and referral of these patients should be studied more closely.

A Chemical Understanding of the Band Convergence in Thermoelectric CoSb 3 Skutterudites: Influence of Electron Population, Local Thermal Expansion, and Bonding Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanus, Riley; Guo, Xingyu; Tang, Yinglu

2017-01-13

N-Type skutterudites, such as Yb xCo 4Sb 12, have recently been shown to exhibit high valley degeneracy with possible band convergence, explaining the excellent thermoelectric efficiency of these materials. Using a combined theoretical and experimental approach involving temperature-dependent synchrotron diffraction, molecular orbital diagrams, and computational studies, the chemical nature of critical features in the band structure is highlighted. We identify how n-type doping on the filler site induces structural changes that are observed in both the diffraction data and computational results. Additionally, we show how chemical n-type doping slightly alters the electronic band structure, moving the high-valley degeneracy secondary conductionmore » band closer to the primary conduction band and thus inducing band convergence.« less

Structural features of LC8-induced self-association of swallow.

PubMed

Kidane, Ariam I; Song, Yujuan; Nyarko, Afua; Hall, Justin; Hare, Michael; Löhr, Frank; Barbar, Elisar

2013-09-03

Cell functions depend on the collective activity of protein networks within which a few proteins, called hubs, participate in a large number of interactions. Dynein light chain LC8, first discovered as a subunit of the motor protein dynein, is considered to have a role broader than that of dynein, and its participation in diverse systems fits the description of a hub. Among its partners is Swallow with which LC8 is essential for proper localization of bicoid mRNA at the anterior cortex of Drosophila oocytes. Why LC8 is essential in this process is not clear, but emerging evidence suggests that LC8 functions by promoting self-association and/or structural organization of its diverse binding partners. This work addresses the energetics and structural features of LC8-induced Swallow self-association distant from LC8 binding. Mutational design based on a hypothetical helical wheel, intermonomer nuclear Overhauser effects assigned to residues expected at interface positions, and circular dichroism spectral characteristics indicate that the LC8-promoted dimer of Swallow is a coiled coil. Secondary chemical shifts and (15)N backbone relaxation identify the boundaries and distinguishing structural features of the coiled coil. Thermodynamic analysis of Swallow polypeptides designed to decouple self-association from LC8 binding reveals that the higher binding affinity of the engineered bivalent Swallow is of purely entropic origin and that the linker separating the coiled coil from the LC8 binding site remains disordered. We speculate that the LC8-promoted coiled coil is critical for bicoid mRNA localization because it favors structural organization of Swallow, which except for the central LC8-promoted coiled coil is primarily disordered.

Structural Features of LC8-Induced Self Association of Swallow†

PubMed Central

Kidane, Ariam I.; Song, Yujuan; Nyarko, Afua; Hall, Justin; Hare, Michael; Löhr, Frank; Barbar, Elisar

2013-01-01

Cell function depends on the collective activity of protein networks within which a few proteins, called hubs, participate in a large number of interactions. Dynein light chain LC8, first discovered as a subunit of the motor protein dynein, is considered to have a role broader than dynein and its participation in diverse systems fits the description of a hub. Among its partners is Swallow with which LC8 is essential for proper localization of bicoid mRNA at the anterior cortex of Drosophila oocytes. Why LC8 is essential in this process is not clear, but emerging evidence suggests that LC8 functions by promoting self-association and/or structural organization of its diverse binding partners. This work addresses the mechanistic and structural features of LC8-induced Swallow self-association distant from LC8 binding. Mutational design based on a hypothetical helical wheel, inter-monomer NOEs assigned to residues expected at interface positions and circular dichroism spectral characteristics indicate that the LC8-promoted dimer of Swallow is a coiled-coil. Secondary chemical shifts and 15N backbone relaxation identify the boundaries and distinguishing structural features of the coiled-coil. Thermodynamic analysis of Swallow polypeptides designed to decouple self-association from LC8 binding reveals that the higher binding affinity of the engineered bivalent Swallow is of purely entropic origin and that the linker separating the coiled-coil from the LC8 binding site remains disordered. We speculate that the LC8-promoted coiled-coil is critical for bicoid mRNA localization because it could induce structural organization of Swallow, which except for the central LC8-promoted coiled-coil is primarily disordered. PMID:23914803

Identifying the Comparative Academic Performance of Secondary Schools

ERIC Educational Resources Information Center

Bendikson, Linda; Hattie, John; Robinson, Viviane

2011-01-01

Purpose: One of the features of the New Zealand secondary schools system is that achievement closely reflects the taught curriculum. The National Certificate of Educational Achievement (NCEA) directly assesses student achievement on the secondary school curriculum through a combination of criterion-based internal and external assessments. The…

Preliminary Investigation and Surficial Mapping of the Faults North and South of Blacktail Butte, Teton County, Wyoming

NASA Astrophysics Data System (ADS)

Wittke, S.

2016-12-01

The Wyoming State Geological Survey has focused on surficial mapping and examination of the location and offset of faults north and south of Blacktail Butte in eastern Jackson Hole, Wyoming. The fault strands south of Blacktail Butte are classified as Late Quaternary, the faults north of the butte are considered Class B structures by the USGS. Little to no detailed studies, including paleoseismic investigations or fault scarp morphology, have been conducted on these fault strands. The acquisition of LiDAR for the Grand Teton National Park and recent aerial photographs provided data necessary for revised mapping and geomorphic interpretation of fault-related features north and south of Blacktail Butte. New fault traces and geomorphic features were identified in the LiDAR data which had not been previously mapped. Mapped fault traces are intermittent, forming a 1.5 km-long graben that extends south from Blacktail Butte and crosses a loess-mantle late-Pleistocene terrace generated from the Pinedale glaciation. Other lineaments were identified that continued for another 0.5 km to the south. With very little vertical offset across the system and comparatively short fault strands, the faults may represent secondary features related to movement on another unidentified fault within the basin. The secondary faults north of Blacktail Butte were mapped based on geomorphic features and through LiDAR-based spatial analysis. The fault scarps are relatively short and are present on alluvial fan and/or terrace deposits related to the Pinedale glaciation or on undated Holocene deposits. The scarps have little net vertical offset, suggesting they could also be secondary features related to movement from another unidentified fault within the basin. Improved understanding of these fault strands is significant because of the vicinity to populated areas within Jackson Hole and the possible relevance to the Teton Fault system. To our knowledge, these fault strands have not been proposed as antithetic to the Teton fault. The faults are located on the eastern edge of the valley, approximately 8-16 km from the Teton fault, and based on their orientation and sense of slip, the Teton fault may be the unidentified fault within the basin. Detailed paleoseismic surveys, including fault trenching, may shed light on the question in the future.

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

PubMed Central

Ding, Feng; Sharma, Shantanu; Chalasani, Poornima; Demidov, Vadim V.; Broude, Natalia E.; Dokholyan, Nikolay V.

2008-01-01

RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 Å deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNAPhe, pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses. PMID:18456842

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

PubMed Central

Zubradt, Meghan; Gupta, Paromita; Persad, Sitara; Lambowitz, Alan M.; Weissman, Jonathan S.; Rouskin, Silvi

2017-01-01

Coupling structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structural studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduces biases and necessitates population-average assessments of RNA structure. Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in non-canonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs to their mature isoforms. These applications illustrate DMS-MaPseq’s capacity to dramatically expand in vivo analysis of RNA structure. PMID:27819661

The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism.

PubMed

Bækkedal, Cecilie; Haugen, Peik

2015-01-01

The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution of spf, show family-specific secondary structural features of Spot 42, and link highly conserved structural regions to mRNA target binding.

Informational technologies in modern educational structure

NASA Astrophysics Data System (ADS)

Fedyanin, A. B.

2017-01-01

The article represents the structure of informational technologies complex that is applied in modern school education, describes the most important educational methods, shows the results of their implementation. It represents the forms and methods of educational process informative support usage, examined in respects of different aspects of their using that take into account also the psychological features of students. A range of anxious facts and dangerous trends connected with the usage and distribution of the informational technologies that are to be taken into account in the educational process of informatization is also indicated in the article. Materials of the article are based on the experience of many years in operation and development of the informational educational sphere on the basis of secondary school of the physics and mathematics specialization.

Functional genomics of gam56: characterisation of the role of a 56 kilodalton sexual stage antigen in oocyst wall formation in Eimeria maxima.

PubMed

Belli, Sabina I; Witcombe, David; Wallach, Michael G; Smith, Nicholas C

2002-12-19

Gam56 (M(r) 56,000) is an antigen found in the sexual (macrogametocyte) stage of the intestinal parasite Eimeria maxima that is implicated in protective immunity. The gene (gam56) encoding this protein was cloned and sequenced. It is a single-copy, intronless gene, that localises to a 1,754 bp transcript, and is first detected at 120 h p.i. The gene predicts two distinct protein domains; a tyrosine-serine rich region, composed of amino acids implicated in oocyst wall formation in Eimeria spp., and a proline-methionine rich region often detected in extensins, protein components of plant cell walls. The tyrosine-serine rich region predicts a secondary structure commonly seen in the structural protein fibroin, a component of the cocoon of the caterpillar Bombyx mori. The inference that gam56 is a structural component of the oocyst wall was confirmed when a specific antibody to gam56 recognised the wall forming bodies in macrogametocytes, and the walls of oocysts and sporocysts. Together, these data identify a developmentally regulated, sexual stage gene in E. maxima that shares primary and secondary structure features in common with intrinsic structural proteins in other parasites such as Schistosoma mansoni and Fasciola hepatica, and other organisms across different phyla, including the caterpillar Bombyx mori. In addition, these findings provide evidence for the molecular mechanisms underlying oocyst wall formation in Eimeria and the role of gametocyte antigens in this process.

Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics

PubMed Central

Hata, Hiroaki; Kitajima, Tetsuro

2018-01-01

Abstract Nucleic acid secondary structure plays an important role in nucleic acid–nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant. PMID:29220504

Mutational robustness accelerates the origin of novel RNA phenotypes through phenotypic plasticity.

PubMed

Wagner, Andreas

2014-02-18

Novel phenotypes can originate either through mutations in existing genotypes or through phenotypic plasticity, the ability of one genotype to form multiple phenotypes. From molecules to organisms, plasticity is a ubiquitous feature of life, and a potential source of exaptations, adaptive traits that originated for nonadaptive reasons. Another ubiquitous feature is robustness to mutations, although it is unknown whether such robustness helps or hinders the origin of new phenotypes through plasticity. RNA is ideal to address this question, because it shows extensive plasticity in its secondary structure phenotypes, a consequence of their continual folding and unfolding, and these phenotypes have important biological functions. Moreover, RNA is to some extent robust to mutations. This robustness structures RNA genotype space into myriad connected networks of genotypes with the same phenotype, and it influences the dynamics of evolving populations on a genotype network. In this study I show that both effects help accelerate the exploration of novel phenotypes through plasticity. My observations are based on many RNA molecules sampled at random from RNA sequence space, and on 30 biological RNA molecules. They are thus not only a generic feature of RNA sequence space but are relevant for the molecular evolution of biological RNA. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Synthesis, characterizations and catalytic studies of a new two-dimensional metal-organic framework based on Co-carboxylate secondary building units

NASA Astrophysics Data System (ADS)

Bagherzadeh, Mojtaba; Ashouri, Fatemeh; Đaković, Marijana

2015-03-01

A metal-organic framework [Co3(BDC)3(DMF)2(H2O)2] was synthesized and structurally characterized. X-ray single crystal analysis revealed that the framework contains a 2D polymeric chain through coordination of 1,4-benzenedicarboxylic acid linker ligand to cobalt centers. The polymer crystallize in monoclinic P21/n space group with a=13.989(3) Å, b=9.6728(17) Å, c=16.707(3) Å, and Z=2. The polymer features a framework based on the perfect octahedral Co-O6 secondary building units. The catalytic activities of [Co3(BDC)3(DMF)2(H2O)2]n for olefins oxidation was conducted. The heterogeneous catalyst could be facilely separated from the reaction mixture, and reused three times without significant degradation in catalytic activity. Furthermore, no contribution from homogeneous catalysis of active species leaching into reaction solution was detected.

How to Care for Your Baby's Teeth

MedlinePlus

... information applies to you and to get more information on this subject. Featured ContentSecondary DrowningRead Article >>Secondary DrowningSensory Processing Disorder (SPD)Read Article >>Sensory Processing Disorder (SPD) ...

Phylogenetic Reconstruction of the Calosphaeriales and Togniniales Using Five Genes and Predicted RNA Secondary Structures of ITS, and Flabellascus tenuirostris gen. et sp. nov.

PubMed Central

Réblová, Martina; Jaklitsch, Walter M.; Réblová, Kamila; Štěpánek, Václav

2015-01-01

The Calosphaeriales is revisited with new collection data, living cultures, morphological studies of ascoma centrum, secondary structures of the internal transcribed spacer (ITS) rDNA and phylogeny based on novel DNA sequences of five nuclear ribosomal and protein-coding loci. Morphological features, molecular evidence and information from predicted RNA secondary structures of ITS converged upon robust phylogenies of the Calosphaeriales and Togniniales. The current concept of the Calosphaeriales includes the Calosphaeriaceae and Pleurostomataceae encompassing five monophyletic genera, Calosphaeria, Flabellascus gen. nov., Jattaea, Pleurostoma and Togniniella, strongly supported by Bayesian and Maximum Likelihood methods. The structural elements of ITS1 form characteristic patterns that are phylogenetically conserved, corroborate observations based on morphology and have a high predictive value at the generic level. Three major clades containing 44 species of Phaeoacremonium were recovered in the closely related Togniniales based on ITS, actin and β-tubulin sequences. They are newly characterized by sexual and RNA structural characters and ecology. This approach is a first step towards understanding of the molecular systematics of Phaeoacremonium and possibly its new classification. In the Calosphaeriales, Jattaea aphanospora sp. nov. and J. ribicola sp. nov. are introduced, Calosphaeria taediosa is combined in Jattaea and epitypified. The sexual morph of Phaeoacremonium cinereum was encountered for the first time on decaying wood and obtained in vitro. In order to achieve a single nomenclature, the genera of asexual morphs linked with the Calosphaeriales are transferred to synonymy of their sexual morphs following the principle of priority, i.e. Calosphaeriophora to Calosphaeria, Phaeocrella to Togniniella and Pleurostomophora to Pleurostoma. Three new combinations are proposed, i.e. Pleurostoma ochraceum comb. nov., P. repens comb. nov. and P. richardsiae comb. nov. The morphology-based key is provided to facilitate identification of genera accepted in the Calosphaeriales. PMID:26699541

Secondary iris recognition method based on local energy-orientation feature

NASA Astrophysics Data System (ADS)

Huo, Guang; Liu, Yuanning; Zhu, Xiaodong; Dong, Hongxing

2015-01-01

This paper proposes a secondary iris recognition based on local features. The application of the energy-orientation feature (EOF) by two-dimensional Gabor filter to the extraction of the iris goes before the first recognition by the threshold of similarity, which sets the whole iris database into two categories-a correctly recognized class and a class to be recognized. Therefore, the former are accepted and the latter are transformed by histogram to achieve an energy-orientation histogram feature (EOHF), which is followed by a second recognition with the chi-square distance. The experiment has proved that the proposed method, because of its higher correct recognition rate, could be designated as the most efficient and effective among its companion studies in iris recognition algorithms.

Isolas of periodic passive Q-switching self-pulsations in the three-level:two-level model for a laser with a saturable absorber.

PubMed

Doedel, Eusebius J; Pando, Carlos L L

2011-11-01

We show that a fundamental feature of the three-level:two-level model, used to describe molecular monomode lasers with a saturable absorber, is the existence of isolas of periodic passive Q-switching (PQS) self-pulsations. A common feature of these closed families of periodic solutions is that they contain regions of stability of the PQS self-pulsation bordered by period-doubling and fold bifurcations, when the control parameter is either the incoherent external pump or the cavity frequency detuning. These findings unveil the fundamental solution structure that is at the origin of the phenomenon known as "period-adding cascades" in our system. Using numerical continuation techniques we determine these isolas systematically, as well as the changes they undergo as secondary parameters are varied.

Performance Characterization of Loctite (Registered Trademark) 242 and 271 Liquid Locking Compounds (LLCs) as a Secondary Locking Feature for International Space Station (ISS) Fasteners

NASA Technical Reports Server (NTRS)

Dube, Michael J.; Gamwell, Wayne R.

2011-01-01

Several International Space Station (ISS) hardware components use Loctite (and other polymer based liquid locking compounds (LLCs)) as a means of meeting the secondary (redundant) locking feature requirement for fasteners. The primary locking method is the fastener preload, with the application of the Loctite compound which when cured is intended to resist preload reduction. The reliability of these compounds has been questioned due to a number of failures during ground testing. The ISS Program Manager requested the NASA Engineering and Safety Center (NESC) to characterize and quantify sensitivities of Loctite being used as a secondary locking feature. The findings and recommendations provided in this investigation apply to the anaerobic LLCs Loctite 242 and 271. No other anaerobic LLCs were evaluated for this investigation. This document contains the findings and recommendations of the NESC investigation

Hierarchical Micro/Nano Structures by Combined Self-Organized Dewetting and Photopatterning of Photoresist Thin Films.

PubMed

Sachan, Priyanka; Kulkarni, Manish; Sharma, Ashutosh

2015-11-17

Photoresists are the materials of choice for micro/nanopatterning and device fabrication but are rarely used as a self-assembly material. We report for the first time a novel interplay of self-assembly and photolithography for fabrication of hierarchical and ordered micro/nano structures. We create self-organized structures by the intensified dewetting of unstable thin (∼10 nm to 1 μm) photoresist films by annealing them in an optimal solvent and nonsolvent liquid mixture that allows spontaneous dewetting to form micro/nano smooth dome-like structures. The density, size (∼100 nm to millimeters), and curvature/contact angle of the dome/droplet structures are controlled by the film thickness, composition of the dewetting liquid, and time of annealing. Ordered dewetted structures are obtained simply by creating spatial variation of viscosity by ultraviolet exposure or by photopatterning before dewetting. Further, the structures thus fabricated are readily photopatterned again on the finer length scales after dewetting. We illustrate the approach by fabricating several three-dimensional structures of varying complexity with secondary and tertiary features.

Efficient RNA structure comparison algorithms.

PubMed

Arslan, Abdullah N; Anandan, Jithendar; Fry, Eric; Monschke, Keith; Ganneboina, Nitin; Bowerman, Jason

2017-12-01

Recently proposed relative addressing-based ([Formula: see text]) RNA secondary structure representation has important features by which an RNA structure database can be stored into a suffix array. A fast substructure search algorithm has been proposed based on binary search on this suffix array. Using this substructure search algorithm, we present a fast algorithm that finds the largest common substructure of given multiple RNA structures in [Formula: see text] format. The multiple RNA structure comparison problem is NP-hard in its general formulation. We introduced a new problem for comparing multiple RNA structures. This problem has more strict similarity definition and objective, and we propose an algorithm that solves this problem efficiently. We also develop another comparison algorithm that iteratively calls this algorithm to locate nonoverlapping large common substructures in compared RNAs. With the new resulting tools, we improved the RNASSAC website (linked from http://faculty.tamuc.edu/aarslan ). This website now also includes two drawing tools: one specialized for preparing RNA substructures that can be used as input by the search tool, and another one for automatically drawing the entire RNA structure from a given structure sequence.

Secondary psychotic features in refugees diagnosed with post-traumatic stress disorder: a retrospective cohort study.

PubMed

Nygaard, Mette; Sonne, Charlotte; Carlsson, Jessica

2017-01-05

A substantial amount of refugees (10-30%) suffer from Post-Traumatic Stress Disorder (PTSD). In Denmark there are different facilities specialised in psychiatric treatment of trauma-affected refugees. A previously published case report from such a facility in Denmark shows that some patients suffer from secondary psychotic symptoms alongside their PTSD. The aim of this study was to illustrate the characteristics and estimate the prevalence of psychotic features in a clinical population of trauma-affected refugees with PTSD. Psychiatric records from 220 consecutive patients at Competence Centre for Transcultural Psychiatry (CTP) were examined, and all the PTSD patients were divided into two groups; one group with secondary psychotic features (PTSD-SP group) and one without (PTSD group). A categorisation and description of the secondary psychotic features was undertaken. One hundred eighty-one patients were diagnosed with PTSD among which psychotic symptoms were identified in 74 (40.9, 95% CI 33.7-48.1%). The majority of symptoms identified were auditory hallucinations (66.2%) and persecutory delusions (50.0%). There were significantly more patients diagnosed with enduring personality change after catastrophic experience in the PTSD-SP group than in the PTSD group (P = 0.009). Furthermore the PTSD-SP group included significantly more patients exposed to torture (P = 0.001) and imprisonment (P = 0.005). This study provides an estimation of PTSD-SP prevalence in a clinical refugee population with PTSD. The study points to the difficulties distinguishing psychotic features from flashbacks and the authors call for attention to psychotic features in PTSD patients in order to improve documentation and understanding of the disorder.

An unconventional family 1 uracil DNA glycosylase in Nitratifractor salsuginis.

PubMed

Li, Jing; Chen, Ran; Yang, Ye; Zhang, Zhemin; Fang, Guang-Chen; Xie, Wei; Cao, Weiguo

2017-12-01

The uracil DNA glycosylase superfamily consists of at least six families with a diverse specificity toward DNA base damage. Family 1 uracil N-glycosylase (UNG) exhibits exclusive specificity on uracil-containing DNA. Here, we report a family 1 UNG homolog from Nitratifractor salsuginis with distinct biochemical features that differentiate it from conventional family 1 UNGs. Globally, the crystal structure of N. salsuginisUNG shows a few additional secondary structural elements. Biochemical and enzyme kinetic analysis, coupled with structural determination, molecular modeling, and molecular dynamics simulations, shows that N. salsuginisUNG contains a salt bridge network that plays an important role in DNA backbone interactions. Disruption of the amino acid residues involved in the salt bridges greatly impedes the enzymatic activity. A tyrosine residue in motif 1 (GQDPY) is one of the distinct sequence features setting family 1 UNG apart from other families. The crystal structure of Y81G mutant indicates that several subtle changes may account for its inactivity. Unlike the conventional family 1 UNG enzymes, N. salsuginisUNG is not inhibited by Ugi, a potent inhibitor specific for family 1 UNG. This study underscores the diversity of paths that a uracil DNA glycosylase may take to acquire its unique structural and biochemical properties during evolution. Structure data are available in the PDB under accession numbers 5X3G and 5X3H. © 2017 Federation of European Biochemical Societies.

CASTp 3.0: computed atlas of surface topography of proteins.

PubMed

Tian, Wei; Chen, Chang; Lei, Xue; Zhao, Jieling; Liang, Jie

2018-06-01

Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.

A Consensus Model of Human Apolipoprotein A-I in its Monomeric and Lipid-free State

PubMed Central

Melchior, John T.; Walker, Ryan G.; Cooke, Allison L.; Morris, Jamie; Castleberry, Mark; Thompson, Thomas B.; Jones, Martin K.; Song, Hyun D.; Rye, Kerry-Anne; Oda, Mike N.; Sorci-Thomas, Mary G.; Thomas, Michael J.; Heinecke, Jay W.; Mei, Xiaohu; Atkinson, David; Segrest, Jere P.; Lund-Katz, Sissel; Phillips, Michael C.; Davidson, W. Sean

2017-01-01

Apolipoprotein (apo)A-I is an organizing scaffold protein that is critical to high density lipoprotein (HDL) structure and metabolism, likely mediating many of its cardioprotective properties. However, HDL biogenesis is poorly understood as lipid-free apoA-I has been notoriously resistant to high resolution structural study. Published models from low resolution techniques share certain features but vary considerably in shape and secondary structure. To tackle this central issue in lipoprotein biology, we assembled an unprecedented team of lipoprotein structural biologists and set out to build a consensus model of monomeric lipid-free human apoA-I. Combining novel and published cross-link constraints, small angle X-ray scattering (SAXS), hydrogen-deuterium exchange (H-DX) and crystallography data, we propose a time averaged model consistent with much of the experimental data published over the last 40 years. The model provides a long sought platform for understanding and testing details of HDL biogenesis, structure and function. PMID:29131142

Structure-directing weak phosphoryl XH...O=P (X = C, N) hydrogen bonds in cyclic oxazaphospholidines and oxazaphosphinanes.

PubMed

van der Lee, A; Rolland, M; Marat, X; Virieux, D; Volle, J N; Pirat, J L

2008-04-01

The structures of six cyclic oxazaphospholidines and three cyclic oxazaphosphinanes have been determined and their supramolecular structures have been compared. The molecules differ with respect to the functional groups attached to the central five- or six-membered rings, but have one phosphoryl group in common. The predominant feature in the supramolecular structures is the existence of relatively weak intermolecular phosphoryl XH...O=P (X = C, N) hydrogen bonds, creating in nearly all cases linear zigzag or double molecular chains. The molecular chains are in general linked to each other via very weak CH...pi or usual hydrogen-bond interactions. A survey of the Cambridge Structural Database on similar XH...O=P interactions shows a very large flexibility of the XH...O angle, which is in agreement with the DFT calculation reported elsewhere. The strength of the XH...O=P interaction can therefore be considered as relatively weak to moderately strong, and is expected to play at least a role in the formation of secondary substructures.

mpMoRFsDB: a database of molecular recognition features in membrane proteins.

PubMed

Gypas, Foivos; Tsaousis, Georgios N; Hamodrakas, Stavros J

2013-10-01

Molecular recognition features (MoRFs) are small, intrinsically disordered regions in proteins that undergo a disorder-to-order transition on binding to their partners. MoRFs are involved in protein-protein interactions and may function as the initial step in molecular recognition. The aim of this work was to collect, organize and store all membrane proteins that contain MoRFs. Membrane proteins constitute ∼30% of fully sequenced proteomes and are responsible for a wide variety of cellular functions. MoRFs were classified according to their secondary structure, after interacting with their partners. We identified MoRFs in transmembrane and peripheral membrane proteins. The position of transmembrane protein MoRFs was determined in relation to a protein's topology. All information was stored in a publicly available mySQL database with a user-friendly web interface. A Jmol applet is integrated for visualization of the structures. mpMoRFsDB provides valuable information related to disorder-based protein-protein interactions in membrane proteins. http://bioinformatics.biol.uoa.gr/mpMoRFsDB

Laser-Based Surface Modification of Microstructure for Carbon Fiber-Reinforced Plastics

NASA Astrophysics Data System (ADS)

Yang, Wenfeng; Sun, Ting; Cao, Yu; Li, Shaolong; Liu, Chang; Tang, Qingru

2018-05-01

Bonding repair is a powerful feature of carbon fiber-reinforced plastics (CFRP). Based on the theory of interface bonding, the interface adhesion strength and reliability of the CFRP structure will be directly affected by the microscopic features of the CFRP surface, including the microstructure, physical, and chemical characteristics. In this paper, laser-based surface modification was compared to Peel-ply, grinding, and polishing to comparatively evaluate the surface microstructure of CFRP. The surface microstructure, morphology, fiber damage, height and space parameters were investigated by scanning electron microscopy (SEM) and laser confocal microscopy (LCM). Relative to the conventional grinding process, laser modification of the CFRP surface can result in more uniform resin removal and better processing control and repeatability. This decreases the adverse impact of surface fiber fractures and secondary damage. The surface properties were significantly optimized, which has been reflected such things as the obvious improvement of surface roughness, microstructure uniformity, and actual area. The improved surface microstructure based on laser modification is more conducive to interface bonding of CFRP structure repair. This can enhance the interfacial adhesion strength and reliability of repair.

Ozone Promotes Chloropicrin Formation by Oxidizing Amines to Nitro Compounds.

PubMed

McCurry, Daniel L; Quay, Amanda N; Mitch, William A

2016-02-02

Chloropicrin formation has been associated with ozonation followed by chlorination, but the reaction pathway and precursors have been poorly characterized. Experiments with methylamine demonstrated that ozonation converts methylamine to nitromethane at ∼100% yield. Subsequent chlorination converts nitromethane to chloropicrin at ∼50% yield under the conditions evaluated. Similarly high yields from other primary amines were limited to those with functional groups on the β-carbon (e.g., the carboxylic acid in glycine) that facilitate carbon-carbon bond cleavage to release nitromethyl anion. Secondary amines featuring these reactive primary amines as functional groups (e.g., secondary N-methylamines) formed chloropicrin at high yields, likely by facile dealkylation to release the primary nitro compound. Chloropicrin yields from tertiary amines were low. Natural water experiments, including derivatization to transform primary and secondary amines to less reactive carbamate functional groups, indicated that primary and secondary amines were the dominant chloropicrin precursors during ozonation/chlorination. Ozonation followed by chlorination of the primary amine side chain of lysine demonstrated low yields (∼0.2%) of chloropicrin, but high yields (∼17%) of dichloronitrolysine, a halonitroalkane structural analogue to chloropicrin. However, chloropicrin yields increased and dichloronitrolysine yields decreased in the absence of hydroxyl radical scavengers, suggesting that future research should characterize the potential occurrence of such halonitroalkane analogues relative to natural radical scavenger (e.g., carbonate) concentrations.

An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations

PubMed Central

2015-01-01

High-density lipoprotein (HDL) retards atherosclerosis by accepting cholesterol from the artery wall. However, the structure of the proposed acceptor, monomeric apolipoprotein A-I (apoA-I), the major protein of HDL, is poorly understood. Two published models for monomeric apoA-I used cross-linking distance constraints to derive best fit conformations. This approach has limitations. (i) Cross-linked peptides provide no information about secondary structure. (ii) A protein chain can be folded in multiple ways to create a best fit. (iii) Ad hoc folding of a secondary structure is unlikely to produce a stable orientation of hydrophobic and hydrophilic residues. To address these limitations, we used a different approach. We first noted that the dimeric apoA-I crystal structure, (Δ185–243)apoA-I, is topologically identical to a monomer in which helix 5 forms a helical hairpin, a monomer with a hydrophobic cleft running the length of the molecule. We then realized that a second crystal structure, (Δ1–43)apoA-I, contains a C-terminal structure that fits snuggly via aromatic and hydrophobic interactions into the hydrophobic cleft. Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations. We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints. We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I. PMID:25423138

R2R--software to speed the depiction of aesthetic consensus RNA secondary structures.

PubMed

Weinberg, Zasha; Breaker, Ronald R

2011-01-04

With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

The dynamics of interacting salt structures and associated fluid flow in the western Norwegian-Danish Basin

NASA Astrophysics Data System (ADS)

Olsen, Mikkel S.; Clausen, Ole R.; Andresen, Katrine J.; Korstgård, John A.

2015-04-01

Minor secondary structures observed along the flanks of major salt structures in the Norwegian-Danish Basin appear to be generated mainly during the early stages of halokinesis. Seismic anomalies in the cover sediments at the flanks of the major salt structures and in relation to one of the secondary structures show several circular patterns. The circular patterns are generally interpreted as faults related to collapsing salt, indicating a subtle and dynamic cannibalization relationship between the secondary structure and the main diapir. High-amplitude reflections interpreted as either entrapped gas along the circular faults or diagenetic changes induced by the fluids originating from the salt-sediment interface generally enhances the seismic appearance of the circular faults, but potentially also disturb the seismic imaging of the faults. Other secondary salt structures, with a similar geometry, do not show sign of collapse, apparently due to a greater distance from the main salt structures and therefore not within the reach of being cannibalized by these. The observations furthermore suggest a trend showing a more advanced development of the main salt structures when the secondary structures are cannibalized. The lateral distribution of the main salt structures thus appears to be controlled not only by the initial thickness of the Zechstein salt, and possible underlying structures, but also by subtle variations in the location and evolution of secondary structures. The secondary structures have a major impact on the drainage of the deep Mesozoic succession as indicated by the fluid flow pattern also observed in the study, which emphasizes that a detailed mapping of salt structures including secondary structures at the flanks is of major importance during evaluation of petroleum systems in areas dominated by halokinesis.

Solution structural ensembles of substrate-free cytochrome P450(cam).

PubMed

Asciutto, Eliana K; Young, Matthew J; Madura, Jeffry; Pochapsky, Susan Sondej; Pochapsky, Thomas C

2012-04-24

Removal of substrate (+)-camphor from the active site of cytochrome P450(cam) (CYP101A1) results in nuclear magnetic resonance-detected perturbations in multiple regions of the enzyme. The (1)H-(15)N correlation map of substrate-free diamagnetic Fe(II) CO-bound CYP101A permits these perturbations to be mapped onto the solution structure of the enzyme. Residual dipolar couplings (RDCs) were measured for (15)N-(1)H amide pairs in two independent alignment media for the substrate-free enzyme and used as restraints in solvated molecular dynamics (MD) simulations to generate an ensemble of best-fit structures of the substrate-free enzyme in solution. Nuclear magnetic resonance-detected chemical shift perturbations reflect changes in the electronic environment of the NH pairs, such as hydrogen bonding and ring current shifts, and are observed for residues in the active site as well as in hinge regions between secondary structural features. RDCs provide information about relative orientations of secondary structures, and RDC-restrained MD simulations indicate that portions of a β-rich region adjacent to the active site shift so as to partially occupy the vacancy left by removal of the substrate. The accessible volume of the active site is reduced in the substrate-free enzyme relative to the substrate-bound structure calculated using the same methods. Both symmetric and asymmetric broadening of multiple resonances observed upon substrate removal as well as localized increased errors in RDC fits suggest that an ensemble of enzyme conformations are present in the substrate-free form.

Role of secondary flows on flow separation induced by shock/boundary layer interaction in supersonic inlets

NASA Astrophysics Data System (ADS)

Morajkar, Rohan

Flow separation in the scramjet air intakes is one of the reasons of failure of these engines which rely on shock waves to achieve flow compression. The shock waves interact with the boundary layers (Shock/ Boundary Layer Interaction or SBLI) on the intake walls inducing adverse pressure gradients causing flow separation. In this experimental study we investigate the role of secondary flows associated with the corners of ducted flows and identify the mechanisms by which they affect flow separation induced by a shock wave interacting with the boundary layers developing along supersonic inlets. The coupling between flow three-dimensionality, shock waves and secondary flows is in fact a key aspect that limits the performance and control of supersonic inlets. The study is conducted at the University of Michigan Glass Supersonic Wind Tunnel (GSWT). This facility replicates some of the features of the three-dimensional (3D) flow-field in a low aspect ratio supersonic inlet. The study uses stereoscopic particle image velocimetry (SPIV) to measure the three-component (3C) velocity field on several orthogonal planes, and thus allows us to identify the length scales of separation, its locations and statistical properties. Furthermore, these measurements allow us to extract the 3D structure of the underlying vortical features, which are important in determining the overall structure of separated regions and their dynamics. The measurements and tools developed are used to study flow fields of three cases: (1) Moderately strong SBLI (Mach 2.75 with 6° deflection), (2) weak SBLI (Mach 2.75 with 4.6° deflection) and (3) secondary corner flows in empty channels. In the configuration of the initial work (moderately strong SBLI), the shock wave system interacts with the boundary layers on the sidewall and the floor of the duct (inlet), thus generating both a swept-shock and an incident-shock interactions. Furthermore, the swept-shock interaction taking place on the sidewalls interacts with the secondary flows in the corners of the tunnel, which are prone to separation. This interaction causes major flow separation on the sidewall as fluid is swept from the sidewall. Flow separation on the floor should be expected given the strength of the SBLI (moderately strong case), but it is instead not observed in the mean flow fields. Our hypothesis is that interacting secondary flows are one of the factors responsible for the sidewall separation and directing the incoming flow towards the center-plane to stabilize and energize the flow on the center of the duct, thus preventing or at least reducing, flow separation on the floor. The secondary flows in an empty tunnel are then investigated to study their evolution and effects on the primary flow field to identify potential separation sites. The results from the empty tunnel experiments are then used to predict locations of flow separations in the moderately strong and weak SBLIs. The predictions were found to be in agreement with the observations.

Molecular, mesoscopic and microscopic structure evolution during amylase digestion of maize starch granules.

PubMed

Shrestha, Ashok K; Blazek, Jaroslav; Flanagan, Bernadine M; Dhital, Sushil; Larroque, Oscar; Morell, Matthew K; Gilbert, Elliot P; Gidley, Michael J

2012-09-01

Cereal starch granules with high (>50%) amylose content are a promising source of nutritionally desirable resistant starch, i.e. starch that escapes digestion in the small intestine, but the structural features responsible are not fully understood. We report the effects of partial enzyme digestion of maize starch granules on amylopectin branch length profiles, double and single helix contents, gelatinisation properties, crystallinity and lamellar periodicity. Comparing results for three maize starches (27, 57, and 84% amylose) that differ in both structural features and amylase-sensitivity allows conclusions to be drawn concerning the rate-determining features operating under the digestion conditions used. All starches are found to be digested by a side-by-side mechanism in which there is no major preference during enzyme attack for amylopectin branch lengths, helix form, crystallinity or lamellar organisation. We conclude that the major factor controlling enzyme susceptibility is granule architecture, with shorter length scales not playing a major role as inferred from the largely invariant nature of numerous structural measures during the digestion process (XRD, NMR, SAXS, DSC, FACE). Results are consistent with digestion rates being controlled by restricted diffusion of enzymes within densely packed granular structures, with an effective surface area for enzyme attack determined by external dimensions (57 or 84% amylose - relatively slow) or internal channels and pores (27% amylose - relatively fast). Although the process of granule digestion is to a first approximation non-discriminatory with respect to structure at molecular and mesoscopic length scales, secondary effects noted include (i) partial crystallisation of V-type helices during digestion of 27% amylose starch, (ii) preferential hydrolysis of long amylopectin branches during the early stage hydrolysis of 27% and 57% but not 84% amylose starches, linked with disruption of lamellar repeating structure and (iii) partial B-type recrystallisation after prolonged enzyme incubation for 57% and 84% amylose starches but not 27% amylose starch. Copyright © 2012 Elsevier Ltd. All rights reserved.

Role of DNA secondary structures in fragile site breakage along human chromosome 10

PubMed Central

Dillon, Laura W.; Pierce, Levi C. T.; Ng, Maggie C. Y.; Wang, Yuh-Hwa

2013-01-01

The formation of alternative DNA secondary structures can result in DNA breakage leading to cancer and other diseases. Chromosomal fragile sites, which are regions of the genome that exhibit chromosomal breakage under conditions of mild replication stress, are predicted to form stable DNA secondary structures. DNA breakage at fragile sites is associated with regions that are deleted, amplified or rearranged in cancer. Despite the correlation, unbiased examination of the ability to form secondary structures has not been evaluated in fragile sites. Here, using the Mfold program, we predict potential DNA secondary structure formation on the human chromosome 10 sequence, and utilize this analysis to compare fragile and non-fragile DNA. We found that aphidicolin (APH)-induced common fragile sites contain more sequence segments with potential high secondary structure-forming ability, and these segments clustered more densely than those in non-fragile DNA. Additionally, using a threshold of secondary structure-forming ability, we refined legitimate fragile sites within the cytogenetically defined boundaries, and identified potential fragile regions within non-fragile DNA. In vitro detection of alternative DNA structure formation and a DNA breakage cell assay were used to validate the computational predictions. Many of the regions identified by our analysis coincide with genes mutated in various diseases and regions of copy number alteration in cancer. This study supports the role of DNA secondary structures in common fragile site instability, provides a systematic method for their identification and suggests a mechanism by which DNA secondary structures can lead to human disease. PMID:23297364

Peptide concentration alters intermediate species in amyloid β fibrillation kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garvey, M., E-mail: megan.garvey@molbiotech.rwth-aachen.de; Morgado, I., E-mail: immorgado@ualg.pt

2013-04-12

Highlights: ► Aβ(1–40) aggregation in vitro has been monitored at different concentrations. ► Aβ(1–40) fibrillation does not always follow conventional kinetic mechanisms. ► We demonstrate non-linear features in the kinetics of Aβ(1–40) fibril formation. ► At high Aβ(1–40) concentrations secondary processes dictate fibrillation speed. ► Intermediate species may play significant roles on final amyloid fibril development. -- Abstract: The kinetic mechanism of amyloid aggregation remains to be fully understood. Investigations into the species present in the different kinetic phases can assist our comprehension of amyloid diseases and further our understanding of the mechanism behind amyloid β (Aβ) (1–40) peptide aggregation.more » Thioflavin T (ThT) fluorescence and transmission electron microscopy (TEM) have been used in combination to monitor Aβ(1–40) aggregation in vitro at both normal and higher than standard concentrations. The observed fibrillation behaviour deviates, in several respects, from standard concepts of the nucleation–polymerisation models and shows such features as concentration-dependent non-linear effects in the assembly mechanism. Aβ(1–40) fibrillation kinetics do not always follow conventional kinetic mechanisms and, specifically at high concentrations, intermediate structures become populated and secondary processes may further modify the fibrillation mechanism.« less

Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment.

PubMed

Li, Yaohang; Liu, Hui; Rata, Ionel; Jakobsson, Eric

2013-02-25

The rapidly increasing number of protein crystal structures available in the Protein Data Bank (PDB) has naturally made statistical analyses feasible in studying complex high-order inter-residue correlations. In this paper, we report a context-based secondary structure potential (CSSP) for assessing the quality of predicted protein secondary structures generated by various prediction servers. CSSP is a sequence-position-specific knowledge-based potential generated based on the potentials of mean force approach, where high-order inter-residue interactions are taken into consideration. The CSSP potential is effective in identifying secondary structure predictions with good quality. In 56% of the targets in the CB513 benchmark, the optimal CSSP potential is able to recognize the native secondary structure or a prediction with Q3 accuracy higher than 90% as best scored in the predicted secondary structures generated by 10 popularly used secondary structure prediction servers. In more than 80% of the CB513 targets, the predicted secondary structures with the lowest CSSP potential values yield higher than 80% Q3 accuracy. Similar performance of CSSP is found on the CASP9 targets as well. Moreover, our computational results also show that the CSSP potential using triplets outperforms the CSSP potential using doublets and is currently better than the CSSP potential using quartets.

Exemplary Secondary Vocational Education: An Exploratory Study of Seven Programs.

ERIC Educational Resources Information Center

Hayward, Becky J.; And Others

A study was conducted to explore the question of what works in secondary vocational education--whether exemplary vocational programs can be identified, whether their key features can be described, and whether there are lessons to be learned that can assist others in devising strategies to improve secondary vocational education. Methodology…

The Speed of Feature-Based Attention: Attentional Advantage Is Slow, but Selection Is Fast

ERIC Educational Resources Information Center

Huang, Liqiang

2010-01-01

When paying attention to a feature (e.g., red), no attentional advantage is gained in perceiving items with this feature in very brief displays. Therefore, feature-based attention seems to be slow. In previous feature-based attention studies, attention has often been measured as the difference in performance in a secondary task. In our recent work…

The macro-structural variability of the human neocortex.

PubMed

Kruggel, Frithjof

2018-05-15

The human neocortex shows a considerable individual structural variability. While primary gyri and sulci are found in all normally developed brains and bear clear-cut gross structural descriptions, secondary structures are highly variable and not present in all brains. The blend of common and individual structures poses challenges when comparing structural and functional results from quantitative neuroimaging studies across individuals, and sets limits on the precision of location information much above the spatial resolution of current neuroimaging methods. This work aimed at quantifying structural variability on the neocortex, and at assessing the spatial relationship between regions common to all brains and their individual structural variants. Based on structural MRI data provided as the "900 Subjects Release" of the Human Connectome Project, a data-driven analytic approach was employed here from which the definition of seven cortical "communities" emerged. Apparently, these communities comprise common regions of structural features, while the individual variability is confined within a community. Similarities between the community structure and the state of the brain development at gestation week 32 lead suggest that communities are segregated early. Subdividing the neocortex into communities is suggested as anatomically more meaningful than the traditional lobar structure. Copyright © 2018 Elsevier Inc. All rights reserved.

Bindings in working memory: The role of object-based attention.

PubMed

Gao, Zaifeng; Wu, Fan; Qiu, Fangfang; He, Kaifeng; Yang, Yue; Shen, Mowei

2017-02-01

Over the past decade, it has been debated whether retaining bindings in working memory (WM) requires more attention than retaining constituent features, focusing on domain-general attention and space-based attention. Recently, we proposed that retaining bindings in WM needs more object-based attention than retaining constituent features (Shen, Huang, & Gao, 2015, Journal of Experimental Psychology: Human Perception and Performance, doi: 10.1037/xhp0000018 ). However, only unitized visual bindings were examined; to establish the role of object-based attention in retaining bindings in WM, more emperical evidence is required. We tested 4 new bindings that had been suggested requiring no more attention than the constituent features in the WM maintenance phase: The two constituent features of binding were stored in different WM modules (cross-module binding, Experiment 1), from auditory and visual modalities (cross-modal binding, Experiment 2), or temporally (cross-time binding, Experiments 3) or spatially (cross-space binding, Experiments 4-6) separated. In the critical condition, we added a secondary object feature-report task during the delay interval of the change-detection task, such that the secondary task competed for object-based attention with the to-be-memorized stimuli. If more object-based attention is required for retaining bindings than for retaining constituent features, the secondary task should impair the binding performance to a larger degree relative to the performance of constituent features. Indeed, Experiments 1-6 consistently revealed a significantly larger impairment for bindings than for the constituent features, suggesting that object-based attention plays a pivotal role in retaining bindings in WM.

Characterising RNA secondary structure space using information entropy

PubMed Central

2013-01-01

Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, however, unclear how this probability distribution changes as a function of the input alignment. As prediction programs typically only return a single secondary structure, better characterisation of the underlying probability space of RNA secondary structures is of great interest. In this work, we show how to efficiently compute the information entropy of the probability distribution over RNA secondary structures produced for RNA alignments by a phylo-SCFG, and implement it for the PPfold model. We also discuss interpretations and applications of this quantity, including how it can clarify reasons for low prediction reliability scores. PPfold and its source code are available from http://birc.au.dk/software/ppfold/. PMID:23368905

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

PubMed Central

Garmann, Rees F.; Gopal, Ajaykumar; Athavale, Shreyas S.; Knobler, Charles M.; Gelbart, William M.; Harvey, Stephen C.

2015-01-01

The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. PMID:25752599

Large space deployable antenna systems

NASA Technical Reports Server (NTRS)

1978-01-01

The design technology is described for manufacturing a 20 m or larger space erectable antenna with high thermal stability, high dynamic stiffness, and minimum stowed size. The selected approach includes a wrap rib design with a cantilever beam basic element and graphite-epoxy composite lenticular cross section ribs. The rib configuration and powered type operated deploying mechanism are described and illustrated. Other features of the parabolic reflector discussed include weight and stowed diameter characteristics, structural dynamics characteristics, orbit thermal aperture limitations, and equivalent element and secondary (on axis) patterns. A block diagram of the multiple beam pattern is also presented.

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra.

PubMed

Micsonai, András; Wien, Frank; Bulyáki, Éva; Kun, Judit; Moussong, Éva; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

2018-06-11

Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

Two new coordination polymers with flexible alicyclic carboxylate and bipyridyl co-ligands bearing trinuclear [Ni3(COO)6] SBUs: Synthesis, crystal structures, and magnetic properties

NASA Astrophysics Data System (ADS)

Zhu, Xian-Dong; Li, Yong; Gao, Jian-Gang; Wang, Fen-Hua; Li, Qing-Hai; Yang, Hong-Xun; Chen, Lei

2017-02-01

Two new coordination polymers generally formulated as [Ni3(Hchda)2(chda)2(bpy)2(H2O)2]n (1) and [Ni3(Hchda)2(chda)2(bpp)2(H2O)2]n (2) [H2chda = 1,1'-cyclohexanediacetic acid, bpy = 4,4'-bipyridine and bpp = 1,3-bis(4-pyridyl)propane], have been successfully assembled through mixed-ligands synthetic strategy with flexible alicyclic carboxylate and bipyridyl ligands. There structures feature trinuclear nickel secondary building units connected via the bridging bipyridyl spacers to form two-dimensional (4,4) grid layer. The nature of the different N-donor auxiliary ligands leads to the discrepancy in supramolecular structure of the two compounds. Magnetic studies indicate the ferromagnetic intra-complex magnetic interaction in the molecule for 1 and 2.

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

DOE PAGES

Boiteau, Rene M.; Hoyt, David W.; Nicora, Carrie D.; ...

2018-01-17

Here, we introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS 2), and NMR in a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS 2 approach is well suited for discovery ofmore » new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases.« less

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boiteau, Rene M.; Hoyt, David W.; Nicora, Carrie D.

Here, we introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS 2), and NMR in a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS 2 approach is well suited for discovery ofmore » new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases.« less

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

PubMed Central

Hoyt, David W.; Nicora, Carrie D.; Kinmonth-Schultz, Hannah A.; Ward, Joy K.

2018-01-01

We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS2), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter out the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture, and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS2 approach is well suited to the discovery of new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases. PMID:29342073

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

Friction at ice-Ih / water interfaces

NASA Astrophysics Data System (ADS)

Louden, Patrick B.; Gezelter, J. Daniel

We present evidence that the prismatic and secondary prism facets of ice-Ih crystals possess structural features that alter the effective hydrophilicity of the ice / water interface. This is shown through molecular dynamics simulations of solid-liquid friction, where the prismatic { 10 1 0 } , secondary prism { 11 2 0 } , basal { 0001 } , and pyramidal { 20 2 1 } facets are drawn through liquid water. We find that the two prismatic facets exhibit differential solid-liquid friction coefficients when compared with the basal and pyramidal facets. These results are complemented by a model solid/liquid interface with tunable hydrophilicity. These simulations provide evidence that the two prismatic faces have a significantly smaller effective surface area in contact with the liquid water. The ice / water interfacial widths for all four crystal facets are similar (using both structural and dynamic measures), and were found to be independent of the shear rate. Additionally, decomposition of orientational time correlation functions show position-dependence for the short- and longer-time decay components close to the interface. Support for this project was provided by the National Science Foundation under Grant CHE-1362211. Computational time was provided by the Center for Research Computing (CRC) at the University of Notre Dame.

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

DOE PAGES

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.; ...

2017-07-18

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

Diagnosis and Management of Iridocorneal Endothelial Syndrome

PubMed Central

Sacchetti, Marta; Mantelli, Flavio; Macchi, Ilaria; Ambrosio, Oriella; Rama, Paolo

2015-01-01

The iridocorneal endothelial (ICE) syndrome is a rare ocular disorder that includes a group of conditions characterized by structural and proliferative abnormalities of the corneal endothelium, the anterior chamber angle, and the iris. Common clinical features include corneal edema, secondary glaucoma, iris atrophy, and pupillary anomalies, ranging from distortion to polycoria. The main subtypes of this syndrome are the progressive iris atrophy, the Cogan-Reese syndrome, and the Chandler syndrome. ICE syndrome is usually diagnosed in women in the adult age. Clinical history and complete eye examination including tonometry and gonioscopy are necessary to reach a diagnosis. Imaging techniques, such as in vivo confocal microscopy and ultrasound biomicroscopy, are used to confirm the diagnosis by revealing the presence of “ICE-cells” on the corneal endothelium and the structural changes of the anterior chamber angle. An early diagnosis is helpful to better manage the most challenging complications such as secondary glaucoma and corneal edema. Treatment of ICE-related glaucoma often requires glaucoma filtering surgery with antifibrotic agents and the use of glaucoma drainage implants should be considered early in the management of these patients. Visual impairment and pain associated with corneal edema can be successfully managed with endothelial keratoplasty. PMID:26451377

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

PubMed Central

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Richard A.; Brown, Steven D.

2017-01-01

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences. PMID:28769883

Structurally coloured secondary particles composed of black and white colloidal particles.

PubMed

Takeoka, Yukikazu; Yoshioka, Shinya; Teshima, Midori; Takano, Atsushi; Harun-Ur-Rashid, Mohammad; Seki, Takahiro

2013-01-01

This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field.

Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles

PubMed Central

Takeoka, Yukikazu; Yoshioka, Shinya; Teshima, Midori; Takano, Atsushi; Harun-Ur-Rashid, Mohammad; Seki, Takahiro

2013-01-01

This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field. PMID:23917891

Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication.

PubMed

Compton, L A; Johnson, W C

1986-05-15

Inverse circular dichroism (CD) spectra are presented for each of the five major secondary structures of proteins: alpha-helix, antiparallel and parallel beta-sheet, beta-turn, and other (random) structures. The fraction of the each secondary structure in a protein is predicted by forming the dot product of the corresponding inverse CD spectrum, expressed as a vector, with the CD spectrum of the protein digitized in the same way. We show how this method is based on the construction of the generalized inverse from the singular value decomposition of a set of CD spectra corresponding to proteins whose secondary structures are known from X-ray crystallography. These inverse spectra compute secondary structure directly from protein CD spectra without resorting to least-squares fitting and standard matrix inversion techniques. In addition, spectra corresponding to the individual secondary structures, analogous to the CD spectra of synthetic polypeptides, are generated from the five most significant CD eigenvectors.

URS DataBase: universe of RNA structures and their motifs.

PubMed

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/. © The Author(s) 2016. Published by Oxford University Press.

URS DataBase: universe of RNA structures and their motifs

PubMed Central

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA–protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification. Database URL: http://server3.lpm.org.ru/urs/ PMID:27242032

Chemical and structural indicators for large redox potentials in Fe-based positive electrode materials.

PubMed

Melot, Brent C; Scanlon, David O; Reynaud, Marine; Rousse, Gwenaëlle; Chotard, Jean-Noël; Henry, Marc; Tarascon, Jean-Marie

2014-07-23

Li-ion batteries have enabled a revolution in the way portable consumer-electronics are powered and will play an important role as large-scale electrochemical storage applications like electric vehicles and grid-storage are developed. The ability to identify and design promising new positive insertion electrodes will be vital in continuing to push Li-ion technology to its fullest potential. Utilizing a combination of computational tools and structural analysis, we report new indicators which will facilitate the recognition of phases with the desired redox potential. Most importantly of these, we find there is a strong correlation between the presence of Li ions sitting in close-proximity to the redox center of polyanionic phases and the open circuit voltage in Fe-based cathodes. This common structural feature suggests that the bonding associated with Li may have a secondary inductive effect which increases the ionic character of Fe bonds beyond what is typically expected based purely on arguments of electronegativity associated with the polyanionic group. This correlation is supported by ab initio calculations which show the Bader charge increases (reflecting an increased ionicity) in a nearly linear fashion with the experimental cell potentials. These features are demonstrated to be consistent across a wide variety of compositions and structures and should help to facilitate the design of new, high-potential, and environmentally sustainable insertion electrodes.

The persuasion network is modulated by drug-use risk and predicts anti-drug message effectiveness.

PubMed

Huskey, Richard; Mangus, J Michael; Turner, Benjamin O; Weber, René

2017-12-01

While a persuasion network has been proposed, little is known about how network connections between brain regions contribute to attitude change. Two possible mechanisms have been advanced. One hypothesis predicts that attitude change results from increased connectivity between structures implicated in affective and executive processing in response to increases in argument strength. A second functional perspective suggests that highly arousing messages reduce connectivity between structures implicated in the encoding of sensory information, which disrupts message processing and thereby inhibits attitude change. However, persuasion is a multi-determined construct that results from both message features and audience characteristics. Therefore, persuasive messages should lead to specific functional connectivity patterns among a priori defined structures within the persuasion network. The present study exposed 28 subjects to anti-drug public service announcements where arousal, argument strength, and subject drug-use risk were systematically varied. Psychophysiological interaction analyses provide support for the affective-executive hypothesis but not for the encoding-disruption hypothesis. Secondary analyses show that video-level connectivity patterns among structures within the persuasion network predict audience responses in independent samples (one college-aged, one nationally representative). We propose that persuasion neuroscience research is best advanced by considering network-level effects while accounting for interactions between message features and target audience characteristics. © The Author (2017). Published by Oxford University Press.

First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications

PubMed Central

Chen, Zhi-Teng; Du, Yu-Zhou

2017-01-01

The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer (AGN), whose dihydrouridine (DHU) arm was reduced to a small loop. There was also a large non-coding region (control region, CR) in the N. nankinensis mitogenome. The 1751 bp CR was the longest and had the highest A+T content (81.8%) among stoneflies. A large tandem repeat region, five potential stem-loop (SL) structures, four tRNA-like structures and four conserved sequence blocks (CSBs) were detected in the elongated CR. The presence of these tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes. These novel features of the elongated CR in N. nankinensis may have functions associated with the process of replication and transcription. Finally, phylogenetic reconstruction suggested that Nemouridae was the sister-group of Capniidae. PMID:28475163

First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications.

PubMed

Chen, Zhi-Teng; Du, Yu-Zhou

2017-05-05

The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer ( AGN ), whose dihydrouridine (DHU) arm was reduced to a small loop. There was also a large non-coding region (control region, CR) in the N. nankinensis mitogenome. The 1751 bp CR was the longest and had the highest A+T content (81.8%) among stoneflies. A large tandem repeat region, five potential stem-loop (SL) structures, four tRNA-like structures and four conserved sequence blocks (CSBs) were detected in the elongated CR. The presence of these tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes. These novel features of the elongated CR in N. nankinensis may have functions associated with the process of replication and transcription. Finally, phylogenetic reconstruction suggested that Nemouridae was the sister-group of Capniidae.

RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.

PubMed

Martinez, Hugo M; Maizel, Jacob V; Shapiro, Bruce A

2008-06-01

Using primary and secondary structure information of an RNA molecule, the program RNA2D3D automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing for the removal of any overlaps introduced by the initial generating procedure and for making conformational changes favorable to targeted features and subsequent refinement. With emphasis on fast exploration of alternative 3D conformations, one may interactively add or delete base-pairs, adjacent stems can be coaxially stacked or unstacked, single strands can be shaped to accommodate special constraints, and arbitrary subsets can be defined and manipulated as rigid bodies. Compaction, whereby base stacking within stems is optimally extended into connecting single strands, is also available as a means of strategically making the structures more compact and revealing folding motifs. Subsequent refinement of the first-order approximation, of modifications, and for the imposing of tertiary constraints is assisted with standard energy refinement techniques. Previously determined coordinates for any part of the molecule are readily incorporated, and any part of the modeled structure can be output as a PDB or XYZ file. Illustrative applications in the areas of ribozymes, viral kissing loops, viral internal ribosome entry sites, and nanobiology are presented.

Microstructure and phase composition characterization in a Co{sub 38}Ni{sub 33}Al{sub 29} ferromagnetic shape memory alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, J.B.

2016-08-15

Transmission electron microscopy was performed to investigate the microstructures of a secondary phase and its surrounding matrix in a Co{sub 38}Ni{sub 33}Al{sub 29} ferromagnetic shape memory alloy. The secondary phase shows a γ′ L1{sub 2} structure exhibiting a dendritic morphology with enclosed B2 austenite regions while the matrix shows the L1{sub 0} martensitic structure. A secondary phase-austenite-martensite sandwich structure with residual austenite ranging from several hundred nanometers to several micrometers wide is observed at the secondary phase-martensite interface due to the depletion of Co and enrichment of Al in the chemical gradient zone and the effect of the strong martensiticmore » start temperature dependency of the element concentrations. The crystallographic orientation relationship of the secondary phase and the B2 austenite fits the Kurdjumov-Sachs relationship. - Highlights: •The secondary phase has a γ′ L1{sub 2} structure exhibiting a dendritic morphology. •A secondary phase-austenite-martensite sandwich structure is observed. •The structural sandwich structure is due to elemental composition variation. •The secondary phase and the B2 austenite fit the Kurdjumov-Sachs relationship.« less

The turn of the screw: an exercise in protein secondary structure.

PubMed

Pikaart, Michael

2011-01-01

An exercise using simple paper strips to illustrate protein helical and sheet secondary structures is presented. Drawing on the rich historical context of the use of physical models in protein biochemistry by early practitioners, in particular Linus Pauling, the purpose of this activity is to cultivate in students a hands-on, intuitive sense of protein secondary structure and to complement the common computer-based structural portrayals often used in teaching biochemistry. As students fold these paper strips into model secondary structures, they will better grasp how intramolecular hydrogen bonds form in the folding of a polypeptide into secondary structure, and how these hydrogen bonds direct the overall shape of helical and sheet structures, including the handedness of the α-helix and the difference between right- and the left-handed twist. Copyright © 2010 Wiley Periodicals, Inc.

Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution

PubMed Central

Chursov, Andrey; Frishman, Dmitrij; Shneider, Alexander

2013-01-01

Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the ‘long-term evolution experiment’. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins. PMID:23783573

Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm.

PubMed

Zhang, Jian; Gao, Bo; Chai, Haiting; Ma, Zhiqiang; Yang, Guifu

2016-08-26

DNA-binding proteins (DBPs) play fundamental roles in many biological processes. Therefore, the developing of effective computational tools for identifying DBPs is becoming highly desirable. In this study, we proposed an accurate method for the prediction of DBPs. Firstly, we focused on the challenge of improving DBP prediction accuracy with information solely from the sequence. Secondly, we used multiple informative features to encode the protein. These features included evolutionary conservation profile, secondary structure motifs, and physicochemical properties. Thirdly, we introduced a novel improved Binary Firefly Algorithm (BFA) to remove redundant or noisy features as well as select optimal parameters for the classifier. The experimental results of our predictor on two benchmark datasets outperformed many state-of-the-art predictors, which revealed the effectiveness of our method. The promising prediction performance on a new-compiled independent testing dataset from PDB and a large-scale dataset from UniProt proved the good generalization ability of our method. In addition, the BFA forged in this research would be of great potential in practical applications in optimization fields, especially in feature selection problems. A highly accurate method was proposed for the identification of DBPs. A user-friendly web-server named iDbP (identification of DNA-binding Proteins) was constructed and provided for academic use.

α-Crystallins Are Small Heat Shock Proteins: Functional and Structural Properties.

PubMed

Tikhomirova, T S; Selivanova, O M; Galzitskaya, O V

2017-02-01

During its life cycle, a cell can be subjected to various external negative effects. Many proteins provide cell protection, including small heat shock proteins (sHsp) that have chaperone-like activity. These proteins have several important functions involving prevention of apoptosis and retention of cytoskeletal integrity; also, sHsp take part in the recovery of enzyme activity. The action mechanism of sHsp is based on the binding of hydrophobic regions exposed to the surface of a molten globule. α-Crystallins presented in chordate cells as two αA- and αB-isoforms are the most studied small heat shock proteins. In this review, we describe the main functions of α-crystallins, features of their secondary and tertiary structures, and examples of their partners in protein-protein interactions.

The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism

PubMed Central

Bækkedal, Cecilie; Haugen, Peik

2015-01-01

The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution of spf, show family-specific secondary structural features of Spot 42, and link highly conserved structural regions to mRNA target binding. PMID:26327359

ProQ3: Improved model quality assessments using Rosetta energy terms

PubMed Central

Uziela, Karolis; Shu, Nanjiang; Wallner, Björn; Elofsson, Arne

2016-01-01

Quality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function. The two new predictors also include residue conservation and terms corresponding to the agreement of a model with predicted secondary structure and surface area, as in ProQ2. We show that the performance of these predictors is on par with ProQ2 and significantly better than all other model quality assessment programs. Furthermore, we show that combining the input features from all three predictors, the resulting predictor ProQ3 performs better than any of the individual methods. ProQ3, ProQRosFA and ProQRosCen are freely available both as a webserver and stand-alone programs at http://proq3.bioinfo.se/. PMID:27698390

Multiscale Processes in Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Surjalal Sharma, A.; Jain, Neeraj

The characteristic scales of the plasma processes in magnetic reconnection range from the elec-tron skin-depth to the magnetohydrodynamic (MHD) scale, and cross-scale coupling among them play a key role. Modeling these processes requires different physical models, viz. kinetic, electron-magnetohydrodynamics (EMHD), Hall-MHD, and MHD. The shortest scale processes are at the electron scale and these are modeled using an EMHD code, which provides many features of the multiscale behavior. In simulations using initial conditions consisting of pertur-bations with many scale sizes the reconnection takes place at many sites and the plasma flows from these interact with each other. This leads to thin current sheets with length less than 10 electron skin depths. The plasma flows also generate current sheets with multiple peaks, as observed by Cluster. The quadrupole structure of the magnetic field during reconnection starts on the electron scale and the interaction of inflow to the secondary sites and outflow from the dominant site generates a nested structure. In the outflow regions, the interaction of the electron outflows generated at the neighboring sites lead to the development of electron vortices. A signature of the nested structure of the Hall field is seen in Cluster observations, and more details of these features are expected from MMS.

GeneratorSE: A Sizing Tool for Variable-Speed Wind Turbine Generators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sethuraman, Latha; Dykes, Katherine L

This report documents a set of analytical models employed by the optimization algorithms within the GeneratorSE framework. The initial values and boundary conditions employed for the generation of the various designs and initial estimates for basic design dimensions, masses, and efficiency for the four different models of generators are presented and compared with empirical data collected from previous studies and some existing commercial turbines. These models include designs applicable for variable-speed, high-torque application featuring direct-drive synchronous generators and low-torque application featuring induction generators. In all of the four models presented, the main focus of optimization is electromagnetic design with themore » exception of permanent-magnet and wire-wound synchronous generators, wherein the structural design is also optimized. Thermal design is accommodated in GeneratorSE as a secondary attribute by limiting the winding current densities to acceptable limits. A preliminary validation of electromagnetic design was carried out by comparing the optimized magnetic loading against those predicted by numerical simulation in FEMM4.2, a finite-element software for analyzing electromagnetic and thermal physics problems for electrical machines. For direct-drive synchronous generators, the analytical models for the structural design are validated by static structural analysis in ANSYS.« less

Meconium pseudocyst secondary to ileum volvulus perforation without peritoneal calcification: a case report.

PubMed

Valladares, Esther; Rodríguez, David; Vela, Antonio; Cabré, Sergi; Lailla, Josep Maria

2010-08-31

A case of giant meconium pseudocyst secondary to ileum volvulus perforation is presented. Conventional radiographic features of meconium peritonitis with secondary meconium pseudocyst formation are well described. Our case is unusual in comparison to other cases reported in the literature and needs to be reported because the meconium pseudocyst presented without the typical ultrasound features (calcifications, polyhydramnios and ascites) and was initially identified as an abdominal mass. We describe the case of a 29-year-old Caucasian woman in her third trimester of pregnancy, in which an abdominal mass was detected in the fetus. The newborn was diagnosed in the early neonatal period with meconium pseudocyst secondary to ileum volvulus perforation. The prenatal appearance of a meconium pseudocyst can be complemented by other signs of bowel obstruction (if present) such as polyhydramnios and fetal bowel dilatation. This is an original case report of interest to all clinicians in the perinatology and fetal ultrasound field. We consider that the utility of this case is the recognition that a meconium pseudocyst might appear without the typical ultrasound features and should be considered as a differential diagnosis when an echogenic intra-abdominal cyst is seen.

How Membrane-Active Peptides Get into Lipid Membranes.

PubMed

Sani, Marc-Antoine; Separovic, Frances

2016-06-21

The structure-function relationship for a family of antimicrobial peptides (AMPs) from the skin of Australian tree frogs is discussed and compared with that of peptide toxins from bee and Australian scorpion venoms. Although these membrane-active peptides induce a similar cellular fate by disrupting the lipid bilayer integrity, their lytic activity is achieved via different modes of action, which are investigated in relation to amino acid sequence, secondary structure, and membrane lipid composition. In order to better understand what structural features govern the interaction between peptides and lipid membranes, cell-penetrating peptides (CPPs), which translocate through the membrane without compromising its integrity, are also discussed. AMPs possess membrane lytic activities that are naturally designed to target the cellular membrane of pathogens or competitors. They are extremely diverse in amino acid composition and often show specificity against a particular strain of microbe. Since our antibiotic arsenal is declining precariously in the face of the rise in multiantibiotic resistance, AMPs increasingly are seen as a promising alternative. In an effort to understand their molecular mechanism, biophysical studies of a myriad of AMPs have been reported, yet no unifying mechanism has emerged, rendering difficult the rational design of drug leads. Similarly, a wide variety of cytotoxic peptides are found in venoms, the best known being melittin, yet again, predicting their activity based on a particular amino acid composition or secondary structure remains elusive. A common feature of these membrane-active peptides is their preference for the lipid environment. Indeed, they are mainly unstructured in solution and, in the presence of lipid membranes, quickly adsorb onto the surface, change their secondary structure, eventually insert into the hydrophobic core of the membrane bilayer, and finally disrupt the bilayer integrity. These steps define the molecular mechanism by which these membrane-active peptides lyse membranes. The last class of membrane-active peptides discussed are the CPPs, which translocate across the lipid bilayer without inducing severe disruption and have potential as drug vehicles. CPPs are typically highly charged and can show antimicrobial activity by targeting an intracellular target rather than via a direct membrane lytic mechanism. A critical aspect in the structure-function relationship of membrane-active peptides is their specific activity relative to the lipid membrane composition of the cell target. Cell membranes have a wide diversity of lipids, and those of eukaryotic and prokaryotic species differ greatly in composition and structure. The activity of AMPs from Australian tree frogs, toxins, and CPPs has been investigated within various lipid systems to assess whether a relationship between peptide and membrane composition could be identified. NMR spectroscopy techniques are being used to gain atomistic details of how these membrane-active peptides interact with model membranes and cells, and in particular, competitive assays demonstrate the difference between affinity and activity for a specific lipid environment. Overall, the interactions between these relatively small sized peptides and various lipid bilayers give insight into how these peptides function at the membrane interface.

Crisis Management for Secondary Education: A Survey of Secondary Education Directors in Greece

ERIC Educational Resources Information Center

Savelides, Socrates; Mihiotis, Athanassios; Koutsoukis, Nikitas-Spiros

2015-01-01

Purpose: The Greek secondary education system lacks a formal crisis management system. The purpose of this paper is to address this problem as follows: elicit current crisis management practices, outline features for designing a formal crisis management system in Greece. Design/methodology/approach: The research is based on a survey conducted with…

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

PubMed Central

Eudes, Richard; Le Tuan, Khanh; Delettré, Jean; Mornon, Jean-Paul; Callebaut, Isabelle

2007-01-01

Background Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. Results The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for α-helices or β-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that β-strands and especially α-helices are generally over-predicted within the limits of typical β and α hydrophobic clusters. Conclusion The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction. PMID:17210072

POLYPOIDAL CHOROIDAL VASCULOPATHY SECONDARY TO A STABLE CHOROIDAL NEVUS.

PubMed

Wong, James G; Lai, Xin Jie; Sarafian, Richard Y; Wong, Hon Seng; Smith, Jeremy B

2016-01-01

Choroidal nevus is the most common ocular fundus tumor in adults. Previous studies have widely discussed the features of choroidal neovascularization secondary to nevus and its treatment options. Polypoidal choroidal vasculopathy (PCV) is an exudative chorioretinopathy that is often underdiagnosed. Clinical features, natural history, and treatment response of PCV are distinct from occult choroidal neovascularization. Polypoidal choroidal vasculopathy secondary to choroidal nevus has not been previously documented. We report a patient with a history of stable choroidal nevus who developed a polypoidal lesion at the edge of the nevus lesion. A white woman who presented with a choroidal nevus and clinical features of PCV was examined using fundoscopy, optical coherence tomography, fluorescein angiography, and indocyanine green angiography. A polypoidal lesion with an associated branching vascular network adjacent to the nevus was demonstrated by optical coherence tomography, fluorescein angiography, and indocyanine green angiography. The patient was asymptomatic and was managed conservatively. Our case showed that PCV developing in association with a stable choroidal nevus. Pathogenic mechanisms of this condition may include chronic degenerative or inflammatory changes at the level of the retinal pigment epithelium resulting in vascular changes. Unlike treatment of occult choroidal neovascularization secondary to nevus, optimal management of PCV secondary to nevus may vary. Indocyanine green angiography is the gold standard for the diagnosis of PCV and is a useful investigation in atypical choroidal neovascularization.

Mass spectrometric study of the negative and positive secondary ions emitted from ethanol microdroplets by MeV-energy heavy ion impact

NASA Astrophysics Data System (ADS)

Kitajima, Kensei; Majima, Takuya; Nishio, Tatsuya; Oonishi, Yoshiki; Mizutani, Shiori; Kohno, Jun-ya; Saito, Manabu; Tsuchida, Hidetsugu

2018-06-01

We have investigated the negative and positive secondary ions emitted from ethanol droplets by 4.0-MeV C3+ impact to reveal the characteristic features of the reaction processes induced by fast heavy ions at the liquid ethanol surface. Analysis of the secondary ions was performed by time-of-flight mass spectrometry for microdroplet targets in a high vacuum environment. Fragment ions, deprotonated cluster ions, and trace amounts of the reaction product ions are observed in the negative secondary ions. The main fragment anions are C2HmO- (m = 1, 3, and 5) and C2H- generated by loss of hydrogen and oxygen atoms. The reaction product anions include deprotonated glycols, larger alcohols, and their dehydrated and dehydrogenated forms generated by secondary reactions between fragments and radicals. Furthermore, C3Hm- (m = 0-2) and C4Hm- (m = 0 and 1) are observed, which could be produced through a plasma state generated in the heavy ion track. Deprotonated ethanol cluster ions, [(EtOH)n - H]-, are observed up to about n = 25. [(EtOH)n - H]- have smaller kinetic energies than the protonated cluster ions (EtOH)nH+. This probably represents the effect of the positive Coulomb potential transiently formed in the ion track. We also discuss the size distributions and structures of the water- and CH2OH-radical-attached ethanol cluster ions.

Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family.

PubMed

Dos Santos, Helena G; Siltberg-Liberles, Jessica

2016-09-19

One of the largest multigene families in Metazoa are the tyrosine kinases (TKs). These are important multifunctional proteins that have evolved as dynamic switches that perform tyrosine phosphorylation and other noncatalytic activities regulated by various allosteric mechanisms. TKs interact with each other and with other molecules, ultimately activating and inhibiting different signaling pathways. TKs are implicated in cancer and almost 30 FDA-approved TK inhibitors are available. However, specific binding is a challenge when targeting an active site that has been conserved in multiple protein paralogs for millions of years. A cassette domain (CD) containing SH3-SH2-Tyrosine Kinase domains reoccurs in vertebrate nonreceptor TKs. Although part of the CD function is shared between TKs, it also presents TK specific features. Here, the evolutionary dynamics of sequence, structure, and phosphorylation across the CD in 17 TK paralogs have been investigated in a large-scale study. We establish that TKs often have ortholog-specific structural disorder and phosphorylation patterns, while secondary structure elements, as expected, are highly conserved. Further, domain-specific differences are at play. Notably, we found the catalytic domain to fluctuate more in certain secondary structure elements than the regulatory domains. By elucidating how different properties evolve after gene duplications and which properties are specifically conserved within orthologs, the mechanistic understanding of protein evolution is enriched and regions supposedly critical for functional divergence across paralogs are highlighted. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

OPTIC NERVE INFILTRATION BY RETINOBLASTOMA: Predictive Clinical Features and Outcome.

PubMed

Kaliki, Swathi; Tahiliani, Prerana; Mishra, Dilip K; Srinivasan, Visweswaran; Ali, Mohammed Hasnat; Reddy, Vijay Anand P

2016-06-01

To identify the clinical features predictive of any optic nerve infiltration and postlaminar optic nerve infiltration by retinoblastoma on histopathology and to report the outcome (metastasis and death) in these patients. Retrospective study. Of the 403 patients who underwent primary enucleation for retinoblastoma, 196 patients had optic nerve tumor infiltration (Group 1) and 207 patients had no evidence of optic nerve tumor infiltration (Group 2). Group 1 included patients with prelaminar (n = 47; 24%), laminar (n = 74; 38%), and postlaminar tumor infiltration with or without involving optic nerve transection (n = 74; 38%). Comparing Group 1 and Group 2, the patients in Group 1 had prolonged duration of symptoms (>6 months) (16% vs. 8%; P = 0.02) and were associated with no vision at presentation (23% vs. 10%; P = 0.01), higher rates of secondary glaucoma (42% vs. 12%; P < 0.0001), iris neovascularization (39% vs. 23%; P < 0.001), and larger tumors (mean tumor thickness, 12.8 mm vs. 12 mm; P = 0.0001). There was a higher prevalence of metastasis in Group 1 than in Group 2 (4% vs. 0%; P = 0.006). On multivariate analysis, clinical features predictive of any optic nerve tumor infiltration secondary glaucoma (hazard ratio = 5.38; P < 0.001) and those predictive of postlaminar optic nerve tumor infiltration included iris neovascularization (hazard ratio = 2.66; P = 0.001) and secondary glaucoma (hazard ratio = 3.13; P < 0.001). In this study, clinical features predictive of any optic nerve tumor infiltration included secondary glaucoma and those predictive of postlaminar optic nerve tumor infiltration included iris neovascularization and secondary glaucoma. Despite adjuvant treatment in those with postlaminar optic nerve tumor infiltration, metastasis occurred in 8% of patients.

Obtaining environmental measures to facilitate vertebrate habitat modeling

USGS Publications Warehouse

Karl, J.W.; Wright, N.M.; Heglund, P.J.; Scott, J.M.

1999-01-01

Published literature generally lacks habitat information needed to adequately model the habitats of most wildlife species at large scales (>1:100,000). We searched in primary and secondary literature for occurrence of several potentially useful habitat measures for 20 species of interest to the Idaho Department of Fish and Game. We found adequate information for modeling only the habitats of certain game species and species of special interest. We suggest that many more researchers could collect simple habitat information regarding vegetation composition and structure, topographic features, soils, temperature, and distance to special landscape features such that current research expenses would not be increased significantly. We recommend that habitat data be consistently reported in peer-reviewed literature or deposited into a central data repository. This will not only help fill the gaps in our current knowledge of wildlife but also place it in a format that is readily accessible by the scientific community.

Histological features of the vomeronasal organ in the giraffe, Giraffa camelopardalis.

PubMed

Kondoh, Daisuke; Nakamura, Kentaro G; Ono, Yurie S; Yuhara, Kazutoshi; Bando, Gen; Watanabe, Kenichi; Horiuchi, Noriyuki; Kobayashi, Yoshiyasu; Sasaki, Motoki; Kitamura, Nobuo

2017-06-01

The vomeronasal organ (VNO) that preferentially detects species-specific substances is diverse among animal species, and its morphological properties seem to reflect the ecological features of animals. This histological study of two female reticulated giraffes (Giraffa camelopardalis reticulata) found that the VNO is developed in giraffes. The lateral and medial regions of the vomeronasal lumen were covered with sensory and nonsensory epithelia, respectively. The vomeronasal glands were positive for periodic acid-Schiff and alcian blue (pH 2.5) stains. The VNO comprises several large veins like others in the order Cetartiodactyla, suggesting that these veins function in a pumping mechanism in this order. In addition, numerous thin-walled vessels located immediately beneath the epithelia covering the lumen entirely surrounded the vomeronasal lumen. This sponge-like structure might function as a specific secondary pump in giraffes. © 2017 Wiley Periodicals, Inc.

Fingerprinting Breast Cancer vs. Normal Mammary Cells by Mass Spectrometric Analysis of Volatiles

NASA Astrophysics Data System (ADS)

He, Jingjing; Sinues, Pablo Martinez-Lozano; Hollmén, Maija; Li, Xue; Detmar, Michael; Zenobi, Renato

2014-06-01

There is increasing interest in the development of noninvasive diagnostic methods for early cancer detection, to improve the survival rate and quality of life of cancer patients. Identification of volatile metabolic compounds may provide an approach for noninvasive early diagnosis of malignant diseases. Here we analyzed the volatile metabolic signature of human breast cancer cell lines versus normal human mammary cells. Volatile compounds in the headspace of conditioned culture medium were directly fingerprinted by secondary electrospray ionization-mass spectrometry. The mass spectra were subsequently treated statistically to identify discriminating features between normal vs. cancerous cell types. We were able to classify different samples by using feature selection followed by principal component analysis (PCA). Additionally, high-resolution mass spectrometry allowed us to propose their chemical structures for some of the most discriminating molecules. We conclude that cancerous cells can release a characteristic odor whose constituents may be used as disease markers.

[Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella].

PubMed

Wang, Pengfei; Wang, Yingfang; Duan, Guangcai; Xue, Zerun; Wang, Linlin; Guo, Xiangjiao; Yang, Haiyan; Xi, Yuanlin

2015-04-01

This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.

Impacts of structuring the electronic health record: Results of a systematic literature review from the perspective of secondary use of patient data.

PubMed

Vuokko, Riikka; Mäkelä-Bengs, Päivi; Hyppönen, Hannele; Lindqvist, Minna; Doupi, Persephone

2017-01-01

To explore the impacts that structuring of electronic health records (EHRs) has had from the perspective of secondary use of patient data as reflected in currently published literature. This paper presents the results of a systematic literature review aimed at answering the following questions; (1) what are the common methods of structuring patient data to serve secondary use purposes; (2) what are the common methods of evaluating patient data structuring in the secondary use context, and (3) what impacts or outcomes of EHR structuring have been reported from the secondary use perspective. The reported study forms part of a wider systematic literature review on the impacts of EHR structuring methods and evaluations of their impact. The review was based on a 12-step systematic review protocol adapted from the Cochrane methodology. Original articles included in the study were divided into three groups for analysis and reporting based on their use focus: nursing documentation, medical use and secondary use (presented in this paper). The analysis from the perspective of secondary use of data includes 85 original articles from 1975 to 2010 retrieved from 15 bibliographic databases. The implementation of structured EHRs can be roughly divided into applications for documenting patient data at the point of care and application for retrieval of patient data (post hoc structuring). Two thirds of the secondary use articles concern EHR structuring methods which were still under development or in the testing phase. of structuring patient data such as codes, terminologies, reference information models, forms or templates and documentation standards were usually applied in combination. Most of the identified benefits of utilizing structured EHR data for secondary use purposes concentrated on information content and quality or on technical quality and reliability, particularly in the case of Natural Language Processing (NLP) studies. A few individual articles evaluated impacts on care processes, productivity and costs, patient safety, care quality or other health impacts. In most articles these endpoints were usually discussed as goals of secondary use and less as evidence-supported impacts, resulting from the use of structured EHR data for secondary purposes. Further studies and more sound evaluation methods are needed for evidence on how EHRs are utilized for secondary purposes, and how structured documentation methods can serve different users' needs, e.g. administration, statistics and research and development, in parallel to medical use purposes. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.

PubMed

Sborgi, Lorenzo; Verma, Abhinav; Muñoz, Victor; de Alba, Eva

2011-01-01

GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein structures.

Dissecting the structural determinants for the difference in mechanical stability of silk and amyloid beta-sheet stacks.

PubMed

Xiao, Senbo; Xiao, Shijun; Gräter, Frauke

2013-06-14

Stacking of β-sheets results in a protein super secondary structure with remarkable mechanical properties. β-Stacks are the determinants of a silk fiber's resilience and are also the building blocks of amyloid fibrils. While both silk and amyloid-type crystals are known to feature a high resistance against rupture, their structural and mechanical similarities and particularities are yet to be fully understood. Here, we systematically compare the rupture force and stiffness of amyloid and spider silk poly-alanine β-stacks of comparable sizes using Molecular Dynamics simulations. We identify the direction of force application as the primary determinant of the rupture strength; β-sheets in silk are orientated along the fiber axis, i.e. the pulling direction, and consequently require high forces in the several nanoNewton range for shearing β-strands apart, while β-sheets in amyloid are oriented vertically to the fiber, allowing a zipper-like rupture at sub-nanoNewton forces. A secondary factor rendering amyloid β-stacks softer and weaker than their spider silk counterparts is the sub-optimal side-chain packing between β-sheets due to the sequence variations of amyloid-forming proteins as opposed to the perfectly packed poly-alanine β-sheets of silk. Taken together, amyloid fibers can reach the stiffness of silk fibers in spite of their softer and weaker β-sheet arrangement as they are missing a softening amorphous matrix.

Mechanistic Study on Electron Capture Dissociation of the Oligosaccharide-Mg2+ Complex

NASA Astrophysics Data System (ADS)

Huang, Yiqun; Pu, Yi; Yu, Xiang; Costello, Catherine E.; Lin, Cheng

2014-08-01

Electron capture dissociation (ECD) has shown great potential in structural characterization of glycans. However, our current understanding of the glycan ECD process is inadequate for accurate interpretation of the complex glycan ECD spectra. Here, we present the first comprehensive theoretical investigation on the ECD fragmentation behavior of metal-adducted glycans, using the cellobiose-Mg2+ complex as the model system. Molecular dynamics simulation was carried out to determine the typical glycan-Mg2+ binding patterns and the lowest-energy conformer identified was used as the initial geometry for density functional theory-based theoretical modeling. It was found that the electron is preferentially captured by Mg2+ and the resultant Mg+• can abstract a hydroxyl group from the glycan moiety to form a carbon radical. Subsequent radical migration and α-cleavage(s) result in the formation of a variety of product ions. The proposed hydroxyl abstraction mechanism correlates well with the major features in the ECD spectrum of the Mg2+-adducted cellohexaose. The mechanism presented here also predicts the presence of secondary, radical-induced fragmentation pathways. These secondary fragment ions could be misinterpreted, leading to erroneous structural determination. The present study highlights an urgent need for continuing investigation of the glycan ECD mechanism, which is imperative for successful development of bioinformatics tools that can take advantage of the rich structural information provided by ECD of metal-adducted glycans.

Nanolayered Features of Collagen-like Peptides

NASA Technical Reports Server (NTRS)

Valluzzi, Regina; Bini, Elisabetta; Haas, Terry; Cebe, Peggy; Kaplan, David L.

2003-01-01

We have been investigating collagen-like model oligopeptides as molecular bases for complex ordered biomimetic materials. The collagen-like molecules incorporate aspects of native collagen sequence and secondary structure. Designed modifications to native primary and secondary structure have been incorporated to control the nanostructure and microstructure of the collagen-like materials produced. We find that the collagen-like molecules form a number of lyotropic rod liquid crystalline phases, which because of their strong temperature dependence in the liquid state can also be viewed as solvent intercalated thermotropic liquid crystals. The liquid crystalline phases formed by the molecules can be captured in the solid state by drying off solvent, resulting in solid nanopatterned (chemically and physically) thermally stable (to greater than 100 C) materials. Designed sequences which stabilize smectic phases have allowed a variety of nanoscale multilayered biopolymeric materials to be developed. Preliminary investigations suggest that chemical patterns running perpendicular to the smectic layer plane can be functionalized and used to localize a variety of organic, inorganic, and organometallic moieties in very simple multilayered nanocomposites. The phase behavior of collagen-like oligopeptide materials is described, emphasizing the correlation between mesophase, molecular orientation, and chemical patterning at the microscale and nanoscale. In many cases, the textures observed for smectic and hexatic phase collagens are remarkably similar to the complex (and not fully understood) helicoids observed in biological collagen-based tissues. Comparisons between biological morphologies and collagen model liquid crystalline (and solidified materials) textures may help us understand the molecular features which impart order and function to the extracellular matrix and to collagen-based mineralized tissues. Initial studies have utilized synthetic collagen-like peptides while future work will also focus on similar sequences generated via genetic engineering methods.

The Design and Usage of the New Data Management Features in NASTRAN

NASA Technical Reports Server (NTRS)

Pamidi, P. R.; Brown, W. K.

1984-01-01

Two new data management features are installed in the April 1984 release of NASTRAN. These two features are the Rigid Format Data Base and the READFILE capability. The Rigid Format Data Base is stored on external files in card image format and can be easily maintained and expanded by the use of standard text editors. This data base provides the user and the NASTRAN maintenance contractor with an easy means for making changes to a Rigid Format or for generating new Rigid Formats without unnecessary compilations and link editing of NASTRAN. Each Rigid Format entry in the data base contains the Direct Matrix Abstraction Program (DMAP), along with the associated restart, DMAP sequence subset and substructure control flags. The READFILE capability allows an user to reference an external secondary file from the NASTRAN primary input file and to read data from this secondary file. There is no limit to the number of external secondary files that may be referenced and read.

An experimental study of secondary vortex structure in mixing layers

NASA Technical Reports Server (NTRS)

Bell, J. H.; Mehta, Rabindra D.

1990-01-01

This report covers the first eight months of an experimental research project on the secondary vortex structure in plane mixing layers. The aim of the project is to obtain quantitative data on the behavior of the secondary structure in a turbulent mixing layer at reasonable reynolds numbers (Re(sub delta(sub w)) approx. 50,000). In particular, we hope to resolve the questions of how the scale of the secondary vortex structure changes with the scale of the mixing layer, and whether the structures are fixed in space, or whether they 'meander' in the spanwise direction.

Convergence of an iterative procedure for large-scale static analysis of structural components

NASA Technical Reports Server (NTRS)

Austin, F.; Ojalvo, I. U.

1976-01-01

The paper proves convergence of an iterative procedure for calculating the deflections of built-up component structures which can be represented as consisting of a dominant, relatively stiff primary structure and a less stiff secondary structure, which may be composed of one or more substructures that are not connected to one another but are all connected to the primary structure. The iteration consists in estimating the deformation of the primary structure in the absence of the secondary structure on the assumption that all mechanical loads are applied directly to the primary structure. The j-th iterate primary structure deflections at the interface are imposed on the secondary structure, and the boundary loads required to produce these deflections are computed. The cycle is completed by applying the interface reaction to the primary structure and computing its updated deflections. It is shown that the mathematical condition for convergence of this procedure is that the maximum eigenvalue of the equation relating primary-structure deflection to imposed secondary-structure deflection be less than unity, which is shown to correspond with the physical requirement that the secondary structure be more flexible at the interface boundary.

Personal goals as predictors of intended classroom goals: comparing elementary and secondary school pre-service teachers.

PubMed

Daniels, Lia M; Frenzel, Anne C; Stupnisky, Robert H; Stewart, Tara L; Perry, Raymond P

2013-09-01

The literature documents fewer classroom mastery goal structures in secondary school compared to elementary. However, little is known about how personal achievement goals may influence classroom goal structures. This is especially true at the level of pre-service teachers. Our objective was to investigate if pre-service teachers' personal goals predicted their intended classroom goal structures. Participants were 125 elementary and 175 secondary school pre-service teachers from two Western Canadian universities. Structural equation modelling was used to examine if the structural relationships and latent means of personal and intended classroom goal structures differed for elementary and secondary school pre-service teachers. The results revealed that personal goals predicted the goal structures that pre-service teachers intended to establish; however, the relationships and means differed between elementary and secondary school pre-service teachers. Specifically, personal mastery-approach goals positively predicted classroom mastery goals much more strongly at the elementary than the secondary level. Furthermore, elementary pre-service teachers had significantly higher latent mean scores on personal mastery-approach goals than their secondary counterparts. It seems possible that the currently documented differences between classroom goal structures noted for elementary compared to secondary school may be based on the personal goals endorsed as pre-service teachers. The results are further discussed in terms of alignment with research on practising teachers' personal and classroom goals and implications for teacher education. © 2012 The British Psychological Society.

Metastable ripple phase of fully hydrated dipalmitoylphosphatidylcholine as studied by small angle x-ray scattering

PubMed Central

Yao, Haruhiko; Matuoka, Sinzi; Tenchov, Boris; Hatta, Ichiro

1991-01-01

Fully hydrated dipalmitoylphosphatidylcholine (DPPC) undergoes liquid crystalline to metastable Pβ, phase transition in cooling. A small angle x-ray scattering study has been performed for obtaining further evidence about the structure of this phase. From a high-resolution observation of x-ray diffraction profiles, a distinct multipeak pattern has become obvious. Among them the (01) reflection in the secondary ripple structure is identified clearly. There are peaks assigned straightforwardly to (10) and (20) reflections in the primary ripple structure and peaks assigned to (10) and (20) reflections in the secondary ripple structure. Therefore the multipeak pattern is due to superposition of the reflections cause by the primary and secondary ripple structures. The lattice parameters are estimated as follows: for the primary ripple structure a = 7.09 nm, b = 13.64 nm, and γ = 95°, and for the secondary ripple structure a = 8.2 nm, b = 26.6 nm, and γ = 90°. The lattice parameters thus obtained for the secondary ripple structure are not conclusive, however. The hydrocarbon chains in the primary ripple structure have been reported as being tilted against the bilayer plane and, on the other hand, the hydrocarbon chains in the secondary ripple structure are likely to be perpendicular to the bilayer plane. This fact seems to be related to a sequential mechanism of phase transitions. On heating from the Lβ, phase where the hydrocarbon chains are tilted the primary ripple structure having tilted hydrocarbon chains takes place and on cooling from the Lα phase where the hydrocarbon chains are not tilted the secondary ripple structure with untilted chains tends to be stabilized. It appears that the truly metastable ripple phase is expressed by the second ripple structure although in the course of the actual cooling transition both the secondary and primary ripple structures form and coexist. PMID:19431787

Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

PubMed Central

Seligmann, Hervé; Raoult, Didier

2018-01-01

We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5′ UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing). PMID:29449833

Structure and Location of the Regulatory β Subunits in the (αβγδ)4 Phosphorylase Kinase Complex* ♦

PubMed Central

Nadeau, Owen W.; Lane, Laura A.; Xu, Dong; Sage, Jessica; Priddy, Timothy S.; Artigues, Antonio; Villar, Maria T.; Yang, Qing; Robinson, Carol V.; Zhang, Yang; Carlson, Gerald M.

2012-01-01

Phosphorylase kinase (PhK) is a hexadecameric (αβγδ)4 complex that regulates glycogenolysis in skeletal muscle. Activity of the catalytic γ subunit is regulated by allosteric activators targeting the regulatory α, β, and δ subunits. Three-dimensional EM reconstructions of PhK show it to be two large (αβγδ)2 lobes joined with D2 symmetry through interconnecting bridges. The subunit composition of these bridges was unknown, although indirect evidence suggested the β subunits may be involved in their formation. We have used biochemical, biophysical, and computational approaches to not only address the quaternary structure of the β subunits within the PhK complex, i.e. whether they compose the bridges, but also their secondary and tertiary structures. The secondary structure of β was determined to be predominantly helical by comparing the CD spectrum of an αγδ subcomplex with that of the native (αβγδ)4 complex. An atomic model displaying tertiary structure for the entire β subunit was constructed using chemical cross-linking, MS, threading, and ab initio approaches. Nearly all this model is covered by two templates corresponding to glycosyl hydrolase 15 family members and the A subunit of protein phosphatase 2A. Regarding the quaternary structure of the β subunits, they were directly determined to compose the four interconnecting bridges in the (αβγδ)4 kinase core, because a β4 subcomplex was observed through both chemical cross-linking and top-down MS of PhK. The predicted model of the β subunit was docked within the bridges of a cryoelectron microscopic density envelope of PhK utilizing known surface features of the subunit. PMID:22969083

Positional Accuracy in Optical Trap-Assisted Nanolithography

NASA Astrophysics Data System (ADS)

Arnold, Craig B.; McLeod, Euan

2009-03-01

The ability to directly print patterns on size scales below 100 nm is important for many applications where the production or repair of high resolution and density features are important. Laser-based direct-write methods have the benefit of quickly and easily being able to modify and create structures on existing devices, but feature sizes are conventionally limited by diffraction. In this presentation, we show how to overcome this limit with a new method of probe-based near-field nanopatterning in which we employ a CW laser to optically trap and manipulate dispersed microspheres against a substrate using a 2-d Bessel beam optical trap. A secondary, pulsed nanosecond laser at 355 nm is directed through the bead and used to modify the surface below the microsphere, taking advantage of the near-field enhancement in order to produce materials modification with feature sizes under 100 nm. Here, we analyze the 3-d positioning accuracy of the microsphere through analytic modeling as a function of experimental parameters. The model is verified in all directions for our experimental conditions and is used to predict the conditions required for improved positional accuracy.

The Laurencia Paradox: An Endless Source of Chemodiversity.

PubMed

Harizani, Maria; Ioannou, Efstathia; Roussis, Vassilios

Nature, the most prolific source of biological and chemical diversity, has provided mankind with treatments for health problems since ancient times and continues to be the most promising reservoir of bioactive chemicals for the development of modern drugs. In addition to the terrestrial organisms that still remain a promising source of new bioactive metabolites, the marine environment, covering approximately 70% of the Earth's surface and containing a largely unexplored biodiversity, offers an enormous resource for the discovery of novel compounds. According to the MarinLit database, more than 27,000 metabolites from marine macro- and microorganisms have been isolated to date providing material and key structures for the development of new products in the pharmaceutical, food, cosmeceutical, chemical, and agrochemical sectors. Algae, which thrive in the euphotic zone, were among the first marine organisms that were investigated as sources of food, nutritional supplements, soil fertilizers, and bioactive metabolites.Red algae of the genus Laurencia are accepted unanimously as one of the richest sources of new secondary metabolites. Their cosmopolitan distribution, along with the chemical variation influenced to a significant degree by environmental and genetic factors, have resulted in an endless parade of metabolites, often featuring multiple halogenation sites.The present contribution, covering the literature until August 2015, offers a comprehensive view of the chemical wealth and the taxonomic problems currently impeding chemical and biological investigations of the genus Laurencia. Since mollusks feeding on Laurencia are, in many cases, bioaccumulating, and utilize algal metabolites as chemical weaponry against natural enemies, metabolites of postulated dietary origin of sea hares that feed on Laurencia species are also included in the present review. Altogether, 1047 secondary metabolites, often featuring new carbocyclic skeletons, have been included.The chapter addresses: (1) the "Laurencia complex", the botanical description and the growth and population dynamics of the genus, as well as its chemical diversity and ecological relations; (2) the secondary metabolites, which are organized according to their chemical structures and are classified into sesquiterpenes, diterpenes, triterpenes, acetogenins, indoles, aromatic compounds, steroids, and miscellaneous compounds, as well as their sources of isolation which are depicted in tabulated form, and (3) the biological activity organized according to the biological target and the ecological functions of Laurencia metabolites.

RNAstructure: software for RNA secondary structure prediction and analysis.

PubMed

Reuter, Jessica S; Mathews, David H

2010-03-15

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.

Study on the Effect of Secondary Banded Structure on the Fatigue Property of Non-Quenched and Tempered Micro Alloyed Steel

NASA Astrophysics Data System (ADS)

Yajie, Cheng; Qingliang, Liao; Yue, Zhang

Due to composition segregation and cooling speed, streamline or banded structure were often obtained in the thermal forming parts along the direction of parts forming. Generally speaking, banded structure doesn't decrease the longitudinal mechanical properties, so the secondary banded structure can't get enough attention. The effect of secondary banded structure on the fatigue properties of micro alloyed DG20Mn and 35CrMo steel was investigated using the axial tensile fatigue test of stress ratio of 0.1. The result shows that secondary banded structure was obtained in the center of the steel parts, because of the composition segregation and the lower cooling rate in center part of steel. Secondary banded structure has no significant effect on axial tensile properties of both DG20Mn and 35CrMo, but decreases the axial tensile fatigue performance of DG20Mn steel. This study suggests that under the high cyclic tensile stress, multi-source damage cracks in steel initiated by large strain of pearlite of secondary banded structure, which is larger than damage strain, is the major factor of the decrease of fatigue life of steel.

antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers.

PubMed

Blin, Kai; Medema, Marnix H; Kazempour, Daniyal; Fischbach, Michael A; Breitling, Rainer; Takano, Eriko; Weber, Tilmann

2013-07-01

Microbial secondary metabolites are a potent source of antibiotics and other pharmaceuticals. Genome mining of their biosynthetic gene clusters has become a key method to accelerate their identification and characterization. In 2011, we developed antiSMASH, a web-based analysis platform that automates this process. Here, we present the highly improved antiSMASH 2.0 release, available at http://antismash.secondarymetabolites.org/. For the new version, antiSMASH was entirely re-designed using a plug-and-play concept that allows easy integration of novel predictor or output modules. antiSMASH 2.0 now supports input of multiple related sequences simultaneously (multi-FASTA/GenBank/EMBL), which allows the analysis of draft genomes comprising multiple contigs. Moreover, direct analysis of protein sequences is now possible. antiSMASH 2.0 has also been equipped with the capacity to detect additional classes of secondary metabolites, including oligosaccharide antibiotics, phenazines, thiopeptides, homo-serine lactones, phosphonates and furans. The algorithm for predicting the core structure of the cluster end product is now also covering lantipeptides, in addition to polyketides and non-ribosomal peptides. The antiSMASH ClusterBlast functionality has been extended to identify sub-clusters involved in the biosynthesis of specific chemical building blocks. The new features currently make antiSMASH 2.0 the most comprehensive resource for identifying and analyzing novel secondary metabolite biosynthetic pathways in microorganisms.

TIME STRUCTURE OF GAMMA-RAY SIGNALS GENERATED IN LINE-OF-SIGHT INTERACTIONS OF COSMIC RAYS FROM DISTANT BLAZARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prosekin, Anton; Aharonian, Felix; Essey, Warren

2012-10-01

Blazars are expected to produce both gamma rays and cosmic rays. Therefore, observed high-energy gamma rays from distant blazars may contain a significant contribution from secondary gamma rays produced along the line of sight by the interactions of cosmic-ray protons with background photons. Unlike the standard models of blazars that consider only the primary photons emitted at the source, models that include the cosmic-ray contribution predict that even {approx}10 TeV photons should be detectable from distant objects with redshifts as high as z {>=} 0.1. Secondary photons contribute to signals of point sources only if the intergalactic magnetic fields aremore » very small, B {approx}< 10{sup -14} G, and their detection can be used to set upper bounds on magnetic fields along the line of sight. Secondary gamma rays have distinct spectral and temporal features. We explore the temporal properties of such signals using a semi-analytical formalism and detailed numerical simulations, which account for all the relevant processes, including magnetic deflections. In particular, we elucidate the interplay of time delays coming from the proton deflections and from the electromagnetic cascade, and we find that, at multi-TeV energies, secondary gamma rays can show variability on timescales of years for B {approx} 10{sup -15} G.« less

DNA Secondary Structure at Chromosomal Fragile Sites in Human Disease

PubMed Central

Thys, Ryan G; Lehman, Christine E; Pierce, Levi C. T; Wang, Yuh-Hwa

2015-01-01

DNA has the ability to form a variety of secondary structures that can interfere with normal cellular processes, and many of these structures have been associated with neurological diseases and cancer. Secondary structure-forming sequences are often found at chromosomal fragile sites, which are hotspots for sister chromatid exchange, chromosomal translocations, and deletions. Structures formed at fragile sites can lead to instability by disrupting normal cellular processes such as DNA replication and transcription. The instability caused by disruption of replication and transcription can lead to DNA breakage, resulting in gene rearrangements and deletions that cause disease. In this review, we discuss the role of DNA secondary structure at fragile sites in human disease. PMID:25937814

In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

PubMed

Martínez-Montiel, Nancy; Morales-Lara, Laura; Hernández-Pérez, Julio M; Martínez-Contreras, Rebeca D

2016-01-01

The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability, physicochemical properties and spatial organization in comparison to the NMD factor depicted for Homo sapiens. These observations strongly support the notion that human and fungal UPF1 could perform equivalent biological activities.

Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks.

PubMed

Babaei, Sepideh; Geranmayeh, Amir; Seyyedsalehi, Seyyed Ali

2010-12-01

The supervised learning of recurrent neural networks well-suited for prediction of protein secondary structures from the underlying amino acids sequence is studied. Modular reciprocal recurrent neural networks (MRR-NN) are proposed to model the strong correlations between adjacent secondary structure elements. Besides, a multilayer bidirectional recurrent neural network (MBR-NN) is introduced to capture the long-range intramolecular interactions between amino acids in formation of the secondary structure. The final modular prediction system is devised based on the interactive integration of the MRR-NN and the MBR-NN structures to arbitrarily engage the neighboring effects of the secondary structure types concurrent with memorizing the sequential dependencies of amino acids along the protein chain. The advanced combined network augments the percentage accuracy (Q₃) to 79.36% and boosts the segment overlap (SOV) up to 70.09% when tested on the PSIPRED dataset in three-fold cross-validation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

New insights from cluster analysis methods for RNA secondary structure prediction

PubMed Central

Rogers, Emily; Heitsch, Christine

2016-01-01

A widening gap exists between the best practices for RNA secondary structure prediction developed by computational researchers and the methods used in practice by experimentalists. Minimum free energy (MFE) predictions, although broadly used, are outperformed by methods which sample from the Boltzmann distribution and data mine the results. In particular, moving beyond the single structure prediction paradigm yields substantial gains in accuracy. Furthermore, the largest improvements in accuracy and precision come from viewing secondary structures not at the base pair level but at lower granularity/higher abstraction. This suggests that random errors affecting precision and systematic ones affecting accuracy are both reduced by this “fuzzier” view of secondary structures. Thus experimentalists who are willing to adopt a more rigorous, multilayered approach to secondary structure prediction by iterating through these levels of granularity will be much better able to capture fundamental aspects of RNA base pairing. PMID:26971529

Low pressure-induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time-resolved infrared spectroscopy.

PubMed

He, Zhipeng; Liu, Zhao; Zhou, Xiaofeng; Huang, He

2018-06-01

The secondary structure transitions of regenerated silk fibroin (RSF) under different external perturbations have been studied extensively, except for pressure. In this work, time-resolved infrared spectroscopy with the attenuated total reflectance (ATR) accessory was employed to follow the secondary structure transitions of RSF in its wet film under low pressure. It has been found that pressure alone is favorable only to the formation of β-sheet structure. Under constant pressure there is an optimum amount of D 2 O in the wet film (D 2 O : film = 2:1) so as to provide the optimal condition for the reorganization of the secondary structure and to have the largest formation of β-sheet structure. Under constant amount of D 2 O and constant pressure, the secondary structure transitions of RSF in its wet film can be divided into three stages along with time. In the first stage, random coil, α-helix, and β-turn were quickly transformed into β-sheet. In the second stage, random coil and β-turn were relatively slowly transformed into β-sheet and α-helix, and the content of α-helix was recovered to the value prior to the application of pressure. In the third and final stage, no measurable changes can be found for each secondary structure. This study may be helpful to understand the secondary structure changes of silk fibroin in silkworm's glands under hydrostatic pressure. © 2018 Wiley Periodicals, Inc.

Daytime encopresis associated with gland mal epileptic seizures: case report.

PubMed

Oyatsi, D P

2005-08-01

Sphincteric incontinence of stool and urine are not unusual features of generalised epileptic seizures. Isolated secondary encopresis as a manifestation of an epileptic seizure is unusual. This report is of, a four year old boy, with daytime secondary non-retentive encopresis. The onset of encopresis was preceded by several episodes of nocturnal generalised tonic clonic epileptic seizures. An electroencephalogram showed features consistent with complex partial seizures. He was commenced on anti-epileptic treatment with phenytoin sodium, and by the third day of treatment, the patient had achieved stool control.

Fourier transform infrared microspectroscopic analysis of the effects of cereal type and variety within a type of grain on structural makeup in relation to rumen degradation kinetics.

PubMed

Walker, Amanda M; Yu, Peiqiang; Christensen, Colleen R; Christensen, David A; McKinnon, John J

2009-08-12

The objectives of this study were to use Fourier transform infrared microspectroscopy (FTIRM) to determine structural makeup (features) of cereal grain endosperm tissue and to reveal and identify differences in protein and carbohydrate structural makeup between different cereal types (corn vs barley) and between different varieties within a grain (barley CDC Bold, CDC Dolly, Harrington, and Valier). Another objective was to investigate how these structural features relate to rumen degradation kinetics. The items assessed included (1) structural differences in protein amide I to nonstructural carbohydrate (NSC, starch) intensity and ratio within cellular dimensions; (2) molecular structural differences in the secondary structure profile of protein, alpha-helix, beta-sheet, and their ratio; (3) structural differences in NSC to amide I ratio profile. From the results, it was observed that (1) comparison between grain types [corn (cv. Pioneer 39P78) vs barley (cv. Harrington)] showed significant differences in structural makeup in terms of NSC, amide I to NSC ratio, and rumen degradation kinetics (degradation ratio, effective degradability of dry matter, protein and NSC) (P < 0.05); (2) comparison between varieties within a grain (barley varieties) also showed significant differences in structural makeup in terms of amide I, NSC, amide I to NSC ratio, alpha-helix and beta-sheet protein structures, and rumen degradation kinetics (effective degradability of dry matter, protein, and NSC) (P < 0.05); (3) correlation analysis showed that the amide I to NSC ratio was strongly correlated with rumen degradation kinetics in terms of the degradation rate (R = 0.91, P = 0.086) and effective degradability of dry matter (R = 0.93, P = 0.071). The results suggest that with the FTIRM technique, the structural makeup differences between cereal types and between different varieties within a type of grain could be revealed. These structural makeup differences were related to the rate and extent of rumen degradation.

An all sulfur analogue of the smallest subunit of F420-non-reducing hydrogenase from Methanococcus voltae--metal binding and structure.

PubMed

Pfeiffer, M; Klein, A; Steinert, P; Schomburg, D

The 25 amino acid long subunit VhuU of the F420-non-reducing hydrogenase from Methanococcus voltae contains selenocysteine within the consensus sequence of known [NiFe] hydrogenases DP(C or U)CxxCxxH (U = selenocysteine). The sulfur-analogue VhuUc was chemically synthesized, purified and its metal binding capability, the catalytic properties, and structural features were investigated. The polypeptide was able to bind nickel, but did not catalyse the heterolytic activation of H2. 2D-NMR spectroscopy revealed an alpha-helical secondary structure for the 15 N-terminal amino acids in 50% TFE. Nickel only binds to the C-terminus, which contains the conserved amino acid motif. Structures derived from the NMR data are compatible with the participation of both sulfur atoms from the conserved cysteine residues in a metal ion binding. Structures obtained from the data sets for Ni.VhuUc as well as Zn.VhuUc showed no further ligands. The informational value for Ni.VhuUc was low due to paramagnetism.

Modeling protein structure at near atomic resolutions with Gorgon.

PubMed

Baker, Matthew L; Abeysinghe, Sasakthi S; Schuh, Stephen; Coleman, Ross A; Abrams, Austin; Marsh, Michael P; Hryc, Corey F; Ruths, Troy; Chiu, Wah; Ju, Tao

2011-05-01

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. Copyright © 2011 Elsevier Inc. All rights reserved.

Which features of primary care affect unscheduled secondary care use? A systematic review.

PubMed

Huntley, Alyson; Lasserson, Daniel; Wye, Lesley; Morris, Richard; Checkland, Kath; England, Helen; Salisbury, Chris; Purdy, Sarah

2014-05-23

To conduct a systematic review to identify studies that describe factors and interventions at primary care practice level that impact on levels of utilisation of unscheduled secondary care. Observational studies at primary care practice level. Studies included people of any age of either sex living in Organisation for Economic Co-operation and Development (OECD) countries with any health condition. The primary outcome measure was unscheduled secondary care as measured by emergency department attendance and emergency hospital admissions. 48 papers were identified describing potential influencing features on emergency department visits (n=24 studies) and emergency admissions (n=22 studies). Patient factors associated with both outcomes were increased age, reduced socioeconomic status, lower educational attainment, chronic disease and multimorbidity. Features of primary care affecting unscheduled secondary care were more complex. Being able to see the same healthcare professional reduced unscheduled secondary care. Generally, better access was associated with reduced unscheduled care in the USA. Proximity to healthcare provision influenced patterns of use. Evidence relating to quality of care was limited and mixed. The majority of research was from different healthcare systems and limited in the extent to which it can inform policy. However, there is evidence that continuity of care is associated with reduced emergency department attendance and emergency hospital admissions. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Grazer responses to variable macroalgal resource conditions facilitate habitat structuring

PubMed Central

Perissinotto, Renzo; Bird, Matthew S.; Pelletier, Noémie

2018-01-01

Consumer responses to altered resource conditions can vary depending on dietary preference, resource characteristics and secondary resource features such as shelter. These can have cascading effects, especially if the consumed resource impacts on overall ecological functioning. In this study, we assessed the dietary composition of grazer communities following seasonal changes in the characteristics of their staple food-source (macroalgae). This was conducted in the living stromatolite pools growing along the coast of South Africa. Stable isotope mixing models suggested that following macroalgal bleaching in summer, metazoan consumers shifted their diet from predominantly macroalgae to a generalist composition. This has important implications for the integrity of the stromatolite matrix and its layered deposition. Where previously in winter stromatolite microalgae comprised a minor component of metazoan consumer diets, in summer, following a change in the resource conditions of macroalgae, microalgae featured more prominently in grazer diets. This seasonal grazing pressure on stromatolite-related resources probably promotes the pattern of annual layering observed in the stromatolite accretion. It also demonstrates a mechanism whereby grazer dietary shifts following a change in their preferred food resource can affect the ecosystem structure of their environment, specifically the stromatolite layering process which responds to microalgal growth or grazing conditions. PMID:29410845

Enhanced lithium storage performances of hierarchical hollow MoS₂ nanoparticles assembled from nanosheets.

PubMed

Wang, Meng; Li, Guangda; Xu, Huayun; Qian, Yitai; Yang, Jian

2013-02-01

MoS(2), because of its layered structure and high theoretical capacity, has been regarded as a potential candidate for electrode materials in lithium secondary batteries. But it suffers from the poor cycling stability and low rate capability. Here, hierarchical hollow nanoparticles of MoS(2) nanosheets with an increased interlayer distance are synthesized by a simple solvothermal reaction at a low temperature. The formation of hierarchical hollow nanoparticles is based on the intermediate, K(2)NaMoO(3)F(3), as a self-sacrificed template. These hollow nanoparticles exhibit a reversible capacity of 902 mA h g(-1) at 100 mA g(-1) after 80 cycles, much higher than the solid counterpart. At a current density of 1000 mA g(-1), the reversible capacity of the hierarchical hollow nanoparticles could be still maintained at 780 mAh g(-1). The enhanced lithium storage performances of the hierarchical hollow nanoparticles in reversible capacities, cycling stability and rate performances can be attributed to their hierarchical surface, hollow structure feature and increased layer distance of S-Mo-S. Hierarchical hollow nanoparticles as an ensemble of these features, could be applied to other electrode materials for the superior electrochemical performance.

Linking imaging spectroscopy and trait data to better understand spatial and temporal variability in functional traits

NASA Astrophysics Data System (ADS)

Townsend, Philip; Kruger, Eric; Wang, Zhihui; Singh, Aditya

2017-04-01

Imaging spectroscopy exhibits great potential for mapping foliar functional traits that are impractical or expensive to regularly measure on the ground, and are essentially impossible to characterize comprehensively across space. Specifically, the high information content in spectroscopic data enables us to identify narrow spectral feature that are associated with vegetation primary and secondary biochemistry (nutrients, pigments, defensive compounds), leaf structure (e.g., leaf mass per area), canopy structure, and physiological capacity. Ultimately, knowledge of the variability in such traits is critical to understanding vegetation productivity, as well as responses to climatic variability, disturbances, pests and pathogens. The great challenge to the use of imaging spectroscopy to supplement trait databases is the development of trait retrieval approaches that are broadly applicable within and between ecosystem types. Here, we outline how we are using the US National Ecological Observatory Network (NEON) to prototype the scaling and comparison of trait distributions derived from field measurements and imagery. We find that algorithms to map traits from imagery are robust across ecosystem types, when controlling for physiognomy and vegetation percent cover, and that among all vegetation types, the chemometric algorithms utilize similar features for mapping of traits.

Direct observation and analysis of york-shell materials using low-voltage high-resolution scanning electron microscopy: Nanometal-particles encapsulated in metal-oxide, carbon, and polymer

NASA Astrophysics Data System (ADS)

Asahina, Shunsuke; Suga, Mitsuo; Takahashi, Hideyuki; Young Jeong, Hu; Galeano, Carolina; Schüth, Ferdi; Terasaki, Osamu

2014-11-01

Nanometal particles show characteristic features in chemical and physical properties depending on their sizes and shapes. For keeping and further enhancing their features, the particles should be protected from coalescence or degradation. One approach is to encapsulate the nanometal particles inside pores with chemically inert or functional materials, such as carbon, polymer, and metal oxides, which contain mesopores to allow permeation of only chemicals not the nanometal particles. Recently developed low-voltage high-resolution scanning electron microscopy was applied to the study of structural, chemical, and electron state of both nanometal particles and encapsulating materials in yolk-shell materials of Au@C, Ru/Pt@C, Au@TiO2, and Pt@Polymer. Progresses in the following categories were shown for the yolk-shell materials: (i) resolution of topographic image contrast by secondary electrons, of atomic-number contrast by back-scattered electrons, and of elemental mapping by X-ray energy dispersive spectroscopy; (ii) sample preparation for observing internal structures; and (iii) X-ray spectroscopy such as soft X-ray emission spectroscopy. Transmission electron microscopy was also used for characterization of Au@C.

DUST AROUND R CORONAE BOREALIS STARS. II. INFRARED EMISSION FEATURES IN AN H-POOR ENVIRONMENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia-Hernandez, D. A.; Rao, N. Kameswara; Lambert, D. L., E-mail: agarcia@iac.es, E-mail: nkrao@iiap.res.in, E-mail: dll@astro.as.utexas.edu

2013-08-20

Residual Spitzer/Infrared Spectrograph spectra for a sample of 31 R Coronae Borealis (RCB) stars are presented and discussed in terms of narrow emission features superimposed on the quasi-blackbody continuous infrared emission. A broad {approx}6-10 {mu}m dust emission complex is seen in the RCBs showing an extreme H-deficiency. A secondary and much weaker {approx}11.5-15 {mu}m broad emission feature is detected in a few RCBs with the strongest {approx}6-10 {mu}m dust complex. The Spitzer infrared spectra reveal for the first time the structure within the {approx}6-10 {mu}m dust complex, showing the presence of strong C-C stretching modes at {approx}6.3 and 8.1 {mu}mmore » as well as of other dust features at {approx}5.9, 6.9, and 7.3 {mu}m, which are attributable to amorphous carbonaceous solids with little or no hydrogen. The few RCBs with only moderate H-deficiencies display the classical ''unidentified infrared bands (UIRs)'' and mid-infrared features from fullerene-related molecules. In general, the characteristics of the RCB infrared emission features are not correlated with the stellar and circumstellar properties, suggesting that the RCB dust features may not be dependent on the present physical conditions around RCB stars. The only exception seems to be the central wavelength of the 6.3 {mu}m feature, which is blueshifted in those RCBs showing also the UIRs, i.e., the RCBs with the smallest H deficiency.« less

Theophylline-Induced Seizures: Clinical and Pathophysiologic Aspects

PubMed Central

Nakada, Tsutomu; Kwee, Ingrid L.; Lerner, Alfred M.; Remler, Michael P.

1983-01-01

The clinical features and management of theophylline-induced seizures are not well appreciated in spite of their unique aspects. These seizures tend to occur in neurologically intact patients and leave no or only minor neurologic sequelae if controlled early. They begin with focal motor seizures with or without secondary generalization and are followed by stupor or coma. They are responsive only to adjustment of theophylline dosage. Should the motor phenomenon persist, it takes the form of epilepsia partialis continua. Extensive workup for a structural brain lesion may be unrewarding. The electroencephalogram typically shows periodic lateralized epileptiform discharges, which may provide a diagnostic clue. PMID:6858124

Genome sequencing reveals complex secondary metabolome in themarine actinomycete Salinispora tropica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Udwary, Daniel W.; Zeigler, Lisa; Asolkar, Ratnakar

2007-05-01

Recent fermentation studies have identified actinomycetes ofthe marine-dwelling genus Salinispora as prolific natural productproducers. To further evaluate their biosynthetic potential, we analyzedall identifiable secondary natural product gene clusters from therecently sequenced 5,184,724 bp S. tropica CNB-440 circular genome. Ouranalysis shows that biosynthetic potential meets or exceeds that shown byprevious Streptomyces genome sequences as well as other naturalproduct-producing actinomycetes. The S. tropica genome features ninepolyketide synthase systems of every known formally classified family,non-ribosomal peptide synthetases and several hybrid clusters. While afew clusters appear to encode molecules previously identified inStreptomyces species,the majority of the 15 biosynthetic loci are novel.Specific chemical information aboutmore » putative and observed natural productmolecules is presented and discussed. In addition, our bioinformaticanalysis was critical for the structure elucidation of the novelpolyenemacrolactam salinilactam A. This study demonstrates the potentialfor genomic analysis to complement and strengthen traditional naturalproduct isolation studies and firmly establishes the genus Salinispora asa rich source of novel drug-like molecules.« less

2003 NASA Seal/Secondary Air System Workshop. Volume 1

NASA Technical Reports Server (NTRS)

Steinetz, Bruce M. (Editor); Hendricks, Robert C. (Editor)

2004-01-01

The following reports were included in the 2003 NASA Seal/Secondary Air System Workshop:Low Emissions Alternative Power (LEAP); Overview of NASA Glenn Seal Developments; NASA Ultra Efficient Engine Technology Project Overview; Development of Higher Temperature Abradable Seals for Industrial Gas Turbines; High Misalignment Carbon Seals for the Fan Drive Gear System Technologies; Compliant Foil Seal Investigations; Test Rig for Evaluating Active Turbine Blade Tip Clearance Control Concepts; Controls Considerations for Turbine Active Clearance Control; Non-Contacting Finger Seal Developments and Design Considerations; Effect of Flow-Induced Radial Load on Brush Seal/Rotor Contact Mechanics; Seal Developments at Flowserve Corporation; Investigations of High Pressure Acoustic Waves in Resonators With Seal-Like Features; Numerical Investigations of High Pressure Acoustic Waves in Resonators; Feltmetal Seal Material Through-Flow; "Bimodal" Nuclear Thermal Rocket (BNTR) Propulsion for Future Human Mars Exploration Missions; High Temperature Propulsion System Structural Seals for Future Space Launch Vehicles; Advanced Control Surface Seal Development for Future Space Vehicles; High Temperature Metallic Seal Development for Aero Propulsion and Gas Turbine Applications; and BrazeFoil Honeycomb.

Secondary metabolites from a marine-derived endophytic fungus Penicillium chrysogenum QEN-24S.

PubMed

Gao, Shu-Shan; Li, Xiao-Ming; Du, Feng-Yu; Li, Chun-Shun; Proksch, Peter; Wang, Bin-Gui

2010-12-27

Penicillium chrysogenum QEN-24S, an endophytic fungus isolated from an unidentified marine red algal species of the genus Laurencia, displayed inhibitory activity against the growth of pathogen Alternaria brassicae in dual culture test. Chemical investigation of this fungal strain resulted in the isolation of four new (1-3 and 5) and one known (4) secondary metabolites. Their structures were identified as two polyketide derivatives penicitides A and B (1 and 2), two glycerol derivatives 2-(2,4-dihydroxy-6-methylbenzoyl)-glycerol (3) and 1-(2,4-dihydroxy-6-methylbenzoyl)- glycerol (4), and one monoterpene derivative penicimonoterpene (5). Penicitides A and B (1 and 2) feature a unique 10-hydroxy- or 7,10-dihydroxy-5,7-dimethylundecyl moiety substituting at C-5 of the α-tetrahydropyrone ring, which is not reported previously among natural products. Compound 5 displayed potent activity against the pathogen A. brassicae, while compound 1 exhibited moderate cytotoxic activity against the human hepatocellular liver carcinoma cell line.

Constructing a New Vision: Undoing Gender through Secondary Education in Honduras

NASA Astrophysics Data System (ADS)

Murphy-Graham, Erin

2009-11-01

This article presents results from a qualitative study on how the Honduran secondary education programme, Sistema de Aprendizaje Tutorial (SAT), attempts to "undo gender" (Deutsch 2007: 122) by encouraging students to rethink gender relations in their everyday lives in a way that reflects their increased consciousness of gender equality. My findings suggest that SAT increased women's gender consciousness and this heightened their desire for change in the domestic sphere. In some instances, women were able to negotiate a new sharing of responsibilities with their spouses. There are several features of SAT that make it a transformative innovation in education: (1) gender is mainstreamed into the curriculum; (2) gender is linked with the larger concept of justice; (3) students engage in reflection, dialogue and debate; (4) teachers are given the opportunity to reflect critically on their understanding of gender in professional development sessions; and (5) it emphasises that undoing gender requires change among individuals and in social structures such as the family.

Nailfold video-capillaroscopy in systemic sclerosis.

PubMed

Cutolo, M; Pizzorni, C; Sulli, A

2004-12-01

The Raynaud's phenomenon (RP) is the most common and significant clinical condition supporting microvascular analysis as soon as possible. Microvascular involvement is a key feature of RP, and several rheumatic diseases are characterized by the presence of the RP. Nailfold capillary microscopy shows an impressive cost/effectiveness ratio: it is simple, noninvasive and inexpensive.Well-recognized videocapillaroscopic patterns (NVC) have been described mainly in scleroderma (SSc) patients complaining of a secondary RP. The peripheral microvascular damage in SSc is characterized by increasing structural alterations of the capillaries (giant capillaries and microhemorrhages) with progressive decrease of their density. The detection of the scleroderma NCV allows early differentiation between primary RP (functional, not disease associated), and secondary RP (disease associated). Other major NVC patterns have been described in the field of rheumatic diseases. Interestingly, correlations are evident between the NCV and the clinical symptoms, severity of the disease and the laboratory findings. Further clinical and epidemiological studies, as well as a standardized and computerized quantitation of the observed damages are required.

Examination of Students' Digital Gaming Habits at Secondary School Level in Elazig Province of Turkey

ERIC Educational Resources Information Center

Mikail, Tel

2015-01-01

In this study, the opinions of the secondary school students on digital games were examined. The research is a screening model research and has a descriptive feature. It was carried out with 521 secondary school students in Elazig (a province in eastern part of Turkey) [MSS1] in 2013. Almost all of the participants use computer. More than half of…

Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software.

PubMed

Pérez, Serge; Tubiana, Thibault; Imberty, Anne; Baaden, Marc

2015-05-01

A molecular visualization program tailored to deal with the range of 3D structures of complex carbohydrates and polysaccharides, either alone or in their interactions with other biomacromolecules, has been developed using advanced technologies elaborated by the video games industry. All the specific structural features displayed by the simplest to the most complex carbohydrate molecules have been considered and can be depicted. This concerns the monosaccharide identification and classification, conformations, location in single or multiple branched chains, depiction of secondary structural elements and the essential constituting elements in very complex structures. Particular attention was given to cope with the accepted nomenclature and pictorial representation used in glycoscience. This achievement provides a continuum between the most popular ways to depict the primary structures of complex carbohydrates to visualizing their 3D structures while giving the users many options to select the most appropriate modes of representations including new features such as those provided by the use of textures to depict some molecular properties. These developments are incorporated in a stand-alone viewer capable of displaying molecular structures, biomacromolecule surfaces and complex interactions of biomacromolecules, with powerful, artistic and illustrative rendering methods. They result in an open source software compatible with multiple platforms, i.e., Windows, MacOS and Linux operating systems, web pages, and producing publication-quality figures. The algorithms and visualization enhancements are demonstrated using a variety of carbohydrate molecules, from glycan determinants to glycoproteins and complex protein-carbohydrate interactions, as well as very complex mega-oligosaccharides and bacterial polysaccharides and multi-stranded polysaccharide architectures. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Multi-centre diagnostic classification of individual structural neuroimaging scans from patients with major depressive disorder.

PubMed

Mwangi, Benson; Ebmeier, Klaus P; Matthews, Keith; Steele, J Douglas

2012-05-01

Quantitative abnormalities of brain structure in patients with major depressive disorder have been reported at a group level for decades. However, these structural differences appear subtle in comparison with conventional radiologically defined abnormalities, with considerable inter-subject variability. Consequently, it has not been possible to readily identify scans from patients with major depressive disorder at an individual level. Recently, machine learning techniques such as relevance vector machines and support vector machines have been applied to predictive classification of individual scans with variable success. Here we describe a novel hybrid method, which combines machine learning with feature selection and characterization, with the latter aimed at maximizing the accuracy of machine learning prediction. The method was tested using a multi-centre dataset of T(1)-weighted 'structural' scans. A total of 62 patients with major depressive disorder and matched controls were recruited from referred secondary care clinical populations in Aberdeen and Edinburgh, UK. The generalization ability and predictive accuracy of the classifiers was tested using data left out of the training process. High prediction accuracy was achieved (~90%). While feature selection was important for maximizing high predictive accuracy with machine learning, feature characterization contributed only a modest improvement to relevance vector machine-based prediction (~5%). Notably, while the only information provided for training the classifiers was T(1)-weighted scans plus a categorical label (major depressive disorder versus controls), both relevance vector machine and support vector machine 'weighting factors' (used for making predictions) correlated strongly with subjective ratings of illness severity. These results indicate that machine learning techniques have the potential to inform clinical practice and research, as they can make accurate predictions about brain scan data from individual subjects. Furthermore, machine learning weighting factors may reflect an objective biomarker of major depressive disorder illness severity, based on abnormalities of brain structure.

Molecular genetics of secondary chemistry in Metarhizium fungi

USDA-ARS?s Scientific Manuscript database

As with many microbes, entomopathogenic fungi from the genus Metarhizium produce a plethora of small molecule metabolites, often referred to as secondary metabolites. Although these intriguing compounds are a conspicuous feature of the biology of the producing fungi, their roles in pathogenicity and...

Clinical and computed tomography features of secondary renal hyperparathyroidism

PubMed Central

Vanbrugghe, Benoît; Blond, Laurent; Carioto, Lisa; Carmel, Eric Norman; Nadeau, Marie-Eve

2011-01-01

An atypical case of secondary renal hyperparathyroidism was diagnosed in a 9-year-old miniature schnauzer after a skull computed tomography (CT) showed the presence of 2 bilateral and symmetrical soft tissue maxillary masses, and osteopenia of the skull. PMID:21532826

The Ramachandran Number: An Order Parameter for Protein Geometry

DOE PAGES

Mannige, Ranjan V.; Kundu, Joyjit; Whitelam, Stephen; ...

2016-08-04

Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as α-helices and β-sheets. Secondary structure is characterized by the local rotational state of the protein backbone, quantified by two dihedral angles called Øand Ψ. Particular types of secondary structure can generally be described by a single (diffuse) location on a two-dimensional plot drawn in the space of the angles Ø andΨ, called a Ramachandran plot. By contrast, a recently-discovered nanomaterial made from peptoids, structural isomers of peptides, displays a secondary-structure motif corresponding to two regions on the Ramachandran plot [Mannige et al., Nature 526, 415 (2015)].more » In order to describe such 'higher-order' secondary structure in a compact way we introduce here a means of describing regions on the Ramachandran plot in terms of a single Ramachandran number, R, which is a structurally meaningful combination of Ø andΨ. We show that the potential applications of R are numerous: it can be used to describe the geometric content of protein structures, and can be used to draw diagrams that reveal, at a glance, the frequency of occurrence of regular secondary structures and disordered regions in large protein datasets. We propose that R might be used as an order parameter for protein geometry for a wide range of applications.« less

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

PubMed Central

Yang, Yuedong; Gao, Jianzhao; Wang, Jihua; Heffernan, Rhys; Hanson, Jack; Paliwal, Kuldip; Zhou, Yaoqi

2018-01-01

Abstract Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82–84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques. As we are approaching to the theoretical limit of three-state prediction (88–90%), alternative to secondary structure prediction (prediction of backbone torsion angles and Cα-atom-based angles and torsion angles) not only has more room for further improvement but also allows direct prediction of three-dimensional fragment structures with constantly improved accuracy. About 20% of all 40-residue fragments in a database of 1199 non-redundant proteins have <6 Å root-mean-squared distance from the native conformations by SPIDER2. More powerful deep learning methods with improved capability of capturing long-range interactions begin to emerge as the next generation of techniques for secondary structure prediction. The time has come to finish off the final stretch of the long march towards protein secondary structure prediction. PMID:28040746

Soft actuators and soft actuating devices

DOEpatents

Yang, Dian; Whitesides, George M.

2017-10-17

A soft buckling linear actuator is described, including: a plurality of substantially parallel bucklable, elastic structural components each having its longest dimension along a first axis; and a plurality of secondary structural components each disposed between and bridging two adjacent bucklable, elastic structural components; wherein every two adjacent bucklable, elastic structural components and the secondary structural components in-between define a layer comprising a plurality of cells each capable of being connected with a fluid inflation or deflation source; the secondary structural components from two adjacent layers are not aligned along a second axis perpendicular to the first axis; and the secondary structural components are configured not to buckle, the bucklable, elastic structural components are configured to buckle along the second axis to generate a linear force, upon the inflation or deflation of the cells. Methods of actuation using the same are also described.

Free energy minimization to predict RNA secondary structures and computational RNA design.

PubMed

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

Effect of centrifugal forces on formation of secondary flow structures in a 180-degree curved artery model under pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Callahan, Shannon; Sajjad, Roshan; Bulusu, Kartik V.; Plesniak, Michael W.

2013-11-01

An experimental investigation of secondary flow structures within a 180-degree bent tube model of a curved artery was performed using phase-averaged, two-component, two-dimensional, particle image velocimetry (2C-2D PIV) under pulsatile inflow conditions. Pulsatile waveforms ranging from simple sinusoidal to physiological inflows were supplied. We developed a novel continuous wavelet transform algorithm (PIVlet 1.2) and applied it to vorticity fields for coherent secondary flow structure detection. Regime maps of secondary flow structures revealed new, deceleration-phase-dependent flow morphologies. The temporal instances where streamwise centrifugal forces dominated were associated with large-scale coherent structures, such as deformed Dean-, Lyne- and Wall-type (D-L-W) vortical structures. Magnitudes of streamwise and cross-stream centrifugal forces tend to balance during deceleration phases. Deceleration events were also associated with spatial reorganization and asymmetry in large-scale D-L-W secondary flow structures. Hence, the interaction between streamwise and cross-stream centrifugal forces that affects secondary flow morphologies is explained using a ``residual force'' parameter i.e., the difference in magnitudes of these forces. Supported by the NSF Grant No. CBET- 0828903 and GW Center for Biomimetics and Bioinspired Engineering.

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

PubMed Central

Vernon, Robert McCoy; Chong, Paul Andrew; Tsang, Brian; Kim, Tae Hun; Bah, Alaji; Farber, Patrick; Lin, Hong

2018-01-01

Protein phase separation is implicated in formation of membraneless organelles, signaling puncta and the nuclear pore. Multivalent interactions of modular binding domains and their target motifs can drive phase separation. However, forces promoting the more common phase separation of intrinsically disordered regions are less understood, with suggested roles for multivalent cation-pi, pi-pi, and charge interactions and the hydrophobic effect. Known phase-separating proteins are enriched in pi-orbital containing residues and thus we analyzed pi-interactions in folded proteins. We found that pi-pi interactions involving non-aromatic groups are widespread, underestimated by force-fields used in structure calculations and correlated with solvation and lack of regular secondary structure, properties associated with disordered regions. We present a phase separation predictive algorithm based on pi interaction frequency, highlighting proteins involved in biomaterials and RNA processing. PMID:29424691

X-ray studies of aluminum alloy of the Al-Mg-Si system subjected to SPD processing

NASA Astrophysics Data System (ADS)

Sitdikov, V. D.; Murashkin, M. Yu; Khasanov, M. R.; Kasatkin, I. A.; Chizhov, P. S.; Bobruk, E. V.

2014-08-01

Recently it has been established that during high pressure torsion dynamic aging takes place in aluminum Al-Mg-Si alloys resulting in formation of nanosized particles of strengthening phases in the aluminum matrix, which greatly improves the electrical conductivity and strength properties. In the present paper structural characterization of ultrafine-grained (UFG) samples of aluminum 6201 alloy produced by severe plastic deformation (SPD) was performed using X-ray diffraction analysis. As a result, structure features (lattice parameter, size of coherent scattering domains) after dynamic aging of UFG samples were determined. The size and distribution of second- phase particles in the Al matrix were assessed with regard to HPT regimes. Impact of the size and distribution of the formed secondary phases on the strength, ductility and electrical conductivity is discussed.

Large Impact Features on Europa: Results of the Galileo Nominal Mission

NASA Technical Reports Server (NTRS)

Moore, Jeffrey M.; Asphaug, Erik; Sullivan, Robert J.; Klemaszewski, James E.; Bender, Kelly C.; Greeley, Ronald; Geissler, Paul E.; McEwen, Alfred S.; Turtle, Elizabeth P.; Phillips, Cynthia B.

1998-01-01

The Galileo Orbiter examined several impact features on Europa at considerably better resolution than was possible from Voyager. The new data allow us to describe the morphology and infer the geology of the largest impact features on Europa, which are probes into the crust. We observe two basic types of large impact features: (1) "classic" impact craters that grossly resemble well-preserved lunar craters of similar size but are more topographically subdued (e.g., Pwyll) and (2) very flat circular features that lack the basic topographic structures of impact craters such as raised rims, a central depression, or central peaks, and which largely owe their identification as impact features to the field of secondary craters radially sprayed about them (e.g., Callanish). Our interpretation is that the classic craters (all <30 km diameter) formed entirely within a solid target at least 5 to 10 km thick that exhibited brittle behavior on time scales of the impact events. Some of the classic craters have a more subdued topography than fresh craters of similar size on other icy bodies such as Ganymede and Callisto, probably due to the enhanced viscous relaxation produced by a steeper thermal gradient on Europa. Pedestal ejecta facies on Europa (and Ganymede) may be produced by the relief-flattening movement of plastically deforming but otherwise solid ice that was warm at the time of emplacement. Callanish and Tyre do not appear to be larger and even more viscously relaxed versions of the classic craters; rather they display totally different morphologies such as distinctive textures and a series of large concentric structural rings cutting impact-feature-related materials. Impact simulations suggest that the distinctive morphologies would not be produced by impact into a solid ice target, but may be explained by impact into an ice layer approximately 10 to 15 km thick overlying a low-viscosity material such as water. The very wide (near antipodal) separation of Callanish and Tyre imply that approximately 10-15 km may have been the global average thickness of the rigid crust of Europa when these impacts occurred. The absence of detectable craters superposed on the interior deposits of Callanish suggests that it is geologically young (< 10(exp 8) years). Hence, it seems likely that our preliminary conclusions about the subsurface structure of Europa apply to the current day.

Large Impact Features on Europa: Results of the Galileo Nominal Mission

USGS Publications Warehouse

Moore, Johnnie N.; Asphaug, E.; Sullivan, R.J.; Klemaszewski, J.E.; Bender, K.C.; Greeley, R.; Geissler, P.E.; McEwen, A.S.; Turtle, E.P.; Phillips, C.B.; Tufts, B.R.; Head, J. W.; Pappalardo, R.T.; Jones, K.B.; Chapman, C.R.; Belton, M.J.S.; Kirk, R.L.; Morrison, D.

1998-01-01

The Galileo Orbiter examined several impact features on Europa at considerably better resolution than was possible from Voyager. The new data allow us to describe the morphology and infer the geology of the largest impact features on Europa, which are probes into the crust. We observe two basic types of large impact features: (1) "classic" impact craters that grossly resemble well-preserved lunar craters of similar size but are more topographically subdued (e.g., Pwyll) and (2) very flat circular features that lack the basic topographic structures of impact craters such as raised rims, a central depression, or central peaks, and which largely owe their identification as impact features to the field of secondary craters radially sprayed about them (e.g., Callanish). Our interpretation is that the classic craters (all <30 km diameter) formed entirely within a solid target at least 5 to 10 km thick that exhibited brittle behavior on time scales of the impact events. Some of the classic craters have a more subdued topography than fresh craters of similar size on other icy bodies such as Ganymede and Callisto, probably due to the enhanced viscous relaxation produced by a steeper thermal gradient on Europa. Pedestal ejecta facies on Europa (and Ganymede) may be produced by the relief-flattening movement of plastically deforming but otherwise solid ice that was warm at the time of emplacement. Callanish and Tyre do not appear to be larger and even more viscously relaxed versions of the classic craters; rather they display totally different morphologies such as distinctive textures and a series of large concentric structural rings cutting impact-feature-related materials. Impact simulations suggest that the distinctive morphologies would not be produced by impact into a solid ice target, but may be explained by impact into an ice layer ~10 to 15 km thick overlying a low-viscosity material such as water. The very wide (near antipodal) separation of Callanish and Tyre imply that ~10-15 km may have been the global average thickness of the rigid crust of Europa when these impacts occurred. The absence of detectable craters superposed on the interior deposits of Callanish suggests that it is geologically young (<108years). Hence, it seems likely that our preliminary conclusions about the subsurface structure of Europa apply to the current day. ?? 1998 Academic Press.

Insights into Structural and Mechanistic Features of Viral IRES Elements

PubMed Central

Martinez-Salas, Encarnacion; Francisco-Velilla, Rosario; Fernandez-Chamorro, Javier; Embarek, Azman M.

2018-01-01

Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of protein synthesis using cap-independent mechanisms. However, distinct types of IRES elements present in the genome of various RNA viruses perform the same function despite lacking conservation of sequence and secondary RNA structure. Likewise, IRES elements differ in host factor requirement to recruit the ribosomal subunits. In spite of this diversity, evolutionarily conserved motifs in each family of RNA viruses preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES activity. Indeed, IRES elements adopting remarkable different structural organizations contain RNA structural motifs that play an essential role in recruiting ribosomes, initiation factors and/or RNA-binding proteins using different mechanisms. Therefore, given that a universal IRES motif remains elusive, it is critical to understand how diverse structural motifs deliver functions relevant for IRES activity. This will be useful for understanding the molecular mechanisms beyond cap-independent translation, as well as the evolutionary history of these regulatory elements. Moreover, it could improve the accuracy to predict IRES-like motifs hidden in genome sequences. This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements. PMID:29354113

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

PubMed Central

Antunes, Deborah; Jorge, Natasha A. N.; Caffarena, Ernesto R.; Passetti, Fabio

2018-01-01

RNA molecules are essential players in many fundamental biological processes. Prokaryotes and eukaryotes have distinct RNA classes with specific structural features and functional roles. Computational prediction of protein structures is a research field in which high confidence three-dimensional protein models can be proposed based on the sequence alignment between target and templates. However, to date, only a few approaches have been developed for the computational prediction of RNA structures. Similar to proteins, RNA structures may be altered due to the interaction with various ligands, including proteins, other RNAs, and metabolites. A riboswitch is a molecular mechanism, found in the three kingdoms of life, in which the RNA structure is modified by the binding of a metabolite. It can regulate multiple gene expression mechanisms, such as transcription, translation initiation, and mRNA splicing and processing. Due to their nature, these entities also act on the regulation of gene expression and detection of small metabolites and have the potential to helping in the discovery of new classes of antimicrobial agents. In this review, we describe software and web servers currently available for riboswitch aptamer identification and secondary and tertiary structure prediction, including applications. PMID:29403526

An Algorithm for Protein Helix Assignment Using Helix Geometry

PubMed Central

Cao, Chen; Xu, Shutan; Wang, Lincong

2015-01-01

Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone Cα atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins. PMID:26132394

Comprehensive Evaluation of Fast-Response, Reynolds-Averaged Navier–Stokes, and Large-Eddy Simulation Methods Against High-Spatial-Resolution Wind-Tunnel Data in Step-Down Street Canyons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayati, Arash Nemati; Stoll, Rob; Kim, J. J.

Three computational fluid dynamics (CFD) methods with different levels of flow-physics modelling are comprehensively evaluated against high-spatial-resolution wind-tunnel velocity data from step-down street canyons (i.e., a short building downwind of a tall building). The first method is a semi-empirical fast-response approach using the Quick Urban Industrial Complex (QUIC-URB) model. The second method solves the Reynolds-averaged Navier–Stokes (RANS) equations, and the third one utilizes a fully-coupled fluid-structure interaction large-eddy simulation (LES) model with a grid-turbulence inflow generator. Unlike typical point-by-point evaluation comparisons, here the entire two-dimensional wind-tunnel dataset is used to evaluate the dynamics of dominant flow topological features in themore » street canyon. Each CFD method is scrutinized for several geometric configurations by varying the downwind-to-upwind building-height ratio (H d/H u) and street canyon-width to building-width aspect ratio (S / W) for inflow winds perpendicular to the upwind building front face. Disparities between the numerical results and experimental data are quantified in terms of their ability to capture flow topological features for different geometric configurations. Ultimately, all three methods qualitatively predict the primary flow topological features, including a saddle point and a primary vortex. But, the secondary flow topological features, namely an in-canyon separation point and secondary vortices, are only well represented by the LES method despite its failure for taller downwind building cases. Misrepresentation of flow-regime transitions, exaggeration of the coherence of recirculation zones and wake fields, and overestimation of downwards vertical velocity into the canyon are the main defects in QUIC-URB, RANS and LES results, respectively. All three methods underestimate the updrafts and, surprisingly, QUIC-URB outperforms RANS for the streamwise velocity component, while RANS is superior to QUIC-URB for the vertical velocity component in the street canyon.« less

Comprehensive Evaluation of Fast-Response, Reynolds-Averaged Navier–Stokes, and Large-Eddy Simulation Methods Against High-Spatial-Resolution Wind-Tunnel Data in Step-Down Street Canyons

DOE PAGES

Hayati, Arash Nemati; Stoll, Rob; Kim, J. J.; ...

2017-05-18

Three computational fluid dynamics (CFD) methods with different levels of flow-physics modelling are comprehensively evaluated against high-spatial-resolution wind-tunnel velocity data from step-down street canyons (i.e., a short building downwind of a tall building). The first method is a semi-empirical fast-response approach using the Quick Urban Industrial Complex (QUIC-URB) model. The second method solves the Reynolds-averaged Navier–Stokes (RANS) equations, and the third one utilizes a fully-coupled fluid-structure interaction large-eddy simulation (LES) model with a grid-turbulence inflow generator. Unlike typical point-by-point evaluation comparisons, here the entire two-dimensional wind-tunnel dataset is used to evaluate the dynamics of dominant flow topological features in themore » street canyon. Each CFD method is scrutinized for several geometric configurations by varying the downwind-to-upwind building-height ratio (H d/H u) and street canyon-width to building-width aspect ratio (S / W) for inflow winds perpendicular to the upwind building front face. Disparities between the numerical results and experimental data are quantified in terms of their ability to capture flow topological features for different geometric configurations. Ultimately, all three methods qualitatively predict the primary flow topological features, including a saddle point and a primary vortex. But, the secondary flow topological features, namely an in-canyon separation point and secondary vortices, are only well represented by the LES method despite its failure for taller downwind building cases. Misrepresentation of flow-regime transitions, exaggeration of the coherence of recirculation zones and wake fields, and overestimation of downwards vertical velocity into the canyon are the main defects in QUIC-URB, RANS and LES results, respectively. All three methods underestimate the updrafts and, surprisingly, QUIC-URB outperforms RANS for the streamwise velocity component, while RANS is superior to QUIC-URB for the vertical velocity component in the street canyon.« less

Comprehensive Evaluation of Fast-Response, Reynolds-Averaged Navier-Stokes, and Large-Eddy Simulation Methods Against High-Spatial-Resolution Wind-Tunnel Data in Step-Down Street Canyons

NASA Astrophysics Data System (ADS)

Hayati, Arash Nemati; Stoll, Rob; Kim, J. J.; Harman, Todd; Nelson, Matthew A.; Brown, Michael J.; Pardyjak, Eric R.

2017-08-01

Three computational fluid dynamics (CFD) methods with different levels of flow-physics modelling are comprehensively evaluated against high-spatial-resolution wind-tunnel velocity data from step-down street canyons (i.e., a short building downwind of a tall building). The first method is a semi-empirical fast-response approach using the Quick Urban Industrial Complex (QUIC-URB) model. The second method solves the Reynolds-averaged Navier-Stokes (RANS) equations, and the third one utilizes a fully-coupled fluid-structure interaction large-eddy simulation (LES) model with a grid-turbulence inflow generator. Unlike typical point-by-point evaluation comparisons, here the entire two-dimensional wind-tunnel dataset is used to evaluate the dynamics of dominant flow topological features in the street canyon. Each CFD method is scrutinized for several geometric configurations by varying the downwind-to-upwind building-height ratio (H_d/H_u) and street canyon-width to building-width aspect ratio ( S / W) for inflow winds perpendicular to the upwind building front face. Disparities between the numerical results and experimental data are quantified in terms of their ability to capture flow topological features for different geometric configurations. Overall, all three methods qualitatively predict the primary flow topological features, including a saddle point and a primary vortex. However, the secondary flow topological features, namely an in-canyon separation point and secondary vortices, are only well represented by the LES method despite its failure for taller downwind building cases. Misrepresentation of flow-regime transitions, exaggeration of the coherence of recirculation zones and wake fields, and overestimation of downwards vertical velocity into the canyon are the main defects in QUIC-URB, RANS and LES results, respectively. All three methods underestimate the updrafts and, surprisingly, QUIC-URB outperforms RANS for the streamwise velocity component, while RANS is superior to QUIC-URB for the vertical velocity component in the street canyon.

Deep sequencing of foot-and-mouth disease virus reveals RNA sequences involved in genome packaging.

PubMed

Logan, Grace; Newman, Joseph; Wright, Caroline F; Lasecka-Dykes, Lidia; Haydon, Daniel T; Cottam, Eleanor M; Tuthill, Tobias J

2017-10-18

Non-enveloped viruses protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. Packaging and capsid assembly in RNA viruses can involve interactions between capsid proteins and secondary structures in the viral genome as exemplified by the RNA bacteriophage MS2 and as proposed for other RNA viruses of plants, animals and human. In the picornavirus family of non-enveloped RNA viruses, the requirements for genome packaging remain poorly understood. Here we show a novel and simple approach to identify predicted RNA secondary structures involved in genome packaging in the picornavirus foot-and-mouth disease virus (FMDV). By interrogating deep sequencing data generated from both packaged and unpackaged populations of RNA we have determined multiple regions of the genome with constrained variation in the packaged population. Predicted secondary structures of these regions revealed stem loops with conservation of structure and a common motif at the loop. Disruption of these features resulted in attenuation of virus growth in cell culture due to a reduction in assembly of mature virions. This study provides evidence for the involvement of predicted RNA structures in picornavirus packaging and offers a readily transferable methodology for identifying packaging requirements in many other viruses. Importance In order to transmit their genetic material to a new host, non-enveloped viruses must protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. For many non-enveloped RNA viruses the requirements for this critical part of the viral life cycle remain poorly understood. We have identified RNA sequences involved in genome packaging of the picornavirus foot-and-mouth disease virus. This virus causes an economically devastating disease of livestock affecting both the developed and developing world. The experimental methods developed to carry out this work are novel, simple and transferable to the study of packaging signals in other RNA viruses. Improved understanding of RNA packaging may lead to novel vaccine approaches or targets for antiviral drugs with broad spectrum activity. Copyright © 2017 Logan et al.

PreSSAPro: a software for the prediction of secondary structure by amino acid properties.

PubMed

Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

2007-10-01

PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in smaller but homogeneous data sets corresponding to protein structural classes, i.e. all-alpha, all-beta, or alpha-beta proteins. Predictions result improved by the use of propensities evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right protein class, if known, or gives a multiple prediction with reference to the different structural classes. The comparison of these predictions represents a novel tool to evaluate what sequence regions can assume different secondary structures depending on the structural class assignment, in the perspective of identifying proteins able to fold in different conformations. The service is available at the URL http://bioinformatica.isa.cnr.it/PRESSAPRO/.

The RNA Newton polytope and learnability of energy parameters.

PubMed

Forouzmand, Elmirasadat; Chitsaz, Hamidreza

2013-07-01

Computational RNA structure prediction is a mature important problem that has received a new wave of attention with the discovery of regulatory non-coding RNAs and the advent of high-throughput transcriptome sequencing. Despite nearly two score years of research on RNA secondary structure and RNA-RNA interaction prediction, the accuracy of the state-of-the-art algorithms are still far from satisfactory. So far, researchers have proposed increasingly complex energy models and improved parameter estimation methods, experimental and/or computational, in anticipation of endowing their methods with enough power to solve the problem. The output has disappointingly been only modest improvements, not matching the expectations. Even recent massively featured machine learning approaches were not able to break the barrier. Why is that? The first step toward high-accuracy structure prediction is to pick an energy model that is inherently capable of predicting each and every one of known structures to date. In this article, we introduce the notion of learnability of the parameters of an energy model as a measure of such an inherent capability. We say that the parameters of an energy model are learnable iff there exists at least one set of such parameters that renders every known RNA structure to date the minimum free energy structure. We derive a necessary condition for the learnability and give a dynamic programming algorithm to assess it. Our algorithm computes the convex hull of the feature vectors of all feasible structures in the ensemble of a given input sequence. Interestingly, that convex hull coincides with the Newton polytope of the partition function as a polynomial in energy parameters. To the best of our knowledge, this is the first approach toward computing the RNA Newton polytope and a systematic assessment of the inherent capabilities of an energy model. The worst case complexity of our algorithm is exponential in the number of features. However, dimensionality reduction techniques can provide approximate solutions to avoid the curse of dimensionality. We demonstrated the application of our theory to a simple energy model consisting of a weighted count of A-U, C-G and G-U base pairs. Our results show that this simple energy model satisfies the necessary condition for more than half of the input unpseudoknotted sequence-structure pairs (55%) chosen from the RNA STRAND v2.0 database and severely violates the condition for ~ 13%, which provide a set of hard cases that require further investigation. From 1350 RNA strands, the observed 3D feature vector for 749 strands is on the surface of the computed polytope. For 289 RNA strands, the observed feature vector is not on the boundary of the polytope but its distance from the boundary is not more than one. A distance of one essentially means one base pair difference between the observed structure and the closest point on the boundary of the polytope, which need not be the feature vector of a structure. For 171 sequences, this distance is larger than two, and for only 11 sequences, this distance is larger than five. The source code is available on http://compbio.cs.wayne.edu/software/rna-newton-polytope.

Finding the target sites of RNA-binding proteins

PubMed Central

Li, Xiao; Kazan, Hilal; Lipshitz, Howard D; Morris, Quaid D

2014-01-01

RNA–protein interactions differ from DNA–protein interactions because of the central role of RNA secondary structure. Some RNA-binding domains (RBDs) recognize their target sites mainly by their shape and geometry and others are sequence-specific but are sensitive to secondary structure context. A number of small- and large-scale experimental approaches have been developed to measure RNAs associated in vitro and in vivo with RNA-binding proteins (RBPs). Generalizing outside of the experimental conditions tested by these assays requires computational motif finding. Often RBP motif finding is done by adapting DNA motif finding methods; but modeling secondary structure context leads to better recovery of RBP-binding preferences. Genome-wide assessment of mRNA secondary structure has recently become possible, but these data must be combined with computational predictions of secondary structure before they add value in predicting in vivo binding. There are two main approaches to incorporating structural information into motif models: supplementing primary sequence motif models with preferred secondary structure contexts (e.g., MEMERIS and RNAcontext) and directly modeling secondary structure recognized by the RBP using stochastic context-free grammars (e.g., CMfinder and RNApromo). The former better reconstruct known binding preferences for sequence-specific RBPs but are not suitable for modeling RBPs that recognize shape and geometry of RNAs. Future work in RBP motif finding should incorporate interactions between multiple RBDs and multiple RBPs in binding to RNA. WIREs RNA 2014, 5:111–130. doi: 10.1002/wrna.1201 PMID:24217996

Unique growth strategy in the Earth's first trees revealed in silicified fossil trunks from China.

PubMed

Xu, Hong-He; Berry, Christopher M; Stein, William E; Wang, Yi; Tang, Peng; Fu, Qiang

2017-11-07

Cladoxylopsida included the earliest large trees that formed critical components of globally transformative pioneering forest ecosystems in the Mid- and early Late Devonian (ca. 393-372 Ma). Well-known cladoxylopsid fossils include the up to ∼1-m-diameter sandstone casts known as Eospermatopteris from Middle Devonian strata of New York State. Cladoxylopsid trunk structure comprised a more-or-less distinct cylinder of numerous separate cauline xylem strands connected internally with a network of medullary xylem strands and, near the base, externally with downward-growing roots, all embedded within parenchyma. However, the means by which this complex vascular system was able to grow to a large diameter is unknown. We demonstrate-based on exceptional, up to ∼70-cm-diameter silicified fossil trunks with extensive preservation of cellular anatomy from the early Late Devonian (Frasnian, ca. 374 Ma) of Xinjiang, China-that trunk expansion is associated with a cylindrical zone of diffuse secondary growth within ground and cortical parenchyma and with production of a large amount of wood containing both rays and growth increments concentrically around individual xylem strands by normal cambia. The xylem system accommodates expansion by tearing of individual strand interconnections during secondary development. This mode of growth seems indeterminate, capable of producing trees of large size and, despite some unique features, invites comparison with secondary development in some living monocots. Understanding the structure and growth of cladoxylopsids informs analysis of canopy competition within early forests with the potential to drive global processes. Published under the PNAS license.

Cellulose-hemicellulose interaction in wood secondary cell-wall

NASA Astrophysics Data System (ADS)

Zhang, Ning; Li, Shi; Xiong, Liming; Hong, Yu; Chen, Youping

2015-12-01

The wood cell wall features a tough and relatively rigid fiber reinforced composite structure. It acts as a pressure vessel, offering protection against mechanical stress. Cellulose microfibrils, hemicellulose and amorphous lignin are the three major components of wood. The structure of secondary cell wall could be imagined as the same as reinforced concrete, in which cellulose microfibrils acts as reinforcing steel bar and hemicellulose-lignin matrices act as the concrete. Therefore, the interface between cellulose and hemicellulose/lignin plays a significant role in determine the mechanical behavior of wood secondary cell wall. To this end, we present a molecular dynamics (MD) simulation study attempting to quantify the strength of the interface between cellulose microfibrils and hemicellulose. Since hemicellulose binds with adjacent cellulose microfibrils in various patterns, the atomistic models of hemicellulose-cellulose composites with three typical binding modes, i.e. bridge, loop and random binding modes are constructed. The effect of the shape of hemicellulose chain on the strength of hemicellulose-cellulose composites under shear loadings is investigated. The contact area as well as hydrogen bonds between cellulose and hemicellulose, together with the covalent bonds in backbone of hemicellulose chain are found to be the controlling parameters which determine the strength of the interfaces in the composite system. For the bridge binding model, the effect of shear loading direction on the strength of the cellulose material is also studied. The obtained results suggest that the shear strength of wood-inspired engineering composites can be optimized through maximizing the formations of the contributing hydrogen bonds between cellulose and hemicellulose.

Clinical characteristics of lung abscess in children: 15-year experience at two university hospitals

PubMed Central

Choi, Mi Suk; Chun, Ji Hye; Lee, Kyung Suk; Rha, Yeong Ho

2015-01-01

Purpose Information on the clinical features of lung abscess, which is uncommon in children, at hospitalizationis helpful to anticipate the disease course and management. There is no report concerning lung abscess in Korean children. We aimed to identify the clinical characteristics of pediatric lung abscess and compare the difference between primary and secondary abscess groups. Methods The medical records of 11 lung abscess patients (7 males and 4 females) from March 1998 to August 2011 at two university hospitals were retrospectively reviewed. The clinical characteristics, symptoms, underlying disease, laboratory and radiologic findings, microbiological results, and treatments were examined. Results Six patients had underlying structural-related problems (e.g., skeletal anomalies). No immunologic or hematologic problem was recorded. The mean ages of the primary and secondary groups were 2.4 and 5.3 years, respectively, but the difference was not statistically significant. The mean length of hospital stay was similar in both groups (22.8 days vs. 21.4 days). Immunologic studies were performed in 3 patients; the results were within the normal range. Most patients had prominent leukocytosis. Seven and 4 patients had right and left lung abscess, respectively. Staphylococcus aureus, Streptococcus pneumoniae, and antimycoplasma antibodies were detected in both groups. Two patients with primary lung abscess were administered antibiotics in the absence of other procedures, while 8 underwent interventional procedures, including 5 with secondary abscess. Conclusion The most common symptoms were fever and cough. All patients in the primary group were younger than 3 years. Structural problems were dominant. Most patients required interventional procedures and antibiotics. PMID:26770223

Clinical characteristics of lung abscess in children: 15-year experience at two university hospitals.

PubMed

Choi, Mi Suk; Chun, Ji Hye; Lee, Kyung Suk; Rha, Yeong Ho; Choi, Sun Hee

2015-12-01

Information on the clinical features of lung abscess, which is uncommon in children, at hospitalizationis helpful to anticipate the disease course and management. There is no report concerning lung abscess in Korean children. We aimed to identify the clinical characteristics of pediatric lung abscess and compare the difference between primary and secondary abscess groups. The medical records of 11 lung abscess patients (7 males and 4 females) from March 1998 to August 2011 at two university hospitals were retrospectively reviewed. The clinical characteristics, symptoms, underlying disease, laboratory and radiologic findings, microbiological results, and treatments were examined. Six patients had underlying structural-related problems (e.g., skeletal anomalies). No immunologic or hematologic problem was recorded. The mean ages of the primary and secondary groups were 2.4 and 5.3 years, respectively, but the difference was not statistically significant. The mean length of hospital stay was similar in both groups (22.8 days vs. 21.4 days). Immunologic studies were performed in 3 patients; the results were within the normal range. Most patients had prominent leukocytosis. Seven and 4 patients had right and left lung abscess, respectively. Staphylococcus aureus, Streptococcus pneumoniae, and antimycoplasma antibodies were detected in both groups. Two patients with primary lung abscess were administered antibiotics in the absence of other procedures, while 8 underwent interventional procedures, including 5 with secondary abscess. The most common symptoms were fever and cough. All patients in the primary group were younger than 3 years. Structural problems were dominant. Most patients required interventional procedures and antibiotics.

An outpatient clinical study of dissociative disorder not otherwise specified.

PubMed

Yanartaş, Ömer; Özmen, Hülya Akar; Citak, Serhat; Zincir, Selma Bozkurt; Sünbül, Esra Aydin

2014-05-01

The relatively high prevalence of the diagnosis of dissociative disorder not otherwise specified is frequently considered to be disproportionate. The disproportionate rate of this diagnosis is thought to be related to nosologic and/or diagnostic issues in dissociative identity disorder. We sought to investigate and compare the symptom patterns of these two clinical entities. We conducted a cross-sectional study involving 1314 participants who were screened with the Dissociative Experience Scale (DES) and the Somatoform Dissociation Questionnaire (SDQ). Of the participants, 272 who scored above the cut-off points for the screening questionnaires (DES score>30 and/or SDQ score>40 points) were invited to complete a structured interview using the Dissociative Disorders Interview Schedule (DDIS); of this subsample, only 190 participants agreed to participate in the second phase of the study. The mean score for the DES was 18.55±17.23, and the mean score for the SDQ was 30.19±13.32. Of the 190 participants, 167 patients were diagnosed as having a dissociative disorder (87.8%). We found that DD-NOS was the most prevalent category of dissociative disorder. There was a significantly larger percentage of patients in the DID group than in the DD-NOS group according to secondary features of DID and Schneiderian symptoms. The secondary features of DID and Schneiderian symptoms appeared to be more specific for DID, while no differences were detected between DID and DD-NOS based on most of the items on the SCL 90R. Further longitudinal studies are needed to determine the features that are similar and dissimilar between DD-NOS and DID. Copyright © 2014 Elsevier Inc. All rights reserved.

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

PubMed

Jabbari, Hosna; Wark, Ian; Montemagno, Carlo

2018-01-01

RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method. The aim of this work is to argue when comparing different methods for RNA pseudoknotted structure prediction, the combination of algorithm and energy model should be considered and a method should not be considered superior or inferior to others if they do not use the same scoring model. We demonstrate that while the folding approach is important in structure prediction, it is not the only important factor in prediction accuracy of a given method as the underlying energy model is also as of great value. Therefore we encourage researchers to pay particular attention in comparing methods with different energy models.

Self-Efficacy, School Resources, Job Stressors and Burnout among Spanish Primary and Secondary School Teachers: A Structural Equation Approach

ERIC Educational Resources Information Center

Betoret, Fernando Domenech

2009-01-01

This study examines the relationship between school resources, teacher self-efficacy, potential multi-level stressors and teacher burnout using structural equation modelling. The causal structure for primary and secondary school teachers was also examined. The sample was composed of 724 primary and secondary Spanish school teachers. The changes…

[Analysis of the primary and secondary structure of the mitochondrial serine transfer RNA in seven species of Lutzomyia].

PubMed

Vivero, Rafael José; Contreras-Gutiérrez, Maria Angélica; Bejarano, Eduar Elías

2007-09-01

Lutzomyia sand flies are involved in the transmission of the parasite Leishmania spp. in America. The taxonomy of these vectors is traditionally based on morphological features of the adult stage, particularly the paired structures of the head and genitalia. Although these characters are useful to distinguish most species of Lutzomyia, morphological identification may be complicated by the similarities within subgenera and species group. To evaluate the utility of mitochondrial serine transfer RNA tRNA Ser for taxonomic identification of Lutzomyia. Seven sand fly species, each representing one of the 27 taxonomic subdivisions in genus Lutzomyia, were analyzed including L. trinidadensis (Oswaldoi group), L. (Psychodopygus) panamensis, L.(Micropygomyia) cayennensis cayennensis, L. dubitans (Migonei group), L. (Lutzomyia) gomezi, L. rangeliana (ungrouped) and L. evansi (Verrucarum group). The mitochondrial tRNA Ser gene, flanked by the cytochrome b and NAD dehydrogenase subunit one genes, was extracted, amplified and sequenced from each specimen. Secondary structure of the tRNA Ser was predicted by comparisons with previously described homologous structures from other dipteran species. The tRNA Ser gene ranged in size from 66 base pairs in L. gomezi to 69 base pairs in L. trinidadensis. Fourteen polymorphic sites, including four insertion-deletion events, were observed in the aligned 70 nucleotide positions. The majority of the substitutions were located in the dihydrouridine, ribothymidine-pseudouridine-cytosine and variable loops, as well as in the basal extreme of the anticodon arm. Changes of primary sequence of the tRNASer provided useful molecular characters for taxonomic identification of the sand fly species under consideration.

Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.

PubMed

Shelar, Ashish; Bansal, Manju

2014-12-01

α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. © 2014 Wiley Periodicals, Inc.

RNApdbee 2.0: multifunctional tool for RNA structure annotation.

PubMed

Zok, Tomasz; Antczak, Maciej; Zurkowski, Michal; Popenda, Mariusz; Blazewicz, Jacek; Adamiak, Ryszard W; Szachniuk, Marta

2018-04-30

In the field of RNA structural biology and bioinformatics, an access to correctly annotated RNA structure is of crucial importance, especially in the secondary and 3D structure predictions. RNApdbee webserver, introduced in 2014, primarily aimed to address the problem of RNA secondary structure extraction from the PDB files. Its new version, RNApdbee 2.0, is a highly advanced multifunctional tool for RNA structure annotation, revealing the relationship between RNA secondary and 3D structure given in the PDB or PDBx/mmCIF format. The upgraded version incorporates new algorithms for recognition and classification of high-ordered pseudoknots in large RNA structures. It allows analysis of isolated base pairs impact on RNA structure. It can visualize RNA secondary structures-including that of quadruplexes-with depiction of non-canonical interactions. It also annotates motifs to ease identification of stems, loops and single-stranded fragments in the input RNA structure. RNApdbee 2.0 is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.

Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.

PubMed

Yehdego, Daniel T; Zhang, Boyu; Kodimala, Vikram K R; Johnson, Kyle L; Taufer, Michela; Leung, Ming-Ying

2013-05-01

Secondary structures of ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Experimental observations and computing limitations suggest that we can approach the secondary structure prediction problem for long RNA sequences by segmenting them into shorter chunks, predicting the secondary structures of each chunk individually using existing prediction programs, and then assembling the results to give the structure of the original sequence. The selection of cutting points is a crucial component of the segmenting step. Noting that stem-loops and pseudoknots always contain an inversion, i.e., a stretch of nucleotides followed closely by its inverse complementary sequence, we developed two cutting methods for segmenting long RNA sequences based on inversion excursions: the centered and optimized method. Each step of searching for inversions, chunking, and predictions can be performed in parallel. In this paper we use a MapReduce framework, i.e., Hadoop, to extensively explore meaningful inversion stem lengths and gap sizes for the segmentation and identify correlations between chunking methods and prediction accuracy. We show that for a set of long RNA sequences in the RFAM database, whose secondary structures are known to contain pseudoknots, our approach predicts secondary structures more accurately than methods that do not segment the sequence, when the latter predictions are possible computationally. We also show that, as sequences exceed certain lengths, some programs cannot computationally predict pseudoknots while our chunking methods can. Overall, our predicted structures still retain the accuracy level of the original prediction programs when compared with known experimental secondary structure.

Walking Down the Chalcogenic Group of the Periodic Table: From Singlet to Triplet Organic Emitters.

PubMed

Kremer, Adrian; Aurisicchio, Claudia; De Leo, Federica; Ventura, Barbara; Wouters, Johan; Armaroli, Nicola; Barbieri, Andrea; Bonifazi, Davide

2015-10-19

The synthesis, X-ray crystal structures, ground- and excited-state UV/Vis absorption spectra, and luminescence properties of chalcogen-doped organic emitters equipped on both extremities with benzoxa-, benzothia-, benzoselena- and benzotellurazole (1X and 2X ) moieties have been reported for the first time. The insertion of the four different chalcogen atoms within the same molecular skeleton enables the investigation of only the chalcogenic effect on the organisation and photophysical properties of the material. Detailed crystal-structure analyses provide evidence of similar packing for 2O -2Se , in which the benzoazoles are engaged in π-π stacking and, for the heavier atoms, in secondary X⋅⋅⋅X and X⋅⋅⋅N bonding interactions. Detailed computational analysis shows that the arrangement is essentially governed by the interplay of van der Waals and secondary bonding interactions. Progressive quenching of the fluorescence and concomitant onset of phosphorescence features with gradually shorter lifetimes are detected as the atomic weight of the chalcogen heteroatom increases, with the tellurium-doped derivatives exhibiting only emission from the lowest triplet excited state. Notably, the phosphorescence spectra of the selenium and tellurium derivatives can be recorded even at room temperature; this is a very rare finding for fully organic emitters. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monte-Carlo Simulations of Heavy Ions Track Structures and Applications

NASA Technical Reports Server (NTRS)

Plante, Ianik; Cucinotta, Francia A.

2013-01-01

In space, astronauts are exposed to protons, high ]energy heavy (HZE) ions that have a high charge (Z) and energy (E), and secondary radiation, including neutrons and recoil nuclei produced by nuclear reactions in spacecraft walls or in tissue. The astronauts can only be partly shielded from these particles. Therefore, on travelling to Mars, it is estimated that every cell nucleus in an astronaut fs body would be hit by a proton or secondary electron (e.g., electrons of the target atoms ionized by the HZE ion) every few days and by an HZE ion about once a month. The risks related to these heavy ions are not well known and of concern for long duration space exploration missions. Medical ion therapy is another situation where human beings can be irradiated by heavy ions, usually to treat cancer. Heavy ions have a peculiar track structure characterized by high levels of energy ]deposition clustering, especially in near the track ends in the so ]called eBragg peak f region. In radiotherapy, these features of heavy ions can provide an improved dose conformation with respect to photons, also considering that the relative biological effectiveness (RBE) of therapeutic ions in the plateau region before the peak is sufficiently low. Therefore, several proton and carbon ion therapy facilities are under construction at this moment

Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins.

PubMed

Lee, Chewook; Kalmar, Lajos; Xue, Bin; Tompa, Peter; Daughdrill, Gary W; Uversky, Vladimir N; Han, Kyou-Hoon

2014-03-01

IDPs function without relying on three-dimensional structures. No clear rationale for such a behavior is available yet. PreSMos are transient secondary structures observed in the target-free IDPs and serve as the target-binding "active" motifs in IDPs. Prolines are frequently found in the flanking regions of PreSMos. Contribution of prolines to the conformational stability of the helical PreSMos in IDPs is investigated. MD simulations are performed for several IDP segments containing a helical PreSMo and the flanking prolines. To measure the influence of flanking-prolines on the structural content of a helical PreSMo calculations were done for wild type as well as for mutant segments with Pro→Asp, His, Lys, or Ala. The change in the helicity due to removal of a proline was measured both for the PreSMo region and for the flanking regions. The α-helical content in ~70% of the helical PreSMos at the early stage of simulation decreases due to replacement of an N-terminal flanking proline by other residues whereas the helix content in nearly all PreSMos increases when the same replacements occur at the C-terminal flanking region. The helix destabilizing/terminating role of the C-terminal flanking prolines is more pronounced than the helix promoting effect of the N-terminal flanking prolines. This work represents a novel example demonstrating that a proline is encoded in an IDP with a defined purpose. The helical PreSMos presage their target-bound conformations. As they most likely mediate IDP-target binding via conformational selection their helical content can be an important feature for IDP function. Copyright © 2013 Elsevier B.V. All rights reserved.

Density functional study of molecular interactions in secondary structures of proteins.

PubMed

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Robust predictions for an oscillatory bispectrum in Planck 2015 data from transient reductions in the speed of sound of the inflaton

NASA Astrophysics Data System (ADS)

Torrado, Jesús; Hu, Bin; Achúcarro, Ana

2017-10-01

We update the search for features in the cosmic microwave background (CMB) power spectrum due to transient reductions in the speed of sound, using Planck 2015 CMB temperature and polarization data. We enlarge the parameter space to much higher oscillatory frequencies of the feature, and define a robust prior independent of the ansatz for the reduction, guaranteed to reproduce the assumptions of the theoretical model. This prior exhausts the regime in which features coming from a Gaussian reduction are easily distinguishable from the baseline cosmology. We find a fit to the ℓ≈20 - 40 minus /plus structure in Planck TT power spectrum, as well as features spanning along higher ℓ's (ℓ≈100 - 1500 ). None of those fits is statistically significant, either in terms of their improvement of the likelihood or in terms of the Bayes ratio. For the higher-ℓ ones, their oscillatory frequency (and their amplitude to a lesser extent) is tightly constrained, so they can be considered robust, falsifiable predictions for their correlated features in the CMB bispectrum. We compute said correlated features, and assess their signal to noise and correlation with the secondary bispectrum of the correlation between the gravitational lensing of the CMB and the integrated Sachs-Wolfe effect. We compare our findings to the shape-agnostic oscillatory template tested in Planck 2015, and we comment on some tantalizing coincidences with some of the traits described in Planck's 2015 bispectrum data.

Pairwise amino acid secondary structural propensities

NASA Astrophysics Data System (ADS)

Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.

2015-04-01

We investigate the propensities for amino acids to form a specific secondary structure when they are paired with other amino acids. Our investigations use molecular dynamics (MD) computer simulations, and we compare the results to those from the Protein Data Bank (PDB). Proper comparison requires weighting of the MD results in a manner consistent with the relative frequency of appearance in the PDB of each possible pair of amino acids. We find that the propensity for an amino acid to assume a secondary structure varies dramatically depending on the amino acid that is before or after it in the primary sequence. This cooperative effect means that when selecting amino acids to facilitate the formation of a secondary structure in peptide engineering experiments, the adjacent amino acids must be considered. We also examine the preference for a secondary structure in bacterial proteins and compare the results to those of human proteins.

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

PubMed Central

2011-01-01

Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file. PMID:21205310

Large Crater Clustering tool

NASA Astrophysics Data System (ADS)

Laura, Jason; Skinner, James A.; Hunter, Marc A.

2017-08-01

In this paper we present the Large Crater Clustering (LCC) tool set, an ArcGIS plugin that supports the quantitative approximation of a primary impact location from user-identified locations of possible secondary impact craters or the long-axes of clustered secondary craters. The identification of primary impact craters directly supports planetary geologic mapping and topical science studies where the chronostratigraphic age of some geologic units may be known, but more distant features have questionable geologic ages. Previous works (e.g., McEwen et al., 2005; Dundas and McEwen, 2007) have shown that the source of secondary impact craters can be estimated from secondary impact craters. This work adapts those methods into a statistically robust tool set. We describe the four individual tools within the LCC tool set to support: (1) processing individually digitized point observations (craters), (2) estimating the directional distribution of a clustered set of craters, back projecting the potential flight paths (crater clusters or linearly approximated catenae or lineaments), (3) intersecting projected paths, and (4) intersecting back-projected trajectories to approximate the local of potential source primary craters. We present two case studies using secondary impact features mapped in two regions of Mars. We demonstrate that the tool is able to quantitatively identify primary impacts and supports the improved qualitative interpretation of potential secondary crater flight trajectories.

Comparative modeling without implicit sequence alignments.

PubMed

Kolinski, Andrzej; Gront, Dominik

2007-10-01

The number of known protein sequences is about thousand times larger than the number of experimentally solved 3D structures. For more than half of the protein sequences a close or distant structural analog could be identified. The key starting point in a classical comparative modeling is to generate the best possible sequence alignment with a template or templates. With decreasing sequence similarity, the number of errors in the alignments increases and these errors are the main causes of the decreasing accuracy of the molecular models generated. Here we propose a new approach to comparative modeling, which does not require the implicit alignment - the model building phase explores geometric, evolutionary and physical properties of a template (or templates). The proposed method requires prior identification of a template, although the initial sequence alignment is ignored. The model is built using a very efficient reduced representation search engine CABS to find the best possible superposition of the query protein onto the template represented as a 3D multi-featured scaffold. The criteria used include: sequence similarity, predicted secondary structure consistency, local geometric features and hydrophobicity profile. For more difficult cases, the new method qualitatively outperforms existing schemes of comparative modeling. The algorithm unifies de novo modeling, 3D threading and sequence-based methods. The main idea is general and could be easily combined with other efficient modeling tools as Rosetta, UNRES and others.

Improved data visualization techniques for analyzing macromolecule structural changes.

PubMed

Kim, Jae Hyun; Iyer, Vidyashankara; Joshi, Sangeeta B; Volkin, David B; Middaugh, C Russell

2012-10-01

The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique. Copyright © 2012 The Protein Society.

Improved data visualization techniques for analyzing macromolecule structural changes

PubMed Central

Kim, Jae Hyun; Iyer, Vidyashankara; Joshi, Sangeeta B; Volkin, David B; Middaugh, C Russell

2012-01-01

The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique. PMID:22898970

Teachers' voices: A comparison of two secondary science teacher preparation programs

NASA Astrophysics Data System (ADS)

Kohlhaas Labuda, Kathryn

This dissertation, using cross-case qualitative methodology, investigates the salient and latent features of two philosophically different university-based secondary science teacher preparation programs. Written documents from the two programs and from the Salish I Research project provided the salient data. New teachers' interview transcripts provided the latent data. This study provides the opportunity to hear teachers voice their perceptions of preparation programs. Three questions were investigated in this research study. First, What are the salient features of two different secondary science teacher preparation programs? Second, What are the latent features of two different secondary science teacher programs as perceived by new teachers? Third, How do new secondary science teachers from different programs perceive their preservice programs? The last question incorporates teachers' perceptions of gaps and coherence in the programs and teachers' recommendations to improve their preservice programs. Salient features of the programs revealed differences in the types of certification, and the amounts and types of required course work. Both programs certified teachers at the secondary science level, but only M program certified their teachers as elementary science specialists. Program M required more semester hours of education and science course work than Program S. Although teachers from both programs perceived little coherence between their science and education courses, S-teachers presented a more fragmented picture of their education program and perceived fewer benefits from the program. Lack of relevance and courses that focused on elementary teaching were perceived as part of the problem. M-teachers perceived some cohesion through the use of cohorts in three consecutive semesters of science methods courses that provided multiple field experiences prior to student teaching. S-teachers did not perceive an organized philosophy of their program. M-teachers' perceptions of the philosophy of their program revolved about research based teaching. S-teachers reported more research experiences. S-teachers perceived better student-science faculty relationship, while M-teachers reported stronger student-education faculty relationships. Teachers from both programs recommended more field experiences that resembled more closely the real life situations of teachers. They recommended smaller classes in both science and education courses. They suggested eliminating or altering courses that were not beneficial.

Structural alterations in rat liver proteins due to streptozotocin-induced diabetes and the recovery effect of selenium: Fourier transform infrared microspectroscopy and neural network study

NASA Astrophysics Data System (ADS)

Bozkurt, Ozlem; Haman Bayari, Sevgi; Severcan, Mete; Krafft, Christoph; Popp, Jürgen; Severcan, Feride

2012-07-01

The relation between protein structural alterations and tissue dysfunction is a major concern as protein fibrillation and/or aggregation due to structural alterations has been reported in many disease states. In the current study, Fourier transform infrared microspectroscopic imaging has been used to investigate diabetes-induced changes on protein secondary structure and macromolecular content in streptozotocin-induced diabetic rat liver. Protein secondary structural alterations were predicted using neural network approach utilizing the amide I region. Moreover, the role of selenium in the recovery of diabetes-induced alterations on macromolecular content and protein secondary structure was also studied. The results revealed that diabetes induced a decrease in lipid to protein and glycogen to protein ratios in diabetic livers. Significant alterations in protein secondary structure were observed with a decrease in α-helical and an increase in β-sheet content. Both doses of selenium restored diabetes-induced changes in lipid to protein and glycogen to protein ratios. However, low-dose selenium supplementation was not sufficient to recover the effects of diabetes on protein secondary structure, while a higher dose of selenium fully restored diabetes-induced alterations in protein structure.

Adsorption of fibrinogen on a biomedical-grade stainless steel 316LVM surface: a PM-IRRAS study of the adsorption thermodynamics, kinetics and secondary structure changes.

PubMed

Desroches, Marie-Josee; Omanovic, Sasha

2008-05-14

Polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) was employed to investigate the interaction of serum protein fibrinogen with a biomedical-grade 316LVM stainless steel surface, in terms of the adsorption thermodynamics, kinetics and secondary structure changes of the protein. Apparent Gibbs energy of adsorption values indicated a highly spontaneous and strong adsorption of fibrinogen onto the surface. The kinetics of fibrinogen adsorption were successfully modeled using a pseudo first-order kinetic model. Deconvolution of the amide I bands indicated that the adsorption of fibrinogen on 316LVM results in significant changes in the protein's secondary structure that occur predominantly within the first minute of adsorption. Among the investigated structures, the alpha-helix structure undergoes the smallest changes, while the beta-sheet and beta-turns structures undergo significant changes. It was shown that lateral interactions between the adsorbed molecules do not play a role in controlling the secondary structure changes. An increase in temperature induced changes in the secondary structure of the protein, characterized by a loss of the alpha-helical content and its transformation into the beta-turns structure.