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.

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.

Secondary structure estimation and properties analysis of stretched Asian and Caucasian hair.

PubMed

Zhou, A J; Liu, H L; Du, Z Q

2015-02-01

In this previous work, we investigated the secondary structure changes of stretched yak hairs by deconvolution, secondary derivation, and curve fitting and determined the number of bands and their positions in order to resolve the protein spectrum of Raman spectroscopy. The secondary structure estimation and properties analysis of stretched Asian and Caucasian hair were investigated by Fourier transform infrared spectroscopy, tensile curves, and measurement of density. The hairs were stretched, dried, and baked at ratios 20%, 40%, 60%, 80% and 100%. The analysis of the amide I band indicated that the transformation from α-helix to β-pleated structure occurred during the stretching process, which could be verified from the tensile analysis. The cysteine oxide in S-O vibration area exhibited that stretching led to the breakage of the disulfide bonds. When the stretching ratio of Caucasian hair was more than a certain ratio, the fiber macromolecular structure was destroyed because Caucasian hair had finer diameter and less medulla than Asian hair. The β turn was easier to retract compared with other conformations, resulted in the content increase. The density measurements revealed that the structure of Caucasian hair was indeed more destroyed than that of Asian hair. The cuticles characterization indicated the length of scales was stretched longer and the thickness became thinner. Caucasian hair tended to collapse to form small fragments at the early stage of stretching. With the increase in stretching ratio, the scales of Caucasian hair lifted up, then flaked off and the scale interval increased accordingly. Asian hair was more easily peeled off than Caucasian hair cuticles with the increase in stretching ratio. The secondary structure of Caucasian hair was destroyed more easily than that of Asian hair. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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.

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

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

PubMed

Danaee, Padideh; Rouches, Mason; Wiley, Michelle; Deng, Dezhong; Huang, Liang; Hendrix, David

2018-05-09

While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, 'bpRNA-1m', of over 100 000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis

PubMed Central

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. Availability http://www.cemb.edu.pk/sw.html Abbreviations RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language. PMID:23055611

Mechanical and thermal disturbances of the PSR Moderate Focus-Mission Structure

NASA Technical Reports Server (NTRS)

Shih, Choon-Foo; Lou, Michael C.

1991-01-01

The primary objective of this paper is to evaluate the optical pointing performance of the PSR Moderate Focus-Mission Structure when subjected to both mechanical and thermal disturbances. The mechanical disturbances are based on secondary mirror chopping. Results indicate that dynamic responses of the primary reflector and the secondary reflector subjected to chopping disturbances of the secondary reflector about its center of mass are within the figure maintenance control capabilities. The effects of modal damping, truss-type secondary support, interface boundary constraints, and alternate configurations, are also evaluated in the analysis. Thermal distortions of the structure were also evaluated based on the on-orbit temperature profiles derived from the submillimeter telescope missions. Results from thermal deformation analysis indicate that figure initialization control is needed for the PSR Moderate Focus-Mission. However, a figure maintenance system may not be required if adequate thermal isolation is incorporated into the support truss design for the PSR Moderate Focus-Mission Structure.

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.

Numerical analysis of exhaust jet secondary combustion in hypersonic flow field

NASA Astrophysics Data System (ADS)

Yang, Tian-Peng; Wang, Jiang-Feng; Zhao, Fa-Ming; Fan, Xiao-Feng; Wang, Yu-Han

2018-05-01

The interaction effect between jet and control surface in supersonic and hypersonic flow is one of the key problems for advanced flight control system. The flow properties of exhaust jet secondary combustion in a hypersonic compression ramp flow field were studied numerically by solving the Navier-Stokes equations with multi-species and combustion reaction effects. The analysis was focused on the flow field structure and the force amplification factor under different jet conditions. Numerical results show that a series of different secondary combustion makes the flow field structure change regularly, and the temperature increases rapidly near the jet exit.

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.

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

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/.

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.

PubMed

Eddy, Sean R

2014-01-01

Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.

Conducting high-value secondary dataset analysis: an introductory guide and resources.

PubMed

Smith, Alexander K; Ayanian, John Z; Covinsky, Kenneth E; Landon, Bruce E; McCarthy, Ellen P; Wee, Christina C; Steinman, Michael A

2011-08-01

Secondary analyses of large datasets provide a mechanism for researchers to address high impact questions that would otherwise be prohibitively expensive and time-consuming to study. This paper presents a guide to assist investigators interested in conducting secondary data analysis, including advice on the process of successful secondary data analysis as well as a brief summary of high-value datasets and online resources for researchers, including the SGIM dataset compendium ( www.sgim.org/go/datasets ). The same basic research principles that apply to primary data analysis apply to secondary data analysis, including the development of a clear and clinically relevant research question, study sample, appropriate measures, and a thoughtful analytic approach. A real-world case description illustrates key steps: (1) define your research topic and question; (2) select a dataset; (3) get to know your dataset; and (4) structure your analysis and presentation of findings in a way that is clinically meaningful. Secondary dataset analysis is a well-established methodology. Secondary analysis is particularly valuable for junior investigators, who have limited time and resources to demonstrate expertise and productivity.

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.

Effects of temperature and SDS on the structure of beta-glycosidase from the thermophilic archaeon Sulfolobus solfataricus.

PubMed Central

D'auria, S; Barone, R; Rossi, M; Nucci, R; Barone, G; Fessas, D; Bertoli, E; Tanfani, F

1997-01-01

The effects of temperature and SDS on the three-dimensional organization and secondary structure of beta-glycosidase from the thermophilic archaeon Sulfolobus solfataricus were investigated by CD, IR spectroscopy and differential scanning calorimetry. CD spectra in the near UV region showed that the detergent caused a remarkable change in the protein tertiary structure, and far-UV CD analysis revealed only a slight effect on secondary structure. Infrared spectroscopy showed that low concentrations of the detergent (up to 0.02%) induced slight changes in the enzyme secondary structure, whereas high concentrations caused the alpha-helix content to increase at high temperatures and prevented protein aggregation. PMID:9169619

Secondary Fire Analysis.

DTIC Science & Technology

1981-09-01

of wood frame and brick veneer, slab on grade construction), killed 33, injured more than 1,000, derailed a train, destroyed 4,000 cars, uprooted most... of a nuclear detonation) in or near structures, with emphasis on critical facil- ities and industries. Assessment of the potential for secondary fires...and/or 517 East Dayshore, Redwood City, CA 94063 DistI pial (DETACHABLE SUMMARY) SECONDARY FIRE ANALYSIS This report presents the results of a

Secondary structural analyses of ITS1 in Paramecium.

PubMed

Hoshina, Ryo

2010-01-01

The nuclear ribosomal RNA gene operon is interrupted by internal transcribed spacer (ITS) 1 and ITS2. Although the secondary structure of ITS2 has been widely investigated, less is known about ITS1 and its structure. In this study, the secondary structure of ITS1 sequences for Paramecium and other ciliates was predicted. Each Paramecium ITS1 forms an open loop with three helices, A through C. Helix B was highly conserved among Paramecium, and similar helices were found in other ciliates. A phylogenetic analysis using the ITS1 sequences showed high-resolution, implying that ITS1 is a good tool for species-level analyses.

Chinese American Post-Secondary Achievement and Attainment: A Cultural and Structural Analysis

ERIC Educational Resources Information Center

Pearce, Richard R.; Lin, Zeng

2007-01-01

In this article, the authors compare Chinese American post-secondary educational attainment with that of White Americans and, in identifying those factors that most strongly account for success, argue that commonalities exist among social structural factors, while distinct differences are evident among cultural capital factors. The article rejects…

FTIR study of secondary structure of bovine serum albumin and ovalbumin

NASA Astrophysics Data System (ADS)

Abrosimova, K. V.; Shulenina, O. V.; Paston, S. V.

2016-11-01

Proteins structure is the critical factor for their functioning. Fourier transform infrared spectroscopy provides a possibility to obtain information about secondary structure of proteins in different states and also in a whole biological samples. Infrared spectra of egg white from the untreated and hard-boiled hen's egg, and also of chicken ovalbumin and bovine serum albumin in lyophilic form and in aqueous solution were studied. Lyophilization of investigated globular proteins is accompanied by the decrease of a-helix structures and the increase in amount of intermolecular β-sheets. Analysis of infrared spectrum of egg white allowed to make an estimation of OVA secondary structure and to observe α-to-β structural transformation as a result of the heat denaturation.

An Amino Acid Code for Irregular and Mixed Protein Packing

PubMed Central

Joo, Hyun; Chavan, Archana; Fraga, Keith; Tsai, Jerry

2015-01-01

To advance our understanding of protein tertiary structure, the development of the knob-socket model is completed in an analysis of the packing in irregular coil and turn secondary structure packing as well as between mixed secondary structure. The knob-socket model simplifies packing based on repeated patterns of 2 motifs: a 3 residue socket for packing within 2° structure and a 4 residue knob-socket for 3° packing. For coil and turn secondary structure, knob-sockets allow identification of a correlation between amino acid composition and tertiary arrangements in space. Coil contributes almost as much as α-helices to tertiary packing. Irregular secondary structure involves 3 residue cliques of consecutive contacting residues or XYZ sockets. In irregular sockets, Gly, Pro, Asp and Ser are favored, while Cys, His, Met and Trp are not. For irregular knobs, the preference order is Arg, Asp, Pro, Asn, Thr, Leu, and Gly, while Cys, His, Met and Trp are not. In mixed packing, the knob amino acid preferences are a function of the socket that they are packing into, whereas the amino acid composition of the sockets does not depend on the secondary structure of the knob. A unique motif of a coil knob with an XYZ β-sheet socket may potentially function to inhibit β-sheet extension. In addition, analysis of the preferred crossing angles for strands within a β-sheet and mixed α-helices/β-sheets identifies canonical packing patterns useful in protein design. Lastly, the knob-socket model abstracts the complexity of protein tertiary structure into an intuitive packing surface topology map. PMID:26370334

Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

PubMed

Wu, Johnny C; Gardner, David P; Ozer, Stuart; Gutell, Robin R; Ren, Pengyu

2009-08-28

The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically derived potential energy has been used in the prediction of protein structure. In the current work, we evaluate the statistical free energy of various secondary structure motifs, including base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtained from the comparative analysis of more than 50,000 RNA sequences stored in the RNA Comparative Analysis Database (rCAD) at the Comparative RNA Web (CRW) Site. Statistical energy was computed from the structural statistics for several datasets. While the statistical energy for a base-pair stack correlates with experimentally derived free energy values, suggesting a Boltzmann-like distribution, variation is observed between different molecules and their location on the phylogenetic tree of life. Our statistical energy values calculated for several structural elements were utilized in the Mfold RNA-folding algorithm. The combined statistical energy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement in the accuracy of secondary structure prediction; the hairpin flanks contribute the most.

Correlation of MFOLD-predicted DNA secondary structures with separation patterns obtained by capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis.

PubMed

Glavac, Damjan; Potocnik, Uros; Podpecnik, Darja; Zizek, Teofil; Smerkolj, Sava; Ravnik-Glavac, Metka

2002-04-01

We have studied 57 different mutations within three beta-globin gene promoter fragments with sizes 52 bp, 77 bp, and 193 bp by fluorescent capillary electrophoresis CE-SSCP analysis. For each mutation and wild type, energetically most-favorable predicted secondary structures were calculated for sense and antisense strands using the MFOLD DNA-folding algorithm in order to investigate if any correlation exists between predicted DNA structures and actual CE migration time shifts. The overall CE-SSCP detection rate was 100% for all mutations in three studied DNA fragments. For shorter 52 bp and 77 bp DNA fragments we obtained a positive correlation between the migration time shifts and difference in free energy values of predicted secondary structures at all temperatures. For longer 193 bp beta-globin gene fragments with 46 mutations MFOLD predicted different secondary structures for 89% of mutated strands at 25 degrees C and 40 degrees C. However, the magnitude of the mobility shifts did not necessarily correlate with their secondary structures and free energy values except for the sense strand at 40 degrees C where this correlation was statistically significant (r = 0.312, p = 0.033). Results of this study provided more direct insight into the mechanism of CE-SSCP and showed that MFOLD prediction could be helpful in making decisions about the running temperatures and in prediction of CE-SSCP data patterns, especially for shorter (50-100 bp) DNA fragments. Copyright 2002 Wiley-Liss, Inc.

Probing the transition state for nucleic acid hybridization using phi-value analysis.

PubMed

Kim, Jandi; Shin, Jong-Shik

2010-04-27

Genetic regulation by noncoding RNA elements such as microRNA and small interfering RNA (siRNA) involves hybridization of a short single-stranded RNA with a complementary segment in a target mRNA. The physical basis of the hybridization process between the structured nucleic acids is not well understood primarily because of the lack of information about the transition-state structure. Here we use transition-state theory, inspired by phi-value analysis in protein folding studies, to provide quantitative analysis of the relationship between changes in the secondary structure stability and the activation free energy. Time course monitoring of the hybridization reaction was performed under pseudo-steady-state conditions using a single fluorophore. The phi-value analysis indicates that the native secondary structure remains intact in the transition state. The nativelike transition state was confirmed via examination of the salt dependence of the hybridization kinetics, indicating that the number of sodium ions associated with the transition state was not substantially affected by changes in the native secondary structure. These results propose that hybridization between structured nucleic acids undergoes a transition state leading to formation of a nucleation complex and then is followed by sequential displacement of preexisting base pairings involving successive small energy barriers. The proposed mechanism might provide new insight into physical processes during small RNA-mediated gene silencing, which is essential to selection of a target mRNA segment for siRNA design.

Constructing Confidence and Identities of Belonging in Mathematics at the Transition to Secondary School

ERIC Educational Resources Information Center

Darragh, Lisa

2013-01-01

This case study investigates students' perspectives on their mathematics learning experiences and identity constructions, in the context of transition to secondary school. In-depth, semi-structured interviews were conducted with six girls, halfway through their first year at their new school. Thematic analysis and discourse analysis were used to…

Sampling And Resolution Enhancement Techniques For The Infrared Analysis Of Adsorbed Proteins.

NASA Astrophysics Data System (ADS)

Fuller, Michael P.; Singh, Bal R.

1989-12-01

In this report, we have analyzed the secondary structures of the dichain form of tetanus neurotoxin using. FT-IR and circular dichroic spectroscopies for a-helix, β-sheets, β-turns and random coils. These results indicate that the secondary structures are significantly different from those reported in earlier studies in that it shows much higher content of ordered structures (~50%) which could be significant for the function of the neurotoxin.

Secondary School Teachers' Experiences of Teaching Pregnant Learners in Limpopo Province, South Africa

ERIC Educational Resources Information Center

Matlala, Sogo F.; Nolte, A. G. W.; Temane, M. A.

2014-01-01

This paper presents the findings of a study on the experiences of secondary school teachers on teaching pregnant learners in Limpopo Province. A qualitative, exploratory, descriptive and contextual design was used. Semi-structured interviews were conducted with ten purposively selected secondary school teachers. Data analysis yielded six themes,…

Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectroscopy as an Analytical Method to Investigate the Secondary Structure of a Model Protein Embedded in Solid Lipid Matrices.

PubMed

Zeeshan, Farrukh; Tabbassum, Misbah; Jorgensen, Lene; Medlicott, Natalie J

2018-02-01

Protein drugs may encounter conformational perturbations during the formulation processing of lipid-based solid dosage forms. In aqueous protein solutions, attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy can investigate these conformational changes following the subtraction of spectral interference of solvent with protein amide I bands. However, in solid dosage forms, the possible spectral contribution of lipid carriers to protein amide I band may be an obstacle to determine conformational alterations. The objective of this study was to develop an ATR FT-IR spectroscopic method for the analysis of protein secondary structure embedded in solid lipid matrices. Bovine serum albumin (BSA) was chosen as a model protein, while Precirol AT05 (glycerol palmitostearate, melting point 58 ℃) was employed as the model lipid matrix. Bovine serum albumin was incorporated into lipid using physical mixing, melting and mixing, or wet granulation mixing methods. Attenuated total reflection FT-IR spectroscopy and size exclusion chromatography (SEC) were performed for the analysis of BSA secondary structure and its dissolution in aqueous media, respectively. The results showed significant interference of Precirol ATO5 with BSA amide I band which was subtracted up to 90% w/w lipid content to analyze BSA secondary structure. In addition, ATR FT-IR spectroscopy also detected thermally denatured BSA solid alone and in the presence of lipid matrix indicating its suitability for the detection of denatured protein solids in lipid matrices. Despite being in the solid state, conformational changes occurred to BSA upon incorporation into solid lipid matrices. However, the extent of these conformational alterations was found to be dependent on the mixing method employed as indicated by area overlap calculations. For instance, the melting and mixing method imparted negligible effect on BSA secondary structure, whereas the wet granulation mixing method promoted more changes. Size exclusion chromatography analysis depicted the complete dissolution of BSA in the aqueous media employed in the wet granulation method. In conclusion, an ATR FT-IR spectroscopic method was successfully developed to investigate BSA secondary structure in solid lipid matrices following the subtraction of lipid spectral interference. The ATR FT-IR spectroscopy could further be applied to investigate the secondary structure perturbations of therapeutic proteins during their formulation development.

Differential Targeting of Unpaired Bases within Duplex DNA by the Natural Compound Clerocidin: A Valuable Tool to Dissect DNA Secondary Structure

PubMed Central

Nadai, Matteo; Palù, Giorgio; Palumbo, Manlio; Richter, Sara N.

2012-01-01

Non-canonical DNA structures have been postulated to mediate protein-nucleic acid interactions and to function as intermediates in the generation of frame-shift mutations when errors in DNA replication occur, which result in a variety of diseases and cancers. Compounds capable of binding to non-canonical DNA conformations may thus have significant diagnostic and therapeutic potential. Clerocidin is a natural diterpenoid which has been shown to selectively react with single-stranded bases without targeting the double helix. Here we performed a comprehensive analysis on several non-canonical DNA secondary structures, namely mismatches, nicks, bulges, hairpins, with sequence variations in both the single-stranded region and the double-stranded flanking segment. By analysis of clerocidin reactivity, we were able to identify the exposed reactive residues which provided information on both the secondary structure and the accessibility of the non-paired sites. Mismatches longer than 1 base were necessary to be reached by clerocidin reactive groups, while 1-base nicks were promptly targeted by clerocidin; in hairpins, clerocidin reactivity increased with the length of the hairpin loop, while, interestingly, reactivity towards bulges reached a maximum in 3-base-long bulges and declined in longer bulges. Electrophoretic mobility shift analysis demonstrated that bulges longer than 3 bases (i.e. 5- and 7-bases) folded or stacked on the duplex region therefore being less accessible by the compound. Clerocidin thus represents a new valuable diagnostic tool to dissect DNA secondary structures. PMID:23285245

Differential targeting of unpaired bases within duplex DNA by the natural compound clerocidin: a valuable tool to dissect DNA secondary structure.

PubMed

Nadai, Matteo; Palù, Giorgio; Palumbo, Manlio; Richter, Sara N

2012-01-01

Non-canonical DNA structures have been postulated to mediate protein-nucleic acid interactions and to function as intermediates in the generation of frame-shift mutations when errors in DNA replication occur, which result in a variety of diseases and cancers. Compounds capable of binding to non-canonical DNA conformations may thus have significant diagnostic and therapeutic potential. Clerocidin is a natural diterpenoid which has been shown to selectively react with single-stranded bases without targeting the double helix. Here we performed a comprehensive analysis on several non-canonical DNA secondary structures, namely mismatches, nicks, bulges, hairpins, with sequence variations in both the single-stranded region and the double-stranded flanking segment. By analysis of clerocidin reactivity, we were able to identify the exposed reactive residues which provided information on both the secondary structure and the accessibility of the non-paired sites. Mismatches longer than 1 base were necessary to be reached by clerocidin reactive groups, while 1-base nicks were promptly targeted by clerocidin; in hairpins, clerocidin reactivity increased with the length of the hairpin loop, while, interestingly, reactivity towards bulges reached a maximum in 3-base-long bulges and declined in longer bulges. Electrophoretic mobility shift analysis demonstrated that bulges longer than 3 bases (i.e. 5- and 7-bases) folded or stacked on the duplex region therefore being less accessible by the compound. Clerocidin thus represents a new valuable diagnostic tool to dissect DNA secondary structures.

Effect of drying methods of microencapsulated Lactobacillus acidophilus and Lactococcus lactis ssp. cremoris on secondary protein structure and glass transition temperature as studied by Fourier transform infrared and differential scanning calorimetry.

PubMed

Dianawati, Dianawati; Mishra, Vijay; Shah, Nagendra P

2013-03-01

Protective mechanisms of casein-based microcapsules containing mannitol on Lactobacillus acidophilus and Lactococcus lactis ssp. cremoris, changes in their secondary protein structures, and glass transition of the microcapsules were studied after spray- or freeze-drying and after 10 wk of storage in aluminum foil pouches containing different desiccants (NaOH, LiCl, or silica gel) at 25°C. An in situ Fourier transform infrared analysis was carried out to recognize any changes in fatty acids (FA) of bacterial cell envelopes, interaction between polar site of cell envelopes and microcapsules, and alteration of their secondary protein structures. Differential scanning calorimetry was used to determine glass transition of microcapsules based on glass transition temperature (T(g)) values. Hierarchical cluster analysis based on functional groups of cell envelopes and secondary protein structures was also carried out to classify the microencapsulated bacteria due to the effects of spray- or freeze-drying and storage for 10 wk. The results showed that drying process did not affect FA and secondary protein structures of bacteria; however, those structures were affected during storage depending upon the type of desiccant used. Interaction between exterior of bacterial cell envelopes and microencapsulant occurred after spray- or freeze-drying; however, these structures were maintained after storage in foil pouch containing sodium hydroxide. Method of drying and type of desiccants influenced the level of similarities of microencapsulated bacteria. Desiccants and method of drying affected glass transition, yet no T(g) ≤25°C was detected. This study demonstrated that the changes in FA and secondary structures of the microencapsulated bacteria still occurred during storage at T(g) above room temperature, indicating that the glassy state did not completely prevent chemical activities. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Influence of Secondary Cooling Mode on Solidification Structure and Macro-segregation Behavior for High-carbon Continuous Casting Bloom

NASA Astrophysics Data System (ADS)

Dou, Kun; Yang, Zhenguo; Liu, Qing; Huang, Yunhua; Dong, Hongbiao

2017-07-01

A cellular automaton-finite element coupling model for high-carbon continuously cast bloom of GCr15 steel is established to simulate the solidification structure and to investigate the influence of different secondary cooling modes on characteristic parameters such as equiaxed crystal ratio, grain size and secondary dendrite arm spacing, in which the effect of phase transformation and electromagnetic stirring is taken into consideration. On this basis, evolution of carbon macro-segregation for GCr15 steel bloom is researched correspondingly via industrial tests. Based on above analysis, the relationship among secondary cooling modes, characteristic parameters for solidification structure as well as carbon macro-segregation is illustrated to obtain optimum secondary cooling strategy and alleviate carbon macro-segregation degree for GCr15 steel bloom in continuous casting process. The evaluating method for element macro-segregation is applicable in various steel types.

On the combinatorics of sparsification.

PubMed

Huang, Fenix Wd; Reidys, Christian M

2012-10-22

We study the sparsification of dynamic programming based on folding algorithms of RNA structures. Sparsification is a method that improves significantly the computation of minimum free energy (mfe) RNA structures. We provide a quantitative analysis of the sparsification of a particular decomposition rule, Λ∗. This rule splits an interval of RNA secondary and pseudoknot structures of fixed topological genus. Key for quantifying sparsifications is the size of the so called candidate sets. Here we assume mfe-structures to be specifically distributed (see Assumption 1) within arbitrary and irreducible RNA secondary and pseudoknot structures of fixed topological genus. We then present a combinatorial framework which allows by means of probabilities of irreducible sub-structures to obtain the expectation of the Λ∗-candidate set w.r.t. a uniformly random input sequence. We compute these expectations for arc-based energy models via energy-filtered generating functions (GF) in case of RNA secondary structures as well as RNA pseudoknot structures. Furthermore, for RNA secondary structures we also analyze a simplified loop-based energy model. Our combinatorial analysis is then compared to the expected number of Λ∗-candidates obtained from the folding mfe-structures. In case of the mfe-folding of RNA secondary structures with a simplified loop-based energy model our results imply that sparsification provides a significant, constant improvement of 91% (theory) to be compared to an 96% (experimental, simplified arc-based model) reduction. However, we do not observe a linear factor improvement. Finally, in case of the "full" loop-energy model we can report a reduction of 98% (experiment). Sparsification was initially attributed a linear factor improvement. This conclusion was based on the so called polymer-zeta property, which stems from interpreting polymer chains as self-avoiding walks. Subsequent findings however reveal that the O(n) improvement is not correct. The combinatorial analysis presented here shows that, assuming a specific distribution (see Assumption 1), of mfe-structures within irreducible and arbitrary structures, the expected number of Λ∗-candidates is Θ(n2). However, the constant reduction is quite significant, being in the range of 96%. We furthermore show an analogous result for the sparsification of the Λ∗-decomposition rule for RNA pseudoknotted structures of genus one. Finally we observe that the effect of sparsification is sensitive to the employed energy model.

Quantifying the benefits to the national economy from secondary applications of NASA technology, executive summary

NASA Technical Reports Server (NTRS)

1976-01-01

The feasibility of systematically quantifying the economic benefits of secondary applications of NASA related R and D was investigated. Based upon the tools of economic theory and econometric analysis, a set of empirical methods was developed and selected applications were made to demonstrate their workability. Analyses of the technological developments related to integrated circuits, cryogenic insulation, gas turbines, and computer programs for structural analysis indicated substantial secondary benefits accruing from NASA's R and D in these areas.

Quantifying the benefits to the national economy from secondary applications of NASA technology

NASA Technical Reports Server (NTRS)

1976-01-01

The feasibility of systematically quantifying the economic benefits of secondary applications of NASA related R and D is investigated. Based upon the tools of economic theory and econometric analysis, it develops a set of empirical methods and makes selected applications to demonstrate their workability. Analyses of the technological developments related to integrated circuits, cryogenic insulation, gas turbines, and computer programs for structural analysis indicated substantial secondary benefits accruing from NASA's R and D in these areas.

Halide salts and their structural properties in presence of secondary amine based molecule: A combined experimental and theoretical analysis

NASA Astrophysics Data System (ADS)

Ghosh, Pritam; Hazra, Abhijit; Ghosh, Meenakshi; Chandra Murmu, Naresh; Banerjee, Priyabrata

2018-04-01

Biologically relevant halide salts and its solution state structural properties are always been significant. In general, exposure of halide salts into polar solution medium results in solvation which in turn separates the cationic and anionic part of the salt. However, the conventional behaviour of salts might alter in presence of any secondary amine based compound, i.e.; moderately strong Lewis acid. In its consequence, to investigate the effect of secondary amine based compound in the salt solution, novel (E)-2-(4-bromobenzylidene)-1-(perfluorophenyl) hydrazine has been synthesized and used as secondary amine source. The secondary amine compound interestingly shows a drastic color change upon exposure to fluoride salts owing to hydrogen bonding interaction. Several experimental methods, e.g.; SCXRD, UV-Vis, FT-IR, ESI-MS and DLS together with modern DFT (i.e.; DFT-D3) have been performed to explore the structural properties of the halide salts upon exposure to secondary amine based compound. The effect of counter cation of the fluoride salt in binding with secondary amine source has also been investigated.

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.

Analysis of Secondary School Students' Perceptions about Information Technologies through a Word Association Test

ERIC Educational Resources Information Center

Eren, Fetah; Sahin, Ismail; Celik, Ismail; Akturk, Ahmet Oguz

2014-01-01

The aim of this study is to discover secondary school students' perceptions related to information technologies and the connections between concepts in their cognitive structures. A word association test consisting of six concepts related to information technologies is used to collect data from 244 secondary school students. Concept maps that…

Comparison of NASTRAN analysis with ground vibration results of UH-60A NASA/AEFA test configuration

NASA Technical Reports Server (NTRS)

Idosor, Florentino; Seible, Frieder

1990-01-01

Preceding program flight tests, a ground vibration test and modal test analysis of a UH-60A Black Hawk helicopter was conducted by Sikorsky Aircraft to complement the UH-60A test plan and NASA/ARMY Modern Technology Rotor Airloads Program. The 'NASA/AEFA' shake test configuration was tested for modal frequencies and shapes and compared with its NASTRAN finite element model counterpart to give correlative results. Based upon previous findings, significant differences in modal data existed and were attributed to assumptions regarding the influence of secondary structure contributions in the preliminary NASTRAN modeling. An analysis of an updated finite element model including several secondary structural additions has confirmed that the inclusion of specific secondary components produces a significant effect on modal frequency and free-response shapes and improves correlations at lower frequencies with shake test data.

Construction and Validation of the Career and Educational Decision Self-Efficacy Inventory for Secondary Students (CEDSIS)

ERIC Educational Resources Information Center

Ho, Esther Sui Chu; Sum, Kwok Wing

2018-01-01

This study aims to construct and validate the Career and Educational Decision Self-Efficacy Inventory for Secondary Students (CEDSIS) by using a sample of 2,631 students in Hong Kong. Principal component analysis yielded a three-factor structure, which demonstrated good model fit in confirmatory factor analysis. High reliability was found for the…

ANALYSIS OF SECONDARY ORGANIC AEROSOL COMPOUNDS FROM THE PHOTOOXIDATION OF D-LIMONENE IN THE PRESENCE OF NO X AND THEIR DETECTION IN AMBIENT PM 2.5

EPA Science Inventory

Chemical analysis of secondary organic aerosol (SOA) from the photooxidation of a d-limonene/NOx/air mixture was carried out. SOA, generated in a smog chamber, was collected on Zefluor filters. To determine the structural characteristics of the compounds, the filter sample...

Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure.

PubMed

Chiusano, M L; D'Onofrio, G; Alvarez-Valin, F; Jabbari, K; Colonna, G; Bernardi, G

1999-09-30

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (alpha-helix, beta-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substitution were found to be significantly different in regions predicted to be alpha-helix, beta-sheet, or coil. Likewise, the nonsynonymous rates also differ, although expectedly at a lower extent, in the three types of secondary structure, suggesting that different selective constraints associated with the different structures are affecting in a similar way the synonymous and nonsynonymous rates. Moreover, the base composition of the third codon positions is different in coding sequence regions corresponding to different secondary structures of proteins.

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

PubMed Central

Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

2016-01-01

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. PMID:26978354

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.

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.

Patient-centered knowledge sharing in healthcare organizations: Identifying the external barriers.

PubMed

Zhou, Lihong

2017-12-01

This paper reports on a research study, which aims to identify, qualify, and theorize the external barriers that prevent and hinder the exercises and activities of patient-centered knowledge sharing (KS) in healthcare organizations. The project adopted a qualitative secondary analysis approach as the overarching methodology to guide the analysis of data collected in a previously completed research study. Specifically, 46 semi-structured interview data were included and analyzed using a thematic analysis approach. The secondary analysis showed that healthcare KS is strongly influenced and hindered by five external barriers: social belief and preference, cultural values, healthcare education structure, political decisions, and economic environment and constraints. Moreover, the research findings suggest that these external barriers cannot be overlooked in KS implementation and operation in healthcare organizations and should be carefully assessed beginning in the early stages of KS design and strategic planning. Based on the secondary analysis, this paper proposes a conceptual model, which will contribute to the development of hypotheses in the future for building a generalized knowledge. The case study used is Chinese healthcare, but the KS problems studied can be shared across international borders.

Tertiary structure-based analysis of microRNA–target interactions

PubMed Central

Gan, Hin Hark; Gunsalus, Kristin C.

2013-01-01

Current computational analysis of microRNA interactions is based largely on primary and secondary structure analysis. Computationally efficient tertiary structure-based methods are needed to enable more realistic modeling of the molecular interactions underlying miRNA-mediated translational repression. We incorporate algorithms for predicting duplex RNA structures, ionic strength effects, duplex entropy and free energy, and docking of duplex–Argonaute protein complexes into a pipeline to model and predict miRNA–target duplex binding energies. To ensure modeling accuracy and computational efficiency, we use an all-atom description of RNA and a continuum description of ionic interactions using the Poisson–Boltzmann equation. Our method predicts the conformations of two constructs of Caenorhabditis elegans let-7 miRNA–target duplexes to an accuracy of ∼3.8 Å root mean square distance of their NMR structures. We also show that the computed duplex formation enthalpies, entropies, and free energies for eight miRNA–target duplexes agree with titration calorimetry data. Analysis of duplex–Argonaute docking shows that structural distortions arising from single-base-pair mismatches in the seed region influence the activity of the complex by destabilizing both duplex hybridization and its association with Argonaute. Collectively, these results demonstrate that tertiary structure-based modeling of miRNA interactions can reveal structural mechanisms not accessible with current secondary structure-based methods. PMID:23417009

Study of multilayered SiGe semiconductor structures by X-ray diffractometry, grazing-incidence X-ray reflectometry, and secondary-ion mass spectrometry

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

Yunin, P. A., E-mail: yunin@ipmras.ru; Drozdov, Yu. N.; Drozdov, M. N.

2013-12-15

In this publication, we report the results of studying a multilayerd nonperiodic SiGe/Si structure by the methods of X-ray diffractometry, grazing-angle X-ray reflectometry, and secondary-ion mass spectrometry (SIMS). Special attention is paid to the processing of the component distribution profile using the SIMS method and to consideration of the most significant experimental distortions introduced by this method. A method for processing the measured composition distribution profile with subsequent consideration of the influence of matrix effects, variation in the etching rate, and remnants of ion sputtering is suggested. The results of such processing are compared with a structure model obtained uponmore » combined analysis of X-ray diffractometry and grazing-angle reflectometry data. Good agreement between the results is established. It is shown that the combined use of independent techniques makes it possible to improve the methods of secondary-ion mass spectrometry and grazing-incidence reflectometry as applied to an analysis of multilayered heteroepitaxial structures (to increase the accuracy and informativity of these methods)« less

Understanding Quality of Life in Adults with Spinal Cord Injury Via SCI-Related Needs and Secondary Complications.

PubMed

Sweet, Shane N; Noreau, Luc; Leblond, Jean; Dumont, Frédéric S

2014-01-01

Understanding the factors that can predict greater quality of life (QoL) is important for adults with spinal cord injury (SCI), given that they report lower levels of QoL than the general population. To build a conceptual model linking SCI-related needs, secondary complications, and QoL in adults with SCI. Prior to testing the conceptual model, we aimed to develop and evaluate the factor structure for both SCI-related needs and secondary complications. Individuals with a traumatic SCI (N = 1,137) responded to an online survey measuring 13 SCI-related needs, 13 secondary complications, and the Life Satisfaction Questionnaire to assess QoL. The SCI-related needs and secondary complications were conceptualized into factors, tested with a confirmatory factor analysis, and subsequently evaluated in a structural equation model to predict QoL. The confirmatory factor analysis supported a 2-factor model for SCI related needs, χ(2)(61, N = 1,137) = 250.40, P <.001, comparative fit index (CFI) = .93, root mean square error of approximation (RMSEA) = .05, standardized root mean square residual (SRMR) = .04, and for 11 of the 13 secondary complications, χ(2)(44, N = 1,137) = 305.67, P < .001, CFI = .91, RMSEA = .060, SRMR = .033. The final 2 secondary complications were kept as observed constructs. In the structural model, both vital and personal development unmet SCI-related needs (β = -.22 and -.20, P < .05, respectively) and the neuro-physiological systems factor (β = -.45, P < .05) were negatively related with QoL. Identifying unmet SCI-related needs of individuals with SCI and preventing or managing secondary complications are essential to their QoL.

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

PubMed Central

Micsonai, András; Wien, Frank; Kernya, Linda; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

2015-01-01

Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. PMID:26038575

Secondary and tertiary isoquinoline alkaloids from Xylopia parviflora.

PubMed

Nishiyama, Yumi; Moriyasu, Masataka; Ichimaru, Momoyo; Iwasa, Kinuko; Kato, Atsushi; Mathenge, Simon G; Chalo Mutiso, Patrick B; Juma, Francis D

2006-12-01

From the secondary and tertiary alkaloidal fractions of the root and the bark of Xylopia parviflora (Annonaceae), the isoquinoline alkaloids, 10,11-dihydroxy-1,2-dimethoxynoraporphine and parvinine were isolated, along with 39 known alkaloids. Their structures were determined on the basis of analysis of spectroscopic data.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

PubMed

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-03-31

With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

PubMed Central

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-01-01

Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules. PMID:18373878

Design and Analysis of Tubular Permanent Magnet Linear Wave Generator

PubMed Central

Si, Jikai; Feng, Haichao; Su, Peng; Zhang, Lufeng

2014-01-01

Due to the lack of mature design program for the tubular permanent magnet linear wave generator (TPMLWG) and poor sinusoidal characteristics of the air gap flux density for the traditional surface-mounted TPMLWG, a design method and a new secondary structure of TPMLWG are proposed. An equivalent mathematical model of TPMLWG is established to adopt the transformation relationship between the linear velocity of permanent magnet rotary generator and the operating speed of TPMLWG, to determine the structure parameters of the TPMLWG. The new secondary structure of the TPMLWG contains surface-mounted permanent magnets and the interior permanent magnets, which form a series-parallel hybrid magnetic circuit, and their reasonable structure parameters are designed to get the optimum pole-arc coefficient. The electromagnetic field and temperature field of TPMLWG are analyzed using finite element method. It can be included that the sinusoidal characteristics of air gap flux density of the new secondary structure TPMLWG are improved, the cogging force as well as mechanical vibration is reduced in the process of operation, and the stable temperature rise of generator meets the design requirements when adopting the new secondary structure of the TPMLWG. PMID:25050388

Influence of high-molecular-weight glutenin subunit composition at Glu-A1 and Glu-D1 loci on secondary and micro structures of gluten in wheat (Triticum aestivum L.).

PubMed

Li, Xuejun; Liu, Tianhong; Song, Lijun; Zhang, Heng; Li, Liqun; Gao, Xin

2016-12-15

As one of critical gluten proteins, high-molecular-weight glutenin subunits (HMW-GS) mainly affect the rheological behaviour of wheat dough. The influence of HMW-GS variations at the Glu-A1 and Glu-D1 loci on both secondary and micro structures of gluten and rheological properties of wheat dough was investigated in this study. Results showed that the Amide I bands of the three near-isogenic lines (NILs) shifted slightly, but the secondary structures differed significantly. The micro structure of gluten in NIL 4 (Ax null) showed bigger apertures and less connection, compared to that in Xinong 1330 (Ax1). The micro structure of gluten in NIL 5 (Dx5+Dy10) showed more compact than that in Xinong 1330 (Dx2+Dy12). Correlation analysis demonstrated that the content of β-sheets and disulfide bonds in gluten has a significant relationship with dough properties. The secondary structures of native gluten are suggested to be used as predictors of wheat quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

Design and analysis of tubular permanent magnet linear wave generator.

PubMed

Si, Jikai; Feng, Haichao; Su, Peng; Zhang, Lufeng

2014-01-01

Due to the lack of mature design program for the tubular permanent magnet linear wave generator (TPMLWG) and poor sinusoidal characteristics of the air gap flux density for the traditional surface-mounted TPMLWG, a design method and a new secondary structure of TPMLWG are proposed. An equivalent mathematical model of TPMLWG is established to adopt the transformation relationship between the linear velocity of permanent magnet rotary generator and the operating speed of TPMLWG, to determine the structure parameters of the TPMLWG. The new secondary structure of the TPMLWG contains surface-mounted permanent magnets and the interior permanent magnets, which form a series-parallel hybrid magnetic circuit, and their reasonable structure parameters are designed to get the optimum pole-arc coefficient. The electromagnetic field and temperature field of TPMLWG are analyzed using finite element method. It can be included that the sinusoidal characteristics of air gap flux density of the new secondary structure TPMLWG are improved, the cogging force as well as mechanical vibration is reduced in the process of operation, and the stable temperature rise of generator meets the design requirements when adopting the new secondary structure of the TPMLWG.

Scientific Explanations in Greek Upper Secondary Physics Textbooks

ERIC Educational Resources Information Center

Velentzas, Athanasios; Halkia, Krystallia

2018-01-01

In this study, an analysis of the structure of scientific explanations included in physics textbooks of upper secondary schools in Greece was completed. In scientific explanations for specific phenomena found in the sample textbooks, the "explanandum" is a logical consequence of the "explanans," which in all cases include at…

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.

The constant region affects antigen binding of antibodies to DNA by altering secondary structure.

PubMed

Xia, Yumin; Janda, Alena; Eryilmaz, Ertan; Casadevall, Arturo; Putterman, Chaim

2013-11-01

We previously demonstrated an important role of the constant region in the pathogenicity of anti-DNA antibodies. To determine the mechanisms by which the constant region affects autoantibody binding, a panel of isotype-switch variants (IgG1, IgG2a, IgG2b) was generated from the murine PL9-11 IgG3 autoantibody. The affinity of the PL9-11 antibody panel for histone was measured by surface plasmon resonance (SPR). Tryptophan fluorescence was used to determine wavelength shifts of the antibody panel upon binding to DNA and histone. Finally, circular dichroism spectroscopy was used to measure changes in secondary structure. SPR analysis revealed significant differences in histone binding affinity between members of the PL9-11 panel. The wavelength shifts of tryptophan fluorescence emission were found to be dependent on the antibody isotype, while circular dichroism analysis determined that changes in antibody secondary structure content differed between isotypes upon antigen binding. Thus, the antigen binding affinity is dependent on the particular constant region expressed. Moreover, the effects of antibody binding to antigen were also constant region dependent. Alteration of secondary structures influenced by constant regions may explain differences in fine specificity of anti-DNA antibodies between antibodies with similar variable regions, as well as cross-reactivity of anti-DNA antibodies with non-DNA antigens. Copyright © 2013 Elsevier Ltd. All rights reserved.

Synthesizing the Evidence on Classroom Goal Structures in Middle and Secondary Schools: A Meta-Analysis and Narrative Review

ERIC Educational Resources Information Center

Givens Rolland, Rebecca

2012-01-01

This meta-analysis and narrative review synthesizes the literature on classroom goal structures and their relationships with student outcomes, focusing additionally on the ways in which these constructs are operationalized across research studies. Specifically, this study evaluates the relationships between students' perceptions of mastery and…

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.

Computation of statistical secondary structure of nucleic acids.

PubMed Central

Yamamoto, K; Kitamura, Y; Yoshikura, H

1984-01-01

This paper presents a computer analysis of statistical secondary structure of nucleic acids. For a given single stranded nucleic acid, we generated "structure map" which included all the annealing structures in the sequence. The map was transformed into "energy map" by rough approximation; here, the energy level of every pairing structure consisting of more than 2 successive nucleic acid pairs was calculated. By using the "energy map", the probability of occurrence of each annealed structure was computed, i.e., the structure was computed statistically. The basis of computation was the 8-queen problem in the chess game. The validity of our computer programme was checked by computing tRNA structure which has been well established. Successful application of this programme to small nuclear RNAs of various origins is demonstrated. PMID:6198622

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.

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

Analysis of spatial and temporal spectra of liquid film surface in annular gas-liquid flow

NASA Astrophysics Data System (ADS)

Alekseenko, Sergey; Cherdantsev, Andrey; Heinz, Oksana; Kharlamov, Sergey; Markovich, Dmitriy

2013-09-01

Wavy structure of liquid film in annular gas-liquid flow without liquid entrainment consists of fast long-living primary waves and slow short-living secondary waves. In present paper, results of spectral analysis of this wavy structure are presented. Application of high-speed LIF technique allowed us to perform such analysis in both spatial and temporal domains. Power spectra in both domains are characterized by one-humped shape with long exponential tail. Influence of gas velocity, liquid Reynolds number, liquid viscosity and pipe diameter on frequency of the waves is investigated. When gravity effect is much lesser than the shear stress, similarity of power spectra at different gas velocities is observed. Using combination of spectral analysis and identification of characteristic lines of primary waves, frequency of generation of secondary waves by primary waves is measured.

Precise structural analysis of α-helical polypeptide by quantum-chemical calculation related to reciprocal side-chain combination of two L-phenylalanine residues

NASA Astrophysics Data System (ADS)

Niimura, Subaru; Kurosu, Hiromichi; Shoji, Akira

2010-04-01

To clarify the positive role of side-chain conformation in the stability of protein secondary structure (main-chain conformation), we successfully calculated the optimization structure of a series of well-defined α-helical octadecapeptides composed of two L-phenylalanine (Phe) and 16 L-alanine (Ala) residues, based on the molecular orbital calculation with density functional theory (DFT/B3LYP/6-31G(d)). From the total energy calculation and the precise secondary structural analysis, we found that the conformational stability of the α-helix is closely related to the reciprocal side-chain combinations (such as positional relation and side-chain conformation) of two Phe residues in this system. Furthermore, we demonstrated that the 1H, 13C, 15N and 17O isotropic chemical shifts of each Phe residue depend on the respective side-chain conformations of the Phe residue.

Proteolytically-induced changes of secondary structural protein conformation of bovine serum albumin monitored by Fourier transform infrared (FT-IR) and UV-circular dichroism spectroscopy

NASA Astrophysics Data System (ADS)

Güler, Günnur; Vorob'ev, Mikhail M.; Vogel, Vitali; Mäntele, Werner

2016-05-01

Enzymatically-induced degradation of bovine serum albumin (BSA) by serine proteases (trypsin and α-chymotrypsin) in various concentrations was monitored by means of Fourier transform infrared (FT-IR) and ultraviolet circular dichroism (UV-CD) spectroscopy. In this study, the applicability of both spectroscopies to monitor the proteolysis process in real time has been proven, by tracking the spectral changes together with secondary structure analysis of BSA as proteolysis proceeds. On the basis of the FTIR spectra and the changes in the amide I band region, we suggest the progression of proteolysis process via conversion of α-helices (1654 cm- 1) into unordered structures and an increase in the concentration of free carboxylates (absorption of 1593 and 1402 cm- 1). For the first time, the correlation between the degree of hydrolysis and the concentration of carboxylic groups measured by FTIR spectroscopy was revealed as well. The far UV-CD spectra together with their secondary structure analysis suggest that the α-helical content decreases concomitant with an increase in the unordered structure. Both spectroscopic techniques also demonstrate that there are similar but less spectral changes of BSA for the trypsin attack than for α-chymotrypsin although the substrate/enzyme ratio is taken the same.

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

[Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].

PubMed

Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian

2009-11-01

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

Influence of high-molecular-weight glutenin subunit composition at Glu-B1 locus on secondary and micro structures of gluten in wheat (Triticum aestivum L.).

PubMed

Gao, Xin; Liu, Tianhong; Yu, Jing; Li, Liqun; Feng, Yi; Li, Xuejun

2016-04-15

Glutenin is one of the critical gluten proteins that affect the processing quality of wheat dough. High-molecular-weight glutenin subunits (HMW-GS) affect rheological behavior of wheat dough. This research demonstrated the effects of four variations of HMW-GS composition at the Glu-B1 locus on secondary and micro structures of gluten and rheological properties of wheat dough, using the bread wheat Xinong 1330 and its three near-isogenic lines (NILs). Results indicated that the Amide I bands of the four wheat lines shifted slightly, but the secondary structure, such as content of α-helices, β-sheets, disulfide bands, tryptophan bands and tyrosine bands, differed significantly among the four NILs. The micro structure of gluten in NIL 2 (Bx14+By15) and NIL 3 (Bx17+By18) showed more cross linkage, with two contrasting patterns. Correlation analysis demonstrated that the content of β-sheets and disulfide bonds has a significant relationship with dough stability, which suggests that the secondary structures could be used as predictors of wheat quality. Copyright © 2015 Elsevier Ltd. All rights reserved.

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions

PubMed Central

Churkin, Alexander; Barash, Danny

2008-01-01

Background RNAmute is an interactive Java application which, given an RNA sequence, calculates the secondary structure of all single point mutations and organizes them into categories according to their similarity to the predicted structure of the wild type. The secondary structure predictions are performed using the Vienna RNA package. A more efficient implementation of RNAmute is needed, however, to extend from the case of single point mutations to the general case of multiple point mutations, which may often be desired for computational predictions alongside mutagenesis experiments. But analyzing multiple point mutations, a process that requires traversing all possible mutations, becomes highly expensive since the running time is O(nm) for a sequence of length n with m-point mutations. Using Vienna's RNAsubopt, we present a method that selects only those mutations, based on stability considerations, which are likely to be conformational rearranging. The approach is best examined using the dot plot representation for RNA secondary structure. Results Using RNAsubopt, the suboptimal solutions for a given wild-type sequence are calculated once. Then, specific mutations are selected that are most likely to cause a conformational rearrangement. For an RNA sequence of about 100 nts and 3-point mutations (n = 100, m = 3), for example, the proposed method reduces the running time from several hours or even days to several minutes, thus enabling the practical application of RNAmute to the analysis of multiple-point mutations. Conclusion A highly efficient addition to RNAmute that is as user friendly as the original application but that facilitates the practical analysis of multiple-point mutations is presented. Such an extension can now be exploited prior to site-directed mutagenesis experiments by virologists, for example, who investigate the change of function in an RNA virus via mutations that disrupt important motifs in its secondary structure. A complete explanation of the application, called MultiRNAmute, is available at [1]. PMID:18445289

Secondary School Teachers' Classroom Activities and Their Perceptions on Effectiveness of the Activity

ERIC Educational Resources Information Center

Guvenc, Hulya

2017-01-01

In the present research, effective and ineffective activities that secondary school teachers used and their perceptions on the effectiveness of the activities are investigated. The data were collected from 20 teachers using semi-structured interviews. Data were analysed using open coding and directed content analysis. Research findings showed that…

Status of Credentialing Structures Related to Secondary Transition: A State-Level Policy Analysis

ERIC Educational Resources Information Center

Simonsen, Monica L.; Novak, Jeanne A.; Mazzotti, Valerie L.

2018-01-01

To understand the current status of transition-related credentialing systems in driving personnel preparation, it is necessary to identify which state education and rehabilitation services agencies are currently providing certification and licensure in the area of secondary transition. The purpose of this study was to examine the current state of…

Comparative Study on the Senior Secondary School Mathematics Curricula Development in Ethiopia and Australia

ERIC Educational Resources Information Center

Meleta, Fufa E.; Zhang, Weizhong

2017-01-01

The main objective of this study is to compare the process of the senior secondary school mathematics curricula development in Ethiopia and Australia. The study was investigated qualitatively with document analysis and semi-structured interview research methods. The documents were collected from Federal Democratic Republic of Ethiopia Ministry of…

Teacher Argumentation in the Secondary Science Classroom: Images of Two Modes of Scientific Inquiry

ERIC Educational Resources Information Center

Gray, Ron E.

2009-01-01

The purpose of this exploratory study was to examine scientific arguments constructed by secondary science teachers during instruction. The analysis focused on how arguments constructed by teachers differed based on the mode of inquiry underlying the topic. Specifically, how did the structure and content of arguments differ between experimentally…

Functional Specialization of Cellulose Synthase Isoforms in a Moss Shows Parallels with Seed Plants1[OPEN

PubMed Central

Li, Xingxing; Huang, Shixin; Van de Meene, Allison M.L.; Tran, Mai L.; Killeavy, Erin; Mercure, Danielle; Burton, Rachel A.

2017-01-01

The secondary cell walls of tracheary elements and fibers are rich in cellulose microfibrils that are helically oriented and laterally aggregated. Support cells within the leaf midribs of mosses deposit cellulose-rich secondary cell walls, but their biosynthesis and microfibril organization have not been examined. Although the Cellulose Synthase (CESA) gene families of mosses and seed plants diversified independently, CESA knockout analysis in the moss Physcomitrella patens revealed parallels with Arabidopsis (Arabidopsis thaliana) in CESA functional specialization, with roles for both subfunctionalization and neofunctionalization. The similarities include regulatory uncoupling of the CESAs that synthesize primary and secondary cell walls, a requirement for two or more functionally distinct CESA isoforms for secondary cell wall synthesis, interchangeability of some primary and secondary CESAs, and some CESA redundancy. The cellulose-deficient midribs of ppcesa3/8 knockouts provided negative controls for the structural characterization of stereid secondary cell walls in wild type P. patens. Sum frequency generation spectra collected from midribs were consistent with cellulose microfibril aggregation, and polarization microscopy revealed helical microfibril orientation only in wild type leaves. Thus, stereid secondary walls are structurally distinct from primary cell walls, and they share structural characteristics with the secondary walls of tracheary elements and fibers. We propose a mechanism for the convergent evolution of secondary walls in which the deposition of aggregated and helically oriented microfibrils is coupled to rapid and highly localized cellulose synthesis enabled by regulatory uncoupling from primary wall synthesis. PMID:28768816

[Peculiarities of secondary structure of serum albumin of some representatives of the animal kingdom].

PubMed

Pekhymenko, G V; Kuchmerovskaia, T M

2011-01-01

Methods of infrared (IR) spectroscopy and circular dichroism (CD) are suitable techniques for detection of proteins structural changes. These methods were used for determinating peculiarities of the secondary structure of serum albumins in some representatives of two classes of reptiles: Horsfield's tortoise (Testudo horsfieldi), water snake (Natrix tessellata) and grass snake (Natrix natrix) and birds: domestic goose (Anser anser), domestic chicken (Gallus domesticus), domestic duck (Anas platyrhyncha) and dove colored (Columba livia). An analysis of IR spectra and spectra obtained by the method of CD of serum albumins of both classes representatives revealed that beta-folding structure and alpha-helical sections that form the alpha-conformation play an important role in conformational structure formation of polypeptide chain and also disordered sites of molecules of these proteins. It was observed that certain redistribution depending on animals species exists, in the formation of secondary structure of serum albumins of the investigated representatives of reptiles and birds classes between the content of beta-folding structure, alpha-helical sections and disordered sites in molecules of these proteins.

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.

24 CFR 3280.903 - General requirements for designing the structure to withstand transportation shock and vibration.

Code of Federal Regulations, 2013 CFR

2013-04-01

... manufactured home shall be designed, in terms of its structural, plumbing, mechanical and electrical systems... subsequent secondary transportation moves. (c) In place of an engineering analysis, either of the following...

24 CFR 3280.903 - General requirements for designing the structure to withstand transportation shock and vibration.

Code of Federal Regulations, 2011 CFR

2011-04-01

... manufactured home shall be designed, in terms of its structural, plumbing, mechanical and electrical systems... subsequent secondary transportation moves. (c) In place of an engineering analysis, either of the following...

24 CFR 3280.903 - General requirements for designing the structure to withstand transportation shock and vibration.

Code of Federal Regulations, 2012 CFR

2012-04-01

... manufactured home shall be designed, in terms of its structural, plumbing, mechanical and electrical systems... subsequent secondary transportation moves. (c) In place of an engineering analysis, either of the following...

24 CFR 3280.903 - General requirements for designing the structure to withstand transportation shock and vibration.

Code of Federal Regulations, 2014 CFR

2014-04-01

... manufactured home shall be designed, in terms of its structural, plumbing, mechanical and electrical systems... subsequent secondary transportation moves. (c) In place of an engineering analysis, either of the following...

The Shape of Literature.

ERIC Educational Resources Information Center

Lansu, Helvi

1965-01-01

The structural analysis of three short stories, arranged to proceed from an elementary to a complex level of form, can illuminate the secondary school student's understanding of literary structure. Representing plot as structure, the basic elements of Richard Connell's "The Most Dangerous Game" can be quickly reviewed to debate and establish the…

Molecular Dynamics Approach in Designing Thermostable Aspergillus niger Xylanase

NASA Astrophysics Data System (ADS)

Malau, N. D.; Sianturi, M.

2017-03-01

Molecular dynamics methods we have applied as a tool in designing thermostable Aspergillus niger Xylanase, by examining Root Mean Square Deviation (RMSD) and The Stability of the Secondary Structure of enzymes structure at its optimum temperature and compare with its high temperature behavior. As RMSD represents structural fluctuation at a particular temperature, a better understanding of this factor will suggest approaches to bioengineer these enzymes to enhance their thermostability. In this work molecular dynamic simulations of Aspergillus niger xylanase (ANX) have been carried at 400K (optimum catalytic temperature) for 2.5 ns and 500K (ANX reported inactive temperature) for 2.5 ns. Analysis have shown that the Root Mean Square Deviation (RMSD) significant increase at higher temperatures compared at optimum temperature and some of the secondary structures of ANX that have been damaged at high temperature. Structural analysis revealed that the fluctuations of the α-helix and β-sheet regions are larger at higher temperatures compared to the fluctuations at optimum temperature.

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.

Multiple-probe analysis of folding and unfolding pathways of human serum albumin. Evidence for a framework mechanism of folding.

PubMed

Santra, Manas Kumar; Banerjee, Abhijit; Krishnakumar, Shyam Sundar; Rahaman, Obaidur; Panda, Dulal

2004-05-01

The changes in the far-UV CD signal, intrinsic tryptophan fluorescence and bilirubin absorbance showed that the guanidine hydrochloride (GdnHCl)-induced unfolding of a multidomain protein, human serum albumin (HSA), followed a two-state process. However, using environment sensitive Nile red fluorescence, the unfolding and folding pathways of HSA were found to follow a three-state process and an intermediate was detected in the range 0.25-1.5 m GdnHCl. The intermediate state displayed 45% higher fluorescence intensity than that of the native state. The increase in the Nile red fluorescence was found to be due to an increase in the quantum yield of the HSA-bound Nile red. Low concentrations of GdnHCl neither altered the binding affinity of Nile red to HSA nor induced the aggregation of HSA. In addition, the secondary structure of HSA was not perturbed during the first unfolding transition (<1.5 m GdnHCl); however, the secondary structure was completely lost during the second transition. The data together showed that the half maximal loss of the tertiary structure occurred at a lower GdnHCl concentration than the loss of the secondary structure. Further kinetic studies of the refolding process of HSA using multiple spectroscopic techniques showed that the folding occurred in two phases, a burst phase followed by a slow phase. An intermediate with native-like secondary structure but only a partial tertiary structure was found to form in the burst phase of refolding. Then, the intermediate slowly folded into the native state. An analysis of the refolding data suggested that the folding of HSA could be best explained by the framework model.

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

[Characterization of structural change of ascorbate peroxidase from Chinese kale during denaturation by circular dichroism].

PubMed

Xi, Jia-Fu; Tang, Lei; Zhang, Jian-Hua; Zhang, Hong-Jian; Chen, Xu-Sheng; Mao, Zhong-Gui

2014-11-01

Circular dichroism (CD) is a special absorption spectrum. The secondary structure of protein such as α-helix, β-sheet and β-turn in the far ultraviolet region (190-250 nm) has a characteristic CD spectrum. In order to understand the activity and structural changes of ascorbate peroxidase from Chinese kale (BaAPX) during denaturation, specific activity and percentage of secondary structure of BaAPX under different time, temperature and concentration were analyzed by CD dynamically. In addition, the percentage of four secondary structures in BaAPX was calculated by CD analysis software Dichroweb. The results show that BaAPX is a full α-type enzyme whose specific activity is positively related to the percentage of α-helix. During denaturation of BaAPX, three kinds of structural changes were proposed: the one-step structural change from initial state (N state) to minimum state of α-helix (R state) under low concentration and low temperature; the one-step structural change from N state to equilibrium state (T state) under high concentration and low temperature; the two-step structural changes from N state through R state to final T state under heat treatment and low temperature renaturation.

Protein structure similarity from Principle Component Correlation analysis.

PubMed

Zhou, Xiaobo; Chou, James; Wong, Stephen T C

2006-01-25

Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC) analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum eigenvalues can be highly effective in clustering structurally or topologically similar proteins. We believe that the PCC analysis of interaction matrix is highly flexible in adopting various structural parameters for protein structure comparison.

Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder.

PubMed

Lorenzo, J Ramiro; Alonso, Leonardo G; Sánchez, Ignacio E

2015-01-01

Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage "Protein and nucleic acid structure and sequence analysis".

Secondary flow structure in a model curved artery: 3D morphology and circulation budget analysis

NASA Astrophysics Data System (ADS)

Bulusu, Kartik V.; Plesniak, Michael W.

2015-11-01

In this study, we examined the rate of change of circulation within control regions encompassing the large-scale vortical structures associated with secondary flows, i.e. deformed Dean-, Lyne- and Wall-type (D-L-W) vortices at planar cross-sections in a 180° curved artery model (curvature ratio, 1/7). Magnetic resonance velocimetry (MRV) and particle image velocimetry (PIV) experiments were performed independently, under the same physiological inflow conditions (Womersley number, 4.2) and using Newtonian blood-analog fluids. The MRV-technique performed at Stanford University produced phase-averaged, three-dimensional velocity fields. Secondary flow field comparisons of MRV-data to PIV-data at various cross-sectional planes and inflow phases were made. A wavelet-decomposition-based approach was implemented to characterize various secondary flow morphologies. We hypothesize that the persistence and decay of arterial secondary flow vortices is intrinsically related to the influence of the out-of-plane flow, tilting, in-plane convection and diffusion-related factors within the control regions. Evaluation of these factors will elucidate secondary flow structures in arterial hemodynamics. Supported by the National Science Foundation under Grant Number CBET-0828903, and GW Center for Biomimetics and Bioinspired Engineering (COBRE). The MRV data were acquired at Stanford University in collaboration with Christopher Elkins and John Eaton.

Do Special Education Interventions Improve Learning of Secondary Content? A Meta-Analysis. Research to Practice. Structured Abstract No. 80

ERIC Educational Resources Information Center

Dragoo, Kyrie

2011-01-01

This is a structured abstract of a meta-analysis conducted by T. E. Scruggs, M. A. Mastropieri, S. Berkeley, and J. E. Graetz, published in "Remedial & Special Education" (2009). The authors of the original paper describe findings from a research synthesis on content area instruction for students with disabilities. Seventy studies…

Obsessive-compulsive symptoms in a normative Chinese sample of youth: prevalence, symptom dimensions, and factor structure of the Leyton Obsessional Inventory--Child Version.

PubMed

Sun, Jing; Boschen, Mark J; Farrell, Lara J; Buys, Nicholas; Li, Zhan-Jiang

2014-08-01

Chinese adolescents face life stresses from multiple sources, with higher levels of stress predictive of adolescent mental health outcomes, including in the area of obsessive-compulsive disorders (OCD). Valid assessment of OCD among this age group is therefore a critical need in China. This study aims to standardise the Chinese version of the Leyton short version scale for adolescents of secondary schools in order to assess this condition. Stratified randomly selected adolescents were selected from four high schools located in Beijing, China. The Chinese version of the Leyton scale was administered to 3221 secondary school students aged between 12 and 18 years. A high response rate was achieved, with 3185 adolescents responding to the survey (98.5 percent). Exploratory factor analysis (EFA) extracted four factors from the scale: compulsive thoughts, concerns of cleanliness, lucky number, repetitiveness and repeated checking. The four-factor structures were confirmed using Confirmatory Factor Analysis (CFA). Overall the four-factor structure had a good model fit and high levels of reliability for each individual dimension and reasonable content validity. Invariance analyses in unconstrained, factor loading, and error variance models demonstrated that the Leyton scale is invariant in relation to the presence or absence OCD, age and gender. Discriminant validity analysis demonstrated that the four-factor structure scale also had excellent ability to differentiate between OCD and non-OCD students, male and female students, and age groups. The dataset was a non-clinical sample of high school students, rather than a sample of individuals with OCD. Future research may examine symptom structure in clinical populations to assess whether this structure fits into both clinical and community population. The structure derived from the Leyton short version scale in a non-clinical secondary school sample of adolescents, suggests that a four-factor solution can be utilised as a screening tool to assess adolescents׳ psychopathological symptoms in the area of OCD in mainland Chinese non-clinical secondary school students. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Structural changes and fluctuations of proteins. I. A statistical thermodynamic model.

PubMed

Ikegami, A

1977-01-01

A general theory of the structural changes and fluctuations of proteins has been proposed based on statistical thermodynamic considerations at the chain level. The "structure" of protein was assumed to be characterized by the state of secondary bonds between unique pairs of specific sites on peptide chains. Every secondary bond changes between the bonded and unbonded states by thermal agitation and the "structure" is continuously fluctuating. The free energy of the "structural state" that is defined by the fraction of secondary bonds in the bonded state has been expressed by the bond energy, the cooperative interaction between bonds, the mixing entropy of bonds, and the entropy of polypeptide chains. The most probable "structural state" can be simply determined by graphical analysis and the effect of temperature or solvent composition on it is discussed. The temperature dependence of the free energy, the probability distribution of structural states and the specific heat have been calculted for two examples of structural change. The theory predicts two different types of structural changes from the ordered to disorderd state, a "structured transition" and a "gradual structural change" with rising temperature. In the "structural transition", the probability distribution has two maxima in the temperature range of transition. In the "gradual structural change", the probabilty distribution has only one maximum during the change. A considerable fraction of secondary bonds is in the unbounded state and is always fluctuating even in the ordered state at room temperature. Such structural flucutations in a single protein molecule have been discussed quantitatively. The theory is extended to include small molecules which bind to the protein molecule and affect the structural state. The changes of structural state caused by specific and non-specific binding and allosteric effects are explained in a unified manner.

Method of identifying hairpin DNA probes by partial fold analysis

DOEpatents

Miller, Benjamin L [Penfield, NY; Strohsahl, Christopher M [Saugerties, NY

2009-10-06

Method of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

Method of identifying hairpin DNA probes by partial fold analysis

DOEpatents

Miller, Benjamin L.; Strohsahl, Christopher M.

2008-10-28

Methods of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

Surface determination through atomically resolved secondary-electron imaging

PubMed Central

Ciston, J.; Brown, H. G.; D'Alfonso, A. J.; Koirala, P.; Ophus, C.; Lin, Y.; Suzuki, Y.; Inada, H.; Zhu, Y.; Allen, L. J.; Marks, L. D.

2015-01-01

Unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we report a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 × 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our work reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO5 units. Dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals. PMID:26082275

Surface determination through atomically resolved secondary-electron imaging

DOE PAGES

Ciston, J.; Brown, H. G.; D’Alfonso, A. J.; ...

2015-06-17

We report that unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we show a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 x 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our workmore » reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO 5 units. Lastly, dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals.« less

A Circular Dichroism Reference Database for Membrane Proteins

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

Wallace,B.; Wien, F.; Stone, T.

2006-01-01

Membrane proteins are a major product of most genomes and the target of a large number of current pharmaceuticals, yet little information exists on their structures because of the difficulty of crystallising them; hence for the most part they have been excluded from structural genomics programme targets. Furthermore, even methods such as circular dichroism (CD) spectroscopy which seek to define secondary structure have not been fully exploited because of technical limitations to their interpretation for membrane embedded proteins. Empirical analyses of circular dichroism (CD) spectra are valuable for providing information on secondary structures of proteins. However, the accuracy of themore » results depends on the appropriateness of the reference databases used in the analyses. Membrane proteins have different spectral characteristics than do soluble proteins as a result of the low dielectric constants of membrane bilayers relative to those of aqueous solutions (Chen & Wallace (1997) Biophys. Chem. 65:65-74). To date, no CD reference database exists exclusively for the analysis of membrane proteins, and hence empirical analyses based on current reference databases derived from soluble proteins are not adequate for accurate analyses of membrane protein secondary structures (Wallace et al (2003) Prot. Sci. 12:875-884). We have therefore created a new reference database of CD spectra of integral membrane proteins whose crystal structures have been determined. To date it contains more than 20 proteins, and spans the range of secondary structures from mostly helical to mostly sheet proteins. This reference database should enable more accurate secondary structure determinations of membrane embedded proteins and will become one of the reference database options in the CD calculation server DICHROWEB (Whitmore & Wallace (2004) NAR 32:W668-673).« less

Transcriptome-Wide Analysis of UTRs in Non-Small Cell Lung Cancer Reveals Cancer-Related Genes with SNV-Induced Changes on RNA Secondary Structure and miRNA Target Sites

PubMed Central

Novotny, Peter; Tang, Xiaojia; Kalari, Krishna R.; Gorodkin, Jan

2014-01-01

Traditional mutation assessment methods generally focus on predicting disruptive changes in protein-coding regions rather than non-coding regulatory regions like untranslated regions (UTRs) of mRNAs. The UTRs, however, are known to have many sequence and structural motifs that can regulate translational and transcriptional efficiency and stability of mRNAs through interaction with RNA-binding proteins and other non-coding RNAs like microRNAs (miRNAs). In a recent study, transcriptomes of tumor cells harboring mutant and wild-type KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) genes in patients with non-small cell lung cancer (NSCLC) have been sequenced to identify single nucleotide variations (SNVs). About 40% of the total SNVs (73,717) identified were mapped to UTRs, but omitted in the previous analysis. To meet this obvious demand for analysis of the UTRs, we designed a comprehensive pipeline to predict the effect of SNVs on two major regulatory elements, secondary structure and miRNA target sites. Out of 29,290 SNVs in 6462 genes, we predict 472 SNVs (in 408 genes) affecting local RNA secondary structure, 490 SNVs (in 447 genes) affecting miRNA target sites and 48 that do both. Together these disruptive SNVs were present in 803 different genes, out of which 188 (23.4%) were previously known to be cancer-associated. Notably, this ratio is significantly higher (one-sided Fisher's exact test p-value = 0.032) than the ratio (20.8%) of known cancer-associated genes (n = 1347) in our initial data set (n = 6462). Network analysis shows that the genes harboring disruptive SNVs were involved in molecular mechanisms of cancer, and the signaling pathways of LPS-stimulated MAPK, IL-6, iNOS, EIF2 and mTOR. In conclusion, we have found hundreds of SNVs which are highly disruptive with respect to changes in the secondary structure and miRNA target sites within UTRs. These changes hold the potential to alter the expression of known cancer genes or genes linked to cancer-associated pathways. PMID:24416147

Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites.

PubMed

Sabarinathan, Radhakrishnan; Wenzel, Anne; Novotny, Peter; Tang, Xiaojia; Kalari, Krishna R; Gorodkin, Jan

2014-01-01

Traditional mutation assessment methods generally focus on predicting disruptive changes in protein-coding regions rather than non-coding regulatory regions like untranslated regions (UTRs) of mRNAs. The UTRs, however, are known to have many sequence and structural motifs that can regulate translational and transcriptional efficiency and stability of mRNAs through interaction with RNA-binding proteins and other non-coding RNAs like microRNAs (miRNAs). In a recent study, transcriptomes of tumor cells harboring mutant and wild-type KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) genes in patients with non-small cell lung cancer (NSCLC) have been sequenced to identify single nucleotide variations (SNVs). About 40% of the total SNVs (73,717) identified were mapped to UTRs, but omitted in the previous analysis. To meet this obvious demand for analysis of the UTRs, we designed a comprehensive pipeline to predict the effect of SNVs on two major regulatory elements, secondary structure and miRNA target sites. Out of 29,290 SNVs in 6462 genes, we predict 472 SNVs (in 408 genes) affecting local RNA secondary structure, 490 SNVs (in 447 genes) affecting miRNA target sites and 48 that do both. Together these disruptive SNVs were present in 803 different genes, out of which 188 (23.4%) were previously known to be cancer-associated. Notably, this ratio is significantly higher (one-sided Fisher's exact test p-value = 0.032) than the ratio (20.8%) of known cancer-associated genes (n = 1347) in our initial data set (n = 6462). Network analysis shows that the genes harboring disruptive SNVs were involved in molecular mechanisms of cancer, and the signaling pathways of LPS-stimulated MAPK, IL-6, iNOS, EIF2 and mTOR. In conclusion, we have found hundreds of SNVs which are highly disruptive with respect to changes in the secondary structure and miRNA target sites within UTRs. These changes hold the potential to alter the expression of known cancer genes or genes linked to cancer-associated pathways.

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/.

The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes.

PubMed

D'Onofrio, Giuseppe; Ghosh, Tapash Chandra

2005-01-17

Fluctuations and increments of both C(3) and G(3) levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC(3) levels, the second shows considerable increments of the GC(3) levels in the human genes. In both data sets, the fluctuations of C(3) and G(3) levels along the coding sequences correlated with the secondary structures of the encoded proteins. The human genes that underwent the compositional transition showed a different increment of the C(3) and G(3) levels within and among the structural units of the proteins. The relative synonymous codon usage (RSCU) of several amino acids were also affected during the compositional transition, showing that there exists a correlation between RSCU and protein secondary structures in human genes. The importance of natural selection for the formation of isochore organization of the human genome has been discussed on the basis of these results.

Effects of high hydrostatic pressure on secondary structure and emulsifying behavior of sweet potato protein

NASA Astrophysics Data System (ADS)

Mehmood Khan, Nasir; Mu, Tai-Hua; Sun, Hong-Nan; Zhang, Miao; Chen, Jing-Wang

2015-04-01

In this study, secondary structures of sweet potato protein (SPP) after high hydrostatic pressure (HHP) treatment (200-600 MPa) were evaluated and emulsifying properties of emulsions with HHP-treated SPP solutions in different pH values (3, 6, and 9) were investigated. Circular dichroism analysis confirmed the modification of the SPP secondary structure. Surface hydrophobicity increased at pH 3 and decreased at 6 and 9. Emulsifying activity index at pH 6 increased with an increase in pressure, whereas emulsifying stability index increased at pH 6 and 9. Oil droplet sizes decreased, while volume frequency distribution of the smaller droplets increased at pH 3 and 6 with the HHP treatment. Emulsion viscosity increased at pH 6 and 9 and pseudo-plastic flow behaviors were not altered for all emulsions produced with HHP-treated SPP. These results suggested that HHP could modify the SPP structure for better emulsifying properties, which could increase the use of SPP emulsion in the food industry.

Phylogenetic analysis of several Thermus strains from Rehai of Tengchong, Yunnan, China.

PubMed

Lin, Lianbing; Zhang, Jie; Wei, Yunlin; Chen, Chaoyin; Peng, Qian

2005-10-01

Several Thermus strains were isolated from 10 hot springs of the Rehai geothermal area in Tengchong, Yunnan province. The diversity of Thermus strains was examined by sequencing the 16S rRNA genes and comparing their sequences. Phylogenetic analysis showed that the 16S rDNA sequences from the Rehai geothermal isolates form four branches in the phylogenetic tree and had greater than 95.9% similarity in the phylogroup. Secondary structure comparison also indicated that the 16S rRNA from the Rehai geothermal isolates have unique secondary structure characteristics in helix 6, helix 9, and helix 10 (reference to Escherichia coli). This research is the first attempt to reveal the diversity of Thermus strains that are distributed in the Rehai geothermal area.

Availability: A Metric for Nucleic Acid Strand Displacement Systems.

PubMed

Olson, Xiaoping; Kotani, Shohei; Padilla, Jennifer E; Hallstrom, Natalya; Goltry, Sara; Lee, Jeunghoon; Yurke, Bernard; Hughes, William L; Graugnard, Elton

2017-01-20

DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks.

The Importance of Model Structure in the Cost-Effectiveness Analysis of Primary Care Interventions for the Management of Hypertension.

PubMed

Peñaloza-Ramos, Maria Cristina; Jowett, Sue; Sutton, Andrew John; McManus, Richard J; Barton, Pelham

2018-03-01

Management of hypertension can lead to significant reductions in blood pressure, thereby reducing the risk of cardiovascular disease. Modeling the course of cardiovascular disease is not without complications, and uncertainty surrounding the structure of a model will almost always arise once a choice of a model structure is defined. To provide a practical illustration of the impact on the results of cost-effectiveness of changing or adapting model structures in a previously published cost-utility analysis of a primary care intervention for the management of hypertension Targets and Self-Management for the Control of Blood Pressure in Stroke and at Risk Groups (TASMIN-SR). The case study assessed the structural uncertainty arising from model structure and from the exclusion of secondary events. Four alternative model structures were implemented. Long-term cost-effectiveness was estimated and the results compared with those from the TASMIN-SR model. The main cost-effectiveness results obtained in the TASMIN-SR study did not change with the implementation of alternative model structures. Choice of model type was limited to a cohort Markov model, and because of the lack of epidemiological data, only model 4 captured structural uncertainty arising from the exclusion of secondary events in the case study model. The results of this study indicate that the main conclusions drawn from the TASMIN-SR model of cost-effectiveness were robust to changes in model structure and the inclusion of secondary events. Even though one of the models produced results that were different to those of TASMIN-SR, the fact that the main conclusions were identical suggests that a more parsimonious model may have sufficed. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

PubMed Central

Zook, James D.; Molugu, Trivikram R.; Jacobsen, Neil E.; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra

2013-01-01

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

Structural and physical properties of collagen extracted from moon jellyfish under neutral pH conditions.

PubMed

Miki, Ayako; Inaba, Satomi; Baba, Takayuki; Kihira, Koji; Fukada, Harumi; Oda, Masayuki

2015-01-01

We extracted collagen from moon jellyfish under neutral pH conditions and analyzed its amino acid composition, secondary structure, and thermal stability. The content of hydroxyproline was 4.3%, which is lower than that of other collagens. Secondary structure analysis using circular dichroism (CD) showed a typical collagen helix. The thermal stability of this collagen at pH 3.0 was lower than those from fish scale and pig skin, which also correlates closely with jellyfish collagen having lower hydroxyproline content. Because the solubility of jellyfish collagen used in this study at neutral pH was quite high, it was possible to analyze its structural and physical properties under physiological conditions. Thermodynamic analysis using CD and differential scanning calorimetry showed that the thermal stability at pH 7.5 was higher than at pH 3.0, possibly due to electrostatic interactions. During the process of unfolding, fibrillation would occur only at neutral pH.

Validation and Utility of the Social Emotional Health Survey-Secondary for Japanese Students

ERIC Educational Resources Information Center

Ito, Ayako; Smith, Douglas C.; You, Sukkyung; Shimoda, Yoshiyuki; Furlong, Michael J.

2015-01-01

The article explores the use of the Social and Emotional Health Survey-Secondary version (SEHS-S) with a sample of 975 Japanese students in Grades 7-9 attending schools located northwest of Tokyo. A confirmatory factor analysis using half the sample confirmed the four-factor structure of the SEHS-S, and further analyses verified its second-order…

Dynamic analysis of the large deployable reflector

NASA Technical Reports Server (NTRS)

Calleson, Robert E.; Scott, A. Don

1987-01-01

The Large Deployable Reflector (LDR) is to be an astronomical observatory orbiting above Earth's obscuring atmosphere and operating in the spectral range between 30 microns and 1000 microns wavelength. The LDR will be used to study such astronomical phenomena as stellar and galactic formation, cosmology, and planetary atmospheres. The LDR will be the first observatory to be erected and assembled in space. This distinction brings with it several major technological challenges such as the development of ultra-lightweight deployable mirrors, advanced mirror fabrication techniques, advanced structures, and control of vibrations due to various sources of excitation. The purpose of this analysis is to provide an assessment of the vibrational response due to secondary mirror chopping and LDR slewing. The dynamic response of two 20-m LDR configurations was studied. Two mirror support configurations were investigated for the Ames concept, the first employs a six-strut secondary mirror support structure, while the second uses a triple-bipod support design. All three configurations were modeled using a tetrahedral truss design for the primary mirror support structure. Response resulting from secondary mirror chopping was obtained for the two Ames configurations, and the response of the primary mirror from slewing was obtained for all three configurations.

Students' understanding of primary and secondary protein structure: drawing secondary protein structure reveals student understanding better than simple recognition of structures.

PubMed

Harle, Marissa; Towns, Marcy H

2013-01-01

The interdisciplinary nature of biochemistry courses requires students to use both chemistry and biology knowledge to understand biochemical concepts. Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations in addition to a fragmented understanding of fundamental biochemistry concepts. This project focuses on students' understanding of primary and secondary protein structure and drawings (representations) of hydrogen-bonding in alpha helices and beta sheets. Analysis demonstrated that students can recognize and identify primary protein structure concepts when given a polypeptide. However, when asked to draw alpha helices and beta sheets and explain the role of hydrogen bonding their drawings students exhibited a fragmented understanding that lacked coherence. Faculty are encouraged to have students draw molecular level representations to make their mental models more explicit, complete, and coherent. This is in contrast to recognition and identification tasks, which do not adequately probe mental models and molecular level understanding. © 2013 by The International Union of Biochemistry and Molecular Biology.

Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum

PubMed Central

Pei, Haisheng; Chen, Zhou; Tan, Xiaoyan; Hu, Jing; Yang, Bin; Sun, Junshe

2017-01-01

Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1–3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP) site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality control in the Ganoderma industry. PMID:28056060

Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum.

PubMed

Zhang, Xiuqing; Xu, Zhangyang; Pei, Haisheng; Chen, Zhou; Tan, Xiaoyan; Hu, Jing; Yang, Bin; Sun, Junshe

2017-01-01

Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1-3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP) site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality control in the Ganoderma industry.

Advanced glycation end products induce differential structural modifications and fibrillation of albumin

NASA Astrophysics Data System (ADS)

Awasthi, Saurabh; Sankaranarayanan, Kamatchi; Saraswathi, N. T.

2016-06-01

Glycation induced amyloid fibrillation is fundamental to the development of many neurodegenerative and cardiovascular complications. Excessive non-enzymatic glycation in conditions such as hyperglycaemia results in the increased accumulation of advanced glycation end products (AGEs). AGEs are highly reactive pro-oxidants, which can lead to the activation of inflammatory pathways and development of oxidative stress. Recently, the effect of non-enzymatic glycation on protein structure has been the major research area, but the role of specific AGEs in such structural alteration and induction of fibrillation remains undefined. In this study, we determined the specific AGEs mediated structural modifications in albumin mainly considering carboxymethyllysine (CML), carboxyethyllysine (CEL), and argpyrimidine (Arg-P) which are the major AGEs formed in the body. We studied the secondary structural changes based on circular dichroism (CD) and spectroscopic analysis. The AGEs induced fibrillation was determined by Congo red binding and examination of scanning and transmission electron micrographs. The amyloidogenic regions in the sequence of BSA were determined using FoldAmyloid. It was observed that CEL modification of BSA leads to the development of fibrillar structures, which was evident from both secondary structure changes and TEM analysis.

Consistent global structures of complex RNA states through multidimensional chemical mapping

PubMed Central

Cheng, Clarence Yu; Chou, Fang-Chieh; Kladwang, Wipapat; Tian, Siqi; Cordero, Pablo; Das, Rhiju

2015-01-01

Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states. DOI: http://dx.doi.org/10.7554/eLife.07600.001 PMID:26035425

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.

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

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

A comparative analysis of the diversity of woody vegetation in old-growth and secondary southern Appalachian cove forests

Treesearch

Lyle J. Guyon; Gary L. Rolfe; John M. Edgington; Guillermo A. Mendoza

2003-01-01

Characteristics of woody vegetation were compared across six different southern Appalachian cove forests. Trees greater than 6.35 cm dbh were point sampled and regeneration was tallied on 25 m² subplots at all study sites. Overstory composition and structure differed between secondary and old-growth sites, which were dominated by yellow-poplar and eastern...

Secondary Mathematics Course Trajectories: Understanding Accumulated Disadvantages in Mathematics in Grades 9-12

ERIC Educational Resources Information Center

Schiller, Kathryn S.; Hunt, Donald J.

2011-01-01

Schools are institutions in which students' course taking creates series of linked learning opportunities continually shaped by not only curricular structures but demographic and academic backgrounds. In contrast to a seven-step normative course sequence reflecting the conventional hierarchical structure of mathematics, analysis of more than…

Development of in-orbit refocusing mechanism for SpaceEye-1 electro-optical payload

NASA Astrophysics Data System (ADS)

Lee, Minwoo; Kim, Jongun; Chang, Jin-Soo; Kang, Myung-Seok

2016-09-01

SpaceEye-1 earth observation satellite, developed by Satrec Initiative Co. Ltd., is a 300 kg scale spacecraft with high resolution electro-optical payload (EOS-D) which performs 1 m GSD, 12 km swath in low earth orbit. Metering structure of EOS-D is manufactured with Carbon Fiber Reinforced Plastic (CFRP). Due to the moisture emission from CFRP metering structure, this spaceborne electro-optical payload undergoes shrinkage after orbit insertion. The shrinkage of metering structure causes change of the distance between primary and secondary mirror. In order to compensate the moisture shrinkage effect, two types of thermal refocusing mechanism were developed, analyzed and applied to EOS-D. Thermal analysis simulating in-orbit thermal condition and thermo-elastic displacement analysis was conducted to calculate the performance of refocusing mechanism. For each EOS-D telescope, analytical refocusing range (displacement change between primary and secondary mirror) was 2.5 um and 3.6 um. Thus, the refocusing mechanism can compensate the dimensional instability of metering structure caused by moisture emission. Furthermore, modal, static and wavefront error analysis was conducted in order to evaluate natural frequency, structural stability and optical performance. As a result, it can be concluded that the refocusing system of EOS-D payload can perform its function in orbit.

Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation.

PubMed

Kachhap, Sangita; Priyadarshini, Pragya; Singh, Balvinder

2017-05-01

Aristaless (Al) and clawless (Cll) homeodomains that are involved in leg development in Drosophila melanogaster are known to bind cooperatively to 5'-(T/C)TAATTAA(T/A)(T/A)G-3' DNA sequence, but the mechanism of their binding to DNA is unknown. Molecular dynamics (MD) studies have been carried out on binary, ternary, and reconstructed protein-DNA complexes involving Al, Cll, and DNA along with binding free energy analysis of these complexes. Analysis of MD trajectories of Cll-3A01, binary complex reveals that C-terminal end of helixIII of Cll, unwind in the absence of Al and remains so in reconstructed ternary complex, Cll-3A01-Al. In addition, this change in secondary structure of Cll does not allow it to form protein-protein interactions with Al in the ternary reconstructed complex. However, secondary structure of Cll and its interactions are maintained in other reconstructed ternary complex, Al-3A01-Cll where Cll binds to Al-3A01, binary complex to form ternary complex. These interactions as observed during MD simulations compare well with those observed in ternary crystal structure. Thus, this study highlights the role of helixIII of Cll and protein-protein interactions while proposing likely mechanism of recognition in ternary complex, Al-Cll-DNA.

Differential accumulation of nif structural gene mRNA in Azotobacter vinelandii.

PubMed

Hamilton, Trinity L; Jacobson, Marty; Ludwig, Marcus; Boyd, Eric S; Bryant, Donald A; Dean, Dennis R; Peters, John W

2011-09-01

Northern analysis was employed to investigate mRNA produced by mutant strains of Azotobacter vinelandii with defined deletions in the nif structural genes and in the intergenic noncoding regions. The results indicate that intergenic RNA secondary structures effect the differential accumulation of transcripts, supporting the high Fe protein-to-MoFe protein ratio required for optimal diazotrophic growth.

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.

A synchronous increase in hydraulic conductive capacity and mechanical support in conifers with relatively uniform xylem structure.

PubMed

Jagels, Richard; Visscher, George E

2006-02-01

The dual function provided by longitudinal tracheids in conifers has led to a generally held trade-off concept that increasing wall thickness and/or volume of latewood tracheids improves mechanical support, while increasing cell diameter and/or volume of earlywood tracheids enhances conductive potential. Yet, some conifers have either uniform cell structure across the growth ring or, at most, a small amount of latewood. How do these trees accomplish the needs for increasing support and conduction with height growth? We examined Metasequoia glyptostroboides, a species that we previously demonstrated improves its mechanical properties with increasing age without a change in specific gravity or secondary wall microfibril angle. In this paper, we showed that lignin and extractive contents are not contributing factors, and through composite structure analysis, we eliminated a role for tracheid length. Using micromorphometric analysis, we demonstrated that as cell diameter increases, total primary wall decreases, secondary wall increases, and strength and conductive capacity increase with no change in specific gravity. Meta-analysis using other species of Cupressaceae, Podocarpaceae, and Araucariaceae provided strong corroborative evidence for this design strategy.

Identification of protein secondary structures by laser induced autofluorescence: A study of urea and GnHCl induced protein denaturation

NASA Astrophysics Data System (ADS)

Siddaramaiah, Manjunath; Satyamoorthy, Kapaettu; Rao, Bola Sadashiva Satish; Roy, Suparna; Chandra, Subhash; Mahato, Krishna Kishore

2017-03-01

In the present study an attempt has been made to interrogate the bulk secondary structures of some selected proteins (BSA, HSA, lysozyme, trypsin and ribonuclease A) under urea and GnHCl denaturation using laser induced autofluorescence. The proteins were treated with different concentrations of urea (3 M, 6 M, 9 M) and GnHCl (2 M, 4 M, 6 M) and the corresponding steady state autofluorescence spectra were recorded at 281 nm pulsed laser excitations. The recorded fluorescence spectra of proteins were then interpreted based on the existing PDB structures of the proteins and the Trp solvent accessibility (calculated using "Scratch protein predictor" at 30% threshold). Further, the influence of rigidity and conformation of the indole ring (caused by protein secondary structures) on the intrinsic fluorescence properties of proteins were also evaluated using fluorescence of ANS-HSA complexes, CD spectroscopy as well as with trypsin digestion experiments. The outcomes obtained clearly demonstrated GnHCl preferably disrupt helix as compared to the beta β-sheets whereas, urea found was more effective in disrupting β-sheets as compared to the helices. The other way round the proteins which have shown detectable change in the intrinsic fluorescence at lower concentrations of GnHCl were rich in helices whereas, the proteins which showed detectable change in the intrinsic fluorescence at lower concentrations of urea were rich in β-sheets. Since high salt concentrations like GnHCl and urea interfere in the secondary structure analysis by circular dichroism Spectrometry, the present method of analyzing secondary structures using laser induced autofluorescence will be highly advantageous over existing tools for the same.

ITS2 sequence-structure phylogeny reveals diverse endophytic Pseudocercospora fungi on poplars.

PubMed

Yan, Dong-Hui; Gao, Qian; Sun, Xiaoming; Song, Xiaoyu; Li, Hongchang

2018-04-01

For matching the new fungal nomenclature to abolish pleomorphic names for a fungus, a genus Pseudocercospora s. str. was suggested to host holomorphic Pseudocercosproa fungi. But the Pseudocercosproa fungi need extra phylogenetic loci to clarify their taxonomy and diversity for their existing and coming species. Internal transcribed spacer 2 (ITS2) secondary structures have been promising in charactering species phylogeny in plants, animals and fungi. In present study, a conserved model of ITS2 secondary structures was confirmed on fungi in Pseudocercospora s. str. genus using RNAshape program. The model has a typical eukaryotic four-helix ITS2 secondary structure. But a single U base occurred in conserved motif of U-U mismatch in Helix 2, and a UG emerged in UGGU motif in Helix 3 to Pseudocercospora fungi. The phylogeny analyses based on the ITS2 sequence-secondary structures with compensatory base change characterizations are able to delimit more species for Pseudocercospora s. str. than phylogenic inferences of traditional multi-loci alignments do. The model was employed to explore the diversity of endophytic Pseudocercospora fungi in poplar trees. The analysis results also showed that endophytic Pseudocercospora fungi were diverse in species and evolved a specific lineage in poplar trees. This work suggested that ITS2 sequence-structures could become as additionally significant loci for species phylogenetic and taxonomic studies on Pseudocerospora fungi, and that Pseudocercospora endophytes could be important roles to Pseudocercospora fungi's evolution and function in ecology.

Impact of target mRNA structure on siRNA silencing efficiency: A large-scale study.

PubMed

Gredell, Joseph A; Berger, Angela K; Walton, S Patrick

2008-07-01

The selection of active siRNAs is generally based on identifying siRNAs with certain sequence and structural properties. However, the efficiency of RNA interference has also been shown to depend on the structure of the target mRNA, primarily through studies using exogenous transcripts with well-defined secondary structures in the vicinity of the target sequence. While these studies provide a means for examining the impact of target sequence and structure independently, the predicted secondary structures for these transcripts are often not reflective of structures that form in full-length, native mRNAs where interactions can occur between relatively remote segments of the mRNAs. Here, using a combination of experimental results and analysis of a large dataset, we demonstrate that the accessibility of certain local target structures on the mRNA is an important determinant in the gene silencing ability of siRNAs. siRNAs targeting the enhanced green fluorescent protein were chosen using a minimal siRNA selection algorithm followed by classification based on the predicted minimum free energy structures of the target transcripts. Transfection into HeLa and HepG2 cells revealed that siRNAs targeting regions of the mRNA predicted to have unpaired 5'- and 3'-ends resulted in greater gene silencing than regions predicted to have other types of secondary structure. These results were confirmed by analysis of gene silencing data from previously published siRNAs, which showed that mRNA target regions unpaired at either the 5'-end or 3'-end were silenced, on average, approximately 10% more strongly than target regions unpaired in the center or primarily paired throughout. We found this effect to be independent of the structure of the siRNA guide strand. Taken together, these results suggest minimal requirements for nucleation of hybridization between the siRNA guide strand and mRNA and that both mRNA and guide strand structure should be considered when choosing candidate siRNAs. (c) 2008 Wiley Periodicals, Inc.

Impact of target mRNA structure on siRNA silencing efficiency: a large-scale study

PubMed Central

Gredell, Joseph A.; Berger, Angela K.; Walton, S. Patrick

2009-01-01

The selection of active siRNAs is generally based on identifying siRNAs with certain sequence and structural properties. However, the efficiency of RNA interference has also been shown to depend on the structure of the target mRNA, primarily through studies using exogenous transcripts with well-defined secondary structures in the vicinity of the target sequence. While these studies provide a means for examining the impact of target sequence and structure independently, the predicted secondary structures for these transcripts are often not reflective of structures that form in full-length, native mRNAs where interactions can occur between relatively remote segments of the mRNAs. Here, using a combination of experimental results and analysis of a large dataset, we demonstrate that the accessibility of certain local target structures on the mRNA is an important determinant in the gene silencing ability of siRNAs. siRNAs targeting the enhanced green fluorescent protein were chosen using a minimal siRNA selection algorithm followed by classification based on the predicted minimum free energy structures of the target transcripts. Transfection into HeLa and HepG2 cells revealed that siRNAs targeting regions of the mRNA predicted to have unpaired 5’- and 3’-ends resulted in greater gene silencing than regions predicted to have other types of secondary structure. These results were confirmed by analysis of gene silencing data from previously published siRNAs, which showed that mRNA target regions unpaired at either the 5’-end or 3’-end were silenced, on average, ~10% more strongly than target regions unpaired in the center or primarily paired throughout. We found this effect to be independent of the structure of the siRNA guide strand. Taken together, these results suggest minimal requirements for nucleation of hybridization between the siRNA guide strand and mRNA and that both mRNA and guide strand structure should be considered when choosing candidate siRNAs. PMID:18306428

PDBFlex: exploring flexibility in protein structures

PubMed Central

Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam

2016-01-01

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193

A high-throughput approach to profile RNA structure.

PubMed

Delli Ponti, Riccardo; Marti, Stefanie; Armaos, Alexandros; Tartaglia, Gian Gaetano

2017-03-17

Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. We trained CROSS using data from high-throughput experiments such as Selective 2΄-Hydroxyl Acylation analyzed by Primer Extension (SHAPE; Mouse and HIV transcriptomes) and Parallel Analysis of RNA Structure (PARS; Human and Yeast transcriptomes) as well as high-quality NMR/X-ray structures (PDB database). The algorithm uses primary structure information alone to predict experimental structural profiles with >80% accuracy, showing high performances on large RNAs such as Xist (17 900 nucleotides; Area Under the ROC Curve AUC of 0.75 on dimethyl sulfate (DMS) experiments). We integrated CROSS in thermodynamics-based methods to predict secondary structure and observed an increase in their predictive power by up to 30%. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nanostructure and molecular mechanics of spider dragline silk protein assemblies

PubMed Central

Keten, Sinan; Buehler, Markus J.

2010-01-01

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre. PMID:20519206

Nanostructure and molecular mechanics of spider dragline silk protein assemblies.

PubMed

Keten, Sinan; Buehler, Markus J

2010-12-06

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 3₁-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.

Availability: A Metric for Nucleic Acid Strand Displacement Systems

PubMed Central

2016-01-01

DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks. PMID:26875531

A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction.

PubMed

Edvardsson, Sverker; Gardner, Paul P; Poole, Anthony M; Hendy, Michael D; Penny, David; Moulton, Vincent

2003-05-01

Noncoding RNA genes produce functional RNA molecules rather than coding for proteins. One such family is the H/ACA snoRNAs. Unlike the related C/D snoRNAs these have resisted automated detection to date. We develop an algorithm to screen the yeast genome for novel H/ACA snoRNAs. To achieve this, we introduce some new methods for facilitating the search for noncoding RNAs in genomic sequences which are based on properties of predicted minimum free-energy (MFE) secondary structures. The algorithm has been implemented and can be generalized to enable screening of other eukaryote genomes. We find that use of primary sequence alone is insufficient for identifying novel H/ACA snoRNAs. Only the use of secondary structure filters reduces the number of candidates to a manageable size. From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened.

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

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Villanueva, Josep; Villegas, Virtudes; Querol, Enrique; Avilés, Francesc X; Serrano, Luis

2002-09-01

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability. Copyright 2002 John Wiley & Sons, Ltd.

Thermal Design and Analysis of the Optical Telescope Assembly for the Gondola for High Altitude Planetary Science

NASA Technical Reports Server (NTRS)

O'Connor, Brian; Brooks, Thomas

2017-01-01

The NASA Gondola for High Altitude Planetary Science (GHAPS) project is an effort to design, build, and fly a balloon-borne platform for planetary science missions. GHAPS observations will be in the 300 nm to 5 micron wavelength region covering UV, visible, and near-mid IR. The primary element of the project is the Optical Telescope Assembly (OTA). It is a one meter aperture narrow-field-of-view telescope that contains the primary and secondary mirrors, the support system/metering structure, a secondary mirror focusing system, baffles, and insulation. This paper presents the thermal design and analysis that has been done to support the design of the OTA. A major part of the thermal analysis was bounding the flight environment for the six potential Columbia Scientific Balloon Facility launch sites. These analyses were used to give input into the Structural Thermal Optical Performance (STOP) analysis of the telescope. Also the analysis was used to select heater sizes for the few OTA associated electronic components. Currently the telescope is scheduled to have its first flight in 2019.

Increasing Elasticity through Changes in the Secondary Structure of Gelatin by Gelation in a Microsized Lipid Space.

PubMed

Sakai, Atsushi; Murayama, Yoshihiro; Fujiwara, Kei; Fujisawa, Takahiro; Sasaki, Saori; Kidoaki, Satoru; Yanagisawa, Miho

2018-04-25

Even though microgels are used in a wide variety of applications, determining their mechanical properties has been elusive because of the difficulties in analysis. In this study, we investigated the surface elasticity of a spherical microgel of gelatin prepared inside a lipid droplet by using micropipet aspiration. We found that gelation inside a microdroplet covered with lipid membranes increased Young's modulus E toward a plateau value E * along with a decrease in gel size. In the case of 5.0 wt % gelatin gelled inside a microsized lipid space, the E * for small microgels with R ≤ 50 μm was 10-fold higher (35-39 kPa) than that for the bulk gel (∼3 kPa). Structural analysis using circular dichroism spectroscopy and a fluorescence indicator for ordered beta sheets demonstrated that the smaller microgels contained more beta sheets in the structure than the bulk gel. Our finding indicates that the confinement size of gelling polymers becomes a factor in the variation of elasticity of protein-based microgels via secondary structure changes.

Increasing Elasticity through Changes in the Secondary Structure of Gelatin by Gelation in a Microsized Lipid Space

PubMed Central

2018-01-01

Even though microgels are used in a wide variety of applications, determining their mechanical properties has been elusive because of the difficulties in analysis. In this study, we investigated the surface elasticity of a spherical microgel of gelatin prepared inside a lipid droplet by using micropipet aspiration. We found that gelation inside a microdroplet covered with lipid membranes increased Young’s modulus E toward a plateau value E* along with a decrease in gel size. In the case of 5.0 wt % gelatin gelled inside a microsized lipid space, the E* for small microgels with R ≤ 50 μm was 10-fold higher (35–39 kPa) than that for the bulk gel (∼3 kPa). Structural analysis using circular dichroism spectroscopy and a fluorescence indicator for ordered beta sheets demonstrated that the smaller microgels contained more beta sheets in the structure than the bulk gel. Our finding indicates that the confinement size of gelling polymers becomes a factor in the variation of elasticity of protein-based microgels via secondary structure changes. PMID:29721530

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

Rtools: a web server for various secondary structural analyses on single RNA sequences.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

2016-07-08

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Resources for Teaching Word Identification.

ERIC Educational Resources Information Center

Schell, Leo M., Ed.; And Others

Only materials specifically designed to teach one or more of the following word identification skills were included in this booklet: sight words, context clues, phonic analysis, structural analysis, and dictionary skills. Materials for grades one through six are stressed, although a few materials suitable for secondary school students are listed.…

AES and SIMS analysis of non-metallic inclusions in a low-carbon chromium-steel.

PubMed

Gammer, Katharina; Rosner, M; Poeckl, G; Hutter, H

2003-05-01

In the final step of secondary metallurgical steel processing, calcium is added. Besides Mg, Ca is the most powerful deoxidiser and desulfurisation agent. It reacts with dissolved oxygen and sulfur and reduces oxides and sulfides thereby forming non-metallic inclusions. Within this paper we present the analysis of such inclusions in a low-carbon chromium-steel. Depending on the time of quenching of the steel sample, different structures were revealed by REM, Auger and SIMS: If the steel was quenched immediately after Ca-addition, non-metallic inclusions that appeared to have "cavities" could be detected with SEM. SIMS investigations of these particles showed ring-shaped structures and revealed that the ring is made up of Al, Ca, Mg, O and S. No secondary ions however could be retrieved from the core inside the ring, thus leaving the nature of the "cavities" unclear. If the steel sample was quenched 3 min after Ca addition, inclusions did not have a ring-shaped structure but a compact one.

Label-free determination of lipid composition and secondary protein structure of human salivary noncancerous and cancerous tissues by Raman microspectroscopy.

PubMed

Brozek-Pluska, Beata; Kopec, Monika; Niedzwiecka, Izabela; Morawiec-Sztandera, Alina

2015-04-07

The applications of optical spectroscopic methods in cancer detection open new possibilities in oncological diagnostics. Raman spectroscopy and Raman imaging represent noninvasive, label-free, and rapidly developing tools in cancer diagnosis. In the study described in this paper Raman microspectroscopy has been employed to examine noncancerous and cancerous human salivary gland tissues of the same patient. The most significant differences between noncancerous and cancerous tissues were found in regions typical for the vibrations of lipids and proteins. The detailed analysis of secondary structures of proteins contained in the cancerous and the noncancerous tissues is also presented.

Defect character at grain boundary facet junctions: Analysis of an asymmetric Σ = 5 grain boundary in Fe

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

Medlin, D. L.; Hattar, K.; Zimmerman, J. A.

Grain boundaries often develop faceted morphologies in systems for which the interfacial free energy depends on the boundary inclination. Although the mesoscale thermodynamic basis for such morphological evolution has been extensively studied, the influence of line defects, such as secondary grain boundary dislocations, on the facet configurations has not been thoroughly explored. In this paper, through a combination of atomistic simulations and electron microscopic observations, we examine in detail the structure of an asymmetric Σ = 5 [001] grain boundary in well-annealed, body-centered cubic (BCC) Fe. The observed boundary forms with a hill-and-valley morphology composed of nanoscale {310} and {210}more » facets. Our analysis clarifies the atomic structure of the {310}/{210} facet junctions and identifies the presence of an array of secondary grain boundary dislocations that are localized to these junctions. Analysis of the Burgers vectors of the grain boundary dislocations, which are of type (1/5)<310> and (1/5)<120>, shows that the defect density is consistent with that required to accommodate a small observed angular deviation from the exact Σ = 5 orientation relationship. As a result, these observations and analysis suggest a crucial role for secondary grain boundary dislocations in dictating the length-scale of grain boundary facets, a consideration which has not been included in prior analyses of facet evolution and equilibrium facet length.« less

Defect character at grain boundary facet junctions: Analysis of an asymmetric Σ = 5 grain boundary in Fe

DOE PAGES

Medlin, D. L.; Hattar, K.; Zimmerman, J. A.; ...

2016-11-16

Grain boundaries often develop faceted morphologies in systems for which the interfacial free energy depends on the boundary inclination. Although the mesoscale thermodynamic basis for such morphological evolution has been extensively studied, the influence of line defects, such as secondary grain boundary dislocations, on the facet configurations has not been thoroughly explored. In this paper, through a combination of atomistic simulations and electron microscopic observations, we examine in detail the structure of an asymmetric Σ = 5 [001] grain boundary in well-annealed, body-centered cubic (BCC) Fe. The observed boundary forms with a hill-and-valley morphology composed of nanoscale {310} and {210}more » facets. Our analysis clarifies the atomic structure of the {310}/{210} facet junctions and identifies the presence of an array of secondary grain boundary dislocations that are localized to these junctions. Analysis of the Burgers vectors of the grain boundary dislocations, which are of type (1/5)<310> and (1/5)<120>, shows that the defect density is consistent with that required to accommodate a small observed angular deviation from the exact Σ = 5 orientation relationship. As a result, these observations and analysis suggest a crucial role for secondary grain boundary dislocations in dictating the length-scale of grain boundary facets, a consideration which has not been included in prior analyses of facet evolution and equilibrium facet length.« less

Correlation between soil physicochemical properties and vegetation parameters in secondary tropical forest in Sabal, Sarawak, Malaysia

NASA Astrophysics Data System (ADS)

Karyati, K.; Ipor, I. B.; Jusoh, I.; Wasli, M. E.

2018-04-01

The tree growth is influenced by soil morphological and physicochemical properties in the site. The purpose of this study was to describe correlation between soil properties under various stage secondary forests and vegetation parameters, such as floristic structure parameters and floristic diversity indices. The vegetation surveys were conducted in 5, 10, and 20 years old at secondary tropical forests in Sarawak, Malaysia. Nine sub plots sized 20 m × 20 m were established within each study site. The Pearson analysis showed that soil physicochemical properties were significantly correlated to floristic structure parameters and floristic diversity indices. The result of PCA clarified the correlation among most important soil properties, floristic structure parameters, and floristic diversity indices. The PC1 represented cation retention capacity and soil texture which were little affected by the fallow age and its also were correlated by floristic structure and diversity. The PC2 was linked to the levels of soil acidity. This property reflected the remnant effects of ash addition and fallow duration, and the significant correlation were showed among pH (H2O), floristic structure and diversity. The PC3 represented the soil compactness. The soil hardness could be influenced by fallow period and it was also correlated by floristic structure.

Simulation of unsteady state performance of a secondary air system by the 1D-3D-Structure coupled method

NASA Astrophysics Data System (ADS)

Wu, Hong; Li, Peng; Li, Yulong

2016-02-01

This paper describes the calculation method for unsteady state conditions in the secondary air systems in gas turbines. The 1D-3D-Structure coupled method was applied. A 1D code was used to model the standard components that have typical geometric characteristics. Their flow and heat transfer were described by empirical correlations based on experimental data or CFD calculations. A 3D code was used to model the non-standard components that cannot be described by typical geometric languages, while a finite element analysis was carried out to compute the structural deformation and heat conduction at certain important positions. These codes were coupled through their interfaces. Thus, the changes in heat transfer and structure and their interactions caused by exterior disturbances can be reflected. The results of the coupling method in an unsteady state showed an apparent deviation from the existing data, while the results in the steady state were highly consistent with the existing data. The difference in the results in the unsteady state was caused primarily by structural deformation that cannot be predicted by the 1D method. Thus, in order to obtain the unsteady state performance of a secondary air system more accurately and efficiently, the 1D-3D-Structure coupled method should be used.

Hydrophobic cluster analysis of G protein-coupled receptors: a powerful tool to derive structural and functional information from 2D-representation of protein sequences.

PubMed

Lentes, K U; Mathieu, E; Bischoff, R; Rasmussen, U B; Pavirani, A

1993-01-01

Current methods for comparative analyses of protein sequences are 1D-alignments of amino acid sequences based on the maximization of amino acid identity (homology) and the prediction of secondary structure elements. This method has a major drawback once the amino acid identity drops below 20-25%, since maximization of a homology score does not take into account any structural information. A new technique called Hydrophobic Cluster Analysis (HCA) has been developed by Lemesle-Varloot et al. (Biochimie 72, 555-574), 1990). This consists of comparing several sequences simultaneously and combining homology detection with secondary structure analysis. HCA is primarily based on the detection and comparison of structural segments constituting the hydrophobic core of globular protein domains, with or without transmembrane domains. We have applied HCA to the analysis of different families of G-protein coupled receptors, such as catecholamine receptors as well as peptide hormone receptors. Utilizing HCA the thrombin receptor, a new and as yet unique member of the family of G-protein coupled receptors, can be clearly classified as being closely related to the family of neuropeptide receptors rather than to the catecholamine receptors for which the shape of the hydrophobic clusters and the length of their third cytoplasmic loop are very different. Furthermore, the potential of HCA to predict relationships between new putative and already characterized members of this family of receptors will be presented.

On the secondary eyewall formation of Hurricane Edouard (2014)

PubMed Central

Abarca, Sergio F.; Montgomery, Michael T.; Braun, Scott A.; Dunion, Jason

2018-01-01

A first observationally-based estimation of departures from gradient wind balance during secondary eyewall formation is presented. The study is based on the Atlantic Hurricane Edouard (2014). This storm was observed during the National Aeronautics and Space Administration’s (NASA) Hurricane and Severe Storm Sentinel (HS3) experiment, a field campaign conducted in collaboration with the National Oceanic and Atmospheric Administration (NOAA). A total of 135 dropsondes are analyzed in two separate time periods: one named the secondary eyewall formation period and the other one referred to as the decaying-double eyewalled storm period. During the secondary eyewall formation period, a time when the storm was observed to have only one eyewall, the diagnosed agradient force has a secondary maxima that coincides with the radial location of the secondary eyewall observed in the second period of study. The maximum spin up tendency of the radial influx of absolute vertical vorticity is within the boundary layer in the region of the eyewall of the storm and the spin up tendency structure elongates radially outward into the secondary region of supergradient wind, where the secondary wind maxima is observed in the second period of study. An analysis of the boundary-layer averaged vertical structure of equivalent potential temperature reveals a conditionally unstable environment in the secondary eyewall formation region. These findings support the hypothesis that deep convective activity in this region contributed to spin up of the boundary layer tangential winds and the formation of a secondary eyewall that is observed during the decaying-double eyewalled storm period. PMID:29651170

On the Secondary Eyewall Formation of Hurricane Edouard (2014)

NASA Technical Reports Server (NTRS)

Abarca, Sergio F.; Montgomery, Michael T.; Braun, Scott A.; Dunion, Jason

2016-01-01

A first observationally-based estimation of departures from gradient wind balance during secondary eyewall formation is presented. The study is based on the Atlantic Hurricane Edouard (2014). This storm was observed during the National Aeronautics and Space Administrations (NASA) Hurricane and Severe Storm Sentinel (HS3) experiment, a field campaign conducted in collaboration with the National Oceanic and Atmospheric Administration (NOAA). A total of 135 dropsondes are analyzed in two separate time periods: one named the secondary eyewall formation period and the other one referred to as the decaying-double eyewalled storm period. During the secondary eyewall formation period, a time when the storm was observed to have only one eyewall, the diagnosed agradient force has a secondary maxima that coincides with the radial location of the secondary eyewall observed in the second period of study. The maximum spin up tendency of the radial influx of absolute vertical vorticity is within the boundary layer in the region of the eyewall of the storm and the spin up tendency structure elongates radially outward into the secondary region of supergradient wind, where the secondary wind maxima is observed in the second period of study. An analysis of the boundary layer averaged vertical structure of equivalent potential temperature reveals a conditionally unstable environment in the secondary eyewall formation region. These findings support the hypothesis that deep convective activity in this region contributed to spin up of the boundary layer tangential winds and the formation of a secondary eyewall that is observed during the decaying-double eyewalled storm period.

On the secondary eyewall formation of Hurricane Edouard (2014).

PubMed

Abarca, Sergio F; Montgomery, Michael T; Braun, Scott A; Dunion, Jason

2016-09-01

A first observationally-based estimation of departures from gradient wind balance during secondary eyewall formation is presented. The study is based on the Atlantic Hurricane Edouard (2014). This storm was observed during the National Aeronautics and Space Administration's (NASA) Hurricane and Severe Storm Sentinel (HS3) experiment, a field campaign conducted in collaboration with the National Oceanic and Atmospheric Administration (NOAA). A total of 135 dropsondes are analyzed in two separate time periods: one named the secondary eyewall formation period and the other one referred to as the decaying-double eyewalled storm period. During the secondary eyewall formation period, a time when the storm was observed to have only one eyewall, the diagnosed agradient force has a secondary maxima that coincides with the radial location of the secondary eyewall observed in the second period of study. The maximum spin up tendency of the radial influx of absolute vertical vorticity is within the boundary layer in the region of the eyewall of the storm and the spin up tendency structure elongates radially outward into the secondary region of supergradient wind, where the secondary wind maxima is observed in the second period of study. An analysis of the boundary-layer averaged vertical structure of equivalent potential temperature reveals a conditionally unstable environment in the secondary eyewall formation region. These findings support the hypothesis that deep convective activity in this region contributed to spin up of the boundary layer tangential winds and the formation of a secondary eyewall that is observed during the decaying-double eyewalled storm period.

Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends.

PubMed

Chuzhanova, Nadia; Abeysinghe, Shaun S; Krawczak, Michael; Cooper, David N

2003-09-01

Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions. Copyright 2003 Wiley-Liss, Inc.

Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

PubMed Central

Hong, Mei

2016-01-01

We have determined refined multidimensional chemical shift ranges for intra-residue correlations (13C–13C, 15N–13C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ~94 % of the 13C NMR data and almost all 15N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the 13C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided command-line Python script (PLUQin), which should be useful in protein structure determination. The refined chemical shift distributions are utilized in a simple quality test (SQAT) that should be applied to new protein NMR data before deposition in a databank, and they could benefit many other chemical-shift based tools. PMID:26787537

Dyeing regions of oxidative hair dyes in human hair investigated by nanoscale secondary ion mass spectrometry.

PubMed

Kojima, Toru; Yamada, Hiromi; Yamamoto, Toshihiko; Matsushita, Yasuyuki; Fukushima, Kazuhiko

2013-06-01

To develop more effective oxidative hair coloring products, it is important to understand the localization of colored chromophores, which are formed from oxidative dyes, in the fine structure of hair. However, the dyeing regions of oxidative hair dyes in the fine structure of hair have not been extensively examined. In this study, we investigated the distribution and localization of colored chromophores formed by an oxidative hair coloring product in the fine structure of human hair by using a stable isotope-labeled oxidative dye with nanoscale secondary ion mass spectrometry (NanoSIMS). First, formation of the colored chromophore from a deuterium-labeled oxidative dye was examined by visible spectra similarly to a study of its formation using nonlabeled oxidative dye. Furthermore, the formation of binuclear indo dye containing deuterium in its chemical structure was confirmed using time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis. As a result of the NanoSIMS image on a cross-sectional dyed hair, although deuterium ions were detected in whole hair cross-section, quite a few of them were detected at particulate regions. These particulate regions of the dyed black hair in which deuterium ions were intensely detected were identified as melanin granules, by comparing the dyeing behaviors of black and white hair. NanoSIMS analysis revealed that melanin granules of black human hair are important dyeing regions in oxidative hair coloring. Copyright © 2013 Elsevier B.V. All rights reserved.

Track structure in radiation biology: theory and applications.

PubMed

Nikjoo, H; Uehara, S; Wilson, W E; Hoshi, M; Goodhead, D T

1998-04-01

A brief review is presented of the basic concepts in track structure and the relative merit of various theoretical approaches adopted in Monte-Carlo track-structure codes are examined. In the second part of the paper, a formal cluster analysis is introduced to calculate cluster-distance distributions. Total experimental ionization cross-sections were least-square fitted and compared with the calculation by various theoretical methods. Monte-Carlo track-structure code Kurbuc was used to examine and compare the spectrum of the secondary electrons generated by using functions given by Born-Bethe, Jain-Khare, Gryzinsky, Kim-Rudd, Mott and Vriens' theories. The cluster analysis in track structure was carried out using the k-means method and Hartigan algorithm. Data are presented on experimental and calculated total ionization cross-sections: inverse mean free path (IMFP) as a function of electron energy used in Monte-Carlo track-structure codes; the spectrum of secondary electrons generated by different functions for 500 eV primary electrons; cluster analysis for 4 MeV and 20 MeV alpha-particles in terms of the frequency of total cluster energy to the root-mean-square (rms) radius of the cluster and differential distance distributions for a pair of clusters; and finally relative frequency distribution for energy deposited in DNA, single-strand break and double-strand breaks for 10MeV/u protons, alpha-particles and carbon ions. There are a number of Monte-Carlo track-structure codes that have been developed independently and the bench-marking presented in this paper allows a better choice of the theoretical method adopted in a track-structure code to be made. A systematic bench-marking of cross-sections and spectra of the secondary electrons shows differences between the codes at atomic level, but such differences are not significant in biophysical modelling at the macromolecular level. Clustered-damage evaluation shows: that a substantial proportion of dose ( 30%) is deposited by low-energy electrons; the majority of DNA damage lesions are of simple type; the complexity of damage increases with increased LET, while the total yield of strand breaks remains constant; and at high LET values nearly 70% of all double-strand breaks are of complex type.

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.

Influence of Professional Preparation and Class Structure on HIV, STD, and Pregnancy Prevention Education

ERIC Educational Resources Information Center

Rhodes, Darson L.; Jozkowski, Kristen N.; Hammig, Bart J.; Ogletree, Roberta J.; Fogarty, Erin C.

2014-01-01

Objective: The purpose of this study was to determine if education about human immunodeficiency virus (HIV)/sexually transmitted disease (STD) and pregnancy prevention is dependent on professional preparation and/or class structure. Design: A secondary data analysis of the 2006 School Health Policies and Programmes Study (SHPPS) was conducted.…

[Structural recovering in Andean successional forests from Porce (Antioquia, Colombia)].

PubMed

Yepes, Adriana P; del Valle, Jorge I; Jaramillo, Sandra L; Orrego, Sergio A

2010-03-01

Places subjected to natural or human disturbance can recover forest through an ecological process called secondary succession. Tropical succession is affected by factors such as disturbances, distance from original forest, surface configuration and local climate. These factors determine the composition of species and the time trend of the succession itself. We studied succession in soils used for cattle ranching over various decades in the Porce Region of Colombia (Andean Colombian forests). A set of twenty five permanent plots was measured, including nine plots (20 x 50 m) in primary forests and sixteen (20 x 25 m) in secondary forests. All trees with diameter > or =1.0 cm were measured. We analyzed stem density, basal area, above-ground biomass and species richness, in a successional process of ca. 43 years, and in primary forests. The secondary forests' age was estimated in previous studies, using radiocarbon dating, aerial photographs and a high-resolution satellite image analysis (7 to >43 years). In total, 1,143 and 1,766 stems were measured in primary and secondary forests, respectively. Basal area (5.7 to 85.4 m2 ha(-1)), above-ground biomass (19.1 to 1,011.5 t ha(-1)) and species richness (4 to 69) directly increased with site age, while steam density decreased (3,180 to 590). Diametric distributions were "J-inverted" for primary forests and even-aged size-class structures for secondary forests. Three species of palms were abundant and exclusive in old secondary forests and primary forests: Oenocarpus mapora, Euterpe precatoria and Oenocarpus bataua. These palms happened in cohorts after forest disturbances. Secondary forest structure was 40% in more than 43 years of forest succession and indicate that many factors are interacting and affecting the forests succession in the area (e.g. agriculture, cattle ranching, mining, etc.).

Korean EFL Teachers' Perceptions of the Impact of EFL Teacher Education upon Their Classroom Teaching Practices

ERIC Educational Resources Information Center

Yook, Cheongmin; Lee, Yong-hun

2016-01-01

This study employed qualitative data collection and analysis methods to investigate the influence of English as a foreign language teacher education programme on Korean teachers' classroom teaching practices. Six in-service secondary-school teachers participated in semi-structured interviews. Thematic analysis was applied to the data collected…

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

Surface topography, nano-mechanics and secondary structure of wheat gluten pretreated by alternate dual-frequency ultrasound and the correlation to enzymolysis.

PubMed

Zhang, Yanyan; Wang, Bei; Zhou, Cunshan; Atungulu, Griffiths G; Xu, Kangkang; Ma, Haile; Ye, Xiaofei; Abdualrahman, Mohammed A Y

2016-07-01

The effects of alternate dual-frequency ultrasound (ADFU) pretreatment on the degree of hydrolysis (DH) of wheat gluten (WG) and angiotensin I-converting enzyme (ACE) inhibitory activity were investigated in this research. The surface topography, nano-mechanics and secondary structure of WG were also determined using atomic force microscope (AFM) and circular dichroism (CD). The correlations of ACE inhibitory activity and DH with surface topography, nano-mechanics and secondary structure of WG were determined using Pearson's correlation analysis. The results showed that with an increase in either pretreatment duration or power, the ACE inhibitory activity of the hydrolysate also increases, reaching maximum at 10 min and 150 W/L, respectively, and then decreases thereafter. Similarly, AFM analysis showed that as the pretreatment duration or power increases, the surface roughness also increase and again a decrease occurs thereafter. As the pretreatment duration or power increased, the Young's modulus and adhesion of WG also increased and then declined. Young's modulus and adhesions average values were compared with ACE inhibitory activity reversely. The result of the CD spectra analysis exhibited losses in the relative percentage of α-helix of WG. Pearson's correlation analysis showed that the average values of Young's modulus and the relative percentage of α-helix correlated with ACE inhibitory activity of the hydrolysates linearly and significantly (P<0.05); the relative percentage of β-sheet correlated linearly with DH of WG significantly (P<0.05). In conclusion, ADFU pretreatment is an efficient method in proteolysis due to its physical and chemical effect on the Young's modulus, α-helix and β-sheet of WG. Copyright © 2015 Elsevier B.V. All rights reserved.

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

How is flow experienced and by whom? Testing flow among occupations.

PubMed

Llorens, Susana; Salanova, Marisa; Rodríguez, Alma M

2013-04-01

The aims of this paper are to test (1) the factorial structure of the frequency of flow experience at work; (2) the flow analysis model in work settings by differentiating the frequency of flow and the frequency of its prerequisites; and (3) whether there are significant differences in the frequency of flow experience depending on the occupation. A retrospective study among 957 employees (474 tile workers and 483 secondary school teachers) using multigroup confirmatory factorial analyses and multiple analyses of variance suggested that on the basis of the flow analysis model in work settings, (1) the frequency of flow experience has a two-factor structure (enjoyment and absorption); (2) the frequency of flow experience at work is produced when both challenge and skills are high and balanced; and (3) secondary school teachers experience flow more frequently than tile workers. Copyright © 2012 John Wiley & Sons, Ltd.

Comparison of red blood cells from gastric cancer patients and healthy persons using FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Liu, Hui; Su, Qinglong; Sheng, Daping; Zheng, Wei; Wang, Xin

2017-02-01

In this paper, FTIR spectroscopy was used to compare gastric cancer patients' red blood cells (RBCs) with healthy persons' RBCs. IR spectra were acquired with high resolution. The A1653/A1543 (the protein secondary structures), A1543/A2958 (the relative content of proteins and lipids), A1106/A1166 (the structure and content changes of sugars) and A1543/A1106 (the relative content of proteins and sugars) ratios of gastric cancer patients' RBCs were significantly different from those of healthy persons' RBCs. Curve fitting results showed that the protein secondary structures and sugars' structures had differences between gastric cancer patients' and healthy persons' RBCs. Additionally, FTIR spectroscopy could obtain 95% sensitivity, 70% specificity, 84.2% accuracy and 80.9% positive predictive value in combination with canconical discriminant analysis. The above results indicate FTIR spectroscopy may be useful for diagnosing gastric cancer.

Discovery of an Unexplored Protein Structural Scaffold of Serine Protease from Big Blue Octopus (Octopus cyanea): A New Prospective Lead Molecule.

PubMed

Panda, Subhamay; Kumari, Leena

2017-01-01

Serine proteases are a group of enzymes that hydrolyses the peptide bonds in proteins. In mammals, these enzymes help in the regulation of several major physiological functions such as digestion, blood clotting, responses of immune system, reproductive functions and the complement system. Serine proteases obtained from the venom of Octopodidae family is a relatively unexplored area of research. In the present work, we tried to effectively utilize comparative composite molecular modeling technique. Our key aim was to propose the first molecular model structure of unexplored serine protease 5 derived from big blue octopus. The other objective of this study was to analyze the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the aid of different bioinformatic tools. In the present study, molecular model has been generated with the help of I-TASSER suite. Afterwards the refined structural model was validated with standard methods. For functional annotation of protein molecule we used Protein Information Resource (PIR) database. Serine protease 5 of big blue octopus was analyzed with different bioinformatical algorithms for the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) were determined using the COACH program. The molecular model data in cooperation to other pertinent post model analysis data put forward molecular insight to proteolytic activity of serine protease 5, which helps in the clear understanding of procoagulant and anticoagulant characteristics of this natural lead molecule. Our approach was to investigate the octopus venom protein as a whole or a part of their structure that may result in the development of new lead molecule. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Significant Natural Product Biosynthetic Potential of Actinorhizal Symbionts of the Genus Frankia, as Revealed by Comparative Genomic and Proteomic Analyses▿

PubMed Central

Udwary, Daniel W.; Gontang, Erin A.; Jones, Adam C.; Jones, Carla S.; Schultz, Andrew W.; Winter, Jaclyn M.; Yang, Jane Y.; Beauchemin, Nicholas; Capson, Todd L.; Clark, Benjamin R.; Esquenazi, Eduardo; Eustáquio, Alessandra S.; Freel, Kelle; Gerwick, Lena; Gerwick, William H.; Gonzalez, David; Liu, Wei-Ting; Malloy, Karla L.; Maloney, Katherine N.; Nett, Markus; Nunnery, Joshawna K.; Penn, Kevin; Prieto-Davo, Alejandra; Simmons, Thomas L.; Weitz, Sara; Wilson, Micheal C.; Tisa, Louis S.; Dorrestein, Pieter C.; Moore, Bradley S.

2011-01-01

Bacteria of the genus Frankia are mycelium-forming actinomycetes that are found as nitrogen-fixing facultative symbionts of actinorhizal plants. Although soil-dwelling actinomycetes are well-known producers of bioactive compounds, the genus Frankia has largely gone uninvestigated for this potential. Bioinformatic analysis of the genome sequences of Frankia strains ACN14a, CcI3, and EAN1pec revealed an unexpected number of secondary metabolic biosynthesis gene clusters. Our analysis led to the identification of at least 65 biosynthetic gene clusters, the vast majority of which appear to be unique and for which products have not been observed or characterized. More than 25 secondary metabolite structures or structure fragments were predicted, and these are expected to include cyclic peptides, siderophores, pigments, signaling molecules, and specialized lipids. Outside the hopanoid gene locus, no cluster could be convincingly demonstrated to be responsible for the few secondary metabolites previously isolated from other Frankia strains. Few clusters were shared among the three species, demonstrating species-specific biosynthetic diversity. Proteomic analysis of Frankia sp. strains CcI3 and EAN1pec showed that significant and diverse secondary metabolic activity was expressed in laboratory cultures. In addition, several prominent signals in the mass range of peptide natural products were observed in Frankia sp. CcI3 by intact-cell matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). This work supports the value of bioinformatic investigation in natural products biosynthesis using genomic information and presents a clear roadmap for natural products discovery in the Frankia genus. PMID:21498757

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

PubMed

Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

2014-01-30

RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

Conformational analysis of α-helical polypeptide included L-proline residue by high-resolution solid-state NMR measurement and quantum chemical calculation

NASA Astrophysics Data System (ADS)

Souma, Hiroyuki; Shoji, Akira; Kurosu, Hiromichi

2008-10-01

We challenged the problem about the stabilization mechanism of an α-helix formation for polypeptides containing L-proline (Pro) residue. We computed the optimized structure of α-helical poly( L-alanine) molecules including a Pro residue, H-(Ala) 8-Pro-(Ala) 9-OH, based on the molecular orbital calculation with density functional theory, B3LYP/6-31G(d) and the 13C and 15N chemical shift values based on the GIAO-CHF method with B3LYP/6-311G(d,p), respectively. It was found that two kinds of optimized structures, 'Bent structure' and 'Included α-helix structure', were preferred structures in H-(Ala) 8-Pro-(Ala) 9-OH. In addition, based on the precise 13C and 15N chemical shift data of the simple model, we successfully analyzed the secondary structure of well-defined synthetic polypeptide H-(Phe-Leu-Ala) 3-Phe C-Pro-Ala N-(Phe-Leu-Ala) 2-OH (FLA-11P), the secondary structure of which was proven to the 'Included α-helix structure'.

Order within disorder: Aggrecan chondroitin sulphate-attachment region provides new structural insights into protein sequences classified as disordered

PubMed Central

Jowitt, Thomas A; Murdoch, Alan D; Baldock, Clair; Berry, Richard; Day, Joanna M; Hardingham, Timothy E

2010-01-01

Structural investigation of proteins containing large stretches of sequences without predicted secondary structure is the focus of much increased attention. Here, we have produced an unglycosylated 30 kDa peptide from the chondroitin sulphate (CS)-attachment region of human aggrecan (CS-peptide), which was predicted to be intrinsically disordered and compared its structure with the adjacent aggrecan G3 domain. Biophysical analyses, including analytical ultracentrifugation, light scattering, and circular dichroism showed that the CS-peptide had an elongated and stiffened conformation in contrast to the globular G3 domain. The results suggested that it contained significant secondary structure, which was sensitive to urea, and we propose that the CS-peptide forms an elongated wormlike molecule based on a dynamic range of energetically equivalent secondary structures stabilized by hydrogen bonds. The dimensions of the structure predicted from small-angle X-ray scattering analysis were compatible with EM images of fully glycosylated aggrecan and a partly glycosylated aggrecan CS2-G3 construct. The semiordered structure identified in CS-peptide was not predicted by common structural algorithms and identified a potentially distinct class of semiordered structure within sequences currently identified as disordered. Sequence comparisons suggested some evidence for comparable structures in proteins encoded by other genes (PRG4, MUC5B, and CBP). The function of these semiordered sequences may serve to spatially position attached folded modules and/or to present polypeptides for modification, such as glycosylation, and to provide templates for the multiple pleiotropic interactions proposed for disordered proteins. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20806220

Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking.

PubMed Central

Harris, M E; Kazantsev, A V; Chen, J L; Pace, N R

1997-01-01

Bacterial ribonuclease P (RNase P), an endonuclease involved in tRNA maturation, is a ribonucleoprotein containing a catalytic RNA. The secondary structure of this ribozyme is well-established, and a low-resolution model of the three-dimensional structure of the ribozyme-substrate complex has been proposed based on site-specific crosslinking and phylogenetic comparative data [Harris ME et al., 1994 EMBO J 13:3953-3963]. However, several substructures of that model were poorly constrained by the available data. In the present analysis, additional constraints between elements within the Escherichia coli RNase P RNA-pre-tRNA complex were determined by intra- and intermolecular crosslinking experiments. Circularly permuted RNase P RNAs were used to position an azidophenacyl photoactive crosslinking agent specifically at strategic sites within the ribozyme-substrate complex. Crosslink sites were mapped by primer extension and confirmed by analysis of the mobility of the crosslinked RNA lariats on denaturing acrylamide gels relative to circular and linear RNA standards. Crosslinked species generally retained significant catalytic activity, indicating that the results reflect the native ribozyme structure. The crosslinking results support the general configuration of the structure model and predicate new positions and orientations for helices that were previously poorly constrained by the data set. The expanded library of crosslinking constraints was used, together with secondary and tertiary structure identified by phylogenetic sequence comparisons, to refine significantly the model of RNase P RNA with bound substrate pre-tRNA. The crosslinking results and data from chemical-modification and mutational studies are discussed in the context of the current structural perspective on this ribozyme. PMID:9174092

Structure and orientation of interfacial proteins determined by sum frequency generation vibrational spectroscopy: method and application.

PubMed

Ye, Shuji; Wei, Feng; Li, Hongchun; Tian, Kangzhen; Luo, Yi

2013-01-01

In situ and real-time characterization of molecular structures and orientation of proteins at interfaces is essential to understand the nature of interfacial protein interaction. Such work will undoubtedly provide important clues to control biointerface in a desired manner. Sum frequency generation vibrational spectroscopy (SFG-VS) has been demonstrated to be a powerful technique to study the interfacial structures and interactions at the molecular level. This paper first systematically introduced the methods for the calculation of the Raman polarizability tensor, infrared transition dipole moment, and SFG molecular hyperpolarizability tensor elements of proteins/peptides with the secondary structures of α-helix, 310-helix, antiparallel β-sheet, and parallel β-sheet, as well as the methodology to determine the orientation of interfacial protein secondary structures using SFG amide I spectra. After that, recent progresses on the determination of protein structure and orientation at different interfaces by SFG-VS were then reviewed, which provides a molecular-level understanding of the structures and interactions of interfacial proteins, specially understanding the nature of driving force behind such interactions. Although this review has focused on analysis of amide I spectra, it will be expected to offer a basic idea for the spectral analysis of amide III SFG signals and other complicated molecular systems such as RNA and DNA. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

Changes in the myosin secondary structure and shrimp surimi gel strength induced by dense phase carbon dioxide.

PubMed

Guo, Minghui; Liu, Shucheng; Ismail, Marliya; Farid, Mohammed M; Ji, Hongwu; Mao, Weijie; Gao, Jing; Li, Chengyong

2017-07-15

Dense phase carbon dioxide (DPCD) could induce protein conformation changes. Myosin and shrimp surimi from Litopenaeus vannamei were treated with DPCD at 5-25MPa and 40-60°C for 20min. Myosin secondary structure was investigated by circular dichroism and shrimp surimi gel strength was determined using textural analysis to develop correlations between them. DPCD had a greater effect on secondary structure and gel strength than heating. With increasing pressure and temperature, the α-helix content of DPCD-treated myosin decreased, while the β-sheet, β-turn and random coil contents increased, and the shrimp surimi gel strength increased. The α-helix content was negatively correlated with gel strength, while the β-sheet, β-turn and random coil contents were positively correlated with gel strength. Therefore, when DPCD induced myosin to form a gel, the α-helix of myosin was unfolded and gradually converted to a β-sheet. Such transformations led to protein-protein interactions and cross-linking, which formed a three-dimensional network to enhance the gel strength. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural changes in gluten protein structure after addition of emulsifier. A Raman spectroscopy study

NASA Astrophysics Data System (ADS)

Ferrer, Evelina G.; Gómez, Analía V.; Añón, María C.; Puppo, María C.

2011-06-01

Food protein product, gluten protein, was chemically modified by varying levels of sodium stearoyl lactylate (SSL); and the extent of modifications (secondary and tertiary structures) of this protein was analyzed by using Raman spectroscopy. Analysis of the Amide I band showed an increase in its intensity mainly after the addition of the 0.25% of SSL to wheat flour to produced modified gluten protein, pointing the formation of a more ordered structure. Side chain vibrations also confirmed the observed changes.

Adaptation and validation of the Spanish version of the Dieting Peer Competitiveness Scale to adolescents of both genders.

PubMed

Pamies-Aubalat, Lidia; Quiles-Marcos, Yolanda; Núñez-Núñez, Rosa M

2013-12-01

This study examined the Dieting Peer Competitiveness Scale; it is an instrument for evaluating this social comparison in young people. This instrumental study has two aims: The objective of the first aim was to present preliminary psychometric data from the Spanish version of the Dieting Peer Competitiveness Scale, including statistical item analysis, research about this instrument's internal structure, and a reliability analysis, from a sample of 1067 secondary school adolescents. The second objective of the study corresponds to confirmatory factor analysis of the scale's internal structure, as well as analysis for evidence of validity from a sample of 1075 adolescents.

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

Role of tryptophan 95 in substrate specificity and structural stability of Sulfolobus solfataricus alcohol dehydrogenase.

PubMed

Pennacchio, Angela; Esposito, Luciana; Zagari, Adriana; Rossi, Mosè; Raia, Carlo A

2009-09-01

A mutant of the thermostable NAD(+)-dependent (S)-stereospecific alcohol dehydrogenase from Sulfolobus solfataricus (SsADH) which has a single substitution, Trp95Leu, located at the substrate binding pocket, was fully characterized to ascertain the role of Trp95 in discriminating between chiral secondary alcohols suggested by the wild-type SsADH crystallographic structure. The Trp95Leu mutant displays no apparent activity with short-chain primary and secondary alcohols and poor activity with aromatic substrates and coenzyme. Moreover, the Trp --> Leu substitution affects the structural stability of the archaeal ADH, decreasing its thermal stability without relevant changes in secondary structure. The double mutant Trp95Leu/Asn249Tyr was also purified to assist in crystallographic analysis. This mutant exhibits higher activity but decreased affinity toward aliphatic alcohols, aldehydes as well as NAD(+) and NADH compared to the wild-type enzyme. The crystal structure of the Trp95Leu/Asn249Tyr mutant apo form, determined at 2.0 A resolution, reveals a large local rearrangement of the substrate site with dramatic consequences. The Leu95 side-chain conformation points away from the catalytic metal center and the widening of the substrate site is partially counteracted by a concomitant change of Trp117 side chain conformation. Structural changes at the active site are consistent with the reduced activity on substrates and decreased coenzyme binding.

Developing Information Skills Test for Malaysian Youth Students Using Rasch Analysis

ERIC Educational Resources Information Center

Karim, Aidah Abdul; Shah, Parilah M.; Din, Rosseni; Ahmad, Mazalah; Lubis, Maimun Aqhsa

2014-01-01

This study explored the psychometric properties of a locally developed information skills test for youth students in Malaysia using Rasch analysis. The test was a combination of 24 structured and multiple choice items with a 4-point grading scale. The test was administered to 72 technical college students and 139 secondary school students. The…

Islam and Muslim Life in Current Bavarian Geography Textbooks

ERIC Educational Resources Information Center

Zecha, Stefanie; Popp, Stephan; Yasar, Aysun

2016-01-01

This paper investigates the Islam and Muslim life in German textbooks. The study is based on the analysis of current Geography textbooks in Bavarian secondary schools. As a first step, the authors developed a system for objective analysis of the textbooks that structures the content in categories. In a second step, the authors used the qualitative…

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.

Dynamic analysis of periodic vibration suppressors with multiple secondary oscillators

NASA Astrophysics Data System (ADS)

Ma, Jiangang; Sheng, Meiping; Guo, Zhiwei; Qin, Qi

2018-06-01

A periodic vibration suppressor with multiple secondary oscillators is examined in this paper to reduce the low-frequency vibration. The band-gap properties of infinite periodic structure and vibration transmission properties of finite periodic structure attached with secondary oscillators with arbitrary degree of freedom are thoroughly analyzed by the plane-wave-expansion method. A simply supported plate with a periodic rectangular array of vibration suppressors is considered. The dynamic model of this periodic structure is established and the equation of harmonic vibration response is theoretically derived and numerically examined. Compared with the simply supported plate without attached suppressors, the proposed plate can obtain better vibration control, and the vibration response can be effectively reduced in several frequency bands owing to the multiple band-gap property. By analyzing the modal properties of the periodic vibration suppressors, the relationship between modal frequencies and the parameters of spring stiffness and mass is established. With the numerical results, the design guidance of the locally resonant structure with multiple secondary oscillators is proposed to provide practical guidance for application. Finally, a practical periodic specimen is designed and fabricated, and then an experiment is carried out to validate the effectiveness of periodic suppressors in the reality. The results show that the experimental band gaps have a good coincidence with those in the theoretical model, and the low-frequency vibration of the plate with periodic suppressors can be effectively reduced in the tuned band gaps. Both the theoretical results and experimental results prove that the design method is effective and the structure with periodic suppressors has a promising application in engineering.

The secondary structure and the thermal unfolding parameters of the S-layer protein from Lactobacillus salivarius.

PubMed

Lighezan, Liliana; Georgieva, Ralitsa; Neagu, Adrian

2016-09-01

Surface layer (S-layer) proteins have been identified in the cell envelope of many organisms, such as bacteria and archaea. They self-assemble, forming monomolecular crystalline arrays. Isolated S-layer proteins are able to recrystallize into regular lattices, which proved useful in biotechnology. Here we investigate the structure and thermal unfolding of the S-layer protein isolated from Lactobacillus salivarius 16 strain of human origin. Using circular dichroism (CD) spectroscopy, and the software CDSSTR from DICHROWEB, CONTINLL from CDPro, as well as CDNN, we assess the fractions of the protein's secondary structural elements at temperatures ranging between 10 and 90 °C, and predict the tertiary class of the protein. To study the thermal unfolding of the protein, we analyze the temperature dependence of the CD signal in the far- and near-UV domains. Fitting the experimental data by two- and three-state models of thermal unfolding, we infer the midpoint temperatures, the temperature dependence of the changes in Gibbs free energy, enthalpy, and entropy of the unfolding transitions in standard conditions, and the temperature dependence of the equilibrium constant. We also estimate the changes in heat capacity at constant pressure in standard conditions. The results indicate that the thermal unfolding of the S-layer protein from L. salivarius is highly cooperative, since changes in the secondary and tertiary structures occur simultaneously. The thermodynamic analysis predicts a "cold" transition, at about -3 °C, of both the secondary and tertiary structures. Our findings may be important for the use of S-layer proteins in biotechnology and in biomedical applications.

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.

Two-dimensional cross correlation analysis of protein unfolding: Portrayal of the thermal denaturation of CMP kinases in the absence and presence of substrates

NASA Astrophysics Data System (ADS)

Schultz, Christian P.; Bârzu, Octavian; Mantsch, Henry H.

2000-03-01

The functional role of CMP kinases is to regenerate mono-phosphate nucleotides in cells by transferring phosphate residues from tri-phosphorylated nucleotides to monophosphorylated nucleotides. These enzymes possess two binding sites and maintain a highly conserved secondary structure. They are essential for cell survival. Herein we compare the infrared spectra of two similar, but not identical enzymes, the CMP kinases from Escherichia coli and Bacillus subtilis. A two-dimensional cross correlation analysis of the infrared spectra reveals differences in the denaturation behavior of the two proteins. Different secondary structure elements show different time-delayed or advanced unfolding events in the two enzymes. When bound to the active sites, the two nucleotide-substrates CMP and ATP exert a stabilizing effect on the structure of both proteins. The changes observed upon thermal denaturation are different for the two enzymes. Model 2D correlations are used to simulate the different denaturation of the two enzymes. Thermal denaturation and aggregation can be distinguished as two processes separated in time.

Design Study of 8 Meter Monolithic Mirror UV/Optical Space Telescope

NASA Technical Reports Server (NTRS)

Stahl, H. Philip

2008-01-01

The planned Ares V launch vehicle with its 10 meter fairing shroud and 55,000 kg capacity to the Sun Earth L2 point enables entirely new classes of space telescopes. NASA MSFC has conducted a preliminary study that demonstrates the feasibility of launching a 6 to 8 meter class monolithic primary mirror telescope to Sun-Earth L2 using an Ares V. Specific technical areas studied included optical design; structural design/analysis including primary mirror support structure, sun shade and secondary mirror support structure; thermal analysis; launch vehicle performance and trajectory; spacecraft including structure, propulsion, GN&C, avionics, power systems and reaction wheels; operations and servicing; mass and power budgets; and system cost.

Realization and testing of a deployable space telescope based on tape springs

NASA Astrophysics Data System (ADS)

Lei, Wang; Li, Chuang; Zhong, Peifeng; Chong, Yaqin; Jing, Nan

2017-08-01

For its compact size and light weight, space telescope with deployable support structure for its secondary mirror is very suitable as an optical payload for a nanosatellite or a cubesat. Firstly the realization of a prototype deployable space telescope based on tape springs is introduced in this paper. The deployable telescope is composed of primary mirror assembly, secondary mirror assembly, 6 foldable tape springs to support the secondary mirror assembly, deployable baffle, aft optic components, and a set of lock-released devices based on shape memory alloy, etc. Then the deployment errors of the secondary mirror are measured with three-coordinate measuring machine to examine the alignment accuracy between the primary mirror and the deployed secondary mirror. Finally modal identification is completed for the telescope in deployment state to investigate its dynamic behavior with impact hammer testing. The results of the experimental modal identification agree with those from finite element analysis well.

R-chie: a web server and R package for visualizing RNA secondary structures

PubMed Central

Lai, Daniel; Proctor, Jeff R.; Zhu, Jing Yun A.; Meyer, Irmtraud M.

2012-01-01

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems. PMID:22434875

Framework for Structural Online Health Monitoring of Aging and Degradation of Secondary Systems due to some Aspects of Erosion

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

Gribok, Andrei; Patnaik, Sobhan; Williams, Christian

This report describes the current state of research related to critical aspects of erosion and selected aspects of degradation of secondary components in nuclear power plants. The report also proposes a framework for online health monitoring of aging and degradation of secondary components. The framework consists of an integrated multi-sensor modality system which can be used to monitor different piping configurations under different degradation conditions. The report analyses the currently known degradation mechanisms and available predictive models. Based on this analysis, the structural health monitoring framework is proposed. The Light Water Reactor Sustainability Program began to evaluate technologies that couldmore » be used to perform online monitoring of piping and other secondary system structural components in commercial NPPs. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real-time measurements, rather than at a pre-determined inspection interval. This transition to condition-based, risk informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for the majority of nuclear power generation costs. There is unanimous agreement between industry experts and academic researchers that identifying and prioritizing inspection locations in secondary piping systems (for example, in raw water piping or diesel piping) would eliminate many excessive in-service inspections. The proposed structural health monitoring framework takes aim at answering this challenge by combining long-range guided wave technologies with other monitoring techniques, which can significantly increase the inspection length and pinpoint the locations that degraded the most. More widely, the report suggests research efforts aimed at developing, validating, and deploying online corrosion monitoring techniques for complex geometries, which are pervasive in NPPs.« less

[Characteristics of soil macrofaunal community structure in secondary forest and forest plantations in western Qinling Mountains of Northwest China].

PubMed

Liu, Ji-Liang; Cao, Jing; Li, Shi-Jie; Pan, Chun-Lin; Pan, Cheng-Chen

2012-09-01

Long-term disturbance of human beings on secondary forest ecosystem would have profound impacts on belowground ecological processes, whereas the community structure and functional diversity of soil fauna would be sensitive to the changes of belowground ecological processes, with significance as an indicator of the changes. In this study, the method of hand-sorting was adopted to investigate the density of soil macrofaunal community in a secondary forest and the Pinus tabulaeformis, Larix kaempferi, Picea abie, and Picea asperata plantations of nearly 30 years old in Xiaolongshan forest area of western Qinling Mountains, and the PCA ordination and one-way ANOVA analysis were applied to analyze the community structure and trophic group composition of soil macrofauna in the five forest types. In the P. tabulaeformis and L. kaempferi plantations, the density of soil macrofaunal community was 3.0 and 2.1 times of that in the secondary forest, respectively, and the consumers/decomposers ratio of the community was obviously higher than that in the secondary forest. Among the plantations, P. tabulaeformis and L. kaempferi plantations had a significantly higher consumers/decomposers ratio of soil macrofaunal community than P. abies and P. asperata plantations. There was an obvious difference in community structure of soil macrofauna among the four plantations. The density of soil macrofaunal community in P. tabulaeformis and L. kaempferi plantations was 3.5 and 2.1 times higher than that in P. asperata plantation, respectively, whereas the group richness of soil macrofaunal community in P. tabulaeformis plantation was 1.5 times of that in P. abies and P. asperata plantations.

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

Structure and Absolute Configuration of Jurassic Polyketide-Derived Spiroborate Pigments Obtained from Microgram Quantities.

PubMed

Wolkenstein, Klaus; Sun, Han; Falk, Heinz; Griesinger, Christian

2015-10-28

Complete structural elucidation of natural products is often challenging due to structural complexity and limited availability. This is true for present-day secondary metabolites, but even more for exceptionally preserved secondary metabolites of ancient organisms that potentially provide insights into the evolutionary history of natural products. Here, we report the full structure and absolute configuration of the borolithochromes, enigmatic boron-containing pigments from a Jurassic putative red alga, from samples of less than 50 μg using microcryoprobe NMR, circular dichroism spectroscopy, and density functional theory calculations and reveal their polyketide origin. The pigments are identified as spiroborates with two pentacyclic sec-butyl-trihydroxy-methyl-benzo[gh]tetraphen-one ligands and less-substituted derivatives. The configuration of the sec-butyl group is found to be (S). Because the exceptional benzo[gh]tetraphene scaffold is otherwise only observed in the recently discovered polyketide clostrubin from a present-day Clostridium bacterium, the Jurassic borolithochromes now can be unambiguously linked to the modern polyketide, providing evidence that the fossil pigments are almost originally preserved secondary metabolites and suggesting that the pigments in fact may have been produced by an ancient bacterium. The borolithochromes differ fundamentally from previously described boronated polyketides and represent the first boronated aromatic polyketides found so far. Our results demonstrate the potential of microcryoprobe NMR in the analysis of previously little-explored secondary metabolites from ancient organisms and reveal the evolutionary significance of clostrubin-type polyketides.

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.

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

Data-directed RNA secondary structure prediction using probabilistic modeling

PubMed Central

Deng, Fei; Ledda, Mirko; Vaziri, Sana; Aviran, Sharon

2016-01-01

Structure dictates the function of many RNAs, but secondary RNA structure analysis is either labor intensive and costly or relies on computational predictions that are often inaccurate. These limitations are alleviated by integration of structure probing data into prediction algorithms. However, existing algorithms are optimized for a specific type of probing data. Recently, new chemistries combined with advances in sequencing have facilitated structure probing at unprecedented scale and sensitivity. These novel technologies and anticipated wealth of data highlight a need for algorithms that readily accommodate more complex and diverse input sources. We implemented and investigated a recently outlined probabilistic framework for RNA secondary structure prediction and extended it to accommodate further refinement of structural information. This framework utilizes direct likelihood-based calculations of pseudo-energy terms per considered structural context and can readily accommodate diverse data types and complex data dependencies. We use real data in conjunction with simulations to evaluate performances of several implementations and to show that proper integration of structural contexts can lead to improvements. Our tests also reveal discrepancies between real data and simulations, which we show can be alleviated by refined modeling. We then propose statistical preprocessing approaches to standardize data interpretation and integration into such a generic framework. We further systematically quantify the information content of data subsets, demonstrating that high reactivities are major drivers of SHAPE-directed predictions and that better understanding of less informative reactivities is key to further improvements. Finally, we provide evidence for the adaptive capability of our framework using mock probe simulations. PMID:27251549

A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

PubMed Central

Sturm, Marc; Quinten, Sascha; Huber, Christian G.; Kohlbacher, Oliver

2007-01-01

We propose a new model for predicting the retention time of oligonucleotides. The model is based on ν support vector regression using features derived from base sequence and predicted secondary structure of oligonucleotides. Because of the secondary structure information, the model is applicable even at relatively low temperatures where the secondary structure is not suppressed by thermal denaturing. This makes the prediction of oligonucleotide retention time for arbitrary temperatures possible, provided that the target temperature lies within the temperature range of the training data. We describe different possibilities of feature calculation from base sequence and secondary structure, present the results and compare our model to existing models. PMID:17567619

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.

VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program.

PubMed

Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid

2014-01-01

The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755.

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

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

Effect of structured physical activity on overall burden and transitions between states of major mobility disability in older persons: secondary analysis of a randomized trial

USDA-ARS?s Scientific Manuscript database

Background: The total time a patient is disabled likely has a greater influence on his or her quality of life than the initial occurrence of disability alone. Objective: To compare the effect of a long-term, structured physical activity program with that of a health education intervention on the pro...

School Structural Characteristics, Student Effort, Peer Associations, and Parental Involvement: The Influence of School- and Individual-Level Factors on Academic Achievement

ERIC Educational Resources Information Center

Stewart, Endya B.

2008-01-01

This research examines the extent to which individual-level and school structural variables are predictors of academic achievement among a sample of 10th grade students abstracted from the National Educational Longitudinal Study database. A secondary analysis of the data produced the following findings. The study results show that individual-level…

Chemical imaging of molecular changes in a hydrated single cell by dynamic secondary ion mass spectrometry and super-resolution microscopy

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

Hua, Xin; Szymanski, Craig; Wang, Zhaoying

2016-01-01

Chemical imaging of single cells is important in capturing biological dynamics. Single cell correlative imaging is realized between structured illumination microscopy (SIM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) using System for Analysis at the Liquid Vacuum Interface (SALVI), a multimodal microreactor. SIM characterized cells and guided subsequent ToF-SIMS analysis. Dynamic ToF-SIMS provided time- and space-resolved cell molecular mapping. Lipid fragments were identified in the hydrated cell membrane. Principal component analysis was used to elucidate chemical component differences among mouse lung cells that uptake zinc oxide nanoparticles. Our results provided submicron chemical spatial mapping for investigations of cell dynamics atmore » the molecular level.« less

Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11

PubMed Central

Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

2015-01-01

We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score=0.736 and RMSD=2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. PMID:26370505

Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.

PubMed

Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

2016-09-01

We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

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.

Teachers' Views on the Impact of Teacher-Student Relationships on School Dropout: A Bourdieusian Analysis of Misrecognition

ERIC Educational Resources Information Center

Nairz-Wirth, Erna; Feldmann, Klaus

2017-01-01

Drawing on Pierre Bourdieu's relational theory this paper shows that many teachers misrecognize the impact of teacher-student relationships on school dropout. The study is based on a series of 60 semi-structured interviews with teachers from Austrian secondary schools. The analysis of the empirical data reveals that many teachers attribute school…

Influence of Lanthanum on Solidification, Microstructure, and Mechanical Properties of Eutectic Al-Si Piston Alloy

NASA Astrophysics Data System (ADS)

Ahmad, R.; Asmael, M. B. A.

2016-07-01

The effects of Lanthanum (La) concentration on the solidification parameters of the α-Al, Al-Si, and Al-Cu phases and on the microstructure, tensile, and hardness properties of eutectic Al-Si-Cu-Mg alloy were systematically investigated. The solidification parameters were examined using computer-aided cooling curve thermal analysis (CA-CCTA). The cooling curve and microstructure analysis showed that La altered the Si structure. The nucleation and growth temperatures of eutectic Si decreased when 0.3 wt.% La was added, and a high depression temperature was obtained with 1.0 wt.% La. High amounts of La considerably modified the Si structure and decreased the area and aspect ratio by 69.9 and 51%, respectively. The thermal analysis result recorded a faster freezing time with the La addition and a 36% alteration in the secondary dendrite arm spacing. Two secondary or ternary La-rich intermetallic phases were formed with needle- and plate-like structures. Furthermore, the mechanical properties were investigated by hardness and tensile tests with different La concentrations. The addition of small amounts of La (0.1 wt.%) significantly improved the ultimate tensile strength and quality index of the Al-Si-Cu-Mg alloy. In addition, the hardness value of Al-11Si-Cu increased by 7-8% with the increasing amount of La added.

On the Surface Mapping using Individual Cluster Impacts

PubMed Central

Fernandez-Lima, F.A.; Eller, M.J.; DeBord, J.D.; Verkhoturov, S.V.; Della-Negra, S.; Schweikert, E.A.

2011-01-01

This paper describes the advantages of using single impacts of large cluster projectiles (e.g. C60 and Au400) for surface mapping and characterization. The analysis of co-emitted time-resolved photon spectra, electron distributions and characteristic secondary ions shows that they can be used as surface fingerprints for target composition, morphology and structure. Photon, electron and secondary ion emission increases with the projectile cluster size and energy. The observed, high abundant secondary ion emission makes cluster projectiles good candidates for surface mapping of atomic and fragment ions (e.g., yield >1 per nominal mass) and molecular ions (e.g., few tens of percent in the 500 < m/z < 1500 range). PMID:22393269

Depth distribution of secondary phases in kesterite Cu 2ZnSnS 4 by angle-resolved X-ray absorption spectroscopy

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

Just, J.; Lützenkirchen-Hecht, D.; Müller, O.

The depth distribution of secondary phases in the solar cell absorber material Cu 2ZnSnS 4 (CZTS) is quantitatively investigated using X-ray Absorption Near Edge Structure (XANES) analysis at the K-edge of sulfur at varying incidence angles. Varying information depths from several nanometers up to the full thickness is achieved. A quantitative profile of the phase distribution is obtained by a self-consistent fit of a multilayer model to the XANES spectra for different angles. Single step co-evaporated CZTS thin-films are found to exhibit zinc and copper sulfide secondary phases preferentially at the front or back interfaces of the film.

Depth distribution of secondary phases in kesterite Cu 2ZnSnS 4 by angle-resolved X-ray absorption spectroscopy

DOE PAGES

Just, J.; Lützenkirchen-Hecht, D.; Müller, O.; ...

2017-12-12

The depth distribution of secondary phases in the solar cell absorber material Cu 2ZnSnS 4 (CZTS) is quantitatively investigated using X-ray Absorption Near Edge Structure (XANES) analysis at the K-edge of sulfur at varying incidence angles. Varying information depths from several nanometers up to the full thickness is achieved. A quantitative profile of the phase distribution is obtained by a self-consistent fit of a multilayer model to the XANES spectra for different angles. Single step co-evaporated CZTS thin-films are found to exhibit zinc and copper sulfide secondary phases preferentially at the front or back interfaces of the film.

Static voltage distribution between turns of secondary winding of air-core spiral strip transformer and its application

NASA Astrophysics Data System (ADS)

Zhang, Hong-bo; Liu, Jin-liang; Cheng, Xin-bing; Zhang, Yu

2011-09-01

The static voltage distribution between winding turns has great impact on output characteristics and lifetime of the air-core spiral strip pulse transformer (ACSSPT). In this paper, winding inductance was calculated by electromagnetic theory, so that the static voltage distribution between turns of secondary winding of ACSSPT was analyzed conveniently. According to theoretical analysis, a voltage gradient because of the turn-to-turn capacitance was clearly noticeable across the ground turns. Simulation results of Pspice and CST EM Studio codes showed that the voltage distribution between turns of secondary winding had linear increments from the output turn to the ground turn. In experiment, the difference in increased voltage between the ground turns and the output turns of a 20-turns secondary winding is almost 50%, which is believed to be responsible for premature breakdown of the insulation, particularly between the ground turns. The experimental results demonstrated the theoretical analysis and simulation results, which had important value for stable and long lifetime ACSSPT design. A new ACSSPT with improved structure has been used successfully in intense electron beam accelerators steadily.

Impact of secondary generated minerals on toxic element immobilization for air pollution control fly ash of a municipal solid waste incinerator.

PubMed

Kitamura, Hiroki; Dahlan, Astryd Viandila; Tian, Yu; Shimaoka, Takayuki; Yamamoto, Takashi; Takahashi, Fumitake

2018-05-12

Impacts of secondary generated minerals on mineralogical and physical immobilization of toxic elements were investigated for chelate-treated air pollution control (APC) fly ash of a municipal solid waste incinerator. Scanning electron microscope (SEM) observation showed that ettringite was generated after the moistening treatment with/without chelate. Although ettringite can incorporate toxic elements into its structure, elemental analysis by energy dispersive X-ray could not find concentrated points of toxic elements in ettringite structure. This implies that mineralogical immobilization of toxic element by the encapsulation to ettringite structure seems to be limited. Physical immobilization was also investigated by SEM observation of the same APC fly ash particles before and after the moistening treatment. The transfer of soluble elements was inhibited only when insoluble minerals such as gypsum were generated and covered the surface of fly ash particles. Neoformed insoluble minerals prevented soluble elements from leaching and transfer. However, such physical immobilization seems to be limited because insoluble mineral formation with surface coverage was monitored only one time of more than 20 observations. Although uncertainty owing to limited samples with limited observations should be considered, this study concludes that mineralogical and physical immobilization of toxic elements by secondary minerals is limited although secondary minerals are always generated on the surface of APC fly ash particles during chelate treatment.

High pressure studies on structural and secondary relaxation dynamics in silyl derivative of D-glucose

NASA Astrophysics Data System (ADS)

Minecka, Aldona; Kamińska, Ewa; Tarnacka, Magdalena; Dzienia, Andrzej; Madejczyk, Olga; Waliłko, Patrycja; Kasprzycka, Anna; Kamiński, Kamil; Paluch, Marian

2017-08-01

In this paper, broadband dielectric spectroscopy was applied to investigate molecular dynamics of 1,2,3,4,6-penta-O-(trimethylsilyl)-D-glucopyranose (S-GLU) at ambient and elevated pressures. Our studies showed that apart from the structural relaxation, one well resolved asymmetric secondary process (initially labeled as β) is observed in the spectra measured at p = 0.1 MPa. Analysis with the use of the coupling model and criterion proposed by Ngai and Capaccioli indicated that the β-process in S-GLU is probably a Johari-Goldstein relaxation of intermolecular origin. Further high pressure experiments demonstrated that there are in fact two secondary processes contributing to the β-relaxation. Therefore, one can postulate that the coupling model is a necessary, but not sufficient criterion to identify the true nature of the given secondary relaxation process. The role of pressure experiments in better understanding of the molecular origin of local mobility seems to be much more important. Interestingly, our research also revealed that the structural relaxation in S-GLU is very sensitive to compression. It was reflected in an extremely high pressure coefficient of the glass transition temperature (dTg/dp = 412 K/GPa). According to the literature data, such a high value of dTg/dp has not been obtained so far for any H-bonded, van der Waals, or polymeric glass-formers.

Discrete Haar transform and protein structure.

PubMed

Morosetti, S

1997-12-01

The discrete Haar transform of the sequence of the backbone dihedral angles (phi and psi) was performed over a set of X-ray protein structures of high resolution from the Brookhaven Protein Data Bank. Afterwards, the new dihedral angles were calculated by the inverse transform, using a growing number of Haar functions, from the lower to the higher degree. New structures were obtained using these dihedral angles, with standard values for bond lengths and angles, and with omega = 0 degree. The reconstructed structures were compared with the experimental ones, and analyzed by visual inspection and statistical analysis. When half of the Haar coefficients were used, all the reconstructed structures were not yet collapsed to a tertiary folding, but they showed yet realized most of the secondary motifs. These results indicate a substantial separation of structural information in the space of Haar transform, with the secondary structural information mainly present in the Haar coefficients of lower degrees, and the tertiary one present in the higher degree coefficients. Because of this separation, the representation of the folded structures in the space of Haar transform seems a promising candidate to encompass the problem of premature convergence in genetic algorithms.

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.

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.

The Effect of a Helix-Coil Transition on the Extension Elasticity

NASA Astrophysics Data System (ADS)

Buhot, Arnaud; Halperin, Avi

2000-03-01

The secondary structure of a polymer affects its deformation behavior in accordance with the Le Chatelier principle. An important example of such secondary structure is the alpha helix encountered in polypeptides. Similar structure was recently proposed for PEO in aqueous media. Our discussion concerns the coupling of the cooperative helix-coil transition and the extension elasticity. In particular, we analyze the extension of a long single chain by use of optical tweezers or AFM. We consider chains that exist in the coil-state when unperturbed. The transition nevertheless occurs because the extension favors the low entropy helical state. As a result, the corresponding force law exhibits a plateau. The analysis of this situation involves two ingredients: (I) the stretching free energy penalty for a rod-coil mutiblock copolymer (II) the entropy associated with the possible placements of the rod and coil blocks.

Probing Conformational Change of Bovine Serum Albumin–Dextran Conjugates under Controlled Dry Heating

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

Xia, Shuqin; Li, Yunqi; Zhao, Qin

2015-04-29

The time-dependent conformational change of bovine serum album (BSA) during Maillard reaction with dextran under controlled dry heating has been studied by small-angle X-ray scattering, fluorescence spectroscopy, dynamic light scattering, and circular dichroism analysis. Through the research on the radii of gyration (R g), intrinsic fluorescence, and secondary structure, conjugates with dextran coating were found to inhibit BSA aggregation and preserve the secondary structure of native BSA against long-time heat treatment during Maillard reaction. The results suggested that the hydrophilic dextran was conjugated to the compact protein surface and enclosed it and more dextran chains were attached to BSA withmore » the increase of the heating time. The study presented here will be beneficial to the understanding of the conformational evolution of BSA molecules during the dry-heating Maillard reaction and to the control of the protein–polysaccharide conjugate structure.« less

Evidence For Rapid Spatiotemporal Changes in Genetic Structure of an Alien Whitefly During Initial Invasion

PubMed Central

Chu, Dong; Guo, Dong; Tao, Yunli; Jiang, Defeng; Li, Jie; Zhang, Youjun

2014-01-01

The sweetpotato whitefly Bemisia tabaci Q species is a recent invader and important pest of agricultural crops in China. This research tested the hypothesis that the Q populations that establish in agricultural fields in northern China each year are derived from multiple secondary introductions and/or local populations that overwinter in greenhouses (the pest cannot survive winters in the field in northern China). Here, we report the evidence that the Q populations in agricultural fields mainly derive from multiple secondary introductions. In addition, the common use of greenhouses during the winter in certain locations in northern China helps increase the genetic diversity and the genetic structure of the pest. The genetic structure information generated from this long-term and large-scale field analysis increases our understanding of B. tabaci Q as an invasive pest and has important implications for B. tabaci Q management. PMID:24637851

A general method for the purification of synthetic oligodeoxyribonucleotides containing strong secondary structure by reversed-phase high-performance liquid chromatography on PRP-1 resin.

PubMed

Germann, M W; Pon, R T; van de Sande, J H

1987-09-01

Synthetic 5'-dimethoxytritylated oligodeoxyribonucleotides, which contained strong secondary structure, were satisfactorily denatured and purified by reversed-phase HPLC on PRP-1 columns when strongly alkaline conditions (0.05 M NaOH) were employed. This procedure was suitable for the purification of hairpin structures, e.g., d(CG)nT4(CG)n (n = 4, 5, 6), and oligo(dG) sequences, e.g., d(G)24, as well as oligodeoxyribonucleotide probes which contained degenerate base sites. Oligodeoxyribonucleotides as long as 50 bases in length were purified. Recovery of injected oligonucleotides was typically 90% or better. The high capacity of the PRP-1 resin also allowed purification to be performed on a preparative scale (2-8 mg per injection). Enzymatic degradation and HPLC analysis indicated that no modification of the heterocyclic bases occurred under the alkaline conditions described.

Characterization of the amino acid contribution to the folding degree of proteins.

PubMed

Estrada, Ernesto

2004-03-01

The folding degree index (Estrada, Bioinformatics 2002;18:697-704) is extended to account for the contribution of amino acids to folding. First, the mathematical formalism for extending the folding degree index is presented. Then, the amino acid contributions to folding degree of several proteins are used to analyze its relation to secondary structure. The possibilities of using these contributions in helping or checking the assignation of secondary structure to amino acids are also introduced. The influence of external factors to the amino acids contribution to folding degree is studied through the temperature effect on ribonuclease A. Finally, the analysis of 3D protein similarity through the use of amino acid contributions to folding degree is studied by selecting a series of lysozymes. These results are compared to that obtained by sequence alignment (2D similarity) and 3D superposition of the structures, showing the uniqueness of the current approach. Copyright 2004 Wiley-Liss, Inc.

Advanced electron microscopy methods for the analysis of MgB2 superconductor

NASA Astrophysics Data System (ADS)

Birajdar, B.; Peranio, N.; Eibl, O.

2008-02-01

Advanced electron microscopy methods used for the analysis of superconducting MgB2 wires and tapes are described. The wires and tapes were prepared by the powder in tube method using different processing technologies and thoroughly characterised for their superconducting properties within the HIPERMAG project. Microstructure analysis on μm to nm length scales is necessary to understand the superconducting properties of MgB2. For the MgB2 phase analysis on μm scale an analytical SEM, and for the analysis on nm scale a energy-filtered STEM is used. Both the microscopes were equipped with EDX detector and field emission gun. Electron microscopy and spectroscopy of MgB2 is challenging because of the boron analysis, carbon and oxygen contamination, and the presence of large number of secondary phases. Advanced electron microscopy involves, combined SEM, EPMA and TEM analysis with artefact free sample preparation, elemental mapping and chemical quantification of point spectra. Details of the acquisition conditions and achieved accuracy are presented. Ex-situ wires show oxygen-free MgB2 colonies (a colony is a dense arrangement of several MgB2 grains) embedded in a porous and oxygen-rich matrix, introducing structural granularity. In comparison, in-situ wires are generally more dense, but show inhibited MgB2 phase formation with significantly higher fraction of B-rich secondary phases. SiC additives in the in-situ wires forms Mg2Si secondary phases. The advanced electron microscopy has been used to extract the microstructure parameters like colony size, B-rich secondary phase fraction, O mole fraction and MgB2 grain size, and establish a microstructure-critical current density model [1]. In summary, conventional secondary electron imaging in SEM and diffraction contrast imaging in the TEM are by far not sufficient and advanced electron microscopy methods are essential for the analysis of superconducting MgB2 wires and tapes.

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

FTIR studies of gluten matrix dehydration after fibre polysaccharide addition.

PubMed

Nawrocka, Agnieszka; Krekora, Magdalena; Niewiadomski, Zbigniew; Miś, Antoni

2018-06-30

FTIR spectroscopy was used to determine changes in secondary structure, as well as water state, in gluten and model doughs supplemented by four fibre polysaccharides (microcrystalline cellulose, inulin, apple pectin and citrus pectin). The gluten and model doughs were obtained from commercially available wheat gluten and model flour, respectively. The polysaccharides were used in five concentrations: 3%, 6%, 9%, 12% and 18%. Analysis of the FTIR spectra indicated that polysaccharides could be divided into two groups: first - microcrystalline cellulose and inulin, second - apple and citrus pectins that induced opposite structural changes. Changes in secondary structure concern mainly β-sheets and β-turns that form aggregated β-structures, suggesting dehydration of the gluten matrix as a result of competition for water between gluten proteins and polysaccharides. Moreover, the positive band at ca. 1226 cm -1 in the spectra of pectin-modified samples indicates formation of 'ether' type hydrogen bonds between gluten proteins and pectins. Copyright © 2018 Elsevier Ltd. All rights reserved.

MS/MS analysis and imaging of lipids across Drosophila brain using secondary ion mass spectrometry.

PubMed

Phan, Nhu T N; Munem, Marwa; Ewing, Andrew G; Fletcher, John S

2017-06-01

Lipids are abundant biomolecules performing central roles to maintain proper functioning of cells and biological bodies. Due to their highly complex composition, it is critical to obtain information of lipid structures in order to identify particular lipids which are relevant for a biological process or metabolic pathway under study. Among currently available molecular identification techniques, MS/MS in secondary ion mass spectrometry (SIMS) imaging has been of high interest in the bioanalytical community as it allows visualization of intact molecules in biological samples as well as elucidation of their chemical structures. However, there have been few applications using SIMS and MS/MS owing to instrumental challenges for this capability. We performed MS and MS/MS imaging to study the lipid structures of Drosophila brain using the J105 and 40-keV Ar 4000 + gas cluster ion source, with the novelty being the use of MS/MS SIMS analysis of intact lipids in the fly brain. Glycerophospholipids were identified by MS/MS profiling. MS/MS was also used to characterize diglyceride fragment ions and to identify them as triacylglyceride fragments. Moreover, MS/MS imaging offers a unique possibility for detailed elucidation of biomolecular distribution with high accuracy based on the ion images of its fragments. This is particularly useful in the presence of interferences which disturb the interpretation of biomolecular localization. Graphical abstract MS/MS was performed during time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis of Drosophila melongaster (fruit fly) to elucidate the structure and origin of different chemical species in the brain including a range of different phospholipid classes (PC, PI, PE) and di- and triacylglycerides (DAG & TAG) species where reference MS/MS spectra provided a potential means of discriminating between the isobaric [M-OH] + ion of DAGs and the [M-RCO] + ion of TAGs.

Computational prediction and biochemical characterization of novel RNA aptamers to Rift Valley fever virus nucleocapsid protein.

PubMed

Ellenbecker, Mary; St Goddard, Jeremy; Sundet, Alec; Lanchy, Jean-Marc; Raiford, Douglas; Lodmell, J Stephen

2015-10-01

Rift Valley fever virus (RVFV) is a potent human and livestock pathogen endemic to sub-Saharan Africa and the Arabian Peninsula that has potential to spread to other parts of the world. Although there is no proven effective and safe treatment for RVFV infections, a potential therapeutic target is the virally encoded nucleocapsid protein (N). During the course of infection, N binds to viral RNA, and perturbation of this interaction can inhibit viral replication. To gain insight into how N recognizes viral RNA specifically, we designed an algorithm that uses a distance matrix and multidimensional scaling to compare the predicted secondary structures of known N-binding RNAs, or aptamers, that were isolated and characterized in previous in vitro evolution experiment. These aptamers did not exhibit overt sequence or predicted structure similarity, so we employed bioinformatic methods to propose novel aptamers based on analysis and clustering of secondary structures. We screened and scored the predicted secondary structures of novel randomly generated RNA sequences in silico and selected several of these putative N-binding RNAs whose secondary structures were similar to those of known N-binding RNAs. We found that overall the in silico generated RNA sequences bound well to N in vitro. Furthermore, introduction of these RNAs into cells prior to infection with RVFV inhibited viral replication in cell culture. This proof of concept study demonstrates how the predictive power of bioinformatics and the empirical power of biochemistry can be jointly harnessed to discover, synthesize, and test new RNA sequences that bind tightly to RVFV N protein. The approach would be easily generalizable to other applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantitation of base substitutions in eukaryotic 5S rRNA: selection for the maintenance of RNA secondary structure.

PubMed

Curtiss, W C; Vournakis, J N

1984-01-01

Eukaryotic 5S rRNA sequences from 34 diverse species were compared by the following method: (1) The sequences were aligned; (2) the positions of substitutions were located by comparison of all possible pairs of sequences; (3) the substitution sites were mapped to an assumed general base pairing model; and (4) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. An analysis of the sequence and structure variability in each region of the molecule is presented. It was found that the degree of base substitution varies over a wide range, from absolute conservation to occurrence of over 90% of the possible observable substitutions. The substitutions are located primarily in stem regions of the 5S rRNA secondary structure. More than 88% of the substitutions in helical regions maintain base pairing. The disruptive substitutions are primarily located at the edges of helical regions, resulting in shortening of the helical regions and lengthening of the adjacent nonpaired regions. Base stacking patterns determined by the R-Y model are mapped onto the general secondary structure. Intrastrand and interstrand stacking could stabilize alternative coaxial structures and limit the conformational flexibility of nonpaired regions. Two short contiguous regions are 100% conserved in all species. This may reflect evolutionary constraints imposed at the DNA level by the requirement for binding of a 5S gene transcription initiation factor during gene expression.

Atoms in Astronomy.

ERIC Educational Resources Information Center

Blanchard, Paul A.

This booklet is part of an American Astronomical Society curriculum project designed to provide teaching materials to teachers of secondary school chemistry, physics, and earth science. A Basic Topics section discusses atomic structure, emphasizing states of matter at high temperature and spectroscopic analysis of light from the stars. A section…

Political Implications of Heavy Television Viewing.

ERIC Educational Resources Information Center

Jackson-Beeck, Marilyn

This paper empirically evaluates the proposition that political conformism, specifically structural, passive, psychological, and defensive conformism, is a function of exposure to mass media. Secondary analysis of data from the National Opinion Research Center's 1975 General Social Survey revealed a significant relationship between TV viewing and…

Microstructure analysis of the secondary pulmonary lobules by 3D synchrotron radiation CT

NASA Astrophysics Data System (ADS)

Fukuoka, Y.; Kawata, Y.; Niki, N.; Umetani, K.; Nakano, Y.; Ohmatsu, H.; Moriyama, N.; Itoh, H.

2014-03-01

Recognition of abnormalities related to the lobular anatomy has become increasingly important in the diagnosis and differential diagnosis of lung abnormalities at clinical routines of CT examinations. This paper aims a 3-D microstructural analysis of the pulmonary acinus with isotropic spatial resolution in the range of several micrometers by using micro CT. Previously, we demonstrated the ability of synchrotron radiation micro CT (SRμCT) using offset scan mode in microstructural analysis of the whole part of the secondary pulmonary lobule. In this paper, we present a semiautomatic method to segment the acinar and subacinar airspaces from the secondary pulmonary lobule and to track small vessels running inside alveolar walls in human acinus imaged by the SRμCT. The method beains with and segmentation of the tissues such as pleural surface, interlobular septa, alveola wall, or vessel using a threshold technique and 3-D connected component analysis. 3-D air space are then conustructed separated by tissues and represented branching patterns of airways and airspaces distal to the terminal bronchiole. A graph-partitioning approach isolated acini whose stems are interactively defined as the terminal bronchiole in the secondary pulmonary lobule. Finally, we performed vessel tracking using a non-linear sate space which captures both smoothness of the trajectories and intensity coherence along vessel orientations. Results demonstrate that the proposed method can extract several acinar airspaces from the 3-D SRμCT image of secondary pulmonary lobule and that the extracted acinar airspace enable an accurate quantitative description of the anatomy of the human acinus for interpretation of the basic unit of pulmonary structure and function.

Chemoinformatic expedition of the chemical space of fungal products.

PubMed

González-Medina, Mariana; Prieto-Martínez, Fernando D; Naveja, J Jesús; Méndez-Lucio, Oscar; El-Elimat, Tamam; Pearce, Cedric J; Oberlies, Nicholas H; Figueroa, Mario; Medina-Franco, José L

2016-08-01

Fungi are valuable resources for bioactive secondary metabolites. However, the chemical space of fungal secondary metabolites has been studied only on a limited basis. Herein, we report a comprehensive chemoinformatic analysis of a unique set of 207 fungal metabolites isolated and characterized in a USA National Cancer Institute funded drug discovery project. Comparison of the molecular complexity of the 207 fungal metabolites with approved anticancer and nonanticancer drugs, compounds in clinical studies, general screening compounds and molecules Generally Recognized as Safe revealed that fungal metabolites have high degree of complexity. Molecular fingerprints showed that fungal metabolites are as structurally diverse as other natural products and have, in general, drug-like physicochemical properties. Fungal products represent promising candidates to expand the medicinally relevant chemical space. This work is a significant expansion of an analysis reported years ago for a smaller set of compounds (less than half of the ones included in the present work) from filamentous fungi using different structural properties.

[Establishment of prescription research technology system in Chinese medicine secondary exploitation based on "component structure" theory].

PubMed

Cheng, Xu-Dong; Feng, Liang; Gu, Jun-Fei; Zhang, Ming-Hua; Jia, Xiao-Bin

2014-11-01

Chinese medicine prescriptions are the wisdom outcomes of traditional Chinese medicine (TCM) clinical treatment determinations which based on differentiation of symptoms and signs. Chinese medicine prescriptions are also the basis of secondary exploitation of TCM. The study on prescription helps to understand the material basis of its efficacy, pharmacological mechanism, which is an important guarantee for the modernization of traditional Chinese medicine. Currently, there is not yet dissertation n the method and technology system of basic research on the prescription of Chinese medicine. This paper focuses on how to build an effective system of prescription research technology. Based on "component structure" theory, a technology system contained four-step method that "prescription analysis, the material basis screening, the material basis of analysis and optimization and verify" was proposed. The technology system analyzes the material basis of the three levels such as Chinese medicine pieces, constituents and the compounds which could respect the overall efficacy of Chinese medicine. Ideas of prescription optimization, remodeling are introduced into the system. The technology system is the combination of the existing research and associates with new techniques and methods, which used for explore the research thought suitable for material basis research and prescription remodeling. The system provides a reference for the secondary development of traditional Chinese medicine, and industrial upgrading.

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.

Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation

PubMed Central

Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

2015-01-01

Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation. PMID:25870416

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.

Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding

PubMed Central

Tischer, Alexander; Auton, Matthew

2013-01-01

We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea–temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea–temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of and that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. PMID:23813497

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

The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis.

PubMed

Rebehmed, Joseph; Quintus, Flavien; Mornon, Jean-Paul; Callebaut, Isabelle

2016-05-01

Several studies have highlighted the leading role of the sequence periodicity of polar and nonpolar amino acids (binary patterns) in the formation of regular secondary structures (RSS). However, these were based on the analysis of only a few simple cases, with no direct mean to correlate binary patterns with the limits of RSS. Here, HCA-derived hydrophobic clusters (HC) which are conditioned binary patterns whose positions fit well those of RSS, were considered. All the HC types, defined by unique binary patterns, which were commonly observed in three-dimensional (3D) structures of globular domains, were analyzed. The 180 HC types with preferences for either α-helices or β-strands distinctly contain basic binary units typical of these RSS. Therefore a general trend supporting the "binary pattern preference" assumption was observed. HC for which observed RSS are in disagreement with their expected behavior (discordant HC) were also examined. They were separated in HC types with moderate preferences for RSS, having "weak" binary patterns and versatile RSS and HC types with high preferences for RSS, having "strong" binary patterns and then displaying nonpolar amino acids at the protein surface. It was shown that in both cases, discordant HC could be distinguished from concordant ones by well-differentiated amino acid compositions. The obtained results could, thus, help to complement the currently available methods for the accurate prediction of secondary structures in proteins from the only information of a single amino acid sequence. This can be especially useful for characterizing orphan sequences and for assisting protein engineering and design. © 2016 Wiley Periodicals, Inc.

A Quantitative Method for the Analysis of Nomothetic Relationships between Idiographic Structures: Dynamic Patterns Create Attractor States for Sustained Posttreatment Change

ERIC Educational Resources Information Center

Fisher, Aaron J.; Newman, Michelle G.; Molenaar, Peter C. M.

2011-01-01

Objective: The present article aimed to demonstrate that the establishment of dynamic patterns during the course of psychotherapy can create attractor states for continued adaptive change following the conclusion of treatment. Method: This study is a secondary analysis of T. D. Borkovec and E. Costello (1993). Of the 55 participants in the…

Sequential protein unfolding through a carbon nanotube pore

NASA Astrophysics Data System (ADS)

Xu, Zhonghe; Zhang, Shuang; Weber, Jeffrey K.; Luan, Binquan; Zhou, Ruhong; Li, Jingyuan

2016-06-01

An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable ``unfoldon'' motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability.An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable ``unfoldon'' motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr00410e

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.

National evaluation of the benefits and risks of greater structuring and coding of the electronic health record: exploratory qualitative investigation.

PubMed

Morrison, Zoe; Fernando, Bernard; Kalra, Dipak; Cresswell, Kathrin; Sheikh, Aziz

2014-01-01

We aimed to explore stakeholder views, attitudes, needs, and expectations regarding likely benefits and risks resulting from increased structuring and coding of clinical information within electronic health records (EHRs). Qualitative investigation in primary and secondary care and research settings throughout the UK. Data were derived from interviews, expert discussion groups, observations, and relevant documents. Participants (n=70) included patients, healthcare professionals, health service commissioners, policy makers, managers, administrators, systems developers, researchers, and academics. Four main themes arose from our data: variations in documentation practice; patient care benefits; secondary uses of information; and informing and involving patients. We observed a lack of guidelines, co-ordination, and dissemination of best practice relating to the design and use of information structures. While we identified immediate benefits for direct care and secondary analysis, many healthcare professionals did not see the relevance of structured and/or coded data to clinical practice. The potential for structured information to increase patient understanding of their diagnosis and treatment contrasted with concerns regarding the appropriateness of coded information for patients. The design and development of EHRs requires the capture of narrative information to reflect patient/clinician communication and computable data for administration and research purposes. Increased structuring and/or coding of EHRs therefore offers both benefits and risks. Documentation standards within clinical guidelines are likely to encourage comprehensive, accurate processing of data. As data structures may impact upon clinician/patient interactions, new models of documentation may be necessary if EHRs are to be read and authored by patients.

National evaluation of the benefits and risks of greater structuring and coding of the electronic health record: exploratory qualitative investigation

PubMed Central

Morrison, Zoe; Fernando, Bernard; Kalra, Dipak; Cresswell, Kathrin; Sheikh, Aziz

2014-01-01

Objective We aimed to explore stakeholder views, attitudes, needs, and expectations regarding likely benefits and risks resulting from increased structuring and coding of clinical information within electronic health records (EHRs). Materials and methods Qualitative investigation in primary and secondary care and research settings throughout the UK. Data were derived from interviews, expert discussion groups, observations, and relevant documents. Participants (n=70) included patients, healthcare professionals, health service commissioners, policy makers, managers, administrators, systems developers, researchers, and academics. Results Four main themes arose from our data: variations in documentation practice; patient care benefits; secondary uses of information; and informing and involving patients. We observed a lack of guidelines, co-ordination, and dissemination of best practice relating to the design and use of information structures. While we identified immediate benefits for direct care and secondary analysis, many healthcare professionals did not see the relevance of structured and/or coded data to clinical practice. The potential for structured information to increase patient understanding of their diagnosis and treatment contrasted with concerns regarding the appropriateness of coded information for patients. Conclusions The design and development of EHRs requires the capture of narrative information to reflect patient/clinician communication and computable data for administration and research purposes. Increased structuring and/or coding of EHRs therefore offers both benefits and risks. Documentation standards within clinical guidelines are likely to encourage comprehensive, accurate processing of data. As data structures may impact upon clinician/patient interactions, new models of documentation may be necessary if EHRs are to be read and authored by patients. PMID:24186957

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.

Optimal packaging of FIV genomic RNA depends upon a conserved long-range interaction and a palindromic sequence within gag.

PubMed

Rizvi, Tahir A; Kenyon, Julia C; Ali, Jahabar; Aktar, Suriya J; Phillip, Pretty S; Ghazawi, Akela; Mustafa, Farah; Lever, Andrew M L

2010-10-15

The feline immunodeficiency virus (FIV) is a lentivirus that is related to human immunodeficiency virus (HIV), causing a similar pathology in cats. It is a potential small animal model for AIDS and the FIV-based vectors are also being pursued for human gene therapy. Previous studies have mapped the FIV packaging signal (ψ) to two or more discontinuous regions within the 5' 511 nt of the genomic RNA and structural analyses have determined its secondary structure. The 5' and 3' sequences within ψ region interact through extensive long-range interactions (LRIs), including a conserved heptanucleotide interaction between R/U5 and gag. Other secondary structural elements identified include a conserved 150 nt stem-loop (SL2) and a small palindromic stem-loop within gag open reading frame that might act as a viral dimerization initiation site. We have performed extensive mutational analysis of these sequences and structures and ascertained their importance in FIV packaging using a trans-complementation assay. Disrupting the conserved heptanucleotide LRI to prevent base pairing between R/U5 and gag reduced packaging by 2.8-5.5 fold. Restoration of pairing using an alternative, non-wild type (wt) LRI sequence restored RNA packaging and propagation to wt levels, suggesting that it is the structure of the LRI, rather than its sequence, that is important for FIV packaging. Disrupting the palindrome within gag reduced packaging by 1.5-3-fold, but substitution with a different palindromic sequence did not restore packaging completely, suggesting that the sequence of this region as well as its palindromic nature is important. Mutation of individual regions of SL2 did not have a pronounced effect on FIV packaging, suggesting that either it is the structure of SL2 as a whole that is necessary for optimal packaging, or that there is redundancy within this structure. The mutational analysis presented here has further validated the previously predicted RNA secondary structure of FIV ψ. Copyright © 2010 Elsevier Ltd. All rights reserved.

Invasive plants have different effects on trophic structure of green and brown food webs in terrestrial ecosystems: a meta-analysis.

PubMed

McCary, Matthew A; Mores, Robin; Farfan, Monica A; Wise, David H

2016-03-01

Although invasive plants are a major source of terrestrial ecosystem degradation worldwide, it remains unclear which trophic levels above the base of the food web are most vulnerable to plant invasions. We performed a meta-analysis of 38 independent studies from 32 papers to examine how invasive plants alter major groupings of primary and secondary consumers in three globally distributed ecosystems: wetlands, woodlands and grasslands. Within each ecosystem we examined if green (grazing) food webs are more sensitive to plant invasions compared to brown (detrital) food webs. Invasive plants have strong negative effects on primary consumers (detritivores, bacterivores, fungivores, and/or herbivores) in woodlands and wetlands, which become less abundant in both green and brown food webs in woodlands and green webs in wetlands. Plant invasions increased abundances of secondary consumers (predators and/or parasitoids) only in woodland brown food webs and green webs in wetlands. Effects of invasive plants on grazing and detrital food webs clearly differed between ecosystems. Overall, invasive plants had the most pronounced effects on the trophic structure of wetlands and woodlands, but caused no detectable changes to grassland trophic structure. © 2016 John Wiley & Sons Ltd/CNRS.

Evaluation of blood adsorption onto dialysis membranes by time-of-flight secondary ion mass spectrometry and near-field infrared microscopy.

PubMed

Aoyagi, Satoka; Abe, Kiyoshi; Yamagishi, Takayuki; Iwai, Hideo; Yamaguchi, Satoru; Sunohara, Takashi

2017-11-01

Blood adsorption onto the inside surface of hollow fiber dialysis membranes was investigated by means of time-of-flight secondary ion mass spectrometry (TOF-SIMS) and near-field infrared microscopy (NFIR) in order to evaluate the biocompatibility and permeability of dialysis membranes. TOF-SIMS is useful for the imaging of particular molecules with a high spatial resolution of approximately 100 nm. In contrast, infrared spectra provide quantitative information and NFIR enables analysis with a high spatial resolution of less than 1 μm, which is close to the resolution of TOF-SIMS. A comparison was made of one of the most widely used dialysis membranes made of polysulfone (PSf), that has an asymmetric and inhomogeneous pore structure, and a newly developed asymmetric cellulose triacetate (ATA) membrane that also has an asymmetric pore structure, even though the conventional cellulose triacetate membrane has a symmetric and homogeneous pore structure. As a result, it was demonstrated that blood adsorption on the inside surface of the ATA membrane is more reduced than that on the PSf membrane. Graphical abstract Analysis of blood adsorption on inside surface of hollow fiber membrane.

Fatigue as a cause, not a consequence of depression and daytime sleepiness: a cross-lagged analysis.

PubMed

Schönberger, Michael; Herrberg, Marlene; Ponsford, Jennie

2014-01-01

To examine the temporal relation between fatigue, depression, and daytime sleepiness after traumatic brain injury. Fatigue is a frequent and disabling consequence of traumatic brain injury (TBI). However, it is unclear whether fatigue is a primary consequence of the structural brain injury or a secondary consequence of injury-related sequelae such as depression and daytime sleepiness. Eighty-eight adults with complicated mild-severe TBI (69% male). Fatigue Severity Scale; depression subscale of the Hospital Anxiety and Depression Scale; Epworth Sleepiness scale at baseline and 6-month follow-up. A cross-lagged path analysis computed within a structural equation modeling framework revealed that fatigue was predictive of depression (β = .20, P < .05) and sleepiness (β = .25, P < .05). However, depression and sleepiness did not predict fatigue (P > .05). The results support the view of fatigue after TBI as "primary fatigue"-that is, a consequence of the structural brain injury rather than a secondary consequence of depression or daytime sleepiness. A rehabilitation approach that assists individuals with brain injury in learning to cope with their neuropsychological and physical limitations in everyday life might attenuate their experience with fatigue.

Role of Polyalanine Domains in -Sheet Formation in Spider Silk Block Copolymers

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

Rabotyagova, O.; Cebe, P; Kaplan, D

2010-01-01

Genetically engineered spider silk-like block copolymers were studied to determine the influence of polyalanine domain size on secondary structure. The role of polyalanine block distribution on {beta}-sheet formation was explored using FT-IR and WAXS. The number of polyalanine blocks had a direct effect on the formation of crystalline {beta}-sheets, reflected in the change in crystallinity index as the blocks of polyalanines increased. WAXS analysis confirmed the crystalline nature of the sample with the largest number of polyalanine blocks. This approach provides a platform for further exploration of the role of specific amino acid chemistries in regulating the assembly of {beta}-sheetmore » secondary structures, leading to options to regulate material properties through manipulation of this key component in spider silks.« less

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.

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.

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

PubMed Central

Rutenberg-Schoenberg, Michael; Simon, Matthew D.

2015-01-01

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

Analysis of secondary particle behavior in multiaperture, multigrid accelerator for the ITER neutral beam injector.

PubMed

Mizuno, T; Taniguchi, M; Kashiwagi, M; Umeda, N; Tobari, H; Watanabe, K; Dairaku, M; Sakamoto, K; Inoue, T

2010-02-01

Heat load on acceleration grids by secondary particles such as electrons, neutrals, and positive ions, is a key issue for long pulse acceleration of negative ion beams. Complicated behaviors of the secondary particles in multiaperture, multigrid (MAMuG) accelerator have been analyzed using electrostatic accelerator Monte Carlo code. The analytical result is compared to experimental one obtained in a long pulse operation of a MeV accelerator, of which second acceleration grid (A2G) was removed for simplification of structure. The analytical results show that relatively high heat load on the third acceleration grid (A3G) since stripped electrons were deposited mainly on A3G. This heat load on the A3G can be suppressed by installing the A2G. Thus, capability of MAMuG accelerator is demonstrated for suppression of heat load due to secondary particles by the intermediate grids.

Biologically active secondary metabolites from fungi. 12.(1) oidiolactones A-F, labdane diterpene derivatives isolated from oidiodendron truncata

PubMed

John; Krohn; Florke; Aust; Draeger; Schulz

1999-09-01

Two known (1 and 2) and four new (3-6) diterpenes named oidiolactones A-F, respectively, and the antibiotic cladosporin were isolated from the fungus Oidiodendron truncata. The structure determination was mainly based on 1D and 2D NMR spectroscopy. The structures of compound 4, displaying an equilibrium between open-chain and cyclized form, and of cladosporin were confirmed by X-ray analysis.

Solution structure of dimeric Mnt repressor (1-76).

PubMed

Burgering, M J; Boelens, R; Gilbert, D E; Breg, J N; Knight, K L; Sauer, R T; Kaptein, R

1994-12-20

Wild-type Mnt repressor of Salmonella bacteriophage P22 is a tetrameric protein of 82 residues per monomer. A C-terminal deletion mutant of the repressor denoted Mnt (1-76) is a dimer in solution. The structure of this dimer has been determined using NMR. The NMR assignments of the majority of the 1H, 15N, and 13C resonances were obtained using 2D and triple-resonance 3D techniques. Elements of secondary structure were identified on the basis of characteristic sequential and medium range NOEs. For the structure determination more than 1000 NOEs per monomer were obtained, and structures were generated using distance geometry and restrained simulated annealing calculations. The discrimination of intra- vs intermonomer NOEs was based upon the observation of intersubunit NOEs in [15N,13C] double half-filtered NOESY experiments. The N-terminal part of Mnt (residues 1-44), which shows a 40% sequence homology with the Arc repressor, has a similar secondary and tertiary structure. Mnt (1-76) continues with a loop region of irregular structure, a third alpha-helix, and a random coil C-terminal peptide. Analysis of the secondary structure NOEs, the exchange rates, and the backbone chemical shifts suggests that the carboxy-terminal third helix is less stable than the remainder of the protein, but the observation of intersubunit NOEs for this part of the protein enables the positioning of this helix. The rsmd's between the backbone atoms of the N-terminal part of the Mnt repressor (residues 5-43, 5'-43') and the Arc repressor is 1.58 A, and between this region and the corresponding part of the MetJ repressor 1.43 A.

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

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/.

Free Energy and Structure of Helix-forming Peptides: A Theoretical Investigation

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim

This thesis focuses on the structure and free energy of helical secondary structures of short peptides in a variety of experimental settings. Specifically, the formation of alpha-, pi- and 310-helices was investigated using large-scale classical molecular dynamics simulations with state-of-the-art force fields. In addition, the recently developed Adaptively Biased Molecular Dynamics (ABMD) and Steered Molecular Dynamics (SMD) methods were used to calculate the corresponding free energies. The most important results are as follows. For the examined peptide homopolymers, the observed minima on the free energy landscapes (based on suitable collective variables such as the radius of gyration, number of hydrogen bonds, and handedness) were associated with alpha-helices and "globular" or "knot-like" configurations only. No evidence was found to indicate that 310- or pi-helices represent equilibrium structures for these systems. In addition, the free energy landscape of short peptide chains formed by mixing two different amino acids were also examined. These results too indicate that the alpha-helix is only equilibrium helical secondary structure, and that the mixing of different amino acids does not result in the introduction of any significant new minima into the free energy landscapes. These results are in agreement with experimental observations insofar as these indicate that helical structural motifs are primary based on alpha-helices, with 310- and pi-helices being observed only rarely. Although pi- and 310-helices represent nonequilibrium structures, we were still able to estimate their free energies by means of SMD simulations. The helical secondary structure of the examined polypeptide chains is due to the formation of hydrogen bonds. However, there are other mechanisms that may allow for the additional stabilization of these structures. Specifically, in the so-called AK-(4,7) protein, the possible presence of disulfide bonds connecting cysteine residues may significantly alter the free energy landscapes and therefore the stability of different helical structures. We therefore examined this issue with ABMD simulations. However, our results show that while the free energy landscapes are indeed significantly altered only the formation of alpha-helices is favored as a secondary structural motif. Since all the results indicate that alpha-helix formation dominates, it is natural to think in terms of an alpha-helix forming propensity for different amino acids. To address this question, we carried out an extensive residue-by-residue population analysis of different amino acid guests in an alanine-based host setting. Such an analysis allows us to rank the different amino acid guests based on whether they increased or decreased the population in the alpha-helix region of the corresponding Ramachandran plots. Our ranking of the different guest amino acids is in reasonable correspondence with the experimental results, although some differences are observed. Finally, using a four-beads coarse-grained model were have investigated the stability of GA88 and GB88 proteins, which are quite similar in terms of their amino acid sequence, by means of 10mus simulations. The results indicate that while the three alpha-helix bundle of the GA88 protein remains stable, the 2beta--alpha--2beta configuration of the GB88 protein does not: the latter rapidly converts to a structure consisting mostly of helices similar to the GA88 protein design. These results indicate that this particular four-bead coarse-grained model is not able to properly grasp the dynamics of the beta-sheet secondary structure and overstabilizes the corresponding helical content.

The Student Experience of Learning Using Networked Technologies: An Emergent Progression of Expanding Awareness

ERIC Educational Resources Information Center

Cutajar, Maria

2017-01-01

This article reports on phenomenographic research which explored the qualitative differences in post-secondary students' accounts of their networked learning experiences. Data was generated using semi-structured interviews with a purposive sample of participants. Phenomenographic analysis led to a configuration of variation in students' accounts…

Developing a Mathematics Education Quality Scale

ERIC Educational Resources Information Center

Ciftci, S. Koza; Karadag, Engin

2016-01-01

The aim of this study was to evaluate students' perceptions of the quality of mathematics education and to develop a reliable and valid measurement tool. The research was conducted with 638 (first study) and 407 (second study) secondary school students in Eskisehir, Turkey. Item discrimination, structural validity (exploratory factor analysis and…

Secondary metabolites produced by solid fermentation of the marine-derived fungus Penicillium commune QSD-17.

PubMed

Gao, Shu-Shan; Shang, Zhuo; Li, Xiao-Ming; Li, Chun-Shun; Cui, Chuan-Ming; Wang, Bin-Gui

2012-01-01

The marine sediment-derived fungus Penicillium commune QSD-17 was re-investigated and cultured on rice solid medium. Two new compounds, isophomenone (1) and 3-deacetylcitreohybridonol (2), together with seven known derivatives (3-9), were identified. Their structures were determined by spectroscopic analysis.

English Grammar in School Textbooks: A Critical Survey.

ERIC Educational Resources Information Center

Collis, Peter; Hollo, Carmella; Mar, Juliet

1997-01-01

Reports findings from a critical analysis of English grammar books and language books with grammar content used in New South Wales (Australia) elementary and secondary schools. Books surveyed showed a low level of awareness of developments in contemporary linguistics, particularly the structural approach to grammar instruction. (Author/MSE)

Dilemmas Concerning the Employment of University Graduates in China

ERIC Educational Resources Information Center

Ren, Shuang; Zhu, Ying; Warner, Malcolm

2017-01-01

This article draws on a "within-subject" design of employment of university graduates in China over two different periods, namely 2008 and 2014. This research was conducted based on semi-structured interviews and secondary data analysis with four groups of key stakeholders including universities, government agencies, labor-market…

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

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…

A boundary element approach to optimization of active noise control sources on three-dimensional structures

NASA Technical Reports Server (NTRS)

Cunefare, K. A.; Koopmann, G. H.

1991-01-01

This paper presents the theoretical development of an approach to active noise control (ANC) applicable to three-dimensional radiators. The active noise control technique, termed ANC Optimization Analysis, is based on minimizing the total radiated power by adding secondary acoustic sources on the primary noise source. ANC Optimization Analysis determines the optimum magnitude and phase at which to drive the secondary control sources in order to achieve the best possible reduction in the total radiated power from the noise source/control source combination. For example, ANC Optimization Analysis predicts a 20 dB reduction in the total power radiated from a sphere of radius at a dimensionless wavenumber ka of 0.125, for a single control source representing 2.5 percent of the total area of the sphere. ANC Optimization Analysis is based on a boundary element formulation of the Helmholtz Integral Equation, and thus, the optimization analysis applies to a single frequency, while multiple frequencies can be treated through repeated analyses.

Analysis of secondary structural elements in human microRNA hairpin precursors.

PubMed

Liu, Biao; Childs-Disney, Jessica L; Znosko, Brent M; Wang, Dan; Fallahi, Mohammad; Gallo, Steven M; Disney, Matthew D

2016-03-01

MicroRNAs (miRNAs) regulate gene expression by targeting complementary mRNAs for destruction or translational repression. Aberrant expression of miRNAs has been associated with various diseases including cancer, thus making them interesting therapeutic targets. The composite of secondary structural elements that comprise miRNAs could aid the design of small molecules that modulate their function. We analyzed the secondary structural elements, or motifs, present in all human miRNA hairpin precursors and compared them to highly expressed human RNAs with known structures and other RNAs from various organisms. Amongst human miRNAs, there are 3808 are unique motifs, many residing in processing sites. Further, we identified motifs in miRNAs that are not present in other highly expressed human RNAs, desirable targets for small molecules. MiRNA motifs were incorporated into a searchable database that is freely available. We also analyzed the most frequently occurring bulges and internal loops for each RNA class and found that the smallest loops possible prevail. However, the distribution of loops and the preferred closing base pairs were unique to each class. Collectively, we have completed a broad survey of motifs found in human miRNA precursors, highly expressed human RNAs, and RNAs from other organisms. Interestingly, unique motifs were identified in human miRNA processing sites, binding to which could inhibit miRNA maturation and hence function.

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.

Statistical analysis of secondary particle distributions in relativistic nucleus-nucleus collisions

NASA Technical Reports Server (NTRS)

Mcguire, Stephen C.

1987-01-01

The use is described of several statistical techniques to characterize structure in the angular distributions of secondary particles from nucleus-nucleus collisions in the energy range 24 to 61 GeV/nucleon. The objective of this work was to determine whether there are correlations between emitted particle intensity and angle that may be used to support the existence of the quark gluon plasma. The techniques include chi-square null hypothesis tests, the method of discrete Fourier transform analysis, and fluctuation analysis. We have also used the method of composite unit vectors to test for azimuthal asymmetry in a data set of 63 JACEE-3 events. Each method is presented in a manner that provides the reader with some practical detail regarding its application. Of those events with relatively high statistics, Fe approaches 0 at 55 GeV/nucleon was found to possess an azimuthal distribution with a highly non-random structure. No evidence of non-statistical fluctuations was found in the pseudo-rapidity distributions of the events studied. It is seen that the most effective application of these methods relies upon the availability of many events or single events that possess very high multiplicities.

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.

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.

How is impulsivity related to depression in adolescence? Evidence from a French validation of the cognitive emotion regulation questionnaire.

PubMed

d'Acremont, Mathieu; Van der Linden, Martial

2007-04-01

The aim of this study was to validate a French version of the Cognitive Emotion Regulation Questionnaire (CERQ; Garnefski, N., Kraaij, V., & Spinhoven, P., 2001. Negative life events, cognitive emotion regulation and emotional problems. Personality and Individual Differences, 30, 1311-1327) and to explore its relationships with impulsivity and depression. Teenagers from a junior secondary (n=107, 13-16 years) and a secondary school (n=110, 15-19 years) completed the CERQ, which assesses regulation strategies in response to negative events. The secondary school adolescents also completed the UPPS Impulsive Behavior Scale (Whiteside, S. P., & Lynam, D. R., 2001. The five factor model and impulsivity: Using a structural model of personality to understand impulsivity. Personality and Individual Differences, 30, 669-689) and the Reynolds Adolescent Depression Scale (Reynolds, W. M., 1987. Reynolds Adolescent Depression Scale: Professional manual. Odessa, FL: Psychological Assessment Resources). Factor analysis for the CERQ confirmed the presence of the nine original regulation strategies. In the secondary school students, impulsivity was related to depression. A path analysis revealed that regulation strategies mediated this relationship. The role of emotion regulation in the development of adolescent psychopathology is discussed.

Managing patient pathways to achieve lung cancer waiting time targets: mixed methods study

PubMed Central

Ip, Hugh; Amer, Tarik; Dangoor, Michael; Zamir, Affan; Gibbings-Isaac, Darryl; Kochhar, Ranjeev; Heymann, Timothy

2012-01-01

Objectives England's National Health Service (NHS) introduced a 62-day target, from referral to treatment, to make lung cancer patient pathways more efficient. This study aims to understand pathway delays that lead to breaches of the target when patients need care in both secondary and tertiary setting, so more than one institution is involved. Design Mixed methods cross case analysis. Setting Two tertiary referral hospitals in London. Participants Database records of 53 patients were analysed. Nineteen sets of patient notes were used for pathway mapping. Seventeen doctors, four nurses, eight managers and administrators were interviewed. Main outcome measures Qualitative methods include pathway mapping and semi-structured interviews. Quantitative analysis of patient pathway times from cancer services records. Results The majority of the patient pathway (68.4%) is spent in secondary centres. There is more variability in the processes of secondary centres but tertiary centres do not have perfect processes either. Three themes emerged from discussions: information flows, pathway performance and the role of the multidisciplinary approach. Conclusions The actions of secondary centres have a greater influence on whether a patient breaches the 62-day target, compared with tertiary centres. Nevertheless variability exists in both, with potential for improvement. PMID:23162682

A Secondary Antibody-Detecting Molecular Weight Marker with Mouse and Rabbit IgG Fc Linear Epitopes for Western Blot Analysis

PubMed Central

Cheng, Ta-Chun; Tung, Yi-Ching; Chu, Pei-Yu; Chuang, Chih-Hung; Hsieh, Yuan-Chin; Huang, Chien-Chiao; Wang, Yeng-Tseng; Kao, Chien-Han; Roffler, Steve R.; Cheng, Tian-Lu

2016-01-01

Molecular weight markers that can tolerate denaturing conditions and be auto-detected by secondary antibodies offer great efficacy and convenience for Western Blotting. Here, we describe M&R LE protein markers which contain linear epitopes derived from the heavy chain constant regions of mouse and rabbit immunoglobulin G (IgG Fc LE). These markers can be directly recognized and stained by a wide range of anti-mouse and anti-rabbit secondary antibodies. We selected three mouse (M1, M2 and M3) linear IgG1 and three rabbit (R1, R2 and R3) linear IgG heavy chain epitope candidates based on their respective crystal structures. Western blot analysis indicated that M2 and R2 linear epitopes are effectively recognized by anti-mouse and anti-rabbit secondary antibodies, respectively. We fused the M2 and R2 epitopes (M&R LE) and incorporated the polypeptide in a range of 15–120 kDa auto-detecting markers (M&R LE protein marker). The M&R LE protein marker can be auto-detected by anti-mouse and anti-rabbit IgG secondary antibodies in standard immunoblots. Linear regression analysis of the M&R LE protein marker plotted as gel mobility versus the log of the marker molecular weights revealed good linearity with a correlation coefficient R2 value of 0.9965, indicating that the M&R LE protein marker displays high accuracy for determining protein molecular weights. This accurate, regular and auto-detected M&R LE protein marker may provide a simple, efficient and economical tool for protein analysis. PMID:27494183

A Secondary Antibody-Detecting Molecular Weight Marker with Mouse and Rabbit IgG Fc Linear Epitopes for Western Blot Analysis.

PubMed

Lin, Wen-Wei; Chen, I-Ju; Cheng, Ta-Chun; Tung, Yi-Ching; Chu, Pei-Yu; Chuang, Chih-Hung; Hsieh, Yuan-Chin; Huang, Chien-Chiao; Wang, Yeng-Tseng; Kao, Chien-Han; Roffler, Steve R; Cheng, Tian-Lu

2016-01-01

Molecular weight markers that can tolerate denaturing conditions and be auto-detected by secondary antibodies offer great efficacy and convenience for Western Blotting. Here, we describe M&R LE protein markers which contain linear epitopes derived from the heavy chain constant regions of mouse and rabbit immunoglobulin G (IgG Fc LE). These markers can be directly recognized and stained by a wide range of anti-mouse and anti-rabbit secondary antibodies. We selected three mouse (M1, M2 and M3) linear IgG1 and three rabbit (R1, R2 and R3) linear IgG heavy chain epitope candidates based on their respective crystal structures. Western blot analysis indicated that M2 and R2 linear epitopes are effectively recognized by anti-mouse and anti-rabbit secondary antibodies, respectively. We fused the M2 and R2 epitopes (M&R LE) and incorporated the polypeptide in a range of 15-120 kDa auto-detecting markers (M&R LE protein marker). The M&R LE protein marker can be auto-detected by anti-mouse and anti-rabbit IgG secondary antibodies in standard immunoblots. Linear regression analysis of the M&R LE protein marker plotted as gel mobility versus the log of the marker molecular weights revealed good linearity with a correlation coefficient R2 value of 0.9965, indicating that the M&R LE protein marker displays high accuracy for determining protein molecular weights. This accurate, regular and auto-detected M&R LE protein marker may provide a simple, efficient and economical tool for protein analysis.

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.

Forcing mechanism of the seasonally asymmetric quasi-biennial oscillation secondary circulation in ERA-40 and MAECHAM5

NASA Astrophysics Data System (ADS)

Peña-Ortiz, C.; Ribera, P.; García-Herrera, R.; Giorgetta, M. A.; García, R. R.

2008-08-01

The seasonality of the quasi-biennial oscillation (QBO) and its secondary circulation is analyzed in the European Reanalysis (ERA-40) and Middle Atmosphere European Centre Hamburg Model (MAECHAM5) general circulation model data sets through the multitaper method-singular value decomposition (MTM-SVD). In agreement with previous studies, the results reveal a strong seasonal dependence of the QBO secondary circulation. This is characterized by a two-cell structure symmetric about the equator during autumn and spring. However, anomalies strongly weaken in the summer hemisphere and strengthen in the winter hemisphere, leading to an asymmetric QBO secondary circulation characterized by a single-cell structure displaced into the winter hemisphere during the solstices. In ERA-40, this asymmetry is more pronounced during the northern than during the southern winter. These results provide the first observation of the QBO secondary circulation asymmetries in the ERA-40 reanalysis data set across the full stratosphere and the lower mesosphere, up to 0.1 hPa. The MTM-SVD reconstruction of the seasonal QBO signals in the residual circulation and the QBO signals in Eliassen Palm (EP) flux divergences suggest a particular mechanism for the seasonal asymmetries of the QBO secondary circulation and its extension across the midlatitudes. The analysis shows that the QBO modulates the EP flux in the winter hemispheric surf zone poleward of the QBO jets. The zonal wind forcing by EP flux divergence is transformed by the Coriolis effect into a meridional wind signal. The seasonality in the stratospheric EP flux and the hemispheric differences in planetary wave forcing cause the observed seasonality in the QBO secondary circulation and its hemispheric differences.

Inquiry practice and identity of beginning secondary science teachers in the online and offline learning community: A longitudinal mixed methods study

NASA Astrophysics Data System (ADS)

Bang, Eunjin

This two-year study explored changes in practices and the emerging identities of beginning secondary science teachers who participated in an online science specific mentoring program. Fourteen beginning secondary science teachers and six experienced secondary science teachers were selected for the study. As a mixed methods study, data were gathered quantitatively and qualitatively. A hierarchical linear modeling was used in order to depict the changes in inquiry-based science practices as a result of content-focused online mentoring program. Qualitative data were collected via monthly semi-structured interviews, pre, post, and follow-up yearly semi-structured interviews, and finally online written dialogues of beginning secondary science teachers and their e-mentors. A mixed method was used that utilized the results of quantitative data, Items for Inquiry-Based Practice (IBP) scores, helped for selecting cases for qualitative analysis. Results indicated that there were no significant differences in IBP scores among the fourteen beginning secondary science teachers; however, three groups were detected: increasing use, no change, and decreasing use in inquiry-based practices. Porsha, who made increasing use, showed four emerging identities throughout two years: watchful-imitator, seeker, collaborator, and junior-leader. Nora, who made no change, showed only two emerging identities: imitator and seeker. Netty, who made decreasing use, showed also two emerging identities: lonely-follower and feeder. Different identities detected in online dialogue, namely Porsha as a whistleblower, Nora as a watchful-imitator, and Netty as a watchful-feeder. The corresponding responses of three beginning secondary science teachers' e-mentors were defender, provider, listener, pusher and umpire. This study provides not only an in-depth picture of the contemporary science education community of practice but also suggest a roadmap to design an effective induction program.

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.

Specific β-Turns Precede PPIIL Structures Binding to Allele-Specific HLA-DRβ1* PBRs in Fully-Protective Malaria Vaccine Components

PubMed Central

Bermudez, Adriana; Alba, Martha P.; Vanegas, Magnolia; Patarroyo, Manuel A.; Patarroyo, Manuel E.

2018-01-01

The 3D structural analysis of 62 peptides derived from highly pathogenic Plasmodium falciparum malaria parasite proteins involved in host cell invasion led to finding a striking association between particular β-turn types located in the N-terminal peripheral flanking residue region (preceding the polyproline II left-handed structures fitting into the HLA-DRβ* allele family) and modified immune protection-inducing protein structure induced long-lasting protective immunity. This is the first time association between two different secondary structures associated with a specific immunological function has been described: full, long-lasting protective immunity. PMID:29682500

Specific β-Turns Precede PPIIL Structures Binding to Allele-Specific HLA-DRβ1* PBRs in Fully-Protective Malaria Vaccine Components.

PubMed

Bermudez, Adriana; Alba, Martha P; Vanegas, Magnolia; Patarroyo, Manuel A; Patarroyo, Manuel E

2018-01-01

The 3D structural analysis of 62 peptides derived from highly pathogenic Plasmodium falciparum malaria parasite proteins involved in host cell invasion led to finding a striking association between particular β-turn types located in the N-terminal peripheral flanking residue region (preceding the polyproline II left-handed structures fitting into the HLA-DRβ * allele family) and modified i mmune protection-inducing protein structure induced long-lasting protective immunity. This is the first time association between two different secondary structures associated with a specific immunological function has been described: full, long-lasting protective immunity.

Specific β-turns precede PPIIL structures binding to allele-specific HLA-DRβ1* PBRs in fully-protective malaria vaccine components

NASA Astrophysics Data System (ADS)

Bermudez, Adriana; Alba, Martha P.; Vanegas, Magnolia; Patarroyo, Manuel A.; Patarroyo, Manuel E.

2018-04-01

The 3D structural analysis of 62 peptides derived from highly pathogenic Plasmodium falciparum malaria parasite proteins involved in host cell invasion led to finding a striking association between particular β-turn types located in the N-terminal peripheral flanking residue region (preceding the polyproline II left-handed structures fitting into the HLA-DRβ* allele family) and modified immune protection-inducing protein structure induced long-lasting protective immunity. This is the first time association between two different secondary structures associated with a specific immunological function has been described: full, long-lasting protective immunity.

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.

Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus

PubMed Central

Leyrat, Cedric; Renner, Max; Harlos, Karl; Huiskonen, Juha T.; Grimes, Jonathan M.

2014-01-01

Summary The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca2+ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca2+ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses. PMID:24316400

The use of information and communication technologies to support working carers of older people - a qualitative secondary analysis.

PubMed

Andersson, Stefan; Magnusson, Lennart; Hanson, Elizabeth

2016-03-01

Family care support services have mainly focused on older spousal carers of older people and have largely overlooked working carers, whom combine paid work with informal/family care responsibilities. Recently, however, information and communication technology (ICT) systems have been identified as a potentially flexible way of supporting working carers. The aim of this study was to describe nursing and support staff's experiences of using ICT for information, e-learning and support of working carers of older people. The study employed a descriptive, qualitative approach conducting a qualitative secondary analysis of two original data sets. In total, seventeen professional staff members from two municipal family carer support units in Sweden that had implemented ICTs were interviewed using a semi-structured interview guide consisting of open-ended questions. Two data sets were merged using latent qualitative content analysis. Secondary analysis produced three subthemes and an overall theme, a virtual road as a carriageway for the support of working carers, consisting of both enabling and hindering aspects in family support. This theme provides access points in both directions and is based on caring instruments that enable nursing staff's support role. The staff's sustainability and ability to support is influenced by caring opportunities and barriers. The findings suggest the ICTs to be flexible structures that provided nursing staff with a means and method to support working carers of older people. To overcome barriers to its use, measures to optimise support for working carers and the older person are needed. The use of ICTs provides nurses with a means to offer support to working carers of older people and enables carers to be informed, to learn and to share their burdens with others when caring for an older family member. © 2015 John Wiley & Sons Ltd.

Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding.

PubMed

Tischer, Alexander; Auton, Matthew

2013-09-01

We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea-temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea-temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of ΔH0 and ΔCP0 that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. © 2013 The Protein Society.

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.

Secondary flow structures in a 180∘ elastic curved vessel with torsion under steady and pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Najjari, Mohammad Reza; Plesniak, Michael W.

2017-11-01

Secondary flow vortical structures were investigated in an elastic 180° curved pipe with and without torsion under steady and pulsatile flow using particle image velocimetry (PIV). The elastic thin-walled curved pipes were constructed using Sylgard 184, and inserted into a bath of refractive index matched fluid to perform PIV. A vortex identification method was employed to identify various vortical structures in the flow. The secondary flow structures in the planar compliant model with dilatation of 0.61%-3.23% under pulsatile flow rate were compared with the rigid vessel model results, and it was found that local vessel compliance has a negligible effect on secondary flow morphology. The secondary flow structures were found to be more sensitive to out of plane curvature (torsion) than to vessel compliance. Torsion distorts the symmetry of secondary flow and results in more complex vortical structures in both steady and pulsatile flows. In high Re number steady flow with torsion, a single dominant vortical structure can be detected at the middle of the 90° cross section. In pulsatile flow with torsion, the split-Dean and Lyne-type vortices with same rotation direction originating from opposite sides of the cross section tend to merge together. supported by GW Center for Biomimetics and Bioinspired Engineering.

A parallel strategy for predicting the secondary structure of polycistronic microRNAs.

PubMed

Han, Dianwei; Tang, Guiliang; Zhang, Jun

2013-01-01

The biogenesis of a functional microRNA is largely dependent on the secondary structure of the microRNA precursor (pre-miRNA). Recently, it has been shown that microRNAs are present in the genome as the form of polycistronic transcriptional units in plants and animals. It will be important to design efficient computational methods to predict such structures for microRNA discovery and its applications in gene silencing. In this paper, we propose a parallel algorithm based on the master-slave architecture to predict the secondary structure from an input sequence. We conducted some experiments to verify the effectiveness of our parallel algorithm. The experimental results show that our algorithm is able to produce the optimal secondary structure of polycistronic microRNAs.

Gel-based and gel-free proteomic analysis of Nicotiana tabacum trichomes identifies proteins involved in secondary metabolism and in the (a)biotic stress response.

PubMed

Van Cutsem, Emmanuel; Simonart, Géraldine; Degand, Hervé; Faber, Anne-Marie; Morsomme, Pierre; Boutry, Marc

2011-02-01

Nicotiana tabacum leaves are covered by trichomes involved in the secretion of large amounts of secondary metabolites, some of which play a major role in plant defense. However, little is known about the metabolic pathways that operate in these structures. We undertook a proteomic analysis of N. tabacum trichomes in order to identify their protein complement. Efficient trichome isolation was obtained by abrading frozen leaves. After homogenization, soluble proteins and a microsomal fraction were prepared by centrifugation. Gel-based and gel-free proteomic analyses were then performed. 2-DE analysis of soluble proteins led to the identification of 1373 protein spots, which were digested and analyzed by MS/MS, leading to 680 unique identifications. Both soluble proteins and microsomal fraction were analyzed by LC MALDI-MS/MS after trypsin digestion, leading to 858 identifications, many of which had not been identified after 2-DE, indicating that the two methods complement each other. Many enzymes putatively involved in secondary metabolism were identified, including enzymes involved in the synthesis of terpenoid precursors and in acyl sugar production. Several transporters were also identified, some of which might be involved in secondary metabolite transport. Various (a)biotic stress response proteins were also detected, supporting the role of trichomes in plant defense. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Synthesis of robalzotan, ebalzotan, and rotigotine precursors via the stereoselective multienzymatic cascade reduction of α,β-unsaturated aldehydes.

PubMed

Brenna, Elisabetta; Gatti, Francesco G; Malpezzi, Luciana; Monti, Daniela; Parmeggiani, Fabio; Sacchetti, Alessandro

2013-05-17

A stereoselective synthesis of bicyclic primary or secondary amines, based on tetralin or chroman structural moieties, is reported. These amines are precursors of important active pharmaceutical ingredients such as rotigotine (Neupro), robalzotan, and ebalzotan. The key step is based on a multienzymatic reduction of an α,β-unsaturated aldehyde or ketone to give the saturated primary or secondary alcohol, in a high yield and with a high ee. The catalytic system consists of the combination of an ene-reductase (ER; i.e., OYE2 or OYE3 belonging to the Old Yellow Enzyme family) with an alcohol dehydrogenase (ADH), applying the in situ substrate feeding product removal technology. By this system the formation of the allylic alcohol side product and the racemization of the chirally unstable α-substituted aldehyde intermediate are minimized. The primary alcohols were elaborated via a Curtius rearrangement. The combination of OYE2 with a Prelog or an anti-Prelog ADH allowed the preparation of the secondary alcohols with ee > 99% and de > 87%. The absolute configuration of the primary amines was unambiguously assigned by comparison with authentic samples. The stereochemistry of secondary alcohols was assigned by X-ray crystal structure and NMR analysis of Mosher esters.

The health benefits of secondary education in adolescents and young adults: An international analysis in 186 low-, middle- and high-income countries from 1990 to 2013.

PubMed

Viner, Russell M; Hargreaves, Dougal S; Ward, Joseph; Bonell, Chris; Mokdad, Ali H; Patton, George

2017-12-01

The health benefits of secondary education have been little studied. We undertook country-level longitudinal analyses of the impact of lengthening secondary education on health outcomes amongst 15-24 year olds. Exposures: average length of secondary and primary education from 1980 to 2013.Data/Outcomes: Country level adolescent fertility rate (AFR), HIV prevalence and mortality rate from 1989/90 to 2013 across 186 low-, middle- and high-income countries.Analysis: Longitudinal mixed effects models, entering secondary and primary education together, adjusted for time varying GDP and country income status. Longitudinal structural marginal models using inverse probability weighting (IPW) to take account of time varying confounding by primary education and GDP. Counterfactual scenarios of no change in secondary education since 1980/1990 were estimated from model coefficients for each outcome. Each additional year of secondary education decreased AFR by 8.4% in mixed effects models and 14.6% in IPW models independent of primary education and GDP. Counterfactual analyses showed the proportion of the reduction in adolescent fertility rate over the study period independently attributable to secondary education was 28% in low income countries. Each additional year of secondary education reduced mortality by 16.9% for 15-19 year and 14.8% for 20-24 year old young women and 11.4% for 15-19 year and 8.8% for 20-24 year old young men. Counterfactual scenarios suggested 12% and 23% of the mortality reduction for 15-19 and 20-24 year old young men was attributable to secondary education in low income countries. Each additional year of secondary education was associated with a 24.5% and 43.1% reduction in HIV prevalence amongst young men and women. The health benefits associated with secondary education were greater than those of primary education and were greatest amongst young women and those from low income countries. Secondary education has the potential to be a social vaccine across many outcomes in low and middle income countries.

Epigenetic modifiers alter the secondary metabolite composition of a plant endophytic fungus, Pestalotiopsis crassiuscula obtained from the leaves of Fragaria chiloensis.

PubMed

Yang, Xiao-Long; Huang, Le; Ruan, Xiao-Li

2014-01-01

The addition of the DNA methyltransferase inhibitor 500 μM 5-azacytidine to the culture medium of a plant endophytic fungus, Pestalotiopsis crassiuscula, obtained from the leaves of Fragaria chiloensis, dramatically altered the profiles of its metabolites and resulted in the isolation of one new coumarin (1), along with six known compounds (2-7). HPLC profiles revealed that only compounds 3, 4, and 7 belonged to the new induced secondary metabolites. The structures of all isolated compounds were elucidated on the basis of extensive analysis of NMR spectra.

[Development of an index system for the comprehensive evaluation on public health emergency events surveillance system in China].

PubMed

Hong, Zhiheng; Ni, Daxin; Cao, Yang; Meng, Ling; Tu, Wenxiao; Li, Leilei; Li, Qun; Jin, Lianmei

2015-06-01

To establish a comprehensive evaluation index system for the China Public Health Emergency Events Surveillance System (CPHEESS). A draft index system was built through literature review and under the consideration of the characteristics on CPHEESS. Delphi method was adapted to determine the final index system. The index system was divided into primary, secondary and tertiary levels. There were 4 primary indicators: System structure, Network platform, Surveillance implementation reports with Data analysis and utilization. There were 16 secondary and 70 tertiary indicators being set, with System structure including 14 tertiary indicators (accounted for 20.00%), 21 Network platforms (accounted for 30.00%). Twenty-four Surveillance implementation reports (accounted for 34.29%), 11 Data analysis and utilization (accounted for 15.71%). The average score of importance of each indicators was 4.29 (3.77-4.94), with an average coefficient variation as 0.14 (0.12-0.16). The mean Chronbach's α index was 0.84 (0.81-0.89). The adaptability of each related facilities indicator was specified. The primary indicators were set in accordance with the characteristics and goals of the surveillance systems. Secondary indicators provided key elements in the management and control of the system while the tertiary indicators were available and operative. The agreement rate of experts was high with good validity and reliability. This index system could be used for CPHEESS in future.

The Globular State of the Single-Stranded RNA: Effect of the Secondary Structure Rearrangements

PubMed Central

Grigoryan, Zareh A.; Karapetian, Armen T.

2015-01-01

The mutual influence of the slow rearrangements of secondary structure and fast collapse of the long single-stranded RNA (ssRNA) in approximation of coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary structure rearrangement is much longer than that for the formation of the tertiary structure. A nonequilibrium phase transition of the 2nd order has been observed. PMID:26345143

Principles for Predicting RNA Secondary Structure Design Difficulty.

PubMed

Anderson-Lee, Jeff; Fisker, Eli; Kosaraju, Vineet; Wu, Michelle; Kong, Justin; Lee, Jeehyung; Lee, Minjae; Zada, Mathew; Treuille, Adrien; Das, Rhiju

2016-02-27

Designing RNAs that form specific secondary structures is enabling better understanding and control of living systems through RNA-guided silencing, genome editing and protein organization. Little is known, however, about which RNA secondary structures might be tractable for downstream sequence design, increasing the time and expense of design efforts due to inefficient secondary structure choices. Here, we present insights into specific structural features that increase the difficulty of finding sequences that fold into a target RNA secondary structure, summarizing the design efforts of tens of thousands of human participants and three automated algorithms (RNAInverse, INFO-RNA and RNA-SSD) in the Eterna massive open laboratory. Subsequent tests through three independent RNA design algorithms (NUPACK, DSS-Opt and MODENA) confirmed the hypothesized importance of several features in determining design difficulty, including sequence length, mean stem length, symmetry and specific difficult-to-design motifs such as zigzags. Based on these results, we have compiled an Eterna100 benchmark of 100 secondary structure design challenges that span a large range in design difficulty to help test future efforts. Our in silico results suggest new routes for improving computational RNA design methods and for extending these insights to assess "designability" of single RNA structures, as well as of switches for in vitro and in vivo applications. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

¹⁵N, ¹³C and ¹H resonance assignments and secondary structure determination of a variable heavy domain of a heavy chain antibody.

PubMed

Prosser, Christine E; Waters, Lorna C; Muskett, Frederick W; Veverka, Vaclav; Addis, Philip W; Griffin, Laura M; Baker, Terry S; Lawson, Alastair D G; Wernery, Ulrich; Kinne, Jorg; Henry, Alistair J; Taylor, Richard J; Carr, Mark D

2014-04-01

Heavy chain antibodies differ in structure to conventional antibodies lacking both the light chain and the first heavy chain constant domain (CH1). Characteristics of the antigen-binding variable heavy domain of the heavy chain antibody (VHH) including the smaller size, high solubility and stability make them an attractive alternative to more traditional antibody fragments for detailed NMR-based structural analysis. Here we report essentially complete backbone and side chain (15)N, (13)C and (1)H assignments for a free VHH. Analysis of the backbone chemical shift data obtained indicates that the VHH is comprised predominantly of β-sheets corresponding to nearly 60% of the protein backbone.

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations

PubMed Central

Porollo, Aleksey; Meller, Jaroslaw

2010-01-01

Molecular simulations offer important mechanistic and functional clues in studies of proteins and other macromolecules. However, interpreting the results of such simulations increasingly requires tools that can combine information from multiple structural databases and other web resources, and provide highly integrated and versatile analysis tools. Here, we present a new web server that integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules. The new tool, dubbed POLYVIEW-MM, enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking. To facilitate structural analysis, POLYVIEW-MM combines interactive view and analysis of conformational changes using Jmol and its tailored extensions, publication quality animation using PyMol, and customizable 2D summary plots that provide an overview of MM, e.g. in terms of changes in secondary structure states and relative solvent accessibility of individual residues in proteins. Furthermore, POLYVIEW-MM integrates visualization with various structural annotations, including automated mapping of known inter-action sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains. URL: http://polyview.cchmc.org/conform.html. PMID:20504857

A possible glycosidic benzophenone with full substitution on B-ring from Psidium guajava leaves.

PubMed

Venditti, Alessandro; Ukwueze, Stanley E

2017-04-01

Bidimensional NMR analysis may be a useful tool to resolve the structure of chemical compounds also in mixture. This letter would demonstrate how these techniques could be applied e.g. to the reported case on identification of benzophenone glycoside from Psidium guajava. A tentative structure for the secondary component, not yet described, was possibly proposed on the basis of observation and critic review of available 1D and 2D NMR spectra.

Secondary flow in a curved artery model with Newtonian and non-Newtonian blood-analog fluids

NASA Astrophysics Data System (ADS)

Najjari, Mohammad Reza; Plesniak, Michael W.

2016-11-01

Steady and pulsatile flows of Newtonian and non-Newtonian fluids through a 180°-curved pipe were investigated using particle image velocimetry (PIV). The experiment was inspired by physiological pulsatile flow through large curved arteries, with a carotid artery flow rate imposed. Sodium iodide (NaI) and sodium thiocyanate (NaSCN) were added to the working fluids to match the refractive index (RI) of the test section to eliminate optical distortion. Rheological measurements revealed that adding NaI or NaSCN changes the viscoelastic properties of non-Newtonian solutions and reduces their shear-thinning property. Measured centerline velocity profiles in the upstream straight pipe agreed well with an analytical solution. In the pulsatile case, secondary flow structures, i.e. deformed-Dean, Dean, Wall and Lyne vortices, were observed in various cross sections along the curved pipe. Vortical structures at each cross section were detected using the d2 vortex identification method. Circulation analysis was performed on each vortex separately during the systolic deceleration phase, and showed that vortices split and rejoin. Secondary flow structures in steady flows were found to be morphologically similar to those in pulsatile flows for sufficiently high Dean number. supported by the George Washington University Center for Biomimetics and Bioinspired Engineering.

Reactivity change of IgE to buckwheat protein treated with high-pressure and enzymatic hydrolysis.

PubMed

Lee, Chaeyoon; In, Sooyeon; Han, Youngshin; Oh, Sangsuk

2016-04-01

Buckwheat is a popular food material in eastern Asian countries that can cause allergenic response. This study was conducted to evaluate the effects of hydrolysis with papain and high-pressure (HP) treatment of buckwheat protein (BWP) on reactivity of immunoglobulin E (IgE) and its secondary structure. Reactivity of IgE was examined by enzyme-linked immunosorbent assay (ELISA) with serum samples from 16 patients allergic to buckwheat. Reactivity of IgE to hydrolysate of BWP with papain showed a maximum decrease of 79.8%. After HP treatment at 600 MPa for 1 min, reactivity of IgE to BWP decreased by up to 55.1%. When extracted, BWP was hydrolyzed with papain overnight following HP treatment at 600 MPa which the reactivity of IgE decreased significantly by up to 87.1%. Significant changes in secondary structure of BWP were observed by circular dichroism (CD) analysis after hydrolysis with papain following HP treatment. Reduction of reactivity of IgE showed a correlation with changes in secondary structure of BWP, which may cause changes in conformational epitopes. This suggests the possibility of decreasing the reactivity of IgE to BWP using combined physical and enzymatic treatments. © 2015 Society of Chemical Industry.

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

A quantum chemical study of the structures, stability, and spectroscopy of halogen- and hydrogen-boned complexes between cyanoacetaldehyde and hypochlorous acids

NASA Astrophysics Data System (ADS)

Tang, Qingjie; Guo, Zhenfu; Li, Qingzhong

2014-03-01

The complexes of cyanoacetaldehyde and hypohalous acid (HOX, X = Cl, Br, and I) have been investigated. They can form six different structures (A, B, C, D, E, and F), the former three structures are mainly combined through a N(O)⋯X halogen bond and the latter three structures are maintained mainly by a N(O)⋯H hydrogen bond, although other weaker interactions are also present in most structures. The hydrogen-bonded structures are more stable than the respective halogen-bonded structures. The Osbnd H and Osbnd X bonds in the halogen- and hydrogen-bonded complexes are lengthened and show an observed red shift, while those in the weaker secondary interactions are contracted and display a small blue shift. The orbital interactions in NBO analysis and the electron densities in AIM analysis provide useful and reliable information for the strength of each type of interaction in different structures.

Arc is a flexible modular protein capable of reversible self-oligomerization

PubMed Central

Myrum, Craig; Baumann, Anne; Bustad, Helene J.; Flydal, Marte Innselset; Mariaule, Vincent; Alvira, Sara; Cuéllar, Jorge; Haavik, Jan; Soulé, Jonathan; Valpuesta, José Maria; Márquez, José Antonio; Martinez, Aurora; Bramham, Clive R.

2015-01-01

The immediate early gene product Arc (activity-regulated cytoskeleton-associated protein) is posited as a master regulator of long-term synaptic plasticity and memory. However, the physicochemical and structural properties of Arc have not been elucidated. In the present study, we expressed and purified recombinant human Arc (hArc) and performed the first biochemical and biophysical analysis of hArc's structure and stability. Limited proteolysis assays and MS analysis indicate that hArc has two major domains on either side of a central more disordered linker region, consistent with in silico structure predictions. hArc's secondary structure was estimated using CD, and stability was analysed by CD-monitored thermal denaturation and differential scanning fluorimetry (DSF). Oligomerization states under different conditions were studied by dynamic light scattering (DLS) and visualized by AFM and EM. Biophysical analyses show that hArc is a modular protein with defined secondary structure and loose tertiary structure. hArc appears to be pyramid-shaped as a monomer and is capable of reversible self-association, forming large soluble oligomers. The N-terminal domain of hArc is highly basic, which may promote interaction with cytoskeletal structures or other polyanionic surfaces, whereas the C-terminal domain is acidic and stabilized by ionic conditions that promote oligomerization. Upon binding of presenilin-1 (PS1) peptide, hArc undergoes a large structural change. A non-synonymous genetic variant of hArc (V231G) showed properties similar to the wild-type (WT) protein. We conclude that hArc is a flexible multi-domain protein that exists in monomeric and oligomeric forms, compatible with a diverse, hub-like role in plasticity-related processes. PMID:25748042

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

2008-01-01

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

Secondary Moments due to Prestressing with Different Bond at the Ultimate Limit State

NASA Astrophysics Data System (ADS)

Halvoník, Jaroslav; Pažma, Peter; Vida, Radoslav

2018-03-01

Secondary effects of prestressing develop in statically indeterminate structures (e.g., continuous beams) due to the restraint of deformations imposed by hyperstatic restraints. These effects may significantly influence internal forces and stresses in prestressed structures. Secondary effects are influenced by the redundancy of a structural system, which raises the question of whether they will remain constant after a change in the structural system, e.g., due to the development of plastic hinge(s) in a critical cross-section(s) or after the development of a kinematic mechanism, or if they will disappear when the structure changes into a sequence of simply supported beams. The paper deals with an investigation of the behavior of continuous post-tensioned beams subjected to an ultimate load with significant secondary effects from prestressing. A total of 6 two-span beams prestressed by tendons with different bonds were tested in a laboratory with a load that changed their structural system into a kinematic mechanism. The internal forces and secondary effects of the prestressing were controlled through measurements of the reactions in all the supports. The results revealed that the secondary effects remained as a permanent part of the action on the experimental beams, even after the development of the kinematic mechanism. The results obtained confirmed that secondary effects should be included in all combinations of actions for verifications of ultimate limit states (ULS).

Rheological and secondary structural characterization of rice flour-zein composites for noodles slit from gluten-free sheeted dough.

PubMed

Jeong, Sungmin; Kim, Hee Won; Lee, Suyong

2017-04-15

Rice flour-zein composites in a hydrated viscoelastic state were utilized to compensate for the role of wheat gluten in gluten-free sheeted dough. The use of zein above its glass transition temperature was able to form a viscoelastic protein network of non-wheat dough with rice flour. The mixing stability and development time of the rice dough were positively increased with increasing levels of zein. The protein secondary structural analysis by FTIR spectroscopy demonstrated that the rice doughs with high levels of zein showed significant increases in β-sheet structures whose intensity was almost doubled by the use of 10% zein. The use of zein at more than 5% (w/w) successfully produced gluten-free dough sheets that could be slit into thin and long noodle strands. In addition, the composites were effective in improving the rheological characteristics of gluten-free noodle strands by increasing their maximum force to extension, compared to wheat-based noodles. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural studies of ROK fructokinase YdhR from Bacillus subtilis : insights into substrate binding and fructose specificity.

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

Nocek, B.; Stein, A.; Jedrzejczak, R.

2011-02-18

The main pathway of bacterial sugar phosphorylation utilizes specific phosphoenolpyruvate phosphotransferase system (PTS) enzymes. In addition to the classic PTS system, a PTS-independent secondary system has been described in which nucleotide-dependent sugar kinases are used for monosaccharide phosphorylation. Fructokinase (FK), which phosphorylates d-fructose with ATP as a cofactor, has been shown to be a member of this secondary system. Bioinformatic analysis has shown that FK is a member of the 'ROK' (bacterial Repressors, uncharacterized Open reading frames, and sugar Kinases) sequence family. In this study, we report the crystal structures of ROK FK from Bacillus subtilis (YdhR) (a) apo andmore » in the presence of (b) ADP and (c) ADP/d-fructose. All structures show that YdhR is a homodimer with a monomer composed of two similar {alpha}/{beta} domains forming a large cleft between domains that bind ADP and d-fructose. Enzymatic activity assays support YdhR function as an ATP-dependent fructose kinase.« less

Synthesis, spectroscopic, DFT studies and biological activity of some ruthenium carbonyl derivatives of bis-(salicylaldehyde)phenylenediimine Schiff base ligand

NASA Astrophysics Data System (ADS)

Ramadan, Ramadan M.; Abu Al-Nasr, Ahmad K.; Ali, Omayma A. M.

2018-06-01

Bis-(salicylaldehyde)phenylenediimine Schiff base (H2salphen) reacted oxidatively with the triruthenium dodecacarbonyl complex, [Ru3(CO)12] to give the dicarbonyl derivative [Ru(CO)2(salphen)], 1. In presence of a secondary ligand L (L = pyridine, triphenyl phosphine, 2-aminobenzimidazole or thiourea), the monocarbonyl derivatives [Ru(CO)(salphen)L], 2-5, were isolated. When the bipyridine (bpy) ligand was used as a secondary ligand, the dicarbonyl complex [Ru(CO)2(Hsalphen)(bpy)], 6, was obtained. In complexes 1-5, the Schiff base ligand acted as a tetradentate, while it coordinated as a bidentate in complex 6. The structure and stoichiometry of the complexes were investigated by the conventional analytical and spectroscopic techniques, which revealed that they have several structural arrangements. The structures of ligand and complexes were verified by theoretical calculations based on accurate DFT approximations. The relative reactivities were estimated using chemical descriptors analysis. Biological activities of the complexes against the Escherchia coli and Staphylococcus aureus bacteria were screened.

IMG-ABC: An Atlas of Biosynthetic Gene Clusters to Fuel the Discovery of Novel Secondary Metabolites

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

Chen, I-Min; Chu, Ken; Ratner, Anna

2014-10-28

In the discovery of secondary metabolites (SMs), large-scale analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of relevant computational resources. We present IMG-ABC (https://img.jgi.doe.gov/abc/) -- An Atlas of Biosynthetic gene Clusters within the Integrated Microbial Genomes (IMG) system1. IMG-ABC is a rich repository of both validated and predicted biosynthetic clusters (BCs) in cultured isolates, single-cells and metagenomes linked with the SM chemicals they produce and enhanced with focused analysis tools within IMG. The underlying scalable framework enables traversal of phylogenetic dark matter and chemical structure space -- serving as a doorwaymore » to a new era in the discovery of novel molecules.« less

[Changes in the secondary and tertiary structure of serum albumin in interactions with ligands of various structures].

PubMed

Trinus, F P; Braver-Chernobul'skaia, B S; Luĭk, A I; Boldeskul, A E; Velichko, A N

1984-01-01

High affinity interactions between blood serum albumin and five substances of various chemical structure, exhibiting distinct physiological activity, were accompanied by alterations in the protein tertiary structure, while the albumin secondary structure was involved in conformational transformation after less effective affinity binding.

High Temperature Unfolding and Low Temperature Refolding Pathway of Chymotrypsin Inhibitor 2 Using Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Malau, N. D.; Sumaryada, T.

2016-01-01

The mechanism that explains the unfolding/refolding process of the protein is still a major problem that has not been fully understood. In this paper we present our study on the unfolding and refolding pathway of Chymotrypsin Inhibitor 2 (CI2) protein through a molecular dynamics simulation technique. The high temperature unfolding simulation were performed at 500 K for 35 ns. While the low temperature refolding simulation performed at 200 K for 35 ns. The unfolding and refolding pathway of protein were analysed by looking at the dynamics of root mean squared deviation (RMSD) and secondary structure profiles. The signatures of unfolding were observed from significant increase of RMSD within the time span of 10 ns to 35 ns. For the refolding process, the initial structure was prepared from the structure of unfolding protein at t=15 ns and T=500 K. Analysis have shown that some of the secondary structures of CI2 protein that have been damaged at high temperature can be refolded back to its initial structure at low temperature simulation. Our results suggest that most of α-helix structure of CI2 protein can be refolded back to its initial state, while only half beta-sheet structure can be reformed.

Multiscale integral analysis of a HT leakage in a fusion nuclear power plant

NASA Astrophysics Data System (ADS)

Velarde, M.; Fradera, J.; Perlado, J. M.; Zamora, I.; Martínez-Saban, E.; Colomer, C.; Briani, P.

2016-05-01

The present work presents an example of the application of an integral methodology based on a multiscale analysis that covers the whole tritium cycle within a nuclear fusion power plant, from a micro scale, analyzing key components where tritium is leaked through permeation, to a macro scale, considering its atmospheric transport. A leakage from the Nuclear Power Plants, (NPP) primary to the secondary side of a heat exchanger (HEX) is considered for the present example. Both primary and secondary loop coolants are assumed to be He. Leakage is placed inside the HEX, leaking tritium in elementary tritium (HT) form to the secondary loop where it permeates through the piping structural material to the exterior. The Heating Ventilation and Air Conditioning (HVAC) system removes the leaked tritium towards the NPP exhaust. The HEX is modelled with system codes and coupled to Computational Fluid Dynamic (CFD) to account for tritium dispersion inside the nuclear power plants buildings and in site environment. Finally, tritium dispersion is calculated with an atmospheric transport code and a dosimetry analysis is carried out. Results show how the implemented methodology is capable of assessing the impact of tritium from the microscale to the atmospheric scale including the dosimetric aspect.

The Novaco Anger Scale--Provocation Inventory (1994 Version) in Dutch Forensic Psychiatric Patients

ERIC Educational Resources Information Center

Hornsveld, Ruud H. J.; Muris, Peter; Kraaimaat, Floris W.

2011-01-01

We examined the psychometric properties of the Novaco Anger Scale--Provocation Inventory (NAS-PI, 1994 version) in Dutch violent forensic psychiatric patients and secondary vocational students. A confirmatory factor analysis of the subscale structure of the NAS was carried out, reliability was investigated, and relations were calculated between…

Mathematics Teaching as Problem Solving: A Framework for Studying Teacher Metacognition Underlying Instructional Practice in Mathematics.

ERIC Educational Resources Information Center

Artzt, Alice F.; Armour-Thomas, Eleanor

1998-01-01

Uses a "teaching as problem solving" perspective to examine the components of metacognition underlying the instructional practice of seven experienced and seven beginning secondary-school mathematics teachers. Data analysis of observations, lesson plans, videotapes, and audiotapes of structured interviews suggests that the metacognition of…

Analysing Teachers' Operations When Teaching Students: What Constitutes Scientific Theories?

ERIC Educational Resources Information Center

Holmqvist, Mona O.; Olander, Clas

2017-01-01

The aim of the study is to analyse teachers' efforts to develop secondary school students' knowledge and argumentation skills of what constitutes scientific theories. The analysis is based on Leontiev's three-level structure of activity (activity, action, and operation), as these levels correspond to the questions why, what, and how content is…

Exploring Student, Family, and School Predictors of Self-Determination Using NLTS2 Data

ERIC Educational Resources Information Center

Shogren, Karrie A.; Garnier Villarreal, Mauricio; Dowsett, Chantelle; Little, Todd D.

2016-01-01

This study conducted secondary analysis of data from the National Longitudinal Transition Study-2 (NLTS2) to examine the degree to which student, family, and school constructs predicted self-determination outcomes. Multi-group structural equation modeling was used to examine predictive relationships between 5 students, 4 family, and 7 school…

Exploring Student, Family, and School Predictors of Self-Determination Using NLTS2 Data

ERIC Educational Resources Information Center

Shogren, Karrie A.; Garnier Villarreal, Mauricio; Dowsett, Chantelle; Little, Todd D.

2016-01-01

This study conducted secondary analysis of data from the National Longitudinal Transition Study-2 (NLTS2) to examine the degree to which student, family, and school constructs predicted self-determination outcomes. Multi-group structural equation modeling was used to examine predictive relationships between 5 student, 4 family, and 7 school…

How Distributed Leadership Can Make a Difference in Teachers' Organizational Commitment? A Qualitative Study

ERIC Educational Resources Information Center

Hulpia, Hester; Devos, Geert

2010-01-01

The present study explores the relation between distributed leadership and teachers' organizational commitment. Semi-structured interviews with teachers and school leaders of secondary schools were conducted. A comparative analysis of four schools with high and four schools with low committed teachers was carried out. Findings revealed differences…

Building Connections: An Interpretative Phenomenological Analysis of Qualitative Research Students' Learning Experiences

ERIC Educational Resources Information Center

Cooper, Robin; Fleischer, Anne; Cotton, Fatima A.

2012-01-01

This paper describes a phenomenological study in which the authors explored students' experiences learning qualitative research in a variety of academic fields. Semi-structured in-depth interviews were conducted with six participants from various academic fields who had completed at least one post-secondary-school-level qualitative research course…

When Projects of "Empowerment" Don't Liberate: Locating Agency in a "Postcolonial" Peace Education

ERIC Educational Resources Information Center

Shirazi, Roozbeh

2011-01-01

By juxtaposing male secondary student and teacher classroom practices with a postcolonial analysis of the structural and discursive forces that characterize education reform in Jordan, this study draws attention to the ways that authoritarian regimes may coopt peace education language and concepts, such as "dialogue" and…

The Relevance of Depressive Symptoms and Social Support to Disability in Women with Multiple Sclerosis or Fibromyalgia

ERIC Educational Resources Information Center

Phillips, Lorraine J.

2010-01-01

Multiple sclerosis and fibromyalgia syndrome may spur substantial disability for those affected. Using structural equation modeling, this secondary analysis examined predictors of disability in women with multiple sclerosis (n = 118) and fibromyalgia syndrome (n = 197) recruited for separate wellness studies. Greater functional limitations, lower…

Whose Model Student? Learner-Centered Discourse and the Post-Secondary Privatization Agenda

ERIC Educational Resources Information Center

Hoben, John

2016-01-01

Using discourse analysis, the author identifies contradictions in privatization discourse in order to highlight how state-based educational reform has used a normative language of student interests to fundamentally redefine the nature of the university's mission and its faculty based governance structures. The author proposes a counter-discourse…

Teacher Behavior Unwanted According to Student's Perceptions

ERIC Educational Resources Information Center

Yildirim, Isa; Akan, Durdagi; Yalçin, Sinan

2016-01-01

This study was conducted in the aim of revealing the misbehaviors of the teachers according to the perceptions of the students. In the study, semi-structured interview was done with 8th grade 45 students, 20 males and 25 females, from three secondary school determined through purposive sampling. The interviews were analyzed with content analysis,…

Classroom Environments and Student Empowerment: An Analysis of Elementary and Secondary Teacher Beliefs

ERIC Educational Resources Information Center

Nichols, Joe D.; Zhang, Guanglan

2011-01-01

This project explored a classroom model of motivation in which the source of student motivation is based on internal mechanisms or structures and classroom student/instructor interactions. It also extended earlier research in which beliefs of veteran, entry level, and preservice teachers have been explored. For this project, 117 elementary…

Opening up "Spaces for Manoeuvre": English Teacher Perspectives on Learner Motivation

ERIC Educational Resources Information Center

Glas, Katharina

2016-01-01

This qualitative study explores teachers' perspectives on learner motivation for English in Chilean secondary schools. Drawing both on motivation theories and on concepts related to teacher cognition, autonomy and agency, the analysis of 19 semi-structured interviews with Chilean English teachers sheds light on the difficulties that many teachers…

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.

Tannin structural elucidation and quantitative ³¹P NMR analysis. 1. Model compounds.

PubMed

Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

2013-10-02

Tannins and flavonoids are secondary metabolites of plants that display a wide array of biological activities. This peculiarity is related to the inhibition of extracellular enzymes that occurs through the complexation of peptides by tannins. Not only the nature of these interactions, but more fundamentally also the structure of these heterogeneous polyphenolic molecules are not completely clear. This first paper describes the development of a new analytical method for the structural characterization of tannins on the basis of tannin model compounds employing an in situ labeling of all labile H groups (aliphatic OH, phenolic OH, and carboxylic acids) with a phosphorus reagent. The ³¹P NMR analysis of ³¹P-labeled samples allowed the unprecedented quantitative and qualitative structural characterization of hydrolyzable tannins, proanthocyanidins, and catechin tannin model compounds, forming the foundations for the quantitative structural elucidation of a variety of actual tannin samples described in part 2 of this series.

Measuring changes in chemistry, composition, and molecular structure within hair fibers by infrared and Raman spectroscopic imaging.

PubMed

Zhang, Guojin; Senak, Laurence; Moore, David J

2011-05-01

Spatially resolved infrared (IR) and Raman images are acquired from human hair cross sections or intact hair fibers. The full informational content of these spectra are spatially correlated to hair chemistry, anatomy, and structural organization through univariate and multivariate data analysis. Specific IR and Raman images from untreated human hair describing the spatial dependence of lipid and protein distribution, protein secondary structure, lipid chain conformational order, and distribution of disulfide cross-links in hair protein are presented in this study. Factor analysis of the image plane acquired with IR microscopy in hair sections, permits delineation of specific micro-regions within the hair. These data indicate that both IR and Raman imaging of molecular structural changes in a specific region of hair will prove to be valuable tools in the understanding of hair structure, physiology, and the effect of various stresses upon its integrity.

Quantifying the Strength of General Factors in Psychopathology: A Comparison of CFA with Maximum Likelihood Estimation, BSEM, and ESEM/EFA Bifactor Approaches.

PubMed

Murray, Aja Louise; Booth, Tom; Eisner, Manuel; Obsuth, Ingrid; Ribeaud, Denis

2018-05-22

Whether or not importance should be placed on an all-encompassing general factor of psychopathology (or p factor) in classifying, researching, diagnosing, and treating psychiatric disorders depends (among other issues) on the extent to which comorbidity is symptom-general rather than staying largely within the confines of narrower transdiagnostic factors such as internalizing and externalizing. In this study, we compared three methods of estimating p factor strength. We compared omega hierarchical and explained common variance calculated from confirmatory factor analysis (CFA) bifactor models with maximum likelihood (ML) estimation, from exploratory structural equation modeling/exploratory factor analysis models with a bifactor rotation, and from Bayesian structural equation modeling (BSEM) bifactor models. Our simulation results suggested that BSEM with small variance priors on secondary loadings might be the preferred option. However, CFA with ML also performed well provided secondary loadings were modeled. We provide two empirical examples of applying the three methodologies using a normative sample of youth (z-proso, n = 1,286) and a university counseling sample (n = 359).

Quantum dots induce charge-specific amyloid-like fibrillation of insulin at physiological conditions

NASA Astrophysics Data System (ADS)

Sukhanova, Alyona; Poly, Simon; Shemetov, Anton; Nabiev, Igor R.

2012-10-01

Agglomeration of some proteins may give rise to aggregates that have been identified as the main cause of amyloid diseases. For example, fibrillation of insulin is related to diabetes mellitus. Quantum dots (QDs) are of special interest as tagging agents for diagnostic and therapeutic studies due to their broad absorption spectra, narrow emission spectra, and high photostability. In this study, PEGylated CdSe/ZnS QDs have been shown to induce the formation of amyloid-like fibrils of human insulin under physiological conditions, this process being dependent on the variation of the surface charge of the nanoparticles (NPs) used. Circular dichroism (CD), protein secondary structure analysis, thioflavin T (ThT) fluorescence assay, and the dynamic light scattering (DLS) technique have been used for comparative analysis of different stages of the fibrillation process. In particular, insulin secondary structure remodelling accompanied by a considerable increase in the rate of amyloid fiber formation have been observed after insulin was mixed with PEGylated QDs. Nanoparticles may significantly influence the rate of protein fibrillation and induce new mechanisms of amyloid diseases, as well as offer opportunities for their treatment.

Polarization-dependent two-photon absorption for the determination of protein secondary structure: A theoretical study

NASA Astrophysics Data System (ADS)

Wanapun, Duangporn; Wampler, Ronald D.; Begue, Nathan J.; Simpson, Garth J.

2008-03-01

A new method for sensitive determination of protein secondary structure via multi-photon absorption is considered theoretically. Perturbation theory is developed to describe the polarization-dependent two-photon absorption (TPA) of α-helix and β-sheet protein secondary structures. The exciton coupling interactions responsible for relatively weak electronic circular dichroism in one-photon absorption are predicted to give rise to large changes in the TPA cross-section (>200%) for circular versus linear incident polarizations, defined as CLD. The CLD effect in TPA is electric dipole-allowed, which explains the much greater sensitivity. These predictions suggest TPA should be a viable means of sensitively probing protein secondary structure.

Effects of proline cis-trans isomerization on TB domain secondary structure.

PubMed Central

Yuan, X.; Werner, J. M.; Knott, V.; Handford, P. A.; Campbell, I. D.; Downing, K.

1998-01-01

The transforming growth factor beta (TGF-beta) binding protein-like (TB) domain is found principally in proteins localized to extracellular matrix fibrils, including human fibrillin-1, the defective protein in the Marfan syndrome. Analysis of the nuclear magnetic resonance (NMR) data for the sixth TB module from human fibrillin-1 has revealed the existence of two stable conformers that differ in the isomerization states of two proline residues. Unusually, the two isoforms do not readily interconvert and are stable on the time scale of milliseconds. We have computed independent structures of the major and minor conformers of TB6 to assess how the domain fold adjusts to incorporate alternatively cis- or trans-prolines. Based on previous observations, it has been suggested that multiple conformers can only be accommodated in flexible regions of protein structure. In contrast, P22, which exists in trans in the major form and cis in the minor form of TB6, is in a rigid region of the domain, which is confirmed by backbone dynamics measurements. Overall, the structures of the major and minor conformers are similar. However, the secondary structure topologies of the two forms differ as a direct consequence of the changes in proline conformation. PMID:9792099

An 8 Meter Monolithic UV/Optical Space Telescope

NASA Technical Reports Server (NTRS)

Stahl, H. Philip; Postman, Marc

2008-01-01

The planned Ares V launch vehicle with its 10 meter fairing and at least 55,600 kg capacity to Earth Sun L2 enables entirely new classes of space telescopes. A consortium from NASA, Space Telescope Science Institute, and aerospace industry are studying an 8-meter monolithic primary mirror UV/optical/NIR space telescope to enable new astrophysical research that is not feasible with existing or near-term missions, either space or ground. This paper briefly reviews the science case for such a mission and presents the results of an on-going technical feasibility study, including: optical design; structural design/analysis including primary mirror support structure, sun shade and secondary mirror support structure; thermal analysis; launch vehicle performance and trajectory; spacecraft including structure, propulsion, GN&C, avionics, power systems and reaction wheels; operations & servicing; mass budget and cost.

DNA secondary structures: stability and function of G-quadruplex structures

PubMed Central

Bochman, Matthew L.; Paeschke, Katrin; Zakian, Virginia A.

2013-01-01

In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription. PMID:23032257

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

Efficient algorithms for probing the RNA mutation landscape.

PubMed

Waldispühl, Jérôme; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2008-08-08

The diversity and importance of the role played by RNAs in the regulation and development of the cell are now well-known and well-documented. This broad range of functions is achieved through specific structures that have been (presumably) optimized through evolution. State-of-the-art methods, such as McCaskill's algorithm, use a statistical mechanics framework based on the computation of the partition function over the canonical ensemble of all possible secondary structures on a given sequence. Although secondary structure predictions from thermodynamics-based algorithms are not as accurate as methods employing comparative genomics, the former methods are the only available tools to investigate novel RNAs, such as the many RNAs of unknown function recently reported by the ENCODE consortium. In this paper, we generalize the McCaskill partition function algorithm to sum over the grand canonical ensemble of all secondary structures of all mutants of the given sequence. Specifically, our new program, RNAmutants, simultaneously computes for each integer k the minimum free energy structure MFE(k) and the partition function Z(k) over all secondary structures of all k-point mutants, even allowing the user to specify certain positions required not to mutate and certain positions required to base-pair or remain unpaired. This technically important extension allows us to study the resilience of an RNA molecule to pointwise mutations. By computing the mutation profile of a sequence, a novel graphical representation of the mutational tendency of nucleotide positions, we analyze the deleterious nature of mutating specific nucleotide positions or groups of positions. We have successfully applied RNAmutants to investigate deleterious mutations (mutations that radically modify the secondary structure) in the Hepatitis C virus cis-acting replication element and to evaluate the evolutionary pressure applied on different regions of the HIV trans-activation response element. In particular, we show qualitative agreement between published Hepatitis C and HIV experimental mutagenesis studies and our analysis of deleterious mutations using RNAmutants. Our work also predicts other deleterious mutations, which could be verified experimentally. Finally, we provide evidence that the 3' UTR of the GB RNA virus C has been optimized to preserve evolutionarily conserved stem regions from a deleterious effect of pointwise mutations. We hope that there will be long-term potential applications of RNAmutants in de novo RNA design and drug design against RNA viruses. This work also suggests potential applications for large-scale exploration of the RNA sequence-structure network. Binary distributions are available at http://RNAmutants.csail.mit.edu/.

RNA structural constraints in the evolution of the influenza A virus genome NP segment

PubMed Central

Gultyaev, Alexander P; Tsyganov-Bodounov, Anton; Spronken, Monique IJ; van der Kooij, Sander; Fouchier, Ron AM; Olsthoorn, René CL

2014-01-01

Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed. PMID:25180940

An orientation analysis method for protein immobilized on quantum dot particles

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Inoue, Masae

2009-11-01

The evaluation of orientation of biomolecules immobilized on nanodevices is crucial for the development of high performance devices. Such analysis requires ultra high sensitivity so as to be able to detect less than one molecular layer on a device. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has sufficient sensitivity to evaluate the uppermost surface structure of a single molecular layer. The objective of this study is to develop an orientation analysis method for proteins immobilized on nanomaterials such as quantum dot particles, and to evaluate the orientation of streptavidin immobilized on quantum dot particles by means of TOF-SIMS. In order to detect fragment ions specific to the protein surface, a monoatomic primary ion source (Ga +) and a cluster ion source (Au 3+) were employed. Streptavidin-immobilized quantum dot particles were immobilized on aminosilanized ITO glass plates at amino groups by covalent bonding. The reference samples streptavidin directly immobilized on ITO plates were also prepared. All samples were dried with a freeze dryer before TOF-SIMS measurement. The positive secondary ion spectra of each sample were obtained using TOF-SIMS with Ga + and Au 3+, respectively, and then they were compared so as to characterize each sample and detect the surface structure of the streptavidin immobilized with the biotin-immobilized quantum dots. The chemical structures of the upper surface of the streptavidin molecules immobilized on the quantum dot particles were evaluated with TOF-SIMS spectra analysis. The indicated surface side of the streptavidin molecules immobilized on the quantum dots includes the biotin binding site.

Influence of perceptions and stereotypes of the nursing role on career choice in secondary students: A regional perspective.

PubMed

Raymond, Anita; James, Ainsley; Jacob, Elisabeth; Lyons, Judith

2018-03-01

This study examined the influence that perceptions and stereotypes of the nursing role had on future career choice of rural secondary students. The study was undertaken to identify a method of attracting final year secondary school students to an undergraduate nursing degree at a rural University. A mixed method study using a pre-post-interventional design. The rural campus of an Australian university. 71 secondary students attending a secondary school career development program at a rural Australian university. Semi structured questionnaires were used for data collection. The surveys were analysed using descriptive statistics and content analysis of open-ended survey questions. The research supports the importance of being aware of young people's impressions about nurses and nursing as a career, to ensure the successful implementation of targeted recruitment. Targeted recruitment strategies can increase students' awareness of the wide variety of pathways within nursing, rather than leaving awareness to what family, friends or career advisers tell them, or how nurses are portrayed on television, movies and the media. Copyright © 2018 Elsevier Ltd. All rights reserved.

Information in general medical practices: the information processing model.

PubMed

Crowe, Sarah; Tully, Mary P; Cantrill, Judith A

2010-04-01

The need for effective communication and handling of secondary care information in general practices is paramount. To explore practice processes on receiving secondary care correspondence in a way that integrates the information needs and perceptions of practice staff both clinical and administrative. Qualitative study using semi-structured interviews with a wide range of practice staff (n = 36) in nine practices in the Northwest of England. Analysis was based on the framework approach using N-Vivo software and involved transcription, familiarization, coding, charting, mapping and interpretation. The 'information processing model' was developed to describe the six stages involved in practice processing of secondary care information. These included the amendment or updating of practice records whilst simultaneously or separately actioning secondary care recommendations, using either a 'one-step' or 'two-step' approach, respectively. Many factors were found to influence each stage and impact on the continuum of patient care. The primary purpose of processing secondary care information is to support patient care; this study raises the profile of information flow and usage within practices as an issue requiring further consideration.

Email communication at the medical primary–secondary care interface: a qualitative exploration

PubMed Central

Sampson, Rod; Barbour, Rosaline; Wilson, Philip

2016-01-01

Background There is little published research into the influence of email communication between primary and secondary care clinicians on patient care. Aim To explore the use of email communication between clinicians across the primary– secondary care interface, and how this may relate to patient care. Design and setting A qualitative study involving primary and secondary care services in the NHS Highland Health Board area, Scotland. Ten GPs and 12 hospital consultants were purposively sampled to reflect diversity. Method Eligible clinicians were invited to take part in a semi-structured interview. Data were analysed using a thematic analysis approach. Results Key themes that emerged for clinicians included general perceptions of email; using email in practice (managing workload, impact on patient journeys, and ‘quick answers’); system issues (variability and governance); relational aspects; and email skills. Conclusion Email communication between primary and secondary care clinicians generally has a positive impact on patient access to specialist expertise. Governance issues around the use of clinical email need to be defined. There may currently be a two-tier health service for those patients (and their GPs) requiring ‘quick answers’. PMID:27162209

Email communication at the medical primary-secondary care interface: a qualitative exploration.

PubMed

Sampson, Rod; Barbour, Rosaline; Wilson, Philip

2016-07-01

There is little published research into the influence of email communication between primary and secondary care clinicians on patient care. To explore the use of email communication between clinicians across the primary- secondary care interface, and how this may relate to patient care. A qualitative study involving primary and secondary care services in the NHS Highland Health Board area, Scotland. Ten GPs and 12 hospital consultants were purposively sampled to reflect diversity. Eligible clinicians were invited to take part in a semi-structured interview. Data were analysed using a thematic analysis approach. Key themes that emerged for clinicians included general perceptions of email; using email in practice (managing workload, impact on patient journeys, and 'quick answers'); system issues (variability and governance); relational aspects; and email skills. Email communication between primary and secondary care clinicians generally has a positive impact on patient access to specialist expertise. Governance issues around the use of clinical email need to be defined. There may currently be a two-tier health service for those patients (and their GPs) requiring 'quick answers'. © British Journal of General Practice 2016.

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

Secondary flow vortical structures in a 180∘ elastic curved vessel with torsion under steady and pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Najjari, Mohammad Reza; Plesniak, Michael W.

2018-01-01

Secondary flow structures in a 180∘ curved pipe model of an artery are studied using particle image velocimetry. Both steady and pulsatile inflow conditions are investigated. In planar curved pipes with steady flow, multiple (two, four, six) vortices are detected. For pulsatile flow, various pairs of vortices, i.e., Dean, deformed-Dean, Lyne-type, and split-Dean, are present in the cross section of the pipe at 90∘ into the bend. The effects of nonplanar curvature (torsion) and vessel dilatation on these vortical structures are studied. Torsion distorts the symmetric secondary flows (which exist in planar curvatures) and can result in formation of more complex vortical structures. For example, the split-Dean and Lyne-type vortices with same rotation direction originating from opposite sides of the cross section tend to merge together in pulsatile flow. The vortical structures in elastic vessels with dilatation (0.61%-3.23%) are also investigated and the results are compared with rigid model results. It was found that the secondary flow structures in rigid and elastic models are similar, and hence the local compliance of the vessel does not affect the morphology of secondary flow structures.

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

PubMed Central

Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2009-01-01

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

Ensemble-based prediction of RNA secondary structures.

PubMed

Aghaeepour, Nima; Hoos, Holger H

2013-04-24

Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches. In this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures. Our new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between false negative and false positive base pair predictions. Finally, AveRNA can make use of arbitrary sets of secondary structure prediction procedures and can therefore be used to leverage improvements in prediction accuracy offered by algorithms and energy models developed in the future. Our data, MATLAB software and a web-based version of AveRNA are publicly available at http://www.cs.ubc.ca/labs/beta/Software/AveRNA.

Advances in single-molecule magnet surface patterning through microcontact printing.

PubMed

Mannini, Matteo; Bonacchi, Daniele; Zobbi, Laura; Piras, Federica M; Speets, Emiel A; Caneschi, Andrea; Cornia, Andrea; Magnani, Agnese; Ravoo, Bart Jan; Reinhoudt, David N; Sessoli, Roberta; Gatteschi, Dante

2005-07-01

We present an implementation of strategies to deposit single-molecule magnets (SMMs) using microcontact printing microCP). We describe different approaches of microCP to print stripes of a sulfur-functionalized dodecamanganese (III, IV) cluster on gold surfaces. Comparison by atomic force microscopy profile analysis of the patterned structures confirms the formation of a chemically stable single layer of SMMs. Images based on chemical contrast, obtained by time-of-flight secondary ion mass spectrometry, confirm the patterned structure.

Biophysical Studies of the Type 1 Repeats of Human Thrombospondin-1 to Characterize the Structural Basis of its Angiostatic Effect

DTIC Science & Technology

1999-08-01

and the digest proceeded for 25 minutes at room temperature. Column fractions were then collected in tubes containing soy- bean trypsin inhibitor (STI...characterization. C. Task 3: Analysis of Secondary Structure Composition using Circular Dichroism 1. Far-UV Circular Dichroism of P3 and P123 The University of...native protiens to determine functional activity of segments of a large modular protein, since non-native fragments and small peptides can yield

Metal matrix composite fabrication processes for high performance aerospace structures

NASA Astrophysics Data System (ADS)

Ponzi, C.

A survey is conducted of extant methods of metal matrix composite (MMC) production in order to serve as a basis for prospective MMC users' selection of a matrix/reinforcement combination, cost-effective primary fabrication methods, and secondary fabrication techniques for the achievement of desired performance levels. Attention is given to the illustrative cases of structural fittings, control-surface connecting rods, hypersonic aircraft air inlet ramps, helicopter swash plates, and turbine rotor disks. Methods for technical and cost analysis modeling useful in process optimization are noted.

Human-mediated and natural dispersal of an invasive fish in the eastern Great Lakes.

PubMed

Johansson, Mattias L; Dufour, Bradley A; Wellband, Kyle W; Corkum, Lynda D; MacIsaac, Hugh J; Heath, Daniel D

2018-06-01

The globally invasive Round Goby (Neogobius melanostomus) was introduced to the Great Lakes around 1990, spreading widely and becoming the dominant benthic fish in many areas. The speed and scope of this invasion is remarkable and calls into question conventional secondary spread models and scenarios. We utilized nine microsatellites to identify large-scale genetic structure in Round Goby populations in the eastern Great Lakes, and assessed the role of colonization vs. secondary transport and dispersal in developing this structure. We identified three clusters, corresponding with Lake Huron, eastern Lake Erie, and western Lake Erie plus eastern Lake Ontario, along with three highly divergent populations. Bottleneck analysis identified founder effects in two divergent populations. Regression analyses of isolation by distance and allelic richness vs. distance from the initial invasion site were consistent with limited migration. However, some populations in eastern Lake Erie and Lake Ontario showed anomalously low genetic distance from the original site of colonization, consistent with secondary transport of large numbers of individuals via ballast water. We conclude that genetic structure of Round Goby in the Great Lakes principally resulted from long-distance secondary transport via ballast water with additional movement of individual via bait buckets and natural dispersal. The success of Round Gobies represents an interesting model for colonization characterization; however, those same attributes present significant challenges for conservation and fisheries management. Current management likely prevents many new species from arriving in the Great Lakes, but fails to address the transport of species within the lakes after they arrive; this is an issue of clear and pressing importance.

Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity, signaling and transformations.

PubMed

Matveev, Vladimir V

2010-06-09

According to the hypothesis explored in this paper, native aggregation is genetically controlled (programmed) reversible aggregation that occurs when interacting proteins form new temporary structures through highly specific interactions. It is assumed that Anfinsen's dogma may be extended to protein aggregation: composition and amino acid sequence determine not only the secondary and tertiary structure of single protein, but also the structure of protein aggregates (associates). Cell function is considered as a transition between two states (two states model), the resting state and state of activity (this applies to the cell as a whole and to its individual structures). In the resting state, the key proteins are found in the following inactive forms: natively unfolded and globular. When the cell is activated, secondary structures appear in natively unfolded proteins (including unfolded regions in other proteins), and globular proteins begin to melt and their secondary structures become available for interaction with the secondary structures of other proteins. These temporary secondary structures provide a means for highly specific interactions between proteins. As a result, native aggregation creates temporary structures necessary for cell activity."One of the principal objects of theoretical research in any department of knowledge is to find the point of view from which the subject appears in its greatest simplicity."Josiah Willard Gibbs (1839-1903).

The roll-up and merging of coherent structures in shallow mixing layers

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

Lam, M. Y., E-mail: celmy@connect.ust.hk; Ghidaoui, M. S.; Kolyshkin, A. A.

2016-09-15

The current study seeks a fundamental explanation to the development of two-dimensional coherent structures (2DCSs) in shallow mixing layers. A nonlinear numerical model based on the depth-averaged shallow water equations is used to investigate the temporal evolution of shallow mixing layers, where the mapping from temporal to spatial results is made using the velocity at the center of the mixing layers. The flow is periodic in the streamwise direction. Transmissive boundary conditions are used in the cross-stream boundaries to prevent reflections. Numerical results are compared to linear stability analysis, mean-field theory, and secondary stability analysis. Results suggest that the onsetmore » and development of 2DCS in shallow mixing layers are the result of a sequence of instabilities governed by linear theory, mean-field theory, and secondary stability theory. The linear instability of the shearing velocity gradient gives the onset of 2DCS. When the perturbations reach a certain amplitude, the flow field of the perturbations changes from a wavy shape to a vortical (2DCS) structure because of nonlinearity. The development of the vertical 2DCS does not appear to follow weakly nonlinear theory; instead, it follows mean-field theory. After the formation of 2DCS, separate 2DCSs merge to form larger 2DCS. In this way, 2DCSs grow and shallow mixing layers develop and grow in scale. The merging of 2DCS in shallow mixing layers is shown to be caused by the secondary instability of the 2DCS. Eventually 2DCSs are dissipated by bed friction. The sequence of instabilities can cause the upscaling of the turbulent kinetic energy in shallow mixing layers.« less

Primary vesicles, vesicle-rich segregation structures and recognition of primary and secondary porosities in lava flows from the Paraná igneous province, southern Brazil

NASA Astrophysics Data System (ADS)

Barreto, Carla Joana S.; de Lima, Evandro F.; Goldberg, Karin

2017-04-01

This study focuses on a volcanic succession of pāhoehoe to rubbly lavas of the Paraná-Etendeka Province exposed in a single road profile in southernmost Brazil. This work provides an integrated approach for examining primary vesicles and vesicle-rich segregation structures at the mesoscopic scale. In addition, this study provides a quantitative analysis of pore types in thin section. We documented distinct distribution patterns of vesicle and vesicle-rich segregation structures according to lava thickness. In compound pāhoehoe lavas, the cooling allows only vesicles (<1 cm size) and pipe vesicles to be frozen into place. In inflated pāhoehoe lavas, vesicles of different sizes are common, including pipe vesicles, and also segregation structures such as proto-cylinders, cylinders, cylinder sheets, vesicle sheets, and pods. In rubbly lavas, only vesicles of varying sizes occur. Gas release from melt caused the formation of primary porosity, while hydrothermal alteration and tectonic fracturing are the main processes that generated secondary porosity. Although several forms of porosity were created in the basaltic lava flows, the precipitation of secondary minerals within the pores has tended to reduce the original porosities. Late-stage fractures could create efficient channel networks for possible hydrocarbon/groundwater migration and entrapment owing to their ability to connect single pores. Quantitative permeability data should be gathered in future studies to confirm the potential of these lavas for store hydrocarbons or groundwater.

Structural vibration passive control and economic analysis of a high-rise building in Beijing

NASA Astrophysics Data System (ADS)

Chen, Yongqi; Cao, Tiezhu; Ma, Liangzhe; Luo, Chaoying

2009-12-01

Performance analysis of the Pangu Plaza under earthquake and wind loads is described in this paper. The plaza is a 39-story steel high-rise building, 191 m high, located in Beijing close to the 2008 Olympic main stadium. It has both fluid viscous dampers (FVDs) and buckling restrained braces or unbonded brace (BRB or UBB) installed. A repeated iteration procedure in its design and analysis was adopted for optimization. Results from the seismic response analysis in the horizontal and vertical directions show that the FVDs are highly effective in reducing the response of both the main structure and the secondary system. A comparative analysis of structural seismic performance and economic impact was conducted using traditional methods, i.e., increased size of steel columns and beams and/or use of an increased number of seismic braces versus using FVD. Both the structural response and economic analysis show that using FVD to absorb seismic energy not only satisfies the Chinese seismic design code for a “rare” earthquake, but is also the most economical way to improve seismic performance both for one-time direct investment and long term maintenance.

Effect of Secondary Cooling Conditions on Solidification Structure and Central Macrosegregation in Continuously Cast High-Carbon Rectangular Billet

NASA Astrophysics Data System (ADS)

Zeng, Jie; Chen, Weiqing

2015-10-01

Solidification structures of high carbon rectangular billet with a size of 180 mm × 240 mm in different secondary cooling conditions were simulated using cellular automaton-finite element (CAFE) coupling model. The adequacy of the model was compared with the simulated and the actual macrostructures of 82B steel. Effects of the secondary cooling water intensity on solidification structures including the equiaxed grain ratio and the equiaxed grain compactness were discussed. It was shown that the equiaxed grain ratio and the equiaxed grain compactness changed in the opposite direction at different secondary cooling water intensities. Increasing the secondary cooling water intensity from 0.9 or 1.1 to 1.3 L/kg could improve the equiaxed grain compactness and decrease the equiaxed grain ratio. Besides, the industrial test was conducted to investigate the effect of different secondary cooling water intensities on the center carbon macrosegregation of 82B steel. The optimum secondary cooling water intensity was 0.9 L/kg, while the center carbon segregation degree was 1.10. The relationship between solidification structure and center carbon segregation was discussed based on the simulation results and the industrial test.

Structural Feasibility Analysis of a Robotically Assembled Very Large Aperture Optical Space Telescope

NASA Technical Reports Server (NTRS)

Wilkie, William Keats; Williams, R. Brett; Agnes, Gregory S.; Wilcox, Brian H.

2007-01-01

This paper presents a feasibility study of robotically constructing a very large aperture optical space telescope on-orbit. Since the largest engineering challenges are likely to reside in the design and assembly of the 150-m diameter primary reflector, this preliminary study focuses on this component. The same technology developed for construction of the primary would then be readily used for the smaller optical structures (secondary, tertiary, etc.). A reasonable set of ground and on-orbit loading scenarios are compiled from the literature and used to define the structural performance requirements and size the primary reflector. A surface precision analysis shows that active adjustment of the primary structure is required in order to meet stringent optical surface requirements. Two potential actuation strategies are discussed along with potential actuation devices at the current state of the art. The finding of this research effort indicate that successful technology development combined with further analysis will likely enable such a telescope to be built in the future.

Large structural modification with conserved conformation: analysis of delta(3)-fused aryl prolines in model beta-turns.

PubMed

Jeannotte, Guillaume; Lubell, William D

2004-11-10

For the first time, the influence of a fused Delta3-arylproline on peptide conformation has been studied by the synthesis and comparison of the conformations of peptides containing proline and pyrrolo-proline, 3 (PyPro). Pyrrolo-proline was demonstrated to be a conservative replacement for Pro in model beta-turns, 4 and 5, as shown by their similar DMSO titration curves, cis/trans-isomer populations, and NOESY spectral data. Pyrrolo-proline may thus be used for studying the structure activity relationships of Pro-containing peptides with minimal modification of secondary structures.

Near-blade flow structure modification

NASA Astrophysics Data System (ADS)

Kura, T.; Fornalik-Wajs, E.

2016-10-01

In this paper, the importance of near-blade flow structure influence on the performance of a centrifugal compressor was discussed. The negative effects of eddies and secondary flows appearance were described, together with the proposal of their reduction. Three-dimensional analyses were performed for the rotors. Focus was placed on the blade's 3D curvature impact on the efficiency of compression, and the influence of blade-shroud tip existence. A few design proposals were investigated - their performance maps were the basis of further analysis. Proposed modification of blade shape changed the near-blade flow structure and improved the compressor performance.

Service evaluation of aircraft composite structural components

NASA Technical Reports Server (NTRS)

Brooks, W. A., Jr.; Dow, M. B.

1973-01-01

The advantages of the use of composite materials in structural applications have been identified in numerous engineering studies. Technology development programs are underway to correct known deficiencies and to provide needed improvements. However, in the final analysis, flight service programs are necessary to develop broader acceptance of, and confidence in, any new class of materials such as composites. Such flight programs, initiated by NASA Langley Research Center, are reviewed. These programs which include the selectively reinforced metal and the all-composite concepts applied to both secondary and primary aircraft structural components, are described and current status is indicated.

Secondary Structure Prediction of Protein Constructs Using Random Incremental Truncation and Vacuum-Ultraviolet CD Spectroscopy

PubMed Central

Pukáncsik, Mária; Orbán, Ágnes; Nagy, Kinga; Matsuo, Koichi; Gekko, Kunihiko; Maurin, Damien; Hart, Darren; Kézsmárki, István; Vertessy, Beata G.

2016-01-01

A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE is excepted to provide key information on the description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. Towards this long-term aim, the random library ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine constructs of UDE were chosen to decipher structural and functional relationships. Vacuum ultraviolet circular dichroism (VUVCD) spectroscopy was performed to define the secondary structure content and location within UDE and its truncated variants. The quantitative analysis demonstrated exclusive α-helical content for the full-length protein, which is preserved in the truncated constructs. Arrangement of α-helical bundles within the truncated protein segments suggested new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues. Here we demonstrate that the combination of ESPRIT and VUVCD spectroscopy provides a new structural description of UDE and confirms that the truncated constructs are useful for further detailed functional studies. PMID:27273007

Evaporation-based method for preparing gelatin foams with aligned tubular pore structures.

PubMed

Frazier, Shane D; Srubar, Wil V

2016-05-01

Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5-30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05-0.22 g/cm(3)) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. Copyright © 2016 Elsevier B.V. All rights reserved.

The predicted secondary structures of class I fructose-bisphosphate aldolases.

PubMed Central

Sawyer, L; Fothergill-Gilmore, L A; Freemont, P S

1988-01-01

The results of several secondary-structure prediction programs were combined to produce an estimate of the regions of alpha-helix, beta-sheet and reverse turns for fructose-bisphosphate aldolases from human and rat muscle and liver, from Trypanosoma brucei and from Drosophila melanogaster. All the aldolase sequences gave essentially the same pattern of secondary-structure predictions despite having sequences up to 50% different. One exception to this pattern was an additional strongly predicted helix in the rat liver and Drosophila enzymes. Regions of relatively high sequence variation generally were predicted as reverse turns, and probably occur as surface loops. Most of the positions corresponding to exon boundaries are located between regions predicted to have secondary-structural elements consistent with a compact structure. The predominantly alternating alpha/beta structure predicted is consistent with the alpha/beta-barrel structure indicated by preliminary high-resolution X-ray diffraction studies on rabbit muscle aldolase [Sygusch, Beaudry & Allaire (1986) Biophys. J. 49, 287a]. Images Fig. 1. (cont.) Fig. 1. PMID:3128269

Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species.

PubMed

Challis, Gregory L; Hopwood, David A

2003-11-25

In this article we briefly review theories about the ecological roles of microbial secondary metabolites and discuss the prevalence of multiple secondary metabolite production by strains of Streptomyces, highlighting results from analysis of the recently sequenced Streptomyces coelicolor and Streptomyces avermitilis genomes. We address this question: Why is multiple secondary metabolite production in Streptomyces species so commonplace? We argue that synergy or contingency in the action of individual metabolites against biological competitors may, in some cases, be a powerful driving force for the evolution of multiple secondary metabolite production. This argument is illustrated with examples of the coproduction of synergistically acting antibiotics and contingently acting siderophores: two well-known classes of secondary metabolite. We focus, in particular, on the coproduction of beta-lactam antibiotics and beta-lactamase inhibitors, the coproduction of type A and type B streptogramins, and the coregulated production and independent uptake of structurally distinct siderophores by species of Streptomyces. Possible mechanisms for the evolution of multiple synergistic and contingent metabolite production in Streptomyces species are discussed. It is concluded that the production by Streptomyces species of two or more secondary metabolites that act synergistically or contingently against biological competitors may be far more common than has previously been recognized, and that synergy and contingency may be common driving forces for the evolution of multiple secondary metabolite production by these sessile saprophytes.

Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species

PubMed Central

Challis, Gregory L.; Hopwood, David A.

2003-01-01

In this article we briefly review theories about the ecological roles of microbial secondary metabolites and discuss the prevalence of multiple secondary metabolite production by strains of Streptomyces, highlighting results from analysis of the recently sequenced Streptomyces coelicolor and Streptomyces avermitilis genomes. We address this question: Why is multiple secondary metabolite production in Streptomyces species so commonplace? We argue that synergy or contingency in the action of individual metabolites against biological competitors may, in some cases, be a powerful driving force for the evolution of multiple secondary metabolite production. This argument is illustrated with examples of the coproduction of synergistically acting antibiotics and contingently acting siderophores: two well-known classes of secondary metabolite. We focus, in particular, on the coproduction of β-lactam antibiotics and β-lactamase inhibitors, the coproduction of type A and type B streptogramins, and the coregulated production and independent uptake of structurally distinct siderophores by species of Streptomyces. Possible mechanisms for the evolution of multiple synergistic and contingent metabolite production in Streptomyces species are discussed. It is concluded that the production by Streptomyces species of two or more secondary metabolites that act synergistically or contingently against biological competitors may be far more common than has previously been recognized, and that synergy and contingency may be common driving forces for the evolution of multiple secondary metabolite production by these sessile saprophytes. PMID:12970466

Acetaldehyde-induced structural and conformational alterations in human immunoglobulin G: A physicochemical and multi-spectroscopic study.

PubMed

Waris, Sana; Habib, Safia; Tantry, Irfan Qadir; Khan, Rizwan Hasan; Mahmood, Riaz; Ali, Asif

2018-07-01

Acetaldehyde is a reactive aldehyde produced as an intermediate of alcohol metabolism and tobacco pyrolysis. It has the potential to interact with different biomolecules in various tissues which results in the formation of stable, unstable and covalent adducts. This causes structural and functional modifications that may lead to severe complications such as cancer. This study has probed the structural modifications in human immunoglobulin G (IgG) as a function of different concentrations of acetaldehyde in the presence of reducing agent, sodium borohydride. Acetaldehyde mediated modifications in IgG have been characterised by various physicochemical techniques. UV-spectrophotometry showed that acetaldehyde modified IgG exhibited marked increase in hyperchromicity. Fluorescence studies revealed a significant quenching of tryptophan fluorescence which resulted in loss of β-sheet secondary structure that was confirmed by circular dichroic analysis. Gross structural changes in the morphology of IgG were confirmed by increase in mass and hydrodynamic radius of this glycoprotein along with the appearance of fibrillar structures in modified IgG, when compared to the granular structure of the native form of IgG observed by scanning electron microscope. The results indicate that acetaldehyde causes alterations in the secondary and tertiary structure of the protein leading to diminution of normal function of IgG molecule. Copyright © 2018 Elsevier B.V. All rights reserved.

Foreland structure - Beartooth Mountains, Montana and Wyoming

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

Clark, D.M.

1996-06-01

Analysis of public drilling records from the AMOCO Beartooth Number 1 and 1 A sidetrack boreholes (SW1/4, SE1/4, Section 19, T.8 S., R.20 E., Carbon County, Montana) continues. Several additional inferences are made about this large foreland structure, and subsequent interpretation of the structural model of the northeast corner of the Beartooth Mountain Block and structural relationship with the Big Horn Basin. The structure is described as a large recumbent to sub-horizontal, synclinal fold with the overturned upper limb out diagonally by the Beartooth Thrust or Thrust Zone and a complex thrust fault zone below the Beartooth Thrust. The singlemore » recorded dip angle and direction of the Beartooth Thrust at depth was 19 degrees to the northwest(?). The dipmeter dip angle on the Beartooth Thrust, 19 degrees, validates foreland structural theory of decreasing dip angles at a vertical depth of 8,232 feet (2,509 m), in the Precambrian crystalline basement. The northwest dip direction may be attributable to secondary structural folding. The record of northwest, southeast, and southwest dip of bedding surfaces and faults in sections of the overturned upper limb, in both boreholes, suggests possible, less intense secondary folding, after thrust fault deformation. Given the overall geometry of this large foreland structure, there is little doubt that the average direction of maximum principal stress (sigma 1) was oriented in a northeast - southwest direction.« less

A Typology of Secondary Stressors Among Refugees of Conflict in the Middle East: The Case of Syrian Refugees in Jordan.

PubMed

Alfadhli, Khalifah; Drury, John

2018-05-10

As the years of displacement accumulate, the burden of secondary stressors (i.e., stressors not directly related to war) increase on the shoulders of millions of refugees, who do not have the option of either returning home due to war or having a sustainable livelihood in the host countries. This paper aims to shed light on the overlooked importance of secondary stressors among refugees of conflict in developing countries; it will do this by highlighting the experience of Syrian refugees in Jordan, and developing a typology of these stressors. We approached this issue using two levels of exploration. In study 1, we used participant observation and 15 in-depth interviews in Irbid, Jordan. Data were analysed qualitatively using thematic analysis to explore the different types of stressors. In study 2, a questionnaire survey among Syrian refugees in Jordan (n = 305) was used to collect data about a wide range of stressors. Responses were subjected to factor analysis to examine the extent to which the stressors could be organized into different factors. The thematic analysis suggested three different types of secondary stressors: financial (money related), environmental (exile structures and feelings created by it), and social (directly related to social relations). The factor analysis of the survey data produced a similar typology, where secondary stressors were found to be grouped into four main factors (financial, services, safety, and relations with out-groups). The final result is a typology of 33 secondary stressors organised in three main themes. Syrian refugees in Jordan suffer the most from financial stressors, due to loss of income and high living expenses. Environmental stressors arise from exile and are either circumstantial (e.g., services and legal requirements) or created by this environment (e.g., instability and lack of familiarity). Social stressors were observed among a considerable section of refugees, varying from stressors due to being targeted as a refugee by the locals (e.g., discrimination) to more traumatic stressors that came from both locals and other refugees (e.g., assault). The typology of secondary stressors suggested by the present analysis needs to be investigated in a larger sample of refugees of conflict in other countries in the Middle East, in order to determine its generality. We suggest that it is a basis for a framework for practitioners and academics working with refugees in the region. Armed conflict, Syrian, Jordan, refugees, forced displacement, exile, daily stressors, secondary stressors, trauma, typology.

Occlusal changes secondary to temporomandibular joint conditions: a critical review and implications for clinical practice

PubMed Central

CALDAS, Waleska; CONTI, Ana Cláudia de Castro Ferreira; JANSON, Guilherme; Paulo César Rodrigues, CONTI

2016-01-01

ABSTRACT The relationship between Temporomandibular Disorders (TMD) and malocclusion is an extremely critical issue in dentistry. Contrary to the old concept that malocclusion causes TMD, occlusal changes, especially those observed as sudden, may be secondary and reflect joint or muscle disorders due to the obvious connection between these structures and the dental occlusion. Objectives The aim of this article is to present the most commonly occlusal changes secondary to TMD. Methods The clinical presentation of these conditions is discussed. Details regarding diagnosis, treatment, and follow-up of patients presenting TMD prior or during treatment are also presented. Conclusions All plans for irreversible therapy should be preceded by a meticulous analysis of TMD signs and symptoms in such a way that patients are not submitted to irreversible treatment, based on an untrue occlusal relationship, secondary to articular and/or muscular disorders. When present, TMD symptoms must always be controlled to reestablish a “normal” occlusion and allow proper treatment strategy. PMID:27556214

Metabolomic tools for secondary metabolite discovery from marine microbial symbionts.

PubMed

Macintyre, Lynsey; Zhang, Tong; Viegelmann, Christina; Martinez, Ignacio Juarez; Cheng, Cheng; Dowdells, Catherine; Abdelmohsen, Usama Ramadam; Gernert, Christine; Hentschel, Ute; Edrada-Ebel, RuAngelie

2014-06-05

Marine invertebrate-associated symbiotic bacteria produce a plethora of novel secondary metabolites which may be structurally unique with interesting pharmacological properties. Selection of strains usually relies on literature searching, genetic screening and bioactivity results, often without considering the chemical novelty and abundance of secondary metabolites being produced by the microorganism until the time-consuming bioassay-guided isolation stages. To fast track the selection process, metabolomic tools were used to aid strain selection by investigating differences in the chemical profiles of 77 bacterial extracts isolated from cold water marine invertebrates from Orkney, Scotland using liquid chromatography-high resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance (NMR) spectroscopy. Following mass spectrometric analysis and dereplication using an Excel macro developed in-house, principal component analysis (PCA) was employed to differentiate the bacterial strains based on their chemical profiles. NMR 1H and correlation spectroscopy (COSY) were also employed to obtain a chemical fingerprint of each bacterial strain and to confirm the presence of functional groups and spin systems. These results were then combined with taxonomic identification and bioassay screening data to identify three bacterial strains, namely Bacillus sp. 4117, Rhodococcus sp. ZS402 and Vibrio splendidus strain LGP32, to prioritize for scale-up based on their chemically interesting secondary metabolomes, established through dereplication and interesting bioactivities, determined from bioassay screening.

A palindrome-mediated mechanism distinguishes translocations involving LCR-B of chromosome 22q11.2.

PubMed

Gotter, Anthony L; Shaikh, Tamim H; Budarf, Marcia L; Rhodes, C Harker; Emanuel, Beverly S

2004-01-01

Two known recurrent constitutional translocations, t(11;22) and t(17;22), as well as a non-recurrent t(4;22), display derivative chromosomes that have joined to a common site within the low copy repeat B (LCR-B) region of 22q11.2. This breakpoint is located between two AT-rich inverted repeats that form a nearly perfect palindrome. Breakpoints within the 11q23, 17q11 and 4q35 partner chromosomes also fall near the center of palindromic sequences. In the present work the breakpoints of a fourth translocation involving LCR-B, a balanced ependymoma-associated t(1;22), were characterized not only to localize this junction relative to known genes, but also to further understand the mechanism underlying these rearrangements. FISH mapping was used to localize the 22q11.2 breakpoint to LCR-B and the 1p21 breakpoint to single BAC clones. STS mapping narrowed the 1p21.2 breakpoint to a 1990 bp AT-rich region, and junction fragments were amplified by nested PCR. Junction fragment-derived sequence indicates that the 1p21.2 breakpoint splits a 278 nt palindrome capable of forming stem-loop secondary structure. In contrast, the 1p21.2 reference genomic sequence from clones in the database does not exhibit this configuration, suggesting a predisposition for regional genomic instability perhaps etiologic for this rearrangement. Given its similarity to known chromosomal fragile site (FRA) sequences, this polymorphic 1p21.2 sequence may represent one of the FRA1 loci. Comparative analysis of the secondary structure of sequences surrounding translocation breakpoints that involve LCR-B with those not involving this region indicate a unique ability of the former to form stem-loop structures. The relative likelihood of forming these configurations appears to be related to the rate of translocation occurrence. Further analysis suggests that constitutional translocations in general occur between sequences of similar melting temperature and propensity for secondary structure.

A palindrome-mediated mechanism distinguishes translocations involving LCR-B of chromosome 22q11.2

PubMed Central

Gotter, Anthony L.; Shaikh, Tamim H.; Budarf, Marcia L.; Rhodes, C. Harker; Emanuel, Beverly S.

2010-01-01

Two known recurrent constitutional translocations, t(11;22) and t(17;22), as well as a non-recurrent t(4;22), display derivative chromosomes that have joined to a common site within the low copy repeat B (LCR-B) region of 22q11.2. This breakpoint is located between two AT-rich inverted repeats that form a nearly perfect palindrome. Breakpoints within the 11q23, 17q11 and 4q35 partner chromosomes also fall near the center of palindromic sequences. In the present work the breakpoints of a fourth translocation involving LCR-B, a balanced ependymoma-associated t(1;22), were characterized not only to localize this junction relative to known genes, but also to further understand the mechanism underlying these rearrangements. FISH mapping was used to localize the 22q11.2 breakpoint to LCR-B and the 1p21 breakpoint to single BAC clones. STS mapping narrowed the 1p21.2 breakpoint to a 1990 bp AT-rich region, and junction fragments were amplified by nested PCR. Junction fragment-derived sequence indicates that the 1p21.2 breakpoint splits a 278 nt palindrome capable of forming stem–loop secondary structure. In contrast, the 1p21.2 reference genomic sequence from clones in the database does not exhibit this configuration, suggesting a predisposition for regional genomic instability perhaps etiologic for this rearrangement. Given its similarity to known chromosomal fragile site (FRA) sequences, this polymorphic 1p21.2 sequence may represent one of the FRA1 loci. Comparative analysis of the secondary structure of sequences surrounding translocation breakpoints that involve LCR-B with those not involving this region indicate a unique ability of the former to form stem–loop structures. The relative likelihood of forming these configurations appears to be related to the rate of translocation occurrence. Further analysis suggests that constitutional translocations in general occur between sequences of similar melting temperature and propensity for secondary structure. PMID:14613967

Design and verification for front mirror-body structure of on-axis three mirror anastigmatic space camera

NASA Astrophysics Data System (ADS)

Wang, Xiaoyong; Guo, Chongling; Hu, Yongli; He, Hongyan

2017-11-01

The primary and secondary mirrors of onaxis three mirror anastigmatic (TMA) space camera are connected and supported by its front mirror-body structure, which affects both imaging performance and stability of the camera. In this paper, the carbon fiber reinforced plastics (CFRP) thin-walled cylinder and titanium alloy connecting rod have been used for the front mirror-body opto-mechanical structure of the long-focus on-axis and TMA space camera optical system. The front mirror-body component structure has then been optimized by finite element analysis (FEA) computing. Each performance of the front mirror-body structure has been tested by mechanics and vacuum experiments in order to verify the validity of such structure engineering design.

Three 3D metal coordination polymers based on triazol-functionalized rigid ligand: Synthesis, topological structure and properties

NASA Astrophysics Data System (ADS)

Meng, Lingkun; Liu, Kang; Liang, Chen; Guo, Xiaolei; Han, Xu; Ren, Siyuan; Ma, Dingxuan; Li, Guanghua; Shi, Zhan; Feng, Shouhua

2018-02-01

By using a triazol-functionalized tricarboxylate, three novel metal coordination polymers, namely, [Zn2L(OH)]·0.5H2O (1), [Co2L(OH)(H2O)]·5.5H2O (2), [Cu2(HL)] (3) L = ［5-(3-(4-carboxyphenyl)-5-methyl-4H-1,2,4-triazol-4-yl)isophthalate］ were synthesized under hydrothermal reactions. All the compounds were characterized by element analysis, IR spectroscopy, thermogravimetric analysis, power X-ray diffrcation and single-crystal X-ray diffrcation. Structural analysis reveals that compounds 1 and 2 have 3D networks with flu topologies where rigid trizaol-functionalized ligands as 4-connected nodes and Zn4(COO)6 or Co4(COO)6 clusters serves as 8-connected secondary building units. Compound 3 has 3D network with pcu topology where Cu4(COO)4 clusters serve as 6-connected secondary building units. Gas adsorption studies reveal that desolvated compoud 1 exhibits high H2 absorption capacity at 77 K and highly selective separation abilities of CO2 and C3H8 over CH4 at room temperature. The results suggest that 1 has potential application in gas storage and separation. In addition, the magnetic properties of compound 2 were also investigated.

Teaching Health Education. A Thematic Analysis of Early Career Teachers' Experiences Following Pre-Service Health Training

ERIC Educational Resources Information Center

Pickett, Karen; Rietdijk, Willeke; Byrne, Jenny; Shepherd, Jonathan; Roderick, Paul; Grace, Marcus

2017-01-01

Purpose: The purpose of this paper is to understand early career teachers' perceptions of the impact of a pre-service health education programme on their health promotion practice in schools and the contextual factors that influence this. Design/methodology/approach: Semi-structured interviews were conducted with 14 primary and secondary trainee…

Teachers' Perceptions of the Impact of Professional Development on Learning and Teaching in a Developing Nation

ERIC Educational Resources Information Center

Mohan, Parmeshwar Prasad; Lingam, Govinda Ishwar; Chand, Deepa Dewali

2017-01-01

This research examined teachers' perceptions of the impact of Professional Development (PD) programmes on learning and teaching in two Fijian secondary schools. Through a qualitative research design, data were gathered using document analysis and semi-structured interviews with 30 teachers from the two case study schools. The major findings to…

Some Preliminary Findings of Structural Changes in Rural Communities Stemming from the "Farm Crisis." Department of Agricultural Economics Staff Paper.

ERIC Educational Resources Information Center

Olsen, Duane A.; And Others

Analysis of secondary data from 1980-85 revealed economic, demographic, social, and psychological effects of the current "farm crisis" on rural communities in Nebraska. Agriculturally dependent counties were found to have a widening income disparity with state and metropolitan county averages, declining retail sales, slower increase in…

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,…

English Proficiency and Admission and Graduation of Post-Secondary Students at a Puerto Rican University

ERIC Educational Resources Information Center

Alea, Jamie

2009-01-01

This dissertation has examined English proficiency as a mediating social factor within the occupational structure of Puerto Rico. It included an analysis of the educational records of 641 students majoring in industrial engineering, nursing, education and finance of the University of Puerto Rico, Mayaguez from 1998-2000. The investigation…

Designing a Structured and Interactive Learning Environment Based on GIS for Secondary Geography Education

ERIC Educational Resources Information Center

Liu, Suxia; Zhu, Xuan

2008-01-01

Geographic information systems (GIS) are computer-based tools for geographic data analysis and spatial visualization. They have become one of the information and communications technologies for education at all levels. This article reviews the current status of GIS in schools, analyzes the requirements of a GIS-based learning environment from…

Innovation and effectiveness: changing the scope of school nurses in New Zealand secondary schools.

PubMed

Kool, Bridget; Thomas, David; Moore, Dennis; Anderson, Angelika; Bennetts, Phillipa; Earp, Karlynne; Dawson, Dianne; Treadwell, Nicky

2008-04-01

To describe the changing role of school nurses in eight New Zealand (NZ) secondary schools from low socio-economic areas with high Pacific Island and Māori rolls. An evaluation of a pilot addressing under-achievement in low-decile schools in Auckland, NZ (2002-05). Annual semi-structured school nurse interviews and analysis of routinely collected school health service data were undertaken. Two patterns of school nurse operation were identified: an embracing pattern, where nurses embraced the concept of providing school-based health services; and a Band-Aid pattern, where only the basics for student health care were provided by school nurses. School nurses with an embracing pattern of practice provided more effective school-based health services. School health services are better served by nurses with structured postgraduate education that fosters the development of a nurse-practitioner role. Co-ordination of school nurses either at a regional or national level is required.

Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein.

PubMed

Lazim, Raudah; Mei, Ye; Zhang, Dawei

2012-03-01

Replica exchange molecular dynamics (REMD) simulation provides an efficient conformational sampling tool for the study of protein folding. In this study, we explore the mechanism directing the structure variation from α/4β-fold protein to 3α-fold protein after mutation by conducting REMD simulation on 42 replicas with temperatures ranging from 270 K to 710 K. The simulation began from a protein possessing the primary structure of GA88 but the tertiary structure of GB88, two G proteins with "high sequence identity." Albeit the large Cα-root mean square deviation (RMSD) of the folded protein (4.34 Å at 270 K and 4.75 Å at 304 K), a variation in tertiary structure was observed. Together with the analysis of secondary structure assignment, cluster analysis and principal component, it provides insights to the folding and unfolding pathway of 3α-fold protein and α/4β-fold protein respectively paving the way toward the understanding of the ongoings during conformational variation.

Matching 4.7-Å XRD Spacing in Amelogenin Nanoribbons and Enamel Matrix

PubMed Central

Sanii, B.; Martinez-Avila, O.; Simpliciano, C.; Zuckermann, R.N.; Habelitz, S.

2014-01-01

The recent discovery of conditions that induce nanoribbon structures of amelogenin protein in vitro raises questions about their role in enamel formation. Nanoribbons of recombinant human full-length amelogenin (rH174) are about 17 nm wide and self-align into parallel bundles; thus, they could act as templates for crystallization of nanofibrous apatite comprising dental enamel. Here we analyzed the secondary structures of nanoribbon amelogenin by x-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) and tested if the structural motif matches previous data on the organic matrix of enamel. XRD analysis showed that a peak corresponding to 4.7 Å is present in nanoribbons of amelogenin. In addition, FTIR analysis showed that amelogenin in the form of nanoribbons was comprised of β-sheets by up to 75%, while amelogenin nanospheres had predominantly random-coil structure. The observation of a 4.7-Å XRD spacing confirms the presence of β-sheets and illustrates structural parallels between the in vitro assemblies and structural motifs in developing enamel. PMID:25048248

Structure of an E. coli integral membrane sulfurtransferase and its structural transition upon SCN- binding defined by EPR-based hybrid method

NASA Astrophysics Data System (ADS)

Ling, Shenglong; Wang, Wei; Yu, Lu; Peng, Junhui; Cai, Xiaoying; Xiong, Ying; Hayati, Zahra; Zhang, Longhua; Zhang, Zhiyong; Song, Likai; Tian, Changlin

2016-01-01

Electron paramagnetic resonance (EPR)-based hybrid experimental and computational approaches were applied to determine the structure of a full-length E. coli integral membrane sulfurtransferase, dimeric YgaP, and its structural and dynamic changes upon ligand binding. The solution NMR structures of the YgaP transmembrane domain (TMD) and cytosolic catalytic rhodanese domain were reported recently, but the tertiary fold of full-length YgaP was not yet available. Here, systematic site-specific EPR analysis defined a helix-loop-helix secondary structure of the YagP-TMD monomers using mobility, accessibility and membrane immersion measurements. The tertiary folds of dimeric YgaP-TMD and full-length YgaP in detergent micelles were determined through inter- and intra-monomer distance mapping and rigid-body computation. Further EPR analysis demonstrated the tight packing of the two YgaP second transmembrane helices upon binding of the catalytic product SCN-, which provides insight into the thiocyanate exportation mechanism of YgaP in the E. coli membrane.

The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles.

PubMed

Kudryashev, Mikhail; Castaño-Díez, Daniel; Deluz, Cédric; Hassaine, Gherici; Grasso, Luigino; Graf-Meyer, Alexandra; Vogel, Horst; Stahlberg, Henning

2016-01-05

The function of membrane proteins is best understood if their structure in the lipid membrane is known. Here, we determined the structure of the mouse serotonin 5-HT3 receptor inserted in lipid bilayers to a resolution of 12 Å without stabilizing antibodies by cryo electron tomography and subtomogram averaging. The reconstruction reveals protein secondary structure elements in the transmembrane region, the extracellular pore, and the transmembrane channel pathway, showing an overall similarity to the available X-ray model of the truncated 5-HT3 receptor determined in the presence of a stabilizing nanobody. Structural analysis of the 5-HT3 receptor embedded in a lipid bilayer allowed the position of the membrane to be determined. Interactions between the densely packed receptors in lipids were visualized, revealing that the interactions were maintained by the short horizontal helices. In combination with methodological improvements, our approach enables the structural analysis of membrane proteins in response to voltage and ligand gating. Copyright © 2016 Elsevier Ltd. All rights reserved.

A secondary data analysis of Internet use in caregivers of persons with dementia.

PubMed

Kim, Heejung; Rose, Karen M; Netemeyer, Richard G; Merwin, Elizabeth I; Williams, Ishan C

2014-12-01

This paper is a secondary data analysis to investigate relationships among caregiver stress appraisal, self-rated health and health-related Internet use. Cross-sectional correlation design. National Alliance for Caregiving telephone survey conducted in the USA was a primary data source collected in 2009 from 258 caregivers of persons with dementia, who used the Internet to perform care-giving tasks. Based on Pearlin's Stress Process Model, structural equation modelling was conducted. Caregivers with poor health reported higher levels of caregiver stress appraised, which was associated with more Internet use for health-related purposes. It is required to develop effective Internet-based resources to meet the needs of highly stressed caregivers of persons with dementia. However, there was no relationship between self-rated health and health-related Internet use in dementia caregiver.

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

LUTE telescope structural design

NASA Technical Reports Server (NTRS)

Ruthven, Gregory

1993-01-01

The major objective of the Lunar Ultraviolet Transit Experiment (LUTE) Telescope Structural Design Study was to investigate the feasibility of designing an ultralightweight 1-m aperture system within optical performance requirements and mass budget constraints. This study uses the results from our previous studies on LUTE as a basis for further developing the LUTE structural architecture. After summarizing our results in Section 2, Section 3 begins with the overall logic we used to determine which telescope 'structural form' should be adopted for further analysis and weight estimates. Specific telescope component analysis showing calculated fundamental frequencies and how they compare with our derived requirements are included. 'First-order' component stress analyses to ensure telescope optical and structural component (i.e. mirrors & main bulkhead) weights are realistic are presented. Layouts of both the primary and tertiary mirrors showing dimensions that are consistent with both our weight and frequency calculations also form part of Section 3. Section 4 presents our calculated values for the predicted thermally induced primary-to-secondary mirror despace motion due to the large temperature range over which LUTE must operate. Two different telescope design approaches (one which utilizes fused quartz metering rods and one which assumes the entire telescope is fabricated from beryllium) are considered in this analysis. We bound the secondary mirror focus mechanism range (in despace) based on these two telescope configurations. In Section 5 we show our overall design of the UVTA (Ultraviolet Telescope Assembly) via an 'exploded view' of the sub-system. The 'exploded view' is annotated to help aid in the understanding of each sub-assembly. We also include a two view layout of the UVTA from which telescope and telescope component dimensions can be measured. We conclude our study with a set of recommendations not only with respect to the LUTE structural architecture but also on other topics related to the overall feasibility of the LUTE telescope sub-system.

Development of methodology for identification the nature of the polyphenolic extracts by FTIR associated with multivariate analysis

NASA Astrophysics Data System (ADS)

Grasel, Fábio dos Santos; Ferrão, Marco Flôres; Wolf, Carlos Rodolfo

2016-01-01

Tannins are polyphenolic compounds of complex structures formed by secondary metabolism in several plants. These polyphenolic compounds have different applications, such as drugs, anti-corrosion agents, flocculants, and tanning agents. This study analyses six different type of polyphenolic extracts by Fourier transform infrared spectroscopy (FTIR) combined with multivariate analysis. Through both principal component analysis (PCA) and hierarchical cluster analysis (HCA), we observed well-defined separation between condensed (quebracho and black wattle) and hydrolysable (valonea, chestnut, myrobalan, and tara) tannins. For hydrolysable tannins, it was also possible to observe the formation of two different subgroups between samples of chestnut and valonea and between samples of tara and myrobalan. Among all samples analysed, the chestnut and valonea showed the greatest similarity, indicating that these extracts contain equivalent chemical compositions and structure and, therefore, similar properties.

Structure and self-assembly of the calcium binding matrix protein of human metapneumovirus.

PubMed

Leyrat, Cedric; Renner, Max; Harlos, Karl; Huiskonen, Juha T; Grimes, Jonathan M

2014-01-07

The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca²⁺ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca²⁺ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

A secondary copulatory structure in a female insect: a clasp for a nuptial meal?

NASA Astrophysics Data System (ADS)

Gwynne, Darryl T.

2002-03-01

Secondary copulatory structures are well-known in male dragonflies and spiders. Here I report a secondary copulatory organ in female ground weta, Hemiandrus pallitarsis (Ensifera, Orthoptera - crickets and allies). The organ, located on the underside of the abdomen, appears to secure the male's genitalia during the transfer of a spermatophylax nuptial meal to this location, an area quite separate from the female's primary copulatory structures, where the sperm ampulla is attached.

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

PubMed Central

Ellington, Roni; Wachira, James

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 discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

RNA secondary structure prediction by using discrete mathematics: an interdisciplinary research experience for undergraduate students.

PubMed

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 discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems.

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

Visualization of RNA structure models within the Integrative Genomics Viewer.

PubMed

Busan, Steven; Weeks, Kevin M

2017-07-01

Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Influence of secondary structure on in-source decay of protein in matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Takayama, Mitsuo; Osaka, Issey; Sakakura, Motoshi

2012-01-01

The susceptibility of the N-Cα bond of the peptide backbone to specific cleavage by in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was studied from the standpoint of the secondary structure of three proteins. A naphthalene derivative, 5-amino-1-naphtol (5,1-ANL), was used as the matrix. The resulting c'-ions, which originate from the cleavage at N-Cα bonds in flexible secondary structures such as turn and bend, and are free from intra-molecular hydrogen-bonded α-helix structure, gave relatively intense peaks. Furthermore, ISD spectra of the proteins showed that the N-Cα bonds of specific amino acid residues, namely Gly-Xxx, Xxx-Asp, and Xxx-Asn, were more susceptible to MALDI-ISD than other amino acid residues. This is in agreement with the observation that Gly, Asp and Asn residues usually located in turns, rather than α-helix. The results obtained indicate that protein molecules embedded into the matrix crystal in the MALDI experiments maintain their secondary structures as determined by X-ray crystallography, and that MALDI-ISD has the capability for providing information concerning the secondary structure of protein.

Secondary flow structures in the presence of Type-IV stent fractures through a bent tube model for curved arteries: Effect of circulation thresholding

NASA Astrophysics Data System (ADS)

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

2013-11-01

A common treatment for atherosclerosis is the opening of narrowed arteries resulting from obstructive lesions by angioplasty and stent implantation to restore unrestricted blood flow. ``Type-IV'' stent fractures involve complete transverse, linear fracture of stent struts, along with displacement of the stent fragments. Experimental data pertaining to secondary flows in the presence of stents that underwent ``Type-IV'' fractures in a bent artery model under physiological inflow conditions were obtained through a two-component, two-dimensional (2C-2D) PIV technique. Concomitant stent-induced flow perturbations result in secondary flow structures with complex, multi-scale morphologies and varying size-strength characteristics. Ultimately, these flow structures may have a role to play in restenosis and progression of atherosclerotic plaque. Vortex circulation thresholds were established with the goal of resolving and tracking iso-circulation secondary flow vortical structures and their morphological changes. This allowed for a parametric evaluation and quantitative representation of secondary flow structures undergoing deformation and spatial reorganization. Supported by NSF Grant No. CBET- 0828903 and GW Center for Biomimetics and Bioinspired Engineering.

Structural and Geophysical Characterization of Oklahoma Basement

NASA Astrophysics Data System (ADS)

Morgan, C.; Johnston, C. S.; Carpenter, B. M.; Reches, Z.

2017-12-01

Oklahoma has experienced a large increase in seismicity since 2009 that has been attributed to wastewater injection. Most earthquakes, including four M5+ earthquakes, nucleated at depths > 4 km, well within the pre-Cambrian crystalline basement, even though wastewater injection occurred almost exclusively in the sedimentary sequence above. To better understand the structural characteristics of the rhyolite and granite that makeup the midcontinent basement, we analyzed a 150 m long core recovered from a basement borehole (Shads 4) in Rogers County, NE Oklahoma. The analysis of the fracture network in the rhyolite core included measurements of fracture inclination, aperture, and density, the examination fracture surface features and fill minerology, as well as x-ray diffraction analysis of secondary mineralization. We also analyzed the highly fractured and faulted segments of the core with a portable gamma-ray detector, magnetometer, and rebound hammer. The preliminary analysis of the fractures within the rhyolite core showed: (1) Fracture density increasing with depth by a factor of 10, from 4 fractures/10m in the upper core segment to 40 fracture/10m at 150 m deeper. (2) The fractures are primarily sub-vertical, inclined 10-20° from the axis of the vertical core. (3) The secondary mineralization is dominated by calcite and epidote. (4) Fracture aperture ranges from 0.35 to 2.35mm based on the thickness of secondary filling. (5) About 8% of the examined fractures display slickenside striations. (6) Increases of elasticity (by rebound hammer) and gamma-ray emissions are systematically correlated with a decrease in magnetic susceptibility in core segments of high fracture density and/or faulting; this observation suggests diagenetic fracture re-mineralization.

[Evaluation of diffuse cerebral atrophy in patients with a history of traumatic brain injury and its relation to cognitive deterioration].

PubMed

Narberhaus, A; Segarra-Castells, M D; Verger-Maestre, K; Serra-Grabulosa, J M; Salgado-Pineda, P; Bartomeus-Jené, F; Mercader-Sobrequés, J M

Diffuse damage secondary to traumatic brain injury (TBI) can be studied through volumetric analysis of several structures that are sensible to this kind of injury, such as corpus callosum, ventricular system, hippocampus, basal ganglia and the volume of cerebrospinal fluid spaces. Our aim is to describe how closed head injury (CHI) occurred in early years produce diffuse damage, and how this damage affects general cognitive functioning at long term. Initially the group of subjects was composed of 27 head injured children and adolescents following paediatric moderate to severe TBI. From this initial group we selected 15 patients without focal lesion, or in case of having suffered focal lesion, this was smaller than 2,600 mm3. These subjects were assessed by means of volumetric analysis of cerebrospinal fluid spaces, corpus callosum, hippocampus and caudate nucleus, comparing the results with a matched control group. We calculated the degree of general cognitive ability of these subjects through tests of intellectual, memory, frontal lobe and motor speed functioning. This study demonstrates that early CHI produce a volume decrease in all measured structures. Corpus callosum atrophy is the factor that better explains general cognitive impairment. Diffuse damage secondary to moderate to severe peadiatric TBI has long term effects on several cerebral structures and on cognitive performance. Corpus callosum atrophy is the best predictor for general cognitive impairment, compared with other affected structures.

Protein Secondary Structures (alpha-helix and beta-sheet) at a Cellular Levle and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

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

Yu,P.

2007-01-01

Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present studymore » were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S-FTIR absorption intensity), increased the percentage of {beta}-sheets (from 37.2% to 49.8%: S-FTIR absorption intensity) and reduced the {alpha}-helix to {beta}-sheet ratio (from 0.3 to 0.7) in the golden flaxseeds, which indicated a negative effect of the roasting on protein values, utilisation and bioavailability. These results were proved by the Cornell Net Carbohydrate Protein System in situ animal trial, which also revealed that roasting increased the amount of protein bound to lignin, and well as of the Maillard reaction protein (both of which are poorly used by ruminants), and increased the level of indigestible and undegradable protein in ruminants. The present results demonstrate the potential of highly spatially resolved synchrotron-based infrared microspectroscopy to locate 'pure' protein in feed tissues, and reveal protein secondary structures and digestive behaviour, making a significant step forward in and an important contribution to protein nutritional research. Further study is needed to determine the sensitivities of protein secondary structures to various heat-processing conditions, and to quantify the relationship between protein secondary structures and the nutrient availability and digestive behaviour of various protein sources. Information from the present study arising from the synchrotron-based IR probing of the protein secondary structures of protein sources at the cellular level will be valuable as a guide to maintaining protein quality and predicting digestive behaviours.« less

Structural elucidation and molecular characterization of Marinobacter sp. α-amylase.

PubMed

Kumar, Sumit; Khan, Rizwan Hasan; Khare, S K

2016-01-01

Halophiles have been perceived as potential source of novel enzymes in recent years. The interest emanates from their ability to catalyze efficiently under high salt and organic solvents. Marinobacter sp. EMB8 α-amylase was found to be active and stable in salt and organic solvents. A study was carried out using circular dichroism (CD), fluorescence spectroscopy, and bioinformatics analysis of similar protein sequence to ascertain molecular basis of salt and solvent adaptability of α-amylase. Structural changes recorded in the presence of varying amounts of NaCl exhibited an increase in negative ellipticity as a function of salt, confirming that salt stabilizes the protein and increases the secondary structure, making it catalytically functional. The data of intrinsic and extrinsic fluorescence (using 1-anilinonaphthalene 8-sulfonate [ANS] as probe) further confirmed the role of salt. The α-amylase was active in the presence of nonpolar solvents, namely, hexane and decane, but inactivated by ethanol. The decrease in the activity was correlated with the loss of tertiary structure in the presence of ethanol. Guanidine hydrochloride and pH denaturation indicated the molten globule state at pH 4.0. Partial N-terminal amino acid sequence of the purified α-amylase revealed the relatedness to Pseudoalteromonas sp. α-amylase. "FVHLFEW" was found as the N-terminal signature sequence. Bioinformatics analysis was done using M. algicola α-amylase protein having the same N-terminal signature sequence. The three-dimensional structure of Marinobacter α-amylase was deduced using the I-TASSER server, which reflected the enrichment of acidic amino acids on the surface, imparting the stability in the presence of salt. Our study clearly indicate that salt is necessary for maintaining the secondary and tertiary structure of halophilic protein, which is a necessary prerequisite for catalysis.

FRAMEWORK FOR STRUCTURAL ONLINE HEALTH MONITORING OF AGING AND DEGRADATION OF SECONDARY PIPING SYSTEMS DUE TO SOME ASPECTS OF EROSION

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

Gribok, Andrei V.; Agarwal, Vivek

This paper describes the current state of research related to critical aspects of erosion and selected aspects of degradation of secondary components in nuclear power plants (NPPs). The paper also proposes a framework for online health monitoring of aging and degradation of secondary components. The framework consists of an integrated multi-sensor modality system, which can be used to monitor different piping configurations under different degradation conditions. The report analyses the currently known degradation mechanisms and available predictive models. Based on this analysis, the structural health monitoring framework is proposed. The Light Water Reactor Sustainability Program began to evaluate technologies thatmore » could be used to perform online monitoring of piping and other secondary system structural components in commercial NPPs. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real time measurements, rather than at a pre-determined inspection interval. This transition to condition-based, risk-informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for the majority of nuclear power generation costs. Furthermore, of the operations and maintenance costs in U.S. plants, approximately 80% are labor costs. To address the issue of rising operating costs and economic viability, in 2017, companies that operate the national nuclear energy fleet started the Delivering the Nuclear Promise Initiative, which is a 3 year program aimed at maintaining operational focus, increasing value, and improving efficiency. There is unanimous agreement between industry experts and academic researchers that identifying and prioritizing inspection locations in secondary piping systems (for example, in raw water piping or diesel piping) would eliminate many excessive in-service inspections. The proposed structural health monitoring framework takes aim at answering this challenge by combining long range guided wave technologies with other monitoring techniques, which can significantly increase the inspection length and pinpoint the locations that degraded the most. More widely, the report suggests research efforts aimed at developing, validating, and deploying online corrosion monitoring techniques for complex geometries, which are pervasive in NPPs.« less

Isolation and characterization of anti-adenoviral secondary metabolites from marine actinobacteria.

PubMed

Strand, Mårten; Carlsson, Marcus; Uvell, Hanna; Islam, Koushikul; Edlund, Karin; Cullman, Inger; Altermark, Björn; Mei, Ya-Fang; Elofsson, Mikael; Willassen, Nils-Peder; Wadell, Göran; Almqvist, Fredrik

2014-01-28

Adenovirus infections in immunocompromised patients are associated with high mortality rates. Currently, there are no effective anti-adenoviral therapies available. It is well known that actinobacteria can produce secondary metabolites that are attractive in drug discovery due to their structural diversity and their evolved interaction with biomolecules. Here, we have established an extract library derived from actinobacteria isolated from Vestfjorden, Norway, and performed a screening campaign to discover anti-adenoviral compounds. One extract with anti-adenoviral activity was found to contain a diastereomeric 1:1 mixture of the butenolide secondary alcohols 1a and 1b. By further cultivation and analysis, we could isolate 1a and 1b in different diastereomeric ratio. In addition, three more anti-adenoviral butenolides 2, 3 and 4 with differences in their side-chains were isolated. In this study, the anti-adenoviral activity of these compounds was characterized and substantial differences in the cytotoxic potential between the butenolide analogs were observed. The most potent butenolide analog 3 displayed an EC50 value of 91 μM and no prominent cytotoxicity at 2 mM. Furthermore, we propose a biosynthetic pathway for these compounds based on their relative time of appearance and structure.

Construction of Zeolite-Like Cluster Organic Frameworks from 3 d-4 d/3 d-3 d Heterometallic Supertetrahedral Secondary Building Units: Syntheses, Structures, and Properties.

PubMed

Lin, Li-Dan; Deng, Chu-Chu; Zhao, D; Li, Xin-Xiong; Zheng, Shou-Tian

2018-01-02

Two zeolite-like cluster organic frameworks based on Cd-Cu/Mn-Cu heterometallic supertetrahedral secondary building units have been successfully constructed under solvothermal conditions, namely, Cu[Cd 4 Cu 6 (L) 4 (H 2 O) 18 ](Ac) 9 ⋅DMA⋅3 H 2 O (1), and Cu[Mn 4 Cu 6 (L) 4 (Ac) 3 (H 2 O) 12 ](Ac) 6 ⋅CH 3 CN⋅13 H 2 O (2), where H 3 L=2-(hydroxymethyl)-2-(pyridin-4-yl)-1,3-propanediol, Ac=CH 3 COO - , DMA=N,N'-dimethylacetamide. Single-crystal X-ray structural analysis reveals that both 1 and 2 exhibit 3-dimensional zeolite-like architectures with similar 4-connected components, but possess definitely different topologies of diamondoid (dia) and uncommon lonsdaleite (lon), respectively. 1 and 2 represent the first cases of zeolite-like cluster organic frameworks containing Cd-Cu/Mn-Cu heterometallic supertetrahedral secondary building units. Furthermore, the magnetic properties and porous nature of 1 and 2 were also studied. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

PubMed Central

Theis, Corinna; Zirbel, Craig L.; zu Siederdissen, Christian Höner; Anthon, Christian; Hofacker, Ivo L.; Nielsen, Henrik; Gorodkin, Jan

2015-01-01

Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D module prediction tools and apply them on a 13-way vertebrate sequence-based alignment. We find that RNA 3D modules predicted by metaRNAmodules and JAR3D are significantly enriched in the screened windows compared to their shuffled counterparts. The initially estimated FDR of 47.0% is lowered to below 25% when certain 3D module predictions are present in the window of the 2D prediction. We discuss the implications and prospects for further development of computational strategies for detection of RNA 2D structure in genomic sequence. PMID:26509713

Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure.

PubMed

Ghosh, Jayadri Sekhar; Bhattacharya, Samik; Pal, Amita

2017-06-01

The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.

Analysis on the workspace of palletizing robot based on AutoCAD

NASA Astrophysics Data System (ADS)

Li, Jin-quan; Zhang, Rui; Guan, Qi; Cui, Fang; Chen, Kuan

2017-10-01

In this paper, a four-degree-of-freedom articulated palletizing robot is used as the object of research. Based on the analysis of the overall configuration of the robot, the kinematic mathematical model is established by D-H method to figure out the workspace of the robot. In order to meet the needs of design and analysis, using AutoCAD secondary development technology and AutoLisp language to develop AutoCAD-based 2D and 3D workspace simulation interface program of palletizing robot. At last, using AutoCAD plugin, the influence of structural parameters on the shape and position of the working space is analyzed when the structure parameters of the robot are changed separately. This study laid the foundation for the design, control and planning of palletizing robots.

Determination of Secondary School Students' Cognitive Structure, and Misconception in Ecological Concepts through Word Association Test

ERIC Educational Resources Information Center

Yücel, Elif Özata; Özkan, Mulis

2015-01-01

In this study, we determined cognitive structures and misconceptions about basic ecological concepts by using "word association" tests on secondary school students, age between 12-14 years. Eighty-nine students participated in this study. Before WAT was generated, basic ecological concepts that take place in the secondary science…

Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.

PubMed

Lin, Luan; McKerrow, Wilson H; Richards, Bryce; Phonsom, Chukiat; Lawrence, Charles E

2018-03-05

The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure Boltzmann ensemble. However because a given RNA secondary structure only contains a fraction of the possible helices that could form from a given sequence, the Boltzmann ensemble is multimodal. Several methods exist for clustering structures and finding those modes. However less focus is given to exploring the underlying reasons for this multimodality: the presence of conflicting basepairs. Information theory, or more specifically mutual information, provides a method to identify those basepairs that are key to the secondary structure. To this end we find most informative basepairs and visualize the effect of these basepairs on the secondary structure. Knowing whether a most informative basepair is present tells us not only the status of the particular pair but also provides a large amount of information about which other pairs are present or not present. We find that a few basepairs account for a large amount of the structural uncertainty. The identification of these pairs indicates small changes to sequence or stability that will have a large effect on structure. We provide a novel algorithm that uses mutual information to identify the key basepairs that lead to a multimodal Boltzmann distribution. We then visualize the effect of these pairs on the overall Boltzmann ensemble.

Secondary electron imaging of monolayer materials inside a transmission electron microscope

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

Cretu, Ovidiu, E-mail: cretu.ovidiu@nims.go.jp; Lin, Yung-Chang; Suenaga, Kazutomo

2015-08-10

A scanning transmission electron microscope equipped with a backscattered and secondary electron detector is shown capable to image graphene and hexagonal boron nitride monolayers. Secondary electron contrasts of the two lightest monolayer materials are clearly distinguished from the vacuum level. A signal difference between these two materials is attributed to electronic structure differences, which will influence the escape probabilities of the secondary electrons. Our results show that the secondary electron signal can be used to distinguish between the electronic structures of materials with atomic layer sensitivity, enhancing its applicability as a complementary signal in the analytical microscope.

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

PubMed Central

Lorenz, William A.; Clote, Peter

2011-01-01

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server and source code available at http://bioinformatics.bc.edu/clotelab/RNAlocopt/. PMID:21297972

Sterilization mechanism of nitrogen gas plasma: induction of secondary structural change in protein.

PubMed

Sakudo, Akikazu; Higa, Masato; Maeda, Kojiro; Shimizu, Naohiro; Imanishi, Yuichiro; Shintani, Hideharu

2013-07-01

The mechanism of action on biomolecules of N₂ gas plasma, a novel sterilization technique, remains unclear. Here, the effect of N₂ gas plasma on protein structure was investigated. BSA, which was used as the model protein, was exposed to N₂ gas plasma generated by short-time high voltage pulses from a static induction thyristor power supply. N₂ gas plasma-treated BSA at 1.5 kilo pulses per second showed evidence of degradation and modification when assessed by Coomassie brilliant blue staining and ultraviolet spectroscopy at 280 nm. Fourier transform infrared spectroscopy analysis was used to determine the protein's secondary structure. When the amide I region was analyzed in the infrared spectra according to curve fitting and Fourier self-deconvolution, N₂ gas plasma-treated BSA showed increased α-helix and decreased β-turn content. Because heating decreased α-helix and increased β-sheet content, the structural changes induced by N₂ gas plasma-treatment of BSA were not caused by high temperatures. Thus, the present results suggest that conformational changes induced by N₂ gas plasma are mediated by mechanisms distinct from heat denaturation. © 2013 The Societies and Wiley Publishing Asia Pty Ltd.

Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias.

PubMed

Barik, Sailen

2017-12-01

A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure. It appears that the AAR genes have evolved by orchestrating a balance between codon usage and mRNA secondary structure. The insights gained here should provide a better understanding of AAR evolution and may assist in designing synthetic genes.

Secondary data analysis of large data sets in urology: successes and errors to avoid.

PubMed

Schlomer, Bruce J; Copp, Hillary L

2014-03-01

Secondary data analysis is the use of data collected for research by someone other than the investigator. In the last several years there has been a dramatic increase in the number of these studies being published in urological journals and presented at urological meetings, especially involving secondary data analysis of large administrative data sets. Along with this expansion, skepticism for secondary data analysis studies has increased for many urologists. In this narrative review we discuss the types of large data sets that are commonly used for secondary data analysis in urology, and discuss the advantages and disadvantages of secondary data analysis. A literature search was performed to identify urological secondary data analysis studies published since 2008 using commonly used large data sets, and examples of high quality studies published in high impact journals are given. We outline an approach for performing a successful hypothesis or goal driven secondary data analysis study and highlight common errors to avoid. More than 350 secondary data analysis studies using large data sets have been published on urological topics since 2008 with likely many more studies presented at meetings but never published. Nonhypothesis or goal driven studies have likely constituted some of these studies and have probably contributed to the increased skepticism of this type of research. However, many high quality, hypothesis driven studies addressing research questions that would have been difficult to conduct with other methods have been performed in the last few years. Secondary data analysis is a powerful tool that can address questions which could not be adequately studied by another method. Knowledge of the limitations of secondary data analysis and of the data sets used is critical for a successful study. There are also important errors to avoid when planning and performing a secondary data analysis study. Investigators and the urological community need to strive to use secondary data analysis of large data sets appropriately to produce high quality studies that hopefully lead to improved patient outcomes. Copyright © 2014 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Structural landscape of base pairs containing post-transcriptional modifications in RNA

PubMed Central

Seelam, Preethi P.; Sharma, Purshotam

2017-01-01

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA. PMID:28341704

Amino acid sequence analysis of the annexin super-gene family of proteins.

PubMed

Barton, G J; Newman, R H; Freemont, P S; Crumpton, M J

1991-06-15

The annexins are a widespread family of calcium-dependent membrane-binding proteins. No common function has been identified for the family and, until recently, no crystallographic data existed for an annexin. In this paper we draw together 22 available annexin sequences consisting of 88 similar repeat units, and apply the techniques of multiple sequence alignment, pattern matching, secondary structure prediction and conservation analysis to the characterisation of the molecules. The analysis clearly shows that the repeats cluster into four distinct families and that greatest variation occurs within the repeat 3 units. Multiple alignment of the 88 repeats shows amino acids with conserved physicochemical properties at 22 positions, with only Gly at position 23 being absolutely conserved in all repeats. Secondary structure prediction techniques identify five conserved helices in each repeat unit and patterns of conserved hydrophobic amino acids are consistent with one face of a helix packing against the protein core in predicted helices a, c, d, e. Helix b is generally hydrophobic in all repeats, but contains a striking pattern of repeat-specific residue conservation at position 31, with Arg in repeats 4 and Glu in repeats 2, but unconserved amino acids in repeats 1 and 3. This suggests repeats 2 and 4 may interact via a buried saltbridge. The loop between predicted helices a and b of repeat 3 shows features distinct from the equivalent loop in repeats 1, 2 and 4, suggesting an important structural and/or functional role for this region. No compelling evidence emerges from this study for uteroglobin and the annexins sharing similar tertiary structures, or for uteroglobin representing a derivative of a primordial one-repeat structure that underwent duplication to give the present day annexins. The analyses performed in this paper are re-evaluated in the Appendix, in the light of the recently published X-ray structure for human annexin V. The structure confirms most of the predictions and shows the power of techniques for the determination of tertiary structural information from the amino acid sequences of an aligned protein family.

Head-Spine Structure Modeling: Enhancements to Secondary Loading Path Model and Validation of Head-Cervical Spine Model.

DTIC Science & Technology

1985-07-01

cervical spine; 𔃽*an axisymmetric finite element analysis of a lumbar vertebral body with comparisons to other models and sJEecific attention to the...AXISYMMETRIC FINITE ELEMENT ANALYSIS OF A LUMBAR VERTEBRAL BODY 37 Model 40 Stress Nomenclature 42 Comparison of Models C and S 47 Comparison with Earlier...left and right sides. Each side of the diaphragm arises as one sternal slip, six costal slips and one lumbar slip. Accordingly, the origin of the

A qualitative, phenomenological study on the lived experiences of science teachers in The Bahamas

NASA Astrophysics Data System (ADS)

Micklewhite, Thalia Vionne

This phenomenological study investigates the lived experiences and perceptions of secondary science teachers in the archipelagic country of The Bahamas and how these teachers make meaning of the secondary science program in The Bahamas through the lens of life in a democratic society. The study's purpose was to answer the question: What are the lived experiences of secondary science teachers in The Bahamas in terms of their working conditions'? Using principles of phenomenological research to approach meaning, in-depth interviewing was conducted with six secondary science teachers on four islands of The Bahamas, including the capital of New Providence. The participants and the selected islands are representative of the diversity of teachers, the population, and school climates and structures throughout the country. Narratives were obtained via three ninety-minute interviews with each participant; and thematic analysis was the instrument by which three central themes emerged. Analysis of narratives reveals that lived experience of secondary science teachers revolve around themes of: (1) The Professional Self, (2) Curriculum Leadership, and (3) Curriculum. Most participants are in the career of secondary science education as second choice but are still committed to the profession. Participants overwhelmingly commented that there was a lack of supportive frameworks for critical elements of their daily work, and a need for clear, visionary and decisive curriculum leadership by The Ministry of Education and private School Boards. Participants also desired more appropriate and alternative science curricula that would meet the need of non-academically inclined Bahamian students. Antecedent to their calls was a pressing recognition that they lacked participatory democratic voice in national secondary science education evidenced by years of unrecognized and unattended suggestions sent to those in authority. As a result of these findings, the researcher was propelled towards the need for a civic association of secondary science educators that could provide voice and recognition for secondary science educators, and founded an association named Bahamas Association of Science Educators (BASE). Further, the study findings highlight the need for the crafting of a national policy in science education which would address many of the concerns of participant secondary science teachers.

Structural analysis of emerging ferrite: Doped nickel zinc ferrite

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

Kumar, Rajinder; Kumar, Hitanshu; Singh, Ragini Raj

2015-08-28

Ni{sub 0.6-x}Zn{sub 0.4}Co{sub x}Fe{sub 2}O{sub 4} (x = 0, 0.033, 0.264) nanoparticles were synthesized by sol-gel method and annealed at 900°C. Structural properties of all prepared samples were examined with X-ray diffraction (XRD). The partial formation of hematite (α-Fe{sub 2}O{sub 3}) secondary phase with spinel phase cubic structure of undoped and cobalt doped nickel zinc ferrite was found by XRD peaks. The variation in crystallite size and other structural parameters with cobalt doping has been calculated for most prominent peak (113) of XRD and has been explained on the basis of cations ionic radii difference.

Isolation and structure elucidation of tetrameric procyanidins from unripe apples (Malus pumila cv. Fuji) by NMR spectroscopy.

PubMed

Nakashima, Shohei; Oda, Chihiro; Masuda, Susumu; Tagashira, Motoyuki; Kanda, Tomomasa

2012-11-01

Procyanidins are plant secondary metabolites widely consumed and known to have various physiological functions, but their bioavailability and mechanism of action are still unclear especially for larger oligomers. One of the reasons is scarce information about the detailed structure of oligomeric procyanidins. As for apple, structures of procyanidin components larger than trimers are scarcely known. In this study, 11 tetrameric procyanidins including two known compounds were isolated from unripe apples (Malus pumila cv. Fuji) and identified by NMR spectroscopic analysis and phloroglucinol degradation. As a result, the detailed structural diversity of tetrameric procyanidins in apple was established. Copyright © 2012 Elsevier Ltd. All rights reserved.

A 'periodic table' for protein structures.

PubMed

Taylor, William R

2002-04-11

Current structural genomics programs aim systematically to determine the structures of all proteins coded in both human and other genomes, providing a complete picture of the number and variety of protein structures that exist. In the past, estimates have been made on the basis of the incomplete sample of structures currently known. These estimates have varied greatly (between 1,000 and 10,000; see for example refs 1 and 2), partly because of limited sample size but also owing to the difficulties of distinguishing one structure from another. This distinction is usually topological, based on the fold of the protein; however, in strict topological terms (neglecting to consider intra-chain cross-links), protein chains are open strings and hence are all identical. To avoid this trivial result, topologies are determined by considering secondary links in the form of intra-chain hydrogen bonds (secondary structure) and tertiary links formed by the packing of secondary structures. However, small additions to or loss of structure can make large changes to these perceived topologies and such subjective solutions are neither robust nor amenable to automation. Here I formalize both secondary and tertiary links to allow the rigorous and automatic definition of protein topology.

A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation.

PubMed

Layton, D M; Bundschuh, R

2005-01-01

Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction algorithms are to changes in these parameters. We found already that for changes corresponding to the actual experimental error to which these parameters have been determined, 30% of the structure are falsely predicted whereas the ground state structure is preserved under parameter perturbation in only 5% of all the cases. We establish that base-pairing probabilities calculated in a thermal ensemble are viable although not a perfect measure for the reliability of the prediction of individual structure elements. Here, a new measure of stability using parameter perturbation is proposed, and its limitations are discussed.

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

1H, 13C, and 15N backbone assignment and secondary structure of the receptor-binding domain of vascular endothelial growth factor.

PubMed Central

Fairbrother, W. J.; Champe, M. A.; Christinger, H. W.; Keyt, B. A.; Starovasnik, M. A.

1997-01-01

Nearly complete sequence-specific 1H, 13C, and 15N resonance assignments are reported for the backbone atoms of the receptor-binding domain of vascular endothelial growth factor (VEGF), a 23-kDa homodimeric protein that is a major regulator of both normal and pathological angiogenesis. The assignment strategy relied on the use of seven 3D triple-resonance experiments [HN(CO)CA, HNCA, HNCO, (HCA)CONH, HN(COCA)HA, HN(CA)HA, and CBCA-(CO)NH] and a 3D 15N-TOCSY-HSQC experiment recorded on a 0.5 mM (12 mg/mL) sample at 500 MHz, pH 7.0, 45 degrees C. Under these conditions, 15N relaxation data show that the protein has a rotational correlation time of 15.0 ns. Despite this unusually long correlation time, assignments were obtained for 94 of the 99 residues; 8 residues lack amide 1H and 15N assignments, presumably due to rapid exchange of the amide 1H with solvent under the experimental conditions used. The secondary structure of the protein was deduced from the chemical shift indices of the 1H alpha, 13C alpha, 13C beta, and 13CO nuclei, and from analysis of backbone NOEs observed in a 3D 15N-NOESY-HSQC spectrum. Two helices and a significant amount of beta-sheet structure were identified, in general agreement with the secondary structure found in a recently determined crystal structure of a similar VEGF construct [Muller YA et al., 1997, Proc Natl Acad Sci USA 94:7192-7197]. PMID:9336848

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

PubMed

Goldschmidt, Felix; Regoes, Roland R; Johnson, David R

2017-09-01

Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity. Because of mechanical constraints imposed by the presence of the primary population, the secondary population forms fractal-like dendritic structures. This divides the advancing secondary population into many small sub-populations and promotes intermixing between the primary and secondary populations. We further developed a mathematical model to simulate the formation of dendritic structures in the secondary population during succession. By introducing mutations in the primary or dendritic secondary populations, we found that mutations are more likely to accumulate in the dendritic secondary populations. Our results thus show that successive range expansion can promote intermixing over the short term and increase genetic diversity over the long term. Our results therefore have potentially important implications for predicting the ecological processes and evolutionary trajectories of microbial communities.

A simple system for the identification of fluorescent dyes capable of reporting differences in secondary structure and hydrophobicity among amyloidogenic protein oligomers

NASA Astrophysics Data System (ADS)

Yates, Emma

2012-02-01

Thioflavin T and Congo Red are fluorescent dyes that are commonly used to identify the presence of amyloid structures, ordered protein aggregates. Despite the ubiquity of their use, little is known about their mechanism of interaction with amyloid fibrils, or whether other dyes, whose photophysics indicate that they may be more responsive to differences in macromolecular secondary structure and hydrophobicity, would be better suited to the identification of pathologically relevant oligomeric species in amyloid diseases. In order to systematically address this question, we have designed a strategy that discretely introduces differences in secondary structure and hydrophobicity amidst otherwise identical polyamino acids. This strategy will enable us to quantify and compare the affinities of Thioflavin T, Congo Red, and other, incompletely explored, fluorescent dyes for different secondary structural elements and hydrophobic motifs. With this information, we will identify dyes that give the most robust and quantitative information about structural differences among the complex population of oligomeric species present along an aggregation pathway between soluble monomers and amyloid fibrils, and correlate the resulting structural information with differential oligomeric toxicity.

Effect of sub- and supercritical CO2 treatment on the properties of Pseudomonas cepacia lipase.

PubMed

Chen, Dawei; Zhang, Houjin; Xu, Jing; Yan, Yunjun

2013-07-10

In this work, we have investigated the influences of sub- and supercritical CO2 treatment on the properties of Pseudomonas cepacia lipase (PCL), including its esterification and transesterification activities, structural changes and stability. Results demonstrated that exposure time to subcritical CO2 treatment had a negative effect on PCL transesterification activity whereas exposure time to supercritical CO2 treatment had a positive effect. But generally, most compressed treatments significantly enhanced PCL esterification activity. Conformational analysis by FT-IR and fluorescence emission spectra revealed that enhanced activities after supercritical CO2 treatment were correlated with the secondary and tertiary structural changes of PCL. Secondary structure changes also appeared to be responsible for enhancement of PCL activities by subcritical CO2 treatment. Compared to native PCL, treated PCL's esterification activity significantly decreased in hydrophilic organic media, while transesterification activity significantly increased in tert-amyl alcohol and acetone. After supercritical treatment, the thermal stability of PCL significantly decreased in esterification reactions, however, there was no significant difference in transesterification reactions. Copyright © 2013 Elsevier Inc. All rights reserved.

Novel Approach to Classify Plants Based on Metabolite-Content Similarity.

PubMed

Liu, Kang; Abdullah, Azian Azamimi; Huang, Ming; Nishioka, Takaaki; Altaf-Ul-Amin, Md; Kanaya, Shigehiko

2017-01-01

Secondary metabolites are bioactive substances with diverse chemical structures. Depending on the ecological environment within which they are living, higher plants use different combinations of secondary metabolites for adaptation (e.g., defense against attacks by herbivores or pathogenic microbes). This suggests that the similarity in metabolite content is applicable to assess phylogenic similarity of higher plants. However, such a chemical taxonomic approach has limitations of incomplete metabolomics data. We propose an approach for successfully classifying 216 plants based on their known incomplete metabolite content. Structurally similar metabolites have been clustered using the network clustering algorithm DPClus. Plants have been represented as binary vectors, implying relations with structurally similar metabolite groups, and classified using Ward's method of hierarchical clustering. Despite incomplete data, the resulting plant clusters are consistent with the known evolutional relations of plants. This finding reveals the significance of metabolite content as a taxonomic marker. We also discuss the predictive power of metabolite content in exploring nutritional and medicinal properties in plants. As a byproduct of our analysis, we could predict some currently unknown species-metabolite relations.

Novel Approach to Classify Plants Based on Metabolite-Content Similarity

PubMed Central

Abdullah, Azian Azamimi; Huang, Ming; Nishioka, Takaaki

2017-01-01

Secondary metabolites are bioactive substances with diverse chemical structures. Depending on the ecological environment within which they are living, higher plants use different combinations of secondary metabolites for adaptation (e.g., defense against attacks by herbivores or pathogenic microbes). This suggests that the similarity in metabolite content is applicable to assess phylogenic similarity of higher plants. However, such a chemical taxonomic approach has limitations of incomplete metabolomics data. We propose an approach for successfully classifying 216 plants based on their known incomplete metabolite content. Structurally similar metabolites have been clustered using the network clustering algorithm DPClus. Plants have been represented as binary vectors, implying relations with structurally similar metabolite groups, and classified using Ward's method of hierarchical clustering. Despite incomplete data, the resulting plant clusters are consistent with the known evolutional relations of plants. This finding reveals the significance of metabolite content as a taxonomic marker. We also discuss the predictive power of metabolite content in exploring nutritional and medicinal properties in plants. As a byproduct of our analysis, we could predict some currently unknown species-metabolite relations. PMID:28164123

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.

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

Integrated Analysis Seismic Inversion and Rockphysics for Determining Secondary Porosity Distribution of Carbonate Reservoir at “FR” Field

NASA Astrophysics Data System (ADS)

Rosid, M. S.; Augusta, F. F.; Haidar, M. W.

2018-05-01

In general, carbonate secondary pore structure is very complex due to the significant diagenesis process. Therefore, the determination of carbonate secondary pore types is an important factor which is related to study of production. This paper mainly deals not only to figure out the secondary pores types, but also to predict the distribution of the secondary pore types of carbonate reservoir. We apply Differential Effective Medium (DEM) for analyzing pore types of carbonate rocks. The input parameter of DEM inclusion model is fraction of porosity and the output parameters are bulk moduli and shear moduli as a function of porosity, which is used as input parameter for creating Vp and Vs modelling. We also apply seismic post-stack inversion technique that is used to map the pore type distribution from 3D seismic data. Afterward, we create porosity cube which is better to use geostatistical method due to the complexity of carbonate reservoir. Thus, the results of this study might show the secondary porosity distribution of carbonate reservoir at “FR” field. In this case, North – Northwest of study area are dominated by interparticle pores and crack pores. Hence, that area has highest permeability that hydrocarbon can be more accumulated.

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.

Maternal Influences on Asian American-Pacific Islander Adolescents' Perceived Maternal Sexual Expectations and Their Sexual Initiation

ERIC Educational Resources Information Center

Kao, Tsui-Sui Annie; Loveland-Cherry, Carol; Guthrie, Barbara

2010-01-01

Maternal influences on adolescents' sexual initiation have been examined over two time points in 433 Asian American-Pacific Islander (AAPI) adolescents in a secondary analysis of the Add Health data set using structural equation modeling. A longitudinal model built on a preliminary qualitative study is used to examine the fit between data and…

Factors Leading African Americans and Black Caribbeans to Use Social Work Services for Treating Mental and Substance Use Disorders

ERIC Educational Resources Information Center

Cheng, Tyrone C.; Robinson, Michael A.

2013-01-01

This secondary analysis of 5,000 African Americans and black Caribbeans explored how their use of social work services to address mental and substance use disorders was associated with the disorder involved as well as their perceived need for services, belief system, family resources, proximity to services, social-structural factors, and…

Introducing Network Analysis into Science Education: Methodological Research Examining Secondary School Students' Understanding of "Decomposition"

ERIC Educational Resources Information Center

Schizas, Dimitrios; Katrana, Evagelia; Stamou, George

2013-01-01

In the present study we used the technique of word association tests to assess students' cognitive structures during the learning period. In particular, we tried to investigate what students living near a protected area in Greece (Dadia forest) knew about the phenomenon of decomposition. Decomposition was chosen as a stimulus word because it…

The Use of Distance Learning in the Educational Process Content and Structure of Educational Platforms--Analysis of the Platform Educans

ERIC Educational Resources Information Center

Igado, Manuel Fandos

2010-01-01

This work provides some considerations that complements the scarcity of researches this field of knowledge of the e-learning specifically referred to secondary education. Distance training programmes (both open source code and not) are becoming increasingly more popular, especially in higher level education. However, there are very few cases of…

Career Decision Self-Efficacy Scale-Short Form: A Rasch Analysis of the Portuguese Version

ERIC Educational Resources Information Center

Miguel, Jose P.; Silva, Jose T.; Prieto, Gerardo

2013-01-01

The present study analyzes the psychometric properties of the Career Decision Self-Efficacy Scale-Short Form (CDSE-SF) in a sample of Portuguese secondary education students using the Rasch model. The results indicate that the 25 items of the CDSE-SF are well fitted to a latent unidimensional structure, as required by Rasch modeling. The response…

Exploring the Association between Transformational Leadership and Teacher's Self-Efficacy in Greek Education System: A Multilevel SEM Model

ERIC Educational Resources Information Center

Gkolia, Aikaterini; Koustelios, Athanasios; Belias, Dimitrios

2018-01-01

The main aim of this study is to examine the effect of principals' transformational leadership on teachers' self-efficacy across 77 different Greek elementary and secondary schools based on a centralized education system. For the investigation of the above effect multilevel Structural Equation Modelling analysis was conducted, recognizing the…

Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms

NASA Technical Reports Server (NTRS)

Kopczynski, E. D.; Bateson, M. M.; Ward, D. M.

1994-01-01

When PCR was used to recover small-subunit (SSU) rRNA genes from a hot spring cyanobacterial mat community, chimeric SSU rRNA sequences which exhibited little or no secondary structural abnormality were recovered. They were revealed as chimeras of SSU rRNA genes of uncultivated species through separate phylogenetic analysis of short sequence domains.

Influence of Using Challenging Tasks in Biology Classrooms on Students' Cognitive Knowledge Structure: An Empirical Video Study

ERIC Educational Resources Information Center

Nawani, Jigna; Rixius, Julia; Neuhaus, Birgit J.

2016-01-01

Empirical analysis of secondary biology classrooms revealed that, on average, 68% of teaching time in Germany revolved around processing tasks. Quality of instruction can thus be assessed by analyzing the quality of tasks used in classroom discourse. This quasi-experimental study analyzed how teachers used tasks in 38 videotaped biology lessons…

Support vector machine based classification of fast Fourier transform spectroscopy of proteins

NASA Astrophysics Data System (ADS)

Lazarevic, Aleksandar; Pokrajac, Dragoljub; Marcano, Aristides; Melikechi, Noureddine

2009-02-01

Fast Fourier transform spectroscopy has proved to be a powerful method for study of the secondary structure of proteins since peak positions and their relative amplitude are affected by the number of hydrogen bridges that sustain this secondary structure. However, to our best knowledge, the method has not been used yet for identification of proteins within a complex matrix like a blood sample. The principal reason is the apparent similarity of protein infrared spectra with actual differences usually masked by the solvent contribution and other interactions. In this paper, we propose a novel machine learning based method that uses protein spectra for classification and identification of such proteins within a given sample. The proposed method uses principal component analysis (PCA) to identify most important linear combinations of original spectral components and then employs support vector machine (SVM) classification model applied on such identified combinations to categorize proteins into one of given groups. Our experiments have been performed on the set of four different proteins, namely: Bovine Serum Albumin, Leptin, Insulin-like Growth Factor 2 and Osteopontin. Our proposed method of applying principal component analysis along with support vector machines exhibits excellent classification accuracy when identifying proteins using their infrared spectra.

Microfibril angle in wood of Scots pine trees (Pinus sylvestris) after irradiation from the Chernobyl nuclear reactor accident.

PubMed

Tulik, Mirela; Rusin, Aleksandra

2005-03-01

The secondary cell wall structure of tracheids of Scots pine (Pinus sylvestris L.), especially the angle of microfibrils in the S(2) layer, was examined in wood deposited prior to and after the Chernobyl accident in 1986. Microscopic analysis was carried out on wood samples collected in October 1997 from breast height of three pine trees 16, 30 and 42 years old. The polluted site was located in a distance of 5 km south from the Chernobyl nuclear power plant where radioactive contamination in 1997 was 3.7 x 10(5) kBq m(-2). Anatomical analysis showed that the structure of the secondary cell wall in tracheids formed after the Chernobyl accident was changed. Changes occurred both in S(2) and S(3) layers. The angle of microfibrils in S(2) layer in wood deposited after the Chernobyl accident was different in comparison to this measured in wood formed prior to the disaster. The intensity of the changes, i.e. alteration of the microfibrils angle in S(2) layer and unusual pattern of the S(3) layer, depended on the age of the tree and was most intensive in a young tree.

A new criterion to evaluate water vapor interference in protein secondary structural analysis by FTIR spectroscopy.

PubMed

Zou, Ye; Ma, Gang

2014-06-04

Second derivative and Fourier self-deconvolution (FSD) are two commonly used techniques to resolve the overlapped component peaks from the often featureless amide I band in Fourier transform infrared (FTIR) curve-fitting approach for protein secondary structural analysis. Yet, the reliability of these two techniques is greatly affected by the omnipresent water vapor in the atmosphere. Several criteria are currently in use as quality controls to ensure the protein absorption spectrum is negligibly affected by water vapor interference. In this study, through a second derivative study of liquid water, we first argue that the previously established criteria cannot guarantee a reliable evaluation of water vapor interference due to a phenomenon that we refer to as sample's absorbance-dependent water vapor interference. Then, through a comparative study of protein and liquid water, we show that a protein absorption spectrum can still be significantly affected by water vapor interference even though it satisfies the established criteria. At last, we propose to use the comparison between the second derivative spectra of protein and liquid water as a new criterion to better evaluate water vapor interference for more reliable second derivative and FSD treatments on the protein amide I band.

Binding of Amphipathic Cell Penetrating Peptide p28 to Wild Type and Mutated p53 as studied by Raman, Atomic Force and Surface Plasmon Resonance spectroscopies.

PubMed

Signorelli, Sara; Santini, Simona; Yamada, Tohru; Bizzarri, Anna Rita; Beattie, Craig W; Cannistraro, Salvatore

2017-04-01

Mutations within the DNA binding domain (DBD) of the tumor suppressor p53 are found in >50% of human cancers and may significantly modify p53 secondary structure impairing its function. p28, an amphipathic cell-penetrating peptide, binds to the DBD through hydrophobic interaction and induces a posttranslational increase in wildtype and mutant p53 restoring functionality. We use mutation analyses to explore which elements of secondary structure may be critical to p28 binding. Molecular modeling, Raman spectroscopy, Atomic Force Spectroscopy (AFS) and Surface Plasmon Resonance (SPR) were used to identify which secondary structure of site-directed and naturally occurring mutant DBDs are potentially altered by discrete changes in hydrophobicity and the molecular interaction with p28. We show that specific point mutations that alter hydrophobicity within non-mutable and mutable regions of the p53 DBD alter specific secondary structures. The affinity of p28 was positively correlated with the β-sheet content of a mutant DBD, and reduced by an increase in unstructured or random coil that resulted from a loss in hydrophobicity and redistribution of surface charge. These results help refine our knowledge of how mutations within p53-DBD alter secondary structure and provide insight on how potential structural alterations in p28 or similar molecules improve their ability to restore p53 function. Raman spectroscopy, AFS, SPR and computational modeling are useful approaches to characterize how mutations within the p53DBD potentially affect secondary structure and identify those structural elements prone to influence the binding affinity of agents designed to increase the functionality of p53. Copyright © 2017 Elsevier B.V. All rights reserved.

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.

PubMed

Chen, Xiang; He, Si-Min; Bu, Dongbo; Zhang, Fa; Wang, Zhiyong; Chen, Runsheng; Gao, Wen

2008-09-15

RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is proved to be NP-hard. Due to kinetic reasons the real RNA secondary structure often has local instead of global minimum free energy. This implies that we may improve the performance of RNA secondary structure prediction by taking kinetics into account and minimize free energy in a local area. we propose a novel algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Still based on MFE criterion, FlexStem adopts comprehensive energy models that allow complex pseudoknots. Unlike classical thermodynamic methods, our approach aims to simulate the RNA folding process by successive addition of maximal stems, reducing the search space while maintaining or even improving the prediction accuracy. This reduced space is constructed by our maximal stem strategy and stem-adding rule induced from elaborate statistical experiments on real RNA secondary structures. The strategy and the rule also reflect the folding characteristic of RNA from a new angle and help compensate for the deficiency of merely relying on MFE in RNA structure prediction. We validate FlexStem by applying it to tRNAs, 5SrRNAs and a large number of pseudoknotted structures and compare it with the well-known algorithms such as RNAfold, PKNOTS, PknotsRG, HotKnots and ILM according to their overall sensitivities and specificities, as well as positive and negative controls on pseudoknots. The results show that FlexStem significantly increases the prediction accuracy through its local search strategy. Software is available at http://pfind.ict.ac.cn/FlexStem/. Supplementary data are available at Bioinformatics online.

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH.

PubMed

Kuramae, Eiko; Gamper, Hannes; van Veen, Johannes; Kowalchuk, George

2011-08-01

Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

The Role of Migration and Single Motherhood in Upper Secondary Education in Mexico

ERIC Educational Resources Information Center

Creighton, Mathew J.; Park, Hyunjoon; Teruel, Graciela M.

2009-01-01

We investigated the link between migration, family structure, and the risk of dropping out of upper secondary school in Mexico. Using two waves of the Mexican Family Life Survey, which includes 1,080 upper secondary students, we longitudinally modeled the role of family structure in the subsequent risk of dropping out, focusing on the role of…

Thermal modeling and analysis of structurally complex spacecraft using the IDEAS system

NASA Technical Reports Server (NTRS)

Garrett, L. B.

1983-01-01

Large antenna satellites of unprecedented sizes are needed for a number of applications. Antenna diameters on the order of 50 meters and upward are required. Such antennas involve the use of large expanses of lattice structures with hundreds or thousands of individual connecting members. In connection with the design of such structures, the consideration of thermal effects represents a crucial factor. Software capabilities have emerged which are coded to include major first order thermal effects and to purposely ignore, in the interest of computational efficiency, the secondary effects. The Interactive Design and Evaluation of Advanced Spacecraft (IDEAS) is one such system. It has been developed for an employment in connection with thermal-structural interaction analyses related to the design of large structurally complex classes of future spacecraft. An IDEAS overview is presented. Attention is given to a typical antenna analysis using IDEAS, the thermal and loading analyses of a tetrahedral truss spacecraft, and ecliptic and polar orbit analyses.

Correlation of RNA secondary structure and attenuation of Sabin vaccine strains of poliovirus in tissue culture.

PubMed

Macadam, A J; Ferguson, G; Burlison, J; Stone, D; Skuce, R; Almond, J W; Minor, P D

1992-08-01

Part of the 5' noncoding regions of all three Sabin vaccine strains of poliovirus contains determinants of attenuation that are shown here to influence the ability of these strains to grow at elevated temperatures in BGM cells. The predicted RNA secondary structure of this region (nt 464-542 in P3/Sabin) suggests that both phenotypes are due to perturbation of base-paired stems. Ts phenotypes of site-directed mutants with defined changes in this region correlated well with predicted secondary structure stabilities. Reversal of base-pair orientation had little effect whereas stem disruption led to marked increases in temperature sensitivity. Phenotypic revertants of such viruses displayed mutations on either side of the stem. Mutations destabilizing stems led to intermediate phenotypes. These results provided evidence for the biological significance of the predicted RNA secondary structure.

Statistical mechanical approach to secondary processes and structural relaxation in glasses and glass formers: a leading model to describe the onset of Johari-Goldstein processes and their relationship with fully cooperative processes.

PubMed

Crisanti, A; Leuzzi, L; Paoluzzi, M

2011-09-01

The interrelation of dynamic processes active on separated time-scales in glasses and viscous liquids is investigated using a model displaying two time-scale bifurcations both between fast and secondary relaxation and between secondary and structural relaxation. The study of the dynamics allows for predictions on the system relaxation above the temperature of dynamic arrest in the mean-field approximation, that are compared with the outcomes of the equations of motion directly derived within the Mode Coupling Theory (MCT) for under-cooled viscous liquids. By varying the external thermodynamic parameters, a wide range of phenomenology can be represented, from a very clear separation of structural and secondary peak in the susceptibility loss to excess wing structures.

IIR filtering based adaptive active vibration control methodology with online secondary path modeling using PZT actuators

NASA Astrophysics Data System (ADS)

Boz, Utku; Basdogan, Ipek

2015-12-01

Structural vibrations is a major cause for noise problems, discomfort and mechanical failures in aerospace, automotive and marine systems, which are mainly composed of plate-like structures. In order to reduce structural vibrations on these structures, active vibration control (AVC) is an effective approach. Adaptive filtering methodologies are preferred in AVC due to their ability to adjust themselves for varying dynamics of the structure during the operation. The filtered-X LMS (FXLMS) algorithm is a simple adaptive filtering algorithm widely implemented in active control applications. Proper implementation of FXLMS requires availability of a reference signal to mimic the disturbance and model of the dynamics between the control actuator and the error sensor, namely the secondary path. However, the controller output could interfere with the reference signal and the secondary path dynamics may change during the operation. This interference problem can be resolved by using an infinite impulse response (IIR) filter which considers feedback of the one or more previous control signals to the controller output and the changing secondary path dynamics can be updated using an online modeling technique. In this paper, IIR filtering based filtered-U LMS (FULMS) controller is combined with online secondary path modeling algorithm to suppress the vibrations of a plate-like structure. The results are validated through numerical and experimental studies. The results show that the FULMS with online secondary path modeling approach has more vibration rejection capabilities with higher convergence rate than the FXLMS counterpart.

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Yang, Zhigang; Okazaki, Yozo; Yonemaru, Jun-ichi; Ebana, Kaworu; Yano, Masahiro; Saito, Kazuki

2015-01-01

Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications. PMID:25267402

Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program

PubMed Central

Miller, Edward B.; Murrett, Colleen S.; Zhu, Kai; Zhao, Suwen; Goldfeld, Dahlia A.; Bylund, Joseph H.; Friesner, Richard A.

2013-01-01

Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess α-helical segments, we employ an alternative dihedral library composed of (ϕ,ψ) angles commonly found in helices. The alternative library is searched over a user-specified range of residues that define the helical bounds. The source of these helical bounds can be from popular secondary structure prediction software or from analysis of past loop predictions where a propensity to form a helix is observed. Due to the maturity of our energy model, the lowest energy loop across all experiments can be selected with an accuracy of sub-Ångström RMSD in 80% of cases, 1.0 to 1.5 Å RMSD in 14% of cases, and poorer than 1.5 Å RMSD in 6% of cases. The effectiveness of our current methods in predicting hairpin-containing loops is explored with hairpins up to 13 residues in length and again reaching an accuracy of sub-Ångström RMSD in 83% of cases, 1.0 to 1.5 Å RMSD in 10% of cases, and poorer than 1.5 Å RMSD in 7% of cases. Finally, we explore the effect of an imprecise surrounding environment, in which side chains, but not the backbone, are initially in perturbed geometries. In these cases, loops perturbed to 3Å RMSD from the native environment were restored to their native conformation with sub-Ångström RMSD. PMID:23814507

Inability of Prevotella bryantii to Form a Functional Shine-Dalgarno Interaction Reflects Unique Evolution of Ribosome Binding Sites in Bacteroidetes

PubMed Central

Accetto, Tomaž; Avguštin, Gorazd

2011-01-01

The Shine-Dalgarno (SD) sequence is a key element directing the translation to initiate at the authentic start codons and also enabling translation initiation to proceed in 5′ untranslated mRNA regions (5′-UTRs) containing moderately strong secondary structures. Bioinformatic analysis of almost forty genomes from the major bacterial phylum Bacteroidetes revealed, however, a general absence of SD sequence, drop in GC content and consequently reduced tendency to form secondary structures in 5′-UTRs. The experiments using the Prevotella bryantii TC1-1 expression system were in agreement with these findings: neither addition nor omission of SD sequence in the unstructured 5′-UTR affected the level of the reporter protein, non-specific nuclease NucB. Further, NucB level in P. bryantii TC1-1, contrary to hMGFP level in Escherichia coli, was five times lower when SD sequence formed part of the secondary structure with a folding energy -5,2 kcal/mol. Also, the extended SD sequences did not affect protein levels as in E. coli. It seems therefore that a functional SD interaction does not take place during the translation initiation in P. bryanttii TC1-1 and possibly other members of phylum Bacteroidetes although the anti SD sequence is present in 16S rRNA genes of their genomes. We thus propose that in the absence of the SD sequence interaction, the selection of genuine start codons in Bacteroidetes is accomplished by binding of ribosomal protein S1 to unstructured 5′-UTR as opposed to coding region which is inaccessible due to mRNA secondary structure. Additionally, we found that sequence logos of region preceding the start codons may be used as taxonomical markers. Depending on whether complete sequence logo or only part of it, such as information content and base proportion at specific positions, is used, bacterial genera or families and in some cases even bacterial phyla can be distinguished. PMID:21857964

Factor analysis of financial and operational performance measures of non-profit hospitals.

PubMed

Das, Dhiman

2009-01-01

To understand the important dimensions of the financial and operational performance of non-profit hospitals. Secondary data for non-profit US hospitals between 1996 and 2004. I use iterative principal factor analysis of hospitals' financial and operational ratios for each year of the study. For factor interpretation, I use oblique rotation. Financial ratios were created using cost report data from HCRIS 2552-96 available from the Centers for Medicaid & Medicare Services (CMS). I identify five factors--capital structure, profitability, activity, liquidity, and an operational factor--that explain most of the variation in the performance of non-profit hospitals. I also find that capital structure is more important than profitability in determining the performance of these hospitals. The importance of capital structure highlights a significant shift in the organization of the non-profit hospitals' finances.

Principals' Administrative Styles and Students' Academic Performance in Taraba State Secondary Schools, Nigeria

ERIC Educational Resources Information Center

Bello, Suleiman; Ibi, Mustapha Baba; Bukar, Ibrahim Bulama

2016-01-01

The study determined the relationship between principals' administrative styles and students' academic performance in Taraba State secondary schools, Nigeria. The objectives of the study were to determine the relationships between initiative structure of leadership styles, consideration structure of leadership styles, participatory structure of…

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.

Secure Secondary Use of Clinical Data with Cloud-based NLP Services. Towards a Highly Scalable Research Infrastructure.

PubMed

Christoph, J; Griebel, L; Leb, I; Engel, I; Köpcke, F; Toddenroth, D; Prokosch, H-U; Laufer, J; Marquardt, K; Sedlmayr, M

2015-01-01

The secondary use of clinical data provides large opportunities for clinical and translational research as well as quality assurance projects. For such purposes, it is necessary to provide a flexible and scalable infrastructure that is compliant with privacy requirements. The major goals of the cloud4health project are to define such an architecture, to implement a technical prototype that fulfills these requirements and to evaluate it with three use cases. The architecture provides components for multiple data provider sites such as hospitals to extract free text as well as structured data from local sources and de-identify such data for further anonymous or pseudonymous processing. Free text documentation is analyzed and transformed into structured information by text-mining services, which are provided within a cloud-computing environment. Thus, newly gained annotations can be integrated along with the already available structured data items and the resulting data sets can be uploaded to a central study portal for further analysis. Based on the architecture design, a prototype has been implemented and is under evaluation in three clinical use cases. Data from several hundred patients provided by a University Hospital and a private hospital chain have already been processed. Cloud4health has shown how existing components for secondary use of structured data can be complemented with text-mining in a privacy compliant manner. The cloud-computing paradigm allows a flexible and dynamically adaptable service provision that facilitates the adoption of services by data providers without own investments in respective hardware resources and software tools.

Potent Cytotoxic Peptides from the Australian Marine Sponge Pipestela candelabra

PubMed Central

Tran, Trong D.; Pham, Ngoc B.; Fechner, Gregory A.; Hooper, John N. A.; Quinn, Ronald J.

2014-01-01

Two consecutive prefractionated fractions of the Australian marine sponge extract, Pipestela candelabra, were identified to be selectively active on the human prostate cancer cells (PC3) compared to the human neonatal foreskin fibroblast non-cancer cells (NFF). Twelve secondary metabolites were isolated in which four compounds are new small peptides. Their structures were characterized by spectroscopic and chemical analysis. These compounds inhibited selectively the growth of prostate cancer cells with IC50 values in the picomolar to sub-micromolar range. Structure-activity relationship of these compounds is discussed. PMID:24901701

Distributed cooperative control of AC microgrids

NASA Astrophysics Data System (ADS)

Bidram, Ali

In this dissertation, the comprehensive secondary control of electric power microgrids is of concern. Microgrid technical challenges are mainly realized through the hierarchical control structure, including primary, secondary, and tertiary control levels. Primary control level is locally implemented at each distributed generator (DG), while the secondary and tertiary control levels are conventionally implemented through a centralized control structure. The centralized structure requires a central controller which increases the reliability concerns by posing the single point of failure. In this dissertation, the distributed control structure using the distributed cooperative control of multi-agent systems is exploited to increase the secondary control reliability. The secondary control objectives are microgrid voltage and frequency, and distributed generators (DGs) active and reactive powers. Fully distributed control protocols are implemented through distributed communication networks. In the distributed control structure, each DG only requires its own information and the information of its neighbors on the communication network. The distributed structure obviates the requirements for a central controller and complex communication network which, in turn, improves the system reliability. Since the DG dynamics are nonlinear and non-identical, input-output feedback linearization is used to transform the nonlinear dynamics of DGs to linear dynamics. Proposed control frameworks cover the control of microgrids containing inverter-based DGs. Typical microgrid test systems are used to verify the effectiveness of the proposed control protocols.

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

PubMed Central

Sloma, Michael F.; Mathews, David H.

2016-01-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

Introduction to bioinformatics.

PubMed

Can, Tolga

2014-01-01

Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.