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Sample records for peptide alignment approach

  1. A graph kernel approach for alignment-free domain–peptide interaction prediction with an application to human SH3 domains

    PubMed Central

    Kundu, Kousik; Costa, Fabrizio; Backofen, Rolf

    2013-01-01

    Motivation: State-of-the-art experimental data for determining binding specificities of peptide recognition modules (PRMs) is obtained by high-throughput approaches like peptide arrays. Most prediction tools applicable to this kind of data are based on an initial multiple alignment of the peptide ligands. Building an initial alignment can be error-prone, especially in the case of the proline-rich peptides bound by the SH3 domains. Results: Here, we present a machine-learning approach based on an efficient graph-kernel technique to predict the specificity of a large set of 70 human SH3 domains, which are an important class of PRMs. The graph-kernel strategy allows us to (i) integrate several types of physico-chemical information for each amino acid, (ii) consider high-order correlations between these features and (iii) eliminate the need for an initial peptide alignment. We build specialized models for each human SH3 domain and achieve competitive predictive performance of 0.73 area under precision-recall curve, compared with 0.27 area under precision-recall curve for state-of-the-art methods based on position weight matrices. We show that better models can be obtained when we use information on the noninteracting peptides (negative examples), which is currently not used by the state-of-the art approaches based on position weight matrices. To this end, we analyze two strategies to identify subsets of high confidence negative data. The techniques introduced here are more general and hence can also be used for any other protein domains, which interact with short peptides (i.e. other PRMs). Availability: The program with the predictive models can be found at http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/SH3PepInt.tar.gz. We also provide a genome-wide prediction for all 70 human SH3 domains, which can be found under http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/Genome-Wide-Predictions.tar.gz. Contact: backofen@informatik.uni-freiburg.de Supplementary

  2. Peptide nanotube aligning side chains onto one side.

    PubMed

    Tabata, Yuki; Mitani, Shota; Kimura, Shunsaku

    2016-06-01

    A novel pseudo cyclic penta-β-peptide composed of a β-naphthylalanine, two β-alanines, and a sequence of ethylenediamine-succinic acid (CP5ES) is synthesized and investigated on peptide nanotube (PNT) formation. When the PNT is formed with the maximum number of intermolecular hydrogen bonds between the cyclic peptides, the sequence enables the alignment of the side chains, naphthyl groups, on one side of the PNT. Microscopic and spectroscopic observations of CP5ES crystals reveal that CP5ES forms rod- or needle-shaped molecular assemblies showing exciton coupling of the Cotton effect and predominant monomer emission, which are different from a reference cyclic tri-β-peptide composed of a β-naphthylalanine and two β-alanines. Insertion of a sequence of ethylenediamine-succinic acid into β-amino acids in the cyclic skeleton is therefore suggested to be effective to make the side chains aligning on one side of the PNT. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. PMID:27282135

  3. Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)

    PubMed Central

    2013-01-01

    Background Small peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of plant development, reproduction and defense responses. However, popular similarity search tools and gene prediction techniques generally fail to identify most members belonging to this class of genes. This is largely due to the high sequence divergence among family members and the limited availability of experimentally verified small peptides to use as training sets for homology search and ab initio prediction. Consequently, there is an urgent need for both experimental and computational studies in order to further advance the accurate prediction of small peptides. Results We present here a homology-based gene prediction program to accurately predict small peptides at the genome level. Given a high-quality profile alignment, SPADA identifies and annotates nearly all family members in tested genomes with better performance than all general-purpose gene prediction programs surveyed. We find numerous mis-annotations in the current Arabidopsis thaliana and Medicago truncatula genome databases using SPADA, most of which have RNA-Seq expression support. We also show that SPADA works well on other classes of small secreted peptides in plants (e.g., self-incompatibility protein homologues) as well as non-secreted peptides outside the plant kingdom (e.g., the alpha-amanitin toxin gene family in the mushroom, Amanita bisporigera). Conclusions SPADA is a free software tool that accurately identifies and predicts the gene structure for short peptides with one or two exons. SPADA is able to incorporate information from profile alignments into the model prediction process and makes use of it to score different candidate models. SPADA achieves high sensitivity and specificity in predicting small plant peptides such as the cysteine-rich peptide families. A systematic application of SPADA to other classes of small peptides by research communities will greatly

  4. Biomimetic alignment of zinc oxide nanoparticles along a peptide nanofiber.

    PubMed

    Tomizaki, Kin-ya; Kubo, Seiya; Ahn, Soo-Ang; Satake, Masahiko; Imai, Takahito

    2012-09-18

    Zinc oxide (ZnO) has potential applications in solar cells, chemical sensors, and piezoelectronic and optoelectronic devices due to its attractive physical and chemical properties. Recently, a solution-phase method has been used to synthesize ZnO crystals with diverse (from simple to hierarchical) nanostructures that is simple, of low cost, and scalable. This method requires template molecules to control the morphology of the ZnO crystals. In this paper, we describe the design and synthesis of two short peptides (RU-003,Ac-AIEKAXEIA-NH(2); RU-027, EAHVMHKVAPRPGGGAIEKAXEIA-NH(2); X = l-2-naphthylalanine) and the characterization of their self-assembled nanostructures. We also report their potential for ZnO mineralization and the alignment of ZnO nanoparticles along peptide nanostructures at room temperature. Interestingly, nonapeptide RU-003 predominantly formed a straight fibrous structure and induced the nucleation of ZnO at its surface, leading to an alignment of ZnO nanoparticles along a peptide nanofiber. This novel method holds promise for the room-temperature fabrication of ZnO catalysts with increased specific surface area, ZnO-gated transistors, and ZnO-based nanomaterials for optical applications. PMID:22954381

  5. A bioengineered peripheral nerve construct using aligned peptide amphiphile nanofibers

    PubMed Central

    Yalom, Anisa; Berns, Eric J.; Stephanopoulos, Nicholas; McClendon, Mark T.; Segovia, Luis A.; Spigelman, Igor; Stupp, Samuel I.; Jarrahy, Reza

    2014-01-01

    Peripheral nerve injuries can result in lifelong disability. Primary coaptation is the treatment of choice when the gap between transected nerve ends is short. Long nerve gaps seen in more complex injuries often require autologous nerve grafts or nerve conduits implemented into the repair. Nerve grafts, however, cause morbidity and functional loss at donor sites, which are limited in number. Nerve conduits, in turn, lack an internal scaffold to support and guide axonal regeneration, resulting in decreased efficacy over longer nerve gap lengths. By comparison, peptide amphiphiles (PAs) are molecules that can self-assemble into nanofibers, which can be aligned to mimic the native architecture of peripheral nerve. As such, they represent a potential substrate for use in a bioengineered nerve graft substitute. To examine this, we cultured Schwann cells with bioactive PAs (RGDS-PA, IKVAV-PA) to determine their ability to attach to and proliferate within the biomaterial. Next, we devised a PA construct for use in a peripheral nerve critical sized defect model. Rat sciatic nerve defects were created and reconstructed with autologous nerve, PLGA conduits filled with various forms of aligned PAs, or left unrepaired. Motor and sensory recovery were determined and compared among groups. Our results demonstrate that Schwann cells are able to adhere to and proliferate in aligned PA gels, with greater efficacy in bioactive PAs compared to the backbone-PA alone. In vivo testing revealed recovery of motor and sensory function in animals treated with conduit/PA constructs comparable to animals treated with autologous nerve grafts. Functional recovery in conduit/PA and autologous graft groups was significantly faster than in animals treated with empty PLGA conduits. Histological examinations also demonstrated increased axonal and Schwann cell regeneration within the reconstructed nerve gap in animals treated with conduit/PA constructs. These results indicate that PA nanofibers may

  6. Partial face recognition: alignment-free approach.

    PubMed

    Liao, Shengcai; Jain, Anil K; Li, Stan Z

    2013-05-01

    Numerous methods have been developed for holistic face recognition with impressive performance. However, few studies have tackled how to recognize an arbitrary patch of a face image. Partial faces frequently appear in unconstrained scenarios, with images captured by surveillance cameras or handheld devices (e.g., mobile phones) in particular. In this paper, we propose a general partial face recognition approach that does not require face alignment by eye coordinates or any other fiducial points. We develop an alignment-free face representation method based on Multi-Keypoint Descriptors (MKD), where the descriptor size of a face is determined by the actual content of the image. In this way, any probe face image, holistic or partial, can be sparsely represented by a large dictionary of gallery descriptors. A new keypoint descriptor called Gabor Ternary Pattern (GTP) is also developed for robust and discriminative face recognition. Experimental results are reported on four public domain face databases (FRGCv2.0, AR, LFW, and PubFig) under both the open-set identification and verification scenarios. Comparisons with two leading commercial face recognition SDKs (PittPatt and FaceVACS) and two baseline algorithms (PCA+LDA and LBP) show that the proposed method, overall, is superior in recognizing both holistic and partial faces without requiring alignment. PMID:23520259

  7. Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

    SciTech Connect

    Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.; Grama, Ananth

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

  8. ARYANA: Aligning Reads by Yet Another Approach

    PubMed Central

    2014-01-01

    Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

  9. Alignment of a model amyloid Peptide fragment in bulk and at a solid surface.

    PubMed

    Hamley, Ian W; Castelletto, Valeria; Moulton, Claire M; Rodríguez-Pérez, José; Squires, Adam M; Eralp, Tugce; Held, Georg; Hicks, Matthew R; Rodger, Alison

    2010-06-24

    The alignment of model amyloid peptide YYKLVFFC is investigated in bulk and at a solid surface using a range of spectroscopic methods employing polarized radiation. The peptide is based on a core sequence of the amyloid beta (Abeta) peptide, KLVFF. The attached tyrosine and cysteine units are exploited to yield information on alignment and possible formation of disulfide or dityrosine links. Polarized Raman spectroscopy on aligned stalks provides information on tyrosine orientation, which complements data from linear dichroism (LD) on aqueous solutions subjected to shear in a Couette cell. LD provides a detailed picture of alignment of peptide strands and aromatic residues and was also used to probe the kinetics of self-assembly. This suggests initial association of phenylalanine residues, followed by subsequent registry of strands and orientation of tyrosine residues. X-ray diffraction (XRD) data from aligned stalks is used to extract orientational order parameters from the 0.48 nm reflection in the cross-beta pattern, from which an orientational distribution function is obtained. X-ray diffraction on solutions subject to capillary flow confirmed orientation in situ at the level of the cross-beta pattern. The information on fibril and tyrosine orientation from polarized Raman spectroscopy is compared with results from NEXAFS experiments on samples prepared as films on silicon. This indicates fibrils are aligned parallel to the surface, with phenyl ring normals perpendicular to the surface. Possible disulfide bridging leading to peptide dimer formation was excluded by Raman spectroscopy, whereas dityrosine formation was probed by fluorescence experiments and was found not to occur except under alkaline conditions. Congo red binding was found not to influence the cross-beta XRD pattern. PMID:20509614

  10. Alignment and Use of Self-Assembled Peptide Nanotubes as Dry-Etching Mask

    NASA Astrophysics Data System (ADS)

    Andersen, Karsten B.; Castillo-León, Jaime; Bakmand, Tanya; Svendsen, Winnie E.

    2012-06-01

    Self-assembled diphenylalanine peptide nanotubes provide a means of achieving nanostructured materials in a very simple and fast way. Recent discoveries have shown that this unique material, in addition to remaining stable under dry conditions, rapidly dissolves in water making it a promising candidate for controlled nanofabrication without organic solvents. The present work demonstrates how this unique structure can be aligned, manipulated and used as both an etching mask in a dry etching procedure and as a lift-off material. As a further demonstration of the potential of this technique, the peptide nanotubes were utilized to fabricate silicon nanowire devices and gold nanoslits in a rapid manner.

  11. Peptide Based Radiopharmaceuticals: Specific Construct Approach

    SciTech Connect

    Som, P; Rhodes, B A; Sharma, S S

    1997-10-21

    The objective of this project was to develop receptor based peptides for diagnostic imaging and therapy. A series of peptides related to cell adhesion molecules (CAM) and immune regulation were designed for radiolabeling with 99mTc and evaluated in animal models as potential diagnostic imaging agents for various disease conditions such as thrombus (clot), acute kidney failure, and inflection/inflammation imaging. The peptides for this project were designed by the industrial partner, Palatin Technologies, (formerly Rhomed, Inc.) using various peptide design approaches including a newly developed rational computer assisted drug design (CADD) approach termed MIDAS (Metal ion Induced Distinctive Array of Structures). In this approach, the biological function domain and the 99mTc complexing domain are fused together so that structurally these domains are indistinguishable. This approach allows construction of conformationally rigid metallo-peptide molecules (similar to cyclic peptides) that are metabolically stable in-vivo. All the newly designed peptides were screened in various in vitro receptor binding and functional assays to identify a lead compound. The lead compounds were formulated in a one-step 99mTc labeling kit form which were studied by BNL for detailed in-vivo imaging using various animals models of human disease. Two main peptides usingMIDAS approach evolved and were investigated: RGD peptide for acute renal failure and an immunomodulatory peptide derived from tuftsin (RMT-1) for infection/inflammation imaging. Various RGD based metallopeptides were designed, synthesized and assayed for their efficacy in inhibiting ADP-induced human platelet aggregation. Most of these peptides displayed biological activity in the 1-100 µM range. Based on previous work by others, RGD-I and RGD-II were evaluated in animal models of acute renal failure. These earlier studies showed that after acute ischemic injury the renal cortex displays

  12. Classroom EFL Writing: The Alignment-Oriented Approach

    ERIC Educational Resources Information Center

    Haiyan, Miao; Rilong, Liu

    2016-01-01

    This paper outlines the alignment-oriented approach in classroom EFL writing. Based on a review of the characteristics of the written language and comparison between the product-focused approach and the process-focused approach, the paper proposes a practical classroom procedure as to how to teach EFL writing. A follow-up empirical study is…

  13. Connectivity independent protein-structure alignment: a hierarchical approach

    PubMed Central

    Kolbeck, Bjoern; May, Patrick; Schmidt-Goenner, Tobias; Steinke, Thomas; Knapp, Ernst-Walter

    2006-01-01

    Background Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE) but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity). Results We perform protein-structure alignment using a two-level hierarchical approach implemented in the program GANGSTA. On the first level, pair contacts and relative orientations between SSEs (i.e. α-helices and β-strands) are maximized with a genetic algorithm (GA). On the second level residue pair contacts from the best SSE alignments are optimized. We have tested the method on visually optimized structure alignments of protein pairs (pairwise mode) and for database scans. For a given protein structure, our method is able to detect significant structural similarity of functionally important folds with non-sequential SSE connectivity. The performance for structure alignments with strictly sequential SSE connectivity is comparable to that of other structure alignment methods. Conclusion As demonstrated for several applications, GANGSTA finds meaningful protein-structure alignments independent of the SSE connectivity. GANGSTA is able to detect structural similarity of protein folds that are assigned to different superfamilies but nevertheless possess similar structures and perform related functions, even if these proteins differ in SSE connectivity. PMID:17118190

  14. Vertically aligned peptide nanostructures using plasma-enhanced chemical vapor deposition.

    PubMed

    Vasudev, Milana C; Koerner, Hilmar; Singh, Kristi M; Partlow, Benjamin P; Kaplan, David L; Gazit, Ehud; Bunning, Timothy J; Naik, Rajesh R

    2014-02-10

    In this study, we utilize plasma-enhanced chemical vapor deposition (PECVD) for the deposition of nanostructures composed of diphenylalanine. PECVD is a solvent-free approach and allows sublimation of the peptide to form dense, uniform arrays of peptide nanostructures on a variety of substrates. The PECVD deposited d-diphenylalanine nanostructures have a range of chemical and physical properties depending on the specific discharge parameters used during the deposition process. PMID:24400716

  15. Aligning Collaborative and Culturally Responsive Evaluation Approaches

    ERIC Educational Resources Information Center

    Askew, Karyl; Beverly, Monifa Green; Jay, Michelle L.

    2012-01-01

    The authors, three African-American women trained as collaborative evaluators, offer a comparative analysis of collaborative evaluation (O'Sullivan, 2004) and culturally responsive evaluation approaches (Frierson, Hood, & Hughes, 2002; Kirkhart & Hopson, 2010). Collaborative evaluation techniques immerse evaluators in the cultural milieu of the…

  16. A two-stage approach to automatic face alignment

    NASA Astrophysics Data System (ADS)

    Wang, Tong; Ai, Haizhou; Huang, Gaofeng

    2003-09-01

    Face alignment is very important in face recognition, modeling and synthesis. Many approaches have been developed for this purpose, such as ASM, AAM, DAM and TC-ASM. After a brief review of all those methods, it is pointed out that these approaches all require a manual initialization to the positions of the landmarks and are very sensitive to it, and despite of all those devoted works the outline of a human face remains a difficult task to be localized precisely. In this paper, a two-stage method to achieve frontal face alignment fully automatically is introduced. The first stage is landmarks' initialization called coarse face alignment. In this stage, after a face is detected by an Adaboost cascade face detector, we use Simple Direct Appearance Model (SDAM) to locate a few key points of human face from the texture according which all the initial landmarks are setup as the coarse alignment. The second stage is fine face alignment that uses a variant of AAM method in which shape variation is predicted from texture reconstruction error together with an embedded ASM refinement for the outline landmarks of the face to achieve the fine alignment. Experiments on a face database of 500 people show that this method is very effective for practical applications.

  17. Protein and Peptide Drug Delivery: Oral Approaches

    PubMed Central

    Shaji, Jessy; Patole, V.

    2008-01-01

    Till recent, injections remained the most common means for administering therapeutic proteins and peptides because of their poor oral bioavailability. However, oral route would be preferred to any other route because of its high levels of patient acceptance and long term compliance, which increases the therapeutic value of the drug. Designing and formulating a polypeptide drug delivery through the gastro intestinal tract has been a persistent challenge because of their unfavorable physicochemical properties, which includes enzymatic degradation, poor membrane permeability and large molecular size. The main challenge is to improve the oral bioavailability from less than 1% to at least 30-50%. Consequently, efforts have intensified over the past few decades, where every oral dosage form used for the conventional small molecule drugs has been used to explore oral protein and peptide delivery. Various strategies currently under investigation include chemical modification, formulation vehicles and use of enzyme inhibitors, absorption enhancers and mucoadhesive polymers. This review summarizes different pharmaceutical approaches which overcome various physiological barriers that help to improve oral bioavailability that ultimately achieve formulation goals for oral delivery. PMID:20046732

  18. Strategic approaches to optimizing peptide ADME properties.

    PubMed

    Di, Li

    2015-01-01

    Development of peptide drugs is challenging but also quite rewarding. Five blockbuster peptide drugs are currently on the market, and six new peptides received first marketing approval as new molecular entities in 2012. Although peptides only represent 2% of the drug market, the market is growing twice as quickly and might soon occupy a larger niche. Natural peptides typically have poor absorption, distribution, metabolism, and excretion (ADME) properties with rapid clearance, short half-life, low permeability, and sometimes low solubility. Strategies have been developed to improve peptide drugability through enhancing permeability, reducing proteolysis and renal clearance, and prolonging half-life. In vivo, in vitro, and in silico tools are available to evaluate ADME properties of peptides, and structural modification strategies are in place to improve peptide developability. PMID:25366889

  19. Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment

    PubMed Central

    Kam, Alfred; Kwak, Daniel; Leung, Clarence; Wu, Chu; Zarour, Eleyine; Sarmenta, Luis; Blanchette, Mathieu; Waldispühl, Jérôme

    2012-01-01

    Background Comparative genomics, or the study of the relationships of genome structure and function across different species, offers a powerful tool for studying evolution, annotating genomes, and understanding the causes of various genetic disorders. However, aligning multiple sequences of DNA, an essential intermediate step for most types of analyses, is a difficult computational task. In parallel, citizen science, an approach that takes advantage of the fact that the human brain is exquisitely tuned to solving specific types of problems, is becoming increasingly popular. There, instances of hard computational problems are dispatched to a crowd of non-expert human game players and solutions are sent back to a central server. Methodology/Principal Findings We introduce Phylo, a human-based computing framework applying “crowd sourcing” techniques to solve the Multiple Sequence Alignment (MSA) problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context. We applied this strategy to improve the alignment of the promoters of disease-related genes from up to 44 vertebrate species. Since the launch in November 2010, we received more than 350,000 solutions submitted from more than 12,000 registered users. Our results show that solutions submitted contributed to improving the accuracy of up to 70% of the alignment blocks considered. Conclusions/Significance We demonstrate that, combined with classical algorithms, crowd computing techniques can be successfully used to help improving the accuracy of MSA. More importantly, we show that an NP-hard computational problem can be embedded in casual game that can be easily played by people without significant scientific training. This suggests that citizen science approaches can be used to exploit the billions of “human-brain peta-flops” of computation that are spent every day playing games. Phylo is

  20. A novel approach to multiple sequence alignment using hadoop data grids.

    PubMed

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

    Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences. PMID:21224205

  1. A statistical approach to determining responses to individual peptides from pooled-peptide ELISpot data.

    PubMed

    Ström, Peter; Støer, Nathalie; Borthwick, Nicola; Dong, Tao; Hanke, Tomáš; Reilly, Marie

    2016-08-01

    To investigate in detail the effect of infection or vaccination on the human immune system, ELISpot assays are used to simultaneously test the immune response to a large number of peptides of interest. Scientists commonly use "peptide pools", where, instead of an individual peptide, a test well contains a group of peptides. Since the response from a well may be due to any or many of the peptides in the pool, pooled assays usually need to be followed by confirmatory assays of a number of individual peptides. We present a statistical method that enables estimation of individual peptide responses from pool responses using the Expectation Maximization (EM) algorithm for "incomplete data". We demonstrate the accuracy and precision of these estimates in simulation studies of ELISpot plates with 90 pools of 6 or 7 peptides arranged in three dimensions and three Mock wells for the estimation of background. In analysis of real pooled data from 6 subjects in a HIV-1 vaccine trial, where 199 peptides were arranged in 80 pools if size 9 or 10, our estimates were in very good agreement with the results from individual-peptide confirmatory assays. Compared to the classical approach, we could identify almost all the same peptides with high or moderate response, with less than half the number of confirmatory tests. Our method facilitates efficient use of the information available in pooled ELISpot data to avoid or reduce the need for confirmatory testing. We provide an easy-to-use free online application for implementing the method, where on uploading two spreadsheets with the pool design and pool responses, the user obtains the estimates of the individual peptide responses. PMID:27196788

  2. Recent developments in protein and peptide parenteral delivery approaches

    PubMed Central

    Patel, Ashaben; Cholkar, Kishore; Mitra, Ashim K

    2014-01-01

    Discovery of insulin in the early 1900s initiated the research and development to improve the means of therapeutic protein delivery in patients. In the past decade, great emphasis has been placed on bringing protein and peptide therapeutics to market. Despite tremendous efforts, parenteral delivery still remains the major mode of administration for protein and peptide therapeutics. Other routes such as oral, nasal, pulmonary and buccal are considered more opportunistic rather than routine application. Improving biological half-life, stability and therapeutic efficacy is central to protein and peptide delivery. Several approaches have been tried in the past to improve protein and peptide in vitro/in vivo stability and performance. Approaches may be broadly categorized as chemical modification and colloidal delivery systems. In this review we have discussed various chemical approaches such as PEGylation, hyperglycosylation, mannosylation, and colloidal carriers including microparticles, nanoparticles, liposomes, carbon nanotubes and micelles for improving protein and peptide delivery. Recent developments on in situ thermosensitive gel-based protein and peptide delivery have also been described. This review summarizes recent developments on some currently existing approaches to improve stability, bioavailability and bioactivity of peptide and protein therapeutics following parenteral administration. PMID:24592957

  3. Two-dimensional replica exchange approach for peptide-peptide interactions

    NASA Astrophysics Data System (ADS)

    Gee, Jason; Shell, M. Scott

    2011-02-01

    The replica exchange molecular dynamics (REMD) method has emerged as a standard approach for simulating proteins and peptides with rugged underlying free energy landscapes. We describe an extension to the original methodology—here termed umbrella-sampling REMD (UREMD)—that offers specific advantages in simulating peptide-peptide interactions. This method is based on the use of two dimensions in the replica cascade, one in temperature as in conventional REMD, and one in an umbrella sampling coordinate between the center of mass of the two peptides that aids explicit exploration of the complete association-dissociation reaction coordinate. To mitigate the increased number of replicas required, we pursue an approach in which the temperature and umbrella dimensions are linked at only fully associated and dissociated states. Coupled with the reweighting equations, the UREMD method aids accurate calculations of normalized free energy profiles and structural or energetic measures as a function of interpeptide separation distance. We test the approach on two families of peptides: a series of designed tetrapeptides that serve as minimal models for amyloid fibril formation, and a fragment of a classic leucine zipper peptide and its mutant. The results for these systems are compared to those from conventional REMD simulations, and demonstrate good convergence properties, low statistical errors, and, for the leucine zippers, an ability to sample near-native structures.

  4. Insights into the molecular architecture of a peptide nanotube using FTIR and solid-state NMR spectroscopic measurements on an aligned sample.

    PubMed

    Middleton, David A; Madine, Jillian; Castelletto, Valeria; Hamley, Ian W

    2013-09-27

    Queuing up: Molecular orientation within macroscopically aligned nanotubes of the peptide AAAAAAK can be studied by solid-state NMR and IR spectroscopy. Line shape analysis of the NMR spectra indicates that the peptide N-H bonds are tilted 65-70° relative to the nanotube long axis. Re-evaluation of earlier X-ray fiber diffraction data suggests that the peptide molecules are hydrogen-bonded in a helical arrangement along the nanotube axis. PMID:23955926

  5. Projection approach to complexity reduction in tomographic alignment of extremely large telescopes.

    PubMed

    Piatrou, Piotr; Chanan, Gary

    2012-02-20

    We describe a complexity reduction approach intended to solve the tomographic alignment problem for the Thirty Meter Telescope by means of its alignment and phasing system (APS) with little loss of information. This approach is computationally efficient enough to perform detailed Monte-Carlo simulations of the APS on a standard PC. We present sample simulations to model error propagation through the system and to build a preliminary APS alignment error budget. PMID:22358159

  6. Aligning graphs and finding substructures by a cavity approach

    NASA Astrophysics Data System (ADS)

    Bradde, S.; Braunstein, A.; Mahmoudi, H.; Tria, F.; Weigt, M.; Zecchina, R.

    2010-02-01

    We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The algorithm allows to analyze large graphs and may find applications in fields such as computational biology. As a proof of concept we use our algorithm to align the similarity graphs of two interacting protein families involved in bacterial signal transduction, and to predict actually interacting protein partners between these families.

  7. An information theoretic approach to macromolecular modeling: I. Sequence alignments.

    PubMed

    Aynechi, Tiba; Kuntz, Irwin D

    2005-11-01

    We are interested in applying the principles of information theory to structural biology calculations. In this article, we explore the information content of an important computational procedure: sequence alignment. Using a reference state developed from exhaustive sequences, we measure alignment statistics and evaluate gap penalties based on first-principle considerations and gap distributions. We show that there are different gap penalties for different alphabet sizes and that the gap penalties can depend on the length of the sequences being aligned. In a companion article, we examine the information content of molecular force fields. PMID:16254389

  8. Selection of peptide ligands for piezoelectric peptide based gas sensors arrays using a virtual screening approach.

    PubMed

    Pizzoni, Daniel; Mascini, Marcello; Lanzone, Valentina; Del Carlo, Michele; Di Natale, Corrado; Compagnone, Dario

    2014-02-15

    Virtual and experimental affinity binding properties of 5 different peptides (cysteinylglycine, glutathione, Cys-Ile-His-Asn-Pro, Cys-Ile-Gln-Pro-Val, Cys-Arg-Gln-Val-Phe) vs. 14 volatile compounds belonging to relevant chemical classes were evaluated. The peptides were selected in order to have a large variability in physicochemical characteristics (including length). In virtual screening a rapid and cost-effective computational methodology for predicting binding scores of small peptide receptors vs. volatile compounds is proposed. Flexibility was considered for both ligands and peptides and each peptide conformer was treated as a possible receptor, generating a dedicated box and then running a docking process vs. all possible conformers of the 14 volatile compounds. The 5 peptides were covalently bound to gold nanoparticles and deposited onto 20 MHz quartz crystal microbalances to realize gas sensors. Gas sensing confirmed that each of the peptide conferred to the gold nanoparticles a particular selectivity pattern able to discriminate the 14 volatile compounds. The largest response was obtained for the pentapeptides Cys-Ile-His-Asn-Pro and Cys-Ile-Gln-Pro-Val while low response was achieved for the dipeptide. The comparative study, carried using a two-tailed T test, demonstrated that virtual screening was able to predict reliably the sensing ability of the pentapeptides. The dipeptide receptor exhibited 29% of virtual-experimental matching vs. 71% of glutathione and up to 93% for the pentapeptides. This virtual screening approach was proved to be a promising tool in predicting the behaviour of sensors array for gas detection. PMID:24060973

  9. The generating function approach for Peptide identification in spectral networks.

    PubMed

    Guthals, Adrian; Boucher, Christina; Bandeira, Nuno

    2015-05-01

    Tandem mass (MS/MS) spectrometry has become the method of choice for protein identification and has launched a quest for the identification of every translated protein and peptide. However, computational developments have lagged behind the pace of modern data acquisition protocols and have become a major bottleneck in proteomics analysis of complex samples. As it stands today, attempts to identify MS/MS spectra against large databases (e.g., the human microbiome or 6-frame translation of the human genome) face a search space that is 10-100 times larger than the human proteome, where it becomes increasingly challenging to separate between true and false peptide matches. As a result, the sensitivity of current state-of-the-art database search methods drops by nearly 38% to such low identification rates that almost 90% of all MS/MS spectra are left as unidentified. We address this problem by extending the generating function approach to rigorously compute the joint spectral probability of multiple spectra being matched to peptides with overlapping sequences, thus enabling the confident assignment of higher significance to overlapping peptide-spectrum matches (PSMs). We find that these joint spectral probabilities can be several orders of magnitude more significant than individual PSMs, even in the ideal case when perfect separation between signal and noise peaks could be achieved per individual MS/MS spectrum. After benchmarking this approach on a typical lysate MS/MS dataset, we show that the proposed intersecting spectral probabilities for spectra from overlapping peptides improve peptide identification by 30-62%. PMID:25423621

  10. Electrospun nanofiber reinforcement of dental composites with electromagnetic alignment approach.

    PubMed

    Uyar, Tansel; Çökeliler, Dilek; Doğan, Mustafa; Koçum, Ismail Cengiz; Karatay, Okan; Denkbaş, Emir Baki

    2016-05-01

    Polymethylmethacrylate (PMMA) is commonly used as a base acrylic denture material with benefits of rapid and easy handling, however, when it is used in prosthetic dentistry, fracturing or cracking problems can be seen due to the relatively low strength issues. Besides, acrylic resin is the still prominent material for denture fabrication due to its handy and low cost features. Numerous proposed fillers that are used to produce PMMA composites, however electrospun polyvinylalcohol (PVA) nanofiber fillers for production of PMMA composite resins are not studied as much as the others. The other focus of the practice is to compare both mechanical properties and efficiency of aligned fibers versus non-aligned PVA nanofibers in PMMA based dental composites. Field-controlled electrospinning system is manufactured and provided good alignment in lab scale as one of contributions. Some novel auxiliary electrodes in controlled structure are augmented to obtain different patterns of alignment with a certain range of fiber diameters. Scanning electron microscopy is used for physical characterization to determine the range of fiber diameters. Non-woven fiber has no unique pattern due to chaotic nature of electrospinning process, but aligned fibers have round pattern or crossed lines. These produced fibers are structured as layer-by-layer form with different features, and these features are used in producing PMMA dental composites with different volume ratios. The maximum flexural strength figure shows that fiber load by weight of 0.25% w/w and above improves in the maximum level. As a result, mechanical properties of PMMA dental composites are improved by using PVA nanofibers as a filler, however the improvement was higher when aligned PVA nanofibers are used. The maximum values were 5.1 MPa (flexural strength), 0.8 GPa (elastic modulus), and 170 kJ/m(3) (toughness) in three-point bending test. In addition to the positive results of aligned and non-aligned nanofibers it was found

  11. CW dipolar broadening EPR spectroscopy and mechanically aligned bilayers used to measure distance and relative orientation between two TOAC spin labels on an antimicrobial peptide

    NASA Astrophysics Data System (ADS)

    Sahu, Indra D.; Hustedt, Eric J.; Ghimire, Harishchandra; Inbaraj, Johnson J.; McCarrick, Robert M.; Lorigan, Gary A.

    2014-12-01

    An EPR membrane alignment technique was applied to measure distance and relative orientations between two spin labels on a protein oriented along the surface of the membrane. Previously we demonstrated an EPR membrane alignment technique for measuring distances and relative orientations between two spin labels using a dual TOAC-labeled integral transmembrane peptide (M2δ segment of Acetylcholine receptor) as a test system. In this study we further utilized this technique and successfully measured the distance and relative orientations between two spin labels on a membrane peripheral peptide (antimicrobial peptide magainin-2). The TOAC-labeled magainin-2 peptides were mechanically aligned using DMPC lipids on a planar quartz support, and CW-EPR spectra were recorded at specific orientations. Global analysis in combination with rigorous spectral simulation was used to simultaneously analyze data from two different sample orientations for both single- and double-labeled peptides. We measured an internitroxide distance of 15.3 Å from a dual TOAC-labeled magainin-2 peptide at positions 8 and 14 that closely matches with the 13.3 Å distance obtained from a model of the labeled magainin peptide. In addition, the angles determining the relative orientations of the two nitroxides have been determined, and the results compare favorably with molecular modeling. This study demonstrates the utility of the technique for proteins oriented along the surface of the membrane in addition to the previous results for proteins situated within the membrane bilayer.

  12. CW Dipolar Broadening EPR Spectroscopy and Mechanically Aligned Bilayers Used to Measure Distance and Relative Orientation between Two TOAC Spin Labels on an Antimicrobial Peptide

    PubMed Central

    Sahu, Indra D.; Hustedt, Eric J.; Ghimire, Harishchandra; Inbaraj, Johnson J.; McCarrick, Robert M.; Lorigan, Gary A.

    2014-01-01

    An EPR membrane alignment technique was applied to measure distance and relative orientations between two spin labels on a protein oriented along the surface of the membrane. Previously we demonstrated an EPR membrane alignment technique for measuring distances and relative orientations between two spin labels using a dual TOAC-labeled integral transmembrane peptide (M2δ segment of Acetylcholine receptor) as a test system. In this study we further utilized this technique and successfully measured the distance and relative orientations between two spin labels on a membrane peripheral peptide (antimicrobial peptide magainin-2). The TOAC-labeled magainin-2 peptides were mechanically aligned using DMPC lipids on a planar quartz support, and CW-EPR spectra were recorded at specific orientations. Global analysis in combination with rigorous spectral simulation was used to simultaneously analyze data from two different sample orientations for both single-and double-labeled peptides. We measured an internitroxide distance of 15.3 Å from a dual TOAC-labeled magainin-2 peptide at positions 8 and 14 that closely matches with the 13.3 Å distance obtained from a model of the labeled magainin peptide. In addition, the angles determining the relative orientations of the two nitroxides have been determined, and the results compare favorably with molecular modeling. This study demonstrates the utility of the technique for proteins oriented along the surface of the membrane in addition to the previous results for proteins situated within the membrane bilayer. PMID:25462949

  13. Optimizing parameters on alignment of PCL/PGA nanofibrous scaffold: An artificial neural networks approach.

    PubMed

    Paskiabi, Farnoush Asghari; Mirzaei, Esmaeil; Amani, Amir; Shokrgozar, Mohammad Ali; Saber, Reza; Faridi-Majidi, Reza

    2015-11-01

    This paper proposes an artificial neural networks approach to finding the effects of electrospinning parameters on alignment of poly(ɛ-caprolactone)/poly(glycolic acid) blend nanofibers. Four electrospinning parameters, namely total polymer concentration, working distance, drum speed and applied voltage were considered as input and the standard deviation of the angles of nanofibers, introducing fibers alignments, as the output of the model. The results demonstrated that drum speed and applied voltage are two critical factors influencing nanofibers alignment, however their effect are entirely interdependent. Their effects also are not independent of other electrospinning parameters. In obtaining aligned electrospun nanofibers, the concentration and working distance can also be effective. In vitro cell culture study on random and aligned nanofibers showed directional growth of cells on aligned fibers. PMID:25450538

  14. The Generating Function Approach for Peptide Identification in Spectral Networks

    PubMed Central

    Guthals, Adrian; Boucher, Christina

    2015-01-01

    Abstract Tandem mass (MS/MS) spectrometry has become the method of choice for protein identification and has launched a quest for the identification of every translated protein and peptide. However, computational developments have lagged behind the pace of modern data acquisition protocols and have become a major bottleneck in proteomics analysis of complex samples. As it stands today, attempts to identify MS/MS spectra against large databases (e.g., the human microbiome or 6-frame translation of the human genome) face a search space that is 10–100 times larger than the human proteome, where it becomes increasingly challenging to separate between true and false peptide matches. As a result, the sensitivity of current state-of-the-art database search methods drops by nearly 38% to such low identification rates that almost 90% of all MS/MS spectra are left as unidentified. We address this problem by extending the generating function approach to rigorously compute the joint spectral probability of multiple spectra being matched to peptides with overlapping sequences, thus enabling the confident assignment of higher significance to overlapping peptide–spectrum matches (PSMs). We find that these joint spectral probabilities can be several orders of magnitude more significant than individual PSMs, even in the ideal case when perfect separation between signal and noise peaks could be achieved per individual MS/MS spectrum. After benchmarking this approach on a typical lysate MS/MS dataset, we show that the proposed intersecting spectral probabilities for spectra from overlapping peptides improve peptide identification by 30–62%. PMID:25423621

  15. Conditions affecting the re-alignment of the antimicrobial peptide PGLa in membranes as monitored by solid state 2H-NMR.

    PubMed

    Tremouilhac, Pierre; Strandberg, Erik; Wadhwani, Parvesh; Ulrich, Anne S

    2006-09-01

    The cationic antimicrobial peptide PGLa is electrostatically attracted to bacterial membranes, binds as an amphiphilic alpha-helix, and is thus able to permeabilize the lipid bilayer. Using solid state (2)H-NMR of non-perturbing Ala-d(3) labels on the peptide, we have characterized the helix alignment under a range of different conditions. Even at a very high peptide-to-lipid ratio (1:20) and in the presence of negatively charged lipids, there was no indication of a toroidal wormhole structure. Instead, PGLa re-aligns from a surface-bound S-state to an obliquely tilted T-state, which is presumably dimeric. An intermediate structure half-way between the S- and T-state was observed in fully hydrated multilamellar DMPC vesicles at 1:50, suggesting a fast exchange between the two states on the time scale of >50 kHz. We demonstrate that this equilibrium is shifted from the S- towards the T-state either upon (i) increasing the peptide concentration, (ii) adding negatively charged DMPG, or (iii) decreasing the level of hydration. The threshold concentration for re-alignment in DMPC is found to be between 1:200 and 1:100 in oriented samples at 96% humidity. In fully hydrated multilamellar DMPC vesicles, it shifts to an effective peptide-to-lipid ratio of 1:50 as some peptides are able to escape into the bulk water phase. PMID:16716250

  16. Prediction of Antimicrobial Peptides Based on Sequence Alignment and Support Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity

    PubMed Central

    Shahrudin, Shahriza

    2015-01-01

    This study concerns an attempt to establish a new method for predicting antimicrobial peptides (AMPs) which are important to the immune system. Recently, researchers are interested in designing alternative drugs based on AMPs because they have found that a large number of bacterial strains have become resistant to available antibiotics. However, researchers have encountered obstacles in the AMPs designing process as experiments to extract AMPs from protein sequences are costly and require a long set-up time. Therefore, a computational tool for AMPs prediction is needed to resolve this problem. In this study, an integrated algorithm is newly introduced to predict AMPs by integrating sequence alignment and support vector machine- (SVM-) LZ complexity pairwise algorithm. It was observed that, when all sequences in the training set are used, the sensitivity of the proposed algorithm is 95.28% in jackknife test and 87.59% in independent test, while the sensitivity obtained for jackknife test and independent test is 88.74% and 78.70%, respectively, when only the sequences that has less than 70% similarity are used. Applying the proposed algorithm may allow researchers to effectively predict AMPs from unknown protein peptide sequences with higher sensitivity. PMID:25802839

  17. A convenient alignment approach for x-ray imaging experiments based on laser positioning devices

    SciTech Connect

    Zhang Da; Donovan, Molly; Wu Xizeng; Liu Hong

    2008-11-15

    This study presents a two-laser alignment approach for facilitating the precise alignment of various imaging and measuring components with respect to the x-ray beam. The first laser constantly pointed to the output window of the source, in a direction parallel to the path along which the components are placed. The second laser beam, originating from the opposite direction, was calibrated to coincide with the first laser beam. Thus, a visible indicator of the direction of the incident x-ray beam was established, and the various components could then be aligned conveniently and accurately with its help.

  18. An Overview of DNA Microarray Grid Alignment and Foreground Separation Approaches

    NASA Astrophysics Data System (ADS)

    Bajcsy, Peter

    2006-12-01

    This paper overviews DNA microarray grid alignment and foreground separation approaches. Microarray grid alignment and foreground separation are the basic processing steps of DNA microarray images that affect the quality of gene expression information, and hence impact our confidence in any data-derived biological conclusions. Thus, understanding microarray data processing steps becomes critical for performing optimal microarray data analysis. In the past, the grid alignment and foreground separation steps have not been covered extensively in the survey literature. We present several classifications of existing algorithms, and describe the fundamental principles of these algorithms. Challenges related to automation and reliability of processed image data are outlined at the end of this overview paper.

  19. RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.

    PubMed

    Kolekar, Pandurang S; Waman, Vaishali P; Kale, Mohan M; Kulkarni-Kale, Urmila

    2016-01-01

    Rhinoviruses (RV) are increasingly being reported to cause mild to severe infections of respiratory tract in humans. RV are antigenically the most diverse species of the genus Enterovirus and family Picornaviridae. There are three species of RV (RV-A, -B and -C), with 80, 32 and 55 serotypes/types, respectively. Antigenic variation is the main limiting factor for development of a cross-protective vaccine against RV.Serotyping of Rhinoviruses is carried out using cross-neutralization assays in cell culture. However, these assays become laborious and time-consuming for the large number of strains. Alternatively, serotyping of RV is carried out by alignment-based phylogeny of both protein and nucleotide sequences of VP1. However, serotyping of RV based on alignment-based phylogeny is a multi-step process, which needs to be repeated every time a new isolate is sequenced. In view of the growing need for serotyping of RV, an alignment-free method based on "return time distribution" (RTD) of amino acid residues in VP1 protein has been developed and implemented in the form of a web server titled RV-Typer. RV-Typer accepts nucleotide or protein sequences as an input and computes return times of di-peptides (k = 2) to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity. It is significantly faster than alignment-based methods. The web server is available at http://bioinfo.net.in/RV-Typer/home.html. PMID:26870949

  20. RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach

    PubMed Central

    Kolekar, Pandurang S.; Waman, Vaishali P.; Kale, Mohan M.; Kulkarni-Kale, Urmila

    2016-01-01

    Rhinoviruses (RV) are increasingly being reported to cause mild to severe infections of respiratory tract in humans. RV are antigenically the most diverse species of the genus Enterovirus and family Picornaviridae. There are three species of RV (RV-A, -B and -C), with 80, 32 and 55 serotypes/types, respectively. Antigenic variation is the main limiting factor for development of a cross-protective vaccine against RV.Serotyping of Rhinoviruses is carried out using cross-neutralization assays in cell culture. However, these assays become laborious and time-consuming for the large number of strains. Alternatively, serotyping of RV is carried out by alignment-based phylogeny of both protein and nucleotide sequences of VP1. However, serotyping of RV based on alignment-based phylogeny is a multi-step process, which needs to be repeated every time a new isolate is sequenced. In view of the growing need for serotyping of RV, an alignment-free method based on “return time distribution” (RTD) of amino acid residues in VP1 protein has been developed and implemented in the form of a web server titled RV-Typer. RV-Typer accepts nucleotide or protein sequences as an input and computes return times of di-peptides (k = 2) to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity. It is significantly faster than alignment-based methods. The web server is available at http://bioinfo.net.in/RV-Typer/home.html. PMID:26870949

  1. Design of Catalytic Peptides and Proteins Through Rational and Combinatorial Approaches.

    PubMed

    Maeda, Yoshiaki; Makhlynets, Olga V; Matsui, Hiroshi; Korendovych, Ivan V

    2016-07-11

    This review focuses on recent progress in noncomputational methods to introduce catalytic function into proteins, peptides, and peptide assemblies. We discuss various approaches to creating catalytic activity and classification of noncomputational methods into rational and combinatorial classes. The section on rational design covers recent progress in the development of short peptides and oligomeric peptide assemblies for various natural and unnatural reactions. The section on combinatorial design describes recent advances in the discovery of catalytic peptides. We present the future prospects of these and other new approaches in a broader context, including implications for functional material design. PMID:27022702

  2. A parallel approach of COFFEE objective function to multiple sequence alignment

    NASA Astrophysics Data System (ADS)

    Zafalon, G. F. D.; Visotaky, J. M. V.; Amorim, A. R.; Valêncio, C. R.; Neves, L. A.; de Souza, R. C. G.; Machado, J. M.

    2015-09-01

    The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

  3. Approaches for Enhancing Oral Bioavailability of Peptides and Proteins

    PubMed Central

    Renukuntla, Jwala; Vadlapudi, Aswani Dutt; Patel, Ashaben; Boddu, Sai HS.; Mitra, Ashim K

    2013-01-01

    Oral delivery of peptide and protein drugs faces immense challenge partially due to the gastrointestinal (GI) environment. In spite of considerable efforts by industrial and academic laboratories, no major breakthrough in the effective oral delivery of polypeptides and proteins has been accomplished. Upon oral administration, gastrointestinal epithelium acts as a physical and biochemical barrier for absorption of proteins resulting in low bioavailability (typically less than 1–2%). An ideal oral drug delivery system should be capable of a) maintaining the integrity of protein molecules until it reaches the site of absorption, b) releasing the drug at the target absorption site, where the delivery system appends to that site by virtue of specific interaction, and c) retaining inside the gastrointestinal tract irrespective of its transitory constraints. Various technologies have been explored to overcome the problems associated with the oral delivery of macromolecules such as insulin, gonadotropin-releasing hormones, calcitonin, human growth factor, vaccines, enkephalins, and interferons, all of which met with limited success. This review article intends to summarize the physiological barriers to oral delivery of peptides and proteins and novel pharmaceutical approaches to circumvent these barriers and enhance oral bioavailability of these macromolecules. PMID:23428883

  4. Novel non-invasive protein and peptide drug delivery approaches.

    PubMed

    Wallis, L; Kleynhans, E; Toit, T Du; Gouws, C; Steyn, D; Steenekamp, J; Viljoen, J; Hamman, J

    2014-01-01

    Protein and peptide based therapeutics are typically administered by injection due to their poor uptake when administered via enteral routes of drug administration. Unfortunately, chronic administration of these drugs through multiple injections presents certain patient related problems and it is difficult to mimic the normal physiological release patterns via this mode of drug administration. A need therefore exists to non-invasively deliver these drugs by means of alternative ways such as via the oral, pulmonary, nasal, transdermal and buccal administration routes. Although some attempts of needle free peptide and protein drug delivery have progressed to the clinical stage, relatively limited success has been achieved in terms of commercially available products. Despite the low frequency of clinical breakthroughs with noninvasive protein drug delivery this far, it remains an active research area with renewed interest not only due to its improved therapeutic potential, but also due to the attractive commercial outcomes it offers. It is the aim of this review article to reflect on the main strategies investigated to overcome the barriers against effective systemic protein drug delivery in different routes of drug administration. Approaches based on chemical modifications and pharmaceutical technologies are discussed with reference to examples of drugs and devices that have shown potential, while attempts that have failed are also briefly outlined. PMID:25106909

  5. An Alignment-Free Approach for Eukaryotic ITS2 Annotation and Phylogenetic Inference

    PubMed Central

    Hidalgo-Yanes, Pedro I.; Pérez-Castillo, Yunierkis; Molina-Ruiz, Reinaldo; Marchal, Kathleen; Vasconcelos, Vítor; Antunes, Agostinho

    2011-01-01

    The ITS2 gene class shows a high sequence divergence among its members that have complicated its annotation and its use for reconstructing phylogenies at a higher taxonomical level (beyond species and genus). Several alignment strategies have been implemented to improve the ITS2 annotation quality and its use for phylogenetic inferences. Although, alignment based methods have been exploited to the top of its complexity to tackle both issues, no alignment-free approaches have been able to successfully address both topics. By contrast, the use of simple alignment-free classifiers, like the topological indices (TIs) containing information about the sequence and structure of ITS2, may reveal to be a useful approach for the gene prediction and for assessing the phylogenetic relationships of the ITS2 class in eukaryotes. Thus, we used the TI2BioP (Topological Indices to BioPolymers) methodology [1], [2], freely available at http://ti2biop.sourceforge.net/ to calculate two different TIs. One class was derived from the ITS2 artificial 2D structures generated from DNA strings and the other from the secondary structure inferred from RNA folding algorithms. Two alignment-free models based on Artificial Neural Networks were developed for the ITS2 class prediction using the two classes of TIs referred above. Both models showed similar performances on the training and the test sets reaching values above 95% in the overall classification. Due to the importance of the ITS2 region for fungi identification, a novel ITS2 genomic sequence was isolated from Petrakia sp. This sequence and the test set were used to comparatively evaluate the conventional classification models based on multiple sequence alignments like Hidden Markov based approaches, revealing the success of our models to identify novel ITS2 members. The isolated sequence was assessed using traditional and alignment-free based techniques applied to phylogenetic inference to complement the taxonomy of the Petrakia sp

  6. Electrode alignment of transverse tripoles using a percutaneous triple-lead approach in spinal cord stimulation.

    PubMed

    Sankarasubramanian, V; Buitenweg, J R; Holsheimer, J; Veltink, P

    2011-02-01

    The aim of this modeling study is to determine the influence of electrode alignment of transverse tripoles on the paresthesia coverage of the pain area in spinal cord stimulation, using a percutaneous triple-lead approach. Transverse tripoles, comprising a central cathode and two lateral anodes, were modeled on the low-thoracic vertebral region (T10-T12) using percutaneous triple-lead configurations, with the center lead on the spinal cord midline. The triple leads were oriented both aligned and staggered. In the staggered configuration, the anodes were offset either caudally (caudally staggered) or rostrally (rostrally staggered) with respect to the midline cathode. The transverse tripolar field steering with the aligned and staggered configurations enabled the estimation of dorsal column fiber thresholds (I(DC)) and dorsal root fiber thresholds (I(DR)) at various anodal current ratios. I(DC) and I(DR) were considerably higher for the aligned transverse tripoles as compared to the staggered transverse tripoles. The aligned transverse tripoles facilitated deeper penetration into the medial dorsal columns (DCs). The staggered transverse tripoles always enabled broad and bilateral DC activation, at the expense of mediolateral steerability. The largest DC recruited area was obtained with the rostrally staggered transverse tripole. Transverse tripolar geometries, using percutaneous leads, allow for selective targeting of either medial or lateral DC fibers, if and only if the transverse tripole is aligned. Steering of anodal currents between the lateral leads of the staggered transverse tripoles cannot target medially confined populations of DC fibers in the spinal cord. An aligned transverse tripolar configuration is strongly recommended, because of its ability to provide more post-operative flexibility than other configurations. PMID:21248383

  7. Electrode alignment of transverse tripoles using a percutaneous triple-lead approach in spinal cord stimulation

    NASA Astrophysics Data System (ADS)

    Sankarasubramanian, V.; Buitenweg, J. R.; Holsheimer, J.; Veltink, P.

    2011-02-01

    The aim of this modeling study is to determine the influence of electrode alignment of transverse tripoles on the paresthesia coverage of the pain area in spinal cord stimulation, using a percutaneous triple-lead approach. Transverse tripoles, comprising a central cathode and two lateral anodes, were modeled on the low-thoracic vertebral region (T10-T12) using percutaneous triple-lead configurations, with the center lead on the spinal cord midline. The triple leads were oriented both aligned and staggered. In the staggered configuration, the anodes were offset either caudally (caudally staggered) or rostrally (rostrally staggered) with respect to the midline cathode. The transverse tripolar field steering with the aligned and staggered configurations enabled the estimation of dorsal column fiber thresholds (IDC) and dorsal root fiber thresholds (IDR) at various anodal current ratios. IDC and IDR were considerably higher for the aligned transverse tripoles as compared to the staggered transverse tripoles. The aligned transverse tripoles facilitated deeper penetration into the medial dorsal columns (DCs). The staggered transverse tripoles always enabled broad and bilateral DC activation, at the expense of mediolateral steerability. The largest DC recruited area was obtained with the rostrally staggered transverse tripole. Transverse tripolar geometries, using percutaneous leads, allow for selective targeting of either medial or lateral DC fibers, if and only if the transverse tripole is aligned. Steering of anodal currents between the lateral leads of the staggered transverse tripoles cannot target medially confined populations of DC fibers in the spinal cord. An aligned transverse tripolar configuration is strongly recommended, because of its ability to provide more post-operative flexibility than other configurations.

  8. Particle alignment reliability in single particle electron cryomicroscopy: a general approach

    PubMed Central

    Vargas, J.; Otón, J.; Marabini, R.; Carazo, J. M.; Sorzano, C. O. S.

    2016-01-01

    Electron Microscopy is reaching new capabilities thanks to the combined effect of new technologies and new image processing methods. However, the reconstruction process is still complex, requiring many steps and elaborated optimization procedures. Therefore, the possibility to reach a wrong structure exists, justifying the need of robust statistical tests. In this work, we present a conceptually simple alignment test, which does not require tilt-pair images, to evaluate the alignment consistency between a set of projection images with respect to a given 3D density map. We test the approach on a number of problems in 3DEM, especially the ranking and evaluation of initial 3D volumes and high resolution 3D maps, where we show its usefulness in providing an objective evaluation for maps that have recently been subject to a strong controversy in the field. Additionally, this alignment statistical test can be linked to the early stages of structure solving of new complexes, streamlining the whole process. PMID:26899789

  9. A Convex Atomic-Norm Approach to Multiple Sequence Alignment and Motif Discovery

    PubMed Central

    Yen, Ian E. H.; Lin, Xin; Zhang, Jiong; Ravikumar, Pradeep; Dhillon, Inderjit S.

    2016-01-01

    Multiple Sequence Alignment and Motif Discovery, known as NP-hard problems, are two fundamental tasks in Bioinformatics. Existing approaches to these two problems are based on either local search methods such as Expectation Maximization (EM), Gibbs Sampling or greedy heuristic methods. In this work, we develop a convex relaxation approach to both problems based on the recent concept of atomic norm and develop a new algorithm, termed Greedy Direction Method of Multiplier, for solving the convex relaxation with two convex atomic constraints. Experiments show that our convex relaxation approach produces solutions of higher quality than those standard tools widely-used in Bioinformatics community on the Multiple Sequence Alignment and Motif Discovery problems. PMID:27559428

  10. CVTree: a Whole-Genome and Alignment-Free Approach to Microbial Phylogeny

    NASA Astrophysics Data System (ADS)

    Hao, Bailin

    The number of sequenced genomes of Archaea, Bacteria, and Fungi accumulates rapidly. Several thousands genomes of these unicellular organisms will be available in a few years. Due to the extremely large difference in genome size and gene content it is difficult to use the traditional alignment-based method to infer phylogeny from the genomes. An alignment-free and whole-genome-based approach called CVTree has been developed and successfully applied to these organisms. As CVTree has been successfully applied to genomes of viruses, chloroplasts, Bacteria, Archaea and fungi, in this brief review we will mainly touch on some mathematical problems related to the foundation of the new approach, including a few yet unsolved problems, such as the violation of the triangular inequalities of the dissimilarity measure used in the CVTree method.

  11. A data-mining approach for multiple structural alignment of proteins.

    PubMed

    Siu, Wing-Yan; Mamoulis, Nikos; Yiu, Siu-Ming; Chan, Ho-Leung

    2010-01-01

    Comparing the 3D structures of proteins is an important but computationally hard problem in bioinformatics. In this paper, we propose studying the problem when much less information or assumptions are available. We model the structural alignment of proteins as a combinatorial problem. In the problem, each protein is simply a set of points in the 3D space, without sequence order information, and the objective is to discover all large enough alignments for any subset of the input. We propose a data-mining approach for this problem. We first perform geometric hashing of the structures such that points with similar locations in the 3D space are hashed into the same bin in the hash table. The novelty is that we consider each bin as a coincidence group and mine for frequent patterns, which is a well-studied technique in data mining. We observe that these frequent patterns are already potentially large alignments. Then a simple heuristic is used to extend the alignments if possible. We implemented the algorithm and tested it using real protein structures. The results were compared with existing tools. They showed that the algorithm is capable of finding conserved substructures that do not preserve sequence order, especially those existing in protein interfaces. The algorithm can also identify conserved substructures of functionally similar structures within a mixture with dissimilar ones. The running time of the program was smaller or comparable to that of the existing tools. PMID:21079664

  12. Prediction of Biofilm Inhibiting Peptides: An In silico Approach

    PubMed Central

    Gupta, Sudheer; Sharma, Ashok K.; Jaiswal, Shubham K.; Sharma, Vineet K.

    2016-01-01

    Approximately 75% of microbial infections found in humans are caused by microbial biofilms. These biofilms are resistant to host immune system and most of the currently available antibiotics. Small peptides are extensively studied for their role as anti-microbial peptides, however, only a limited studies have shown their potential as inhibitors of biofilm. Therefore, to develop a unique computational method aimed at the prediction of biofilm inhibiting peptides, the experimentally validated biofilm inhibiting peptides sequences were used to extract sequence based features and to identify unique sequence motifs. Biofilm inhibiting peptides were observed to be abundant in positively charged and aromatic amino acids, and also showed selective abundance of some dipeptides and sequence motifs. These individual sequence based features were utilized to construct Support Vector Machine-based prediction models and additionally by including sequence motifs information, the hybrid models were constructed. Using 10-fold cross validation, the hybrid model displayed the accuracy and Matthews Correlation Coefficient (MCC) of 97.83% and 0.87, respectively. On the validation dataset, the hybrid model showed the accuracy and MCC value of 97.19% and 0.84, respectively. The validated model and other tools developed for the prediction of biofilm inhibiting peptides are available freely as web server at http://metagenomics.iiserb.ac.in/biofin/ and http://metabiosys.iiserb.ac.in/biofin/. PMID:27379078

  13. A flux-coordinate independent field-aligned approach to plasma turbulence simulations

    NASA Astrophysics Data System (ADS)

    Hariri, F.; Ottaviani, M.

    2013-11-01

    This work illustrates a new approach to field-aligned coordinates for plasma turbulence simulations which is not based on flux variables. The method employs standard Cartesian or polar coordinates to discretize the fields. Parallel derivatives are computed directly along a coordinate that follows the local field, and poloidal derivatives are computed in the original Cartesian frame. Several advantages of this approach are presented. The tests on a drift-wave model demonstrate that the method is well suited to exploit the flute property of small parallel gradients by minimizing the number of degrees of freedom needed to treat a given problem in an accurate and efficient manner.

  14. First-Principles Approach to Energy Level Alignment at Aqueous Semiconductor Interfaces

    NASA Astrophysics Data System (ADS)

    Hybertsen, Mark

    2015-03-01

    We have developed a first principles method to calculate the energy level alignment between semiconductor band edges and reference energy levels at aqueous interfaces. This alignment is fundamental to understand the electrochemical characteristics of any semiconductor electrode in general and the potential for photocatalytic activity in particular. For example, in the search for new photo-catalytic materials, viable candidates must demonstrate both efficient absorption of the solar spectrum and an appropriate alignment of the band edge levels in the semiconductor to the redox levels for the target reactions. In our approach, the interface-specific contribution to the electrostatic step across the interface is evaluated using density functional theory (DFT) based molecular dynamics to sample the physical interface structure and the corresponding change in the electrostatic potential at the interface. The reference electronic levels in the semiconductor and in the water are calculated using the GW approach, which naturally corrects for errors inherent in the use of Kohn-Sham energy eigenvalues to approximate the electronic excitation energies in each material. Taken together, our calculations provide the alignment of the semiconductor valence band edge to the centroid of the highest occupied 1b1 level in water. The known relationship of the 1b1 level to the normal hydrogen electrode completes the connection to electrochemical levels. We discuss specific results for GaN, ZnO, and TiO2. The effect of interface structural motifs, such as different degrees of water dissociation, and of dynamical characteristics, will be presented together with available experimental data. Work supported by the US Department of Energy, Office of Basic Energy Sciences under Contract No. DE-AC02-98CH10886.

  15. Peptide library approach to uncover phosphomimetic inhibitors of the BRCA1 C-terminal domain.

    PubMed

    White, E Railey; Sun, Luxin; Ma, Zhong; Beckta, Jason M; Danzig, Brittany A; Hacker, David E; Huie, Melissa; Williams, David C; Edwards, Ross A; Valerie, Kristoffer; Glover, J N Mark; Hartman, Matthew C T

    2015-05-15

    Many intracellular protein-protein interactions are mediated by the phosphorylation of serine, and phosphoserine-containing peptides can inhibit these interactions. However, hydrolysis of the phosphate by phosphatases, and the poor cell permeability associated with phosphorylated peptides has limited their utility in cellular and in vivo contexts. Compounding the problem, strategies to replace phosphoserine in peptide inhibitors with easily accessible mimetics (such as Glu or Asp) routinely fail. Here, we present an in vitro selection strategy for replacement of phosphoserine. Using mRNA display, we created a 10 trillion member structurally diverse unnatural peptide library. From this library, we found a peptide that specifically binds to the C-terminal domain (BRCT)2 of breast cancer associated protein 1 (BRCA1) with an affinity comparable to phosphorylated peptides. A crystal structure of the peptide bound reveals that the pSer-x-x-Phe motif normally found in BRCA1 (BRCT)2 binding partners is replaced by a Glu-x-x-4-fluoroPhe and that the peptide picks up additional contacts on the protein surface not observed in cognate phosphopeptide binding. Expression of the peptide in human cells led to defects in DNA repair by homologous recombination, a process BRCA1 is known to coordinate. Overall, this work validates a new in vitro selection approach for the development of inhibitors of protein-protein interactions mediated by serine phosphorylation. PMID:25654734

  16. Peptide Library Approach to Uncover Phosphomimetic Inhibitors of the BRCA1 C-Terminal Domain

    PubMed Central

    White, E. Railey; Sun, Luxin; Ma, Zhong; Beckta, Jason M.; Danzig, Brittany A.; Hacker, David E.; Huie, Melissa; Williams, David C.; Edwards, Ross A.; Valerie, Kristoffer; Mark Glover, J. N.; Hartman, Matthew C. T.

    2015-01-01

    Many intracellular protein–protein interactions are mediated by the phosphorylation of serine, and phosphoserine-containing peptides can inhibit these interactions. However, hydrolysis of the phosphate by phosphatases, and the poor cell permeability associated with phosphorylated peptides has limited their utility in cellular and in vivo contexts. Compounding the problem, strategies to replace phosphoserine in peptide inhibitors with easily accessible mimetics (such as Glu or Asp) routinely fail. Here, we present an in vitro selection strategy for replacement of phosphoserine. Using mRNA display, we created a 10 trillion member structurally diverse unnatural peptide library. From this library, we found a peptide that specifically binds to the C-terminal domain (BRCT)2 of breast cancer associated protein 1 (BRCA1) with an affinity comparable to phosphorylated peptides. A crystal structure of the peptide bound reveals that the pSer-x-x-Phe motif normally found in BRCA1 (BRCT)2 binding partners is replaced by a Glu-x-x-4-fluoroPhe and that the peptide picks up additional contacts on the protein surface not observed in cognate phosphopeptide binding. Expression of the peptide in human cells led to defects in DNA repair by homologous recombination, a process BRCA1 is known to coordinate. Overall, this work validates a new in vitro selection approach for the development of inhibitors of protein–protein interactions mediated by serine phosphorylation. PMID:25654734

  17. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra.

    PubMed

    Wang, Jian; Anania, Veronica G; Knott, Jeff; Rush, John; Lill, Jennie R; Bourne, Philip E; Bandeira, Nuno

    2014-04-01

    The combination of chemical cross-linking and mass spectrometry has recently been shown to constitute a powerful tool for studying protein-protein interactions and elucidating the structure of large protein complexes. However, computational methods for interpreting the complex MS/MS spectra from linked peptides are still in their infancy, making the high-throughput application of this approach largely impractical. Because of the lack of large annotated datasets, most current approaches do not capture the specific fragmentation patterns of linked peptides and therefore are not optimal for the identification of cross-linked peptides. Here we propose a generic approach to address this problem and demonstrate it using disulfide-bridged peptide libraries to (i) efficiently generate large mass spectral reference data for linked peptides at a low cost and (ii) automatically train an algorithm that can efficiently and accurately identify linked peptides from MS/MS spectra. We show that using this approach we were able to identify thousands of MS/MS spectra from disulfide-bridged peptides through comparison with proteome-scale sequence databases and significantly improve the sensitivity of cross-linked peptide identification. This allowed us to identify 60% more direct pairwise interactions between the protein subunits in the 20S proteasome complex than existing tools on cross-linking studies of the proteasome complexes. The basic framework of this approach and the MS/MS reference dataset generated should be valuable resources for the future development of new tools for the identification of linked peptides. PMID:24493012

  18. Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.

    PubMed

    Bonham-Carter, Oliver; Steele, Joe; Bastola, Dhundy

    2014-11-01

    Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base-base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel-Ziv techniques from data compression. PMID:23904502

  19. Electrospinning of peptide and protein fibres: approaching the molecular scale.

    PubMed

    Nuansing, Wiwat; Frauchiger, Daniela; Huth, Florian; Rebollo, Amaia; Hillenbrand, Rainer; Bittner, Alexander M

    2013-01-01

    For the example of peptides and proteins, we contrast "natural" self-assembly, i.e. aggregation in solutions, with "forced" assembly by electrospinning, i.e. by application of strong electrical fields to concentrated solutions. We were able to spin fibres that contain short stretches of diameters down to 5 nm; the ultimate aim is a fibre of the size of a single molecule. Besides their wide biochemical relevance, small peptides can assemble to defined supramolecular structures such as fibres and tubes. While the main driving mechanism in electrospinning is certainly based on electrostatics, aromatic groups in peptides might play a directing role. We used fluorenyl and phenyl, whose i-stacking is not manifested in vibrational spectra, but is clearly visible in their crystal structures. The main differences between solid phases and single molecules are found for O-H and N-H stretching and bending vibrations, due to extensive hydrogen bonding in solids. However, we found that only proteins, but not peptides, can be spun into ultrathin fibres. Therefore, nanoscale analysis by SEM and AFM, and by infrared near-field microscopy are especially useful. The comparison of the amide bands from the infrared and Raman spectra, combined with circular dichroism spectroscopy, allowed us to assign secondary structures. Our results are not only useful for interpreting and refining current theories of self-assembly and electrospinning, but also for creating new scaffolds for the growth of sensitive cells. PMID:24611278

  20. Physician clinical alignment and integration: a community-academic hospital approach.

    PubMed

    Salas-Lopez, Debbie; Weiss, Sandra Jarva; Nester, Brian; Whalen, Thomas

    2014-01-01

    An overwhelming need for change in the U.S. healthcare delivery system, coupled with the need to improve clinical and financial outcomes, has prompted hospitals to direct renewed efforts toward achieving high quality and cost-effectiveness. Additionally, with the dawn of accountable care organizations and increasing focus on patient expectations, hospitals have begun to seek physician partners through clinical alignment. Contrary to the unsuccessful alignment strategies of the 1990s, today's efforts are more mutually beneficial, driven by the need to achieve better care coordination, increased access to infrastructure, improved quality, and lower costs. In this article, we describe a large, academic, tertiary care hospital's approach to developing and implementing alignment and integration models with its collaboration-ready physicians and physician groups. We developed four models--short of physicians' employment with the organization--tailored to meet the needs of both the physician group and the hospital: (1) medical directorship (group physicians are appointed to serve as medical directors of a clinical area), (2) professional services agreement (specific clinical services, such as overnight admissions help, are contracted), (3) co-management services agreement (one specialty group co-manages all services within the specialty service lines), and (4) lease arrangement (closest in scope to employment, in which the hospital pays all expenses and receives all revenue). Successful hospital-physician alignment requires careful planning and the early engagement of legal counsel to ensure compliance with federal statutes. Establishing an integrated system with mutually identified goals better positions hospitals to deliver cost-effective and high-quality care under the new paradigm of healthcare reform. PMID:24988674

  1. First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces

    SciTech Connect

    Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.

    2014-10-21

    A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.

  2. First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces

    DOE PAGESBeta

    Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.

    2014-10-21

    A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and themore » dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.« less

  3. A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions

    PubMed Central

    Abnousi, Armen; Broschat, Shira L.; Kalyanaraman, Ananth

    2016-01-01

    Background Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to compute protein clusters, to annotate sequence function, and to compute evolutionary relationships among protein sequences. A number of approaches exist for identifying and characterizing protein families based on their domains, and because domains represent conserved portions of a protein sequence, the primary computation involved in protein family characterization is identification of such conserved regions. However, identifying conserved regions from large collections (millions) of protein sequences presents significant challenges. Methods In this paper we present a new, alignment-free method for detecting conserved regions in protein sequences called NADDA (No-Alignment Domain Detection Algorithm). Our method exploits the abundance of exact matching short subsequences (k-mers) to quickly detect conserved regions, and the power of machine learning is used to improve the prediction accuracy of detection. We present a parallel implementation of NADDA using the MapReduce framework and show that our method is highly scalable. Results We have compared NADDA with Pfam and InterPro databases. For known domains annotated by Pfam, accuracy is 83%, sensitivity 96%, and specificity 44%. For sequences with new domains not present in the training set an average accuracy of 63% is achieved when compared to Pfam. A boost in results in comparison with InterPro demonstrates the ability of NADDA to capture conserved regions beyond those present in Pfam. We have also compared NADDA with ADDA and MKDOM2, assuming Pfam as ground-truth. On average NADDA shows comparable accuracy, more balanced sensitivity and specificity, and being alignment-free, is significantly faster. Excluding the one-time cost of training, runtimes on a single processor were 49s, 10,566s, and 456s

  4. A New Approach to the Oral Administration of Insulin and Other Peptide Drugs

    NASA Astrophysics Data System (ADS)

    Saffran, Murray; Sudesh Kumar, G.; Savariar, Celin; Burnham, Jeffrey C.; Williams, Frederick; Neckers, Douglas C.

    1986-09-01

    The oral administration of peptide drugs is well known to be precluded by their digestion in the stomach and small intestine. As a new approach to oral delivery, peptide drugs were coated with polymers cross-linked with azoaromatic groups to form an impervious film to protect orally administered drugs from digestion in the stomach and small intestine. When the azopolymer-coated drug reached the large intestine, the indigenous microflora reduced the azo bonds, broke the cross-links, and degraded the polymer film, thereby releasing the drug into the lumen of the colon for local action or for absorption. The ability of the azopolymer coating to protect and deliver orally administered peptide drugs was demonstrated in rats with the peptide hormones vasopressin and insulin.

  5. Coupling in silico and in vitro analysis of peptide-MHC binding: a bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes.

    PubMed

    Doytchinova, Irini A; Walshe, Valerie A; Jones, Nicola A; Gloster, Simone E; Borrow, Persephone; Flower, Darren R

    2004-06-15

    The ability to define and manipulate the interaction of peptides with MHC molecules has immense immunological utility, with applications in epitope identification, vaccine design, and immunomodulation. However, the methods currently available for prediction of peptide-MHC binding are far from ideal. We recently described the application of a bioinformatic prediction method based on quantitative structure-affinity relationship methods to peptide-MHC binding. In this study we demonstrate the predictivity and utility of this approach. We determined the binding affinities of a set of 90 nonamer peptides for the MHC class I allele HLA-A*0201 using an in-house, FACS-based, MHC stabilization assay, and from these data we derived an additive quantitative structure-affinity relationship model for peptide interaction with the HLA-A*0201 molecule. Using this model we then designed a series of high affinity HLA-A2-binding peptides. Experimental analysis revealed that all these peptides showed high binding affinities to the HLA-A*0201 molecule, significantly higher than the highest previously recorded. In addition, by the use of systematic substitution at principal anchor positions 2 and 9, we showed that high binding peptides are tolerant to a wide range of nonpreferred amino acids. Our results support a model in which the affinity of peptide binding to MHC is determined by the interactions of amino acids at multiple positions with the MHC molecule and may be enhanced by enthalpic cooperativity between these component interactions. PMID:15187128

  6. Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from Scarce Clinical Samples.

    PubMed

    Heyder, Tina; Kohler, Maxie; Tarasova, Nataliya K; Haag, Sabrina; Rutishauser, Dorothea; Rivera, Natalia V; Sandin, Charlotta; Mia, Sohel; Malmström, Vivianne; Wheelock, Åsa M; Wahlström, Jan; Holmdahl, Rikard; Eklund, Anders; Zubarev, Roman A; Grunewald, Johan; Ytterberg, A Jimmy

    2016-09-01

    Immune-mediated diseases strongly associating with human leukocyte antigen (HLA) alleles are likely linked to specific antigens. These antigens are presented to T cells in the form of peptides bound to HLA molecules on antigen presenting cells, e.g. dendritic cells, macrophages or B cells. The identification of HLA-DR-bound peptides presents a valuable tool to investigate the human immunopeptidome. The lung is likely a key player in the activation of potentially auto-aggressive T cells prior to entering target tissues and inducing autoimmune disease. This makes the lung of exceptional interest and presents an ideal paradigm to study the human immunopeptidome and to identify antigenic peptides.Our previous investigation of HLA-DR peptide presentation in the lung required high numbers of cells (800 × 10(6) bronchoalveolar lavage (BAL) cells). Because BAL from healthy nonsmokers typically contains 10-15 × 10(6) cells, there is a need for a highly sensitive approach to study immunopeptides in the lungs of individual patients and controls.In this work, we analyzed the HLA-DR immunopeptidome in the lung by an optimized methodology to identify HLA-DR-bound peptides from low cell numbers. We used an Epstein-Barr Virus (EBV) immortalized B cell line and bronchoalveolar lavage (BAL) cells obtained from patients with sarcoidosis, an inflammatory T cell driven disease mainly occurring in the lung. Specifically, membrane complexes were isolated prior to immunoprecipitation, eluted peptides were identified by nanoLC-MS/MS and processed using the in-house developed ClusterMHCII software. With the optimized procedure we were able to identify peptides from 10 × 10(6) cells, which on average correspond to 10.9 peptides/million cells in EBV-B cells and 9.4 peptides/million cells in BAL cells. This work presents an optimized approach designed to identify HLA-DR-bound peptides from low numbers of cells, enabling the investigation of the BAL immunopeptidome from individual patients

  7. Analysis of the proteolysis of bioactive peptides using a peptidomics approach

    PubMed Central

    Kim, Yun-Gon; Lone, Anna Mari; Saghatelian, Alan

    2014-01-01

    Identifying the peptidases that inactivate bioactive peptides (e.g. peptide hormones and neuropeptides) in mammals is an important unmet challenge. This protocol describes a recent approach that combines liquid chromatography-mass spectrometry peptidomics to identify endogenous cleavage sites of a bioactive peptide, the subsequent biochemical purification of a candidate peptidase based on these cleavage sites, and validation of the candidate peptidase’s role in the physiological regulation of the bioactive peptide by examining a peptidase knockout mouse. We highlight successful application of this protocol to discover that insulin-degrading enzyme (IDE) regulates physiological calcitonin gene-related peptide (CGRP) levels and detail the key stages and steps in this approach. This protocol requires 7 days of work; however, the total time for this protocol is highly variable because of its dependence on the availability of biological reagents, namely purified enzymes and knockout mice. The protocol is valuable because it expedites the characterization of mammalian peptidases, such as IDE, which in certain instances can be used to develop novel therapeutics. PMID:23949379

  8. A new approach to implant alignment and ligament balancing in total knee arthroplasty focussing on joint loads.

    PubMed

    Zimmermann, Frauke; Schwenninger, Christoph; Nolten, Ulrich; Firmbach, Franz Peter; Elfring, Robert; Radermacher, Klaus

    2012-08-01

    Preservation and recovery of the mechanical leg axis as well as good rotational alignment of the prosthesis components and well-balanced ligaments are essential for the longevity of total knee arthroplasty (TKA). In the framework of the OrthoMIT project, the genALIGN system, a new navigated implantation approach based on intra-operative force-torque measurements, has been developed. With this system, optical or magnetic position tracking as well as any fixation of invasive rigid bodies are no longer necessary. For the alignment of the femoral component along the mechanical axis, a sensor-integrated instrument measures the torques resulting from the deviation between the instrument's axis and the mechanical axis under manually applied axial compression load. When both axes are coaxial, the resulting torques equal zero, and the tool axis can be fixed with respect to the bone. For ligament balancing and rotational alignment of the femoral component, the genALIGN system comprises a sensor-integrated tibial trial inlay measuring the amplitude and application points of the forces transferred between femur and tibia. Hereby, the impact of ligament tensions on knee joint loads can be determined over the whole range of motion. First studies with the genALIGN system, including a comparison with an imageless navigation system, show the feasibility of the concept. PMID:22868781

  9. Quantification of chemical peptide reactivity for screening contact allergens: a classification tree model approach.

    PubMed

    Gerberick, G Frank; Vassallo, Jeffrey D; Foertsch, Leslie M; Price, Brad B; Chaney, Joel G; Lepoittevin, Jean-Pierre

    2007-06-01

    In the interest of reducing animal use, in vitro alternatives for skin sensitization testing are under development. One unifying characteristic of chemical allergens is the requirement that they react with proteins for the effective induction of skin sensitization. The majority of chemical allergens are electrophilic and react with nucleophilic amino acids. To determine whether and to what extent reactivity correlates with skin sensitization potential, 82 chemicals comprising allergens of different potencies and nonallergenic chemicals were evaluated for their ability to react with reduced glutathione (GSH) or with two synthetic peptides containing either a single cysteine or lysine. Following a 15-min reaction time with GSH, or a 24-h reaction time with the two synthetic peptides, the samples were analyzed by high-performance liquid chromatography. UV detection was used to monitor the depletion of GSH or the peptides. The peptide reactivity data were compared with existing local lymph node assay data using recursive partitioning methodology to build a classification tree that allowed a ranking of reactivity as minimal, low, moderate, and high. Generally, nonallergens and weak allergens demonstrated minimal to low peptide reactivity, whereas moderate to extremely potent allergens displayed moderate to high peptide reactivity. Classifying minimal reactivity as nonsensitizers and low, moderate, and high reactivity as sensitizers, it was determined that a model based on cysteine and lysine gave a prediction accuracy of 89%. The results of these investigations reveal that measurement of peptide reactivity has considerable potential utility as a screening approach for skin sensitization testing, and thereby for reducing reliance on animal-based test methods. PMID:17400584

  10. Developing a New Teaching Approach for the Chemical Bonding Concept Aligned with Current Scientific and Pedagogical Knowledge

    ERIC Educational Resources Information Center

    Nahum, Tami Levy; Mamlok-Naaman, Rachel; Hofstein, Avi; Krajcik, Joseph

    2007-01-01

    The traditional pedagogical approach for teaching chemical bonding is often overly simplistic and not aligned with the most up-to-date scientific models. As a result, high-school students around the world lack fundamental understanding of chemical bonding. In order to improve students' understanding of this concept, it was essential to propose a…

  11. Biofunctionalization of Surfaces with Peptides, Proteins, or Subcellular Organelles: Single-Molecule Studies and Nanomedical Approach

    NASA Astrophysics Data System (ADS)

    Katranidis, A.; Choli-Papadopoulou, T.

    Immobilization of biologically active proteins and enzymes on surfaces is very important for the production of biofunctionalized surfaces for applications in medicine such as biosensors and in the diagnostics field. There are various approaches to immobilize and control the release of peptides/proteins from different surfaces. The identification of successful techniques to functionalize a particular material is a challenge. On the other hand, biomaterials are at the moment of great benefit for medicinal purposes and a lot of knowledge from different fields is required in order to design biomimetic scaffolds or biomimetic materials. The used methodologies are different for different materials and are mainly based on the special chemistry of the surfaces. Peptides with distinct properties are desired instead of entire proteins. However, in some cases, proteins cannot be replaced by peptide segments and therefore biochemical knowledge, such as in protein and/or genetic engineering is required.

  12. A targeted proteomics approach to the identification of peptides modified by reactive metabolites.

    PubMed

    Tzouros, Manuel; Pähler, Axel

    2009-05-01

    Covalent binding of reactive metabolites is generally accepted as one underlying mechanism of drug-induced toxicity. However, identification of protein targets by reactive metabolites still remains a challenge due to their low abundance. Here, we report the development of a highly selective proteomics workflow for the targeted identification of peptides modified by reactive metabolites. An equimolar mixture of non- and radiolabeled furan containing 2-amino-pyrimidine drug candidate (1 and 14C(1)-1) along with rat liver microsomes were used for the in vitro generation of reactive metabolites. Liver microsomal proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, modified protein bands were highlighted by autoradiography and in-gel digested, and peptides were fractionated by strong cation exchange chromatography. Fractions enriched in modified peptides, as determined by radioactivity levels, were subjected to nanoLC-MS/MS and unambiguously detected based on their unique 12C/14C MS isotope pattern fingerprint. The peptide detection step could be automated using isotope pattern recognition software. Peptide sequencing, identification of the site of modification, and reactive metabolite characterization were achieved by MS2 and MS3 experiments using high-resolution and accurate mass detection. This approach led to the identification of four modified peptides originating from three drug-metabolizing enzymes, MGST1, FMO1, and P450 2C11. These revealed modifications by five different metabolite structures. This approach is generally suitable for the identification and characterization of modified proteins and metabolite structures involved in covalent binding and may serve as a valuable tool to link protein targets with clinically relevant toxicities. PMID:19317514

  13. Signal-3L: A 3-layer approach for predicting signal peptides.

    PubMed

    Shen, Hong-Bin; Chou, Kuo-Chen

    2007-11-16

    Functioning as an "address tag" that directs nascent proteins to their proper cellular and extracellular locations, signal peptides have become a crucial tool in finding new drugs or reprogramming cells for gene therapy. To effectively and timely use such a tool, however, the first important thing is to develop an automated method for rapidly and accurately identifying the signal peptide for a given nascent protein. With the avalanche of new protein sequences generated in the post-genomic era, the challenge has become even more urgent and critical. In this paper, we have developed a novel method for predicting signal peptide sequences and their cleavage sites in human, plant, animal, eukaryotic, Gram-positive, and Gram-negative protein sequences, respectively. The new predictor is called Signal-3L that consists of three prediction engines working, respectively, for the following three progressively deepening layers: (1) identifying a query protein as secretory or non-secretory by an ensemble classifier formed by fusing many individual OET-KNN (optimized evidence-theoretic K nearest neighbor) classifiers operated in various dimensions of PseAA (pseudo amino acid) composition spaces; (2) selecting a set of candidates for the possible signal peptide cleavage sites of a query secretory protein by a subsite-coupled discrimination algorithm; (3) determining the final cleavage site by fusing the global sequence alignment outcome for each of the aforementioned candidates through a voting system. Signal-3L is featured by high success prediction rates with short computational time, and hence is particularly useful for the analysis of large-scale datasets. Signal-3L is freely available as a web-server at http://chou.med.harvard.edu/bioinf/Signal-3L/ or http://202.120.37.186/bioinf/Signal-3L, where, to further support the demand of the related areas, the signal peptides identified by Signal-3L for all the protein entries in Swiss-Prot databank that do not have signal peptide

  14. One-Pot Photochemical Ring-Opening/Cleavage Approach for the Synthesis and Decoding of Cyclic Peptide Libraries.

    PubMed

    Liang, Xinxia; Vézina-Dawod, Simon; Bédard, François; Porte, Karine; Biron, Eric

    2016-03-01

    A novel dual ring-opening/cleavage strategy to determine the sequence of cyclic peptides from one bead, one compound libraries is described. The approach uses a photolabile residue within the macrocycle and as a linker to allow a simultaneous ring opening and cleavage from the beads upon UV irradiation and provide linearized molecules. Cyclic peptides of five to nine residues were synthesized and the generated linear peptides successfully sequenced by tandem mass spectrometry. PMID:26914725

  15. A biomimetic approach for enhancing the in vivo half-life of peptides

    PubMed Central

    Penchala, Sravan C; Miller, Mark R; Pal, Arindom; Dong, Jin; Madadi, Nikhil R.; Xie, Jinghang; Joo, Hyun; Tsai, Jerry; Batoon, Patrick; Samoshin, Vyacheslav; Franz, Andreas; Cox, Trever; Miles, Jesse; Chan, William K; Park, Miki S; Alhamadsheh, Mamoun M

    2015-01-01

    The tremendous therapeutic potential of peptides has not yet been realized, mainly due to their short in vivo half-life. While conjugation to macromolecules has been a mainstay approach for enhancing the half-life of proteins, the steric hindrance of macromolecules often harms the binding of peptides to target receptors, compromising the in vivo efficacy. Here we report a new strategy for enhancing the in vivo half-life of peptides without compromising their potency. Our approach involves endowing peptides with a small-molecule that binds reversibly to the serum protein, transthyretin. Although there are few reversible albumin-binding molecules, we are unaware of designed small molecules that bind reversibly to other serum proteins and are used for half-life extension in vivo. We show here that our strategy was indeed effective in enhancing the half-life of an agonist for GnRH receptor while maintaining its binding affinity, which was translated into superior in vivo efficacy. PMID:26344696

  16. A three-dimensional vertically aligned functionalized multilayer graphene architecture: an approach for graphene-based thermal interfacial materials.

    PubMed

    Liang, Qizhen; Yao, Xuxia; Wang, Wei; Liu, Yan; Wong, Ching Ping

    2011-03-22

    Thermally conductive functionalized multilayer graphene sheets (fMGs) are efficiently aligned in large-scale by a vacuum filtration method at room temperature, as evidenced by SEM images and polarized Raman spectroscopy. A remarkably strong anisotropy in properties of aligned fMGs is observed. High electrical (∼386 S cm(-1)) and thermal conductivity (∼112 W m(-1) K(-1) at 25 °C) and ultralow coefficient of thermal expansion (∼-0.71 ppm K(-1)) in the in-plane direction of A-fMGs are obtained without any reduction process. Aligned fMGs are vertically assembled between contacted silicon/silicon surfaces with pure indium as a metallic medium. Thus-constructed three-dimensional vertically aligned fMG thermal interfacial material (VA-fMG TIM) architecture has significantly higher equivalent thermal conductivity (75.5 W m(-1) K(-1)) and lower contact thermal resistance (5.1 mm2 K W(-1)), compared with their counterpart from A-fMGs that are recumbent between silicon surfaces. This finding provides a throughout approach for a graphene-based TIM assembly as well as knowledge of vertically aligned graphene architectures, which may not only facilitate graphene's application in current demanding thermal management but also promote its widespread applications in electrodes of energy storage devices, conductive polymeric composites, etc. PMID:21384860

  17. Advances in peptidic and peptidomimetic-based approaches to inhibit STAT signaling in human diseases.

    PubMed

    Szelag, Malgorzata; Wesoly, Joanna; Bluyssen, Hans A R

    2016-01-01

    STATs promote fundamental cellular processes, marking them as convergence points of many oncogenic and inflammatory pathways. Therefore, aberrant activation of STAT signaling is implicated in a plethora of human diseases, like cancer, inflammation and auto-immunity. Identification of STAT-specific inhibitors is the topic of great practical importance, and various inhibitory strategies are being pursued. An interesting approach includes peptides and peptide-like biopolymers, because they allow the manipulation of STAT signaling without the transfer of genetic material. Phosphopeptides and peptidomimetics directly target STATs by inhibiting dimerization. Despite that a large number of efficient peptide- based STAT3-specific inhibitors have been reported to date, none of them was able to meet the pharmacological requirements to serve as a potent anti-cancer drug. The existing limitations, like metabolic instability and poor cell permeability during in vivo tests, excluded these macromolecules from further clinical development. To overcome these liabilities, in the last five years many advances have been made to develop next generation STAT-specific inhibitors. Here we discuss the pitfalls of current STAT inhibitory strategies and review the progress on the development of peptide-like prodrugs directly targeting STATs. Novel strategies involve screening of high-complexity libraries of random peptides, as specific STAT3 or STAT5 DNA-binding inhibitors, to construct cell permeable peptide aptamers and aptides for cancer therapy. Another new direction is synthesis of negative dominant α-helical mimetics of the STAT3 N-domain, preventing oligomerization on DNA. Moreover, construction of phosphopeptide conjugates with molecules mediating cellular uptake offers new therapeutic possibilities in treatment of cancer, asthma and allergy. PMID:26521960

  18. A combined NMR and computational approach to investigate peptide binding to a designed Armadillo repeat protein.

    PubMed

    Ewald, Christina; Christen, Martin T; Watson, Randall P; Mihajlovic, Maja; Zhou, Ting; Honegger, Annemarie; Plückthun, Andreas; Caflisch, Amedeo; Zerbe, Oliver

    2015-05-22

    The specific recognition of peptide sequences by proteins plays an important role both in biology and in diagnostic applications. Here we characterize the relatively weak binding of the peptide neurotensin (NT) to the previously developed Armadillo repeat protein VG_328 by a multidisciplinary approach based on solution NMR spectroscopy, mutational studies, and molecular dynamics (MD) simulations, totaling 20μs for all MD runs. We describe assignment challenges arising from the repetitive nature of the protein sequence, and we present novel approaches to address them. Partial assignments obtained for VG_328 in combination with chemical shift perturbations allowed us to identify the repeats not involved in binding. Their subsequent elimination resulted in a reduced-size binder with very similar affinity for NT, for which near-complete backbone assignments were achieved. A binding mode suggested by automatic docking and further validated by explicit solvent MD simulations is consistent with paramagnetic relaxation enhancement data collected using spin-labeled NT. Favorable intermolecular interactions are observed in the MD simulations for the residues that were previously shown to contribute to binding in an Ala scan of NT. We further characterized the role of residues within the N-cap for protein stability and peptide binding. Our multidisciplinary approach demonstrates that an initial low-resolution picture for a low-micromolar-peptide binder can be refined through the combination of NMR, protein design, docking, and MD simulations to establish its binding mode, even in the absence of crystallographic data, thereby providing valuable information for further design. PMID:25816772

  19. A Simple Approach to Reproducing IMAGE/RPI-Derived Field-Aligned Electron Density Profiles During Plasmaspheric Refilling

    NASA Astrophysics Data System (ADS)

    Webb, P. A.; Reinisch, B. W.; Huang, X.; Reynolds, M. A.; Benson, R. F.; Green, J. L.

    2002-12-01

    Magnetic field-aligned electron-density (Ne) profiles can be calculated from active soundings using the Radio Plasma Imager (RPI) on the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) satellite. By observing these profiles under different geomagnetic conditions, the underlying physics that control the Ne distribution can be investigated. In this presentation RPI observations will be used to show that a magnetic field line depleted of plasma has an Ne distribution approximating a collisionless (CL) profile, while a saturated field line has a diffusive equilibrium (DE) profile. Furthermore, by using the RPI-derived profiles it is possible to observe the transition from the depleted CL profile to the saturated DE profile. Using computationally simple CL and DE models as upper and lower boundaries respectively, methods to vary the distribution between these two extremes that reproduces the refilling of the field-aligned Ne profiles observed by RPI will be presented. Furthermore, the results of this approach will be compared with the Multi-Species Kinetic Plasmasphere Model (MSKPM), a kinetic field-aligned model that simulates the plasmaspheric refilling by single particles from the underlying exosphere. Comparisons of the Global Plasmasphere Ionosphere Density (GPID) model with IMAGE Ne observations from passive and active RPI operations will demonstrate the increased accuracy of GPID when the improved CL-DE field-aligned Ne distribution is included in the model.

  20. Variant fatty acid-like molecules Conjugation, novel approaches for extending the stability of therapeutic peptides

    PubMed Central

    Li, Ying; Wang, Yuli; Wei, Qunchao; Zheng, Xuemin; Tang, Lida; Kong, Dexin; Gong, Min

    2015-01-01

    The multiple physiological properties of glucagon-like peptide-1 (GLP-1) make it a promising drug candidate for the treatment of type 2 diabetes. However, the in vivo half-life of GLP-1 is short due to rapid degradation by dipeptidyl peptidase-IV (DPP-IV) and renal clearance. The poor stability of GLP-1 has significantly limited its clinical utility; however, many studies are focused on extending its stability. Fatty acid conjugation is a traditional approach for extending the stability of therapeutic peptides because of the high binding affinity of human serum albumin for fatty acids. However, the conjugate requires a complex synthetic approach, usually involving Lys and occasionally involving a linker. In the current study, we conjugated the GLP-1 molecule with fatty acid derivatives to simplify the synthesis steps. Human serum albumin binding assays indicated that the retained carboxyl groups of the fatty acids helped maintain a tight affinity to HSA. The conjugation of fatty acid-like molecules improved the stability and increased the binding affinity of GLP-1 to HSA. The use of fatty acid-like molecules as conjugating components allowed variant conjugation positions and freed carboxyl groups for other potential uses. This may be a novel, long-acting strategy for the development of therapeutic peptides. PMID:26658631

  1. Computational Amide I Spectroscopy for Refinement of Disordered Peptide Ensembles: Maximum Entropy and Related Approaches

    NASA Astrophysics Data System (ADS)

    Reppert, Michael; Tokmakoff, Andrei

    The structural characterization of intrinsically disordered peptides (IDPs) presents a challenging biophysical problem. Extreme heterogeneity and rapid conformational interconversion make traditional methods difficult to interpret. Due to its ultrafast (ps) shutter speed, Amide I vibrational spectroscopy has received considerable interest as a novel technique to probe IDP structure and dynamics. Historically, Amide I spectroscopy has been limited to delivering global secondary structural information. More recently, however, the method has been adapted to study structure at the local level through incorporation of isotope labels into the protein backbone at specific amide bonds. Thanks to the acute sensitivity of Amide I frequencies to local electrostatic interactions-particularly hydrogen bonds-spectroscopic data on isotope labeled residues directly reports on local peptide conformation. Quantitative information can be extracted using electrostatic frequency maps which translate molecular dynamics trajectories into Amide I spectra for comparison with experiment. Here we present our recent efforts in the development of a rigorous approach to incorporating Amide I spectroscopic restraints into refined molecular dynamics structural ensembles using maximum entropy and related approaches. By combining force field predictions with experimental spectroscopic data, we construct refined structural ensembles for a family of short, strongly disordered, elastin-like peptides in aqueous solution.

  2. Variant fatty acid-like molecules Conjugation, novel approaches for extending the stability of therapeutic peptides.

    PubMed

    Li, Ying; Wang, Yuli; Wei, Qunchao; Zheng, Xuemin; Tang, Lida; Kong, Dexin; Gong, Min

    2015-01-01

    The multiple physiological properties of glucagon-like peptide-1 (GLP-1) make it a promising drug candidate for the treatment of type 2 diabetes. However, the in vivo half-life of GLP-1 is short due to rapid degradation by dipeptidyl peptidase-IV (DPP-IV) and renal clearance. The poor stability of GLP-1 has significantly limited its clinical utility; however, many studies are focused on extending its stability. Fatty acid conjugation is a traditional approach for extending the stability of therapeutic peptides because of the high binding affinity of human serum albumin for fatty acids. However, the conjugate requires a complex synthetic approach, usually involving Lys and occasionally involving a linker. In the current study, we conjugated the GLP-1 molecule with fatty acid derivatives to simplify the synthesis steps. Human serum albumin binding assays indicated that the retained carboxyl groups of the fatty acids helped maintain a tight affinity to HSA. The conjugation of fatty acid-like molecules improved the stability and increased the binding affinity of GLP-1 to HSA. The use of fatty acid-like molecules as conjugating components allowed variant conjugation positions and freed carboxyl groups for other potential uses. This may be a novel, long-acting strategy for the development of therapeutic peptides. PMID:26658631

  3. Combined Systems Approaches Reveal Highly Plastic Responses to Antimicrobial Peptide Challenge in Escherichia coli

    PubMed Central

    Kozlowska, Justyna; Vermeer, Louic S.; Rogers, Geraint B.; Rehnnuma, Nabila; Amos, Sarah-Beth T. A.; Koller, Garrit; McArthur, Michael; Bruce, Kenneth D.; Mason, A. James

    2014-01-01

    Obtaining an in-depth understanding of the arms races between peptides comprising the innate immune response and bacterial pathogens is of fundamental interest and will inform the development of new antibacterial therapeutics. We investigated whether a whole organism view of antimicrobial peptide (AMP) challenge on Escherichia coli would provide a suitably sophisticated bacterial perspective on AMP mechanism of action. Selecting structurally and physically related AMPs but with expected differences in bactericidal strategy, we monitored changes in bacterial metabolomes, morphological features and gene expression following AMP challenge at sub-lethal concentrations. For each technique, the vast majority of changes were specific to each AMP, with such a plastic response indicating E. coli is highly capable of discriminating between specific antibiotic challenges. Analysis of the ontological profiles generated from the transcriptomic analyses suggests this approach can accurately predict the antibacterial mode of action, providing a fresh, novel perspective for previous functional and biophysical studies. PMID:24789011

  4. Modeling of the Binding of Peptide Blockers to Voltage-Gated Potassium Channels: Approaches and Evidence

    PubMed Central

    Novoseletsky, V. N.; Volyntseva, A. D.; Shaitan, K. V.; Kirpichnikov, M. P.; Feofanov, A. V.

    2016-01-01

    Modeling of the structure of voltage-gated potassium (KV) channels bound to peptide blockers aims to identify the key amino acid residues dictating affinity and provide insights into the toxin-channel interface. Computational approaches open up possibilities for in silico rational design of selective blockers, new molecular tools to study the cellular distribution and functional roles of potassium channels. It is anticipated that optimized blockers will advance the development of drugs that reduce over activation of potassium channels and attenuate the associated malfunction. Starting with an overview of the recent advances in computational simulation strategies to predict the bound state orientations of peptide pore blockers relative to KV-channels, we go on to review algorithms for the analysis of intermolecular interactions, and then take a look at the results of their application. PMID:27437138

  5. Aligning Game Activity with Educational Goals: Following a Constrained Design Approach to Instructional Computer Games

    ERIC Educational Resources Information Center

    Shelton, Brett E.; Scoresby, Jon

    2011-01-01

    We discuss the design, creation and implementation of an instructional game for use in a high school poetry class following a commitment to an educational game design principle of "alignment". We studied groups of instructional designers and an interactive fiction computer game they built. The game was implemented in a 9th grade English classroom…

  6. An Approach to Enhance Alignment and Myelination of Dorsal Root Ganglion Neurons.

    PubMed

    Liu, Chun; Chan, Christina

    2016-01-01

    Axon regeneration is a chaotic process due largely to unorganized axon alignment. Therefore, in order for a sufficient number of regenerated axons to bridge the lesion site, properly organized axonal alignment is required. Since demyelination after nerve injury strongly impairs the conductive capacity of surviving axons, remyelination is critical for successful functioning of regenerated nerves. Previously, we demonstrated that mesenchymal stem cells (MSCs) aligned on a pre-stretch induced anisotropic surface because the cells can sense a larger effective stiffness in the stretched direction than in the perpendicular direction. We also showed that an anisotropic surface arising from a mechanical pre-stretched surface similarly affects alignment, as well as growth and myelination of axons. Here, we provide a detailed protocol for preparing a pre-stretched anisotropic surface, the isolation and culture of dorsal root ganglion (DRG) neurons on a pre-stretched surface, and show the myelination behavior of a co-culture of DRG neurons with Schwann cells (SCs) on a pre-stretched surface. PMID:27585118

  7. Identification and characterization of Aβ peptide interactors in Alzheimer’s disease by structural approaches

    PubMed Central

    Philibert, Keith D.; Marr, Robert A.; Norstrom, Eric M.; Glucksman, Marc J.

    2014-01-01

    Currently, there are very limited pharmaceutical interventions for Alzheimer’s disease (AD) to alleviate the amyloid burden implicated in the pathophysiology of the disease. Alzheimer’s disease is characterized immunohistologically by the accumulation of senile plaques in the brain with afflicted patients progressively losing short-term memory and, ultimately, cognition. Although significant improvements in clinical diagnosis and care for AD patients have been made, effective treatments for this devastating disease remain elusive. A key component of the amyloid burden of AD comes from accumulation of the amyloid-beta (Aβ) peptide which comes from processing of the amyloid precursor protein (APP) by enzymes termed secretases, leading to production of these toxic Aβ peptides of 40–42 amino acids. New therapeutic approaches for reducing Aβ are warranted after the most logical avenues of inhibiting secretase activity appear less than optimal in ameliorating the progression of AD.Novel therapeutics may be gleaned from proteomics biomarker initiatives to yield detailed molecular interactions of enzymes and their potential substrates. Explicating the APPome by deciphering protein complexes forming in cells is a complementary approach to unveil novel molecular interactions with the amyloidogenic peptide precursor to both understand the biology and develop potential upstream drug targets. Utilizing these strategies we have identified EC 3.4.24.15 (EP24.15), a zinc metalloprotease related to neprilysin (NEP), with the ability to catabolize Aβ 1–42 by examining first potential in silico docking and then verification by mass spectrometry. In addition, a hormone carrier protein, transthyreitin (TTR), was identified and with its abundance in cerebrospinal fluid (CSF), found to clear Aβ by inhibiting formation of oligomeric forms of Aβ peptide. The confluence of complementary strategies may allow new therapeutic avenues as well as biomarkers for AD that will aid in

  8. From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins.

    PubMed

    Verdes, Aida; Anand, Prachi; Gorson, Juliette; Jannetti, Stephen; Kelly, Patrick; Leffler, Abba; Simpson, Danny; Ramrattan, Girish; Holford, Mandë

    2016-01-01

    Animal venoms comprise a diversity of peptide toxins that manipulate molecular targets such as ion channels and receptors, making venom peptides attractive candidates for the development of therapeutics to benefit human health. However, identifying bioactive venom peptides remains a significant challenge. In this review we describe our particular venomics strategy for the discovery, characterization, and optimization of Terebridae venom peptides, teretoxins. Our strategy reflects the scientific path from mollusks to medicine in an integrative sequential approach with the following steps: (1) delimitation of venomous Terebridae lineages through taxonomic and phylogenetic analyses; (2) identification and classification of putative teretoxins through omics methodologies, including genomics, transcriptomics, and proteomics; (3) chemical and recombinant synthesis of promising peptide toxins; (4) structural characterization through experimental and computational methods; (5) determination of teretoxin bioactivity and molecular function through biological assays and computational modeling; (6) optimization of peptide toxin affinity and selectivity to molecular target; and (7) development of strategies for effective delivery of venom peptide therapeutics. While our research focuses on terebrids, the venomics approach outlined here can be applied to the discovery and characterization of peptide toxins from any venomous taxa. PMID:27104567

  9. From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins

    PubMed Central

    Verdes, Aida; Anand, Prachi; Gorson, Juliette; Jannetti, Stephen; Kelly, Patrick; Leffler, Abba; Simpson, Danny; Ramrattan, Girish; Holford, Mandë

    2016-01-01

    Animal venoms comprise a diversity of peptide toxins that manipulate molecular targets such as ion channels and receptors, making venom peptides attractive candidates for the development of therapeutics to benefit human health. However, identifying bioactive venom peptides remains a significant challenge. In this review we describe our particular venomics strategy for the discovery, characterization, and optimization of Terebridae venom peptides, teretoxins. Our strategy reflects the scientific path from mollusks to medicine in an integrative sequential approach with the following steps: (1) delimitation of venomous Terebridae lineages through taxonomic and phylogenetic analyses; (2) identification and classification of putative teretoxins through omics methodologies, including genomics, transcriptomics, and proteomics; (3) chemical and recombinant synthesis of promising peptide toxins; (4) structural characterization through experimental and computational methods; (5) determination of teretoxin bioactivity and molecular function through biological assays and computational modeling; (6) optimization of peptide toxin affinity and selectivity to molecular target; and (7) development of strategies for effective delivery of venom peptide therapeutics. While our research focuses on terebrids, the venomics approach outlined here can be applied to the discovery and characterization of peptide toxins from any venomous taxa. PMID:27104567

  10. Simple, Inexpensive, and Rapid Approach to Fabricate Cross-Shaped Memristors Using an Inorganic-Nanowire-Digital-Alignment Technique and a One-Step Reduction Process.

    PubMed

    Xu, Wentao; Lee, Yeongjun; Min, Sung-Yong; Park, Cheolmin; Lee, Tae-Woo

    2016-01-20

    A rapid, scalable, and designable approach to produce a cross-shaped memristor array is demonstrated using an inorganic-nanowire digital-alignment technique and a one-step reduction process. Two-dimensional arrays of perpendicularly aligned, individually conductive Cu-nanowires with a nanometer-scale Cux O layer sandwiched at each cross point are produced. PMID:26585580

  11. Curve aligning approach for gait authentication based on a wearable accelerometer.

    PubMed

    Sun, Hu; Yuao, Tao

    2012-06-01

    Gait authentication based on a wearable accelerometer is a novel biometric which can be used for identity identification, medical rehabilitation and early detection of neurological disorders. The method for matching gait patterns tells heavily on authentication performances. In this paper, curve aligning is introduced as a new method for matching gait patterns and it is compared with correlation and dynamic time warping (DTW). A support vector machine (SVM) is proposed to fuse pattern-matching methods in a decision level. Accelerations collected from ankles of 22 walking subjects are processed for authentications in our experiments. The fusion of curve aligning with backward-forward accelerations and DTW with vertical accelerations promotes authentication performances substantially and consistently. This fusion algorithm is tested repeatedly. Its mean and standard deviation of equal error rates are 0.794% and 0.696%, respectively, whereas among all presented non-fusion algorithms, the best one shows an EER of 3.03%. PMID:22621972

  12. A Brief Review of Computer-Assisted Approaches to Rational Design of Peptide Vaccines.

    PubMed

    Nandy, Ashesh; Basak, Subhash C

    2016-01-01

    The growing incidences of new viral diseases and increasingly frequent viral epidemics have strained therapeutic and preventive measures; the high mutability of viral genes puts additional strains on developmental efforts. Given the high cost and time requirements for new drugs development, vaccines remain as a viable alternative, but there too traditional techniques of live-attenuated or inactivated vaccines have the danger of allergenic reactions and others. Peptide vaccines have, over the last several years, begun to be looked on as more appropriate alternatives, which are economically affordable, require less time for development and hold the promise of multi-valent dosages. The developments in bioinformatics, proteomics, immunogenomics, structural biology and other sciences have spurred the growth of vaccinomics where computer assisted approaches serve to identify suitable peptide targets for eventual development of vaccines. In this mini-review we give a brief overview of some of the recent trends in computer assisted vaccine development with emphasis on the primary selection procedures of probable peptide candidates for vaccine development. PMID:27153063

  13. Novel Approach to Prepare {sup 99m}Tc-Based Multivalent RGD Peptides

    SciTech Connect

    Shuang Liu

    2012-10-24

    This project presents a novel approach to prepare the {sup 99m}Tc-bridged multivalent RGD (arginine-glycine-aspartate) peptides. This project will focus on fundamentals of {sup 99m}Tc radiochemistry. The main objective of this project is to demonstrate the proof-of-principle for the proposed radiotracers. Once a kit formulation is developed for preparation of the {sup 99m}Tc-bridged multivalent RGD peptides, various tumor-bearing animal models will be used to evaluate their potential for SPECT (single photon-emission computed tomography) imaging of cancer. We have demonstrated that (1) multimerization of cyclic RGD peptides enhances the integrin {alpha}{sub v}{beta}{sub 3} bonding affinity and radiotracer tumor uptake; (2) addition of G{sub 3} or PEG{sub 4} linkers makes it possible for two RGD motifs in 3P-RGD{sub 2} and 3G-RGD{sub 2} to achieve simultaneous integrin {alpha}{sub v}{beta}{sub 3} binding; and (3) multimers are actually bivalent (not multivalent), the presence of extra RGD motifs can enhance the tumor retention time of the radiotracer.

  14. A Brief Review of Computer-Assisted Approaches to Rational Design of Peptide Vaccines

    PubMed Central

    Nandy, Ashesh; Basak, Subhash C.

    2016-01-01

    The growing incidences of new viral diseases and increasingly frequent viral epidemics have strained therapeutic and preventive measures; the high mutability of viral genes puts additional strains on developmental efforts. Given the high cost and time requirements for new drugs development, vaccines remain as a viable alternative, but there too traditional techniques of live-attenuated or inactivated vaccines have the danger of allergenic reactions and others. Peptide vaccines have, over the last several years, begun to be looked on as more appropriate alternatives, which are economically affordable, require less time for development and hold the promise of multi-valent dosages. The developments in bioinformatics, proteomics, immunogenomics, structural biology and other sciences have spurred the growth of vaccinomics where computer assisted approaches serve to identify suitable peptide targets for eventual development of vaccines. In this mini-review we give a brief overview of some of the recent trends in computer assisted vaccine development with emphasis on the primary selection procedures of probable peptide candidates for vaccine development. PMID:27153063

  15. Processing of chromatographic data for chemometric analysis of peptide profiles from cheese extracts: a novel approach.

    PubMed

    Piraino, Paolo; Parente, Eugenio; McSweeney, Paul L H

    2004-11-17

    Chemometric analysis of chromatograms plays a fundamental role in characterization of foods or in detection of adulteration. Data for multivariate analysis of chromatographic profiles are usually obtained by visual matching (VM) of peaks, the identities of which, as for peptide profiles from cheese extracts, are often unknown. To avoid the main disadvantages of VM, which is subjective and time-consuming, a novel approach was developed. Fuzzy logic was employed to handle in a systematic way uncertainty in the position of peptide peaks, and chromatograms were processed by a rule-based membership function. Processed data consisted of classes of retention time wherein peak heights were accumulated by using the distance from the center of the class as a weight. The novel approach (fuzzy approach, FA) was compared with VM by using a real data set and by performing multivariate descriptive statistical techniques (principal component analysis, multidimensional scaling, and nonhierarchical cluster analysis). FA provided a fast, reliable, and objective alternative to VM and could be successfully applied for chemometric analysis of chromatographic profiles whenever knowledge of the identity of peaks is lacking or unnecessary. PMID:15537294

  16. Production of angiotensin-I-converting enzyme inhibitory peptides from β-lactoglobulin- and casein-derived peptides: an integrative approach.

    PubMed

    Welderufael, Fisseha T; Gibson, Trevor; Jauregi, Paula

    2012-01-01

    Angiotensin I-converting enzyme (ACE) inhibition is one of the mechanisms by which reduction in blood pressure is exerted. Whey proteins are a rich source of ACE inhibitory peptides and have shown a blood pressure reduction effect i.e. antihypertensive activity. The aim of this work was to develop a simplified process using a combination of adsorption and microfiltration steps for the production of hydrolysates from whey with high ACE inhibitory activity and potency; the latter was measured as the IC50, which is the peptide concentration required to reduce ACE activity by half. This process integrates the selective separation of β-lactoglobulin- and casein-derived peptides (CDP) from rennet whey and their hydrolysis, which results in partially pure, less complex hydrolysates with high bioactive potency. Hydrolysis was carried out with protease N "Amano" in a thermostatically controlled membrane reactor operated in a batch mode. By applying the integrative approach it was possible to produce from the same feedstock two different hydrolysates that exhibited high ACE inhibition. One hydrolysate was mainly composed of casein-derived peptides with IC50=285 μg/mL. In this hydrolysate we identified the well-known potent ACE-inhibitor and antihypertensive tripeptide Ile-Pro-Pro (IPP) and another novel octapeptide Gln-Asp-Lys-Thr-Glu-Ile-Pro-Thr (QDKTEIPT). The second hydrolysate was mainly composed of β-lactoglobulin derived peptides with IC50=28 μg/mL. This hydrolysate contained a tetrapeptide (Ile-Ile-Ala-Glu) IIAE as one of the two major peptides. A further advantage to this process is that enzyme activity was substantially increased as enzyme product inhibition was reduced. PMID:22467199

  17. MetaMHCpan, A Meta Approach for Pan-Specific MHC Peptide Binding Prediction.

    PubMed

    Xu, Yichang; Luo, Cheng; Mamitsuka, Hiroshi; Zhu, Shanfeng

    2016-01-01

    Recent computational approaches in bioinformatics can achieve high performance, by which they can be a powerful support for performing real biological experiments, making biologists pay more attention to bioinformatics than before. In immunology, predicting peptides which can bind to MHC alleles is an important task, being tackled by many computational approaches. However, this situation causes a serious problem for immunologists to select the appropriate method to be used in bioinformatics. To overcome this problem, we develop an ensemble prediction-based Web server, which we call MetaMHCpan, consisting of two parts: MetaMHCIpan and MetaMHCIIpan, for predicting peptides which can bind MHC-I and MHC-II, respectively. MetaMHCIpan and MetaMHCIIpan use two (MHC2SKpan and LApan) and four (TEPITOPEpan, MHC2SKpan, LApan, and MHC2MIL) existing predictors, respectively. MetaMHCpan is available at http://datamining-iip.fudan.edu.cn/MetaMHCpan/index.php/pages/view/info . PMID:27076335

  18. Transparent aligners: An invisible approach to correct mild skeletal class III malocclusion.

    PubMed

    Yezdani, A Arif

    2015-04-01

    This case report highlights the treatment of a mild skeletal class III malocclusion with an invisible thermoplastic retainer. A 15-year-old female patient presented with a mild skeletal class III malocclusion with a retrognathic maxilla, orthognathic mandible, a low mandibular plane angle with Angle's class III malocclusion with maxillary lateral incisors in anterior cross-bite with crowding of maxillary anteriors, imbricated and rotated mandibular incisors and deep bite. Accurate upper and lower impressions and a bite registration were taken with polyvinyl siloxane rubber base impression material. This was then sent to the lab for the processing of a series of ClearPath aligners. The ClearPath virtual set-up sent from the lab provided the treatment plan and interproximal reduction estimation complete with posttreatment results. This enabled the clinician to actively participate in the treatment plan and provide the necessary suggestions. The ClearPath three-dimensional aligner was found to have effectively corrected the anterior cross-bite and crowding of the maxillary anteriors. PMID:26015738

  19. A Parallel Non-Alignment Based Approach to Efficient Sequence Comparison using Longest Common Subsequences

    NASA Astrophysics Data System (ADS)

    Bhowmick, S.; Shafiullah, M.; Rai, H.; Bastola, D.

    2010-11-01

    Biological sequence comparison programs have revolutionized the practice of biochemistry, and molecular and evolutionary biology. Pairwise comparison of genomic sequences is a popular method of choice for analyzing genetic sequence data. However the quality of results from most sequence comparison methods are significantly affected by small perturbations in the data and furthermore, there is a dearth of computational tools to compare sequences beyond a certain length. In this paper, we describe a parallel algorithm for comparing genetic sequences using an alignment free-method based on computing the Longest Common Subsequence (LCS) between genetic sequences. We validate the quality of our results by comparing the phylogenetic tress obtained from ClustalW and LCS. We also show through complexity analysis of the isoefficiency and by empirical measurement of the running time that our algorithm is very scalable.

  20. Fast statistical alignment.

    PubMed

    Bradley, Robert K; Roberts, Adam; Smoot, Michael; Juvekar, Sudeep; Do, Jaeyoung; Dewey, Colin; Holmes, Ian; Pachter, Lior

    2009-05-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/. PMID:19478997

  1. Multi-Beam Approach for Accelerating Alignment and Calibration of HyspIRI-Like Imaging Spectrometers

    NASA Technical Reports Server (NTRS)

    Eastwood, Michael L.; Green, Robert O.; Mouroulis, Pantazis; Hochberg, Eric B.; Hein, Randall C.; Kroll, Linley A.; Geier, Sven; Coles, James B.; Meehan, Riley

    2012-01-01

    A paper describes an optical stimulus that produces more consistent results, and can be automated for unattended, routine generation of data analysis products needed by the integration and testing team assembling a high-fidelity imaging spectrometer system. One key attribute of the system is an arrangement of pick-off mirrors that provides multiple input beams (five in this implementation) to simultaneously provide stimulus light to several field angles along the field of view of the sensor under test, allowing one data set to contain all the information that previously required five data sets to be separately collected. This stimulus can also be fed by quickly reconfigured sources that ultimately provide three data set types that would previously be collected separately using three different setups: Spectral Response Function (SRF), Cross-track Response Function (CRF), and Along-track Response Function (ARF), respectively. This method also lends itself to expansion of the number of field points if less interpolation across the field of view is desirable. An absolute minimum of three is required at the beginning stages of imaging spectrometer alignment.

  2. Aligning Goals, Assessments, and Activities: An Approach to Teaching PCR and Gel Electrophoresis

    PubMed Central

    Robertson, Amber L.; Batzli, Janet; Harris, Michelle; Miller, Sarah

    2008-01-01

    Polymerase chain reaction (PCR) and gel electrophoresis have become common techniques used in undergraduate molecular and cell biology labs. Although students enjoy learning these techniques, they often cannot fully comprehend and analyze the outcomes of their experiments because of a disconnect between concepts taught in lecture and experiments done in lab. Here we report the development and implementation of novel exercises that integrate the biological concepts of DNA structure and replication with the techniques of PCR and gel electrophoresis. Learning goals were defined based on concepts taught throughout the cell biology lab course and learning objectives specific to the PCR and gel electrophoresis lab. Exercises developed to promote critical thinking and target the underlying concepts of PCR, primer design, gel analysis, and troubleshooting were incorporated into an existing lab unit based on the detection of genetically modified organisms. Evaluative assessments for each exercise were aligned with the learning goals and used to measure student learning achievements. Our analysis found that the exercises were effective in enhancing student understanding of these concepts as shown by student performance across all learning goals. The new materials were particularly helpful in acquiring relevant knowledge, fostering critical-thinking skills, and uncovering prevalent misconceptions. PMID:18316813

  3. A computational design approach for virtual screening of peptide interactions across K+ channel families☆

    PubMed Central

    Doupnik, Craig A.; Parra, Katherine C.; Guida, Wayne C.

    2014-01-01

    Ion channels represent a large family of membrane proteins with many being well established targets in pharmacotherapy. The ‘druggability’ of heteromeric channels comprised of different subunits remains obscure, due largely to a lack of channel-specific probes necessary to delineate their therapeutic potential in vivo. Our initial studies reported here, investigated the family of inwardly rectifying potassium (Kir) channels given the availability of high resolution crystal structures for the eukaryotic constitutively active Kir2.2 channel. We describe a ‘limited’ homology modeling approach that can yield chimeric Kir channels having an outer vestibule structure representing nearly any known vertebrate or invertebrate channel. These computationally-derived channel structures were tested ""in silico for ‘docking’ to NMR structures of tertiapin (TPN), a 21 amino acid peptide found in bee venom. TPN is a highly selective and potent blocker for the epithelial rat Kir1.1 channel, but does not block human or zebrafish Kir1.1 channel isoforms. Our Kir1.1 channel-TPN docking experiments recapitulated published in vitro ""findings for TPN-sensitive and TPN-insensitive channels. Additionally, in silico site-directed mutagenesis identified ‘hot spots’ within the channel outer vestibule that mediate energetically favorable docking scores and correlate with sites previously identified with in vitro thermodynamic mutant-cycle analysis. These ‘proof-of-principle’ results establish a framework for virtual screening of re-engineered peptide toxins for interactions with computationally derived Kir channels that currently lack channel-specific blockers. When coupled with electrophysiological validation, this virtual screening approach may accelerate the drug discovery process, and can be readily applied to other ion channels families where high resolution structures are available. PMID:25709757

  4. Peptide-Based Anti-PCSK9 Vaccines - An Approach for Long-Term LDLc Management

    PubMed Central

    Galabova, Gergana; Brunner, Sylvia; Winsauer, Gabriele; Juno, Claudia; Wanko, Bettina; Mairhofer, Andreas; Lührs, Petra; Schneeberger, Achim; von Bonin, Arne; Mattner, Frank; Schmidt, Walter; Staffler, Guenther

    2014-01-01

    Background Low Density Lipoprotein (LDL) hypercholesterolemia, and its associated cardiovascular diseases, are some of the leading causes of death worldwide. The ability of proprotein convertase subtilisin/kexin 9 (PCSK9) to modulate circulating LDL cholesterol (LDLc) concentrations made it a very attractive target for LDLc management. To date, the most advanced approaches for PCSK9 inhibition are monoclonal antibody (mAb) therapies. Although shown to lower LDLc significantly, mAbs face functional limitations because of their relatively short in vivo half-lives necessitating frequent administration. Here, we evaluated the long-term efficacy and safety of PCSK9-specific active vaccines in different preclinical models. Methods and Finding PCSK9 peptide-based vaccines were successfully selected by our proprietary technology. To test their efficacy, wild-type (wt) mice, Ldlr+/− mice, and rats were immunized with highly immunogenic vaccine candidates. Vaccines induced generation of high-affine PCSK9-specific antibodies in all species. Group mean total cholesterol (TC) concentration was reduced by up to 30%, and LDLc up to 50% in treated animals. Moreover, the PCSK9 vaccine-induced humoral immune response persisted for up to one year in mice, and reduced cholesterol levels significantly throughout the study. Finally, the vaccines were well tolerated in all species tested. Conclusions Peptide-based anti-PCSK9 vaccines induce the generation of antibodies that are persistent, high-affine, and functional for up to one year. They are powerful and safe tools for long-term LDLc management, and thus may represent a novel therapeutic approach for the prevention and/or treatment of LDL hypercholesterolemia-related cardiovascular diseases in humans. PMID:25474576

  5. Innovative scatterometry approach for self-aligned quadruple patterning (SAQP) process control

    NASA Astrophysics Data System (ADS)

    Gunay-Demirkol, Anil; Altamirano Sanchez, Efrain; Heraud, Stephane; Godny, Stephane; Charley, Anne-Laure; Leray, Philippe; Urenski, Ronen; Cohen, Oded; Turovets, Igor; Wolfling, Shay

    2016-03-01

    In this work, capabilities of scatterometry at various steps of the self-aligned quadruple patterning (SAQP) process flow for 7nm (N7) technology node are demonstrated including the pitch walk measurement on the final fin etch step. The scatterometry solutions for each step are verified using reference metrology and the capability to follow the planned process design-of-experiment (DOE) and the sensitivity to catch the small process variations are demonstrated. Pitch walk, which is pitch variation in the four line/space (L/S) populations, is one of the main process challenges for SAQP. Scatterometry, which is a versatile optical technique for critical dimensions (CD) and shape metrology, can find the direct measurement of pitch walk challenging because it is a very weak parameter. In this work, the pitch walk measurement is managed via scatterometry using an advanced technique of parallel interpretation of scatterometry pads with varying pitches. The three populations of trenches could be clearly distinguished with the scatterometry and the consistency with the reference data and with the process DOE are presented. In addition, the root cause of the within-wafer non-uniformity of fin CD is determined. The measurements were done on-site at IMEC as a part of the process development and control of the IMEC SAQP processes [1]. All in all, in this work it is demonstrated that scatterometry is capable of monitoring each process step of FEOL SAQP and it can measure three different space populations separately and extract pitch walk information at the final fin etch step.

  6. Toward automated chromatographic fingerprinting: A non-alignment approach to gas chromatography mass spectrometry data.

    PubMed

    Vestner, Jochen; de Revel, Gilles; Krieger-Weber, Sibylle; Rauhut, Doris; du Toit, Maret; de Villiers, André

    2016-03-10

    In contrast to targeted analysis of volatile compounds, non-targeted approaches take information of known and unknown compounds into account, are inherently more comprehensive and give a more holistic representation of the sample composition. Although several non-targeted approaches have been developed, there's still a demand for automated data processing tools, especially for complex multi-way data such as chromatographic data obtained from multichannel detectors. This work was therefore aimed at developing a data processing procedure for gas chromatography mass spectrometry (GC-MS) data obtained from non-targeted analysis of volatile compounds. The developed approach uses basic matrix manipulation of segmented GC-MS chromatograms and PARAFAC multi-way modelling. The approach takes retention time shifts and peak shape deformations between samples into account and can be done with the freely available N-way toolbox for MATLAB. A demonstration of the new fingerprinting approach is presented using an artificial GC-MS data set and an experimental full-scan GC-MS data set obtained for a set of experimental wines. PMID:26893085

  7. Radiolabeled heterobivalent peptidic ligands: an approach with high future potential for in vivo imaging and therapy of malignant diseases.

    PubMed

    Fischer, Gabriel; Schirrmacher, Ralf; Wängler, Björn; Wängler, Carmen

    2013-06-01

    Two-pronged synergism: We review the recently developed approach of using heterobivalent peptide ligands that interact concomitantly with different receptors on tumor cells. These ligands exhibit highly favorable tumor-targeting properties and pave the way for the development of drugs for specific, sensitive, and noninvasive tumor imaging and therapy. PMID:23564566

  8. Overcoming synthetic Abeta peptide aging: a new approach to an age-old problem.

    PubMed

    Manzoni, Claudia; Colombo, Laura; Messa, Massimo; Cagnotto, Alfredo; Cantù, Laura; Del Favero, Elena; Salmona, Mario

    2009-01-01

    Investigations of amyloidogenic diseases use synthetic peptides for cell-free and in vitro studies. However, amyloidogenic peptides often show intrinsic variability that markedly affects the reproducibility of experiments. Proof of physicochemical and biological variability with different batches of amyloidogenic peptides have been reported in literature. Here, we show that differences can be observed even within the same batch of Abeta1-42 peptide after storing lyophilised samples at -20 degrees C. This change (referred to as 'peptide aging') was reproduced with Abeta1-40 peptide samples by using a series of lyophilisation cycles, showing that lyophilisation, rather than preserving the physicochemical and biological features of Abeta peptides, introduces wide variability. To counteract synthetic peptide aging, we set up a procedure involving the sequential use of trifluoroacetic acid, formic acid and sodium hydroxide solutions that disaggregate preformed seeds and enriched Abeta peptide solutions into monomers and low-molecular-weight oligomers. This procedure enabled us to obtain reproducible physicochemical and biological features of Abeta peptides, irrespective of their age. PMID:20536398

  9. Structural re-alignment in an immunologic surface region of ricin A chain

    SciTech Connect

    Zemla, A T; Zhou, C E

    2007-07-24

    We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.

  10. A self-assembly pathway to aligned monodomain gels

    SciTech Connect

    Zhang, Shuming; Greenfield, Megan A.; Mata, Alvaro; Palmer, Liam C.; Bitton, Ronit; Mantei, Jason R.; Aparicio, Conrado; Olvera de la Cruz, Monica; Stupp, Samuel I.

    2010-09-27

    Aggregates of charged amphiphilic molecules have been found to access a structure at elevated temperature that templates alignment of supramolecular fibrils over macroscopic scales. The thermal pathway leads to a lamellar plaque structure with fibrous texture that breaks on cooling into large arrays of aligned nanoscale fibres and forms a strongly birefringent liquid. By manually dragging this liquid crystal from a pipette onto salty media, it is possible to extend this alignment over centimetres in noodle-shaped viscoelastic strings. Using this approach, the solution of supramolecular filaments can be mixed with cells at physiological temperatures to form monodomain gels of aligned cells and filaments. The nature of the self-assembly process and its biocompatibility would allow formation of cellular wires in situ that have any length and customized peptide compositions for use in biological applications.

  11. A self-assembly pathway to aligned monodomain gels

    SciTech Connect

    Zhang, Shuming; Greenfield, Megan A.; Mata, Alvaro; Palmer, Liam C.; Bitton, Ronit; Mantei, Jason R.; Aparicio, Conrado; Olvera de la Cruz, Monica; Stupp, Samuel I.

    2010-06-13

    Aggregates of charged amphiphilic molecules have been found to access a structure at elevated temperature that templates alignment of supramolecular fibrils over macroscopic scales. The thermal pathway leads to a lamellar plaque structure with fibrous texture that breaks on cooling into large arrays of aligned nanoscale fibres and forms a strongly birefringent liquid. By manually dragging this liquid crystal from a pipette onto salty media, it is possible to extend this alignment over centimetres in noodle-shaped viscoelastic strings. Using this approach, the solution of supramolecular filaments can be mixed with cells at physiological temperatures to form monodomain gels of aligned cells and filaments. The nature of the self-assembly process and its biocompatibility would allow formation of cellular wires in situ that have any length and customized peptide compositions for use in biological applications.

  12. Aligning physical elements with persons' attitude: an approach using Rasch measurement theory

    NASA Astrophysics Data System (ADS)

    Camargo, F. R.; Henson, B.

    2013-09-01

    Affective engineering uses mathematical models to convert the information obtained from persons' attitude to physical elements into an ergonomic design. However, applications in the domain have not in many cases met measurement assumptions. This paper proposes a novel approach based on Rasch measurement theory to overcome the problem. The research demonstrates that if data fit the model, further variables can be added to a scale. An empirical study was designed to determine the range of compliance where consumers could obtain an impression of a moisturizer cream when touching some product containers. Persons, variables and stimulus objects were parameterised independently on a linear continuum. The results showed that a calibrated scale preserves comparability although incorporating further variables.

  13. New Milk Protein-Derived Peptides with Potential Antimicrobial Activity: An Approach Based on Bioinformatic Studies

    PubMed Central

    Dziuba, Bartłomiej; Dziuba, Marta

    2014-01-01

    New peptides with potential antimicrobial activity, encrypted in milk protein sequences, were searched for with the use of bioinformatic tools. The major milk proteins were hydrolyzed in silico by 28 enzymes. The obtained peptides were characterized by the following parameters: molecular weight, isoelectric point, composition and number of amino acid residues, net charge at pH 7.0, aliphatic index, instability index, Boman index, and GRAVY index, and compared with those calculated for known 416 antimicrobial peptides including 59 antimicrobial peptides (AMPs) from milk proteins listed in the BIOPEP database. A simple analysis of physico-chemical properties and the values of biological activity indicators were insufficient to select potentially antimicrobial peptides released in silico from milk proteins by proteolytic enzymes. The final selection was made based on the results of multidimensional statistical analysis such as support vector machines (SVM), random forest (RF), artificial neural networks (ANN) and discriminant analysis (DA) available in the Collection of Anti-Microbial Peptides (CAMP database). Eleven new peptides with potential antimicrobial activity were selected from all peptides released during in silico proteolysis of milk proteins. PMID:25141106

  14. Graphene oxide-peptide nanoassembly as a general approach for monitoring the activity of histone deacetylases.

    PubMed

    Liang, Ping; Li, Qing; Wu, Zhan; Jiang, Jian-Hui; Yu, Ru-Qin

    2016-06-20

    A novel fluorescent sensor using graphene oxide (GO)-peptide nanoassembly is developed for histone deacetylases (HDACs) based on deacetylation mediated cleavage of substrate peptides, which provides a simple, cost-effective platform for monitoring the activity of HDACs. PMID:27194207

  15. On the co-alignment of solar telescopes. A new approach to solar pointing

    NASA Astrophysics Data System (ADS)

    Staiger, J.

    2013-06-01

    Helioseismological measurements require long observing times and thus may be adversely affected by lateral image drifts as caused by pointing instabilities. At the Vacuum Tower Telescope VTT, Tenerife we have recorded drift values of up to 5" per hour under unstable thermal conditions (dome opening, strong day-to-day thermal gradients). Typically drifts of 0.5" - 1.0" per hour may be encountered under more favorable conditions. Past experience has shown that most high-resolution solar telescopes may be affected by this problem to some degree. This inherent shortcoming of solar pointing is caused by the fact that the guiding loop can be closed only within the guiding beam but not within the telescope's main beam. We have developed a new approach to this problem. We correlate continuum brightness patterns observed from within the telescope main beam with patterns originating from a full disk telescope. We show that brightness patterns of sufficient size are unique with respect to solar location at any instant of time and may serve as a location identifier. We make use of the fact that averaged location information of solar structures is invariant with respect to telescope resolution. We have carried out tests at the VTT together with SDO. We have used SDO as a full disk reference. We were able to reduce lateral image drifts by an order of magnitude.

  16. Horizontal carbon nanotube alignment.

    PubMed

    Cole, Matthew T; Cientanni, Vito; Milne, William I

    2016-09-21

    The production of horizontally aligned carbon nanotubes offers a rapid means of realizing a myriad of self-assembled near-atom-scale technologies - from novel photonic crystals to nanoscale transistors. The ability to reproducibly align anisotropic nanostructures has huge technological value. Here we review the present state-of-the-art in horizontal carbon nanotube alignment. For both in and ex situ approaches, we quantitatively assess the reported linear packing densities alongside the degree of alignment possible for each of these core methodologies. PMID:27546174

  17. Carcinogenesis of renal cell carcinoma reflected in HLA ligands: A novel approach for synergistic peptide vaccination design.

    PubMed

    Klatt, Martin G; Kowalewski, Daniel J; Schuster, Heiko; Di Marco, Moreno; Hennenlotter, Jörg; Stenzl, Arnulf; Rammensee, Hans-Georg; Stevanović, Stefan

    2016-08-01

    Despite recent advances in immunotherapy of renal cell carcinoma (RCC), peptide vaccination strategies still lack an approach for personalized peptide vaccination that takes intra- and inter-tumoral heterogeneity and biological characteristics into account. In this study, we use an immunoprecipitation and mass spectrometry-based approach supplemented by network analysis of HLA ligands to target this goal. By analyzing HLA-presented peptides for HLA class I and II of 11 malignant and 6 non-malignant kidney tissue samples, more than 2,700 peptides and 1,600 corresponding source proteins were identified. A high overlap with HLA ligands derived from peripheral blood mononuclear cells (PBMCs) was detected most likely due to tumor-infiltrating inflammatory cells and therefore excluded from network analysis. Subsequent biological function analysis of HLA ligands by the GeneMANIA online platform showed enrichment for well established, but also novel, pathways and biological processes involved in carcinogenesis of RCC almost exclusively in malignant tissue samples. By exploring source proteins involved in these overrepresented pathways, we verified various known tumor-associated antigens (TAAs) for RCC (e.g., CA9, EGLN3, IGFBP3, MMP7, PAX2, VEGFA, or EGFR) but could also detect novel TAAs for RCC (e.g., PLOD2, LOX, ENPEP, or TGFBI). Some of these new TAAs had already been shown to elicit a T cell response in cancer patients. Thus, network analysis of HLA ligands provided a new platform for implementing personalized, multipeptide vaccines with potentially synergistic antitumor effects. PMID:27622074

  18. Identification of novel serum peptide biomarkers for high-altitude adaptation: a comparative approach.

    PubMed

    Yang, Juan; Li, Wenhua; Liu, Siyuan; Yuan, Dongya; Guo, Yijiao; Jia, Cheng; Song, Tusheng; Huang, Chen

    2016-01-01

    We aimed to identify serum biomarkers for screening individuals who could adapt to high-altitude hypoxia at sea level. HHA (high-altitude hypoxia acclimated; n = 48) and HHI (high-altitude hypoxia illness; n = 48) groups were distinguished at high altitude, routine blood tests were performed for both groups at high altitude and at sea level. Serum biomarkers were identified by comparing serum peptidome profiling between HHI and HHA groups collected at sea level. Routine blood tests revealed the concentration of hemoglobin and red blood cells were significantly higher in HHI than in HHA at high altitude. Serum peptidome profiling showed that ten significantly differentially expressed peaks between HHA and HHI at sea level. Three potential serum peptide peaks (m/z values: 1061.91, 1088.33, 4057.63) were further sequence identified as regions of the inter-α trypsin inhibitor heavy chain H4 fragment (ITIH4 347-356), regions of the inter-α trypsin inhibitor heavy chain H1 fragment (ITIH1 205-214), and isoform 1 of fibrinogen α chain precursor (FGA 588-624). Expression of their full proteins was also tested by ELISA in HHA and HHI samples collected at sea level. Our study provided a novel approach for identifying potential biomarkers for screening people at sea level who can adapt to high altitudes. PMID:27150491

  19. Identification of novel serum peptide biomarkers for high-altitude adaptation: a comparative approach

    NASA Astrophysics Data System (ADS)

    Yang, Juan; Li, Wenhua; Liu, Siyuan; Yuan, Dongya; Guo, Yijiao; Jia, Cheng; Song, Tusheng; Huang, Chen

    2016-05-01

    We aimed to identify serum biomarkers for screening individuals who could adapt to high-altitude hypoxia at sea level. HHA (high-altitude hypoxia acclimated; n = 48) and HHI (high-altitude hypoxia illness; n = 48) groups were distinguished at high altitude, routine blood tests were performed for both groups at high altitude and at sea level. Serum biomarkers were identified by comparing serum peptidome profiling between HHI and HHA groups collected at sea level. Routine blood tests revealed the concentration of hemoglobin and red blood cells were significantly higher in HHI than in HHA at high altitude. Serum peptidome profiling showed that ten significantly differentially expressed peaks between HHA and HHI at sea level. Three potential serum peptide peaks (m/z values: 1061.91, 1088.33, 4057.63) were further sequence identified as regions of the inter-α trypsin inhibitor heavy chain H4 fragment (ITIH4 347–356), regions of the inter-α trypsin inhibitor heavy chain H1 fragment (ITIH1 205–214), and isoform 1 of fibrinogen α chain precursor (FGA 588–624). Expression of their full proteins was also tested by ELISA in HHA and HHI samples collected at sea level. Our study provided a novel approach for identifying potential biomarkers for screening people at sea level who can adapt to high altitudes.

  20. Identification of novel serum peptide biomarkers for high-altitude adaptation: a comparative approach

    PubMed Central

    Yang, Juan; Li, Wenhua; Liu, Siyuan; Yuan, Dongya; Guo, Yijiao; Jia, Cheng; Song, Tusheng; Huang, Chen

    2016-01-01

    We aimed to identify serum biomarkers for screening individuals who could adapt to high-altitude hypoxia at sea level. HHA (high-altitude hypoxia acclimated; n = 48) and HHI (high-altitude hypoxia illness; n = 48) groups were distinguished at high altitude, routine blood tests were performed for both groups at high altitude and at sea level. Serum biomarkers were identified by comparing serum peptidome profiling between HHI and HHA groups collected at sea level. Routine blood tests revealed the concentration of hemoglobin and red blood cells were significantly higher in HHI than in HHA at high altitude. Serum peptidome profiling showed that ten significantly differentially expressed peaks between HHA and HHI at sea level. Three potential serum peptide peaks (m/z values: 1061.91, 1088.33, 4057.63) were further sequence identified as regions of the inter-α trypsin inhibitor heavy chain H4 fragment (ITIH4 347–356), regions of the inter-α trypsin inhibitor heavy chain H1 fragment (ITIH1 205–214), and isoform 1 of fibrinogen α chain precursor (FGA 588–624). Expression of their full proteins was also tested by ELISA in HHA and HHI samples collected at sea level. Our study provided a novel approach for identifying potential biomarkers for screening people at sea level who can adapt to high altitudes. PMID:27150491

  1. Cancer therapeutic approach based on conformational stabilization of mutant p53 protein by small peptides.

    PubMed

    Tal, Perry; Eizenberger, Shay; Cohen, Elad; Goldfinger, Naomi; Pietrokovski, Shmuel; Oren, Moshe; Rotter, Varda

    2016-03-15

    The p53 tumor suppressor serves as a major barrier against malignant transformation. Over 50% of tumors inactivate p53 by point mutations in its DNA binding domain. Most mutations destabilize p53 protein folding, causing its partial denaturation at physiological temperature. Thus a high proportion of human tumors overexpress a potential potent tumor suppressor in a non-functional, misfolded form. The equilibrium between the properly folded and misfolded states of p53 may be affected by molecules that interact with p53, stabilizing its native folding and restoring wild type p53 activity to cancer cells. To select for mutant p53 (mutp53) reactivating peptides, we adopted the phage display technology, allowing interactions between mutp53 and random peptide libraries presented on phages and enriching for phage that favor the correctly folded p53 conformation. We obtained a large database of potential reactivating peptides. Lead peptides were synthesized and analyzed for their ability to restore proper p53 folding and activity. Remarkably, many enriched peptides corresponded to known p53-binding proteins, including RAD9. Importantly, lead peptides elicited dramatic regression of aggressive tumors in mouse xenograft models. Such peptides might serve as novel agents for human cancer therapy. PMID:26943582

  2. Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach.

    PubMed

    Sheikholeslami, Somayyeh; Pandey, R B; Dragneva, Nadiya; Floriano, Wely; Rubel, Oleg; Barr, Stephen A; Kuang, Zhifeng; Berry, Rajiv; Naik, Rajesh; Farmer, Barry

    2014-05-28

    Binding of a solvated peptide A1 ((1)E (2)P (3)L (4)Q (5)L (6)K (7)M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of temperature (T). Quantitative differences (e.g., the extent of binding within a temperature range) and qualitative similarities are observed in results from three simulated potentials. Differences in variations of both local and global physical quantities suggest a need for such analysis with multiple inputs in assessing the reliability of both quantitative and qualitative observations. While all three potentials indicate binding at low T and unbinding at high T, the extent of binding of peptide with the temperature differs. Unlike un-solvated peptides (with little variation in binding among residues), solvation accentuates the differences in residue binding. As a result the binding of solvated peptide at low temperatures is found to be anchored by three residues, (1)E, (4)Q, and (6)K (different from that with the un-solvated peptide). Binding to unbinding transition can be described by the variation of the transverse (with respect to graphene sheet) component of the radius of gyration of the peptide (a potential order parameter) as a function of temperature. PMID:24880319

  3. Cancer therapeutic approach based on conformational stabilization of mutant p53 protein by small peptides

    PubMed Central

    Tal, Perry; Eizenberger, Shay; Cohen, Elad; Goldfinger, Naomi; Pietrokovski, Shmuel; Oren, Moshe; Rotter, Varda

    2016-01-01

    The p53 tumor suppressor serves as a major barrier against malignant transformation. Over 50% of tumors inactivate p53 by point mutations in its DNA binding domain. Most mutations destabilize p53 protein folding, causing its partial denaturation at physiological temperature. Thus a high proportion of human tumors overexpress a potential potent tumor suppressor in a non-functional, misfolded form. The equilibrium between the properly folded and misfolded states of p53 may be affected by molecules that interact with p53, stabilizing its native folding and restoring wild type p53 activity to cancer cells. To select for mutant p53 (mutp53) reactivating peptides, we adopted the phage display technology, allowing interactions between mutp53 and random peptide libraries presented on phages and enriching for phage that favor the correctly folded p53 conformation. We obtained a large database of potential reactivating peptides. Lead peptides were synthesized and analyzed for their ability to restore proper p53 folding and activity. Remarkably, many enriched peptides corresponded to known p53-binding proteins, including RAD9. Importantly, lead peptides elicited dramatic regression of aggressive tumors in mouse xenograft models. Such peptides might serve as novel agents for human cancer therapy. PMID:26943582

  4. Conformational flexibility in designing peptides for immunology: the molecular dynamics approach.

    PubMed

    Stavrakoudis, Athanassios

    2010-09-01

    Computational modeling techniques and computer simulations have become a routine in biological sciences and have gained great attention from researchers. Molecular dynamics simulation is a valuable tool towards an understanding of the complex structure of biological systems, especially in the study of the flexibility of the biological molecules such as peptides or proteins. Peptides play a very important role in human physiology and control many of the processes involved in the immune system response. Designing new and optimal peptide vaccines is one of the hottest challenges of the 21(st) century science and it brings together researchers from different fields. Molecular dynamics simulations have proven to be a helpful tool assisting laboratory work, saving financial sources and opening possibilities for exploring properties of the molecular systems that are hardly accessible by conventional experimental methods. Present review is dedicated to the recent contributions in applications of molecular dynamics simulations in peptide design for immunological purposes, such as B or T cell epitopes. PMID:20412039

  5. A Postgenomic Approach to Identification of Mycobacterium leprae-Specific Peptides as T-Cell Reagents

    PubMed Central

    Dockrell, Hazel M.; Brahmbhatt, Shweta; Robertson, Brian D.; Britton, Sven; Fruth, Uli; Gebre, Negussie; Hunegnaw, Mesfin; Hussain, Rabia; Manandhar, Rakesh; Murillo, Luis; Pessolani, Maria Cristina V.; Roche, Paul; Salgado, Jorge L.; Sampaio, Elizabeth; Shahid, Firdaus; Thole, Jelle E. R.; Young, Douglas B.

    2000-01-01

    To identify Mycobacterium leprae-specific human T-cell epitopes, which could be used to distinguish exposure to M. leprae from exposure to Mycobacterium tuberculosis or to environmental mycobacteria or from immune responses following Mycobacterium bovis BCG vaccination, 15-mer synthetic peptides were synthesized based on data from the M. leprae genome, each peptide containing three or more predicted HLA-DR binding motifs. Eighty-one peptides from 33 genes were tested for their ability to induce T-cell responses, using peripheral blood mononuclear cells (PBMC) from tuberculoid leprosy patients (n = 59) and healthy leprosy contacts (n = 53) from Brazil, Ethiopia, Nepal, and Pakistan and 20 United Kingdom blood bank donors. Gamma interferon (IFN-γ) secretion proved more sensitive for detection of PBMC responses to peptides than did lymphocyte proliferation. Many of the peptides giving the strongest responses in leprosy donors compared to subjects from the United Kingdom, where leprosy is not endemic, have identical, or almost identical, sequences in M. leprae and M. tuberculosis and would not be suitable as diagnostic tools. Most of the peptides recognized by United Kingdom donors showed promiscuous recognition by subjects expressing differing HLA-DR types. The majority of the novel T-cell epitopes identified came from proteins not previously recognized as immune targets, many of which are cytosolic enzymes. Fifteen of the tested peptides had ≥5 of 15 amino acid mismatches between the equivalent M. leprae and M. tuberculosis sequences; of these, eight gave specificities of ≥90% (percentage of United Kingdom donors who were nonresponders for IFN-γ secretion), with sensitivities (percentage of responders) ranging from 19 to 47% for tuberculoid leprosy patients and 21 to 64% for healthy leprosy contacts. A pool of such peptides, formulated as a skin test reagent, could be used to monitor exposure to leprosy or as an aid to early diagnosis. PMID:10992494

  6. Peptidyl Molecular Imaging Contrast Agents Using a New Solid Phase Peptide Synthesis Approach

    PubMed Central

    Yoo, Byunghee; Pagel, Mark D.

    2008-01-01

    A versatile method is disclosed for solid phase peptide synthesis (SPPS) of molecular imaging contrast agents. A DO3A moiety was derivatized to introduce a CBZ-protected amino group and then coupled to a polymeric support. CBZ cleavage with Et2AlCl/thioanisole was optimized for SPPS. Amino acids were then coupled to the aminoDOTA loaded resin using conventional step-wise Fmoc SPPS to create a product with DOTA coupled to the C-terminus of the peptide. In a second study, the DO3A moiety was coupled to a glycine-loaded polymeric support, and amino acids were then coupled to the amino-DOTA-peptide loaded resin using SPPS, to incorporate DOTA within the peptide sequence. The peptide-(Tm3+-DOTA) amide showed a PARAmagnetic Chemical Exchange Saturation Transfer (PARACEST) effect, which demonstrated the utility of this contrast agent for molecular imaging. These results demonstrate the advantages of exploiting SPPS methodologies through the development of unique DOTA derivatives to create peptide-based molecular imaging contrast agents. PMID:17330953

  7. dPABBs: A Novel in silico Approach for Predicting and Designing Anti-biofilm Peptides

    PubMed Central

    Sharma, Arun; Gupta, Pooja; Kumar, Rakesh; Bhardwaj, Anshu

    2016-01-01

    Increasingly, biofilms are being recognised for their causative role in persistent infections (like cystic fibrosis, otitis media, diabetic foot ulcers) and nosocomial diseases (biofilm-infected vascular catheters, implants and prosthetics). Given the clinical relevance of biofilms and their recalcitrance to conventional antibiotics, it is imperative that alternative therapeutics are proactively sought. We have developed dPABBs, a web server that facilitates the prediction and design of anti-biofilm peptides. The six SVM and Weka models implemented on dPABBs were observed to identify anti-biofilm peptides on the basis of their whole amino acid composition, selected residue features and the positional preference of the residues (maximum accuracy, sensitivity, specificity and MCC of 95.24%, 92.50%, 97.73% and 0.91, respectively, on the training datasets). On the N-terminus, it was seen that either of the cationic polar residues, R and K, is present at all five positions in case of the anti-biofilm peptides, whereas in the QS peptides, the uncharged polar residue S is preponderant at the first (also anionic polar residues D, E), third and fifth positions. Positive predictions were also obtained for 29 FDA-approved peptide drugs and ten antimicrobial peptides in clinical development, indicating at their possible repurposing for anti-biofilm therapy. dPABBs is freely accessible on: http://ab-openlab.csir.res.in/abp/antibiofilm/. PMID:26912180

  8. dPABBs: A Novel in silico Approach for Predicting and Designing Anti-biofilm Peptides.

    PubMed

    Sharma, Arun; Gupta, Pooja; Kumar, Rakesh; Bhardwaj, Anshu

    2016-01-01

    Increasingly, biofilms are being recognised for their causative role in persistent infections (like cystic fibrosis, otitis media, diabetic foot ulcers) and nosocomial diseases (biofilm-infected vascular catheters, implants and prosthetics). Given the clinical relevance of biofilms and their recalcitrance to conventional antibiotics, it is imperative that alternative therapeutics are proactively sought. We have developed dPABBs, a web server that facilitates the prediction and design of anti-biofilm peptides. The six SVM and Weka models implemented on dPABBs were observed to identify anti-biofilm peptides on the basis of their whole amino acid composition, selected residue features and the positional preference of the residues (maximum accuracy, sensitivity, specificity and MCC of 95.24%, 92.50%, 97.73% and 0.91, respectively, on the training datasets). On the N-terminus, it was seen that either of the cationic polar residues, R and K, is present at all five positions in case of the anti-biofilm peptides, whereas in the QS peptides, the uncharged polar residue S is preponderant at the first (also anionic polar residues D, E), third and fifth positions. Positive predictions were also obtained for 29 FDA-approved peptide drugs and ten antimicrobial peptides in clinical development, indicating at their possible repurposing for anti-biofilm therapy. dPABBs is freely accessible on: http://ab-openlab.csir.res.in/abp/antibiofilm/. PMID:26912180

  9. Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach

    PubMed Central

    Oany, Arafat Rahman; Emran, Abdullah-Al; Jyoti, Tahmina Pervin

    2014-01-01

    Human coronavirus (HCoV), a member of Coronaviridae family, is the causative agent of upper respiratory tract infections and “atypical pneumonia”. Despite severe epidemic outbreaks on several occasions and lack of antiviral drug, not much progress has been made with regard to an epitope-based vaccine designed for HCoV. In this study, a computational approach was adopted to identify a multiepitope vaccine candidate against this virus that could be suitable to trigger a significant immune response. Sequences of the spike proteins were collected from a protein database and analyzed with an in silico tool, to identify the most immunogenic protein. Both T cell immunity and B cell immunity were checked for the peptides to ensure that they had the capacity to induce both humoral and cell-mediated immunity. The peptide sequence from 88–94 amino acids and the sequence KSSTGFVYF were found as the most potential B cell and T cell epitopes, respectively. Furthermore, conservancy analysis was also done using in silico tools and showed a conservancy of 64.29% for all epitopes. The peptide sequence could interact with as many as 16 human leukocyte antigens (HLAs) and showed high cumulative population coverage, ranging from 75.68% to 90.73%. The epitope was further tested for binding against the HLA molecules, using in silico docking techniques, to verify the binding cleft epitope interaction. The allergenicity of the epitopes was also evaluated. This computational study of design of an epitope-based peptide vaccine against HCoVs allows us to determine novel peptide antigen targets in spike proteins on intuitive grounds, albeit the preliminary results thereof require validation by in vitro and in vivo experiments. PMID:25187696

  10. Binding of a C-end rule peptide to neuropilin-1 receptor: A molecular modeling approach

    PubMed Central

    Haspel, Nurit; Zanuy, David; Nussinov, Ruth; Teesalu, Tambet; Ruoslahti, Erkki; Aleman, Carlos

    2011-01-01

    Neuropilin-1 (NRP-1) is a receptor that plays an essential role in angiogenesis, vascular permeability and nervous system development. Previous studies have shown that peptides with an N-terminal Arg, especially peptides with the four residue consensus sequence R/K/XXR/K bind to NRP-1 cell surfaces. Peptides containing such consensus sequences promote binding and internalization into cells, while blocking the C-terminal Arg (or Lys) prevents the internalization. In this study we use molecular dynamics simulations to model the structural properties of the NRP-1 complex with a prototypic CendR peptide, RPAR. Our simulations show that RPAR binds NRP-1 through specific interactions of the RPAR C-terminus: three hydrogen bonds and a salt bridge anchor the ligand in the receptor pocket. The modeling results were used as the starting point for a systematic computational study of new RPAR analogs based on chemical modifications of its natural amino acids. Comparison of the structural properties of the new peptide - receptor complexes with the original organization suggest that some of the analogs can increase the binding affinity while reducing the natural sensitivity of RXXR to endogenous proteases. PMID:21247217

  11. Combined Bioinformatic and Rational Design Approach To Develop Antimicrobial Peptides against Mycobacterium tuberculosis.

    PubMed

    Pearson, C Seth; Kloos, Zachary; Murray, Brian; Tabe, Ebot; Gupta, Monica; Kwak, Jun Ha; Karande, Pankaj; McDonough, Kathleen A; Belfort, Georges

    2016-05-01

    Drug-resistant pathogens are a growing problem, and novel strategies are needed to combat this threat. Among the most significant of these resistant pathogens is Mycobacterium tuberculosis, which is an unusually difficult microbial target due to its complex membrane. Here, we design peptides for specific activity against M. tuberculosis using a combination of "database filtering" bioinformatics, protein engineering, and de novo design. Several variants of these peptides are structurally characterized to validate the design process. The designed peptides exhibit potent activity (MIC values as low as 4 μM) against M. tuberculosis and also exhibit broad activity against a host of other clinically relevant pathogenic bacteria such as Gram-positive bacteria (Streptococcus) and Gram-negative bacteria (Escherichia coli). They also display excellent selectivity, with low cytotoxicity against cultured macrophages and lung epithelial cells. These first-generation antimicrobial peptides serve as a platform for the design of antibiotics and for investigating structure-activity relationships in the context of the M. tuberculosis membrane. The antimicrobial peptide design strategy is expected to be generalizable for any pathogen for which an activity database can be created. PMID:26902758

  12. Generation of Small 32P-Labeled Peptides as a Potential Approach to Colorectal Cancer Therapy

    PubMed Central

    Abraham, John M.; Cheng, Yulan; Hamilton, James P.; Paun, Bogdan; Jin, Zhe; Agarwal, Rachana; Kan, Takatsugu; David, Stefan; Olaru, Alexandru; Yang, Jian; Ito, Tetsuo; Selaru, Florin M.; Mori, Yuriko; Meltzer, Stephen J.

    2008-01-01

    Cancers have been revealed to be extremely heterogenous in terms of the frequency and types of mutations present in cells from different malignant tumors. Thus, it is likely that uniform clinical treatment is not optimal for all patients, and that the development of individualized therapeutic regimens may be beneficial. We describe the generation of multiple, unique small peptides nine to thirty-four amino acids in length which, when labeled with the radioisotope 32P, bind with vastly differing efficiencies to cell lines derived from different colon adenocarcinomas. In addition, the most effective of these peptides permanently transfers the 32P radioisotope to colorectal cancer cellular proteins within two hours at a rate that is more than 150 times higher than in cell lines derived from other cancers or from the normal tissues tested. Currently, the only two FDA-approved radioimmunotherapeutic agents in use both employ antibodies directed against the B cell marker CD20 for the treatment of non-Hodgkin's lymphoma. By using the method described herein, large numbers of different 32P-labeled peptides can be readily produced and assayed against a broad spectrum of cancer types. This report proposes the development and use of 32P-labeled peptides as potential individualized peptide-binding therapies for the treatment of colon adenocarcinoma patients. PMID:18575578

  13. Continuum Approaches to Understanding Ion and Peptide Interactions with the Membrane

    PubMed Central

    Latorraca, Naomi R.; Callenberg, Keith M.; Boyle, Jon P.; Grabe, Michael

    2014-01-01

    Experimental and computational studies have shown that cellular membranes deform to stabilize the inclusion of transmembrane (TM) proteins harboring charge. Recent analysis suggests that membrane bending helps to expose charged and polar residues to the aqueous environment and polar head groups. We previously used elasticity theory to identify membrane distortions that minimize the insertion of charged TM peptides into the membrane. Here, we extend our work by showing that it also provides a novel, computationally efficient method for exploring the energetics of ion and small peptide penetration into membranes. First, we show that the continuum method accurately reproduces energy profiles and membrane shapes generated from molecular simulations of bare ion permeation at a fraction of the computational cost. Next, we demonstrate that the dependence of the ion insertion energy on the membrane thickness arises primarily from the elastic properties of the membrane. Moreover, the continuum model readily provides a free energy decomposition into components not easily determined from molecular dynamics. Finally, we show that the energetics of membrane deformation strongly depend on membrane patch size both for ions and peptides. This dependence is particularly strong for peptides based on simulations of a known amphipathic, membrane binding peptide from the human pathogen Toxoplasma gondii. In total, we address shortcomings and advantages that arise from using a variety of computational methods in distinct biological contexts. PMID:24652510

  14. A continuous peptide epitope reacting with pandemic influenza AH1N1 predicted by bioinformatic approaches.

    PubMed

    Carrillo-Vazquez, Jonathan P; Correa-Basurto, José; García-Machorro, Jazmin; Campos-Rodríguez, Rafael; Moreau, Violaine; Rosas-Trigueros, Jorge L; Reyes-López, Cesar A; Rojas-López, Marlon; Zamorano-Carrillo, Absalom

    2015-09-01

    Computational identification of potential epitopes with an immunogenic capacity challenges immunological research. Several methods show considerable success, and together with experimental studies, the efficiency of the algorithms to identify potential peptides with biological activity has improved. Herein, an epitope was designed by combining bioinformatics, docking, and molecular dynamics simulations. The hemagglutinin protein of the H1N1 influenza pandemic strain served as a template, owing to the interest of obtaining a scheme of immunization. Afterward, we performed enzyme-linked immunosorbent assay (ELISA) using the epitope to analyze if any antibodies in human sera before and after the influenza outbreak in 2009 recognize this peptide. Also, a plaque reduction neutralization test induced by virus-neutralizing antibodies and the IgG determination showed the biological activity of this computationally designed peptide. The results of the ELISAs demonstrated that the serum of both prepandemic and pandemic recognized the epitope. Moreover, the plaque reduction neutralization test evidenced the capacity of the designed peptide to neutralize influenza virus in Madin-Darby canine cells. PMID:25788327

  15. A Discovery-Oriented Approach to Solid-Phase Peptide Synthesis

    ERIC Educational Resources Information Center

    Bockman, Matthew R.; Miedema, Christopher J.; Brennan, Brian B.

    2012-01-01

    In this discovery-oriented laboratory experiment, students use solid-phase synthesis techniques to construct a dipeptide containing an unknown amino acid. Following synthesis and cleavage from the polymeric support, electrospray ionization-mass spectrometry is employed to identify the unknown amino acid that was used in the peptide coupling. This…

  16. MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines

    PubMed Central

    Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I.; Marcotte, Edward M.

    2011-01-01

    Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for all possible PSMs and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for all detected proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses. PMID:21488652

  17. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

    PubMed

    Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I; Marcotte, Edward M

    2011-07-01

    Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for every possible PSM and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for most proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses. PMID:21488652

  18. The rational search for selective anticancer derivatives of the peptide Trichogin GA IV: a multi-technique biophysical approach.

    PubMed

    Dalzini, Annalisa; Bergamini, Christian; Biondi, Barbara; De Zotti, Marta; Panighel, Giacomo; Fato, Romana; Peggion, Cristina; Bortolus, Marco; Maniero, Anna Lisa

    2016-01-01

    Peptaibols are peculiar peptides produced by fungi as weapons against other microorganisms. Previous studies showed that peptaibols are promising peptide-based drugs because they act against cell membranes rather than a specific target, thus lowering the possibility of the onset of multi-drug resistance, and they possess non-coded α-amino acid residues that confer proteolytic resistance. Trichogin GA IV (TG) is a short peptaibol displaying antimicrobial and cytotoxic activity. In the present work, we studied thirteen TG analogues, adopting a multidisciplinary approach. We showed that the cytotoxicity is tuneable by single amino-acids substitutions. Many analogues maintain the same level of non-selective cytotoxicity of TG and three analogues are completely non-toxic. Two promising lead compounds, characterized by the introduction of a positively charged unnatural amino-acid in the hydrophobic face of the helix, selectively kill T67 cancer cells without affecting healthy cells. To explain the determinants of the cytotoxicity, we investigated the structural parameters of the peptides, their cell-binding properties, cell localization, and dynamics in the membrane, as well as the cell membrane composition. We show that, while cytotoxicity is governed by the fine balance between the amphipathicity and hydrophobicity, the selectivity depends also on the expression of negatively charged phospholipids on the cell surface. PMID:27039838

  19. The rational search for selective anticancer derivatives of the peptide Trichogin GA IV: a multi-technique biophysical approach

    PubMed Central

    Dalzini, Annalisa; Bergamini, Christian; Biondi, Barbara; De Zotti, Marta; Panighel, Giacomo; Fato, Romana; Peggion, Cristina; Bortolus, Marco; Maniero, Anna Lisa

    2016-01-01

    Peptaibols are peculiar peptides produced by fungi as weapons against other microorganisms. Previous studies showed that peptaibols are promising peptide-based drugs because they act against cell membranes rather than a specific target, thus lowering the possibility of the onset of multi-drug resistance, and they possess non-coded α-amino acid residues that confer proteolytic resistance. Trichogin GA IV (TG) is a short peptaibol displaying antimicrobial and cytotoxic activity. In the present work, we studied thirteen TG analogues, adopting a multidisciplinary approach. We showed that the cytotoxicity is tuneable by single amino-acids substitutions. Many analogues maintain the same level of non-selective cytotoxicity of TG and three analogues are completely non-toxic. Two promising lead compounds, characterized by the introduction of a positively charged unnatural amino-acid in the hydrophobic face of the helix, selectively kill T67 cancer cells without affecting healthy cells. To explain the determinants of the cytotoxicity, we investigated the structural parameters of the peptides, their cell-binding properties, cell localization, and dynamics in the membrane, as well as the cell membrane composition. We show that, while cytotoxicity is governed by the fine balance between the amphipathicity and hydrophobicity, the selectivity depends also on the expression of negatively charged phospholipids on the cell surface. PMID:27039838

  20. Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy.

    PubMed

    Berlin, C; Kowalewski, D J; Schuster, H; Mirza, N; Walz, S; Handel, M; Schmid-Horch, B; Salih, H R; Kanz, L; Rammensee, H-G; Stevanović, S; Stickel, J S

    2015-03-01

    Identification of physiologically relevant peptide vaccine targets calls for the direct analysis of the entirety of naturally presented human leukocyte antigen (HLA) ligands, termed the HLA ligandome. In this study, we implemented this direct approach using immunoprecipitation and mass spectrometry to define acute myeloid leukemia (AML)-associated peptide vaccine targets. Mapping the HLA class I ligandomes of 15 AML patients and 35 healthy controls, more than 25 000 different naturally presented HLA ligands were identified. Target prioritization based on AML exclusivity and high presentation frequency in the AML cohort identified a panel of 132 LiTAAs (ligandome-derived tumor-associated antigens), and 341 corresponding HLA ligands (LiTAPs (ligandome-derived tumor-associated peptides)) represented subset independently in >20% of AML patients. Functional characterization of LiTAPs by interferon-γ ELISPOT (Enzyme-Linked ImmunoSpot) and intracellular cytokine staining confirmed AML-specific CD8(+) T-cell recognition. Of note, our platform identified HLA ligands representing several established AML-associated antigens (e.g. NPM1, MAGED1, PRTN3, MPO, WT1), but found 80% of them to be also represented in healthy control samples. Mapping of HLA class II ligandomes provided additional CD4(+) T-cell epitopes and potentially synergistic embedded HLA ligands, allowing for complementation of a multipeptide vaccine for the immunotherapy of AML. PMID:25092142

  1. A Cell-Based Approach for the Biosynthesis/Screening of Cyclic Peptide Libraries against Bacterial Toxins

    SciTech Connect

    Camarero, J A; Kimura, R; Woo, Y; Cantor, J; Steenblock, E

    2007-10-24

    Available methods for developing and screening small drug-like molecules able to knockout toxins or pathogenic microorganisms have some limitations. In order to be useful, these new methods must provide high-throughput analysis and identify specific binders in a short period of time. To meet this need, we are developing an approach that uses living cells to generate libraries of small biomolecules, which are then screened inside the cell for activity. Our group is using this new, combined approach to find highly specific ligands capable of disabling anthrax Lethal Factor (LF) as proof of principle. Key to our approach is the development of a method for the biosynthesis of libraries of cyclic peptides, and an efficient screening process that can be carried out inside the cell.

  2. Alignment validation

    SciTech Connect

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under constructionat CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector andthe muon system requires an accurate alignment of all detector elements. Alignmentinformation is deduced from dedicated hardware alignment systems and the reconstruction of charged particles. However, the system is degenerate which means the data is insufficient to constrain all alignment degrees of freedom, so the techniques are prone to converging on wrong geometries. This deficiency necessitates validation and monitoring of the alignment. An exhaustive discussion of means to validate is subject to this document, including examples and plans from all four LHC experiments, as well as other high energy experiments.

  3. Computational approaches for designing potent and selective analogs of peptide toxins as novel therapeutics

    PubMed Central

    Kuyucak, Serdar; Norton, Raymond S

    2015-01-01

    Peptide toxins provide valuable therapeutic leads for many diseases. As they bind to their targets with high affinity, potency is usually ensured. However, toxins also bind to off-target receptors, causing potential side effects. Thus, a major challenge in generating drugs from peptide toxins is ensuring their specificity for their intended targets. Computational methods can play an important role in solving such design problems through construction of accurate models of receptor–toxin complexes and calculation of binding free energies. Here we review the computational methods used for this purpose and their application to toxins targeting ion channels. We describe ShK and HsTX1 toxins, high-affinity blockers of the voltage-gated potassium channel Kv1.3, which could be developed as therapeutic agents for autoimmune diseases. PMID:25406005

  4. Peptides and proteins used to enhance gold nanoparticle delivery to the brain: preclinical approaches

    PubMed Central

    Velasco-Aguirre, Carolina; Morales, Francisco; Gallardo-Toledo, Eduardo; Guerrero, Simon; Giralt, Ernest; Araya, Eyleen; Kogan, Marcelo J

    2015-01-01

    An exciting and emerging field in nanomedicine involves the use of gold nanoparticles (AuNPs) in the preclinical development of new strategies for the treatment and diagnosis of brain-related diseases such as neurodegeneration and cerebral tumors. The treatment of many brain-related disorders with AuNPs, which possess useful physical properties, is limited by the blood–brain barrier (BBB). The BBB highly regulates the substances that can permeate into the brain. Peptides and proteins may represent promising tools to improve the delivery of AuNPs to the central nervous system (CNS). In this review, we summarize the potential applications of AuNPs to CNS disorders, discuss different strategies based on the use of peptides or proteins to improve the delivery of AuNPs to the brain, and examine the intranasal administration route, which bypasses the BBB. We also analyze the potential neurotoxicity of AuNPs and the perspectives and new challenges concerning the use of peptides and proteins to enhance the delivery of AuNPs to the brain. The majority of the work described in this review is in a preclinical stage of experimentation, or in select cases, in clinical trials in humans. We note that the use of AuNPs still requires substantial study before being translated into human applications. However, for further clinical research, the issues related to the potential use of AuNPs must be analyzed. PMID:26300639

  5. Aligned Nanofibers for Regenerating Arteries, Nerves, and Muscles

    NASA Astrophysics Data System (ADS)

    McClendon, Mark Trosper

    annular gap containing PA solution with a rotating rod. Using the shear aligning properties of PA solutions this rotating surface in contact with the PA solution induced a high degree of alignment in the nanofibers which was subsequently locked in place by introducing gelating calcium ions. again say something about what this fabrication procedure entails Cells encapsulated within these tubes responded to the alignment by extending in the circumferential direction mimicking the same cellular alignment observed in native arteries. A similar design strategy was also used to align nanofibers within the core of biopolymer nerve conduits, and these scaffolds were implanted in a rat sciatic nerve model. Histological and behavioral observations confirmed that PA implants sustained regeneration rates comparable to autologous grafts and significantly better than empty biopolymer grafts. Furthermore, these nanofiber gels were used as a vehicle to deliver stem cells into muscle tissue. A specialized injector was designed to introduce aligned PA gels into mouse leg muscles in a 1cm long channel. Bioluminescence and histology showed that stem cell engraftment into myofibers was greatly enhanced when delivered by PA gels compared to saline solution. The final section of this thesis describes a new series of PA molecules designed to degrade upon exposure to UV lightstate here why is this of interest in the context of the work described in the thesis. This was done to understand the degradation behavior of PA nanofibers and provide a controlled approach to changing the rheological properties post gelation.The three PA molecules in this series contained the same peptide sequence V3A3E3, while varying the location of a nitrobenzyl UV-reactive group along the backbone of the molecule. This system allowed for a quick reaction that cleaves the molecule at the reactive nitrobenzyl site without introducing any other reactive molecules. While all three molecules produced nanofibers that remained

  6. Segmentation of precursor mass range using "tiling" approach increases peptide identifications for MS1-based label-free quantification.

    PubMed

    Vincent, Catherine E; Potts, Gregory K; Ulbrich, Arne; Westphall, Michael S; Atwood, James A; Coon, Joshua J; Weatherly, D Brent

    2013-03-01

    Label-free quantification is a powerful tool for the measurement of protein abundances by mass spectrometric methods. To maximize quantifiable identifications, MS(1)-based methods must balance the collection of survey scans and fragmentation spectra while maintaining reproducible extracted ion chromatograms (XIC). Here we present a method which increases the depth of proteome coverage over replicate data-dependent experiments without the requirement of additional instrument time or sample prefractionation. Sampling depth is increased by restricting precursor selection to a fraction of the full MS(1) mass range for each replicate; collectively, the m/z segments of all replicates encompass the full MS(1) range. Although selection windows are narrowed, full MS(1) spectra are obtained throughout the method, enabling the collection of full mass range MS(1) chromatograms such that label-free quantitation can be performed for any peptide in any experiment. We term this approach "binning" or "tiling" depending on the type of m/z window utilized. By combining the data obtained from each segment, we find that this approach increases the number of quantifiable yeast peptides and proteins by 31% and 52%, respectively, when compared to normal data-dependent experiments performed in replicate. PMID:23350991

  7. A Novel Peptide Thrombopoietin Mimetic Designing and Optimization Using Computational Approach

    PubMed Central

    Singh, Vimal Kishor; Kumar, Neeraj; Kalsan, Manisha; Saini, Abhishek; Chandra, Ramesh

    2016-01-01

    Thrombopoietin receptor (TPOR) is a cytokine receptor protein present on the cell surface. The activation of TPOR by thrombopoietin (TPO) (a glycoprotein hormone) triggers an intracellular cascade of megakaryocytopoiesis for the formation of platelets. Recent studies on ex vivo megakaryocytopoiesis have evolved the possibilities of therapeutics uses. These findings have paved the way for the development of various TPO alternatives (recombinant TPO, peptide, and non-peptide TPO mimetics), which are useful in regenerative medicine. However, these alternatives possess various limitations such as induction of autoimmune effects, high production cost, low specificity, and hence activity. In the present study, a novel peptidic TPO mimetic was designed through computational studies by studying the binding sites of TPO and TMP to TPOR and analogs of known mimetics. Screening of combinatorial library was done through molecular docking using ClusPro. These studies indicated mimetic-9 as a significant molecule since it was found to have better binding score of −938.8 kcal/mol with seven hydrogen bonds and a high number of hydrophobic interactions, than known mimetic TMP with docking score of −798.4 kcal/mol and TMP dimer with docking score of −811.9 kcal/mol for TPOR. Mimetic9-TPOR complex was further assessed by the molecular dynamics simulation, and their complex was found to be stable with an RMSD value of 0.091 Å. While studying the parameters, mimetic-9 was found to have overall good physiochemical properties with positive grand average hydropathy (GRAVY) score and high instability index score and was found to be localized in the extracellular region. The designed mimetic-9 might prove to be a useful lead molecule for mimicking the role of TPO for in vitro platelet production with higher efficiency.

  8. Atrial natriuretic peptide and circadian blood pressure regulation: clues from a chronobiological approach.

    PubMed

    Portaluppi, F; Vergnani, L; degli Uberti, E C

    1993-06-01

    A critical review of the data available in the literature today permits a better understanding of the multiple actions of atrial natriuretic peptide (ANP) on the cardiovascular system. Moreover, the results of chronobiological studies suggest a role for this peptide in the determination of the circadian rhythm of blood pressure (BP). ANP can affect BP by several mechanisms, including modification of renal function and vascular tone, counteraction of the renin-angiotensin-aldosterone system, and action on brain regulatory sites. A series of interrelated events may follow from very small changes in the plasma levels of ANP. The endpoints are blood volume and BP reduction, but they are rapidly offset (mainly by reactive sympathetic activation) as soon as blood volume or pressure is threatened. The circadian rhythms of BP and ANP are antiphasic under normal conditions and in essential hypertension. The loss in the nocturnal decrease of BP is accompanied by a comparable loss in the nocturnal surge of ANP in hypertensive renal failure and hypotensive heart failure. In the latter condition, BP and ANP variabilities correlate significantly both before and after therapy-induced functional recovery, independently of the mean BP levels. Autonomic function modulates the secretion of ANP, which seems more apt to determine only transient changes in BP levels, as suggested by the short half-life of the peptide and the buffering role of its clearance receptors. There is now sufficient evidence that ANP contributes to short-term control over BP and electrolyte balance, in contrast and in opposition to the renin-angiotensin-aldosterone system, which is involved primarily in long-term BP control. By interfering with other well-established neurohormonal factors, ANP appears to be an additional modulator of the circadian rhythm of BP. PMID:8391398

  9. A novel multi-epitope peptide vaccine against cancer: an in silico approach.

    PubMed

    Nezafat, Navid; Ghasemi, Younes; Javadi, Gholamreza; Khoshnoud, Mohammad Javad; Omidinia, Eskandar

    2014-05-21

    Cancer immunotherapy has an outstanding position in cancer prevention and treatment. In this kind of therapy, the immune system is activated to eliminate cancerous cells. Multi-epitope peptide cancer vaccines are manifesting as the next generation of cancer immunotherapy. In the present study, we have implemented various strategies to design an efficient multi-epitope vaccine. CD8+ cytolytic T lymphocytes (CTLs) epitopes, which have a pivotal role in cellular immune responses, helper epitopes and adjuvant, are three crucial components of peptide vaccine. CTL epitopes were determined from two high immunogenic protein Wilms tumor-1 (WT1) and human papillomavirus (HPV) E7 by various servers, which apply different algorithms. CTL epitopes were linked together by AAY and HEYGAEALERAG motifs to enhance epitope presentation. Pan HLA DR-binding epitope (PADRE) peptide sequence and helper epitopes, which have defined from Tetanus toxin fragment C (TTFrC) by various servers, were used to induce CD4+ helper T lymphocytes (HTLs) responses. Additionally, helper epitopes were conjugated together via GPGPG motifs that stimulate HTL immunity. Heparin-Binding Hemagglutinin (HBHA), a novel TLR4 agonist was employed as an adjuvant to polarize CD4+ T cells toward T-helper 1 to induce strong CTL responses. Moreover, the EAAAK linker was introduced to N and C terminals of HBHA for efficient separation. 3D model of protein was generated and predicted B cell epitopes were determined from the surface of built structure. Our protein contains several linear and conformational B cell epitopes, which suggests the antibody triggering property of this novel vaccine. Hence, our final protein can be used for prophylactic or therapeutic usages, because it can potentially stimulate both cellular and humoral immune responses. PMID:24512916

  10. Inspiration from the mirror: D-amino acid containing peptides in biomedical approaches.

    PubMed

    Feng, Zhaoqianqi; Xu, Bing

    2016-06-01

    D-amino acids, the enantiomers of naturally abundant L-amino acids, bear unique stereochemistry properties that lead to the resistance towards most of the endogenous enzymes. Previous works have demonstrated applications of D-amino acids in therapeutic development with the aid of mirror-image phage display and retro-inverso peptide synthesis. In this review, we highlight the recent progress and challenges in the exploration of D-amino acids at the interface of chemistry and life science. First, we will introduce some progress made in traditional application of D-amino acids to enhance biostability of peptide therapeutics. Then, we discuss some works that explore the relatively underexplored interactions between the enzyme and D-amino acids and enzymatic reactions of D-amino acids. To highlight the enzymatic reactions of D-amino acids, we will describe several emerging works on the enzyme-instructed self-assembly (EISA) and their potential application in selective anti-inflammatory or anticancer therapies. At the end, we briefly mention the challenges and possible future directions. PMID:27159920

  11. Photodissociation of TEMPO-modified peptides: new approaches to radical-directed dissociation of biomolecules.

    PubMed

    Marshall, David L; Hansen, Christopher S; Trevitt, Adam J; Oh, Han Bin; Blanksby, Stephen J

    2014-03-14

    Radical-directed dissociation of gas phase ions is emerging as a powerful and complementary alternative to traditional tandem mass spectrometric techniques for biomolecular structural analysis. Previous studies have identified that coupling of 2-[(2,2,6,6-tetramethylpiperidin-1-oxyl)methyl]benzoic acid (TEMPO-Bz) to the N-terminus of a peptide introduces a labile oxygen-carbon bond that can be selectively activated upon collisional activation to produce a radical ion. Here we demonstrate that structurally-defined peptide radical ions can also be generated upon UV laser photodissociation of the same TEMPO-Bz derivatives in a linear ion-trap mass spectrometer. When subjected to further mass spectrometric analyses, the radical ions formed by a single laser pulse undergo identical dissociations as those formed by collisional activation of the same precursor ion, and can thus be used to derive molecular structure. Mapping the initial radical formation process as a function of photon energy by photodissociation action spectroscopy reveals that photoproduct formation is selective but occurs only in modest yield across the wavelength range (300-220 nm), with the photoproduct yield maximised between 235 and 225 nm. Based on the analysis of a set of model compounds, structural modifications to the TEMPO-Bz derivative are suggested to optimise radical photoproduct yield. Future development of such probes offers the advantage of increased sensitivity and selectivity for radical-directed dissociation. PMID:24473158

  12. Proline Editing: A General and Practical Approach to the Synthesis of Functionally and Structurally Diverse Peptides. Analysis of Steric versus Stereoelectronic Effects of 4-Substituted Prolines on Conformation within Peptides

    PubMed Central

    Pandey, Anil K.; Naduthambi, Devan; Thomas, Krista M.; Zondlo, Neal J.

    2013-01-01

    Functionalized proline residues have diverse applications. Herein we describe a practical approach, proline editing, for the synthesis of peptides with stereospecifically modified proline residues. Peptides are synthesized by standard solid-phase-peptide-synthesis to incorporate Fmoc-Hydroxyproline (4R-Hyp). In an automated manner, the Hyp hydroxyl is protected and the remainder of the peptide synthesized. After peptide synthesis, the Hyp protecting group is orthogonally removed and Hyp selectively modified to generate substituted proline amino acids, with the peptide main chain functioning to “protect” the proline amino and carboxyl groups. In a model tetrapeptide (Ac-TYPN-NH2), 4R-Hyp was stereospecifically converted to 122 different 4-substituted prolyl amino acids, with 4R or 4S stereochemistry, via Mitsunobu, oxidation, reduction, acylation, and substitution reactions. 4-Substituted prolines synthesized via proline editing include incorporated structured amino acid mimetics (Cys, Asp/Glu, Phe, Lys, Arg, pSer/pThr), recognition motifs (biotin, RGD), electron-withdrawing groups to induce stereoelectronic effects (fluoro, nitrobenzoate), handles for heteronuclear NMR (19F:fluoro; pentafluorophenyl or perfluoro-tert-butyl ether; 4,4-difluoro; 77SePh) and other spectroscopies (fluorescence, IR: cyanophenyl ether), leaving groups (sulfonate, halide, NHS, bromoacetate), and other reactive handles (amine, thiol, thioester, ketone, hydroxylamine, maleimide, acrylate, azide, alkene, alkyne, aryl halide, tetrazine, 1,2-aminothiol). Proline editing provides access to these proline derivatives with no solution phase synthesis. All peptides were analyzed by NMR to identify stereoelectronic and steric effects on conformation. Proline derivatives were synthesized to permit bioorthogonal conjugation reactions, including azide-alkyne, tetrazinetrans-cyclooctene, oxime, reductive amination, native chemical ligation, Suzuki, Sonogashira, cross-metathesis, and Diels

  13. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  14. Pairwise Sequence Alignment Library

    Energy Science and Technology Software Center (ESTSC)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprintmore » that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

  15. An Approach to Identifying the Effect of Technique Asymmetries on Body Alignment in Swimming Exemplified by a Case Study of a Breaststroke Swimmer

    PubMed Central

    Sanders, Ross H.; Fairweather, Malcolm M.; Alcock, Alison; McCabe, Carla B.

    2015-01-01

    Despite the importance of maintaining good alignment to minimize resistive drag in swimming there is a paucity of literature relating to the effect of technique asymmetries on rotations of the body about a vertical axis (yaw). The purpose of this paper was to present an approach to analyzing the effect of technique asymmetries on rotations in swimming, exemplifying the process with a case study of a breaststroke swimmer. The kinematics and angular kinetics of an elite female international breaststroke swimmer performing a ‘fatigue set’ of four 100m swims were derived from digitized three-dimensional video data using a 13 segment body model. Personalised anthropometric data required to quantify accurately segment and whole body centres of mass and segmental angular momentum were obtained by the elliptical zone method. Five episodes of torques producing yaw occurred in the stroke cycle sampled for each 100m swim of this swimmer. These torques were linked to bilateral differences in upper limb kinematics during 1) out-sweep; 2) in-sweep; 3) upper limb recovery; and lower limb kinematics during 4) Lower limb recovery and 5) the kick. It has been shown that by quantifying whole body torques, in conjunction with the kinematic movement patterns, the effect of technique asymmetries on body alignment can be assessed. Assessment of individual swimmers in this manner provides a solid foundation for planning interventions in strength, flexibility, and technique to improve alignment and performance. Key points A unique (not been attempted previously) study of yaw in breaststroke swimming that yields new knowledge of how technique and strength asymmetries affects body alignment. Establishes an approach to investigation of yaw in swimming using 3D videography and inverse dynamics. Exemplifies the approach with a case study. The case study illustrated the potential of the approach to enable detailed assessment of yaw and to explain how the yaw is produced in terms of the

  16. Alignment fixture

    DOEpatents

    Bell, Grover C.; Gibson, O. Theodore

    1980-01-01

    A part alignment fixture is provided which may be used for precise variable lateral and tilt alignment relative to the fixture base of various shaped parts. The fixture may be used as a part holder for machining or inspection of parts or alignment of parts during assembly and the like. The fixture includes a precisely machined diameter disc-shaped hub adapted to receive the part to be aligned. The hub is nested in a guide plate which is adapted to carry two oppositely disposed pairs of positioning wedges so that the wedges may be reciprocatively positioned by means of respective micrometer screws. The sloping faces of the wedges contact the hub at respective quadrants of the hub periphery. The lateral position of the hub relative to the guide plate is adjusted by positioning the wedges with the associated micrometer screws. The tilt of the part is adjusted relative to a base plate, to which the guide plate is pivotally connected by means of a holding plate. Two pairs of oppositely disposed wedges are mounted for reciprocative lateral positioning by means of separate micrometer screws between flanges of the guide plate and the base plate. Once the wedges are positioned to achieve the proper tilt of the part or hub on which the part is mounted relative to the base plate, the fixture may be bolted to a machining, inspection, or assembly device.

  17. PINALOG: a novel approach to align protein interaction networks—implications for complex detection and function prediction

    PubMed Central

    Phan, Hang T. T.; Sternberg, Michael J. E.

    2012-01-01

    Motivation: Analysis of protein–protein interaction networks (PPINs) at the system level has become increasingly important in understanding biological processes. Comparison of the interactomes of different species not only provides a better understanding of species evolution but also helps with detecting conserved functional components and in function prediction. Method and Results: Here we report a PPIN alignment method, called PINALOG, which combines information from protein sequence, function and network topology. Alignment of human and yeast PPINs reveals several conserved subnetworks between them that participate in similar biological processes, notably the proteasome and transcription related processes. PINALOG has been tested for its power in protein complex prediction as well as function prediction. Comparison with PSI-BLAST in predicting protein function in the twilight zone also shows that PINALOG is valuable in predicting protein function. Availability and implementation: The PINALOG web-server is freely available from http://www.sbg.bio.ic.ac.uk/~pinalog. The PINALOG program and associated data are available from the Download section of the web-server. Contact: m.sternberg@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22419782

  18. Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data.

    PubMed

    Tu, Chengjian; Sheng, Quanhu; Li, Jun; Ma, Danjun; Shen, Xiaomeng; Wang, Xue; Shyr, Yu; Yi, Zhengping; Qu, Jun

    2015-11-01

    The two key steps for analyzing proteomic data generated by high-resolution MS are database searching and postprocessing. While the two steps are interrelated, studies on their combinatory effects and the optimization of these procedures have not been adequately conducted. Here, we investigated the performance of three popular search engines (SEQUEST, Mascot, and MS Amanda) in conjunction with five filtering approaches, including respective score-based filtering, a group-based approach, local false discovery rate (LFDR), PeptideProphet, and Percolator. A total of eight data sets from various proteomes (e.g., E. coli, yeast, and human) produced by various instruments with high-accuracy survey scan (MS1) and high- or low-accuracy fragment ion scan (MS2) (LTQ-Orbitrap, Orbitrap-Velos, Orbitrap-Elite, Q-Exactive, Orbitrap-Fusion, and Q-TOF) were analyzed. It was found combinations involving Percolator achieved markedly more peptide and protein identifications at the same FDR level than the other 12 combinations for all data sets. Among these, combinations of SEQUEST-Percolator and MS Amanda-Percolator provided slightly better performances for data sets with low-accuracy MS2 (ion trap or IT) and high accuracy MS2 (Orbitrap or TOF), respectively, than did other methods. For approaches without Percolator, SEQUEST-group performs the best for data sets with MS2 produced by collision-induced dissociation (CID) and IT analysis; Mascot-LFDR gives more identifications for data sets generated by higher-energy collisional dissociation (HCD) and analyzed in Orbitrap (HCD-OT) and in Orbitrap Fusion (HCD-IT); MS Amanda-Group excels for the Q-TOF data set and the Orbitrap Velos HCD-OT data set. Therefore, if Percolator was not used, a specific combination should be applied for each type of data set. Moreover, a higher percentage of multiple-peptide proteins and lower variation of protein spectral counts were observed when analyzing technical replicates using Percolator

  19. LPXRFa peptide system in the European sea bass: A molecular and immunohistochemical approach.

    PubMed

    Paullada-Salmerón, José A; Cowan, Mairi; Aliaga-Guerrero, María; Gómez, Ana; Zanuy, Silvia; Mañanos, Evaristo; Muñoz-Cueto, José A

    2016-01-01

    Gonadotropin-inhibitory hormone (GnIH) is a neuropeptide that suppresses reproduction in birds and mammals by inhibiting GnRH and gonadotropin secretion. GnIH orthologs with a C-terminal LPXRFamide (LPXRFa) motif have been identified in teleost fish. Although recent work also suggests its role in fish reproduction, studies are scarce and controversial, and have mainly focused on cyprinids. In this work we cloned a full-length cDNA encoding an LPXRFa precursor in the European sea bass, Dicentrarchus labrax. In contrast to other teleosts, the sea bass LPXRFa precursor contains only two putative RFamide peptides, termed sbLPXRFa1 and sbLPXRFa2. sblpxrfa transcripts were expressed predominantly in the olfactory bulbs/telencephalon, diencephalon, midbrain tegmentum, retina, and gonads. We also developed a specific antiserum against sbLPXRFa2, which revealed sbLPXRFa-immunoreactive (ir) perikarya in the olfactory bulbs-terminal nerve, ventral telencephalon, caudal preoptic area, dorsal mesencephalic tegmentum, and rostral rhombencephalon. These sbLPXRFa-ir cells profusely innervated the preoptic area, hypothalamus, optic tectum, semicircular torus, and caudal midbrain tegmentum, but conspicuous projections also reached the olfactory bulbs, ventral/dorsal telencephalon, habenula, ventral thalamus, pretectum, rostral midbrain tegmentum, posterior tuberculum, reticular formation, and viscerosensory lobe. The retina, pineal, vascular sac, and pituitary were also targets of sbLPXRFa-ir cells. In the pituitary, this innervation was observed close to follicle-stimulating hormone (FSH), luteinizing hormone (LH) and growth hormone (GH) cells. Tract-tracing retrograde labeling suggests that telencephalic and preoptic sbLPXRFa cells might represent the source of pituitary innervation. The immunohistochemical distribution of sbLPXRFa cells and fibers suggest that LPXRFa peptides might be involved in some functions as well as reproduction, such as feeding, growth, and behavior. PMID

  20. Lutetium-177-labeled gastrin releasing peptide receptor binding analogs: a novel approach to radionuclide therapy.

    PubMed

    Panigone, S; Nunn, A D

    2006-12-01

    Optimization of therapy for individual patients remains a goal of clinical practice. Radionuclide imaging can identify those patients who may benefit from subsequent targeted therapy by providing regional information on the distribution of the target. An ideal situation may be when the imaging and the therapeutic compounds are the same agent. Two antibodies ([ [90Y]ibritumomab, [131I]tositumomab) are now approved for the systemic radiotherapy of non-Hodgkin's lymphoma. The main hurdle is to deliver higher absorbed doses to the more refractory solid tumors paying particular regard to the bone marrow toxicity. The low dose is thought to be a result of the large size of antibodies slowing delivery to the target. Peptides having high affinity to receptors expressed on cancer cells are a promising alternative. They are usually rapidly excreted from the body through renal and/or hepatobiliary excretion thus creating a prolonged accumulation of the radioactivity in the kidneys, which represents a recognized issue for systemic radiotherapy. The first radiopeptide developed was a somatostatin analogue, which led to a major breakthrough in the field. Beside the kidney issue, somatostatin use remains limited to few cancers that express receptors in sufficiently large quantities, mainly neuroendocrine tumors. The gastrin releasing peptide (GRP) receptor is an attractive target for development of new radiopeptides with diagnostic and therapeutic potential. This is based upon the functional expression of GRP receptors in several of the more prevalent cancers including prostate, breast, and small cell lung cancer. This review covers the efforts currently underway to develop new and clinically promising GRP-receptor specific molecules labeled with imageable and therapeutic radionuclides. PMID:17043628

  1. A peptide immunization approach to counteract a Staphylococcus aureus protease defense against host immunity.

    PubMed

    Jordan, Robert E; Fernandez, Jeffrey; Brezski, Randall J; Greenplate, Allison R; Knight, David M; Raju, T Shantha; Lynch, A Simon

    2016-04-01

    Pathogens that induce acute and chronic infections, as well as certain cancers, employ numerous strategies to thwart host cellular and humoral immune defenses. One proposed evasion mechanism against humoral immunity is a localized expression of extracellular proteases that cleave the IgG hinge and disable host IgG functions. Host immunity appears to be prepared to counter such a proteolytic tactic by providing a group of autoantibodies, denoted anti-hinge antibodies that specifically bind to cleaved IgGs and provide compensating functional restoration in vitro. These respective counter-measures highlight the complex interrelationships among pathogens and host immunity and suggested to us a possible means for therapeutic intervention. In this study, we combined an investigation of pathogen-mediated proteolysis of host IgGs with an immunization strategy to boost host anti-hinge antibodies. In a Staphylococcus aureus infection model using an artificial tissue cage (wiffle ball) implanted into rabbits, cleaved rabbit IgGs were detected in abundance in the abscesses of untreated animals early after infection. However, in animals previously immunized with peptide analogs of the cleaved IgG hinge to generate substantial anti-hinge antibody titers, S. aureus colony formation was markedly reduced compared to control animals or those similarly immunized with a scrambled peptide sequence. The results of this study demonstrate that extensive local proteolysis of IgGs occurs in a test abscess setting and that immunization to increase host anti-hinge antibodies provided substantial acute protection against bacterial growth. PMID:26905931

  2. Conditional alignment random fields for multiple motion sequence alignment.

    PubMed

    Kim, Minyoung

    2013-11-01

    We consider the multiple time-series alignment problem, typically focusing on the task of synchronizing multiple motion videos of the same kind of human activity. Finding an optimal global alignment of multiple sequences is infeasible, while there have been several approximate solutions, including iterative pairwise warping algorithms and variants of hidden Markov models. In this paper, we propose a novel probabilistic model that represents the conditional densities of the latent target sequences which are aligned with the given observed sequences through the hidden alignment variables. By imposing certain constraints on the target sequences at the learning stage, we have a sensible model for multiple alignments that can be learned very efficiently by the EM algorithm. Compared to existing methods, our approach yields more accurate alignment while being more robust to local optima and initial configurations. We demonstrate its efficacy on both synthetic and real-world motion videos including facial emotions and human activities. PMID:24051737

  3. Mass balance approaches for estimating the intestinal absorption and metabolism of peptides and analogues: theoretical development and applications

    NASA Technical Reports Server (NTRS)

    Sinko, P. J.; Leesman, G. D.; Amidon, G. L.

    1993-01-01

    A theoretical analysis for estimating the extent of intestinal peptide and peptide analogue absorption was developed on the basis of a mass balance approach that incorporates convection, permeability, and reaction. The macroscopic mass balance analysis (MMBA) was extended to include chemical and enzymatic degradation. A microscopic mass balance analysis, a numerical approach, was also developed and the results compared to the MMBA. The mass balance equations for the fraction of a drug absorbed and reacted in the tube were derived from the general steady state mass balance in a tube: [formula: see text] where M is mass, z is the length of the tube, R is the tube radius, Pw is the intestinal wall permeability, kr is the reaction rate constant, C is the concentration of drug in the volume element over which the mass balance is taken, VL is the volume of the tube, and vz is the axial velocity of drug. The theory was first applied to the oral absorption of two tripeptide analogues, cefaclor (CCL) and cefatrizine (CZN), which degrade and dimerize in the intestine. Simulations using the mass balance equations, the experimental absorption parameters, and the literature stability rate constants yielded a mean estimated extent of CCL (250-mg dose) and CZN (1000-mg dose) absorption of 89 and 51%, respectively, which was similar to the mean extent of absorption reported in humans (90 and 50%). It was proposed previously that 15% of the CCL dose spontaneously degraded systematically; however, our simulations suggest that significant CCL degradation occurs (8 to 17%) presystemically in the intestinal lumen.(ABSTRACT TRUNCATED AT 250 WORDS).

  4. A Comprehensive Approach to Clustering of Expressed Human Gene Sequence: The Sequence Tag Alignment and Consensus Knowledge Base

    PubMed Central

    Miller, Robert T.; Christoffels, Alan G.; Gopalakrishnan, Chella; Burke, John; Ptitsyn, Andrey A.; Broveak, Tania R.; Hide, Winston A.

    1999-01-01

    The expressed human genome is being sequenced and analyzed by disparate groups producing disparate data. The majority of the identified coding portion is in the form of expressed sequence tags (ESTs). The need to discover exonic representation and expression forms of full-length cDNAs for each human gene is frustrated by the partial and variable quality nature of this data delivery. A highly redundant human EST data set has been processed into integrated and unified expressed transcript indices that consist of hierarchically organized human transcript consensi reflecting gene expression forms and genetic polymorphism within an index class. The expression index and its intermediate outputs include cleaned transcript sequence, expression, and alignment information and a higher fidelity subset, SANIGENE. The STACK_PACK clustering system has been applied to dbEST release 121598 (GenBank version 110). Sixty-four percent of 1,313,103 Homo sapiens ESTs are condensed into 143,885 tissue level multiple sequence clusters; linking through clone-ID annotations produces 68,701 total assemblies, such that 81% of the original input set is captured in a STACK multiple sequence or linked cluster. Indexing of alignments by substituent EST accession allows browsing of the data structure and its cross-links to UniGene. STACK metaclusters consolidate a greater number of ESTs by a factor of 1.86 with respect to the corresponding UniGene build. Fidelity comparison with genome reference sequence AC004106 demonstrates consensus expression clusters that reflect significantly lower spurious repeat sequence content and capture alternate splicing within a whole body index cluster and three STACK v.2.3 tissue-level clusters. Statistics of a staggered release whole body index build of STACK v.2.0 are presented. PMID:10568754

  5. ALIGNING JIG

    DOEpatents

    Culver, J.S.; Tunnell, W.C.

    1958-08-01

    A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

  6. Phage display allows identification of zona pellucida-binding peptides with species-specific properties: novel approach for development of contraceptive vaccines for wildlife.

    PubMed

    Samoylova, Tatiana I; Cochran, Anna M; Samoylov, Alexandre M; Schemera, Bettina; Breiteneicher, Adam H; Ditchkoff, Stephen S; Petrenko, Valery A; Cox, Nancy R

    2012-12-31

    Multiple phage-peptide constructs, where the peptides mimic sperm epitopes that bind to zona pellucida (ZP) proteins, were generated via selection from a phage display library using a novel approach. Selections were designed to allow for identification of ZP-binding phage clones with potential species-specific properties, an important feature for wildlife oral vaccines as the goal is to control overpopulation of a target species while not affecting non-target species' reproduction. Six phage-peptide antigens were injected intramuscularly into pigs and corresponding immune responses evaluated. Administration of the antigens into pigs stimulated production of anti-peptide antibodies, which were shown to act as anti-sperm antibodies. Potentially, such anti-sperm antibodies could interfere with sperm delivery or function in the male or female genital tract, leading to contraceptive effects. Staining of semen samples collected from different mammalian species, including pig, cat, dog, bull, and mouse, with anti-sera from pigs immunized with ZP-binding phage allowed identification of phage-peptide constructs with different levels of species specificity. Based on the intensity of the immune responses and specificity of these responses in different species, two of the antigens with fusion peptide sequences GEGGYGSHD and GQQGLNGDS were recognized as the most promising candidates for development of contraceptive vaccines for wild pigs. PMID:23079080

  7. Image alignment

    DOEpatents

    Dowell, Larry Jonathan

    2014-04-22

    Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishing features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.

  8. Ligand and Structure-Based Approaches for the Identification of Peptide Deformylase Inhibitors as Antibacterial Drugs

    PubMed Central

    Gao, Jian; Liang, Li; Zhu, Yasheng; Qiu, Shengzhi; Wang, Tao; Zhang, Ling

    2016-01-01

    Peptide deformylase (PDF) is a metalloprotease catalyzing the removal of a formyl group from newly synthesized proteins, which makes it an important antibacterial drug target. Given the importance of PDF inhibitors like actinonin in antibacterial drug discovery, several reported potent PDF inhibitors were used to develop pharmacophore models using the Galahad module of Sybyl 7.1 software. Generated pharmacophore models were composed of two donor atom centers, four acceptor atom centers and two hydrophobic groups. Model-1 was screened against the Zinc database and several compounds were retrieved as hits. Compounds with Qfit values of more than 60 were employed to perform a molecular docking study with the receptor Escherichia coli PDF, then compounds with docking score values of more than 6 were used to predict the in silico pharmacokinetic and toxicity risk via OSIRIS property explorer. Two known PDF inhibitors were also used to perform a molecular docking study with E. coli PDF as reference molecules. The results of the molecular docking study were validated by reproducing the crystal structure of actinonin. Molecular docking and in silico pharmacokinetic and toxicity prediction studies suggested that ZINC08740166 has a relatively high docking score of 7.44 and a drug score of 0.78. PMID:27428963

  9. Ligand and Structure-Based Approaches for the Identification of Peptide Deformylase Inhibitors as Antibacterial Drugs.

    PubMed

    Gao, Jian; Liang, Li; Zhu, Yasheng; Qiu, Shengzhi; Wang, Tao; Zhang, Ling

    2016-01-01

    Peptide deformylase (PDF) is a metalloprotease catalyzing the removal of a formyl group from newly synthesized proteins, which makes it an important antibacterial drug target. Given the importance of PDF inhibitors like actinonin in antibacterial drug discovery, several reported potent PDF inhibitors were used to develop pharmacophore models using the Galahad module of Sybyl 7.1 software. Generated pharmacophore models were composed of two donor atom centers, four acceptor atom centers and two hydrophobic groups. Model-1 was screened against the Zinc database and several compounds were retrieved as hits. Compounds with Qfit values of more than 60 were employed to perform a molecular docking study with the receptor Escherichia coli PDF, then compounds with docking score values of more than 6 were used to predict the in silico pharmacokinetic and toxicity risk via OSIRIS property explorer. Two known PDF inhibitors were also used to perform a molecular docking study with E. coli PDF as reference molecules. The results of the molecular docking study were validated by reproducing the crystal structure of actinonin. Molecular docking and in silico pharmacokinetic and toxicity prediction studies suggested that ZINC08740166 has a relatively high docking score of 7.44 and a drug score of 0.78. PMID:27428963

  10. Gold Alignment and Internal Dissipation

    NASA Astrophysics Data System (ADS)

    Lazarian, A.

    1997-07-01

    The measures of mechanical alignment are obtained for both prolate and oblate grains whose temperatures are comparable to the grain kinetic energy divided by k, the Boltzmann constant. For such grains, the alignment of angular momentum, J, with the axis of maximal inertia, a, is only partial, which substantially alters the mechanical alignment as compared with the results obtained by Lazarian and Roberge, Hanany, & Messinger under the assumption of perfect alignment. We also describe Gold alignment when the Barnett dissipation is suppressed and derive an analytical expression that relates the measure of alignment to the parameters of grain nonsphericity and the direction of the gas-grain drift. This solution provides the lower limit for the measure of alignment, while the upper limit is given by the method derived by Lazarian. Using the results of a recent study of incomplete internal relaxation by Lazarian & Roberge, we find measures of alignment for the whole range of ratios of grain rotational energy to kTs, where Ts is the grain temperature. To describe alignment for mildly supersonic drifts, we suggest an analytical approach that provides good correspondence with the results of direct numerical simulations by Roberge, Hanany, & Messinger. We also extend our approach to account for simultaneous action of the Gold and Davis-Greenstein mechanisms.

  11. A genomic approach highlights common and diverse effects and determinants of susceptibility on the yeast Saccharomyces cerevisiae exposed to distinct antimicrobial peptides

    PubMed Central

    2010-01-01

    Background The mechanism of action of antimicrobial peptides (AMP) was initially correlated with peptide membrane permeation properties. However, recent evidences indicate that action of a number of AMP is more complex and involves specific interactions at cell envelopes or with intracellular targets. In this study, a genomic approach was undertaken on the model yeast Saccharomyces cerevisiae to characterize the antifungal effect of two unrelated AMP. Results Two differentiated peptides were used: the synthetic cell-penetrating PAF26 and the natural cytolytic melittin. Transcriptomic analyses demonstrated distinctive gene expression changes for each peptide. Quantitative RT-PCR confirmed differential expression of selected genes. Gene Ontology (GO) annotation of differential gene lists showed that the unique significant terms shared by treatment with both peptides were related to the cell wall (CW). Assays with mutants lacking CW-related genes including those of MAPK signaling pathways revealed genes having influence on sensitivity to peptides. Fluorescence microscopy and flow cytometry demonstrated PAF26 interaction with cells and internalization that correlated with cell killing in sensitive CW-defective mutants such as Δecm33 or Δssd1. GO annotation also showed differential responses between peptides, which included ribosomal biogenesis, ARG genes from the metabolism of amino groups (specifically induced by PAF26), or the reaction to unfolded protein stress. Susceptibility of deletion mutants confirmed the involvement of these processes. Specifically, mutants lacking ARG genes from the metabolism of arginine pathway were markedly more resistant to PAF26 and had a functional CW. In the deletant in the arginosuccinate synthetase (ARG1) gene, PAF26 interaction occurred normally, thus uncoupling peptide interaction from cell killing. The previously described involvement of the glycosphingolipid gene IPT1 was extended to the peptides studied here. Conclusions

  12. MUSE optical alignment procedure

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

    2012-09-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

  13. A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments

    SciTech Connect

    Matzke, Melissa M.; Brown, Joseph N.; Gritsenko, Marina A.; Metz, Thomas O.; Pounds, Joel G.; Rodland, Karin D.; Shukla, Anil K.; Smith, Richard D.; Waters, Katrina M.; McDermott, Jason E.; Webb-Robertson, Bobbie-Jo M.

    2013-02-01

    Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used to identify and quantify peptides in complex biological samples. In particular, label-free shotgun proteomics is highly effective for the identification of peptides and subsequently obtaining a global protein profile of a sample. As a result, this approach is widely used for discovery studies. Typically, the objective of these discovery studies is to identify proteins that are affected by some condition of interest (e.g. disease, exposure). However, for complex biological samples, label-free LC-MS proteomics experiments measure peptides and do not directly yield protein quantities. Thus, protein quantification must be inferred from one or more measured peptides. In recent years, many computational approaches to relative protein quantification of label-free LC-MS data have been published. In this review, we examine the most commonly employed quantification approaches to relative protein abundance from peak intensity values, evaluate their individual merits, and discuss challenges in the use of the various computational approaches.

  14. The use of a neutral peptide aptamer scaffold to anchor BH3 peptides constitutes a viable approach to studying their function

    PubMed Central

    Stadler, L K J; Tomlinson, D C; Lee, T; Knowles, M A; Ko Ferrigno, P

    2014-01-01

    The B-cell CLL/lymphoma-2 (Bcl-2) family of proteins are important regulators of the intrinsic pathway of apoptosis, and their interactions, driven by Bcl-2 homology (BH) domains, are of great interest in cancer research. Particularly, the BH3 domain is of clinical relevance, as it promotes apoptosis through activation of Bcl-2-associated x protein (Bax) and Bcl-2 antagonist killer (Bak), as well as by antagonising the anti-apoptotic Bcl-2 family members. Although investigated extensively in vitro, the study of the BH3 domain alone inside cells is more problematic because of diminished secondary structure of the unconstrained peptide and a lack of stability. In this study, we report the successful use of a novel peptide aptamer scaffold – Stefin A quadruple mutant – to anchor and present the BH3 domains from Bcl-2-interacting mediator of cell death (Bim), p53 upregulated modulator of apoptosis (Puma), Bcl-2-associated death promoter (Bad) and Noxa, and demonstrate its usefulness in the study of the BH3 domains in vivo. When expressed intracellularly, anchored BH3 peptides exhibit much the same binding specificities previously established in vitro, however, we find that, at endogenous expression levels, Bcl-2 does not bind to any of the anchored BH3 domains tested. Nonetheless, when expressed inside cells the anchored PUMA and Bim BH3 α-helices powerfully induce cell death in the absence of efficient targeting to the mitochondrial membrane, whereas the Noxa helix requires a membrane insertion domain in order to kill Mcl-1-dependent myeloma cells. Finally, the binding of the Bim BH3 peptide to Bax was the only interaction with a pro-apoptotic effector protein observed in this study. PMID:24481451

  15. Development of an anti-microbial peptide-mediated liposomal delivery system: a novel approach towards pH-responsive anti-microbial peptides.

    PubMed

    Zhang, Qianyu; Tang, Jie; Ran, Rui; Liu, Yayuan; Zhang, Zhirong; Gao, Huile; He, Qin

    2016-05-01

    On one hand, the application of anti-microbial peptides (AMPs) in the construction of AMPs-mediated drug delivery system has not yet been fully exploited; on the other hand, its non-selectivity in vivo has also limited its clinical application. In this work, we chose one pH-responsive peptide, [D]-H6L9, and functionalized it onto the surface of liposomes (D-Lip). The protonation of histidines in the sequence of [D]-H6L9 under pH 6.3 could switch the surface charge of D-Lip from negative (under pH 7.4) to positive (under pH 6.3), and the cellular uptake and tumor spheroids uptake were increased accordingly. Lysosome co-localization assay suggested that there was only little overlap of D-Lip with lysosomes in 12 h, which indicated that D-Lip could escape lysosomes effectively. In vivo biodistribution assay on C26 tumor-bearing BALB/C mice showed that DiR-labeled D-Lip could reach tumors as much as PEG-Lip, and both tumor slices and quantitative measurement of dispersed cells of in vivo tumors by flow cytometry demonstrated that D-Lip could be taken up by tumors more efficiently. Therefore, we have established an anti-microbial peptide-mediated liposomal delivery system for tumor delivery. PMID:25693639

  16. Evaluation of two approaches for aligning data obtained from a motion capture system and an in-shoe pressure measurement system.

    PubMed

    Kim, Sunwook; Nussbaum, Maury A

    2014-01-01

    An in-shoe pressure measurement (IPM) system can be used to measure center of pressure (COP) locations, and has fewer restrictions compared to the more conventional approach using a force platform. The insole of an IPM system, however, has its own coordinate system. To use an IPM system along with a motion capture system, there is thus a need to align the coordinate systems of the two measurement systems. To address this need, the current study examined two different approaches-rigid body transformation and nonlinear mapping (i.e., multilayer feed-forward neural network (MFNN))-to express COP measurements from an IPM system in the coordinate system of a motion capture system. Ten participants (five male and five female) completed several simulated manual material handling (MMH) activities, and during these activities the performance of the two approaches was assessed. Results indicated that: (1) performance varied between MMH activity types; and (2) a MFNN performed better than or comparable to the rigid body transformation, depending on the specific input variable sets used. Further, based on the results obtained, it was argued that a nonlinear mapping vs. rigid body transformation approach may be more effective to account for shoe deformation during MMH or potentially other types of physical activity. PMID:25222032

  17. A peptidomic approach to study the contribution of added casein proteins to the peptide profile in Spanish dry-fermented sausages.

    PubMed

    Mora, Leticia; Escudero, Elizabeth; Aristoy, M-Concepción; Toldrá, Fidel

    2015-11-01

    Peptidomics is a necessary alternative in the analysis of naturally generated peptides in dry-fermented processing. The intense proteolysis occurred during the processing of dry-fermented sausages is due to the action of endopeptidases and exopeptidases from both, endogenous muscle origin and lactic acid bacteria (LAB) added in the starter. Sodium caseinate is frequently used as an additive in this type of products because of its emulsifying properties, and consequently influences the protein profile available during the proteolysis. In this study, a mass spectrometry approach has been used to determine the impact of added sodium caseinate in the final peptide profile as well as to analyse its possible influence in the presence of certain previously described casein-derived bioactive peptides. PMID:26116420

  18. Peptides (P1, P2 and its mutations) binding with a graphene sheet: an all-atom to all-residue hierarchical coarse-grained approach

    NASA Astrophysics Data System (ADS)

    Kuang, Zhifeng; Farmer, Barry; Pandey, Ras

    2013-03-01

    Binding of peptide P2 (EPLQLKM) [1] and its mutations (P2G, P2Q) to a graphene sheet are studied by a coarse-grained computer simulation. Our hierarchical coarse-grained approach involves all-atom MD simulation to assess the binding interaction of each residue with the graphene sheet. Data from all-atom simulations are then used as input to phenomenological interaction in a coarse-grained MC simulation [2]. Binding of each peptide and its residue in corresponding sequence (P2, P2G, P2Q) are evaluated by analyzing the adsorption of each residue, its mobility, and structural profiles. Although it is difficult to identify overall morphological differences in adsorbed peptides by visual inspections, quantitative analysis of the conformational changes of adsorbed peptides shows variations in size among P2E and its mutations. Results on binding of peptide P1 (HSSYWYAFNNKT) may also be presented if data become available. This work is supported by the Air Force Research Laboratory.

  19. IUS prerelease alignment

    NASA Technical Reports Server (NTRS)

    Evans, F. A.

    1978-01-01

    Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

  20. Novel isotopic N, N-Dimethyl Leucine (iDiLeu) Reagents Enable Absolute Quantification of Peptides and Proteins Using a Standard Curve Approach

    NASA Astrophysics Data System (ADS)

    Greer, Tyler; Lietz, Christopher B.; Xiang, Feng; Li, Lingjun

    2015-01-01

    Absolute quantification of protein targets using liquid chromatography-mass spectrometry (LC-MS) is a key component of candidate biomarker validation. One popular method combines multiple reaction monitoring (MRM) using a triple quadrupole instrument with stable isotope-labeled standards (SIS) for absolute quantification (AQUA). LC-MRM AQUA assays are sensitive and specific, but they are also expensive because of the cost of synthesizing stable isotope peptide standards. While the chemical modification approach using mass differential tags for relative and absolute quantification (mTRAQ) represents a more economical approach when quantifying large numbers of peptides, these reagents are costly and still suffer from lower throughput because only two concentration values per peptide can be obtained in a single LC-MS run. Here, we have developed and applied a set of five novel mass difference reagents, isotopic N, N-dimethyl leucine (iDiLeu). These labels contain an amine reactive group, triazine ester, are cost effective because of their synthetic simplicity, and have increased throughput compared with previous LC-MS quantification methods by allowing construction of a four-point standard curve in one run. iDiLeu-labeled peptides show remarkably similar retention time shifts, slightly lower energy thresholds for higher-energy collisional dissociation (HCD) fragmentation, and high quantification accuracy for trypsin-digested protein samples (median errors <15%). By spiking in an iDiLeu-labeled neuropeptide, allatostatin, into mouse urine matrix, two quantification methods are validated. The first uses one labeled peptide as an internal standard to normalize labeled peptide peak areas across runs (<19% error), whereas the second enables standard curve creation and analyte quantification in one run (<8% error).

  1. Novel isotopic N, N-dimethyl leucine (iDiLeu) reagents enable absolute quantification of peptides and proteins using a standard curve approach

    PubMed Central

    Greer, Tyler; Lietz, Christopher B.; Xiang, Feng; Li, Lingjun

    2014-01-01

    Absolute quantification of protein targets using liquid chromatography-mass spectrometry (LC-MS) is a key component of candidate biomarker validation. One popular method combines multiple reaction monitoring (MRM) using a triple quadrupole instrument with stable isotope-labeled standards (SIS) for absolute quantification (AQUA). LC-MRM AQUA assays are sensitive and specific, but they are also expensive due to the cost of synthesizing stable isotope peptide standards. While the chemical modification approach using Mass Differential Tags for Relative and Absolute Quantification (mTRAQ) represents a more economical approach when quantifying large numbers of peptides, these reagents are costly and still suffer from lower throughput because only two concentration values per peptide can be obtained in a single LC-MS run. Here, we have developed and applied a set of five novel mass difference reagents, isotopic N,N-dimethyl leucine (iDiLeu). These labels contain an amine reactive group, triazine ester, are cost effective due to their synthetic simplicity, and have increased throughput compared to previous LC-MS quantification methods by allowing construction of a four-point standard curve in one run. iDiLeu-labeled peptides show remarkably similar retention time shifts, slightly lower energy thresholds for higher-energy collisional dissociation (HCD) fragmentation, and high quantification accuracy for trypsin-digested protein samples (median errors <15%). By spiking in an iDiLeu-labeled neuropeptide, allatostatin, into mouse urine matrix, two quantification methods are validated. The first uses one labeled peptide as an internal standard to normalize labeled peptide peak areas across runs (<19% error) while the second enables standard curve creation and analyte quantification in one run (<8% error). PMID:25377360

  2. An effective and effecient peptide binding prediction approach for a broad set of HLA-DR molecules based on ordered weighted averaging of binding pocket profiles

    PubMed Central

    2013-01-01

    Background The immune system must detect a wide variety of microbial pathogens, such as viruses, bacteria, fungi and parasitic worms, to protect the host against disease. Antigenic peptides displayed by MHC II (class II Major Histocompatibility Complex) molecules is a pivotal process to activate CD4+ TH cells (Helper T cells). The activated TH cells can differentiate into effector cells which assist various cells in activating against pathogen invasion. Each MHC locus encodes a great number of allele variants. Yet this limited number of MHC molecules are required to display enormous number of antigenic peptides. Since the peptide binding measurements of MHC molecules by biochemical experiments are expensive, only a few of the MHC molecules have suffecient measured peptides. To perform accurate binding prediction for those MHC alleles without suffecient measured peptides, a number of computational algorithms were proposed in the last decades. Results Here, we propose a new MHC II binding prediction approach, OWA-PSSM, which is a significantly extended version of a well known method called TEPITOPE. The TEPITOPE method is able to perform prediction for only 50 MHC alleles, while OWA-PSSM is able to perform prediction for much more, up to 879 HLA-DR molecules. We evaluate the method on five benchmark datasets. The method is demonstrated to be the best one in identifying binding cores compared with several other popular state-of-the-art approaches. Meanwhile, the method performs comparably to the TEPITOPE and NetMHCIIpan2.0 approaches in identifying HLA-DR epitopes and ligands, and it performs significantly better than TEPITOPEpan in the identification of HLA-DR ligands and MultiRTA in identifying HLA-DR T cell epitopes. Conclusions The proposed approach OWA-PSSM is fast and robust in identifying ligands, epitopes and binding cores for up to 879 MHC II molecules. PMID:24565049

  3. A room temperature approach for the fabrication of aligned TiO₂ nanotube arrays on transparent conductive substrates.

    PubMed

    Zeng, Ruosha; Li, Ke; Sheng, Xia; Chen, Liping; Zhang, Haijiao; Feng, Xinjian

    2016-03-14

    A novel solution approach is reported for the fabrication of TiO₂ nanotube arrays on transparent conductive substrates via in situ conversion from nanowires. The as-prepared nanotube arrays not only demonstrate a larger surface area in comparison with the primary NWs, but also longer charge carrier lifetime than that of randomly packed nanoparticle films. PMID:26892268

  4. A rational approach to select immunogenic peptides that induce IFN-γ response against Toxoplasma gondii in human leukocytes.

    PubMed

    Cardona, Néstor I; Moncada, Diego M; Gómez-Marin, Jorge E

    2015-12-01

    The ideal vaccine to prevent toxoplasmosis in humans would comprise antigens that elicit a protective T cell type 1 response with high IFN-γ production. Here, we report the use of a bioinformatics pipeline to discover peptides based on biochemical characteristics that predict strong IFN-γ response by human leukocytes. We selected peptide sequences that previously were reported to induce IFN-γ to identify the biophysical characteristics that will predict HLA-A*02 high-affinity epitopes. We found that the protein motif pattern FL...L..[VL] was common in previously reported highly immunogenic sequences. We have selected new peptides with a length of 9 residues with affinities from 2 to 21 nM with peptide signal and transmembrane domains and predicted to be cleaved at the proteasome to perform ELISPOT assays with human leukocytes. Within 9 peptides with the highest scores for IFN-γ production, four peptides elicited IFN-γ levels in a range from 252 to 1763 SFC/1e6. Our pipeline uncovered Toxoplasma proteins with peptides that are processed by MHC class 1 in humans. Our results suggest that our rational strategy for the selection of immunogenic epitopes could be used to select peptides as candidates for inclusion in epitope-based vaccines. PMID:26210043

  5. An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets.

    PubMed

    Lee, Su Jin; Hyun, Soonsil; Kieft, Jeffrey S; Yu, Jaehoon

    2009-02-18

    The hairpin RNA motif is one of the most frequently observed secondary structures and is often targeted by therapeutic agents. An amphiphilic peptide with seven lysine and eight leucine residues and its derivatives were designed for use as ligands against RNA hairpin motifs. We hypothesized that variations in both the hydrophobic leucine-rich and hydrophilic lysine-rich spheres of these amphiphilic peptides would create extra attractive interactions with hairpin RNA targets. A series of alanine-scanned peptides were probed to identify the most influential lysine residues in the hydrophilic sphere. The binding affinities of these modified peptides with several hairpins, such as RRE, TAR from HIV, a short hairpin from IRES of HCV, and a hairpin from the 16S A-site stem from rRNA, were determined. Since the hairpin from IRES of HCV was the most susceptible to the initial series of alanine-scanned peptides, studies investigating how further variations in the peptides effect binding employed the IRES hairpin. Next, the important Lys residues were substituted by shorter chain amines, such as ornithine, to place the peptide deeper into the hairpin groove. In a few cases, a 70-fold improved binding was observed for peptides that contained the specifically located shorter amine side chains. To further explore changes in binding affinities brought about by alterations in the hydrophobic sphere, tryptophan residues were introduced in place of leucine. A few peptides with tryptophan in specific positions also displayed 70-fold improved binding affinities. Finally, double mutant peptides incorporating both specifically located shorter amine side chains in the hydrophilic region and tryptophan residues in the hydrophobic region were synthesized. The binding affinities of peptides containing the simple double modification were observed to be 80 times lower, and their binding specificities were increased 40-fold. The results of this effort provide important information about

  6. Effect of graded hydration on the dynamics of an ion channel peptide: a fluorescence approach.

    PubMed

    Kelkar, Devaki A; Chattopadhyay, Amitabha

    2005-02-01

    Water plays an important role in determining the folding, structure, dynamics, and, in turn, the function of proteins. We have utilized a combination of fluorescence approaches such as the wavelength-selective fluorescence approach to monitor the effect of varying degrees of hydration on the organization and dynamics of the functionally important tryptophan residues of gramicidin in reverse micelles formed by sodium bis(2-ethylhexyl) sulfosuccinate. Our results show that tryptophans in gramicidin, present in the single-stranded beta6.3 conformation, experience slow solvent relaxation giving rise to red-edge excitation shift (REES). In addition, changes in fluorescence polarization with increasing excitation or emission wavelength reinforce that the gramicidin tryptophans are localized in motionally restricted regions of the reverse micelle. Interestingly, the extent of REES is found to be independent of the [water]/[surfactant] molar ratio (w(o)). We attribute this to heterogeneity in gramicidin tryptophan localization. Fluorescence intensity and mean fluorescence lifetime of the gramicidin tryptophans show significant reductions with increasing w(o) indicating sensitivity to increased polarity. Since the dynamics of hydration is related to folding, structure, and eventually function of proteins, we conclude that REES could prove to be a potentially sensitive tool to explore the dynamics of proteins under conditions of changing hydration. PMID:15542551

  7. Effect of Graded Hydration on the Dynamics of an Ion Channel Peptide: A Fluorescence Approach

    PubMed Central

    Kelkar, Devaki A.; Chattopadhyay, Amitabha

    2005-01-01

    Water plays an important role in determining the folding, structure, dynamics, and, in turn, the function of proteins. We have utilized a combination of fluorescence approaches such as the wavelength-selective fluorescence approach to monitor the effect of varying degrees of hydration on the organization and dynamics of the functionally important tryptophan residues of gramicidin in reverse micelles formed by sodium bis(2-ethylhexyl) sulfosuccinate. Our results show that tryptophans in gramicidin, present in the single-stranded β6.3 conformation, experience slow solvent relaxation giving rise to red-edge excitation shift (REES). In addition, changes in fluorescence polarization with increasing excitation or emission wavelength reinforce that the gramicidin tryptophans are localized in motionally restricted regions of the reverse micelle. Interestingly, the extent of REES is found to be independent of the [water]/[surfactant] molar ratio (wo). We attribute this to heterogeneity in gramicidin tryptophan localization. Fluorescence intensity and mean fluorescence lifetime of the gramicidin tryptophans show significant reductions with increasing wo indicating sensitivity to increased polarity. Since the dynamics of hydration is related to folding, structure, and eventually function of proteins, we conclude that REES could prove to be a potentially sensitive tool to explore the dynamics of proteins under conditions of changing hydration. PMID:15542551

  8. A Stochastic Hill Climbing Approach for Simultaneous 2D Alignment and Clustering of Cryogenic Electron Microscopy Images.

    PubMed

    Reboul, Cyril F; Bonnet, Frederic; Elmlund, Dominika; Elmlund, Hans

    2016-06-01

    A critical step in the analysis of novel cryogenic electron microscopy (cryo-EM) single-particle datasets is the identification of homogeneous subsets of images. Methods for solving this problem are important for data quality assessment, ab initio 3D reconstruction, and analysis of population diversity due to the heterogeneous nature of macromolecules. Here we formulate a stochastic algorithm for identification of homogeneous subsets of images. The purpose of the method is to generate improved 2D class averages that can be used to produce a reliable 3D starting model in a rapid and unbiased fashion. We show that our method overcomes inherent limitations of widely used clustering approaches and proceed to test the approach on six publicly available experimental cryo-EM datasets. We conclude that, in each instance, ab initio 3D reconstructions of quality suitable for initialization of high-resolution refinement are produced from the cluster centers. PMID:27184214

  9. Analysis of endogenous peptides bound by soluble MHC class I molecules: a novel approach for identifying tumor-specific antigens.

    PubMed

    Barnea, Eilon; Beer, Ilan; Patoka, Renana; Ziv, Tamar; Kessler, Ofra; Tzehoval, Esther; Eisenbach, Lea; Zavazava, Nicholas; Admon, Arie

    2002-01-01

    The Human MHC Project aims at comprehensive cataloging of peptides presented within the context of different human leukocyte antigens (HLA) expressed by cells of various tissue origins, both in health and in disease. Of major interest are peptides presented on cancer cells, which include peptides derived from tumor antigens that are of interest for immunotherapy. Here, HLA-restricted tumor-specific antigens were identified by transfecting human breast, ovarian and prostate tumor cell lines with truncated genes of HLA-A2 and HLA-B7. Soluble HLA secreted by these cell lines were purified by affinity chromatography and analyzed by nano-capillary electrospray ionization-tandem mass spectrometry. Typically, a large peptide pool was recovered and sequenced including peptides derived from MAGE-B2 and mucin and other new tumor-derived antigens that may serve as potential candidates for immunotherapy. PMID:11782012

  10. State strategies of governance in biomedical innovation: aligning conceptual approaches for understanding 'Rising Powers' in the global context

    PubMed Central

    2011-01-01

    Background 'Innovation' has become a policy focus in its own right in many states as they compete to position themselves in the emerging knowledge economies. Innovation in biomedicine is a global enterprise in which 'Rising Power' states figure prominently, and which undoubtedly will re-shape health systems and health economies globally. Scientific and technological innovation processes and policies raise difficult issues in the domains of science/technology, civil society, and the economic and healthcare marketplace. The production of knowledge in these fields is complex, uncertain, inter-disciplinary and inter-institutional, and subject to a continuing political struggle for advantage. As part of this struggle, a wide variety of issues - regulation, intellectual property, ethics, scientific boundaries, healthcare market formation - are raised and policy agendas negotiated. Methods A range of social science disciplines and approaches have conceptualised such innovation processes. Against a background of concepts such as the competition state and the developmental state, and national innovation systems, we give an overview of a range of approaches that have potential for advancing understanding of governance of global life science and biomedical innovation, with special reference to the 'Rising Powers', in order to examine convergences and divergences between them. Conceptual approaches that we focus on include those drawn from political science/political economy, sociology of technology; Innovation Studies and Science & Technology Studies. The paper is part of a project supported by the UK ESRC's Rising Powers programme. Results We show convergences and complementarities between the approaches discussed, and argue that the role of the national state itself has become relatively neglected in much of the relevant theorising. Conclusions We conclude that an approach is required that enables innovation and governance to be seen as 'co-producing' each other in a multi

  11. A Novel Peptide-Binding Motifs Inference Approach to Understand Deoxynivalenol Molecular Toxicity

    PubMed Central

    Hassan, Yousef I.; Watts, Christena; Li, Xiu-Zhen; Zhou, Ting

    2015-01-01

    Deoxynivalenol (DON) is a type B trichothecene mycotoxin that is commonly detected in cereals and grains world-wide. The low-tolerated levels of this mycotoxin, especially in mono-gastric animals, reflect its bio-potency. The toxicity of DON is conventionally attributed to its ability to inhibit ribosomal protein biosynthesis, but recent advances in molecular tools have elucidated novel mechanisms that further explain DON’s toxicological profile, complementing the diverse symptoms associated with its exposure. This article summarizes the recent findings related to novel mechanisms of DON toxicity as well as how structural modifications to DON alter its potency. In addition, it explores feasible ways of expanding our understating of DON-cellular targets and their roles in DON toxicity, clearance, and detoxification through the utilization of computational biology approaches. PMID:26043274

  12. A Novel Two-Stage Tandem Mass Spectrometry Approach and Scoring Scheme for the Identification of O-GlcNAc Modified Peptides

    NASA Astrophysics Data System (ADS)

    Hahne, Hannes; Kuster, Bernhard

    2011-05-01

    The modification of serine and threonine residues in proteins by a single N-acetylglucosamine (O-GlcNAc) residue is an emerging post-translational modification (PTM) with broad biological implications. However, the systematic or large-scale analysis of this PTM is hampered by several factors, including low stoichiometry and the lability of the O-glycosidic bond during tandem mass spectrometry. Using a library of 72 synthetic glycopeptides, we developed a two-stage tandem MS approach consisting of pulsed Q dissociation (PQD) for O-GlcNAc peptide detection and electron transfer dissociation (ETD) for identification and site localization. Based on a set of O-GlcNAc specific fragment ions, we further developed a score (OScore) that discriminates O-GlcNAc peptide spectra from spectra of unmodified peptides with 95% sensitivity and >99% specificity. Integrating the OScore into the two-stage LC-MS/MS approach detected O-GlcNAc peptides in the low fmol range and at 10-fold better sensitivity than a single data-dependent ETD tandem MS experiment.

  13. Glucagon-like peptide-1 (GLP-1) and protective effects in cardiovascular disease: a new therapeutic approach for myocardial protection

    PubMed Central

    2013-01-01

    Glucagon-like peptide-1 (GLP-1) is a member of the proglucagon incretin family implicated in the control of appetite and satiety. GLP-1 has insulinotropic, insulinomimetic, and glucagonostatic effects, thereby exerting multiple complementary actions to lower blood glucose in subjects with type 2 diabetes mellitus. A major advantage over conventional insulin is the fact that the insulinotropic actions of GLP-1 are dependent upon ambient glucose concentration, mitigating the risks of hypoglycemia. Recently, the crucial role of GLP-1 in cardiovascular disease has been suggested in both preclinical and clinical studies. The experimental data indicate GLP-1 and its analogs to have direct effects on the cardiovascular system, in addition to their classic glucoregulatory actions. Clinically, beneficial effects of GLP-1 have also been demonstrated in patients with myocardial ischemia and heart failure. GLP-1 has recently been demonstrated to be a more effective alternative in treating myocardial injury. This paper provides a review on the current evidence supporting the use of GLP-1 in experimental animal models and human trials with the ischemic and non-ischemic heart and discusses their molecular mechanisms and potential as a new therapeutic approach. PMID:23777457

  14. A combined cheminformatic and bioinformatic approach to address the proteolytic stability challenge in peptide-based drug discovery.

    PubMed

    Bayden, Alexander S; Gomez, Edwin F; Audie, Joseph; Chakravorty, Dhruva K; Diller, David J

    2015-11-01

    We have created models to predict cleavage sites for several human proteases including caspase-1, caspase-3, caspase-6, caspase-7, cathepsin B, cathepsin D, cathepsin G, cathepsin K, cathepsin L, elastase-2, granzyme A, granzyme B, matrix metallopeptidase-2 (MMP2), MMP7, MMP9, thrombin, and trypsin-1. Rather than representing the sequence pattern around the potential cleavage site through a series of flags with each flag representing one of the 20 standard amino acids, we first represent each amino acid by its calculated properties. For these calculated properties, we use validated cheminformatic descriptors, such as molecular weight, logP, and polar surface area, of the individual amino acids. Finally, the cleavage site-specific descriptors are calculated through various combinations of the individual amino acid descriptors for the residues surrounding the cleavage site. Some of these combinations do not take into account the location of the residue, as long as it is in a prescribed neighborhood of the potential cleavage site, whereas others are sensitive to the precise order of the residues in the sequence. The key advantage of this approach is that it allows one to perform meaningful calculations with nonstandard amino acids for which little or no data exists. Finally, using both docking and molecular dynamics simulations, we examine the potential for and limitations of protease crystal structures to impact the design of proteolytically stable peptides. PMID:26270398

  15. Increase of anti-HIV activity of C-peptide fusion inhibitors using a bivalent drug design approach.

    PubMed

    Ling, Yanbo; Xue, Huifang; Jiang, Xifeng; Cai, Lifeng; Liu, Keliang

    2013-09-01

    We reported the design of fusion inhibitors with improved activity using a multivalent inhibitor design strategy. First, we chose C29 as the template sequence, which is a 29-mer peptide derived from HIV-1 gp41 CHR domain and has anti-HIV activity of IC50 118 nM in a cell-cell fusion assay. We optimized the crosslink sites and linkers of the template peptide. We found that N-terminal crosslink caused activity improvement based on the multivalent co-operative effect. Especially, the IC50 of peptide (CAcaC29)2 was improved from 49.02 (monomeric form) to 5.71 nM. Compared with long peptides, short peptides may be more suitable to analyze the co-operative effect. So we selected a shorter peptide C22 to synthesize the bivalent inhibitors. Due its weak helicity, no co-operative effect appeared. Therefore, we chose SC22EK, which were introduced salt bridges to consolidate the helicity based on the natural sequence C22. The cross-linked (CAcaSC22EK)2 was four times more potent than the monomer SC22EK in anti-HIV activity, with an IC50 value of 4.92 nM close to the high active peptide fusion inhibitor C34. The strategy used in this study may be used to design new fusion inhibitors to interfere similar processes. PMID:23906421

  16. Predicting protein-ligand and protein-peptide interfaces

    NASA Astrophysics Data System (ADS)

    Bertolazzi, Paola; Guerra, Concettina; Liuzzi, Giampaolo

    2014-06-01

    The paper deals with the identification of binding sites and concentrates on interactions involving small interfaces. In particular we focus our attention on two major interface types, namely protein-ligand and protein-peptide interfaces. As concerns protein-ligand binding site prediction, we classify the most interesting methods and approaches into four main categories: (a) shape-based methods, (b) alignment-based methods, (c) graph-theoretic approaches and (d) machine learning methods. Class (a) encompasses those methods which employ, in some way, geometric information about the protein surface. Methods falling into class (b) address the prediction problem as an alignment problem, i.e. finding protein-ligand atom pairs that occupy spatially equivalent positions. Graph theoretic approaches, class (c), are mainly based on the definition of a particular graph, known as the protein contact graph, and then apply some sophisticated methods from graph theory to discover subgraphs or score similarities for uncovering functional sites. The last class (d) contains those methods that are based on the learn-from-examples paradigm and that are able to take advantage of the large amount of data available on known protein-ligand pairs. As for protein-peptide interfaces, due to the often disordered nature of the regions involved in binding, shape similarity is no longer a determining factor. Then, in geometry-based methods, geometry is accounted for by providing the relative position of the atoms surrounding the peptide residues in known structures. Finally, also for protein-peptide interfaces, we present a classification of some successful machine learning methods. Indeed, they can be categorized in the way adopted to construct the learning examples. In particular, we envisage three main methods: distance functions, structure and potentials and structure alignment.

  17. Moving beyond Rules: The Development of a Central Nervous System Multiparameter Optimization (CNS MPO) Approach To Enable Alignment of Druglike Properties

    PubMed Central

    2010-01-01

    The interplay among commonly used physicochemical properties in drug design was examined and utilized to create a prospective design tool focused on the alignment of key druglike attributes. Using a set of six physicochemical parameters ((a) lipophilicity, calculated partition coefficient (ClogP); (b) calculated distribution coefficient at pH = 7.4 (ClogD); (c) molecular weight (MW); (d) topological polar surface area (TPSA); (e) number of hydrogen bond donors (HBD); (f) most basic center (pKa)), a druglikeness central nervous system multiparameter optimization (CNS MPO) algorithm was built and applied to a set of marketed CNS drugs (N = 119) and Pfizer CNS candidates (N = 108), as well as to a large diversity set of Pfizer proprietary compounds (N = 11 303). The novel CNS MPO algorithm showed that 74% of marketed CNS drugs displayed a high CNS MPO score (MPO desirability score ≥ 4, using a scale of 0−6), in comparison to 60% of the Pfizer CNS candidates. This analysis suggests that this algorithm could potentially be used to identify compounds with a higher probability of successfully testing hypotheses in the clinic. In addition, a relationship between an increasing CNS MPO score and alignment of key in vitro attributes of drug discovery (favorable permeability, P-glycoprotein (P-gp) efflux, metabolic stability, and safety) was seen in the marketed CNS drug set, the Pfizer candidate set, and the Pfizer proprietary diversity set. The CNS MPO scoring function offers advantages over hard cutoffs or utilization of single parameters to optimize structure−activity relationships (SAR) by expanding medicinal chemistry design space through a holistic assessment approach. Based on six physicochemical properties commonly used by medicinal chemists, the CNS MPO function may be used prospectively at the design stage to accelerate the identification of compounds with increased probability of success. PMID:22778837

  18. Moving Away from the Reference Genome: Evaluating a Peptide Sequencing Tagging Approach for Single Amino Acid Polymorphism Identifications in the Genus Populus

    SciTech Connect

    Abraham, Paul E; Adams, Rachel M; Tuskan, Gerald A; Hettich, Robert {Bob} L

    2013-01-01

    The genetic diversity across natural populations of the model organism, Populus, is extensive, containing a single nucleotide polymorphism roughly every 200 base pairs. When deviations from the reference genome occur in coding regions, they can impact protein sequences. Rather than relying on a static reference database to profile protein expression, we employed a peptide sequence tagging (PST) approach capable of decoding the plasticity of the Populus proteome. Using shotgun proteomics data from two genotypes of P. trichocarpa, a tag-based approach enabled the detection of 6,653 unexpected sequence variants. Through manual validation, our study investigated how the most abundant chemical modification (methionine oxidation) could masquerade as a sequence variant (AlaSer) when few site-determining ions existed. In fact, precise localization of an oxidation site for peptides with more than one potential placement was indeterminate for 70% of the MS/MS spectra. We demonstrate that additional fragment ions made available by high energy collisional dissociation enhances the robustness of the peptide sequence tagging approach (81% of oxidation events could be exclusively localized to a methionine). We are confident that augmenting fragmentation processes for a PST approach will further improve the identification of single amino acid polymorphism in Populus and potentially other species as well.

  19. Communication About Sexuality in Advanced Illness Aligns With a Palliative Care Approach to Patient-Centered Care.

    PubMed

    Leung, Margaret W; Goldfarb, Shari; Dizon, Don S

    2016-02-01

    Treatment-related sexual complications are common in cancer patients although rarely discussed in the palliative care setting. Sexuality is an important survivorship issue and remains relevant even in the terminal setting. There are multiple barriers in dialoguing about intimacy and sexual functioning from the patient and provider perspectives. Palliative care providers, while not expected to be sexual health experts, can provide comprehensive patient-centered care by including sexual health as part of their evaluation. They can explore how sexual dysfunction can impair functioning and utilize an interdisciplinary approach to manage symptoms. Palliative care providers can help patients identify their goals of care and explore what anticipated sexual changes and treat-related side effects are tolerable and intolerable to the patient's quality of life. Principles on addressing sexuality in the palliative setting and practical ways of incorporating sexual history into the palliative care assessment are provided. PMID:26769116

  20. Probabilistic Mixture Regression Models for Alignment of LC-MS Data

    PubMed Central

    Befekadu, Getachew K.; Tadesse, Mahlet G.; Tsai, Tsung-Heng; Ressom, Habtom W.

    2010-01-01

    A novel framework of a probabilistic mixture regression model (PMRM) is presented for alignment of liquid chromatography-mass spectrometry (LC-MS) data with respect to both retention time (RT) and mass-to-charge ratio (m/z). The expectation maximization algorithm is used to estimate the joint parameters of spline-based mixture regression models and prior transformation density models. The latter accounts for the variability in RT points, m/z values, and peak intensities. The applicability of PMRM for alignment of LC-MS data is demonstrated through three datasets. The performance of PMRM is compared with other alignment approaches including dynamic time warping, correlation optimized warping, and continuous profile model in terms of coefficient variation of replicate LC-MS runs and accuracy in detecting differentially abundant peptides/proteins. PMID:20837998

  1. A gynecologic oncology group phase II trial of two p53 peptide vaccine approaches: subcutaneous injection and intravenous pulsed dendritic cells in high recurrence risk ovarian cancer patients

    PubMed Central

    Rahma, Osama E.; Ashtar, Ed; Czystowska, Malgorzata; Szajnik, Marta E.; Wieckowski, Eva; Bernstein, Sarah; Herrin, Vincent E.; Shams, Mortada A.; Steinberg, Seth M.; Merino, Maria; Gooding, William; Visus, Carmen; DeLeo, Albert B.; Wolf, Judith K.; Bell, Jeffrey G.; Berzofsky, Jay A.; Whiteside, Theresa L.; Khleif, Samir N.

    2013-01-01

    Purpose Peptide antigens have been administered by different approaches as cancer vaccine therapy, including direct injection or pulsed onto dendritic cells; however, the optimal delivery method is still debatable. In this study, we describe the immune response elicited by two vaccine approaches using the wild-type (wt) p53 vaccine. Experimental design Twenty-one HLA-A2.1 patients with stage III, IV, or recurrent ovarian cancer over-expressing the p53 protein with no evidence of disease were treated in two cohorts. Arm A received SC wt p53:264-272 peptide admixed with Montanide and GM-CSF. Arm B received wt p53:264-272 peptide-pulsed dendritic cells IV. Interleukin-2 (IL-2) was administered to both cohorts in alternative cycles. Results Nine of 13 patients (69%) in arm A and 5 of 6 patients (83%) in arm B developed an immunologic response as determined by ELISPOT and tetramer assays. The vaccine caused no serious systemic side effects. IL-2 administration resulted in grade 3 and 4 toxicities in both arms and directly induced the expansion of T regulatory cells. The median overall survival was 40.8 and 29.6 months for arm A and B, respectively; the median progression-free survival was 4.2 and. 8.7 months, respectively. Conclusion We found that using either vaccination approach generates comparable specific immune responses against the p53 peptide with minimal toxicity. Accordingly, our findings suggest that the use of less demanding SC approach may be as effective. Furthermore, the use of low-dose SC IL-2 as an adjuvant might have interfered with the immune response. Therefore, it may not be needed in future trials. PMID:21927947

  2. QSBR study of bitter taste of peptides: application of GA-PLS in combination with MLR, SVM, and ANN approaches.

    PubMed

    Soltani, Somaieh; Haghaei, Hossein; Shayanfar, Ali; Vallipour, Javad; Asadpour Zeynali, Karim; Jouyban, Abolghasem

    2013-01-01

    Detailed information about the relationships between structures and properties/activities of peptides as drugs and nutrients is useful in the development of drugs and functional foods containing peptides as active compounds. The bitterness of the peptides is an undesirable property which should be reduced during drug/nutrient production, and quantitative structure bitter taste relationship (QSBR) studies can help researchers to design less bitter peptides with higher target efficiency. Calculated structural parameters were used to develop three different QSBR models (i.e., multiple linear regression, support vector machine, and artificial neural network) to predict the bitterness of 229 peptides (containing 2-12 amino acids, obtained from the literature). The developed models were validated using internal and external validation methods, and the prediction errors were checked using mean percentage deviation and absolute average error values. All developed models predicted the activities successfully (with prediction errors less than experimental error values), whereas the prediction errors for nonlinear methods were less than those for linear methods. The selected structural descriptors successfully differentiated between bitter and nonbitter peptides. PMID:24371826

  3. Development and optimization of on-line 2-dimensional chromatographic approaches for eliminating matrix effects and improving bioanalysis of peptides in human plasma using UHPLC-MS/MS.

    PubMed

    Ismaiel, Omnia A; Jenkins, Rand G

    2014-05-01

    Online 2-dimensional chromatographic approaches for eliminating matrix effects and optimizing bioanalysis of peptides using ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) were studied. Three therapeutic peptides (octreotide, desmopressin, and vasopressin) were selected as model analytes. Human plasma was precipitated with acetonitrile; peptides were analyzed on C(8), C(18), Phenyl and HILIC ACQUITY UPLC columns. For simpler online clean-up applications, a C(18) pre-column was coupled to the analytical column via a switching valve. For more complex heart-cutting applications, two analytical columns were used with optional online dilution to refocus the analyte peaks prior to the second dimension separation. This allows the use of MS incompatible mobile phases, such as TFA, in the first dimension separation. Online clean-up effectiveness was investigated by monitoring phospholipids. Flushing direction, mobile phase composition, flow rate and transfer window were evaluated. Phospholipids were readily retained on reversed-phase columns, and the peptides were reproducibly transferred, individually or as a group, to the second column using appropriate transfer windows. The best peak shapes were obtained when the second dimension column was more retentive (e.g. C(18) vs. C(8)). However, C(8) to HILIC gave broad unresolved peaks due to mobile phase mismatch. Trapped phospholipids were efficiently removed from either guard columns or first dimensional columns by forward- or back-flushing at high flows; however, back-flushing was more efficient with lower flow rates on larger columns. PMID:23918459

  4. N-terminal sequence tagging using reliably determined b2 ions: a useful approach to deconvolute tandem mass spectra of co-fragmented peptides in proteomics.

    PubMed

    Kryuchkov, Fedor; Verano-Braga, Thiago; Kjeldsen, Frank

    2014-05-30

    With the recent introduction of higher-energy collisional dissociation (HCD) in Orbitrap mass spectrometry, the popularity of that technique has grown tremendously in the proteomics society. HCD spectra, however, are characterized by a limited distribution of bn-type ions, which permit the generation of reliable sequence tags based on complementary b,y pairs both for de novo sequencing and sequence tagging strategies. Instead, most peptide HCD spectra (~95%) are dominated with b2 ions. In this work, we analyzed positive predictive values of b2 ions in HCD, and found that b2 ions can be determined with >97% certainty in the presence of a2 and its complementary yn-2 ions. Analytically, b2 ions provide information on the composition of the first two N-terminal amino acids in peptides. Their utilization in N-terminal sequence tagging leads to a significant decrease in false discovery rate by filtering out false positives while retaining true positive identifications. As a consequence, the number of peptide spectrum matches (PSMs) increased by 4.8% at fixed FDR (1%). This approach allows for deconvolution of mixture spectra and increased the number of PSM to 9.2% in a complex human sample and to 24% in a complex sample of synthetic peptides at 1% FDR. PMID:24726481

  5. Development of surface modified biodegradable polymeric nanoparticles to deliver GSE24.2 peptide to cells: a promising approach for the treatment of defective telomerase disorders.

    PubMed

    Egusquiaguirre, Susana P; Manguán-García, Cristina; Pintado-Berninches, Laura; Iarriccio, Laura; Carbajo, Daniel; Albericio, Fernando; Royo, Miriam; Pedraz, José Luís; Hernández, Rosa M; Perona, Rosario; Igartua, Manuela

    2015-04-01

    The aim of the present study was to develop a novel strategy to deliver intracellularly the peptide GSE24.2 for the treatment of Dyskeratosis congenita (DC) and other defective telomerase disorders. For this purpose, biodegradable polymeric nanoparticles using poly(lactic-co-glycolic acid) (PLGA NPs) or poly(lactic-co-glycolic acid)-poly ethylene glycol (PLGA-PEG NPs) attached to either polycations or cell-penetrating peptides (CPPs) were prepared in order to increase their cellular uptake. The particles exhibited an adequate size and zeta potential, with good peptide loading and a biphasic pattern obtained in the in vitro release assay, showing an initial burst release and a later sustained release. GSE24.2 structural integrity after encapsulation was assessed using SDS-PAGE, revealing an unaltered peptide after the NPs elaboration. According to the cytotoxicity results, cell viability was not affected by uncoated polymeric NPs, but the incorporation of surface modifiers slightly decreased the viability of cells. The intracellular uptake exhibited a remarkable improvement of the internalization, when the NPs were conjugated to the CPPs. Finally, the bioactivity, addressed by measuring DNA damage rescue and telomerase reactivation, showed that some formulations had the lowest cytotoxicity and highest biological activity. These results proved that GSE24.2-loaded NPs could be delivered to cells, and therefore, become an effective approach for the treatment of DC and other defective telomerase syndromes. PMID:25660910

  6. Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping--a novel approach to assess intermolecular protein contacts.

    PubMed Central

    Bennett, K. L.; Kussmann, M.; Björk, P.; Godzwon, M.; Mikkelsen, M.; Sørensen, P.; Roepstorff, P.

    2000-01-01

    The intermolecular contact regions between monomers of the homodimeric DNA binding protein ParR and the interaction between the glycoproteins CD28 and CD80 were investigated using a strategy that combined chemical cross-linking with differential MALDI-MS analyses. ParR dimers were modified in vitro with the thiol-cleavable cross-linker 3,3'-dithio-bis(succinimidylproprionate) (DTSSP), proteolytically digested with trypsin and analyzed by MALDI-MS peptide mapping. Comparison of the peptide maps obtained from digested cross-linked ParR dimers in the presence and absence of a thiol reagent strongly supported a "head-to-tail" arrangement of the monomers in the dimeric complex. Glycoprotein fusion constructs CD28-IgG and CD80-Fab were cross-linked in vitro by DTSSP, characterized by nonreducing SDS-PAGE, digested in situ with trypsin and analyzed by MALDI-MS peptide mapping (+/- thiol reagent). The data revealed the presence of an intermolecular cross-link between the receptor regions of the glycoprotein constructs, as well as a number of unexpected but nonetheless specific interactions between the fusion domains of CD28-IgG and the receptor domain of CD80-Fab. The strategy of chemical cross-linking combined with differential MALDI-MS peptide mapping (+ thiol reagent) enabled localization of the interface region(s) of the complexes studied and clearly demonstrates the utility of such an approach to obtain structural information on interacting noncovalent complexes. PMID:10975572

  7. DNA Align Editor: DNA Alignment Editor Tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The SNPAlignEditor is a DNA sequence alignment editor that runs on Windows platforms. The purpose of the program is to provide an intuitive, user-friendly tool for manual editing of multiple sequence alignments by providing functions for input, editing, and output of nucleotide sequence alignments....

  8. Polycyclic peptide therapeutics.

    PubMed

    Baeriswyl, Vanessa; Heinis, Christian

    2013-03-01

    Owing to their excellent binding properties, high stability, and low off-target toxicity, polycyclic peptides are an attractive molecule format for the development of therapeutics. Currently, only a handful of polycyclic peptides are used in the clinic; examples include the antibiotic vancomycin, the anticancer drugs actinomycin D and romidepsin, and the analgesic agent ziconotide. All clinically used polycyclic peptide drugs are derived from natural sources, such as soil bacteria in the case of vancomycin, actinomycin D and romidepsin, or the venom of a fish-hunting coil snail in the case of ziconotide. Unfortunately, nature provides peptide macrocyclic ligands for only a small fraction of therapeutic targets. For the generation of ligands of targets of choice, researchers have inserted artificial binding sites into natural polycyclic peptide scaffolds, such as cystine knot proteins, using rational design or directed evolution approaches. More recently, large combinatorial libraries of genetically encoded bicyclic peptides have been generated de novo and screened by phage display. In this Minireview, the properties of existing polycyclic peptide drugs are discussed and related to their interesting molecular architectures. Furthermore, technologies that allow the development of unnatural polycyclic peptide ligands are discussed. Recent application of these technologies has generated promising results, suggesting that polycyclic peptide therapeutics could potentially be developed for a broad range of diseases. PMID:23355488

  9. Mapping protein-protein interactions with phage-displayed combinatorial peptide libraries and alanine scanning.

    PubMed

    Kokoszka, Malgorzata E; Kay, Brian K

    2015-01-01

    One avenue for inferring the function of a protein is to learn what proteins it may bind to in the cell. Among the various methodologies, one way for doing so is to affinity select peptide ligands from a phage-displayed combinatorial peptide library and then to examine if the proteins that carry such peptide sequences interact with the target protein in the cell. With the protocols described in this chapter, a laboratory with skills in microbiology, molecular biology, and protein biochemistry can readily identify peptides in the library that bind selectively, and with micromolar affinity, to a given target protein on the time scale of 2 months. To illustrate this approach, we use a library of bacteriophage M13 particles, which display 12-mer combinatorial peptides, to affinity select different peptide ligands for two different targets, the SH3 domain of the human Lyn protein tyrosine kinase and a segment of the yeast serine/threonine protein kinase Cbk1. The binding properties of the selected peptide ligands are then dissected by sequence alignment, Kunkel mutagenesis, and alanine scanning. Finally, the peptide ligands can be used to predict cellular interacting proteins and serve as the starting point for drug discovery. PMID:25616333

  10. Aligning for Innovation - Alignment Strategy to Drive Innovation

    NASA Technical Reports Server (NTRS)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  11. Peptides of presenilin-1 bind the amyloid precursor protein ectodomain and offer a novel and specific therapeutic approach to reduce ß-amyloid in Alzheimer's disease.

    PubMed

    Dewji, Nazneen N; Singer, S Jonathan; Masliah, Eliezer; Rockenstein, Edward; Kim, Mihyun; Harber, Martha; Horwood, Taylor

    2015-01-01

    β-Amyloid (Aβ) accumulation in the brain is widely accepted to be critical to the development of Alzheimer's disease (AD). Current efforts at reducing toxic Aβ40 or 42 have largely focused on modulating γ-secretase activity to produce shorter, less toxic Aβ, while attempting to spare other secretase functions. In this paper we provide data that offer the potential for a new approach for the treatment of AD. The method is based on our previous findings that the production of Aβ from the interaction between the β-amyloid precursor protein (APP) and Presenilin (PS), as part of the γ-secretase complex, in cell culture is largely inhibited if the entire water-soluble NH2-terminal domain of PS is first added to the culture. Here we demonstrate that two small, non-overlapping water-soluble peptides from the PS-1 NH2-terminal domain can substantially and specifically inhibit the production of total Aβ as well as Aβ40 and 42 in vitro and in vivo in the brains of APP transgenic mice. These results suggest that the inhibitory activity of the entire amino terminal domain of PS-1 on Aβ production is largely focused in a few smaller sequences within that domain. Using biolayer interferometry and confocal microscopy we provide evidence that peptides effective in reducing Aβ give a strong, specific and biologically relevant binding with the purified ectodomain of APP 695. Finally, we demonstrate that the reduction of Aβ by the peptides does not affect the catalytic activities of β- or γ-secretase, or the level of APP. P4 and P8 are the first reported protein site-specific small peptides to reduce Aβ production in model systems of AD. These peptides and their derivatives offer new potential drug candidates for the treatment of AD. PMID:25923432

  12. Strategy-aligned fuzzy approach for market segment evaluation and selection: a modular decision support system by dynamic network process (DNP)

    NASA Astrophysics Data System (ADS)

    Mohammadi Nasrabadi, Ali; Hosseinpour, Mohammad Hossein; Ebrahimnejad, Sadoullah

    2013-05-01

    In competitive markets, market segmentation is a critical point of business, and it can be used as a generic strategy. In each segment, strategies lead companies to their targets; thus, segment selection and the application of the appropriate strategies over time are very important to achieve successful business. This paper aims to model a strategy-aligned fuzzy approach to market segment evaluation and selection. A modular decision support system (DSS) is developed to select an optimum segment with its appropriate strategies. The suggested DSS has two main modules. The first one is SPACE matrix which indicates the risk of each segment. Also, it determines the long-term strategies. The second module finds the most preferred segment-strategies over time. Dynamic network process is applied to prioritize segment-strategies according to five competitive force factors. There is vagueness in pairwise comparisons, and this vagueness has been modeled using fuzzy concepts. To clarify, an example is illustrated by a case study in Iran's coffee market. The results show that success possibility of segments could be different, and choosing the best ones could help companies to be sure in developing their business. Moreover, changing the priority of strategies over time indicates the importance of long-term planning. This fact has been supported by a case study on strategic priority difference in short- and long-term consideration.

  13. Accelerator and transport line survey and alignment

    SciTech Connect

    Ruland, R.E.

    1991-10-01

    This paper summarizes the survey and alignment processes of accelerators and transport lines and discusses the propagation of errors associated with these processes. The major geodetic principles governing the survey and alignment measurement space are introduced and their relationship to a lattice coordinate system shown. The paper continues with a broad overview about the activities involved in the step sequence from initial absolute alignment to final smoothing. Emphasis is given to the relative alignment of components, in particular to the importance of incorporating methods to remove residual systematic effects in surveying and alignment operations. Various approaches to smoothing used at major laboratories are discussed. 47 refs., 19 figs., 1 tab.

  14. Biochemical functionalization of peptide nanotubes with phage displayed peptides.

    PubMed

    Swaminathan, Swathi; Cui, Yue

    2016-09-01

    The development of a general approach for the biochemical functionalization of peptide nanotubes (PNTs) could open up existing opportunities in both fundamental studies as well as a variety of applications. PNTs are spontaneously assembled organic nanostructures made from peptides. Phage display has emerged as a powerful approach for identifying selective peptide binding motifs. Here, we demonstrate for the first time the biochemical functionalization of PNTs via peptides identified from a phage display peptide library. The phage-displayed peptides are shown to recognize PNTs. These advances further allow for the development of bifunctional peptides for the capture of bacteria and the self-assembly of silver particles onto PNTs. We anticipate that these results could provide significant opportunities for using PNTs in both fundamental studies and practical applications, including sensors and biosensors nanoelectronics, energy storage devices, drug delivery, and tissue engineering. PMID:27479451

  15. Biochemical functionalization of peptide nanotubes with phage displayed peptides

    NASA Astrophysics Data System (ADS)

    Swaminathan, Swathi; Cui, Yue

    2016-09-01

    The development of a general approach for the biochemical functionalization of peptide nanotubes (PNTs) could open up existing opportunities in both fundamental studies as well as a variety of applications. PNTs are spontaneously assembled organic nanostructures made from peptides. Phage display has emerged as a powerful approach for identifying selective peptide binding motifs. Here, we demonstrate for the first time the biochemical functionalization of PNTs via peptides identified from a phage display peptide library. The phage-displayed peptides are shown to recognize PNTs. These advances further allow for the development of bifunctional peptides for the capture of bacteria and the self-assembly of silver particles onto PNTs. We anticipate that these results could provide significant opportunities for using PNTs in both fundamental studies and practical applications, including sensors and biosensors nanoelectronics, energy storage devices, drug delivery, and tissue engineering.

  16. Antagonistic peptide technology for functional dissection of CLE peptides revisited

    PubMed Central

    Czyzewicz, Nathan; Wildhagen, Mari; Cattaneo, Pietro; Stahl, Yvonne; Pinto, Karine Gustavo; Aalen, Reidunn B.; Butenko, Melinka A.; Simon, Rüdiger; Hardtke, Christian S.; De Smet, Ive

    2015-01-01

    In the Arabidopsis thaliana genome, over 1000 putative genes encoding small, presumably secreted, signalling peptides can be recognized. However, a major obstacle in identifying the function of genes encoding small signalling peptides is the limited number of available loss-of-function mutants. To overcome this, a promising new tool, antagonistic peptide technology, was recently developed. Here, this antagonistic peptide technology was tested on selected CLE peptides and the related IDA peptide and its usefulness in the context of studies of peptide function discussed. Based on the analyses, it was concluded that the antagonistic peptide approach is not the ultimate means to overcome redundancy or lack of loss-of-function lines. However, information collected using antagonistic peptide approaches (in the broad sense) can be very useful, but these approaches do not work in all cases and require a deep insight on the interaction between the ligand and its receptor to be successful. This, as well as peptide ligand structure considerations, should be taken into account before ordering a wide range of synthetic peptide variants and/or generating transgenic plants. PMID:26136270

  17. Antagonistic peptide technology for functional dissection of CLE peptides revisited.

    PubMed

    Czyzewicz, Nathan; Wildhagen, Mari; Cattaneo, Pietro; Stahl, Yvonne; Pinto, Karine Gustavo; Aalen, Reidunn B; Butenko, Melinka A; Simon, Rüdiger; Hardtke, Christian S; De Smet, Ive

    2015-08-01

    In the Arabidopsis thaliana genome, over 1000 putative genes encoding small, presumably secreted, signalling peptides can be recognized. However, a major obstacle in identifying the function of genes encoding small signalling peptides is the limited number of available loss-of-function mutants. To overcome this, a promising new tool, antagonistic peptide technology, was recently developed. Here, this antagonistic peptide technology was tested on selected CLE peptides and the related IDA peptide and its usefulness in the context of studies of peptide function discussed. Based on the analyses, it was concluded that the antagonistic peptide approach is not the ultimate means to overcome redundancy or lack of loss-of-function lines. However, information collected using antagonistic peptide approaches (in the broad sense) can be very useful, but these approaches do not work in all cases and require a deep insight on the interaction between the ligand and its receptor to be successful. This, as well as peptide ligand structure considerations, should be taken into account before ordering a wide range of synthetic peptide variants and/or generating transgenic plants. PMID:26136270

  18. Antimicrobial peptides

    PubMed Central

    2014-01-01

    With increasing antibiotics resistance, there is an urgent need for novel infection therapeutics. Since antimicrobial peptides provide opportunities for this, identification and optimization of such peptides have attracted much interest during recent years. Here, a brief overview of antimicrobial peptides is provided, with focus placed on how selected hydrophobic modifications of antimicrobial peptides can be employed to combat also more demanding pathogens, including multi-resistant strains, without conferring unacceptable toxicity. PMID:24758244

  19. MALDI TOF/TOF-Based Approach for the Identification of d- Amino Acids in Biologically Active Peptides and Proteins.

    PubMed

    Koehbach, Johannes; Gruber, Christian W; Becker, Christian; Kreil, David P; Jilek, Alexander

    2016-05-01

    Several biologically active peptides contain a d- amino acid in a well-defined position, which is position 2 in all peptide epimers isolated to date from vertebrates and also some from invertebrates. The detection of such D- residues by standard analytical techniques is challenging. In tandem mass spectrometric (MS) analysis, although fragment masses are the same for all stereoisomers, peak intensities are known to depend on chirality. Here, we observe that the effect of a d- amino acid in the second N-terminal position on the fragmentation pattern in matrix assisted laser desorption time-of-flight spectrometry (MALDI-TOF/TOF MS) strongly depends on the peptide sequence. Stereosensitive fragmentation (SF) is correlated to a neighborhood effect, but the d- residue also exerts an overall effect influencing distant bonds. In a fingerprint analysis, multiple peaks can thus serve to identify the chirality of a sample in short time and potentially high throughput. Problematic variations between individual spots could be successfully suppressed by cospotting deuterated analogues of the epimers. By identifying the [d-Leu2] isomer of the predicted peptide GH-2 (gene derived bombininH) in skin secretions of the toad Bombina orientalis, we demonstrated the analytical power of SF-MALDI-TOF/TOF measurements. In conclusion, SF-MALDI-TOF/TOF MS combines high sensitivity, versatility, and the ability to complement other methods. PMID:26985971

  20. A bottom-up approach to build the hyperpolarizability of peptides and proteins from their amino acids.

    PubMed

    Duboisset, Julien; Deniset-Besseau, Ariane; Benichou, Emmanuel; Russier-Antoine, Isabelle; Lascoux, Noelle; Jonin, Christian; Hache, François; Schanne-Klein, Marie-Claire; Brevet, Pierre-François

    2013-08-29

    We experimentally demonstrate that some peptides and proteins lend themselves to an elementary analysis where their first hyperpolarizability can be decomposed into the coherent superposition of the first hyperpolarizability of their elementary units. We then show that those elementary units can be associated with the amino acids themselves in the case of nonaromatic amino acids and nonresonant second harmonic generation. As a case study, this work investigates the experimentally determined first hyperpolarizability of rat tail Type I collagen and compares it to that of the shorter peptide [(PPG)10]3, where P and G are the one-letter code for Proline and Glycine, respectively, and that of the triamino acid peptides PPG and GGG. An absolute value of (0.16 ± 0.01) × 10(-30) esu for the first hyperpolarizability of nonaromatic amino acids is then obtained by using the newly defined 0.087 × 10(-30) esu reference value for water. By using a collagen like model, the microscopic hyperpolarizability along the peptide bond can be evaluated at (0.7 ± 0.1) × 10(-30) esu. PMID:23879840

  1. Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach

    SciTech Connect

    Economou, Nicoleta J.; Zentner, Isaac J.; Lazo, Edwin; Jakoncic, Jean; Stojanoff, Vivian; Weeks, Stephen D.; Grasty, Kimberly C.; Cocklin, Simon; Loll, Patrick J.

    2013-04-01

    Using a carrier-protein strategy, the structure of teicoplanin bound to its bacterial cell-wall target has been determined. The structure reveals the molecular determinants of target recognition, flexibility in the antibiotic backbone and intrinsic radiation sensitivity of teicoplanin. Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a d-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein–peptide–antibiotic complex. The 2.05 Å resolution MBP–peptide–teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance.

  2. Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach

    PubMed Central

    Economou, Nicoleta J.; Zentner, Isaac J.; Lazo, Edwin; Jakoncic, Jean; Stojanoff, Vivian; Weeks, Stephen D.; Grasty, Kimberly C.; Cocklin, Simon; Loll, Patrick J.

    2013-01-01

    Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a d-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein–peptide–antibiotic complex. The 2.05 Å resolution MBP–peptide–teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance. PMID:23519660

  3. MALDI TOF/TOF-Based Approach for the Identification of d- Amino Acids in Biologically Active Peptides and Proteins

    PubMed Central

    2016-01-01

    Several biologically active peptides contain a d- amino acid in a well-defined position, which is position 2 in all peptide epimers isolated to date from vertebrates and also some from invertebrates. The detection of such D- residues by standard analytical techniques is challenging. In tandem mass spectrometric (MS) analysis, although fragment masses are the same for all stereoisomers, peak intensities are known to depend on chirality. Here, we observe that the effect of a d- amino acid in the second N-terminal position on the fragmentation pattern in matrix assisted laser desorption time-of-flight spectrometry (MALDI-TOF/TOF MS) strongly depends on the peptide sequence. Stereosensitive fragmentation (SF) is correlated to a neighborhood effect, but the d- residue also exerts an overall effect influencing distant bonds. In a fingerprint analysis, multiple peaks can thus serve to identify the chirality of a sample in short time and potentially high throughput. Problematic variations between individual spots could be successfully suppressed by cospotting deuterated analogues of the epimers. By identifying the [d-Leu2] isomer of the predicted peptide GH-2 (gene derived bombininH) in skin secretions of the toad Bombina orientalis, we demonstrated the analytical power of SF-MALDI-TOF/TOF measurements. In conclusion, SF-MALDI-TOF/TOF MS combines high sensitivity, versatility, and the ability to complement other methods. PMID:26985971

  4. Target alignment in the National Ignition Facility

    SciTech Connect

    Vann, C.S.; Bliss, E.S.; Murray, J.E.

    1994-06-06

    Accurate placement of hundreds of focused laser beams on target is necessary to achieve success in the National Ignition Facility (NIF). The current system requirement is {le}7 {mu}rad error in output pointing and {le}1 mm error in focusing. To accommodate several system shots per day, a target alignment system must be able to align the target to chamber center, inject an alignment beam to represent each shot beam, and point and focus the alignment beams onto the target in about one hour. At Lawrence Livermore National Laboratory, we have developed a target alignment concept and built a prototype to validate the approach. The concept comprises three systems: the chamber center reference, target alignment sensor, and target alignment beams.

  5. MHC2SKpan: a novel kernel based approach for pan-specific MHC class II peptide binding prediction

    PubMed Central

    2013-01-01

    Background Computational methods for the prediction of Major Histocompatibility Complex (MHC) class II binding peptides play an important role in facilitating the understanding of immune recognition and the process of epitope discovery. To develop an effective computational method, we need to consider two important characteristics of the problem: (1) the length of binding peptides is highly flexible; and (2) MHC molecules are extremely polymorphic and for the vast majority of them there are no sufficient training data. Methods We develop a novel string kernel MHC2SK (MHC-II String Kernel) method to measure the similarities among peptides with variable lengths. By considering the distinct features of MHC-II peptide binding prediction problem, MHC2SK differs significantly from the recently developed kernel based method, GS (Generic String) kernel, in the way of computing similarities. Furthermore, we extend MHC2SK to MHC2SKpan for pan-specific MHC-II peptide binding prediction by leveraging the binding data of various MHC molecules. Results MHC2SK outperformed GS in allele specific prediction using a benchmark dataset, which demonstrates the effectiveness of MHC2SK. Furthermore, we evaluated the performance of MHC2SKpan using various benckmark data sets from several different perspectives: Leave-one-allele-out (LOO), 5-fold cross validation as well as independent data testing. MHC2SKpan has achieved comparable performance with NetMHCIIpan-2.0 and outperformed NetMHCIIpan-1.0, TEPITOPEpan and MultiRTA, being statistically significant. MHC2SKpan can be freely accessed at http://datamining-iip.fudan.edu.cn/service/MHC2SKpan/index.html. PMID:24564280

  6. Exploiting non-linear relationships between retention time and molecular structure of peptides originating from proteomes and comparing three multivariate approaches.

    PubMed

    Žuvela, Petar; Macur, Katarzyna; Jay Liu, J; Bączek, Tomasz

    2016-08-01

    Peptides' retention time prediction is gaining increasing popularity in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics. This is a promising approach for improving successful proteome mapping, useful both in identification and quantification workflows. In this work, a quantitative structure-retention relationships (QSRR) model for its direct prediction from the molecular structure of 185 peptides originating from 8 well-characterized proteins and two Bacillus subtilis proteomes has been developed. Genetic Algorithm (GA) was used for selection of a subset of molecular descriptors coupled with three machine learning methods: Support Vector Regression (SVR), Artificial Neural Networks (ANN), and kernel Partial Least Squares (kPLS) for regression. Final GA-SVR, GA-ANN, and GA-kPLS models were validated through an external validation set of 95 peptides originating from the human epithelial HeLa cells proteomes. Robustness and stability was ensured by defining their applicability domain. The descriptors of the developed models were interpreted confirming a causal relationship between parameters of molecular structure and retention time. GA-SVR model has shown to be superior over the others in terms of both predictive ability, and interpretation of the selected descriptors. PMID:26856456

  7. Shuttle-cargo fusion molecules of transport peptides and the hD2/3 receptor antagonist fallypride: a feasible approach to preserve ligand-receptor binding?

    PubMed

    Wängler, Carmen; Chowdhury, Shafinaz; Höfner, Georg; Djurova, Petia; Purisima, Enrico O; Bartenstein, Peter; Wängler, Björn; Fricker, Gert; Wanner, Klaus T; Schirrmacher, Ralf

    2014-05-22

    To determine if the conjugation of a small receptor ligand to a peptidic carrier to potentially facilitate transport across the blood-brain barrier (BBB) by "molecular Trojan horse" transcytosis is feasible, we synthesized several transport peptide-fallypride fusion molecules as model systems and determined their binding affinities to the hD2 receptor. Although they were affected by conjugation, the binding affinities were found to be still in the nanomolar range (between 1.5 and 64.2 nM). In addition, homology modeling of the receptor and docking studies for the most potent compounds were performed, elucidating the binding modes of the fusion molecules and the structure elements contributing to the observed high receptor binding. Furthermore, no interaction between the hybrid compounds and P-gp, the main excretory transporter of the BBB, was found. From these results, it can be inferred that the approach to deliver small neuroreceptor ligands across the BBB by transport peptide carriers is feasible. PMID:24779610

  8. Aligned Nanofibers for Regenerating Arteries, Nerves, and Muscles

    NASA Astrophysics Data System (ADS)

    McClendon, Mark Trosper

    annular gap containing PA solution with a rotating rod. Using the shear aligning properties of PA solutions this rotating surface in contact with the PA solution induced a high degree of alignment in the nanofibers which was subsequently locked in place by introducing gelating calcium ions. again say something about what this fabrication procedure entails Cells encapsulated within these tubes responded to the alignment by extending in the circumferential direction mimicking the same cellular alignment observed in native arteries. A similar design strategy was also used to align nanofibers within the core of biopolymer nerve conduits, and these scaffolds were implanted in a rat sciatic nerve model. Histological and behavioral observations confirmed that PA implants sustained regeneration rates comparable to autologous grafts and significantly better than empty biopolymer grafts. Furthermore, these nanofiber gels were used as a vehicle to deliver stem cells into muscle tissue. A specialized injector was designed to introduce aligned PA gels into mouse leg muscles in a 1cm long channel. Bioluminescence and histology showed that stem cell engraftment into myofibers was greatly enhanced when delivered by PA gels compared to saline solution. The final section of this thesis describes a new series of PA molecules designed to degrade upon exposure to UV lightstate here why is this of interest in the context of the work described in the thesis. This was done to understand the degradation behavior of PA nanofibers and provide a controlled approach to changing the rheological properties post gelation.The three PA molecules in this series contained the same peptide sequence V3A3E3, while varying the location of a nitrobenzyl UV-reactive group along the backbone of the molecule. This system allowed for a quick reaction that cleaves the molecule at the reactive nitrobenzyl site without introducing any other reactive molecules. While all three molecules produced nanofibers that remained

  9. Adipokinetic hormone-immunoreactive peptide in the endocrine and central nervous system of several insect species: a comparative immunocytochemical approach.

    PubMed

    Schooneveld, H; Romberg-Privee, H M; Veenstra, J A

    1985-02-01

    The distribution of intrinsic glandular cells containing adipokinetic hormone (AKH)-like material in the corpora cardiaca (CC) and the occurrence of immunoreactive neurons in the nervous system in 19 species belonging to nine insect orders was studied by means of an immunocytochemical method (peroxidase-antiperoxidase), with antisera raised against an AKH analogue [( Tyr1]-AKH). The CC gland cells in Locusta migratoria migratorioides and Schistocerca americana gregaria were strongly immunoreactive. Those in other orders showed less or no immunoreactivity indicating that AKH has a very restricted distribution. Neurons containing immunoreactive material were found in the brain and ventral ganglia in all species investigated. As the specificity of the antiserum has not been determined, it is not known whether this peptide is identical to AKH. Considering the distribution of their axons, these neurons may be involved with one or more of the following functions: (1) nervous communication within the central nervous system; (2) communication with the stomatogastric nervous system; (3) possible release of peptide from the CC; (4) release of neuropeptide in or from the corpus allatum. A combination of these features has been found in only a few of the species investigated. The immunocytochemical study demonstrated significant differences among species belonging to Apterygota, Hemi-, and Holometabola in the number of neurons, the length and degree of branching of their axon, and the amount of immunoreactive peptide stored therein. PMID:3979801

  10. A Novel Peptide Binding Prediction Approach for HLA-DR Molecule Based on Sequence and Structural Information

    PubMed Central

    Li, Zhao; Zhao, Yilei; Pan, Gaofeng; Tang, Jijun; Guo, Fei

    2016-01-01

    MHC molecule plays a key role in immunology, and the molecule binding reaction with peptide is an important prerequisite for T cell immunity induced. MHC II molecules do not have conserved residues, so they appear as open grooves. As a consequence, this will increase the difficulty in predicting MHC II molecules binding peptides. In this paper, we aim to propose a novel prediction method for MHC II molecules binding peptides. First, we calculate sequence similarity and structural similarity between different MHC II molecules. Then, we reorder pseudosequences according to descending similarity values and use a weight calculation formula to calculate new pocket profiles. Finally, we use three scoring functions to predict binding cores and evaluate the accuracy of prediction to judge performance of each scoring function. In the experiment, we set a parameter α in the weight formula. By changing α value, we can observe different performances of each scoring function. We compare our method with the best function to some popular prediction methods and ultimately find that our method outperforms them in identifying binding cores of HLA-DR molecules. PMID:27340658

  11. Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach*

    PubMed Central

    Carr, Steven A.; Abbatiello, Susan E.; Ackermann, Bradley L.; Borchers, Christoph; Domon, Bruno; Deutsch, Eric W.; Grant, Russell P.; Hoofnagle, Andrew N.; Hüttenhain, Ruth; Koomen, John M.; Liebler, Daniel C.; Liu, Tao; MacLean, Brendan; Mani, DR; Mansfield, Elizabeth; Neubert, Hendrik; Paulovich, Amanda G.; Reiter, Lukas; Vitek, Olga; Aebersold, Ruedi; Anderson, Leigh; Bethem, Robert; Blonder, Josip; Boja, Emily; Botelho, Julianne; Boyne, Michael; Bradshaw, Ralph A.; Burlingame, Alma L.; Chan, Daniel; Keshishian, Hasmik; Kuhn, Eric; Kinsinger, Christopher; Lee, Jerry S.H.; Lee, Sang-Won; Moritz, Robert; Oses-Prieto, Juan; Rifai, Nader; Ritchie, James; Rodriguez, Henry; Srinivas, Pothur R.; Townsend, R. Reid; Van Eyk, Jennifer; Whiteley, Gordon; Wiita, Arun; Weintraub, Susan

    2014-01-01

    Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this “fit-for-purpose” approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and

  12. Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach

    SciTech Connect

    Carr, Steven A.; Abbateillo, Susan E.; Ackermann, Bradley L.; Borchers, Christoph H.; Domon, Bruno; Deutsch, Eric W.; Grant, Russel; Hoofnagle, Andrew N.; Huttenhain, Ruth; Koomen, John M.; Liebler, Daniel; Liu, Tao; MacLean, Brendan; Mani, DR; Mansfield, Elizabeth; Neubert, Hendrik; Paulovich, Amanda G.; Reiter, Lukas; Vitek, Olga; Aebersold, Ruedi; Anderson, Leigh N.; Bethem, Robert; Blonder, Josip; Boja, Emily; Botelho, Julianne; Boyne, Michael; Bradshaw, Ralph A.; Burlingame, Alma S.; Chan, Daniel W.; Keshishian, Hasmik; Kuhn, Eric; Kingsinger, Christopher R.; Lee, Jerry S.; Lee, Sang-Won; Moritz, Robert L.; Oses-Prieto, Juan; Rifai, Nader; Ritchie, James E.; Rodriguez, Henry; Srinivas, Pothur R.; Townsend, Reid; Van Eyk , Jennifer; Whiteley, Gordon; Wiita, Arun; Weintraub, Susan

    2014-01-14

    Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this “fit-for-purpose” approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and

  13. PSAR: measuring multiple sequence alignment reliability by probabilistic sampling

    PubMed Central

    Kim, Jaebum; Ma, Jian

    2011-01-01

    Multiple sequence alignment, which is of fundamental importance for comparative genomics, is a difficult problem and error-prone. Therefore, it is essential to measure the reliability of the alignments and incorporate it into downstream analyses. We propose a new probabilistic sampling-based alignment reliability (PSAR) score. Instead of relying on heuristic assumptions, such as the correlation between alignment quality and guide tree uncertainty in progressive alignment methods, we directly generate suboptimal alignments from an input multiple sequence alignment by a probabilistic sampling method, and compute the agreement of the input alignment with the suboptimal alignments as the alignment reliability score. We construct the suboptimal alignments by an approximate method that is based on pairwise comparisons between each single sequence and the sub-alignment of the input alignment where the chosen sequence is left out. By using simulation-based benchmarks, we find that our approach is superior to existing ones, supporting that the suboptimal alignments are highly informative source for assessing alignment reliability. We apply the PSAR method to the alignments in the UCSC Genome Browser to measure the reliability of alignments in different types of regions, such as coding exons and conserved non-coding regions, and use it to guide cross-species conservation study. PMID:21576232

  14. Strategies for active alignment of lenses

    NASA Astrophysics Data System (ADS)

    Langehanenberg, Patrik; Heinisch, Josef; Wilde, Chrisitan; Hahne, Felix; Lüerß, Bernd

    2015-10-01

    Today's optical systems require up-to-date assembly and joining technology. The trend of keeping dimensions as small as possible while maintaining or increasing optical imaging performance leaves little to no room for mechanical lens adjustment equipment that may remain in the final product. In this context active alignment of optical elements opens up possibilities for the fast and cost-economic manufacturing of lenses and lens assemblies with highest optical performance. Active alignment for lens manufacturing is the precise alignment of the optical axis of a lens with respect to an optical or mechanical reference axis (e.g. housing) including subsequent fixation by glue. In this contribution we will describe different approaches for active alignment and outline strengths and limitations of the different methods. Using the SmartAlign principle, highest quality cemented lenses can be manufactured without the need for high precision prealignment, while the reduction to a single alignment step greatly reduces the cycle time. The same strategies can also be applied to bonding processes. Lenses and lens groups can be aligned to both mechanical and optical axes to maximize the optical performance of a given assembly. In hybrid assemblies using both mechanical tolerances and active alignment, SmartAlign can be used to align critical lens elements anywhere inside the system for optimized total performance. Since all geometrical parameters are re-measured before each alignment, this process is especially suited for complex and time-consuming production processes where the stability of the reference axis would otherwise be critical. For highest performance, lenses can be actively aligned using up to five degrees of freedom. In this way, SmartAlign enables the production of ultra-precise mounted lenses with an alignment precision below 1 μm.

  15. Achieving Organisational Change through Values Alignment

    ERIC Educational Resources Information Center

    Branson, Christopher M.

    2008-01-01

    Purpose: The purpose of this paper is to, first, establish the interdependency between the successful achievement of organisational change and the attainment of values alignment within an organisation's culture and then, second, to describe an effective means for attaining such values alignment. Design/methodology/approach: Literature from the…

  16. Directed peptide amphiphile assembly using aqueous liquid crystal templates in magnetic fields.

    PubMed

    van der Asdonk, Pim; Keshavarz, Masoumeh; Christianen, Peter C M; Kouwer, Paul H J

    2016-08-21

    An alignment technique based on the combination of magnetic fields and a liquid crystal (LC) template uses the advantages of both approaches: the magnetic fields offer non-contact methods that apply to all sample sizes and shapes, whilst the LC templates offer high susceptibilities. The combination introduces a route to control the spatial organization of materials with low intrinsic susceptibilities. We demonstrate that we can unidirectionally align one such material, peptide amphiphiles in water, on a centimeter scale at a tenfold lower magnetic field by using a lyotropic chromonic liquid crystal as a template. We can transform the aligned supramolecular assemblies into optically active π-conjugated polymers after photopolymerization. Lastly, by reducing the magnetic field strength needed for addressing these assemblies, we are able to create more complex structures by initiating self-assembly of our supramolecular materials under competing alignment forces between the magnetically induced alignment of the assemblies (with a positive diamagnetic anisotropy) and the elastic force dominated alignment of the template (with a negative diamagnetic anisotropy), which is directed orthogonally. Although the approach is still in its infancy and many critical parameters need optimization, we believe that it is a very promising technique to create tailor-made complex structures of (aqueous) functional soft matter. PMID:27320385

  17. Neutral endopeptidase-resistant C-type natriuretic peptide variant represents a new therapeutic approach for treatment of fibroblast growth factor receptor 3-related dwarfism.

    PubMed

    Wendt, Daniel J; Dvorak-Ewell, Melita; Bullens, Sherry; Lorget, Florence; Bell, Sean M; Peng, Jeff; Castillo, Sianna; Aoyagi-Scharber, Mika; O'Neill, Charles A; Krejci, Pavel; Wilcox, William R; Rimoin, David L; Bunting, Stuart

    2015-04-01

    Achondroplasia (ACH), the most common form of human dwarfism, is caused by an activating autosomal dominant mutation in the fibroblast growth factor receptor-3 gene. Genetic overexpression of C-type natriuretic peptide (CNP), a positive regulator of endochondral bone growth, prevents dwarfism in mouse models of ACH. However, administration of exogenous CNP is compromised by its rapid clearance in vivo through receptor-mediated and proteolytic pathways. Using in vitro approaches, we developed modified variants of human CNP, resistant to proteolytic degradation by neutral endopeptidase, that retain the ability to stimulate signaling downstream of the CNP receptor, natriuretic peptide receptor B. The variants tested in vivo demonstrated significantly longer serum half-lives than native CNP. Subcutaneous administration of one of these CNP variants (BMN 111) resulted in correction of the dwarfism phenotype in a mouse model of ACH and overgrowth of the axial and appendicular skeletons in wild-type mice without observable changes in trabecular and cortical bone architecture. Moreover, significant growth plate widening that translated into accelerated bone growth, at hemodynamically tolerable doses, was observed in juvenile cynomolgus monkeys that had received daily subcutaneous administrations of BMN 111. BMN 111 was well tolerated and represents a promising new approach for treatment of patients with ACH. PMID:25650377

  18. Segmentation of precursor mass range using ‘tiling’ approach increases peptide identifications for MS1-based label-free quantification

    PubMed Central

    Vincent, Catherine E.; Potts, Gregory K.; Ulbrich, Arne; Westphall, Michael S.; Atwood, James A.; Coon, Joshua J.; Weatherly, D. Brent

    2013-01-01

    Label-free quantification is a powerful tool for the measurement of protein abundances by mass spectrometric methods. To maximize quantifiable identifications, MS1-based methods must balance the collection of survey scans and fragmentation spectra while maintaining reproducible extracted ion chromatograms (XIC). Here we present a method which increases the depth of proteome coverage over replicate data-dependent experiments without the requirement of additional instrument time or sample pre-fractionation. Sampling depth is increased by restricting precursor selection to a fraction of the full MS1 mass range for each replicate; collectively, the m/z segments of all replicates encompass the full MS1 range. Although selection windows are narrowed, full MS1 spectra are obtained throughout the method, enabling the collection of full mass range MS1 chromatograms such that label-free quantitation can be performed for any peptide in any experiment. We term this approach “binning” or “tiling” depending on the type of m/z window utilized. By combining the data obtained from each segment, we find that this approach increases the number of quantifiable yeast peptides and proteins by 31% and 52%, respectively, when compared to normal data-dependent experiments performed in replicate. PMID:23350991

  19. Comparison of marmoset and human FSH using synthetic peptides of the β-subunit L2 loop region and anti-peptide antibodies.

    PubMed

    Kutteyil, Susha S; Kulkarni, Bhalchandra J; Mojidra, Rahul; Joseph, Shaini; Pathak, Bhakti R; Mahale, Smita D

    2016-06-01

    Follicle stimulating hormone (FSH) is a glycoprotein hormone required for female and male gametogenesis in vertebrates. Common marmoset (Callithrix jacchus) is a New World primate monkey, used as animal model in biomedical research. Observations like, requirement of extremely high dose of human FSH in marmosets for superovulation compared to other primates and generation of antibodies in marmoset against human FSH after repeated superovulation cycles, point towards the possibility that FSH-FSH receptor (FSHR) interaction in marmosets might be different than in the humans. In this study we attempted to understand some of these structural differences using FSH peptides and anti-peptide antibody approach. Based on sequence alignment, in silico modeling and docking studies, L2 loop of FSH β-subunit (L2β) was found to be different between marmoset and human. Hence, peptides corresponding to region 32-50 of marmoset and human L2β loop were synthesized, purified and characterized. The peptides displayed dissimilarity in terms of molecular mass, predicted isoelectric point, predicted charge and in the ability to inhibit hormone-receptor interaction. Polyclonal antibodies generated against both the peptides were found to exhibit specific binding for the corresponding peptide and parent FSH in ELISA and Western blotting respectively and exhibited negligible reactivity to cross-species peptide and FSH in ELISA. The anti-peptide antibody against marmoset FSH was also able to detect native FSH in marmoset plasma samples and pituitary sections. In summary, the L2β loop of marmoset and human FSH has distinct receptor interaction ability and immunoreactivity indicating possibility of subtle conformational and biochemical differences between the two regions which may affect the FSH-FSHR interaction in these two primates. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. PMID:27282136

  20. Nearest Alignment Space Termination

    Energy Science and Technology Software Center (ESTSC)

    2006-07-13

    Near Alignment Space Termination (NAST) is the Greengenes algorithm that matches up submitted sequences with the Greengenes database to look for similarities and align the submitted sequences based on those similarities.

  1. Liquid crystal alignment in cylindrical microcapillaries

    NASA Astrophysics Data System (ADS)

    Chychłowski, M.; Yaroshchuk, O.; Kravchuk, R.; Woliński, T.

    2011-09-01

    A variety of alignment configurations of liquid crystals (LCs) inside the glassy cylindrical capillaries is realized by using alignment materials providing different anchoring. The radial configuration with central disclination line is obtained for homeotropic boundary conditions. In turn, the axial, transversal and tilted alignment structures are realized by using materials for planar anchoring. The uniformity and controlling of the latter structures were provided by photoalignment method. This approach can be further used to control LC alignment in the photonic crystal fibers recognized as advanced elements for different optical devices.

  2. Liquid crystal alignment in cylindrical microcapillaries

    NASA Astrophysics Data System (ADS)

    Chychłowski, M.; Yaroshchuk, O.; Kravchuk, R.; Woliński, T.

    2012-03-01

    A variety of alignment configurations of liquid crystals (LCs) inside the glassy cylindrical capillaries is realized by using alignment materials providing different anchoring. The radial configuration with central disclination line is obtained for homeotropic boundary conditions. In turn, the axial, transversal and tilted alignment structures are realized by using materials for planar anchoring. The uniformity and controlling of the latter structures were provided by photoalignment method. This approach can be further used to control LC alignment in the photonic crystal fibers recognized as advanced elements for different optical devices.

  3. Innovative optical alignment technique for CMP wafers

    NASA Astrophysics Data System (ADS)

    Sugaya, Ayako; Kanaya, Yuho; Nakajima, Shinichi; Nagayama, Tadashi; Shiraishi, Naomasa

    2002-07-01

    Detecting position of the wafers such as after CMP process is critical theme of current and forthcoming IC manufacturing. The alignment system must be with high accuracy for any process. To satisfy such requirements, we have studied and analyzed factors that have made alignment difficult. From the result of the studies, we have developed new optical alignment techniques which improve the accuracy of FIA (alignment sensor of Nikon's NSR series) and examined them. The approaches are optimizing the focus position, developing an advanced algorithm for position detection, and selecting a suitable mark design. For experiment, we have developed the special wafers that make it possible to evaluate the influence of CMP processes. The experimental results show that the overlay errors decrease dramatically with the new alignment techniques. FIA with these new techniques will be much accurate and suitable alignment sensor for CMP and other processes of future generation ULSI production.

  4. Multiple alignment using hidden Markov models

    SciTech Connect

    Eddy, S.R.

    1995-12-31

    A simulated annealing method is described for training hidden Markov models and producing multiple sequence alignments from initially unaligned protein or DNA sequences. Simulated annealing in turn uses a dynamic programming algorithm for correctly sampling suboptimal multiple alignments according to their probability and a Boltzmann temperature factor. The quality of simulated annealing alignments is evaluated on structural alignments of ten different protein families, and compared to the performance of other HMM training methods and the ClustalW program. Simulated annealing is better able to find near-global optima in the multiple alignment probability landscape than the other tested HMM training methods. Neither ClustalW nor simulated annealing produce consistently better alignments compared to each other. Examination of the specific cases in which ClustalW outperforms simulated annealing, and vice versa, provides insight into the strengths and weaknesses of current hidden Maxkov model approaches.

  5. Shiva automatic pinhole alignment

    SciTech Connect

    Suski, G.J.

    1980-09-05

    This paper describes a computer controlled closed loop alignment subsystem for Shiva, which represents the first use of video sensors for large laser alignment at LLNL. The techniques used on this now operational subsystem are serving as the basis for all closed loop alignment on Nova, the 200 terawatt successor to Shiva.

  6. A proteomic approach for studying insect phylogeny: CAPA peptides of ancient insect taxa (Dictyoptera, Blattoptera) as a test case

    PubMed Central

    Roth, Steffen; Fromm, Bastian; Gäde, Gerd; Predel, Reinhard

    2009-01-01

    Background Neuropeptide ligands have to fit exactly into their respective receptors and thus the evolution of the coding regions of their genes is constrained and may be strongly conserved. As such, they may be suitable for the reconstruction of phylogenetic relationships within higher taxa. CAPA peptides of major lineages of cockroaches (Blaberidae, Blattellidae, Blattidae, Polyphagidae, Cryptocercidae) and of the termite Mastotermes darwiniensis were chosen to test the above hypothesis. The phylogenetic relationships within various groups of the taxon Dictyoptera (praying mantids, termites and cockroaches) are still highly disputed. Results Tandem mass spectrometry of neuropeptides from perisympathetic organs was used to obtain sequence data of CAPA peptides from single specimens; the data were analysed by Maximum Parsimony and Bayesian Interference. The resulting cladograms, taking 61 species into account, show a topology which is in general agreement with recent molecular and morphological phylogenetic analyses, including the recent phylogenetic arrangement placing termites within the cockroaches. When sequence data sets from other neuropeptides, viz. adipokinetic hormones and sulfakinins, were included, the general topology of the cladogram did not change but bootstrap values increased considerably. Conclusion This study represents the first comprehensive survey of neuropeptides of insects for solely phylogenetic purposes and concludes that sequences of short neuropeptides are suitable to complement molecular biological and morphological data for the reconstruction of phylogenetic relationships. PMID:19257902

  7. An integrated, peptide-based approach to site-specific protein immobilization for detection of biomolecular interactions.

    PubMed

    Kruis, Ilmar C; Löwik, Dennis W P M; Boelens, Wilbert C; van Hest, Jan C M; Pruijn, Ger J M

    2016-09-21

    We have developed an integrated solution for the site-specific immobilization of proteins on a biosensor surface, which may be widely applicable for high throughput analytical purposes. The gold surface of a biosensor was coated with an anti-fouling layer of zwitterionic peptide molecules from which leucine zipper peptides protrude. Proteins of interest, the autoantigenic proteins La and U1A, were immobilized via a simple incubation procedure by using the complementary leucine zipper sequence as a genetically fused binding tag. This tag forms a strong coiled-coil interaction that is stable during multiple consecutive measurements and under common regeneration conditions. Visualization of the immobilized proteins of interest via antibody binding with multiplex surface plasmon resonance imaging demonstrated 2.5 times higher binding responses than when these proteins were randomly attached to the surface via the commonly applied activated ester-mediated coupling. The proteins could also be immobilized in a leucine zipper-dependent manner directly from complex mixtures like bacterial lysates, eliminating the need for laborious purification steps. This method allows the production of uniform functional protein arrays by control over immobilized protein orientation and geometry and is compatible with high-throughput procedures. PMID:27328408

  8. CARNA--alignment of RNA structure ensembles.

    PubMed

    Sorescu, Dragos Alexandru; Möhl, Mathias; Mann, Martin; Backofen, Rolf; Will, Sebastian

    2012-07-01

    Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool 'CARNA'. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large flexibility in the input, ranging from fixed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, 'CARNA' optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared with already costly Sankoff-style alignment, 'CARNA' solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although 'CARNA' is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA. PMID:22689637

  9. Concepts for Biologically Active Peptides

    PubMed Central

    Kastin, Abba J.; Pan, Weihong

    2012-01-01

    Here we review a unique aspect of CNS research on biologically active peptides that started against a background of prevalent dogmas but ended by exerting considerable influence on the field. During the course of refuting some doctrines, we introduced several concepts that were unconventional and paradigm-shifting at the time. We showed that (1) hypothalamic peptides can act ‘up’ on the brain as well as ‘down’ on the pituitary, (2) peripheral peptides can affect the brain, (3) peptides can cross the blood-brain barrier, (4) the actions of peptides can persist longer than their half-lives in blood, (5) perinatal administration of peptides can exert actions persisting into adulthood, (6) a single peptide can have more than one action, (7) dose-response relationships of peptides need not be linear, (8) the brain produces antiopiate as well as opiate peptides, (9) there is a selective high affinity endogenous peptide ligand for the mu-opiate receptor, (10) a peptide’s name does not restrict its effects, and (11) astrocytes assume an active role in response to metabolic disturbance and hyperleptinemia. The evolving questions in our laboratories reflect the diligent effort of the neuropeptide community to identify the roles of peptides in the CNS. The next decade is expected to see greater progress in the following areas: (a) interactions of peptides with other molecules in the CNS; (b) peptide involvement in cell-cell interactions; and (c) peptides in neuropsychiatric, autoimmune, and neurodegenerative diseases. The development of peptidomics and gene silencing approaches will expedite the formation of many new concepts in a new era. PMID:20726835

  10. Girder Alignment Plan

    SciTech Connect

    Wolf, Zackary; Ruland, Robert; LeCocq, Catherine; Lundahl, Eric; Levashov, Yurii; Reese, Ed; Rago, Carl; Poling, Ben; Schafer, Donald; Nuhn, Heinz-Dieter; Wienands, Uli; /SLAC

    2010-11-18

    The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which includes efficiency and high accuracy. The motivation for girder alignment involves the following considerations. Using beam based alignment, the girder position will be adjusted until the beam goes through the center of the quadrupole and beam finder wire. For the machine to work properly, the undulator axis must be on this line and the center of the undulator beam pipe must be on this line. The physics reasons for the undulator axis and undulator beam pipe axis to be centered on the beam are different, but the alignment tolerance for both are similar. In addition, the beam position monitor must be centered on the beam to preserve its calibration. Thus, the undulator, undulator beam pipe, quadrupole, beam finder wire, and beam position monitor axes must all be aligned to a common line. All relative alignments are equally important, not just, for example, between quadrupole and undulator. We begin by making the common axis the nominal beam axis in the girder coordinate system. All components will be initially aligned to this axis. A more accurate alignment will then position the components relative to each other, without incorporating the girder itself.