WorldWideScience

Sample records for acid sequences visualized

  1. WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or amino acids sequences.

    Science.gov (United States)

    Zika, Radek; Paces, Jan; Pavlícek, Adam; Paces, Václav

    2004-07-01

    Web Alignment Visualization Server contains a set of web-tools designed for quick generation of publication-quality color figures of multiple alignments of nucleotide or amino acids sequences. It can be used for identification of conserved regions and gaps within many sequences using only common web browsers. The server is accessible at http://wavis.img.cas.cz.

  2. WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or amino acids sequences

    OpenAIRE

    Zika, Radek; Pačes, Jan; Pavlíček, Adam; Pačes, Václav

    2004-01-01

    Web Alignment Visualization Server contains a set of web-tools designed for quick generation of publication-quality color figures of multiple alignments of nucleotide or amino acids sequences. It can be used for identification of conserved regions and gaps within many sequences using only common web browsers. The server is accessible at http://wavis.img.cas.cz.

  3. Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Nielsen, Morten

    2012-01-01

    Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active...... related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein...

  4. Recalling visual serial order for verbal sequences

    NARCIS (Netherlands)

    Logie, R.H.; Saito, S.; Morita, A.; Varma, S.; Norris, D.

    2016-01-01

    We report three experiments in which participants performed written serial recall of visually presented verbal sequences with items varying in visual similarity. In Experiments 1 and 2 native speakers of Japanese recalled visually presented Japanese Kanji characters. In Experiment 3, native speakers

  5. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole;

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...... about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. Availability : MatrixPlot can be obtained on request, and can also be accessed online at http://www. cbs.dtu.dk/services/MatrixPlot. Contact : gorodkin@cbs.dtu.dk...

  6. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence non-specific learning during......Voluntary limb modifications must be integrated with basic walking patterns during visually guided walking. Here we tested whether voluntary gait modifications can become more automatic with practice. We challenged walking control by presenting visual stepping targets that instructed subjects...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...

  7. Robot Sequencing and Visualization Program (RSVP)

    Science.gov (United States)

    Cooper, Brian K.; Maxwell,Scott A.; Hartman, Frank R.; Wright, John R.; Yen, Jeng; Toole, Nicholas T.; Gorjian, Zareh; Morrison, Jack C

    2013-01-01

    The Robot Sequencing and Visualization Program (RSVP) is being used in the Mars Science Laboratory (MSL) mission for downlink data visualization and command sequence generation. RSVP reads and writes downlink data products from the operations data server (ODS) and writes uplink data products to the ODS. The primary users of RSVP are members of the Rover Planner team (part of the Integrated Planning and Execution Team (IPE)), who use it to perform traversability/articulation analyses, take activity plan input from the Science and Mission Planning teams, and create a set of rover sequences to be sent to the rover every sol. The primary inputs to RSVP are downlink data products and activity plans in the ODS database. The primary outputs are command sequences to be placed in the ODS for further processing prior to uplink to each rover. RSVP is composed of two main subsystems. The first, called the Robot Sequence Editor (RoSE), understands the MSL activity and command dictionaries and takes care of converting incoming activity level inputs into command sequences. The Rover Planners use the RoSE component of RSVP to put together command sequences and to view and manage command level resources like time, power, temperature, etc. (via a transparent realtime connection to SEQGEN). The second component of RSVP is called HyperDrive, a set of high-fidelity computer graphics displays of the Martian surface in 3D and in stereo. The Rover Planners can explore the environment around the rover, create commands related to motion of all kinds, and see the simulated result of those commands via its underlying tight coupling with flight navigation, motor, and arm software. This software is the evolutionary replacement for the Rover Sequencing and Visualization software used to create command sequences (and visualize the Martian surface) for the Mars Exploration Rover mission.

  8. Coding visual features extracted from video sequences.

    Science.gov (United States)

    Baroffio, Luca; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

    2014-05-01

    Visual features are successfully exploited in several applications (e.g., visual search, object recognition and tracking, etc.) due to their ability to efficiently represent image content. Several visual analysis tasks require features to be transmitted over a bandwidth-limited network, thus calling for coding techniques to reduce the required bit budget, while attaining a target level of efficiency. In this paper, we propose, for the first time, a coding architecture designed for local features (e.g., SIFT, SURF) extracted from video sequences. To achieve high coding efficiency, we exploit both spatial and temporal redundancy by means of intraframe and interframe coding modes. In addition, we propose a coding mode decision based on rate-distortion optimization. The proposed coding scheme can be conveniently adopted to implement the analyze-then-compress (ATC) paradigm in the context of visual sensor networks. That is, sets of visual features are extracted from video frames, encoded at remote nodes, and finally transmitted to a central controller that performs visual analysis. This is in contrast to the traditional compress-then-analyze (CTA) paradigm, in which video sequences acquired at a node are compressed and then sent to a central unit for further processing. In this paper, we compare these coding paradigms using metrics that are routinely adopted to evaluate the suitability of visual features in the context of content-based retrieval, object recognition, and tracking. Experimental results demonstrate that, thanks to the significant coding gains achieved by the proposed coding scheme, ATC outperforms CTA with respect to all evaluation metrics. PMID:24818244

  9. Temporal integration windows for naturalistic visual sequences.

    Directory of Open Access Journals (Sweden)

    Scott L Fairhall

    Full Text Available There is increasing evidence that the brain possesses mechanisms to integrate incoming sensory information as it unfolds over time-periods of 2-3 seconds. The ubiquity of this mechanism across modalities, tasks, perception and production has led to the proposal that it may underlie our experience of the subjective present. A critical test of this claim is that this phenomenon should be apparent in naturalistic visual experiences. We tested this using movie-clips as a surrogate for our day-to-day experience, temporally scrambling them to require (re- integration within and beyond the hypothesized 2-3 second interval. Two independent experiments demonstrate a step-wise increase in the difficulty to follow stimuli at the hypothesized 2-3 second scrambling condition. Moreover, only this difference could not be accounted for by low-level visual properties. This provides the first evidence that this 2-3 second integration window extends to complex, naturalistic visual sequences more consistent with our experience of the subjective present.

  10. Visualization of the sequence of a couple splitting outside shop

    DEFF Research Database (Denmark)

    2015-01-01

    Visualization of tracks of couple walking together before splitting and one goes into shop the other waits outside. The visualization represents the sequence described in figure 7 in the publication 'Taking the temperature of pedestrian movement in public spaces'......Visualization of tracks of couple walking together before splitting and one goes into shop the other waits outside. The visualization represents the sequence described in figure 7 in the publication 'Taking the temperature of pedestrian movement in public spaces'...

  11. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian;

    2013-01-01

    BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, se...

  12. Chip-based sequencing nucleic acids

    Science.gov (United States)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  13. Enhanced learning of natural visual sequences in newborn chicks.

    Science.gov (United States)

    Wood, Justin N; Prasad, Aditya; Goldman, Jason G; Wood, Samantha M W

    2016-07-01

    To what extent are newborn brains designed to operate over natural visual input? To address this question, we used a high-throughput controlled-rearing method to examine whether newborn chicks (Gallus gallus) show enhanced learning of natural visual sequences at the onset of vision. We took the same set of images and grouped them into either natural sequences (i.e., sequences showing different viewpoints of the same real-world object) or unnatural sequences (i.e., sequences showing different images of different real-world objects). When raised in virtual worlds containing natural sequences, newborn chicks developed the ability to recognize familiar images of objects. Conversely, when raised in virtual worlds containing unnatural sequences, newborn chicks' object recognition abilities were severely impaired. In fact, the majority of the chicks raised with the unnatural sequences failed to recognize familiar images of objects despite acquiring over 100 h of visual experience with those images. Thus, newborn chicks show enhanced learning of natural visual sequences at the onset of vision. These results indicate that newborn brains are designed to operate over natural visual input. PMID:27079969

  14. Visually lossless compression of digital hologram sequences

    OpenAIRE

    Darakis E.; Kowiel M.; Nasanen R.; Naughton T.J.

    2010-01-01

    Digital hologram sequences have great potential for the recording of 3D scenes of moving macroscopic objects as their numerical reconstruction can yield a range of perspective views of the scene. Digital holograms inherently have large information content and lossless coding of holographic data is rather inefficient due to the speckled nature of the interference fringes they contain. Lossy coding of still holograms and hologram sequences has shown promising results. By definition,...

  15. Programming Using Visual Basic for Nucleic Acid Sequences Analysis%Visual BASIC编程在核酸序列分析中的应用研究初探

    Institute of Scientific and Technical Information of China (English)

    葛威; 鲍大鹏; 董战峰; 施铮

    2004-01-01

    利用可视化的编程语言Visual BASIC编写了一个简易实用的核酸序列分析程序,能够自动实现对已知核酸序列的分子质量、Tm值、碱基组成的测定、各种核酸序列的转换和氨基酸序列的推导.同时也详细描述了核酸序列自动分析各功能实现的Visual BASIC语言编程过程.

  16. Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

    Science.gov (United States)

    Mai, Te-Lun; Hu, Geng-Ming; Chen, Chi-Ming

    2016-07-01

    Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences. PMID:27267620

  17. ProSAT+: visualizing sequence annotations on 3D structure.

    Science.gov (United States)

    Stank, Antonia; Richter, Stefan; Wade, Rebecca C

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org. PMID:27284084

  18. Reverse sequencing syllables of spoken words activates primary visual cortex.

    Science.gov (United States)

    Ino, Tadashi; Asada, Tomohiko; Hirose, Syuichi; Ito, Jin; Fukuyama, Hidenao

    2003-10-27

    Using fMRI, we investigated the neural correlates for sequencing the individual syllables of spoken words in reverse order. The comparison of this task to a control task requiring subjects to repeat identical syllables given acoustically revealed the activation of the primary visual cortex. Because one syllable is generally expressed by one kana character (Japanese phonogram), most subjects used a strategy in which the kana character string corresponding to the word was imagined visually and then read mentally in reverse order to perform the task effectively. Such strategy was not used during a control condition. These results suggest that the primary visual cortex plays a role in the generation of an imagined string.

  19. Comparative Amino Acid Sequences of Dengue Viruses

    OpenAIRE

    Haishi, Shozo; TANAKA Mariko; Igarashi, Akira

    1990-01-01

    Amino acid (AA) sequences of 4 serotype of dengue viruses deduced from their nucleotide (nt) sequences of genomic RNA were analyzed for each genome segment and each stretch of 10 AA residues. Precursor of membrane protein (pM), and 4 nonstructural proteins (NS1, NS3, NS4B, NS5) were highly conserved, while another nonstructural protein (NS2A) was least conserved among 5 strains of dengue viruses. When homology was compared among heterotypic viruses, type 1 and type 3 dengue viruses showed clo...

  20. Motor sequence learning occurs despite disrupted visual and proprioceptive feedback

    Directory of Open Access Journals (Sweden)

    Boyd Lara A

    2008-07-01

    Full Text Available Abstract Background Recent work has demonstrated the importance of proprioception for the development of internal representations of the forces encountered during a task. Evidence also exists for a significant role for proprioception in the execution of sequential movements. However, little work has explored the role of proprioceptive sensation during the learning of continuous movement sequences. Here, we report that the repeated segment of a continuous tracking task can be learned despite peripherally altered arm proprioception and severely restricted visual feedback regarding motor output. Methods Healthy adults practiced a continuous tracking task over 2 days. Half of the participants experienced vibration that altered proprioception of shoulder flexion/extension of the active tracking arm (experimental condition and half experienced vibration of the passive resting arm (control condition. Visual feedback was restricted for all participants. Retention testing was conducted on a separate day to assess motor learning. Results Regardless of vibration condition, participants learned the repeated segment demonstrated by significant improvements in accuracy for tracking repeated as compared to random continuous movement sequences. Conclusion These results suggest that with practice, participants were able to use residual afferent information to overcome initial interference of tracking ability related to altered proprioception and restricted visual feedback to learn a continuous motor sequence. Motor learning occurred despite an initial interference of tracking noted during acquisition practice.

  1. 77 FR 65537 - Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Sequence...

    Science.gov (United States)

    2012-10-29

    ... Amino Acid Sequence Disclosures ACTION: Proposed collection; comment request. SUMMARY: The United States....'' SUPPLEMENTARY INFORMATION: I. Abstract Patent applications that contain nucleotide and/or amino acid...

  2. Detection of nucleic acid sequences by invader-directed cleavage

    Science.gov (United States)

    Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  3. Sensory information in perceptual-motor sequence learning: visual and/or tactile stimuli

    OpenAIRE

    Abrahamse, Elger L.; Lubbe, van der, S.; Verwey, Willem B.

    2009-01-01

    Sequence learning in serial reaction time (SRT) tasks has been investigated mostly with unimodal stimulus presentation. This approach disregards the possibility that sequence acquisition may be guided by multiple sources of sensory information simultaneously. In the current study we trained participants in a SRT task with visual only, tactile only, or bimodal (visual and tactile) stimulus presentation. Sequence performance for the bimodal and visual only training groups was similar, while bot...

  4. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    Science.gov (United States)

    Pabinger, Stephan; Ernst, Karina; Pulverer, Walter; Kallmeyer, Rainer; Valdes, Ana M; Metrustry, Sarah; Katic, Denis; Nuzzo, Angelo; Kriegner, Albert; Vierlinger, Klemens; Weinhaeusel, Andreas

    2016-01-01

    Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely

  5. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Toon Rosseel

    Full Text Available Sequence Independent Single Primer Amplification is one of the most widely used random amplification approaches in virology for sequencing template preparation. This technique relies on oligonucleotides consisting of a 3' random part used to prime complementary DNA synthesis and a 5' defined tag sequence for subsequent amplification. Recently, this amplification method was combined with next generation sequencing to obtain viral sequences. However, these studies showed a biased distribution of the resulting sequence reads over the analyzed genomes. The aim of this study was to elucidate the mechanisms that lead to biased sequence depth when using random amplification. Avian paramyxovirus type 8 was used as a model RNA virus to investigate these mechanisms. We showed, based on in silico analysis of the sequence depth in relation to GC-content, predicted RNA secondary structure and sequence complementarity to the 3' part of the tag sequence, that the tag sequence has the main contribution to the observed bias in sequence depth. We confirmed this finding experimentally using both fragmented and non-fragmented viral RNAs as well as primers differing in random oligomer length (6 or 12 nucleotides and in the sequence of the amplification tag. The observed oligonucleotide annealing bias can be reduced by extending the random oligomer sequence and by in silico combining sequence data from SISPA experiments using different 5' defined tag sequences. These findings contribute to the optimization of random nucleic acid amplification protocols that are currently required for downstream applications such as viral metagenomics and microarray analysis.

  6. Peptide Nucleic Acids Having Enhanced Binding Affinity and Sequence Specificity

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. Methods of increasing binding affinity and sequence specificity of peptide nucleic aci...

  7. MEANS AND METHODS FOR CLONING NUCLEIC ACID SEQUENCES

    NARCIS (Netherlands)

    Geertsma, Eric Robin; Poolman, Berend

    2008-01-01

    The invention provides means and methods for efficiently cloning nucleic acid sequences of interest in micro-organisms that are less amenable to conventional nucleic acid manipulations, as compared to, for instance, E.coli. The present invention enables high-throughput cloning (and, preferably, expr

  8. Timing of Visual Bodily Behavior in Repair Sequences: Evidence from Three Languages

    Science.gov (United States)

    Floyd, Simeon; Manrique, Elizabeth; Rossi, Giovanni; Torreira, Francisco

    2016-01-01

    This article expands the study of other-initiated repair in conversation--when one party signals a problem with producing or perceiving another's turn at talk--into the domain of visual bodily behavior. It presents one primary cross-linguistic finding about the timing of visual bodily behavior in repair sequences: if the party who initiates repair…

  9. Visual Sequence Learning in Infancy: Domain-General and Domain-Specific Associations with Language

    Science.gov (United States)

    Shafto, Carissa L.; Conway, Christopher M.; Field, Suzanne L.; Houston, Derek M.

    2012-01-01

    Research suggests that nonlinguistic sequence learning abilities are an important contributor to language development (Conway, Bauernschmidt, Huang, & Pisoni, 2010). The current study investigated visual sequence learning (VSL) as a possible predictor of vocabulary development in infants. Fifty-eight 8.5-month-old infants were presented with a…

  10. Visual Analytics of Temporal Event Sequences in News Streams

    OpenAIRE

    Krstajic, Milos

    2014-01-01

    Finding new ways of extracting and analyzing useful information from exploding volumes of unstructured and semi-structured text sources has become one of the greatest challenges in the era of big data. After new technologies have enabled efficient solutions for collecting and storing these data, the next step in computer science research is to develop scalable approaches for efficient analysis of dynamics in text streams. This dissertation addresses this challenge by examining how visual anal...

  11. Visual Sequence Learning in Infancy: Domain-General and Domain-Specific Associations with Language

    OpenAIRE

    2011-01-01

    Research suggests that non-linguistic sequence learning abilities are an important contributor to language development (Conway, Bauernschmidt, Huang, & Pisoni, 2010). The current study investigated visual sequence learning as a possible predictor of vocabulary development in infants. Fifty-eight 8.5-month-old infants were presented with a three-location spatiotemporal sequence of multi-colored geometric shapes. Early language skills were assessed using the MacArthur-Bates CDI. Analyses of chi...

  12. Amino acid sequences of proteins from Leptospira serovar pomona

    Directory of Open Access Journals (Sweden)

    Alves Selmo F

    2000-01-01

    Full Text Available This report describes a partial amino acid sequences from three putative outer envelope proteins from Leptospira serovar pomona. In order to obtain internal fragments for protein sequencing, enzymatic and chemical digestion was performed. The enzyme clostripain was used to digest the proteins 32 and 45 kDa. In situ digestion of 40 kDa molecular weight protein was accomplished using cyanogen bromide. The 32 kDa protein generated two fragments, one of 21 kDa and another of 10 kDa that yielded five residues. A fragment of 24 kDa that yielded nineteen residues of amino acids was obtained from 45 kDa protein. A fragment with a molecular weight of 20 kDa, yielding a twenty amino acids sequence from the 40 kDa protein.

  13. Visual programming for next-generation sequencing data analytics

    OpenAIRE

    Milicchio, Franco; Rose, Rebecca; Bian, Jiang; Min, Jae; Prosperi, Mattia

    2016-01-01

    Background High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone. Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) ...

  14. Representation of protein-sequence information by amino acid subalphabets

    DEFF Research Database (Denmark)

    Andersen, C.A.F.; Brunak, Søren

    2004-01-01

    Within computational biology, algorithms are constructed with the aim of extracting knowledge from biological data, in particular, data generated by the large genome projects, where gene and protein sequences are produced in high volume. In this article, we explore new ways of representing protein......-sequence information, using machine learning strategies, where the primary goal is the discovery of novel powerful representations for use in AI techniques. In the case of proteins and the 20 different amino acids they typically contain, it is also a secondary goal to discover how the current selection of amino acids...

  15. On Quantum Algorithm for Multiple Alignment of Amino Acid Sequences

    Science.gov (United States)

    Iriyama, Satoshi; Ohya, Masanori

    2009-02-01

    The alignment of genome sequences or amino acid sequences is one of fundamental operations for the study of life. Usual computational complexity for the multiple alignment of N sequences with common length L by dynamic programming is O(LN). This alignment is considered as one of the NP problems, so that it is desirable to find a nice algorithm of the multiple alignment. Thus in this paper we propose the quantum algorithm for the multiple alignment based on the works12,1,2 in which the NP complete problem was shown to be the P problem by means of quantum algorithm and chaos information dynamics.

  16. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.

    Science.gov (United States)

    Derr, Julien; Manapat, Michael L; Rajamani, Sudha; Leu, Kevin; Xulvi-Brunet, Ramon; Joseph, Isaac; Nowak, Martin A; Chen, Irene A

    2012-05-01

    During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.

  17. The amino-acid sequence of kangaroo pancreatic ribonuclease.

    Science.gov (United States)

    Gaastra, W; Welling, G W; Beintema, J J

    1978-05-01

    Red kangaroo (Macropus rufus) ribonuclease was isolated from pancreatic tissue by affinity chromatography. The amino acid sequence was determined by automatic sequencing of overlapping large fragments and by analysis of shorter peptides obtained by digestion with a number of proteolytic enzymes. The polypeptide chain consists of 122 amino acid residues. Compared to other ribonucleases, the N-terminal residue and residue 114 are deleted. In other pancreatic ribonucleases position 114 is occupied by a cis proline residue in an external loop at the surface of the molecule. Other remarkable substitutions are the presence of a tyrosine residue at position 123 instead of a serine which forms a hydrogen bond with the pyrimidine ring of a nucleotide substrate, and a number of hydrophobichydrophilic interchanges in the sequence 51-55, which forms part of an alpha-helix in bovine ribonuclease and exhibits few substitutions in the placental mammals. Kangaroo ribonuclease contains no carbohydrate, although the enzyme possesses a recognition site for carbohydrate attachment in the sequence Asn-Val-Thr (62-64). The enzyme differs at about 35-40% of the positions from all other mammalian pancreatic ribonucleases sequenced to date, which is in agreement with the early divergence between the marsupials and the placental mammals. From fragmentary data a tentative sequence of red-necked wallaby (Macropus rufogriseus) pancreatic ribonuclease has been derived. Eight differences with the kangaroo sequence were found. PMID:658039

  18. Age-Related Declines in Early Sensory Memory: Identification of Rapid Auditory and Visual Stimulus Sequences

    Science.gov (United States)

    Fogerty, Daniel; Humes, Larry E.; Busey, Thomas A.

    2016-01-01

    Age-related temporal-processing declines of rapidly presented sequences may involve contributions of sensory memory. This study investigated recall for rapidly presented auditory (vowel) and visual (letter) sequences presented at six different stimulus onset asynchronies (SOA) that spanned threshold SOAs for sequence identification. Younger, middle-aged, and older adults participated in all tasks. Results were investigated at both equivalent performance levels (i.e., SOA threshold) and at identical physical stimulus values (i.e., SOAs). For four-item sequences, results demonstrated best performance for the first and last items in the auditory sequences, but only the first item for visual sequences. For two-item sequences, adults identified the second vowel or letter significantly better than the first. Overall, when temporal-order performance was equated for each individual by testing at SOA thresholds, recall accuracy for each position across the age groups was highly similar. These results suggest that modality-specific processing declines of older adults primarily determine temporal-order performance for rapid sequences. However, there is some evidence for a second amodal processing decline in older adults related to early sensory memory for final items in a sequence. This selective deficit was observed particularly for longer sequence lengths and was not accounted for by temporal masking. PMID:27199737

  19. Age-Related Declines in Early Sensory Memory: Identification of Rapid Auditory and Visual Stimulus Sequences.

    Science.gov (United States)

    Fogerty, Daniel; Humes, Larry E; Busey, Thomas A

    2016-01-01

    Age-related temporal-processing declines of rapidly presented sequences may involve contributions of sensory memory. This study investigated recall for rapidly presented auditory (vowel) and visual (letter) sequences presented at six different stimulus onset asynchronies (SOA) that spanned threshold SOAs for sequence identification. Younger, middle-aged, and older adults participated in all tasks. Results were investigated at both equivalent performance levels (i.e., SOA threshold) and at identical physical stimulus values (i.e., SOAs). For four-item sequences, results demonstrated best performance for the first and last items in the auditory sequences, but only the first item for visual sequences. For two-item sequences, adults identified the second vowel or letter significantly better than the first. Overall, when temporal-order performance was equated for each individual by testing at SOA thresholds, recall accuracy for each position across the age groups was highly similar. These results suggest that modality-specific processing declines of older adults primarily determine temporal-order performance for rapid sequences. However, there is some evidence for a second amodal processing decline in older adults related to early sensory memory for final items in a sequence. This selective deficit was observed particularly for longer sequence lengths and was not accounted for by temporal masking. PMID:27199737

  20. PyVDT: A PsychoPy-Based Visual Sequence Detection Task

    OpenAIRE

    Hansen, Mads

    2016-01-01

    PyVDT is a computerized test consisting of two brief visual sequence detection tasks in which participants watch single digits displayed on screen and respond whenever target digit sequences (even – odd – even) are displayed. The total duration of the test is around five minutes. PyVDT is a reimplementation of the Visual Monitoring Task (VMT), a task thought to measure working memory.PyVDT uses the PsychoPy API to display digits, to plot diagnostic information, and to output log files and res...

  1. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures

    OpenAIRE

    Fördös Gergely; Biro Jan C

    2005-01-01

    Abstract Background The interacting residues of protein and nucleic acid sequences are close to each other – they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB) contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. Results SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid...

  2. Subfamily logos: visualization of sequence deviations at alignment positions with high information content

    Directory of Open Access Journals (Sweden)

    Beitz Eric

    2006-06-01

    Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

  3. 3matrix and 3motif: a protein structure visualization system for conserved sequence motifs

    OpenAIRE

    Bennett, Steven P.; Lu, Lin; Brutlag, Douglas L.

    2003-01-01

    Computational methods such as sequence alignment and motif construction are useful in grouping related proteins into families, as well as helping to annotate new proteins of unknown function. These methods identify conserved amino acids in protein sequences, but cannot determine the specific functional or structural roles of conserved amino acids without additional study. In this work, we present 3matrix (http://3matrix.stanford.edu) and 3motif (http://3motif.stanford.edu), a web-based sequen...

  4. Abstract Rule Learning for Visual Sequences in 8- and 11-Month-Olds

    Science.gov (United States)

    Johnson, Scott P.; Fernandes, Keith J.; Frank, Michael C.; Kirkham, Natasha; Marcus, Gary; Rabagliati, Hugh; Slemmer, Jonathan A.

    2009-01-01

    The experiments reported here investigated the development of a fundamental component of cognition: to recognize and generalize abstract relations. Infants were presented with simple rule-governed patterned sequences of visual shapes (ABB, AAB, and ABA) that could be discriminated from differences in the position of the repeated element (late,…

  5. Learning of Grammar-Like Visual Sequences by Adults with and without Language-Learning Disabilities

    Science.gov (United States)

    Aguilar, Jessica M.; Plante, Elena

    2014-01-01

    Purpose: Two studies examined learning of grammar-like visual sequences to determine whether a general deficit in statistical learning characterizes this population. Furthermore, we tested the hypothesis that difficulty in sustaining attention during the learning task might account for differences in statistical learning. Method: In Study 1,…

  6. Visual Statistical Learning Works after Binding the Temporal Sequences of Shapes and Spatial Positions

    Directory of Open Access Journals (Sweden)

    Osamu Watanabe

    2011-05-01

    Full Text Available The human visual system can acquire the statistical structures in temporal sequences of object feature changes, such as changes in shape, color, and its combination. Here we investigate whether the statistical learning for spatial position and shape changes operates separately or not. It is known that the visual system processes these two types of information separately; the spatial information is processed in the parietal cortex, whereas object shapes and colors are detected in the temporal pathway, and, after that, we perceive bound information in the two streams. We examined whether the statistical learning operates before or after binding the shape and the spatial information by using the “re-paired triplet” paradigm proposed by Turk-Browne, Isola, Scholl, and Treat (2008. The result showed that observers acquired combined sequences of shape and position changes, but no statistical information in individual sequence was obtained. This finding suggests that the visual statistical learning works after binding the temporal sequences of shapes and spatial structures and would operate in the higher-order visual system; this is consistent with recent ERP (Abla & Okanoya, 2009 and fMRI (Turk-Browne, Scholl, Chun, & Johnson, 2009 studies.

  7. PyVDT: A PsychoPy-Based Visual Sequence Detection Task

    Directory of Open Access Journals (Sweden)

    Mads Hansen

    2016-06-01

    Full Text Available PyVDT is a computerized test consisting of two brief visual sequence detection tasks in which participants watch single digits displayed on screen and respond whenever target digit sequences (even – odd – even are displayed. The total duration of the test is around five minutes. PyVDT is a reimplementation of the Visual Monitoring Task (VMT, a task thought to measure working memory. PyVDT uses the PsychoPy API to display digits, to plot diagnostic information, and to output log files and results. It is available for download on Figshare and GitHub. PyVDT is free software and has minimal software and hardware requirements. Thus, PyVDT provides a readily available visual monitoring task for use in experiments within cognitive science and related fields.

  8. The amino acid sequence of Escherichia coli cyanase.

    Science.gov (United States)

    Chin, C C; Anderson, P M; Wold, F

    1983-01-10

    The amino acid sequence of the enzyme cyanase (cyanate hydrolase) from Escherichia coli has been determined by automatic Edman degradation of the intact protein and of its component peptides. The primary peptides used in the sequencing were produced by cyanogen bromide cleavage at the methionine residues, yielding 4 peptides plus free homoserine from the NH2-terminal methionine, and by trypsin cleavage at the 7 arginine residues after acetylation of the lysines. Secondary peptides required for overlaps and COOH-terminal sequences were produced by chymotrypsin or clostripain cleavage of some of the larger peptides. The complete sequence of the cyanase subunit consists of 156 amino acid residues (Mr 16,350). Based on the observation that the cysteine-containing peptide is obtained as a disulfide-linked dimer, it is proposed that the covalent structure of cyanase is made up of two subunits linked by a disulfide bond between the single cystine residue in each subunit. The native enzyme (Mr 150,000) then appears to be a complex of four or five such subunit dimers.

  9. Isolating Visual and Proprioceptive Components of Motor Sequence Learning in ASD.

    Science.gov (United States)

    Sharer, Elizabeth A; Mostofsky, Stewart H; Pascual-Leone, Alvaro; Oberman, Lindsay M

    2016-05-01

    In addition to defining impairments in social communication skills, individuals with autism spectrum disorder (ASD) also show impairments in more basic sensory and motor skills. Development of new skills involves integrating information from multiple sensory modalities. This input is then used to form internal models of action that can be accessed when both performing skilled movements, as well as understanding those actions performed by others. Learning skilled gestures is particularly reliant on integration of visual and proprioceptive input. We used a modified serial reaction time task (SRTT) to decompose proprioceptive and visual components and examine whether patterns of implicit motor skill learning differ in ASD participants as compared with healthy controls. While both groups learned the implicit motor sequence during training, healthy controls showed robust generalization whereas ASD participants demonstrated little generalization when visual input was constant. In contrast, no group differences in generalization were observed when proprioceptive input was constant, with both groups showing limited degrees of generalization. The findings suggest, when learning a motor sequence, individuals with ASD tend to rely less on visual feedback than do healthy controls. Visuomotor representations are considered to underlie imitative learning and action understanding and are thereby crucial to social skill and cognitive development. Thus, anomalous patterns of implicit motor learning, with a tendency to discount visual feedback, may be an important contributor in core social communication deficits that characterize ASD. Autism Res 2016, 9: 563-569. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.

  10. Isolating Visual and Proprioceptive Components of Motor Sequence Learning in ASD.

    Science.gov (United States)

    Sharer, Elizabeth A; Mostofsky, Stewart H; Pascual-Leone, Alvaro; Oberman, Lindsay M

    2016-05-01

    In addition to defining impairments in social communication skills, individuals with autism spectrum disorder (ASD) also show impairments in more basic sensory and motor skills. Development of new skills involves integrating information from multiple sensory modalities. This input is then used to form internal models of action that can be accessed when both performing skilled movements, as well as understanding those actions performed by others. Learning skilled gestures is particularly reliant on integration of visual and proprioceptive input. We used a modified serial reaction time task (SRTT) to decompose proprioceptive and visual components and examine whether patterns of implicit motor skill learning differ in ASD participants as compared with healthy controls. While both groups learned the implicit motor sequence during training, healthy controls showed robust generalization whereas ASD participants demonstrated little generalization when visual input was constant. In contrast, no group differences in generalization were observed when proprioceptive input was constant, with both groups showing limited degrees of generalization. The findings suggest, when learning a motor sequence, individuals with ASD tend to rely less on visual feedback than do healthy controls. Visuomotor representations are considered to underlie imitative learning and action understanding and are thereby crucial to social skill and cognitive development. Thus, anomalous patterns of implicit motor learning, with a tendency to discount visual feedback, may be an important contributor in core social communication deficits that characterize ASD. Autism Res 2016, 9: 563-569. © 2015 International Society for Autism Research, Wiley Periodicals, Inc. PMID:26442448

  11. Nucleotide sequence and corresponding amino acid sequence of the gene for the major antigen of foot and mouth disease virus.

    OpenAIRE

    Kurz, C; Forss, S; Küpper, H; K Strohmaier; Schaller, H

    1981-01-01

    A segment of 1160 nucleotides of the FMDV genome has been sequenced using three overlapping fragments of cloned cDNA from FMDV strain O1K. This sequence contains the coding sequence for the viral capsid protein VP1 as shown by its homology to known and newly determined amino acid sequences from this man antigenic polypeptide of the FMDV virion. The structural gene for VP1 comprises 639 nucleotides which specify a sequence of 213 amino acids for the VP1 protein. The coding sequence is not flan...

  12. Correlation between fibroin amino acid sequence and physical silk properties.

    Science.gov (United States)

    Fedic, Robert; Zurovec, Michal; Sehnal, Frantisek

    2003-09-12

    The fiber properties of lepidopteran silk depend on the amino acid repeats that interact during H-fibroin polymerization. The aim of our research was to relate repeat composition to insect biology and fiber strength. Representative regions of the H-fibroin genes were sequenced and analyzed in three pyralid species: wax moth (Galleria mellonella), European flour moth (Ephestia kuehniella), and Indian meal moth (Plodia interpunctella). The amino acid repeats are species-specific, evidently a diversification of an ancestral region of 43 residues, and include three types of regularly dispersed motifs: modifications of GSSAASAA sequence, stretches of tripeptides GXZ where X and Z represent bulky residues, and sequences similar to PVIVIEE. No concatenations of GX dipeptide or alanine, which are typical for Bombyx silkworms and Antheraea silk moths, respectively, were found. Despite different repeat structure, the silks of G. mellonella and E. kuehniella exhibit similar tensile strength as the Bombyx and Antheraea silks. We suggest that in these latter two species, variations in the repeat length obstruct repeat alignment, but sufficiently long stretches of iterated residues get superposed to interact. In the pyralid H-fibroins, interactions of the widely separated and diverse motifs depend on the precision of repeat matching; silk is strong in G. mellonella and E. kuehniella, with 2-3 types of long homogeneous repeats, and nearly 10 times weaker in P. interpunctella, with seven types of shorter erratic repeats. The high proportion of large amino acids in the H-fibroin of pyralids has probably evolved in connection with the spinning habit of caterpillars that live in protective silk tubes and spin continuously, enlarging the tubes on one end and partly devouring the other one. The silk serves as a depot of energetically rich and essential amino acids that may be scarce in the diet. PMID:12816957

  13. Cervical cancer risk factors and feasibility of visual inspection with acetic acid screening in Sudan

    DEFF Research Database (Denmark)

    Ibrahim, Ahmed; Rasch, Vibeke; Pukkala, Eero;

    2011-01-01

    To assess the risk factors of cervical cancer and the feasibility and acceptability of a visual inspection with acetic acid (VIA) screening method in a primary health center in Khartoum, Sudan.......To assess the risk factors of cervical cancer and the feasibility and acceptability of a visual inspection with acetic acid (VIA) screening method in a primary health center in Khartoum, Sudan....

  14. Nucleic acid sequence detection using multiplexed oligonucleotide PCR

    Science.gov (United States)

    Nolan, John P.; White, P. Scott

    2006-12-26

    Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

  15. fluff: exploratory analysis and visualization of high-throughput sequencing data.

    Science.gov (United States)

    Georgiou, Georgios; van Heeringen, Simon J

    2016-01-01

    In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org. Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff. PMID:27547532

  16. Timing and sequence of brain activity in top-down control of visual-spatial attention.

    OpenAIRE

    Tineke Grent-'t-Jong; Woldorff, Marty G.

    2007-01-01

    Recent brain imaging studies using functional magnetic resonance imaging (fMRI) have implicated a frontal-parietal network in the top-down control of attention. However, little is known about the timing and sequence of activations within this network. To investigate these timing questions, we used event-related electrical brain potentials (ERPs) and a specially designed visual-spatial attentional-cueing paradigm, which were applied as part of a multi-methodological approach that included a cl...

  17. HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data.

    Science.gov (United States)

    Ward, Ben J; van Oosterhout, Cock

    2016-03-01

    HYBRIDCHECK is a software package to visualize the recombination signal in large DNA sequence data set, and it can be used to analyse recombination, genetic introgression, hybridization and horizontal gene transfer. It can scan large (multiple kb) contigs and whole-genome sequences of three or more individuals. HYBRIDCHECK is written in the r software for OS X, Linux and Windows operating systems, and it has a simple graphical user interface. In addition, the r code can be readily incorporated in scripts and analysis pipelines. HYBRIDCHECK implements several ABBA-BABA tests and visualizes the effects of hybridization and the resulting mosaic-like genome structure in high-density graphics. The package also reports the following: (i) the breakpoint positions, (ii) the number of mutations in each introgressed block, (iii) the probability that the identified region is not caused by recombination and (iv) the estimated age of each recombination event. The divergence times between the donor and recombinant sequence are calculated using a JC, K80, F81, HKY or GTR correction, and the dating algorithm is exceedingly fast. By estimating the coalescence time of introgressed blocks, it is possible to distinguish between hybridization and incomplete lineage sorting. HYBRIDCHECK is libré software and it and its manual are free to download from http://ward9250.github.io/HybridCheck/. PMID:26394708

  18. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

    Directory of Open Access Journals (Sweden)

    Francisco Alexandre P

    2012-05-01

    Full Text Available Abstract Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

  19. Carbon nanotube-based labels for highly sensitive colorimetric and aggregation-based visual detection of nucleic acids

    International Nuclear Information System (INIS)

    A novel carbon nanotube (CNT) derived label capable of dramatic signal amplification of nucleic acid detection and direct visual detection of target hybridization has been developed. Highly sensitive colorimetric detection of human acute lymphocytic leukemia (ALL) related oncogene sequences amplified by the novel CNT-based label was demonstrated. Atomic force microscope (AFM) images confirmed that a monolayer of horseradish peroxidase and detection probe molecules was immobilized along the carboxylated CNT carrier. The resulting CNT labels significantly enhanced the nucleic acid assay sensitivity by at least 1000 times compared to that of conventional labels used in enzyme-linked oligosorbent assay (ELOSA). An excellent detection limit of 1 x 10-12 M (60 x 10-18 mol in 60 μl) and a four-order wide dynamic range of target concentration were achieved. Hybridizations using these labels were coupled to a concentration-dependent formation of visible dark aggregates. Targets can thus be detected simply with visual inspection, eliminating the need for expensive and sophisticated detection systems. The approach holds promise for ultrasensitive and low cost visual inspection and colorimetric nucleic acid detection in point-of-care and early disease diagnostic application

  20. 37 CFR 1.822 - Symbols and format to be used for nucleotide and/or amino acid sequence data.

    Science.gov (United States)

    2010-07-01

    ... for nucleotide and/or amino acid sequence data. 1.822 Section 1.822 Patents, Trademarks, and... Amino Acid Sequences § 1.822 Symbols and format to be used for nucleotide and/or amino acid sequence data. (a) The symbols and format to be used for nucleotide and/or amino acid sequence data...

  1. Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

    Energy Technology Data Exchange (ETDEWEB)

    Myers, G.; Foley, B.; Korber, B. [eds.] [Los Alamos National Lab., NM (United States). Theoretical Div.; Mellors, J.W. [ed.] [Univ. of Pittsburgh, PA (United States); Jeang, K.T. [ed.] [National Institutes of Health, Bethesda, MD (United States). Molecular Virology Section; Wain-Hobson, S. [Pasteur Inst., Paris (France)] [ed.

    1997-04-01

    This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. While this publication could take the form of a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.

  2. CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.

    Directory of Open Access Journals (Sweden)

    Eric Talevich

    2016-04-01

    Full Text Available Germline copy number variants (CNVs and somatic copy number alterations (SCNAs are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.

  3. Amino acid sequences used for clusterintg (Multi FASTA format) - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Gclust Server Amino acid sequences used for clusterintg (Multi FASTA format) Data detail Data name Amino acid sequence...s used for clusterintg (Multi FASTA format) Description of data contents Amino acid sequences of p...a entries - FASTA format header: ID and the annotation information of the sequence... Site Policy | Contact Us Amino acid sequences used for clusterintg (Multi FASTA format) - Gclust Server | LSDB Archive ...

  4. Transcriptome Sequencing in Response to Salicylic Acid in Salvia miltiorrhiza.

    Science.gov (United States)

    Zhang, Xiaoru; Dong, Juane; Liu, Hailong; Wang, Jiao; Qi, Yuexin; Liang, Zongsuo

    2016-01-01

    Salvia miltiorrhiza is a traditional Chinese herbal medicine, whose quality and yield are often affected by diseases and environmental stresses during its growing season. Salicylic acid (SA) plays a significant role in plants responding to biotic and abiotic stresses, but the involved regulatory factors and their signaling mechanisms are largely unknown. In order to identify the genes involved in SA signaling, the RNA sequencing (RNA-seq) strategy was employed to evaluate the transcriptional profiles in S. miltiorrhiza cell cultures. A total of 50,778 unigenes were assembled, in which 5,316 unigenes were differentially expressed among 0-, 2-, and 8-h SA induction. The up-regulated genes were mainly involved in stimulus response and multi-organism process. A core set of candidate novel genes coding SA signaling component proteins was identified. Many transcription factors (e.g., WRKY, bHLH and GRAS) and genes involved in hormone signal transduction were differentially expressed in response to SA induction. Detailed analysis revealed that genes associated with defense signaling, such as antioxidant system genes, cytochrome P450s and ATP-binding cassette transporters, were significantly overexpressed, which can be used as genetic tools to investigate disease resistance. Our transcriptome analysis will help understand SA signaling and its mechanism of defense systems in S. miltiorrhiza. PMID:26808150

  5. A noncontrast-enhanced pulse sequence optimized to visualize human peripheral vessels

    International Nuclear Information System (INIS)

    The purpose of this paper is to present a pulse sequence optimized to visualize human peripheral vessels. The optimized MR technique is a 3D multi-shot balanced non-SSFP gradient echo pulse sequence with fat suppression. Several imaging parameters were adjusted to find the best compromise between the contrast of vascular structures and muscle, fat, and bone. Most of the optimization was performed in the knee and calf regions using multi-channel SENSE coils. To verify potential clinical use, images of both healthy volunteers and volunteers with varicose veins were produced. The balanced non-SSFP sequence can produce high-spatial-resolution images of the human peripheral vessels without the need for an intravenous contrast agent. Both arteries and veins are displayed along with other body fluids. Due to the high spatial resolution of the axial plane source or reconstructed images, the need for procedures to separate arteries from veins is limited. We demonstrate that high signals from synovial joint fluid and cystic structures can be suppressed by applying an inversion prepulse but at the expense of reduced image signal-to-noise and overall image quality. (orig.)

  6. A noncontrast-enhanced pulse sequence optimized to visualize human peripheral vessels

    Energy Technology Data Exchange (ETDEWEB)

    Gjesdal, Kjell-Inge [Sunnmoere MR-Klinikk, Aalesund (Norway); Storaas, Tryggve [Ullevaal University Hospital, Section for Diagnostic Physics, Department of Radiology, Oslo (Norway); Geitung, Jonn-Terje [Haraldsplass University Hospital, Department of Radiology, Bergen (Norway)

    2009-01-15

    The purpose of this paper is to present a pulse sequence optimized to visualize human peripheral vessels. The optimized MR technique is a 3D multi-shot balanced non-SSFP gradient echo pulse sequence with fat suppression. Several imaging parameters were adjusted to find the best compromise between the contrast of vascular structures and muscle, fat, and bone. Most of the optimization was performed in the knee and calf regions using multi-channel SENSE coils. To verify potential clinical use, images of both healthy volunteers and volunteers with varicose veins were produced. The balanced non-SSFP sequence can produce high-spatial-resolution images of the human peripheral vessels without the need for an intravenous contrast agent. Both arteries and veins are displayed along with other body fluids. Due to the high spatial resolution of the axial plane source or reconstructed images, the need for procedures to separate arteries from veins is limited. We demonstrate that high signals from synovial joint fluid and cystic structures can be suppressed by applying an inversion prepulse but at the expense of reduced image signal-to-noise and overall image quality. (orig.)

  7. Natural vs. random protein sequences: Discovering combinatorics properties on amino acid words.

    Science.gov (United States)

    Santoni, Daniele; Felici, Giovanni; Vergni, Davide

    2016-02-21

    Casual mutations and natural selection have driven the evolution of protein amino acid sequences that we observe at present in nature. The question about which is the dominant force of proteins evolution is still lacking of an unambiguous answer. Casual mutations tend to randomize protein sequences while, in order to have the correct functionality, one expects that selection mechanisms impose rigid constraints on amino acid sequences. Moreover, one also has to consider that the space of all possible amino acid sequences is so astonishingly large that it could be reasonable to have a well tuned amino acid sequence indistinguishable from a random one. In order to study the possibility to discriminate between random and natural amino acid sequences, we introduce different measures of association between pairs of amino acids in a sequence, and apply them to a dataset of 1047 natural protein sequences and 10,470 random sequences, carefully generated in order to preserve the relative length and amino acid distribution of the natural proteins. We analyze the multidimensional measures with machine learning techniques and show that, to a reasonable extent, natural protein sequences can be differentiated from random ones.

  8. Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Dicty_cDB Contig sequence...s and their annotation (amino acid sequence and results of homology search), and ex...pression profile Data detail Data name Contig sequences and their annotation (amino acid sequence and result...s of homology search), and expression profile Description of data contents Contig sequences of cDNA sequen...ces of Dictyostelium discoideum and their annotation (amino acid sequence and resul

  9. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures

    Directory of Open Access Journals (Sweden)

    Fördös Gergely

    2005-07-01

    Full Text Available Abstract Background The interacting residues of protein and nucleic acid sequences are close to each other – they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. Results SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user a. selects a structure from PDB; b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s c. defines a distance from these atoms (3–15 Å. The SeqX tool detects every residue that is located within the defined distances from the defined "backbone" atom(s; provides a DotPlot-like visualization (Residues Contact Map, and calculates the frequency of every possible residue pairs (Residue Contact Table in the observed structure. It is possible to exclude +/- 1 to 10 neighbor residues in the same polymeric chain from detection, which greatly improves the specificity of detections (up to 60% when tested on dsDNA. Results obtained on protein structures showed highly significant correlations with results obtained from literature (p Conclusion The tool is simple and easy to use and provides a quick and reliable visualization and analyses of residue co-locations in protein and nucleic acid structures. Availability and requirements http://janbiro.com/Downloads.html SeqX, Java J2SE Runtime Environment 5.0 (available from [see Additional file 1] http://www.sun.com and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors. Additional File 1 SeqX_1.041_05601.jar. see this article Click here for file

  10. The complete amino acid sequence of the basic nuclear protein of bull spermatozoa

    NARCIS (Netherlands)

    Coelingh, J.P.; Monfoort, Cornelis H.; Rozijn, Thomas H.; Gevers Leuven, Jan A.; Schiphof, R.; Steyn-Parvé, Elizabeth P.; Braunitzer, Gerhard; Schrank, Barbara; Ruhfus, Annette

    1972-01-01

    The complete amino acid sequence of the basic nuclear protein of bull spermatozoa has been established. The sequence was partially deduced by characterization of peptides isolated from thermolysine and chymotryptic digests of the reduced and S-aminoethylated protein. The complete sequence of the fir

  11. Analysis and dynamic 3D visualization of cerebral blood flow combining 3D and 4D MR image sequences

    Science.gov (United States)

    Forkert, Nils Daniel; Säring, Dennis; Fiehler, Jens; Illies, Till; Möller, Dietmar; Handels, Heinz

    2009-02-01

    In this paper we present a method for the dynamic visualization of cerebral blood flow. Spatio-temporal 4D magnetic resonance angiography (MRA) image datasets and 3D MRA datasets with high spatial resolution were acquired for the analysis of arteriovenous malformations (AVMs). One of the main tasks is the combination of the information of the 3D and 4D MRA image sequences. Initially, in the 3D MRA dataset the vessel system is segmented and a 3D surface model is generated. Then, temporal intensity curves are analyzed voxelwise in the 4D MRA image sequences. A curve fitting of the temporal intensity curves to a patient individual reference curve is used to extract the bolus arrival times in the 4D MRA sequences. After non-linear registration of both MRA datasets the extracted hemodynamic information is transferred to the surface model where the time points of inflow can be visualized color coded dynamically over time. The dynamic visualizations computed using the curve fitting method for the estimation of the bolus arrival times were rated superior compared to those computed using conventional approaches for bolus arrival time estimation. In summary the procedure suggested allows a dynamic visualization of the individual hemodynamic situation and better understanding during the visual evaluation of cerebral vascular diseases.

  12. Nucleotide Sequence of a Chicken Vitellogenin Gene and Derived Amino Acid Sequence of the Encoded Yolk Precursor Protein

    NARCIS (Netherlands)

    Schip, Fred D. van het; Samallo, John; Broos, Jaap; Ophuis, Jan; Mojet, Mart; Gruber, Max; AB, Geert

    1987-01-01

    The gene encoding the major vitellogenin from chicken has been completely sequenced and its exon-intron organization has been established. The gene is 20,342 base-pairs long and contains 35 exons with a combined length of 5787 base-pairs. They encode the 1850-amino acid pre-peptide of vitellogenin,

  13. AllelicImbalance: An R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing

    DEFF Research Database (Denmark)

    Gådin, Jesper R.; van't Hooft, Ferdinand M.; Eriksson, Per;

    2015-01-01

    the possible biases. Results: We present AllelicImblance, a software program that is designed to detect, manage, and visualize allelic imbalances comprehensively. The purpose of this software is to allow users to pose genetic questions in any RNA sequencing experiment quickly, enhancing the general utility...

  14. The amino acid sequence of elephant (Elephas maximus) myoglobin and the phylogeny of Proboscidea.

    Science.gov (United States)

    Dene, H; Goodman, M; Romero-Herrera, A E

    1980-02-13

    The complete amino acid sequence of skeletal myoglobin from the Asian elephant (Elephas maximus) is reported. The functional significance of variations seen when this sequence is compared with that of sperm whale myoglobin is explored in the light of the crystallographic model available for the latter molecule. The phylogenetic implications of the elephant myoglobin amino acid sequence are evaluated by using the maximum parsimony technique. A similar analysis is also presented which incorporates all of the proteins sequenced from the elephant. These results are discussed with respect to current views on proboscidean phylogeny.

  15. A conversational system for the computer analysis of nucleic acid sequences.

    OpenAIRE

    Sege, R; Söll, D.; Ruddle, F H; Queen, C

    1981-01-01

    We present a conversational system for the computer analysis of nucleic acid and protein sequences based on the well-known Queen and Korn program (1). The system can be used by persons with only minimal knowledge of computers.

  16. cDNA-derived amino acid sequences of myoglobins from nine species of whales and dolphins.

    Science.gov (United States)

    Iwanami, Kentaro; Mita, Hajime; Yamamoto, Yasuhiko; Fujise, Yoshihiro; Yamada, Tadasu; Suzuki, Tomohiko

    2006-10-01

    We determined the myoglobin (Mb) cDNA sequences of nine cetaceans, of which six are the first reports of Mb sequences: sei whale (Balaenoptera borealis), Bryde's whale (Balaenoptera edeni), pygmy sperm whale (Kogia breviceps), Stejneger's beaked whale (Mesoplodon stejnegeri), Longman's beaked whale (Indopacetus pacificus), and melon-headed whale (Peponocephala electra), and three confirm the previously determined chemical amino acid sequences: sperm whale (Physeter macrocephalus), common minke whale (Balaenoptera acutorostrata) and pantropical spotted dolphin (Stenella attenuata). We found two types of Mb in the skeletal muscle of pantropical spotted dolphin: Mb I with the same amino acid sequence as that deposited in the protein database, and Mb II, which differs at two amino acid residues compared with Mb I. Using an alignment of the amino acid or cDNA sequences of cetacean Mb, we constructed a phylogenetic tree by the NJ method. Clustering of cetacean Mb amino acid and cDNA sequences essentially follows the classical taxonomy of cetaceans, suggesting that Mb sequence data is valid for classification of cetaceans at least to the family level. PMID:16962803

  17. Multiple Genome Sequences of Important Beer-Spoiling Lactic Acid Bacteria

    Science.gov (United States)

    Geissler, Andreas J.; Vogel, Rudi F.

    2016-01-01

    Seven strains of important beer-spoiling lactic acid bacteria were sequenced using single-molecule real-time sequencing. Complete genomes were obtained for strains of Lactobacillus paracollinoides, Lactobacillus lindneri, and Pediococcus claussenii. The analysis of these genomes emphasizes the role of plasmids as the genomic foundation of beer-spoiling ability. PMID:27795248

  18. Amino Acid Sequence - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ll_sequence_amino_db.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST...ta.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_ine_full_sequence_amino_db.fasta.zip Fi...date History of This Database Site Policy | Contact Us Amino Acid Sequence - KOME | LSDB Archive ...

  19. A study to visualize and determine the sequencing of intersecting ink lines.

    Science.gov (United States)

    Ozbek, Nil; Braz, André; López-López, Maria; García-Ruiz, Carmen

    2014-01-01

    Determining the sequencing of intersecting ink lines is one of the current problems for forensic document examiners. The way two inks will distribute and interact with each other and the paper at the crossing is a dynamic process that can be affected by many variables. Thus, the main purpose of this manuscript is to visualize and have a more comprehensive understanding of this process as well as study a methodology for determining the correct order of intersecting ink lines. For this, overlapping layers of different types of inks from writing instruments and printers were cross-sectioned and examined with a microscope. Results from pen/pen crossings showed that liquid-liquid and gel-gel intersections tended to form a double layer but oil-oil intersections usually formed mixtures. Additionally, oil-liquid and oil-gel intersections tended to form a double layer whenever the oil ink was on top and liquid-gel intersections tended to form a double layer for almost all crossings with exception of the ones involving a gel pen ink from one manufacturer. Results from pen/printer crossings showed the formation of a double layer only when the printer ink was on top of the pen ink. On the other permutation, the pen ink tended to penetrate through the printer ink producing the mixture of both inks. The inks drying time was found to be an important factor affecting the interaction between two inks in a crossing, particularly crossings involving gel pen inks. On the contrary, the type of paper and the writing pressure showed no significant influence on the inks distribution at the crossing. The methodology developed was reproducible with overlapping layers but there were many experimental difficulties during the validation process of intersections representing real crossings. Moreover, interpretation was dependent on the operator's eye which was a limiting factor.

  20. Complete Genome Sequence of Streptomyces clavuligerus F613-1, an Industrial Producer of Clavulanic Acid

    Science.gov (United States)

    Zhong, Chuanqing; Zong, Gongli; Fu, Jiafang; Liu, Zhong; Zhang, Guimin; Qin, Ronghuo

    2016-01-01

    Streptomyces clavuligerus strain F613-1 is an industrial strain with high-yield clavulanic acid production. In this study, the complete genome sequence of S. clavuligerus strain F613-1 was determined, including one linear chromosome and one linear plasmid, carrying numerous sets of genes involving in the biosynthesis of clavulanic acid. PMID:27660792

  1. Complete Genome Sequence of Streptomyces clavuligerus F613-1, an Industrial Producer of Clavulanic Acid.

    Science.gov (United States)

    Cao, Guangxiang; Zhong, Chuanqing; Zong, Gongli; Fu, Jiafang; Liu, Zhong; Zhang, Guimin; Qin, Ronghuo

    2016-01-01

    Streptomyces clavuligerus strain F613-1 is an industrial strain with high-yield clavulanic acid production. In this study, the complete genome sequence of S. clavuligerus strain F613-1 was determined, including one linear chromosome and one linear plasmid, carrying numerous sets of genes involving in the biosynthesis of clavulanic acid. PMID:27660792

  2. Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome

    Science.gov (United States)

    Pinto, Ameet J.; Sharp, Jonathan O.; Yoder, Michael J.

    2016-01-01

    Bacteria belonging to the family Acidimicrobiaceae are frequently encountered in heavy metal-contaminated acidic environments. However, their phylogenetic and metabolic diversity is poorly resolved. We present draft genome sequences of two novel and phylogenetically distinct Acidimicrobiaceae members assembled from an acid mine drainage biofilm metagenome. PMID:26769942

  3. Complete Genome Sequence of Streptomyces clavuligerus F613-1, an Industrial Producer of Clavulanic Acid.

    Science.gov (United States)

    Cao, Guangxiang; Zhong, Chuanqing; Zong, Gongli; Fu, Jiafang; Liu, Zhong; Zhang, Guimin; Qin, Ronghuo

    2016-01-01

    Streptomyces clavuligerus strain F613-1 is an industrial strain with high-yield clavulanic acid production. In this study, the complete genome sequence of S. clavuligerus strain F613-1 was determined, including one linear chromosome and one linear plasmid, carrying numerous sets of genes involving in the biosynthesis of clavulanic acid.

  4. Complete amino acid sequence of human intestinal aminopeptidase N as deduced from cloned cDNA

    DEFF Research Database (Denmark)

    Cowell, G M; Kønigshøfer, E; Danielsen, E M;

    1988-01-01

    The complete primary structure (967 amino acids) of an intestinal human aminopeptidase N (EC 3.4.11.2) was deduced from the sequence of a cDNA clone. Aminopeptidase N is anchored to the microvillar membrane via an uncleaved signal for membrane insertion. A domain constituting amino acid 250-555 p...

  5. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

    Science.gov (United States)

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

    2015-05-01

    We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

  6. Parvalbumins from coelacanth muscle. III. Amino acid sequence of the major component.

    Science.gov (United States)

    Jauregui-Adell, J; Pechere, J F

    1978-09-26

    The primary structure of the major parvalbumin (pI = 4.52) from coelacanth muscle (Latimeria chalumnae) has been determined. Sequence analysis of the tryptic peptides, in some cases obtained with beta-trypsin, accounts for the total amino acid content of the protein. Chymotryptic peptides provide appropriate sequence overlaps, to complete the localization of the tryptic peptides. Examination of the amino acid sequence of this protein shows the typical structure of a beta-parvalbumin. Its position in the dendrogram of related calcium-binding proteins corresponds to that usually accepted for crossopterygians.

  7. Sequencing and computational analysis of complete genome sequences of Citrus yellow mosaic badna virus from acid lime and pummelo.

    Science.gov (United States)

    Borah, Basanta K; Johnson, A M Anthony; Sai Gopal, D V R; Dasgupta, Indranil

    2009-08-01

    Citrus yellow mosaic badna virus (CMBV), a member of the Family Caulimoviridae, Genus Badnavirus, is the causative agent of Citrus mosaic disease in India. Although the virus has been detected in several citrus species, only two full-length genomes, one each from Sweet orange and Rangpur lime, are available in publicly accessible databases. In order to obtain a better understanding of the genetic variability of the virus in other citrus mosaic-affected citrus species, we performed the cloning and sequence analysis of complete genomes of CMBV from two additional citrus species, Acid lime and Pummelo. We show that CMBV genomes from the two hosts share high homology with previously reported CMBV sequences and hence conclude that the new isolates represent variants of the virus present in these species. Based on in silico sequence analysis, we predict the possible function of the protein encoded by one of the five ORFs.

  8. Two distinct ferredoxins from Rhodobacter capsulatus: complete amino acid sequences and molecular evolution.

    Science.gov (United States)

    Saeki, K; Suetsugu, Y; Yao, Y; Horio, T; Marrs, B L; Matsubara, H

    1990-09-01

    Two distinct ferredoxins were purified from Rhodobacter capsulatus SB1003. Their complete amino acid sequences were determined by a combination of protease digestion, BrCN cleavage and Edman degradation. Ferredoxins I and II were composed of 64 and 111 amino acids, respectively, with molecular weights of 6,728 and 12,549 excluding iron and sulfur atoms. Both contained two Cys clusters in their amino acid sequences. The first cluster of ferredoxin I and the second cluster of ferredoxin II had a sequence, CxxCxxCxxxCP, in common with the ferredoxins found in Clostridia. The second cluster of ferredoxin I had a sequence, CxxCxxxxxxxxCxxxCM, with extra amino acids between the second and third Cys, which has been reported for other photosynthetic bacterial ferredoxins and putative ferredoxins (nif-gene products) from nitrogen-fixing bacteria, and with a unique occurrence of Met. The first cluster of ferredoxin II had a CxxCxxxxCxxxCP sequence, with two additional amino acids between the second and third Cys, a characteristics feature of Azotobacter-[3Fe-4S] [4Fe-4S]-ferredoxin. Ferredoxin II was also similar to Azotobacter-type ferredoxins with an extended carboxyl (C-) terminal sequence compared to the common Clostridium-type. The evolutionary relationship of the two together with a putative one recently found to be encoded in nifENXQ region in this bacterium [Moreno-Vivian et al. (1989) J. Bacteriol. 171, 2591-2598] is discussed. PMID:2277040

  9. Visualization of cranial nerves I-XII: value of 3D CISS and T2-weighted FSE sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yousry, I.; Camelio, S.; Wiesmann, M.; Brueckmann, H.; Yousry, T.A. [Department of Neuroradiology, Klinikum Grosshadern, Ludwig-Maximilians University, Marchioninistrasse 15, D-81377 Munich (Germany); Schmid, U.D. [Neurosurgical Unit, Klinik im Park, 8000 Zurich (Switzerland); Horsfield, M.A. [Department of Medical Physics, University of Leicester, Leicester LE1 5WW (United Kingdom)

    2000-07-01

    The aim of this study was to evaluate the sensitivity of the three-dimensional constructive interference of steady state (3D CISS) sequence (slice thickness 0.7 mm) and that of the T2-weighted fast spin echo (T2-weighted FSE) sequence (slice thickness 3 mm) for the visualization of all cranial nerves in their cisternal course. Twenty healthy volunteers were examined using the T2-weighted FSE and the 3D CISS sequences. Three observers evaluated independently the cranial nerves NI-NXII in their cisternal course. The rates for successful visualization of each nerve for 3D CISS (and for T2-weighted FSE in parentheses) were as follows: NI, NII, NV, NVII, NVIII 40 of 40 (40 of 40), NIII 40 of 40 (18 of 40), NIV 19 of 40 (3 of 40), NVI 39 of 40 (5 of 40), NIX, X, XI 40 of 40 (29 of 40), and NXII 40 of 40 (4 of 40). Most of the cranial nerves can be reliably assessed when using the 3D CISS and the T2-weighted FSE sequences. Increasing the spatial resolution when using the 3D CISS sequence increases the reliability of the identification of the cranial nerves NIII-NXII. (orig.)

  10. Complete amino acid sequence and structure characterization of the taste-modifying protein, miraculin.

    Science.gov (United States)

    Theerasilp, S; Hitotsuya, H; Nakajo, S; Nakaya, K; Nakamura, Y; Kurihara, Y

    1989-04-25

    The taste-modifying protein, miraculin, has the unusual property of modifying sour taste into sweet taste. The complete amino acid sequence of miraculin purified from miracle fruits by a newly developed method (Theerasilp, S., and Kurihara, Y. (1988) J. Biol. Chem. 263, 11536-11539) was determined by an automatic Edman degradation method. Miraculin was a single polypeptide with 191 amino acid residues. The calculated molecular weight based on the amino acid sequence and the carbohydrate content (13.9%) was 24,600. Asn-42 and Asn-186 were linked N-glycosidically to carbohydrate chains. High homology was found between the amino acid sequences of miraculin and soybean trypsin inhibitor. PMID:2708331

  11. Protein chemotaxonomy. XIII. Amino acid sequence of ferredoxin from Panax ginseng.

    Science.gov (United States)

    Mino, Yoshiki

    2006-08-01

    The complete amino acid sequence of [2Fe-2S] ferredoxin from Panax ginseng (Araliaceae) has been determined by automated Edman degradation of the entire S-carboxymethylcysteinyl protein and of the peptides obtained by enzymatic digestion. This ferredoxin has a unique amino acid sequence, which includes an insertion of Tyr at the 3rd position from the amino-terminus and a deletion of two amino acid residues at the carboxyl terminus. This ferredoxin had 18 differences in its amino acid sequence compared to that of Petroselinum sativum (Umbelliferae). In contrast, 23-33 differences were observed compared to other dicotyledonous plants. This suggests that Panax ginseng is related taxonomically to umbelliferous plants. PMID:16880642

  12. Visualization of Early Events in Acetic Acid Denaturation of HIV-1 Protease: A Molecular Dynamics Study

    OpenAIRE

    Borkar, Aditi Narendra; Rout, Manoj Kumar; Hosur, Ramakrishna V.

    2011-01-01

    Protein denaturation plays a crucial role in cellular processes. In this study, denaturation of HIV-1 Protease (PR) was investigated by all-atom MD simulations in explicit solvent. The PR dimer and monomer were simulated separately in 9 M acetic acid (9 M AcOH) solution and water to study the denaturation process of PR in acetic acid environment. Direct visualization of the denaturation dynamics that is readily available from such simulations has been presented. Our simulations in 9 M AcOH re...

  13. Omega-3 fatty acids modify human cortical visual processing--a double-blind, crossover study.

    Directory of Open Access Journals (Sweden)

    Isabelle Bauer

    Full Text Available While cardiovascular and mood benefits of dietary omega-3 fatty acids such as docosahexaenoic acid (DHA and eicosapentaenoic acid (EPA are manifest, direct neurophysiological evidence of their effects on cortical activity is still limited. Hence we chose to examine the effects of two proprietary fish oil products with different EPA:DHA ratios (EPA-rich, high EPA:DHA; DHA-rich on mental processing speed and visual evoked brain activity. We proposed that nonlinear multifocal visual evoked potentials (mfVEP would be sensitive to any alteration of the neural function induced by omega-3 fatty acid supplementation, because the higher order kernel responses directly measure the degree of recovery of the neural system as a function of time following stimulation. Twenty-two healthy participants aged 18-34, with no known neurological or psychiatric disorder and not currently taking any nutritional supplementation, were recruited. A double-blind, crossover design was utilized, including a 30-day washout period, between two 30-day supplementation periods of the EPA-rich and DHA-rich diets (with order of diet randomized. Psychophysical choice reaction times and multi-focal nonlinear visual evoked potential (VEP testing were performed at baseline (No Diet, and after each supplementation period. Following the EPA-rich supplementation, for stimulation at high luminance contrast, a significant reduction in the amplitude of the first slice of the second order VEP kernel response, previously related to activation in the magnocellular pathway, was observed. The correlations between the amplitude changes of short latency second and first order components were significantly different for the two supplementations. Significantly faster choice reaction times were observed psychophysically (compared with baseline performance under the EPA-rich (but not DHA-rich supplementation, while simple reaction times were not affected. The reduced nonlinearities observed under the

  14. Visualizing digestive organ morphology and function using differential fatty acid metabolism in live zebrafish

    OpenAIRE

    Carten, Juliana Debrito; Bradford, Mary Katherine; Farber, Steven Arthur

    2011-01-01

    Lipids are essential for cellular function as sources of fuel, critical signaling molecules and membrane components. Deficiencies in lipid processing and transport underlie many metabolic diseases. To better understand metabolic function as it relates to disease etiology, a whole animal approach is advantageous, one in which multiple organs and cell types can be assessed simultaneously in vivo. Towards this end, we have developed an assay to visualize fatty acid (FA) metabolism in larval zebr...

  15. Amino acid sequence heterogeneity of the chromosomal encoded Borrelia burgdorferi sensu lato major antigen P100.

    Science.gov (United States)

    Fellinger, W; Farencena, A; Redl, B; Sambri, V; Cevenini, R; Stöffler, G

    1995-04-01

    The entire nucleotide sequence of the chromosomal encoded major antigen p100 of the European Borrelia garinii isolate B29 was determined and the deduced amino acid sequence was compared to the homologous antigen p83 of the North American Borrelia burgdorferi sensu stricto strain B31 and the p100 of the European Borrelia afzelii (group VS461) strain PKo. p100 of strain B29 shows 87% amino acid sequence identity to strain B31 and 79.2% to strain PKo, p100 of strain B31 and PKo shows 62.5% identity to each other. In addition, partial nucleotide sequences of the most heterogeneous region of the p100 gene of two other Borrelia garinii isolates (PBi and VS286) have been determined and the deduced amino acid sequences were compared with all p100 of Borrelia garinii published so far. We found an amino acid sequence identity between 88.6 and 100% within the same genospecies. The N-terminal part of the p100 proteins is highly conserved whereas a striking heterogeneous region within the C-terminal part of the proteins was observed.

  16. Coding Local and Global Binary Visual Features Extracted From Video Sequences.

    Science.gov (United States)

    Baroffio, Luca; Canclini, Antonio; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

    2015-11-01

    Binary local features represent an effective alternative to real-valued descriptors, leading to comparable results for many visual analysis tasks while being characterized by significantly lower computational complexity and memory requirements. When dealing with large collections, a more compact representation based on global features is often preferred, which can be obtained from local features by means of, e.g., the bag-of-visual word model. Several applications, including, for example, visual sensor networks and mobile augmented reality, require visual features to be transmitted over a bandwidth-limited network, thus calling for coding techniques that aim at reducing the required bit budget while attaining a target level of efficiency. In this paper, we investigate a coding scheme tailored to both local and global binary features, which aims at exploiting both spatial and temporal redundancy by means of intra- and inter-frame coding. In this respect, the proposed coding scheme can conveniently be adopted to support the analyze-then-compress (ATC) paradigm. That is, visual features are extracted from the acquired content, encoded at remote nodes, and finally transmitted to a central controller that performs the visual analysis. This is in contrast with the traditional approach, in which visual content is acquired at a node, compressed and then sent to a central unit for further processing, according to the compress-then-analyze (CTA) paradigm. In this paper, we experimentally compare the ATC and the CTA by means of rate-efficiency curves in the context of two different visual analysis tasks: 1) homography estimation and 2) content-based retrieval. Our results show that the novel ATC paradigm based on the proposed coding primitives can be competitive with the CTA, especially in bandwidth limited scenarios. PMID:26080384

  17. DNA Data Visualization (DDV: Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes.

    Directory of Open Access Journals (Sweden)

    Tomasz Neugebauer

    Full Text Available Data visualization methods are necessary during the exploration and analysis activities of an increasingly data-intensive scientific process. There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. Software for data visualization should allow the researchers to create accessible data visualization interfaces that can be exported and shared with others on the web. Herein, novel software developed for generating DNA data visualization interfaces is described. The software converts DNA data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection. Nucleotide composition frequencies and GC skew of a selected sequence segment can be obtained through the interface. The software was used to generate DNA data visualization of human and bacterial chromosomes. Examples of visually detectable features such as short and long direct repeats, long terminal repeats, mobile genetic elements, heterochromatic segments in microbial and human chromosomes, are presented. The software and its source code are available for download and further development. The visualization interfaces generated with the software allow for the immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins. The visualization interfaces generated with the software are readily accessible through a web browser. This software is a useful research and teaching tool for genetics and structural genomics.

  18. Introduction of restriction enzyme sites in protein-coding DNA sequences by site-specific mutagenesis not affecting the amino acid sequence: a computer program.

    OpenAIRE

    Arentzen, R; Ripka, W. C.

    1984-01-01

    Structure/function relationship studies of proteins are greatly facilitated by recombinant DNA technology which allows specific amino acid mutations to be made at the DNA sequence level by site-specific mutagenesis employing synthetic oligonucleotides. This technique has been successfully used to alter one or two amino acids in a protein. Replacement of existing DNA sequence coding for several amino acids with new synthetic DNA fragments would be facilitated by the presence of unique restrict...

  19. Protein location prediction using atomic composition and global features of the amino acid sequence

    Energy Technology Data Exchange (ETDEWEB)

    Cherian, Betsy Sheena, E-mail: betsy.skb@gmail.com [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India); Nair, Achuthsankar S. [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India)

    2010-01-22

    Subcellular location of protein is constructive information in determining its function, screening for drug candidates, vaccine design, annotation of gene products and in selecting relevant proteins for further studies. Computational prediction of subcellular localization deals with predicting the location of a protein from its amino acid sequence. For a computational localization prediction method to be more accurate, it should exploit all possible relevant biological features that contribute to the subcellular localization. In this work, we extracted the biological features from the full length protein sequence to incorporate more biological information. A new biological feature, distribution of atomic composition is effectively used with, multiple physiochemical properties, amino acid composition, three part amino acid composition, and sequence similarity for predicting the subcellular location of the protein. Support Vector Machines are designed for four modules and prediction is made by a weighted voting system. Our system makes prediction with an accuracy of 100, 82.47, 88.81 for self-consistency test, jackknife test and independent data test respectively. Our results provide evidence that the prediction based on the biological features derived from the full length amino acid sequence gives better accuracy than those derived from N-terminal alone. Considering the features as a distribution within the entire sequence will bring out underlying property distribution to a greater detail to enhance the prediction accuracy.

  20. ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences.

    Science.gov (United States)

    Jehl, Peter; Manguy, Jean; Shields, Denis C; Higgins, Desmond G; Davey, Norman E

    2016-07-01

    Low-throughput experiments and high-throughput proteomic and genomic analyses have created enormous quantities of data that can be used to explore protein function and evolution. The ability to consolidate these data into an informative and intuitive format is vital to our capacity to comprehend these distinct but complementary sources of information. However, existing tools to visualize protein-related data are restricted by their presentation, sources of information, functionality or accessibility. We introduce ProViz, a powerful browser-based tool to aid biologists in building hypotheses and designing experiments by simplifying the analysis of functional and evolutionary features of proteins. Feature information is retrieved in an automated manner from resources describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterization of functional regions. These features are mapped to evolutionary information from precomputed multiple sequence alignments. Data are displayed in an interactive and information-rich yet intuitive visualization, accessible through a simple protein search interface. This allows users with limited bioinformatic skills to rapidly access data pertinent to their research. Visualizations can be further customized with user-defined data either manually or using a REST API. ProViz is available at http://proviz.ucd.ie/.

  1. ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences.

    Science.gov (United States)

    Jehl, Peter; Manguy, Jean; Shields, Denis C; Higgins, Desmond G; Davey, Norman E

    2016-07-01

    Low-throughput experiments and high-throughput proteomic and genomic analyses have created enormous quantities of data that can be used to explore protein function and evolution. The ability to consolidate these data into an informative and intuitive format is vital to our capacity to comprehend these distinct but complementary sources of information. However, existing tools to visualize protein-related data are restricted by their presentation, sources of information, functionality or accessibility. We introduce ProViz, a powerful browser-based tool to aid biologists in building hypotheses and designing experiments by simplifying the analysis of functional and evolutionary features of proteins. Feature information is retrieved in an automated manner from resources describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterization of functional regions. These features are mapped to evolutionary information from precomputed multiple sequence alignments. Data are displayed in an interactive and information-rich yet intuitive visualization, accessible through a simple protein search interface. This allows users with limited bioinformatic skills to rapidly access data pertinent to their research. Visualizations can be further customized with user-defined data either manually or using a REST API. ProViz is available at http://proviz.ucd.ie/. PMID:27085803

  2. Sequence divergence, polymorphism and evolution of the middle-wave and long-wave visual pigment genes of great apes and Old World monkeys.

    Science.gov (United States)

    Dulai, K S; Bowmaker, J K; Mollon, J D; Hunt, D M

    1994-10-01

    In man, the spectral shift between the middle-wave (MW) and long-wave (LW) visual pigments is largely achieved by amino acid substitution at two codons, both located in exon 5. A third amino acid site coded by exon 3 is polymorphic between pigments. We have studied the equivalent regions of the cone opsin genes in two members of the Hominidea (the gorilla, Gorilla gorilla and the chimpanzee, Pan troglodytes) and in three members of the Cercopithecoidea family of Old World primates (the diana monkey, Cercopithecus diana, the talapoin monkey, Miopithecus talapoin, and the crab-eating macaque, Macaca fascicularis). No variation in the codons that specify the amino acids involved in spectral tuning were found. We predict therefore that the MW and LW pigments of gorilla and chimpanzee have similar spectral characteristics to those of man. Multiple copies of the same opsin gene sequence were identified in the chimpanzee, talapoin and macaque and we also show that non-human Old World primates are similar to man in showing a bunching of polymorphic sites in exon 3. We discuss the ancestry of the separate MW and LW genes of Old World primates and the equivalent polymorphic gene of the marmoset, a New World primate. PMID:7975287

  3. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

    Science.gov (United States)

    Loh, Yong-Hwee Eddie; Shen, Li

    2016-01-01

    The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

  4. Sequence Pattern Correlation of Amino Acid in Collision-induced Dissociation Electrospray Ionization Mass Spectrometry

    Institute of Scientific and Technical Information of China (English)

    SONG,Hao-Wei(宋浩威); YUE,Gui-Hua(岳贵花); LU,Yu(陆宇); YANG,Peng-Yuan(杨芃原); WANG,Hong-Hai(王洪海)

    2002-01-01

    A novel approach of sequence pattern correlation has been applied to predict an expected amino acid sequence from CID ESI-MS spectra. The proposed approach deduces sequence patterns with no help from known protein database such that it is useful to identify an unknown peptide or new protein. The algorithm applies a cross-correlation to match an experimental CID spectrum with predicted sequence pattern generated from fragmentation information. The fragmentation knowledge of both y-series and other non y-series are utilized to generate the predicted sequence patterns. In contrast to the normal de novo approach, the proposed approach is insensitive to mass tolerance and non-susceptive to spectral integrality with no need for selection of a starting point.

  5. Fetal magnetic resonance imaging of normal spinal cord: Evaluating cord visualization and conus medullaris position by T2-weighted sequences

    Directory of Open Access Journals (Sweden)

    Yen-Ling Huang

    2014-08-01

    Full Text Available Background: Prenatal magnetic resonance (MR imaging demonstration of the normal spinal cord and the conus medullaris location has not been well studied. We compared balanced fast field echo (bFFE with single-shot turbo spin-echo (SSh-TSE MR sequences for visualizing the normal spinal cord and position of conus medullaris in fetuses. Methods: This retrospective study was approved by the Institutional Review Board of Chang Gung Medical Foundation. We reviewed the MR images of 141 fetuses aged between 16 and 39 gestational weeks, to determine the position of the conus and visualize the spinal cord by using a signal intensity ratio of cerebral spinal fluid (CSF to the spinal cord. Results: Of the 75 subjects having normal spinal cord and being examined by both bFFE and SSh-TSE studies, the signal intensity ratio of CSF/cord was greater on bFFE images (2.18 ± 0.53 than that on SSh-TSE images (1.21 ± 0.13 (p < 0.05. The conus level identified in the 50 subjects, in whom the lumbosacral spine was appropriately imaged, was located from L1 to L5 levels. The ascendance of the conus correlated moderately with gestational age. Conclusions: With greater signal contrast ratio of CSF to spinal cord, bFFE sequence, when compared with SSh-TSE sequence, provides better visualization of normal spinal cord. The fetal conus medullaris ascends from L5 to L1 levels as the gestational age increases.

  6. SeqVISTA: a graphical tool for sequence feature visualization and comparison

    Directory of Open Access Journals (Sweden)

    Niu Tianhua

    2003-01-01

    Full Text Available Abstract Background Many readers will sympathize with the following story. You are viewing a gene sequence in Entrez, and you want to find whether it contains a particular sequence motif. You reach for the browser's "find in page" button, but those darn spaces every 10 bp get in the way. And what if the motif is on the opposite strand? Subsequently, your favorite sequence analysis software informs you that there is an interesting feature at position 13982–14013. By painstakingly counting the 10 bp blocks, you are able to examine the sequence at this location. But now you want to see what other features have been annotated close by, and this information is buried several screenfuls higher up the web page. Results SeqVISTA presents a holistic, graphical view of features annotated on nucleotide or protein sequences. This interactive tool highlights the residues in the sequence that correspond to features chosen by the user, and allows easy searching for sequence motifs or extraction of particular subsequences. SeqVISTA is able to display results from diverse sequence analysis tools in an integrated fashion, and aims to provide much-needed unity to the bioinformatics resources scattered around the Internet. Our viewer may be launched on a GenBank record by a single click of a button installed in the web browser. Conclusion SeqVISTA allows insights to be gained by viewing the totality of sequence annotations and predictions, which may be more revealing than the sum of their parts. SeqVISTA runs on any operating system with a Java 1.4 virtual machine. It is freely available to academic users at http://zlab.bu.edu/SeqVISTA.

  7. 37 CFR 1.821 - Nucleotide and/or amino acid sequence disclosures in patent applications.

    Science.gov (United States)

    2010-07-01

    ... Director of the Federal Register in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of WIPO... Biotechnology Invention Disclosures Application Disclosures Containing Nucleotide And/or Amino Acid Sequences... Listing” referred to in paragraph (c) of this section must also be submitted in computer readable...

  8. Nucleic acid sequence-based amplification with oligochromatography for detection of Trypanosoma brucei in clinical samples

    NARCIS (Netherlands)

    C.M. Mugasa; T. Laurent; G.J. Schoone; P.A. Kager; G.W. Lubega; H.D.F.H. Schallig

    2009-01-01

    Molecular tools, such as real-time nucleic acid sequence-based amplification (NASBA) and PCR, have been developed to detect Trypanosoma brucei parasites in blood for the diagnosis of human African trypanosomiasis (HAT). Despite good sensitivity, these techniques are not implemented in HAT control pr

  9. Software scripts for quality checking of high-throughput nucleic acid sequencers.

    Science.gov (United States)

    Lazo, G R; Tong, J; Miller, R; Hsia, C; Rausch, C; Kang, Y; Anderson, O D

    2001-06-01

    We have developed a graphical interface to allow the researcher to view and assess the quality of sequencing results using a series of program scripts developed to process data generated by automated sequencers. The scripts are written in Perl programming language and are executable under the cgibin directory of a Web server environment. The scripts direct nucleic acid sequencing trace file data output from automated sequencers to be analyzed by the phred molecular biology program and are displayed as graphical hypertext mark-up language (HTML) pages. The scripts are mainly designed to handle 96-well microtiter dish samples, but the scripts are also able to read data from 384-well microtiter dishes 96 samples at a time. The scripts may be customized for different laboratory environments and computer configurations. Web links to the sources and discussion page are provided. PMID:11414222

  10. Agreement Between Visual Inspection with Acetic Acid and Papanicolaous Smear as Screening Methods for Cervical Cancer

    International Nuclear Information System (INIS)

    Objective: To determine degree of agreement between visual inspection with acetic acid (VIA) and Papanicolaous (Pap) smear as screening methods for cervical cancer. Study Design: A cross-sectional study. Place and Duration of Study: Department of Obstetrics and Gynaecology, Sir Ganga Ram Hospital, Lahore, from July to December 2012. Methodology: Two hundred and fifty women in reproductive age group presenting with various gynaecological complaints were included in the study. A Papanicolaous smear was taken and visual inspection with 5% acetic acid was done. VIA was reported as positive or negative according to acetowhite changes and cytology result was graded as CIN 1, 2, 3 and squamous carcinoma. Those women who showed positive result with either VIA or Pap smear or both were further subjected to colposcopic directed biopsy which was taken as gold standard. Results were computed using Statistical Package for Social Sciences (SPSS) version 16 and statistical test used was kappa. Results: Out of 250 women, VIA was positive in 55 (22%) patients and Pap smear was abnormal in 27 (10.8%). Histological diagnosis of CIN/cancer was made in 36 out of a total 62 patients who underwent biopsy. Conclusion: There was a fair agreement between VIA and Pap smear, with VIA detecting more abnormalities than cytology. In the absence of Pap smear availability, VIA may be a reasonable cervical cancer screening method, especially in low resource settings. (author)

  11. Clinical utility of 5-aminolevulinic acid HCl to better visualize and more completely remove gliomas

    Directory of Open Access Journals (Sweden)

    Halani SH

    2016-09-01

    Full Text Available Sameer H Halani,1 D Cory Adamson1,2 1Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA; 2Neurosurgery Section, Atlanta VA Medical Center, Decatur, GA, USA Abstract: Surgical resection is typically the first line of treatment for gliomas. However, the neurosurgeon faces a major challenge in achieving maximal resection in high-grade gliomas as these infiltrative tumors make it difficult to discern tumor margins from normal brain with conventional white-light microscopy alone. To aid in resection of these infiltrative tumors, fluorescence-guided surgery has gained much popularity in intraoperative visualization of malignant gliomas, with 5-aminolevulinic acid (5-ALA leading the way. First introduced in an article in Neurosurgery, 5-ALA has since become a safe, effective, and inexpensive method to visualize and improve resection of gliomas. This has undoubtedly led to improvements in the clinical course of patients as demonstrated by the increased overall and progression-free survival in patients with such devastating disease. This literature review aims to discuss the major studies and trials demonstrating the clinical utility of 5-ALA and its ability to aid in complete resection of malignant gliomas. Keywords: aminolevulinic acid, 5-ALA, fluorescence, glioblastoma multiforme, high-grade glioma, resection

  12. Visualization of early events in acetic acid denaturation of HIV-1 protease: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Aditi Narendra Borkar

    Full Text Available Protein denaturation plays a crucial role in cellular processes. In this study, denaturation of HIV-1 Protease (PR was investigated by all-atom MD simulations in explicit solvent. The PR dimer and monomer were simulated separately in 9 M acetic acid (9 M AcOH solution and water to study the denaturation process of PR in acetic acid environment. Direct visualization of the denaturation dynamics that is readily available from such simulations has been presented. Our simulations in 9 M AcOH reveal that the PR denaturation begins by separation of dimer into intact monomers and it is only after this separation that the monomer units start denaturing. The denaturation of the monomers is flagged off by the loss of crucial interactions between the α-helix at C-terminal and surrounding β-strands. This causes the structure to transit from the equilibrium dynamics to random non-equilibrating dynamics. Residence time calculations indicate that denaturation occurs via direct interaction of the acetic acid molecules with certain regions of the protein in 9 M AcOH. All these observations have helped to decipher a picture of the early events in acetic acid denaturation of PR and have illustrated that the α-helix and the β-sheet at the C-terminus of a native and functional PR dimer should maintain both the stability and the function of the enzyme and thus present newer targets for blocking PR function.

  13. Automatic classification of lung tumour heterogeneity according to a visual-based score system in dynamic contrast enhanced CT sequences

    Science.gov (United States)

    Bevilacqua, Alessandro; Baiocco, Serena

    2016-03-01

    Computed tomography (CT) technologies have been considered for a long time as one of the most effective medical imaging tools for morphological analysis of body parts. Contrast Enhanced CT (CE-CT) also allows emphasising details of tissue structures whose heterogeneity, inspected through visual analysis, conveys crucial information regarding diagnosis and prognosis in several clinical pathologies. Recently, Dynamic CE-CT (DCE-CT) has emerged as a promising technique to perform also functional hemodynamic studies, with wide applications in the oncologic field. DCE-CT is based on repeated scans over time performed after intravenous administration of contrast agent, in order to study the temporal evolution of the tracer in 3D tumour tissue. DCE-CT pushes towards an intensive use of computers to provide automatically quantitative information to be used directly in clinical practice. This requires that visual analysis, representing the gold-standard for CT image interpretation, gains objectivity. This work presents the first automatic approach to quantify and classify the lung tumour heterogeneities based on DCE-CT image sequences, so as it is performed through visual analysis by experts. The approach developed relies on the spatio-temporal indices we devised, which also allow exploiting temporal data that enrich the knowledge of the tissue heterogeneity by providing information regarding the lesion status.

  14. HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences

    Directory of Open Access Journals (Sweden)

    Firth Andrew E

    2007-12-01

    Full Text Available Abstract Background The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (~3.2 kb but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses. Results These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters and comparative genome analysis results (e.g. blastn, tblastx. It also contains analyses based on curated HBV alignments. Information about conserved regions – including primary conservation (e.g. CDS-Plotcon and RNA secondary structure predictions (e.g. Alidot – is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences. Conclusion HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.

  15. GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Stærfeldt, Hans Henrik; Rotenberg, Eva;

    2009-01-01

    , standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. [Supplemental material including interactive...... atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/]....

  16. Studies on adenosine triphosphate transphosphorylases. Amino acid sequence of rabbit muscle ATP-AMP transphosphorylase.

    Science.gov (United States)

    Kuby, S A; Palmieri, R H; Frischat, A; Fischer, A H; Wu, L H; Maland, L; Manship, M

    1984-05-22

    The total amino acid sequence of rabbit muscle adenylate kinase has been determined, and the single polypeptide chain of 194 amino acid residues starts with N-acetylmethionine and ends with leucyllysine at its carboxyl terminus, in agreement with the earlier data on its amino acid composition [Mahowald, T. A., Noltmann, E. A., & Kuby, S. A. (1962) J. Biol. Chem. 237, 1138-1145] and its carboxyl-terminus sequence [Olson, O. E., & Kuby, S. A. (1964) J. Biol. Chem. 239, 460-467]. Elucidation of the primary structure was based on tryptic and chymotryptic cleavages of the performic acid oxidized protein, cyanogen bromide cleavages of the 14C-labeled S-carboxymethylated protein at its five methionine sites (followed by maleylation of peptide fragments), and tryptic cleavages at its 12 arginine sites of the maleylated 14C-labeled S-carboxymethylated protein. Calf muscle myokinase, whose sequence has also been established, differs primarily from the rabbit muscle myokinase's sequence in the following: His-30 is replaced by Gln-30; Lys-56 is replaced by Met-56; Ala-84 and Asp 85 are replaced by Val-84 and Asn-85. A comparison of the four muscle-type adenylate kinases, whose covalent structures have now been determined, viz., rabbit, calf, porcine, and human [for the latter two sequences see Heil, A., Müller, G., Noda, L., Pinder, T., Schirmer, H., Schirmer, I., & Von Zabern, I. (1974) Eur. J. Biochem. 43, 131-144, and Von Zabern, I., Wittmann-Liebold, B., Untucht-Grau, R., Schirmer, R. H., & Pai, E. F. (1976) Eur. J. Biochem. 68, 281-290], demonstrates an extraordinary degree of homology.(ABSTRACT TRUNCATED AT 250 WORDS)

  17. Complete nucleic acid sequence of Penaeus stylirostris densovirus (PstDNV) from India.

    Science.gov (United States)

    Rai, Praveen; Safeena, Muhammed P; Karunasagar, Iddya; Karunasagar, Indrani

    2011-06-01

    Infectious hypodermal and hematopoietic necrosis virus (IHHNV) of shrimp, recently been classified as Penaeus stylirostris densovirus (PstDNV). The complete nucleic acid sequence of PstDNV from India was obtained by cloning and sequencing of different DNA fragment of the virus. The genome organisation of PstDNV revealed that there were three major coding domains: a left ORF (NS1) of 2001 bp, a mid ORF (NS2) of 1092 bp and a right ORF (VP) of 990 bp. The complete genome and amino acid sequences of three proteins viz., NS1, NS2 and VP were compared with the genomes of the virus reported from Hawaii, China and Mexico and with partial sequence available from isolates from different regions. The phylogenetic analysis of shrimp, insect and vertebrate parvovirus sequences showed that the Indian PstDNV isolate is phylogenetically more closely related to one of the three isolates from Taiwan (AY355307), and two isolates (AY362547 and AY102034) from Thailand. PMID:21402111

  18. Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

    Directory of Open Access Journals (Sweden)

    Alexandre S. Boutorine

    2013-12-01

    Full Text Available This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i sequence-specific peptides and proteins; (ii triplex-forming oligonucleotides and (iii polyamide oligo(N-methylpyrrole/N-methylimidazole minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.

  19. The amino acid sequence of cytochrome c from Cucurbita maxima L. (pumpkin)

    Science.gov (United States)

    Thompson, E. W.; Richardson, M.; Boulter, D.

    1971-01-01

    The amino acid sequence of pumpkin cytochrome c was determined on 2μmol of protein. Some evidence was found for the occurrence of two forms of cytochrome c, whose sequences differed in three positions. Pumpkin cytochrome c consists of 111 residues and is homologous with mitochondrial cytochromes c from other plants. Experimental details are given in a supplementary paper that has been deposited as Supplementary Publication SUP 50005 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1971), 121, 7. PMID:5131733

  20. Human apolipoprotein C-II: complete nucleic acid sequence of preapolipoprotein C-II.

    OpenAIRE

    Fojo, S S; Law, S W; Brewer, H B

    1984-01-01

    Apolipoprotein (apo) C-II is a cofactor for lipoprotein lipase, the enzyme that catalyzes the hydrolysis of triglycerides on plasma triglyceride-rich lipoproteins. The complete coding sequence of apoC-II mRNA has been determined from an apoC-II clone isolated from a human liver cDNA library. A 17-base-long synthetic oligonucleotide based on amino acid residues 5-10 of apoC-II was utilized as a hybridization probe to select recombinant plasmids containing the apoC-II sequence. Two thousand fou...

  1. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...... alignment by 'reverse translation' of the aligned protein sequences. In the resulting DNA alignment, gaps occur in groups of three corresponding to entire codons, and analogous codon positions are therefore always lined up. These features are useful when constructing multiple DNA alignments for phylogenetic...

  2. Nucleotide and amino acid sequences of human intestinal alkaline phosphatase: close homology to placental alkaline phosphatase

    International Nuclear Information System (INIS)

    A cDNA clone for human adult intestinal alkaline phosphatase (ALP) [orthophosphoric-monoester phosphohydrolase (alkaline optimum); EC 3.1.3.1] was isolated from a λgt11 expression library. The cDNA insert of this clone is 2513 base pairs in length and contains an open reading frame that encodes a 528-amino acid polypeptide. This deduced polypeptide contains the first 40 amino acids of human intestinal ALP, as determined by direct protein sequencing. Intestinal ALP shows 86.5% amino acid identity to placental (type 1) ALP and 56.6% amino acid identity to liver/bone/kidney ALP. In the 3'-untranslated regions, intestinal and placental ALP cDNAs are 73.5% identical (excluding gaps). The evolution of this multigene enzyme family is discussed

  3. Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, I; Loots, G; Giardine, B; Hou, M; Ma, J; Hardison, R; Stubbs, L; Miller, W

    2004-07-14

    Multiple sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the tba multi-aligner program for rapid identification of local sequence conservation and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short-and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multi-species comparisons of the GATA3 gene locus and the identification of elements that are conserved differently in avians than in other genomes allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://bio.cse.psu.edu/.

  4. Sequence-specific nucleic acid detection from binary pore conductance measurement

    OpenAIRE

    Esfandiari, Leyla; Monbouquette, Harold G.; Jacob J. Schmidt

    2012-01-01

    We describe a platform for sequence-specific nucleic acid (NA) detection utilizing a micropipette tapered to a 2 μm diameter pore and 3 μm diameter polystyrene beads to which uncharged peptide nucleic acid (PNA) probe molecules have been conjugated. As the target NAs hybridize to the complementary PNA-beads, the beads acquire negative charge and become electrophoretically mobile. An applied electric field guides these NA-PNA-beads toward the pipette tip, which they obstruct, leading to an ind...

  5. Visualization of the mycelia of wood-rotting fungi by fluorescence in situ hybridization using a peptide nucleic acid probe.

    Science.gov (United States)

    Nakada, Yuji; Nakaba, Satoshi; Matsunaga, Hiroshi; Funada, Ryo; Yoshida, Makoto

    2013-01-01

    White rot fungus, Phanerochaete chrysosporium, and brown rot fungus, Postia placenta, grown on agar plates, were visualized by fluorescence in situ hybridization (FISH) using a peptide nucleic acid (PNA) probe. Mycelia grown on wood chips were also clearly detected by PNA-FISH following blocking treatment. To the best of our knowledge, this is the first report on the visualization of fungi in wood by FISH. PMID:23391931

  6. Self-Sequencing of Amino Acids and Origins of Polyfunctional Protocells

    Science.gov (United States)

    Fox, Sidney W.

    1984-12-01

    The primal role of the origins of proteins in molecular evolution is discussed. On the basis of this premise, the significance of the experimentally established self-sequencing of amino acids under simulated geological conditions is explained as due to the fact that the products are highly nonrandom and accordingly contain many kinds of information. When such thermal proteins are aggregated into laboratory protocells, an action that occurs readily, the resultant protocells also contain many kinds of information. Residue-by-residue order, enzymic activities, and lipid quality accordingly occur within each preparation of proteinoid (thermal protein). In this paper are reviewed briefly the phenomenon of self-sequencing of amino acids, its relationship to evolutionary processes, other significance of such self-ordering, and the experimental evidence for original polyfunctional protocells.

  7. Anti-peptide aptamers recognize amino acid sequence and bind a protein epitope.

    OpenAIRE

    Xu, W; Ellington, A. D.

    1996-01-01

    In vitro selection of nucleic acid binding species (aptamers) is superficially similar to the immune response. Both processes produce biopolymers that can recognize targets with high affinity and specificity. While antibodies are known to recognize the sequence and conformation of protein surface features (epitopes), very little is known about the precise interactions between aptamers and their epitopes. Therefore, aptamers that could recognize a particular epitope, a peptide fragment of huma...

  8. Amino acid sequences mediating vascular cell adhesion molecule 1 binding to integrin alpha 4: homologous DSP sequence found for JC polyoma VP1 coat protein

    Directory of Open Access Journals (Sweden)

    Michael Andrew Meyer

    2013-07-01

    Full Text Available The JC polyoma viral coat protein VP1 was analyzed for amino acid sequences homologies to the IDSP sequence which mediates binding of VLA-4 (integrin alpha 4 to vascular cell adhesion molecule 1. Although the full sequence was not found, a DSP sequence was located near the critical arginine residue linked to infectivity of the virus and binding to sialic acid containing molecules such as integrins (3. For the JC polyoma virus, a DSP sequence was found at residues 70, 71 and 72 with homology also noted for the mouse polyoma virus and SV40 virus. Three dimensional modeling of the VP1 molecule suggests that the DSP loop has an accessible site for interaction from the external side of the assembled viral capsid pentamer.

  9. Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model

    CERN Document Server

    Irbäck, Anders; Potthast, Frank

    2008-01-01

    Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences.

  10. Sequence-selective targeting of duplex DNA by peptide nucleic acids

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2010-01-01

    Sequence-selective gene targeting constitutes an attractive drug-discovery approach for genetic therapy, with the aim of reducing or enhancing the activity of specific genes at the transcriptional level, or as part of a methodology for targeted gene repair. The pseudopeptide DNA mimic peptide...... nucleic acid (PNA) can recognize duplex DNA with high sequence specificity and affinity in triplex, duplex and double-duplex invasive modes or non-invasive triplex modes. Novel PNA modification has improved the affinity for DNA recognition via duplex invasion, double-duplex invasion and triplex...... recognition considerably. Such modifications have also resulted in new approaches to targeted gene repair and sequence-selective double-strand cleavage of genomic DNA....

  11. Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC.

    Science.gov (United States)

    Robeyns, Koen; Herdewijn, Piet; Van Meervelt, Luc

    2008-02-13

    CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal structure of a carbocyclic-based nucleic acid, is presented. This particular sequence was built with left-handed building blocks and crystallizes as a left-handed double helix. The helix can be characterized as belonging to the (mirrored) A-type family. Crystallographic data were processed up to 1.53 A, and the octamer sequence crystallizes in the space group R32. The sugar puckering is found to adopt the 3H2 half-chair conformation which mimics the C3'-endo conformation of the ribose sugar. The double helices stack on top of each other to form continuous helices, and static disorder is observed due to this end-to-end stacking.

  12. Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

    Directory of Open Access Journals (Sweden)

    Andreas Martin Lisewski

    Full Text Available The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions and in structure (structural defects trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a sensitive to random errors and (b restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials.

  13. Characterization of the microbial acid mine drainage microbial community using culturing and direct sequencing techniques.

    Science.gov (United States)

    Auld, Ryan R; Myre, Maxine; Mykytczuk, Nadia C S; Leduc, Leo G; Merritt, Thomas J S

    2013-05-01

    We characterized the bacterial community from an AMD tailings pond using both classical culturing and modern direct sequencing techniques and compared the two methods. Acid mine drainage (AMD) is produced by the environmental and microbial oxidation of minerals dissolved from mining waste. Surprisingly, we know little about the microbial communities associated with AMD, despite the fundamental ecological roles of these organisms and large-scale economic impact of these waste sites. AMD microbial communities have classically been characterized by laboratory culturing-based techniques and more recently by direct sequencing of marker gene sequences, primarily the 16S rRNA gene. In our comparison of the techniques, we find that their results are complementary, overall indicating very similar community structure with similar dominant species, but with each method identifying some species that were missed by the other. We were able to culture the majority of species that our direct sequencing results indicated were present, primarily species within the Acidithiobacillus and Acidiphilium genera, although estimates of relative species abundance were only obtained from direct sequencing. Interestingly, our culture-based methods recovered four species that had been overlooked from our sequencing results because of the rarity of the marker gene sequences, likely members of the rare biosphere. Further, direct sequencing indicated that a single genus, completely missed in our culture-based study, Legionella, was a dominant member of the microbial community. Our results suggest that while either method does a reasonable job of identifying the dominant members of the AMD microbial community, together the methods combine to give a more complete picture of the true diversity of this environment. PMID:23485423

  14. Colorimetric and visual determination of dicyandiamide using gallic acid-capped gold nanoparticles

    International Nuclear Information System (INIS)

    A new method is presented for the visual detection of dicyandiamide (DCD). Gold nanoparticles (AuNPs) capped with gallic acid (GA) were synthesized in a single step at room temperature, using GA as both the reducing agent and stabilizer. In the presence of DCD, the hydrogen-bonding interaction between GA and DCD induces the aggregation of AuNPs, associated with a color change from red to gray that can be observed with bare eye. DCD could be quantified by photometry as the red shift of the maximal absorption band is linearly related to the logarithm of concentration of DCD in the 0.1 to 500 μM concentration range, with a regression coefficient of 0.9987 and a 80 nM detection limit (at an SNR of 3). The proposed method was successfully applied to the detection of DCD in spiked dairy samples. (author)

  15. An interactive environment for agile analysis and visualization of ChIP-sequencing data

    DEFF Research Database (Denmark)

    Lerdrup, Mads; Johansen, Jens Vilstrup; Agrawal-Singh, Shuchi;

    2016-01-01

    and established a new screening approach to analyze more than 900 datasets from mouse embryonic stem cells for factors potentially associated with Polycomb recruitment. EaSeq, which is freely available and works on a standard personal computer, can substantially increase the throughput of many analysis workflows......To empower experimentalists with a means for fast and comprehensive chromatin immunoprecipitation sequencing (ChIP-seq) data analyses, we introduce an integrated computational environment, EaSeq. The software combines the exploratory power of genome browsers with an extensive set of interactive...

  16. Complete Genome Sequence of the Probiotic Lactic Acid Bacterium Lactobacillus Rhamnosus

    Directory of Open Access Journals (Sweden)

    Samat Kozhakhmetov

    2014-01-01

    Full Text Available Introduction: Lactobacilli are a bacteria commonly found in the gastrointestinal tract. Some species of this genus have probiotic properties. The most common of these is Lactobacillus rhamnosus, a microoganism, generally regarded as safe (GRAS. It is also a homofermentative L-(+-lactic acid producer. The genus Lactobacillus is characterized by an extraordinary degree of the phenotypic and genotypic diversity. However, the studies of the genus were conducted mostly with the unequally distributed, non-random choice of species for sequencing; thus, there is only one representative genome from the Lactobacillus rhamnosus clade available to date. The aim of this study was to characterize the genome sequencing of selected strains of Lactobacilli. Methods: 109 samples were isolated from national domestic dairy products in the laboratory of Center for life sciences. After screaning isolates for probiotic properties, a highly active Lactobacillus spp strain was chosen. Genomic DNA was extracted according to the manufacturing protocol (Wizard® Genomic DNA Purification Kit. The Lactobacillus rhamnosus strain was identified as the highly active Lactobacillus strain accoridng to its morphological, cultural, physiological, and biochemical properties, and a genotypic analysis. Results: The genome of Lactobacillus rhamnosus was sequenced using the Roche 454 GS FLX (454 GS FLX platforms. The initial draft assembly was prepared from 14 large contigs (20 all contigs by the Newbler gsAssembler 2.3 (454 Life Sciences, Branford, CT. Conclusion: A full genome-sequencing of selected strains of lactic acid bacteria was made during the study.

  17. Prediction of protein motions from amino acid sequence and its application to protein-protein interaction

    Directory of Open Access Journals (Sweden)

    Wako Hiroshi

    2010-07-01

    Full Text Available Abstract Background Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter involves only rotational and translational motions as a rigid body. Normal Model Analysis (NMA can derive these two motions, but its application remains limited because it necessitates the gathering of complete structural information. Results In this work, we present a novel method for predicting two kinds of protein motions in ordered structures. The prediction uses only information from the amino acid sequence. We prepared a dataset of the internal and external motions of segments in many proteins by application of NMA. Subsequently, we analyzed the relation between thermal motion assessed from X-ray crystallographic B-factor and internal/external motions calculated by NMA. Results show that attributes of amino acids related to the internal motion have different features from those related to the B-factors, although those related to the external motion are correlated strongly with the B-factors. Next, we developed a method to predict internal and external motions from amino acid sequences based on the Random Forest algorithm. The proposed method uses information associated with adjacent amino acid residues and secondary structures predicted from the amino acid sequence. The proposed method exhibited moderate correlation between predicted internal and external motions with those calculated by NMA. It has the highest prediction accuracy compared to a naïve model and three published predictors. Conclusions Finally, we applied the proposed method predicting the internal motion to a set of 20 proteins that undergo large conformational change upon protein-protein interaction. Results show significant overlaps between the

  18. Method and software for using m-sequences to characterize parallel components of higher-order visual tracking behavior in Drosophila

    Directory of Open Access Journals (Sweden)

    Jacob W. Aptekar

    2014-10-01

    Full Text Available A moving visual figure may contain first-order signals defined by variation in mean luminance, as well as second-order signals defined by constant mean luminance and variation in luminance envelope, or higher-order signals that cannot be estimated by taking higher moments of the luminance distribution. Separating these properties of a moving figure to experimentally probe the visual subsystems that encode them is technically challenging and has resulted in debated mechanisms of visual object detection by flies. Our prior work took a white noise systems identification approach using a commercially available electronic display system to characterize the spatial variation in the temporal dynamics of two distinct subsystems for first- and higher-order components of visual figure tracking. The method relied on the use of single pixel displacements of two visual stimuli according to two binary maximum length shift register sequences (m-sequences and cross-correlation of each m-sequence with time-varying flight steering measurements. The resultant spatio-temporal action fields represent temporal impulse responses parameterized by the azimuthal location of the visual figure, one STAF for first-order and another for higher-order components of compound stimuli. Here we review m-sequence and reverse correlation procedures, then describe our application in detail, provide Matlab code, validate the STAFs, and demonstrate the utility and robustness of STAFs by predicting the results of other published experimental procedures. This method has demonstrated how two relatively modest innovations on classical white noise analysis—the inclusion of space as a way to organize response kernels and the use of linear decoupling to measure the response to two channels of visual information simultaneously—could substantially improve our basic understanding of visual processing in the fly.

  19. Amino acid selective unlabeling for sequence specific resonance assignments in proteins

    Energy Technology Data Exchange (ETDEWEB)

    Krishnarjuna, B.; Jaipuria, Garima; Thakur, Anushikha [Indian Institute of Science, NMR Research Centre (India); D' Silva, Patrick, E-mail: patrick@biochem.iisc.ernet.in [Indian Institute of Science, Department of Biochemistry (India); Atreya, Hanudatta S., E-mail: hsatreya@sif.iisc.ernet.in [Indian Institute of Science, NMR Research Centre (India)

    2011-01-15

    Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective 'unlabeling' or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly {sup 13}C/{sup 15}N labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {l_brace}{sup 12}CO{sub i}-{sup 15}N{sub i+1}{r_brace}-filtered HSQC, which aids in linking the {sup 1}H{sup N}/{sup 15}N resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i - 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to {sup 2}H labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of {sup 14}N at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies.

  20. N-terminal amino acid sequences and some characteristics of fibrinolytic/hemorrhagic metalloproteinases purified from Bothrops jararaca venom.

    Science.gov (United States)

    Maruyama, Masugi; Sugiki, Masahiko; Anai, Keita; Yoshida, Etsuo

    2002-08-01

    We determined the N-terminal amino acid sequences of the fibrinolytic/hemorrhagic metalloproteinases (jararafibrases I, III and IV) purified from Bothrops jararaca venom. The N-terminal amino acid sequences of jararafibrase I and its degradation products were identical to those of jararhagin, another hemorrhagic metalloproteinase purified from the same snake venom. Together with enzymatic and immunological properties, we concluded that those two enzymes are identical. The N-terminal amino acid sequence of jararafibrase III was quite similar to C-type lectin isolated from Crotalus atrox, and the protein had a hemagglutinating activity on intact rat red blood cells. PMID:12165326

  1. Protein sequence analysis by incorporating modified chaos game and physicochemical properties into Chou's general pseudo amino acid composition.

    Science.gov (United States)

    Xu, Chunrui; Sun, Dandan; Liu, Shenghui; Zhang, Yusen

    2016-10-01

    In this contribution we introduced a novel graphical method to compare protein sequences. By mapping a protein sequence into 3D space based on codons and physicochemical properties of 20 amino acids, we are able to get a unique P-vector from the 3D curve. This approach is consistent with wobble theory of amino acids. We compute the distance between sequences by their P-vectors to measure similarities/dissimilarities among protein sequences. Finally, we use our method to analyze four datasets and get better results compared with previous approaches. PMID:27375218

  2. Bacteria obtained from a sequencing batch reactor that are capable of growth on dehydroabietic acid.

    Science.gov (United States)

    Mohn, W W

    1995-06-01

    Eleven isolates capable of growth on the resin acid dehydroabietic acid (DhA) were obtained from a sequencing batch reactor designed to treat a high-strength process stream from a paper mill. The isolates belonged to two groups, represented by strains DhA-33 and DhA-35, which were characterized. In the bioreactor, bacteria like DhA-35 were more abundant than those like DhA-33. The population in the bioreactor of organisms capable of growth on DhA was estimated to be 1.1 x 10(6) propagules per ml, based on a most-probable-number determination. Analysis of small-subunit rRNA partial sequences indicated that DhA-33 was most closely related to Sphingomonas yanoikuyae (Sab = 0.875) and that DhA-35 was most closely related to Zoogloea ramigera (Sab = 0.849). Both isolates additionally grew on other abietanes, i.e., abietic and palustric acids, but not on the pimaranes, pimaric and isopimaric acids. For DhA-33 and DhA-35 with DhA as the sole organic substrate, doubling times were 2.7 and 2.2 h, respectively, and growth yields were 0.30 and 0.25 g of protein per g of DhA, respectively. Glucose as a cosubstrate stimulated growth of DhA-33 on DhA and stimulated DhA degradation by the culture. Pyruvate as a cosubstrate did not stimulate growth of DhA-35 on DhA and reduced the specific rate of DhA degradation of the culture. DhA induced DhA and abietic acid degradation activities in both strains, and these activities were heat labile. Cell suspensions of both strains consumed DhA at a rate of 6 mumol mg of protein-1 h-1.(ABSTRACT TRUNCATED AT 250 WORDS)

  3. Comparison of Visual Inspection with acetic acid and Pap smear in cervical cancer screening at a tertiary care hospital

    International Nuclear Information System (INIS)

    Objective: To determine the accuracy of visual inspection with acetic acid in comparison with Pap smear against colposcopic directed biopsy, for detection of pre-cancerous lesion. Methods: The comparative cross-sectional study was conducted at the Maternal and Child Health Centre (MCHC), Pakistan Institute of Medical Sciences (PIMS), Islamabad, from January to December 2010. Every married women with age range 19 to 51 years underwent conventional cytology and visual inspection with 5% acetic acid. Distinct acetowhite areas were taken as positive, while cervical intra-epithelial neoplasia on cytology was labelled as Pap smear positive. Colposcopic directed biopsy was taken as the gold standard. SPSS 13 was used for statistical analysis. Results: Of 519 subjects, 70(13.4%) were screened positive and 29(5.6%) were biopsy positive for cervical intra-epithelial neoplasia. Of these, 26(37.1 %) were positive on visual inspection; 14 (20 %) on cytology; and 30 (42.8%) on combined test. The sensitivity of visual inspection was 78.5% vs 61.1% for Pap smear (p<0.001). The specificity of visual inspection was 99.3% vs 99.4% for cytology (p<0.1). Significantly higher sensitivity and specificity was found for the combined test than either of the two alone; 93.1% and 99.1% respectively (p<0.001). The positive predictive value of visual inspection vs pap was 84.6% vs 78.5% (p<0.001) and negative predictive value was 98.6% vs 96.5% (p<0.1). Both values of combined test were significantly higher than either of the two tests alone (p<0.01). Conclusion: Visual inspection with acetic acid has significantly higher sensitivity than Pap smear and may replace pap smear as a primary screening tool for universal screening. Combined test with higher predictive accuracy may be used for opportunistic screening. (author)

  4. Development of a SCAR (sequence-characterised amplified region) marker for acid resistance-related gene in Lactobacillus plantarum.

    Science.gov (United States)

    Liu, Shu-Wen; Li, Kai; Yang, Shi-Ling; Tian, Shu-Fen; He, Ling

    2015-03-01

    A sequence characterised amplified region marker was developed to determine an acid resistance-related gene in Lactobacillus plantarum. A random amplified polymorphic DNA marker named S116-680 was reported to be closely related to the acid resistance of the strains. The DNA band corresponding to this marker was cloned and sequenced with the induction of specific designed PCR primers. The results of PCR test helped to amplify a clear specific band of 680 bp in the tested acid-resistant strains. S116-680 marker would be useful to explore the acid-resistant mechanism of L. plantarum and to screen desirable malolactic fermentation strains.

  5. Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

    Directory of Open Access Journals (Sweden)

    Ruan Jishou

    2007-04-01

    Full Text Available Abstract Background Traditionally, it is believed that the native structure of a protein corresponds to a global minimum of its free energy. However, with the growing number of known tertiary (3D protein structures, researchers have discovered that some proteins can alter their structures in response to a change in their surroundings or with the help of other proteins or ligands. Such structural shifts play a crucial role with respect to the protein function. To this end, we propose a machine learning method for the prediction of the flexible/rigid regions of proteins (referred to as FlexRP; the method is based on a novel sequence representation and feature selection. Knowledge of the flexible/rigid regions may provide insights into the protein folding process and the 3D structure prediction. Results The flexible/rigid regions were defined based on a dataset, which includes protein sequences that have multiple experimental structures, and which was previously used to study the structural conservation of proteins. Sequences drawn from this dataset were represented based on feature sets that were proposed in prior research, such as PSI-BLAST profiles, composition vector and binary sequence encoding, and a newly proposed representation based on frequencies of k-spaced amino acid pairs. These representations were processed by feature selection to reduce the dimensionality. Several machine learning methods for the prediction of flexible/rigid regions and two recently proposed methods for the prediction of conformational changes and unstructured regions were compared with the proposed method. The FlexRP method, which applies Logistic Regression and collocation-based representation with 95 features, obtained 79.5% accuracy. The two runner-up methods, which apply the same sequence representation and Support Vector Machines (SVM and Naïve Bayes classifiers, obtained 79.2% and 78.4% accuracy, respectively. The remaining considered methods are

  6. Nucleic and amino acid sequences relating to a novel transketolase, and methods for the expression thereof

    Energy Technology Data Exchange (ETDEWEB)

    Croteau, Rodney Bruce (Pullman, WA); Wildung, Mark Raymond (Colfax, WA); Lange, Bernd Markus (Pullman, WA); McCaskill, David G. (Pullman, WA)

    2001-01-01

    cDNAs encoding 1-deoxyxylulose-5-phosphate synthase from peppermint (Mentha piperita) have been isolated and sequenced, and the corresponding amino acid sequences have been determined. Accordingly, isolated DNA sequences (SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7) are provided which code for the expression of 1-deoxyxylulose-5-phosphate synthase from plants. In another aspect the present invention provides for isolated, recombinant DXPS proteins, such as the proteins having the sequences set forth in SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:8. In other aspects, replicable recombinant cloning vehicles are provided which code for plant 1-deoxyxylulose-5-phosphate synthases, or for a base sequence sufficiently complementary to at least a portion of 1-deoxyxylulose-5-phosphate synthase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding a plant 1-deoxyxylulose-5-phosphate synthase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant 1-deoxyxylulose-5-phosphate synthase that may be used to facilitate its production, isolation and purification in significant amounts. Recombinant 1-deoxyxylulose-5-phosphate synthase may be used to obtain expression or enhanced expression of 1-deoxyxylulose-5-phosphate synthase in plants in order to enhance the production of 1-deoxyxylulose-5-phosphate, or its derivatives such as isopentenyl diphosphate (BP), or may be otherwise employed for the regulation or expression of 1-deoxyxylulose-5-phosphate synthase, or the production of its products.

  7. Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.

    Directory of Open Access Journals (Sweden)

    Xiaoyu Wang

    Full Text Available Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals.

  8. Sequence-defined bioactive macrocycles via an acid-catalysed cascade reaction

    Science.gov (United States)

    Porel, Mintu; Thornlow, Dana N.; Phan, Ngoc N.; Alabi, Christopher A.

    2016-06-01

    Synthetic macrocycles derived from sequence-defined oligomers are a unique structural class whose ring size, sequence and structure can be tuned via precise organization of the primary sequence. Similar to peptides and other peptidomimetics, these well-defined synthetic macromolecules become pharmacologically relevant when bioactive side chains are incorporated into their primary sequence. In this article, we report the synthesis of oligothioetheramide (oligoTEA) macrocycles via a one-pot acid-catalysed cascade reaction. The versatility of the cyclization chemistry and modularity of the assembly process was demonstrated via the synthesis of >20 diverse oligoTEA macrocycles. Structural characterization via NMR spectroscopy revealed the presence of conformational isomers, which enabled the determination of local chain dynamics within the macromolecular structure. Finally, we demonstrate the biological activity of oligoTEA macrocycles designed to mimic facially amphiphilic antimicrobial peptides. The preliminary results indicate that macrocyclic oligoTEAs with just two-to-three cationic charge centres can elicit potent antibacterial activity against Gram-positive and Gram-negative bacteria.

  9. Heterodimeric l-amino acid oxidase enzymes from Egyptian Cerastes cerastes venom: Purification, biochemical characterization and partial amino acid sequencing

    Directory of Open Access Journals (Sweden)

    A.E. El Hakim

    2015-12-01

    Full Text Available Two l-amino acid oxidase enzyme isoforms, Cc-LAAOI and Cc-LAAOII were purified to apparent homogeneity from Cerastes cerastes venom in a sequential two-step chromatographic protocol including; gel filtration and anion exchange chromatography. The native molecular weights of the isoforms were 115 kDa as determined by gel filtration on calibrated Sephacryl S-200 column, while the monomeric molecular weights of the enzymes were, 60, 56 kDa and 60, 53 kDa for LAAOI and LAAOII, respectively. The tryptic peptides of the two isoforms share high sequence homology with other snake venom l-amino acid oxidases. The optimal pH and temperature values of Cc-LAAOI and Cc-LAAOII were 7.8, 50 °C and 7, 60 °C, respectively. The two isoenzymes were thermally stable up to 70 °C. The Km and Vmax values were 0.67 mM, 0.135 μmol/min for LAAOI and 0.82 mM, 0.087 μmol/min for LAAOII. Both isoenzymes displayed high catalytic preference to long-chain, hydrophobic and aromatic amino acids. The Mn2+ ion markedly increased the LAAO activity for both purified isoforms, while Na+, K+, Ca2+, Mg2+ and Ba2+ ions showed a non-significant increase in the enzymatic activity of both isoforms. Furthermore, Zn2+, Ni2+, Co2+, Cu2+ and AL3+ ions markedly inhibited the LAAOI and LAAOII activities. l-Cysteine and reduced glutathione completely inhibited the LAAO activity of both isoenzymes, whereas, β-mercaptoethanol, O-phenanthroline and PMSF completely inhibited the enzymatic activity of LAAOII. Furthermore, iodoacitic acid inhibited the enzymatic activity of LAAOII by 46% and had no effect on the LAAOI activity.

  10. Amino acid sequence and variant forms of favin, a lectin from Vicia faba.

    Science.gov (United States)

    Hopp, T P; Hemperly, J J; Cunningham, B A

    1982-04-25

    We have determined the complete amino acid sequence (182 residues) of the beta chain of favin, the glucose-binding lectin from fava beans (Vicia faba), and have established that the carbohydrate moiety is attached to Asn 168. Together with the sequence of the alpha chain previously reported (Hemperly, J. J., Hopp, T. P., Becker, J. W., and Cunningham, B. A. (1979) J. Biol. Chem. 254, 6803-6810), these data complete the analysis of the primary structure of the lectin. We have also examined minor polypeptides that appear in all preparations of favin. Two lower molecular weight species (Mr = 9,500-11,600) appear to be fragments of the beta chain resulting from cleavage following Asn 76, whereas six high molecular weight forms (Mr = 25,000 or greater) appear to include aggregates of the beta chain and possibly some alternative products of chain processing. PMID:7068646

  11. Morphological tranformation of calcite crystal growth by prismatic "acidic" polypeptide sequences.

    Energy Technology Data Exchange (ETDEWEB)

    Kim, I; Giocondi, J L; Orme, C A; Collino, J; Evans, J S

    2007-02-13

    Many of the interesting mechanical and materials properties of the mollusk shell are thought to stem from the prismatic calcite crystal assemblies within this composite structure. It is now evident that proteins play a major role in the formation of these assemblies. Recently, a superfamily of 7 conserved prismatic layer-specific mollusk shell proteins, Asprich, were sequenced, and the 42 AA C-terminal sequence region of this protein superfamily was found to introduce surface voids or porosities on calcite crystals in vitro. Using AFM imaging techniques, we further investigate the effect that this 42 AA domain (Fragment-2) and its constituent subdomains, DEAD-17 and Acidic-2, have on the morphology and growth kinetics of calcite dislocation hillocks. We find that Fragment-2 adsorbs on terrace surfaces and pins acute steps, accelerates then decelerates the growth of obtuse steps, forms clusters and voids on terrace surfaces, and transforms calcite hillock morphology from a rhombohedral form to a rounded one. These results mirror yet are distinct from some of the earlier findings obtained for nacreous polypeptides. The subdomains Acidic-2 and DEAD-17 were found to accelerate then decelerate obtuse steps and induce oval rather than rounded hillock morphologies. Unlike DEAD-17, Acidic-2 does form clusters on terrace surfaces and exhibits stronger obtuse velocity inhibition effects than either DEAD-17 or Fragment-2. Interestingly, a 1:1 mixture of both subdomains induces an irregular polygonal morphology to hillocks, and exhibits the highest degree of acute step pinning and obtuse step velocity inhibition. This suggests that there is some interplay between subdomains within an intra (Fragment-2) or intermolecular (1:1 mixture) context, and sequence interplay phenomena may be employed by biomineralization proteins to exert net effects on crystal growth and morphology.

  12. Cervical cancer risk factors and feasibility of visual inspection with acetic acid screening in Sudan

    Directory of Open Access Journals (Sweden)

    Ibrahim A

    2011-04-01

    Full Text Available Ahmed Ibrahim1, Vibeke Rasch2, Eero Pukkala3, Arja R Aro11Unit for Health Promotion Research, University of Southern Denmark, Esbjerg, Denmark; 2Department of Obstetrics and Gynecology, Odense University Hospital, Odense, Denmark; 3Institute for Statistical and Epidemiological Cancer Research, Finnish Cancer Registry, Helsinki, FinlandObjectives: To assess the risk factors of cervical cancer and the feasibility and acceptability of a visual inspection with acetic acid (VIA screening method in a primary health center in Khartoum, Sudan.Methods: A cross-sectional prospective pilot study of 100 asymptomatic women living in Khartoum State in Sudan was carried out from December 2008 to January 2009. The study was performed at the screening center in Khartoum. Six nurses and two physicians were trained by a gynecologic oncologist. The patients underwent a complete gynecological examination and filled in a questionnaire on risk factors and feasibility and acceptability. They were screened for cervical cancer by application of 3%–5% VIA. Women with a positive test were referred for colposcopy and treatment.Results: Sixteen percent of screened women were tested positive. Statistically significant associations were observed between being positive with VIA test and the following variables: uterine cervix laceration (odds ratio [OR] 18.6; 95% confidence interval [CI]: 4.64–74.8, assisted vaginal delivery (OR 13.2; 95% CI: 2.95–54.9, parity (OR 5.78; 95% CI: 1.41–23.7, female genital mutilation (OR 4.78; 95% CI: 1.13–20.1, and episiotomy (OR 5.25; 95% CI: 1.15–23.8. All these associations remained statistically significant after adjusting for age, educational level, employment, and potential confounding factors such as smoking, number of sexual partners, and use of contraceptive method. Furthermore, the VIA screening method was found to be feasible and acceptable to participants.Conclusion: This pilot study showed that women who have uterine

  13. Complete Genome Sequence of Lactococcus lactis IO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels of l-Lactic Acid

    OpenAIRE

    Kato, Hiroaki; Shiwa, Yuh; Oshima, Kenshiro; Machii, Miki; Araya-Kojima, Tomoko; Zendo, Takeshi; Shimizu-Kadota, Mariko; Hattori, Masahira; Sonomoto, Kenji; Yoshikawa, Hirofumi

    2012-01-01

    We report the complete genome sequence of Lactococcus lactis IO-1 (= JCM7638). It is a nondairy lactic acid bacterium, produces nisin Z, ferments xylose, and produces predominantly l-lactic acid at high xylose concentrations. From ortholog analysis with other five L. lactis strains, IO-1 was identified as L. lactis subsp. lactis.

  14. The human receptor for urokinase plasminogen activator. NH2-terminal amino acid sequence and glycosylation variants

    DEFF Research Database (Denmark)

    Behrendt, N; Rønne, E; Ploug, M;

    1990-01-01

    The receptor for human urokinase-type plasminogen activator (u-PA) was purified from phorbol 12-myristate 13-acetate-stimulated U937 cells by temperature-induced phase separation of detergent extracts, followed by affinity chromatography with immobilized diisopropyl fluorophosphate-treated u......, but no N-acetyl-D-galactosamine. Glycosylation is responsible for substantial heterogeneity in the receptor on phorbol ester-stimulated U937 cells, and also for molecular weight variations among various cell lines. The amino acid composition and the NH2-terminal amino acid sequence are reported...... amino-terminal fragment; 2) the identical electrophoretic mobilities observed for cross-linked conjugates, formed between either the purified protein or the u-PA receptor on intact U937 cells and the above ligands; 3) the identity of the apparent molecular weight of the purified protein...

  15. Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues

    OpenAIRE

    Schwartz, Russell; Istrail, Sorin; King, Jonathan

    2001-01-01

    Patterns of hydrophobic and hydrophilic residues play a major role in protein folding and function. Long, predominantly hydrophobic strings of 20–22 amino acids each are associated with transmembrane helices and have been used to identify such sequences. Much less attention has been paid to hydrophobic sequences within globular proteins. In prior work on computer simulations of the competition between on-pathway folding and off-pathway aggregate formation, we found that long sequences of cons...

  16. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.

    Directory of Open Access Journals (Sweden)

    James B Howard

    Full Text Available Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification

  17. Nanostructure of native pectin sugar acid gels visualized by atomic force microscopy.

    Science.gov (United States)

    Fishman, Marshall L; Cooke, Peter H; Coffin, David R

    2004-01-01

    Height and phase shift images of high methoxyl sugar acid gels (HMSAG) of pectin were obtained by atomic force microscopy in the tapping mode. Images revealed that pores in these gels were fluid and flattened out when measured as a function of time. These images revealed for the first time the structure of adsorbed sugar on pectin in the hydrated native gels and how the pectin framework is organized within these gels. Segmentation of images revealed that the underlying pectin framework contained combinations of rods, segmented rods, and kinked rods connected end to end and laterally. The open network of strands was similar to pectin aggregates from 5 mM NaCl solution imaged earlier by electron microscopy (Fishman et al., Arch. Biochem. Biophys. 1992, 294, 253). Area measurements revealed that the ratio of bound sugar to pectin was in excess of 100 to 1 (w/w). Furthermore, images indicated relatively small differences in the organization of native commercial citrus pectin, orange albedo pectin, and lime albedo pectin gels at optimal pH as determined in this study. The findings are consistent with earlier gel strength measurements of these gels. In addition, values of gel strength were consistent with values of molar mass and viscosity of the constituent pectins in that they increased in the same order. Finally, we demonstrated the advantage of simultaneous visualization of height and phase shift images for observing and quantitating the nanostructure of relatively soft gels which are fully hydrated with a buffer. PMID:15002992

  18. PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome

    Directory of Open Access Journals (Sweden)

    Martinetz Thomas

    2011-06-01

    Full Text Available Abstract Background Results of phylogenetic analysis are often visualized as phylogenetic trees. Such a tree can typically only include up to a few hundred sequences. When more than a few thousand sequences are to be included, analyzing the phylogenetic relationships among them becomes a challenging task. The recent frequent outbreaks of influenza A viruses have resulted in the rapid accumulation of corresponding genome sequences. Currently, there are more than 7500 influenza A virus genomes in the database. There are no efficient ways of representing this huge data set as a whole, thus preventing a further understanding of the diversity of the influenza A virus genome. Results Here we present a new algorithm, "PhyloMap", which combines ordination, vector quantization, and phylogenetic tree construction to give an elegant representation of a large sequence data set. The use of PhyloMap on influenza A virus genome sequences reveals the phylogenetic relationships of the internal genes that cannot be seen when only a subset of sequences are analyzed. Conclusions The application of PhyloMap to influenza A virus genome data shows that it is a robust algorithm for analyzing large sequence data sets. It utilizes the entire data set, minimizes bias, and provides intuitive visualization. PhyloMap is implemented in JAVA, and the source code is freely available at http://www.biochem.uni-luebeck.de/public/software/phylomap.html

  19. MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species

    Science.gov (United States)

    Baek, Jeong-Ho; Kim, Junah; Kim, Chang-Kug; Sohn, Seong-Han; Choi, Dongsu; Ratnaparkhe, Milind B.; Kim, Do-Wan; Lee, Tae-Ho

    2016-01-01

    Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution. So far, some web applications have been developed to determine and visualize multiple homology regions at once. However, the applications are not fully convenient for biologists because some of them do not include the function of synteny determination but visualize the multiple synteny plots by allowing users to upload their synteny data by determining the synteny based only on BLAST similarity information, with some algorithms not designed for synteny determination. Here, we introduce a web application that determines and visualizes multiple synteny from two types of files, simplified browser extensible data and protein sequence file by MCScanX algorithm, which have been used in many synteny studies. PMID:27594782

  20. MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User's Sequence of Interest Compared to Public Plant Species.

    Science.gov (United States)

    Baek, Jeong-Ho; Kim, Junah; Kim, Chang-Kug; Sohn, Seong-Han; Choi, Dongsu; Ratnaparkhe, Milind B; Kim, Do-Wan; Lee, Tae-Ho

    2016-01-01

    Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution. So far, some web applications have been developed to determine and visualize multiple homology regions at once. However, the applications are not fully convenient for biologists because some of them do not include the function of synteny determination but visualize the multiple synteny plots by allowing users to upload their synteny data by determining the synteny based only on BLAST similarity information, with some algorithms not designed for synteny determination. Here, we introduce a web application that determines and visualizes multiple synteny from two types of files, simplified browser extensible data and protein sequence file by MCScanX algorithm, which have been used in many synteny studies.

  1. MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User's Sequence of Interest Compared to Public Plant Species.

    Science.gov (United States)

    Baek, Jeong-Ho; Kim, Junah; Kim, Chang-Kug; Sohn, Seong-Han; Choi, Dongsu; Ratnaparkhe, Milind B; Kim, Do-Wan; Lee, Tae-Ho

    2016-01-01

    Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution. So far, some web applications have been developed to determine and visualize multiple homology regions at once. However, the applications are not fully convenient for biologists because some of them do not include the function of synteny determination but visualize the multiple synteny plots by allowing users to upload their synteny data by determining the synteny based only on BLAST similarity information, with some algorithms not designed for synteny determination. Here, we introduce a web application that determines and visualizes multiple synteny from two types of files, simplified browser extensible data and protein sequence file by MCScanX algorithm, which have been used in many synteny studies. PMID:27594782

  2. Barley polyamine oxidase: Characterisation and analysis of the cofactor and the N-terminal amino acid sequence

    DEFF Research Database (Denmark)

    Radova, A.; Sebela, M.; Galuszka, P.;

    2001-01-01

    was further confirmed by measuring the fluorescence spectra, Barley PAO is an acidic protein (pI 5.4) containing 3% of neutral sugars: its molecular mass determined by SDS-PAGE was 56 kDa, whilst gel permeation chromatography revealed the higher value of 76 kDa. The N-terminal amino acid sequence of barley...

  3. Draft Genome Sequences of Gluconobacter cerinus CECT 9110 and Gluconobacter japonicus CECT 8443, Acetic Acid Bacteria Isolated from Grape Must

    Science.gov (United States)

    Sainz, Florencia

    2016-01-01

    We report here the draft genome sequences of Gluconobacter cerinus strain CECT9110 and Gluconobacter japonicus CECT8443, acetic acid bacteria isolated from grape must. Gluconobacter species are well known for their ability to oxidize sugar alcohols into the corresponding acids. Our objective was to select strains to oxidize effectively d-glucose. PMID:27365351

  4. The Effect of Using a Visual Representation Tool in a Teaching-Learning Sequence for Teaching Newton's Third Law

    Science.gov (United States)

    Savinainen, Antti; Mäkynen, Asko; Nieminen, Pasi; Viiri, Jouni

    2015-09-01

    This paper presents a research-based teaching-learning sequence (TLS) that focuses on the notion of interaction in teaching Newton's third law (N3 law) which is, as earlier studies have shown, a challenging topic for students to learn. The TLS made systematic use of a visual representation tool—an interaction diagram (ID)—highlighting interactions between objects and addressing the learning demand related to N3 law. This approach had been successful in enhancing students' understanding of N3 law in pilot studies conducted by teacher-researchers. However, it was unclear whether teachers, who have neither been involved with the research nor received intensive tutoring, could replicate the positive results in ordinary school settings. To address this question, we present an empirical study conducted in 10 Finnish upper secondary schools with students (n = 261, aged 16) taking their mandatory physics course. The study design involved three groups: the heavy ID group (the TLS with seven to eight exercises on IDs), the light ID group (two to three exercises on IDs) and the no ID group (no exercises on IDs). The heavy and light ID groups answered eight ID questions, and all the students answered four questions on N3 law after teaching the force concept. The findings clearly suggest that systematic use of the IDs in teaching the force concept significantly fostered students' understanding of N3 law even with teachers who have no intensive tutoring or research background.

  5. Learning multisensory representations for auditory-visual transfer of sequence category knowledge: a probabilistic language of thought approach.

    Science.gov (United States)

    Yildirim, Ilker; Jacobs, Robert A

    2015-06-01

    If a person is trained to recognize or categorize objects or events using one sensory modality, the person can often recognize or categorize those same (or similar) objects and events via a novel modality. This phenomenon is an instance of cross-modal transfer of knowledge. Here, we study the Multisensory Hypothesis which states that people extract the intrinsic, modality-independent properties of objects and events, and represent these properties in multisensory representations. These representations underlie cross-modal transfer of knowledge. We conducted an experiment evaluating whether people transfer sequence category knowledge across auditory and visual domains. Our experimental data clearly indicate that we do. We also developed a computational model accounting for our experimental results. Consistent with the probabilistic language of thought approach to cognitive modeling, our model formalizes multisensory representations as symbolic "computer programs" and uses Bayesian inference to learn these representations. Because the model demonstrates how the acquisition and use of amodal, multisensory representations can underlie cross-modal transfer of knowledge, and because the model accounts for subjects' experimental performances, our work lends credence to the Multisensory Hypothesis. Overall, our work suggests that people automatically extract and represent objects' and events' intrinsic properties, and use these properties to process and understand the same (and similar) objects and events when they are perceived through novel sensory modalities.

  6. Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence

    Directory of Open Access Journals (Sweden)

    Pelletier Eric

    2010-10-01

    Full Text Available Abstract Background Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabolic aspects such as the Stickland reaction, coenzyme-B12- and selenium-dependent reactions of amino acids. With the goal of revisiting its carbon, nitrogen, and energy metabolism, and comparing studies with other clostridia, its genome has been sequenced and analyzed. Results C. sticklandii is one of the best biochemically studied proteolytic clostridial species. Useful additional information has been obtained from the sequencing and annotation of its genome, which is presented in this paper. Besides, experimental procedures reveal that C. sticklandii degrades amino acids in a preferential and sequential way. The organism prefers threonine, arginine, serine, cysteine, proline, and glycine, whereas glutamate, aspartate and alanine are excreted. Energy conservation is primarily obtained by substrate-level phosphorylation in fermentative pathways. The reactions catalyzed by different ferredoxin oxidoreductases and the exergonic NADH-dependent reduction of crotonyl-CoA point to a possible chemiosmotic energy conservation via the Rnf complex. C. sticklandii possesses both the F-type and V-type ATPases. The discovery of an as yet unrecognized selenoprotein in the D-proline reductase operon suggests a more detailed mechanism for NADH-dependent D-proline reduction. A rather unusual metabolic feature is the presence of genes for all the enzymes involved in two different CO2-fixation pathways: C. sticklandii harbours both the glycine synthase/glycine reductase and the Wood-Ljungdahl pathways. This unusual pathway combination has retrospectively been observed in only four other sequenced microorganisms. Conclusions Analysis of the C

  7. Isolation and amino acid sequences of squirrel monkey (Saimiri sciurea) insulin and glucagon

    International Nuclear Information System (INIS)

    It was reported two decades ago that insulin was not detectable in the glucose-stimulated state in Saimiri sciurea, the New World squirrel monkey, by a radioimmunoassay system developed with guinea pig anti-pork insulin antibody and labeled park insulin. With the same system, reasonable levels were observed in rhesus monkeys and chimpanzees. This suggested that New World monkeys, like the New World hystricomorph rodents such as the guinea pig and the coypu, might have insulins whose sequences differ markedly from those of Old World mammals. In this report the authors describe the purification and amino acid sequences of squirrel monkey insulin and glucagon. They demonstrate that the substitutions at B29, B27, A2, A4, and A17 of squirrel monkey insulin are identical with those previously found in another New World primate, the owl monkey (Aotus trivirgatus). The immunologic cross-reactivity of this insulin in their immunoassay system is only a few percent of that of human insulin. It appears that the peptides of the New World monkeys have diverged less from those of the Old World mammals than have those of the New World hystricomorph rodents. The striking improvements in peptide purification and sequencing have the potential for adding new information concerning the evolutionary divergence of species

  8. Complete amino acid sequence of the myoglobin from the Pacific spotted dolphin, Stenella attenuata graffmani.

    Science.gov (United States)

    Jones, B N; Wang, C C; Dwulet, F E; Lehman, L D; Meuth, J L; Bogardt, R A; Gurd, F R

    1979-04-25

    The complete amino acid sequence of the major component myoglobin from the Pacific spotted dolphin, Stenella attenuata graffmani, was determined by the automated Edman degradation of several large peptides obtained by specific cleavage of the protein. The acetimidated apomyoglobin was selectively cleaved at its two methionyl residues with cyanogen bromide and at its three arginyl residues by trypsin. By subjecting four of these peptides and the apomyoglobin to automated Edman degradation, over 80% of the primary structure of the protein was obtained. The remainder of the covalent structure was determined by the sequence analysis of peptides that resulted from further digestion of the central cyanogen bromide fragment. This fragment was cleaved at its glutamyl residues with staphylococcal protease and its lysyl residues with trypsin. The action of trypsin was restricted to the lysyl residues by chemical modification of the single arginyl residue of the fragment with 1,2-cyclohexanedione. The primary structure of this myoglobin proved to be identical with that from the Atlantic bottlenosed dolphin and Pacific common dolphin but differs from the myoglobins of the killer whale and pilot whale at two positions. The above sequence identities and differences reflect the close taxonomic relationship of these five species of Cetacea. PMID:454657

  9. ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

    Directory of Open Access Journals (Sweden)

    Meiler Arno

    2012-09-01

    Full Text Available Abstract Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

  10. Human liver phosphatase 2A: cDNA and amino acid sequence of two catalytic subunit isotypes

    Energy Technology Data Exchange (ETDEWEB)

    Arino, J.; Woon, Chee Wai; Brautigan, D.L.; Miller, T.B. Jr.; Johnson, G.L. (Univ. of Massachusetts Medical School, Worcester (USA))

    1988-06-01

    Two cDNA clones were isolated from a human liver library that encode two phosphatase 2A catalytic subunits. The two cDNAs differed in eight amino acids (97% identity) with three nonconservative substitutions. All of the amino acid substitutions were clustered in the amino-terminal domain of the protein. Amino acid sequence of one human liver clone (HL-14) was identical to the rabbit skeletal muscle phosphatase 2A cDNA (with 97% nucleotide identity). The second human liver clone (HL-1) is encoded by a separate gene, and RNA gel blot analysis indicates that both mRNAs are expressed similarly in several human clonal cell lines. Sequence comparison with phosphatase 1 and 2A indicates highly divergent amino acid sequences at the amino and carboxyl termini of the proteins and identifies six highly conserved regions between the two proteins that are predicted to be important for phosphatase enzymatic activity.

  11. Amino acid sequences of neuropeptides in the sinus gland of the land crab Cardisoma carnifex: a novel neuropeptide proteolysis site.

    Science.gov (United States)

    Newcomb, R W

    1987-08-01

    The sinus gland is a major neurosecretory structure in Crustacea. Five peptides, labeled C, D, E, F, and I, isolated from the sinus gland of the land crab have been hypothesized to arise from the incomplete proteolysis at two internal sites on a single biosynthetic intermediate peptide "H", based on amino acid composition additivities and pulse-chase radiolabeling studies. The presence of only a single major precursor for the sinus gland peptides implies that peptide H may be synthesized on a common precursor with crustacean hyperglycemic hormone forms, "J" and "L," and a peptide, "K," similar to peptides with molt inhibiting activity. Here I report amino acid sequences of these peptides. The amino terminal sequence of the parent peptide, H, (and the homologous fragments) proved refractory to Edman degradation. Data from amino acid analysis and carboxypeptidase digestion of the naturally occurring fragments and of fragments produced by endopeptidase digestion were used together with Edman degradation to obtain the sequences. Amino acid analysis of fragments of the naturally occurring "overlap" peptides (those produced by internal cleavage at one site on H) was used to obtain the sequences across the cleavage sites. The amino acid sequence of the land crab peptide H is Arg-Ser-Ala-Asp-Gly-Phe-Gly-Arg-Met-Glu-Ser-Leu-Leu-Thr-Ser-Leu-Arg-Gly- Ser-Ala-Glu- Ser-Pro-Ala-Ala-Leu-Gly-Glu-Ala-Ser-Ala-Ala-His-Pro-Leu-Glu. In vivo cleavage at one site involves excision of arginine from the sequence Leu-Arg-Gly, whereas cleavage at the other site involves excision of serine from the sequence Glu-Ser-Leu. Proteolysis at the latter sequence has not been previously reported in intact secretory granules. The aspartate at position 4 is possibly covalently modified.

  12. Enzyme-free translation of DNA into sequence-defined synthetic polymers structurally unrelated to nucleic acids

    Science.gov (United States)

    Niu, Jia; Hili, Ryan; Liu, David R.

    2013-04-01

    The translation of DNA sequences into corresponding biopolymers enables the production, function and evolution of the macromolecules of life. In contrast, methods to generate sequence-defined synthetic polymers with similar levels of control have remained elusive. Here, we report the development of a DNA-templated translation system that enables the enzyme-free translation of DNA templates into sequence-defined synthetic polymers that have no necessary structural relationship with nucleic acids. We demonstrate the efficiency, sequence-specificity and generality of this translation system by oligomerizing building blocks including polyethylene glycol, α-(D)-peptides, and β-peptides in a DNA-programmed manner. Sequence-defined synthetic polymers with molecular weights of 26 kDa containing 16 consecutively coupled building blocks and 90 densely functionalized β-amino acid residues were translated from DNA templates using this strategy. We integrated the DNA-templated translation system developed here into a complete cycle of translation, coding sequence replication, template regeneration and re-translation suitable for the iterated in vitro selection of functional sequence-defined synthetic polymers unrelated in structure to nucleic acids.

  13. Repetitive sequence based polymerase chain reaction to differentiate close bacteria strains in acidic sites

    Institute of Scientific and Technical Information of China (English)

    XIE Ming; YIN Hua-qun; LIU Yi; LIU Jie; LIU Xue-duan

    2008-01-01

    To study the diversity of bacteria strains newly isolated from several acid mine drainage(AMD) sites in China,repetitive sequence based polymerase chain reaction (rep-PCR),a well established technology for diversity analysis of closely related bacteria strains,was conducted on 30 strains of bacteria Leptospirillum ferriphilium,8 strains of bacteria Acidithiobacillus ferrooxidans,as well as the Acidithiobacillus ferrooxidans type strain ATCC (American Type Culture Collection) 23270.The results showed that,using ERIC and BOX primer sets,rep-PCR produced highly discriminatory banding patterns.Phylogenetic analysis based on ERIC-PCR banding types was made and the results indicated that rep-PCR could be used as a rapid and highly discriminatory screening technique in studying bacterial diversity,especially in differentiating bacteria within one species in AMD.

  14. Trypsin inhibitors from ridged gourd (Luffa acutangula Linn.) seeds: purification, properties, and amino acid sequences.

    Science.gov (United States)

    Haldar, U C; Saha, S K; Beavis, R C; Sinha, N K

    1996-02-01

    Two trypsin inhibitors, LA-1 and LA-2, have been isolated from ridged gourd (Luffa acutangula Linn.) seeds and purified to homogeneity by gel filtration followed by ion-exchange chromatography. The isoelectric point is at pH 4.55 for LA-1 and at pH 5.85 for LA-2. The Stokes radius of each inhibitor is 11.4 A. The fluorescence emission spectrum of each inhibitor is similar to that of the free tyrosine. The biomolecular rate constant of acrylamide quenching is 1.0 x 10(9) M-1 sec-1 for LA-1 and 0.8 x 10(9) M-1 sec-1 for LA-2 and that of K2HPO4 quenching is 1.6 x 10(11) M-1 sec-1 for LA-1 and 1.2 x 10(11) M-1 sec-1 for LA-2. Analysis of the circular dichroic spectra yields 40% alpha-helix and 60% beta-turn for La-1 and 45% alpha-helix and 55% beta-turn for LA-2. Inhibitors LA-1 and LA-2 consist of 28 and 29 amino acid residues, respectively. They lack threonine, alanine, valine, and tryptophan. Both inhibitors strongly inhibit trypsin by forming enzyme-inhibitor complexes at a molar ratio of unity. A chemical modification study suggests the involvement of arginine of LA-1 and lysine of LA-2 in their reactive sites. The inhibitors are very similar in their amino acid sequences, and show sequence homology with other squash family inhibitors. PMID:8924202

  15. Canine amino acid transport system Xc(-): cDNA sequence, distribution and cystine transport activity in lens epithelial cells.

    Science.gov (United States)

    Maruo, Takuya; Kanemaki, Nobuyuki; Onda, Ken; Sato, Reiichiro; Ichihara, Nobuteru; Ochiai, Hideharu

    2014-04-01

    The cystine transport activity of a lens epithelial cell line originated from a canine mature cataract was investigated. The distinct cystine transport activity was observed, which was inhibited to 28% by extracellular 1 mM glutamate. The cDNA sequences of canine cysteine/glutamate exchanger (xCT) and 4F2hc were determined. The predicted amino acid sequences were 527 and 533 amino acid polypeptides, respectively. The amino acid sequences of canine xCT and 4F2hc showed high similarities (>80%) to those of humans. The expression of xCT in lens epithelial cell line was confirmed by western blot analysis. RT-PCR analysis revealed high level expression only in the brain, and it was below the detectable level in other tissues.

  16. Human Retroviruses and AIDS. A compilation and analysis of nucleic acid and amino acid sequences: I--II; III--V

    Energy Technology Data Exchange (ETDEWEB)

    Myers, G.; Korber, B. [eds.] [Los Alamos National Lab., NM (United States); Wain-Hobson, S. [ed.] [Laboratory of Molecular Retrovirology, Pasteur Inst.; Smith, R.F. [ed.] [Baylor Coll. of Medicine, Houston, TX (United States). Dept. of Pharmacology; Pavlakis, G.N. [ed.] [National Cancer Inst., Frederick, MD (United States). Cancer Research Facility

    1993-12-31

    This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (I) HIV and SIV Nucleotide Sequences; (II) Amino Acid Sequences; (III) Analyses; (IV) Related Sequences; and (V) Database Communications. Information within all the parts is updated at least twice in each year, which accounts for the modes of binding and pagination in the compendium.

  17. Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences

    KAUST Repository

    Chen, Peng

    2013-07-23

    Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K-nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state-of-the-art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx. © 2013 Wiley Periodicals, Inc.

  18. Lactic acid production from potato peel waste by anaerobic sequencing batch fermentation using undefined mixed culture.

    Science.gov (United States)

    Liang, Shaobo; McDonald, Armando G; Coats, Erik R

    2015-11-01

    Lactic acid (LA) is a necessary industrial feedstock for producing the bioplastic, polylactic acid (PLA), which is currently produced by pure culture fermentation of food carbohydrates. This work presents an alternative to produce LA from potato peel waste (PPW) by anaerobic fermentation in a sequencing batch reactor (SBR) inoculated with undefined mixed culture from a municipal wastewater treatment plant. A statistical design of experiments approach was employed using set of 0.8L SBRs using gelatinized PPW at a solids content range from 30 to 50 g L(-1), solids retention time of 2-4 days for yield and productivity optimization. The maximum LA production yield of 0.25 g g(-1) PPW and highest productivity of 125 mg g(-1) d(-1) were achieved. A scale-up SBR trial using neat gelatinized PPW (at 80 g L(-1) solids content) at the 3 L scale was employed and the highest LA yield of 0.14 g g(-1) PPW and a productivity of 138 mg g(-1) d(-1) were achieved with a 1 d SRT. PMID:25708409

  19. Cloning and sequence analysis of putative type II fatty acid synthase genes from Arachis hypogaea L.

    Indian Academy of Sciences (India)

    Meng-Jun Li; Ai-Qin Li; Han Xia; Chuan-Zhi Zhao; Chang-Sheng Li; Shu-Bo Wan; Yu-Ping Bi; Xing-Jun Wang

    2009-06-01

    The cultivated peanut is a valuable source of dietary oil and ranks fifth among the world oil crops. Plant fatty acid biosynthesis is catalysed by type II fatty acid synthase (FAS) in plastids and mitochondria. By constructing a full-length cDNA library derived from immature peanut seeds and homology-based cloning, candidate genes of acyl carrier protein (ACP), malonyl-CoA:ACP transacylase, -ketoacyl-ACP synthase (I, II, III), -ketoacyl-ACP reductase, -hydroxyacyl-ACP dehydrase and enoyl-ACP reductase were isolated. Sequence alignments revealed that primary structures of type II FAS enzymes were highly conserved in higher plants and the catalytic residues were strictly conserved in Escherichia coli and higher plants. Homologue numbers of each type II FAS gene expressing in developing peanut seeds varied from 1 in KASII, KASIII and HD to 5 in ENR. The number of single-nucleotide polymorphisms (SNPs) was quite different in each gene. Peanut type II FAS genes were predicted to target plastids except ACP2 and ACP3. The results suggested that peanut may contain two type II FAS systems in plastids and mitochondria. The type II FAS enzymes in higher plants may have similar functions as those in E. coli.

  20. Application of peptide nucleic acids containing azobenzene self-assembled electrochemical biosensors in detecting DNA sequences

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Hybridization of peptide nucleic acids probe containing azobenzene (NH2-TNT4, N-PNAs) with DNA was performed by covalently immobilizing of NH2-TNT4 in sequence on the 3-mercaptopropionic acid self-assembled monolayer modified gold electrode with the helps of N-(3-dimethylaminopropy1)-N’-ethylcarbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS), and the hybrid was coded as N-PNAs/DNA. Using [Fe(CN)6]4-/3- (1:1) as the electrochemical indicator, the electrochemical properties of the N-PNAs self-assembled monolayer (N-PNAs-SAMs) and N-PNAs/DNA hybridization system under the conditions of before and after UV light irradiation were characterized with cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectra (EIS). Results showed that the redox currents decreased with the increase of irradiation time, suggesting that the ability of the charge transfer on the electrode surface was weakened and the conformation of hybrid system had been changed, and the control of PNAs/DNA hybridization could be realized by UV light irradiation.

  1. Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids

    OpenAIRE

    Kim, Ki-Hyun; Nielsen, Peter E.; Glazer, Peter M.

    2007-01-01

    Sequence-specific DNA-binding molecules such as triple helix-forming oligonucleotides (TFOs) provide a means for inducing site-specific mutagenesis and recombination at chromosomal sites in mammalian cells. However, the utility of TFOs is limited by the requirement for homopurine stretches in the target duplex DNA. Here, we report the use of pseudo-complementary peptide nucleic acids (pcPNAs) for intracellular gene targeting at mixed sequence sites. Due to steric hindrance, pcPNAs are unable ...

  2. Nucleotide and amino acid sequence coding for polypeptides of foot-and-mouth disease virus type A12.

    OpenAIRE

    Robertson, B H; Grubman, M J; Weddell, G N; Moore, D.M.; Welsh, J D; Fischer, T.; Dowbenko, D J; Yansura, D G; Small, B.; Kleid, D G

    1985-01-01

    The coding region for the structural and nonstructural polypeptides of the type A12 foot-and-mouth disease virus genome has been identified by nucleotide sequencing of cloned DNA derived from the viral RNA. In addition, 704 nucleotides in the 5' untranslated region between the polycytidylic acid tract and the probable initiation codon of the first translated gene, P16-L, have been sequenced. This region has several potential initiation codons, one of which appears to be a low-frequency altern...

  3. Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides

    Science.gov (United States)

    McMillen, Chelsea L.; Wright, Patience M.; Cassady, Carolyn J.

    2016-05-01

    Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

  4. Homology analyses of the protein sequences of fatty acid synthases from chicken liver, rat mammary gland, and yeast

    International Nuclear Information System (INIS)

    Homology analyses of the protein sequences of chicken liver and rat mammary gland fatty acid synthases were carried out. The amino acid sequences of the chicken and rat enzymes are 67% identical. If conservative substitutions are allowed, 78% of the amino acids are matched. A region of low homologies exists between the functional domains, in particular around amino acid residues 1059-1264 of the chicken enzyme. Homologies between the active sites of chicken and rat and of chicken and yeast enzymes have been analyzed by an alignment method. A high degree of homology exists between the active sites of the chicken and rat enzymes. However, the chicken and yeast enzymes show a lower degree of homology. The DADPH-binding dinucleotide folds of the β-ketoacyl reductase and the enoyl reductase sites were identified by comparison with a known consensus sequence for the DADP- and FAD-binding dinucleotide folds. The active sites of all of the enzymes are primarily in hydrophobic regions of the protein. This study suggests that the genes for the functional domains of fatty acid synthase were originally separated, and these genes were connected to each other by using different connecting nucleotide sequences in different species. An alternative explanation for the differences in rat and chicken is a common ancestry and mutations in the joining regions during evolution

  5. Homology analyses of the protein sequences of fatty acid synthases from chicken liver, rat mammary gland, and yeast

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Soo-Ik (Harvard Medical School, Boston, MA (USA)); Hammes, G.G. (Univ. of California, Santa Barbara (USA))

    1989-11-01

    Homology analyses of the protein sequences of chicken liver and rat mammary gland fatty acid synthases were carried out. The amino acid sequences of the chicken and rat enzymes are 67% identical. If conservative substitutions are allowed, 78% of the amino acids are matched. A region of low homologies exists between the functional domains, in particular around amino acid residues 1059-1264 of the chicken enzyme. Homologies between the active sites of chicken and rat and of chicken and yeast enzymes have been analyzed by an alignment method. A high degree of homology exists between the active sites of the chicken and rat enzymes. However, the chicken and yeast enzymes show a lower degree of homology. The DADPH-binding dinucleotide folds of the {beta}-ketoacyl reductase and the enoyl reductase sites were identified by comparison with a known consensus sequence for the DADP- and FAD-binding dinucleotide folds. The active sites of all of the enzymes are primarily in hydrophobic regions of the protein. This study suggests that the genes for the functional domains of fatty acid synthase were originally separated, and these genes were connected to each other by using different connecting nucleotide sequences in different species. An alternative explanation for the differences in rat and chicken is a common ancestry and mutations in the joining regions during evolution.

  6. The complete amino acid sequence of a mannose-binding lectin from "Kidachi Aloe" (Aloe arborescens Miller var. natalensis Berger).

    Science.gov (United States)

    Koike, T; Titani, K; Suzuki, M; Beppu, H; Kuzuya, H; Maruta, K; Shimpo, K; Fujita, K

    1995-09-01

    The complete amino acid sequence of a mannose-binding lectin purified from the leaf skin of "Kidachi Aloe" (Aloe arborescens Miller var. natalensis Berger) is presented. The 109-residue sequence of the subunit was determined by analysis of peptides of the intact or S-pyridylethylated protein generated by digestion with cyanogen bromide, BNPS-skatole, Achromobacter protease I, or trypsin. The subunit contains an intrachain disulfide bridge. The sequence is highly homologous to that of a mannose-binding lectin from snowdrop bulb. PMID:7669035

  7. The developmental transcriptome landscape of bovine skeletal muscle defined by Ribo-Zero ribonucleic acid sequencing.

    Science.gov (United States)

    Sun, X; Li, M; Sun, Y; Cai, H; Li, R; Wei, X; Lan, X; Huang, Y; Lei, C; Chen, H

    2015-12-01

    Ribonucleic acid sequencing (RNA-Seq) libraries are normally prepared with oligo(dT) selection of poly(A)+ mRNA, but it depends on intact total RNA samples. Recent studies have described Ribo-Zero technology, a novel method that can capture both poly(A)+ and poly(A)- transcripts from intact or fragmented RNA samples. We report here the first application of Ribo-Zero RNA-Seq for the analysis of the bovine embryonic, neonatal, and adult skeletal muscle whole transcriptome at an unprecedented depth. Overall, 19,893 genes were found to be expressed, with a high correlation of expression levels between the calf and the adult. Hundreds of genes were found to be highly expressed in the embryo and decreased at least 10-fold after birth, indicating their potential roles in embryonic muscle development. In addition, we present for the first time the analysis of global transcript isoform discovery in bovine skeletal muscle and identified 36,694 transcript isoforms. Transcriptomic data were also analyzed to unravel sequence variations; 185,036 putative SNP and 12,428 putative short insertions-deletions (InDel) were detected. Specifically, many stop-gain, stop-loss, and frameshift mutations were identified that probably change the relative protein production and sequentially affect the gene function. Notably, the numbers of stage-specific transcripts, alternative splicing events, SNP, and InDel were greater in the embryo than in the calf and the adult, suggesting that gene expression is most active in the embryo. The resulting view of the transcriptome at a single-base resolution greatly enhances the comprehensive transcript catalog and uncovers the global trends in gene expression during bovine skeletal muscle development. PMID:26641174

  8. Genome Sequence of a Candidate World Health Organization Reference Strain of Zika Virus for Nucleic Acid Testing

    Science.gov (United States)

    Trösemeier, Jan-Hendrik; Musso, Didier; Blümel, Johannes; Thézé, Julien; Pybus, Oliver G.

    2016-01-01

    We report here the sequence of a candidate reference strain of Zika virus (ZIKV) developed on behalf of the World Health Organization (WHO). The ZIKV reference strain is intended for use in nucleic acid amplification (NAT)-based assays for the detection and quantification of ZIKV RNA. PMID:27587826

  9. Genome Sequence of Corynebacterium glutamicum ATCC 14067, Which Provides Insight into Amino Acid Biosynthesis in Coryneform Bacteria

    OpenAIRE

    Lv, Yangyong; Liao, Juanjun; Wu, Zhanhong; Han, Shuangyan; Lin, Ying; Zheng, Suiping

    2012-01-01

    We report the genome sequence of Corynebacterium glutamicum ATCC 14067 (once named Brevibacterium flavum), which is useful for taxonomy research and further molecular breeding in amino acid production. Preliminary comparison with those of the reported coryneform strains revealed some notable differences that might be related to the difficulties in molecular manipulation.

  10. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk

    Science.gov (United States)

    Meneghel, Julie; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes. PMID:26941141

  11. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.

    Science.gov (United States)

    Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine; Fonseca, Fernanda

    2016-03-03

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes.

  12. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.

    Science.gov (United States)

    Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine; Fonseca, Fernanda

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes. PMID:26941141

  13. N-terminal amino acid sequence of Bacillus licheniformis alpha-amylase: comparison with Bacillus amyloliquefaciens and Bacillus subtilis Enzymes.

    OpenAIRE

    Kuhn, H; Fietzek, P P; Lampen, J. O.

    1982-01-01

    The thermostable, liquefying alpha-amylase from Bacillus licheniformis was immunologically cross-reactive with the thermolabile, liquefying alpha-amylase from Bacillus amyloliquefaciens. Their N-terminal amino acid sequences showed extensive homology with each other, but not with the saccharifying alpha-amylases of Bacillus subtilis.

  14. Genome Sequence of a Candidate World Health Organization Reference Strain of Zika Virus for Nucleic Acid Testing.

    Science.gov (United States)

    Trösemeier, Jan-Hendrik; Musso, Didier; Blümel, Johannes; Thézé, Julien; Pybus, Oliver G; Baylis, Sally A

    2016-01-01

    We report here the sequence of a candidate reference strain of Zika virus (ZIKV) developed on behalf of the World Health Organization (WHO). The ZIKV reference strain is intended for use in nucleic acid amplification (NAT)-based assays for the detection and quantification of ZIKV RNA. PMID:27587826

  15. Amino acid sequence of Coprinus macrorhizus peroxidase and cDNA sequence encoding Coprinus cinereus peroxidase. A new family of fungal peroxidases.

    Science.gov (United States)

    Baunsgaard, L; Dalbøge, H; Houen, G; Rasmussen, E M; Welinder, K G

    1993-04-01

    Sequence analysis and cDNA cloning of Coprinus peroxidase (CIP) were undertaken to expand the understanding of the relationships of structure, function and molecular genetics of the secretory heme peroxidases from fungi and plants. Amino acid sequencing of Coprinus macrorhizus peroxidase, and cDNA sequencing of Coprinus cinereus peroxidase showed that the mature proteins are identical in amino acid sequence, 343 residues in size and preceded by a 20-residue signal peptide. Their likely identity to peroxidase from Arthromyces ramosus is discussed. CIP has an 8-residue, glycine-rich N-terminal extension blocked with a pyroglutamate residue which is absent in other fungal peroxidases. The presence of pyroglutamate, formed by cyclization of glutamine, and the finding of a minor fraction of a variant form lacking the N-terminal residue, indicate that signal peptidase cleavage is followed by further enzymic processing. CIP is 40-45% identical in amino-acid sequence to 11 lignin peroxidases from four fungal species, and 42-43% identical to the two known Mn-peroxidases. Like these white-rot fungal peroxidases, CIP has an additional segment of approximately 40 residues at the C-terminus which is absent in plant peroxidases. Although CIP is much more similar to horseradish peroxidase (HRP C) in substrate specificity, specific activity and pH optimum than to white-rot fungal peroxidases, the sequences of CIP and HRP C showed only 18% identity. Hence, CIP qualifies as the first member of a new family of fungal peroxidases. The nine invariant residues present in all plant, fungal and bacterial heme peroxidases are also found in CIP. The present data support the hypothesis that only one chromosomal CIP gene exists. In contrast, a large number of secretory plant and fungal peroxidases are expressed from several peroxidase gene clusters. Analyses of three batches of CIP protein and of 49 CIP clones revealed the existence of only two highly similar alleles indicating less

  16. Colorimetric and visual read-out determination of cyanuric acid exploiting the interaction between melamine and silver nanoparticles

    International Nuclear Information System (INIS)

    We present two colorimetric procedures for the determination of cyanuric acid, using silver nanoparticle-based (AgNPs) probes. The first is making use of melamine-modified AgNPs which bind to cyanuric acid through hydrogen bonding to form a large conjugate network that enhances the aggregation of AgNPs to produce an absorbance peak at 640 nm and a green coloration. In the second assay, melamine is directly added to the sample in order to form a stable complex with cyanuric acid. AgNPs are then added, resulting in the formation of an absorbance peaking at 525 nm and a color change from green (blank sample) to purple or orange-red as a function of cyanuric acid concentration. Matrix effects, that originate from the interaction of alkaline earth metals with the charged surface of the AgNPs, are mitigated through a matrix-matched calibration. In this manner, spectral transitions can be selectively attributed to the concentration of cyanuric acid, which can be even visually quantified at low mg L−1 levels with minimum sample pre-treatment and without sophisticated instrumentation. (author)

  17. Extraction of Sequence Conservation Features for the Prioritization of Candidate Single Amino Acid Polymorphisms

    Directory of Open Access Journals (Sweden)

    Jiaxin Wu

    2011-03-01

    Full Text Available Although remarkable success has been achieved by genome-wide association (GWA studies over the past few years, genetic variants discovered in GWA studies can typically account for only a small fraction of heritability of most common diseases. As such, the identification of multiple rare variants that are associated with complex diseases has been receiving more and more attentions. However, most of the recently developed statistical approaches for detecting association of rare variants with diseases require the selection of functional variants before the successive analysis, making an effective bioinformatics method for filtering out non-relevant rare variants indispensible. In this paper, we focus on a specific type of genetic variants called single amino acid polymorphisms (SAAPs. We propose to prioritize candidate SAAPs for a specific disease according to their association scores that are calculated using a guilt-by-association model with a set of features derived from protein sequences. We validate the proposed approach in a systematic way and demonstrate that the proposed model is powerful in distinguishing disease-associated SAAPs for the specific disease of interest.

  18. A randomized trial comparing the diagnostic accuracy of visual inspection with acetic acid to Visual Inspection with Lugol's Iodine for cervical cancer screening in HIV-infected women.

    Directory of Open Access Journals (Sweden)

    Megan J Huchko

    Full Text Available Visual inspection with Acetic Acid (VIA and Visual Inspection with Lugol’s Iodine (VILI are increasingly recommended in various cervical cancer screening protocols in low-resource settings. Although VIA is more widely used, VILI has been advocated as an easier and more specific screening test. VILI has not been well-validated as a stand-alone screening test, compared to VIA or validated for use in HIV-infected women. We carried out a randomized clinical trial to compare the diagnostic accuracy of VIA and VILI among HIV-infected women. Women attending the Family AIDS Care and Education Services (FACES clinic in western Kenya were enrolled and randomized to undergo either VIA or VILI with colposcopy. Lesions suspicious for cervical intraepithelial neoplasia 2 or greater (CIN2+ were biopsied. Between October 2011 and June 2012, 654 were randomized to undergo VIA or VILI. The test positivity rates were 26.2% for VIA and 30.6% for VILI (p = 0.22. The rate of detection of CIN2+ was 7.7% in the VIA arm and 11.5% in the VILI arm (p = 0.10. There was no significant difference in the diagnostic performance of VIA and VILI for the detection of CIN2+. Sensitivity and specificity were 84.0% and 78.6%, respectively, for VIA and 84.2% and 76.4% for VILI. The positive and negative predictive values were 24.7% and 98.3% for VIA, and 31.7% and 97.4% for VILI. Among women with CD4+ count < 350, VILI had a significantly decreased specificity (66.2% compared to VIA in the same group (83.9%, p = 0.02 and compared to VILI performed among women with CD4+ count ≥ 350 (79.7%, p = 0.02. VIA and VILI had similar diagnostic accuracy and rates of CIN2+ detection among HIV-infected women.

  19. A randomized trial comparing the diagnostic accuracy of visual inspection with acetic acid to Visual Inspection with Lugol's Iodine for cervical cancer screening in HIV-infected women.

    Science.gov (United States)

    Huchko, Megan J; Sneden, Jennifer; Zakaras, Jennifer M; Smith-McCune, Karen; Sawaya, George; Maloba, May; Bukusi, Elizabeth Ann; Cohen, Craig R

    2015-01-01

    Visual inspection with Acetic Acid (VIA) and Visual Inspection with Lugol’s Iodine (VILI) are increasingly recommended in various cervical cancer screening protocols in low-resource settings. Although VIA is more widely used, VILI has been advocated as an easier and more specific screening test. VILI has not been well-validated as a stand-alone screening test, compared to VIA or validated for use in HIV-infected women. We carried out a randomized clinical trial to compare the diagnostic accuracy of VIA and VILI among HIV-infected women. Women attending the Family AIDS Care and Education Services (FACES) clinic in western Kenya were enrolled and randomized to undergo either VIA or VILI with colposcopy. Lesions suspicious for cervical intraepithelial neoplasia 2 or greater (CIN2+) were biopsied. Between October 2011 and June 2012, 654 were randomized to undergo VIA or VILI. The test positivity rates were 26.2% for VIA and 30.6% for VILI (p = 0.22). The rate of detection of CIN2+ was 7.7% in the VIA arm and 11.5% in the VILI arm (p = 0.10). There was no significant difference in the diagnostic performance of VIA and VILI for the detection of CIN2+. Sensitivity and specificity were 84.0% and 78.6%, respectively, for VIA and 84.2% and 76.4% for VILI. The positive and negative predictive values were 24.7% and 98.3% for VIA, and 31.7% and 97.4% for VILI. Among women with CD4+ count HIV-infected women.

  20. Decreased load on general motor preparation and visual-working memory while preparing familiar as compared to unfamiliar movement sequences

    NARCIS (Netherlands)

    Kleine, de Elian; Lubbe, van der Rob

    2011-01-01

    Learning movement sequences is thought to develop from an initial controlled attentive phase to a more automatic inattentive phase. Furthermore, execution of sequences becomes faster with practice, which may result from changes at a general motor processing level rather than at an effector specific

  1. Evolution of vertebrate IgM: complete amino acid sequence of the constant region of Ambystoma mexicanum mu chain deduced from cDNA sequence.

    Science.gov (United States)

    Fellah, J S; Wiles, M V; Charlemagne, J; Schwager, J

    1992-10-01

    cDNA clones coding for the constant region of the Mexican axolotl (Ambystoma mexicanum) mu heavy immunoglobulin chain were selected from total spleen RNA, using a cDNA polymerase chain reaction technique. The specific 5'-end primer was an oligonucleotide homologous to the JH segment of Xenopus laevis mu chain. One of the clones, JHA/3, corresponded to the complete constant region of the axolotl mu chain, consisting of a 1362-nucleotide sequence coding for a polypeptide of 454 amino acids followed in 3' direction by a 179-nucleotide untranslated region and a polyA+ tail. The axolotl C mu is divided into four typical domains (C mu 1-C mu 4) and can be aligned with the Xenopus C mu with an overall identity of 56% at the nucleotide level. Percent identities were particularly high between C mu 1 (59%) and C mu 4 (71%). The C-terminal 20-amino acid segment which constitutes the secretory part of the mu chain is strongly homologous to the equivalent sequences of chondrichthyans and of other tetrapods, including a conserved N-linked oligosaccharide, the penultimate cysteine and the C-terminal lysine. The four C mu domains of 13 vertebrate species ranging from chondrichthyans to mammals were aligned and compared at the amino acid level. The significant number of mu-specific residues which are conserved into each of the four C mu domains argues for a continuous line of evolution of the vertebrate mu chain. This notion was confirmed by the ability to reconstitute a consistent vertebrate evolution tree based on the phylogenic parsimony analysis of the C mu 4 sequences. PMID:1382992

  2. 基于视觉感受的景观空间序列组织%Landscape Space Sequence Organization Based on Visual Sense

    Institute of Scientific and Technical Information of China (English)

    梁晓宇; 吕建伟

    2014-01-01

    With the continuous improvement of people’s livi-ng standard, the landscape space sequence organization probl-em has become the overal problem of city design. This paper takes the landscape space sequence organization as the resear-ch object, and gives a brief description of landscape space seq-uence, analyzes landscape space sequence organization based on visual sense, and finally puts forward the strategy of land-scape space sequence plot.%随着人们生活水平的不断提高,景观空间序列组织问题已经成为城市设计的整体性问题。本文以景观空间序列组织作为研究对象,对景观空间序列进行简述,分析基于视觉感受的景观空间序列组织,最后提出景观空间序列的情节策略。

  3. Imagery May Arise from Associations Formed through Sensory Experience: A Network of Spiking Neurons Controlling a Robot Learns Visual Sequences in Order to Perform a Mental Rotation Task

    Science.gov (United States)

    McKinstry, Jeffrey L.; Fleischer, Jason G.; Chen, Yanqing; Gall, W. Einar; Edelman, Gerald M.

    2016-01-01

    Mental imagery occurs “when a representation of the type created during the initial phases of perception is present but the stimulus is not actually being perceived.” How does the capability to perform mental imagery arise? Extending the idea that imagery arises from learned associations, we propose that mental rotation, a specific form of imagery, could arise through the mechanism of sequence learning–that is, by learning to regenerate the sequence of mental images perceived while passively observing a rotating object. To demonstrate the feasibility of this proposal, we constructed a simulated nervous system and embedded it within a behaving humanoid robot. By observing a rotating object, the system learns the sequence of neural activity patterns generated by the visual system in response to the object. After learning, it can internally regenerate a similar sequence of neural activations upon briefly viewing the static object. This system learns to perform a mental rotation task in which the subject must determine whether two objects are identical despite differences in orientation. As with human subjects, the time taken to respond is proportional to the angular difference between the two stimuli. Moreover, as reported in humans, the system fills in intermediate angles during the task, and this putative mental rotation activates the same pathways that are activated when the system views physical rotation. This work supports the proposal that mental rotation arises through sequence learning and the idea that mental imagery aids perception through learned associations, and suggests testable predictions for biological experiments. PMID:27653977

  4. EST sequences and their annotation (amino acid sequence and results of homology search) - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available and VS) derived from five developmental stages. Clone ID ID of cDNA clone Atlas ID ID of Atlas database ( ht...tp://dictycdb.biol.tsukuba.ac.jp/~tools/bin/ISH/index.html ) and link to Atlas database NBRP ID ID of cDNA c...ir annotations (amino acid sequence, homology search results (with target DBs: dicty EST-DB, DNA-DB and prot...ein-DB)). Links to the Atlas database ( http://dictycdb.biol.tsukuba.ac.jp/~tools/bin/ISH/index.html ), whic

  5. Gene structure and amino acid sequence of Latimeria chalumnae (coelacanth) myelin DM20: phylogenetic relation of the fish.

    Science.gov (United States)

    Tohyama, Y; Kasama-Yoshida, H; Sakuma, M; Kobayashi, Y; Cao, Y; Hasegawa, M; Kojima, H; Tamai, Y; Tanokura, M; Kurihara, T

    1999-07-01

    The structure of Latimeria chalumnae (coelacanth) proteolipid protein/DM20 gene excluding exon 1 was determined, and the amino acid sequence of Latimeria DM20 corresponding to exons 2-7 was deduced. The nucleotide sequence of exon 3 suggests that only DM20 isoform is expressed in Latimeria. The structure of proteolipid protein/DM20 gene is well preserved among human, dog, mouse, and Latimeria. Southern blot analysis indicates that Latimeria DM20 gene is a single-copy gene. When the amino acid sequences of DM20 were compared among various species, Latimeria was more similar to tetrapods than other fishes including lungfish, confirming the previous finding by immunoreactivity (Waehneldt and Malotka 1989 J. Neurochem. 52:1941-1943). However, when phylogenetic trees were constructed from the DM20 sequences, lungfish was clearly the closest to tetrapods. Latimeria was situated outside of lungfish by the maximum likelihood method. The apparent similarity of Latimeria DM20 to tetrapod proteolipid protein/DM20 is explained by the slow amino acid substitution rate of Latimeria DM20.

  6. Sparse Representations-Based Super-Resolution of Key-Frames Extracted from Frames-Sequences Generated by a Visual Sensor Network

    Directory of Open Access Journals (Sweden)

    Muhammad Sajjad

    2014-02-01

    Full Text Available Visual sensor networks (VSNs usually generate a low-resolution (LR frame-sequence due to energy and processing constraints. These LR-frames are not very appropriate for use in certain surveillance applications. It is very important to enhance the resolution of the captured LR-frames using resolution enhancement schemes. In this paper, an effective framework for a super-resolution (SR scheme is proposed that enhances the resolution of LR key-frames extracted from frame-sequences captured by visual-sensors. In a VSN, a visual processing hub (VPH collects a huge amount of visual data from camera sensors. In the proposed framework, at the VPH, key-frames are extracted using our recent key-frame extraction technique and are streamed to the base station (BS after compression. A novel effective SR scheme is applied at BS to produce a high-resolution (HR output from the received key-frames. The proposed SR scheme uses optimized orthogonal matching pursuit (OOMP for sparse-representation recovery in SR. OOMP does better in terms of detecting true sparsity than orthogonal matching pursuit (OMP. This property of the OOMP helps produce a HR image which is closer to the original image. The K-SVD dictionary learning procedure is incorporated for dictionary learning. Batch-OMP improves the dictionary learning process by removing the limitation in handling a large set of observed signals. Experimental results validate the effectiveness of the proposed scheme and show its superiority over other state-of-the-art schemes.

  7. Sparse representations-based super-resolution of key-frames extracted from frames-sequences generated by a visual sensor network.

    Science.gov (United States)

    Sajjad, Muhammad; Mehmood, Irfan; Baik, Sung Wook

    2014-02-21

    Visual sensor networks (VSNs) usually generate a low-resolution (LR) frame-sequence due to energy and processing constraints. These LR-frames are not very appropriate for use in certain surveillance applications. It is very important to enhance the resolution of the captured LR-frames using resolution enhancement schemes. In this paper, an effective framework for a super-resolution (SR) scheme is proposed that enhances the resolution of LR key-frames extracted from frame-sequences captured by visual-sensors. In a VSN, a visual processing hub (VPH) collects a huge amount of visual data from camera sensors. In the proposed framework, at the VPH, key-frames are extracted using our recent key-frame extraction technique and are streamed to the base station (BS) after compression. A novel effective SR scheme is applied at BS to produce a high-resolution (HR) output from the received key-frames. The proposed SR scheme uses optimized orthogonal matching pursuit (OOMP) for sparse-representation recovery in SR. OOMP does better in terms of detecting true sparsity than orthogonal matching pursuit (OMP). This property of the OOMP helps produce a HR image which is closer to the original image. The K-SVD dictionary learning procedure is incorporated for dictionary learning. Batch-OMP improves the dictionary learning process by removing the limitation in handling a large set of observed signals. Experimental results validate the effectiveness of the proposed scheme and show its superiority over other state-of-the-art schemes.

  8. Convergent evolution of the red- and green-like visual pigment genes in fish, Astyanax fasciatus, and human

    International Nuclear Information System (INIS)

    The authors have isolated and sequenced genes from the blind cave fish, Astyanax fasciatus, that are homologous to the human red and green visual pigment genes. The data strongly suggest that, like human, these fish have one red-like visual pigment gene and multiple green-like visual pigment genes. By comparing the DNA sequences of the human and fish visual pigment genes and knowing their phylogenetic relationship, one can infer the direction of amino acid substitutions in the red and green visual pigments. The results indicate that the red pigments in human and fish evolved from the green pigment independently by identical amino acid substitutions in only a few key positions

  9. Visually driven chaining of elementary swim patterns into a goal-directed motor sequence: a virtual reality study of zebrafish prey capture.

    Science.gov (United States)

    Trivedi, Chintan A; Bollmann, Johann H

    2013-01-01

    Prey capture behavior critically depends on rapid processing of sensory input in order to track, approach, and catch the target. When using vision, the nervous system faces the problem of extracting relevant information from a continuous stream of input in order to detect and categorize visible objects as potential prey and to select appropriate motor patterns for approach. For prey capture, many vertebrates exhibit intermittent locomotion, in which discrete motor patterns are chained into a sequence, interrupted by short periods of rest. Here, using high-speed recordings of full-length prey capture sequences performed by freely swimming zebrafish larvae in the presence of a single paramecium, we provide a detailed kinematic analysis of first and subsequent swim bouts during prey capture. Using Fourier analysis, we show that individual swim bouts represent an elementary motor pattern. Changes in orientation are directed toward the target on a graded scale and are implemented by an asymmetric tail bend component superimposed on this basic motor pattern. To further investigate the role of visual feedback on the efficiency and speed of this complex behavior, we developed a closed-loop virtual reality setup in which minimally restrained larvae recapitulated interconnected swim patterns closely resembling those observed during prey capture in freely moving fish. Systematic variation of stimulus properties showed that prey capture is initiated within a narrow range of stimulus size and velocity. Furthermore, variations in the delay and location of swim triggered visual feedback showed that the reaction time of secondary and later swims is shorter for stimuli that appear within a narrow spatio-temporal window following a swim. This suggests that the larva may generate an expectation of stimulus position, which enables accelerated motor sequencing if the expectation is met by appropriate visual feedback.

  10. Complete genome sequence of Enterococcus mundtii QU 25, an efficient L-(+)-lactic acid-producing bacterium.

    Science.gov (United States)

    Shiwa, Yuh; Yanase, Hiroaki; Hirose, Yuu; Satomi, Shohei; Araya-Kojima, Tomoko; Watanabe, Satoru; Zendo, Takeshi; Chibazakura, Taku; Shimizu-Kadota, Mariko; Yoshikawa, Hirofumi; Sonomoto, Kenji

    2014-08-01

    Enterococcus mundtii QU 25, a non-dairy bacterial strain of ovine faecal origin, can ferment both cellobiose and xylose to produce l-lactic acid. The use of this strain is highly desirable for economical l-lactate production from renewable biomass substrates. Genome sequence determination is necessary for the genetic improvement of this strain. We report the complete genome sequence of strain QU 25, primarily determined using Pacific Biosciences sequencing technology. The E. mundtii QU 25 genome comprises a 3 022 186-bp single circular chromosome (GC content, 38.6%) and five circular plasmids: pQY182, pQY082, pQY039, pQY024, and pQY003. In all, 2900 protein-coding sequences, 63 tRNA genes, and 6 rRNA operons were predicted in the QU 25 chromosome. Plasmid pQY024 harbours genes for mundticin production. We found that strain QU 25 produces a bacteriocin, suggesting that mundticin-encoded genes on plasmid pQY024 were functional. For lactic acid fermentation, two gene clusters were identified-one involved in the initial metabolism of xylose and uptake of pentose and the second containing genes for the pentose phosphate pathway and uptake of related sugars. This is the first complete genome sequence of an E. mundtii strain. The data provide insights into lactate production in this bacterium and its evolution among enterococci.

  11. Gastropod arginine kinases from Cellana grata and Aplysia kurodai. Isolation and cDNA-derived amino acid sequences.

    Science.gov (United States)

    Suzuki, T; Inoue, N; Higashi, T; Mizobuchi, R; Sugimura, N; Yokouchi, K; Furukohri, T

    2000-12-01

    Arginine kinase (AK) was isolated from the radular muscle of the gastropod molluscs Cellana grata (subclass Prosobranchia) and Aplysia kurodai (subclass Opisthobranchia), respectively, by ammonium sulfate fractionation, Sephadex G-75 gel filtration and DEAE-ion exchange chromatography. The denatured relative molecular mass values were estimated to be 40 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The isolated enzyme from Aplysia gave a Km value of 0.6 mM for arginine and a Vmax value of 13 micromole Pi min(-1) mg protein(-1) for the forward reaction. These values are comparable to other molluscan AKs. The cDNAs encoding Cellana and Aplysia AKs were amplified by polymerase chain reaction, and the nucleotide sequences of 1,608 and 1,239 bp, respectively, were determined. The open reading frame for Cellana AK is 1044 nucleotides in length and encodes a protein with 347 amino acid residues, and that for A. kurodai is 1077 nucleotides and 354 residues. The cDNA-derived amino acid sequences were validated by chemical sequencing of internal lysyl endopeptidase peptides. The amino acid sequences of Cellana and Aplysia AKs showed the highest percent identity (66-73%) with those of the abalone Nordotis and turbanshell Battilus belonging to the same class Gastropoda. These AK sequences still have a strong homology (63-71%) with that of the chiton Liolophura (class Polyplacophora), which is believed to be one of the most primitive molluscs. On the other hand, these AK sequences are less homologous (55-57%) with that of the clam Pseudocardium (class Bivalvia), suggesting that the biological position of the class Polyplacophora should be reconsidered. PMID:11281267

  12. Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

    Directory of Open Access Journals (Sweden)

    Yan Koon-Kiu

    2007-11-01

    Full Text Available Abstract Background The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic parameters of these three basic processes is contained in the proteome-wide distribution of sequence identities of pairs of paralogous proteins. Results We introduce a simple mathematical framework based on a stochastic birth-and-death model that allows one to extract some of this information and apply it to the set of all pairs of paralogous proteins in H. pylori, E. coli, S. cerevisiae, C. elegans, D. melanogaster, and H. sapiens. It was found that the histogram of sequence identities p generated by an all-to-all alignment of all protein sequences encoded in a genome is well fitted with a power-law form ~ p-γ with the value of the exponent γ around 4 for the majority of organisms used in this study. This implies that the intra-protein variability of substitution rates is best described by the Gamma-distribution with the exponent α ≈ 0.33. Different features of the shape of such histograms allow us to quantify the ratio between the genome-wide average deletion/duplication rates and the amino-acid substitution rate. Conclusion We separately measure the short-term ("raw" duplication and deletion rates rdup∗ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGaemOCai3aa0baaSqaaiabbsgaKjabbwha1jabbchaWbqaaiabgEHiQaaaaaa@3283@, rdel∗ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGaemOCai3aa0baaSqaaiabbsga

  13. JRC GMO-Amplicons, a collection of nucleic acid sequences related to genetically modified organisms

    OpenAIRE

    PETRILLO MAURO; ANGERS ALEXANDRE; HENRIKSSON PETER; Bonfini, Laura; PATAK DENNSTEDT Alexandre; KREYSA JOACHIM

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico...

  14. Identification of novel rice low phytic acid mutations via TILLING by sequencing

    Science.gov (United States)

    Phytic acid (myo-inositol-1,2,3,4,5,6-hexakisphosphate or InsP6) accounts for 75-85% of the total phosphorus in seeds. Low phytic acid (lpa) mutants exhibit decreases in seed InsP6 with corresponding increases in inorganic P which, unlike phytic acid P, is readily utilized by humans and monogastric ...

  15. Purification, characterization, and amino acid sequencing of a. delta. /sup 5/-3-oxosteroid isomerase from Pseudomonas putida biotype B

    Energy Technology Data Exchange (ETDEWEB)

    Linden, K.G.

    1986-01-01

    Studies were performed on the ..delta../sup 5/-3-oxosteroid isomerase from Pseudomonas putida biotype B. The studies have involved three broad areas: improvement in the purification of the enzyme, further characterization of the purified enzyme, and completion of the amino acid sequence of the enzyme. For the purification of the enzyme, techniques for removing the isomerase from whole cells were studied, the effects of ionic strength on the binding of the isomerase to steroidal affinity resins was explored, and a new affinity resin was developed. Absorption spectra and the proton NMR spectra of the isomerase were obtained. Amino acid sequencing of the oxosteroid isomerase indicates that the enzyme is a dimeric protein consisting of two identical subunits each consisting of a polypeptide chain of 131 residues and a M/sub r/ = 14,536.

  16. Real-Time Nucleic Acid Sequence-Based Amplification Using Molecular Beacons for Detection of Enterovirus RNA in Clinical Specimens

    OpenAIRE

    Landry, Marie L.; Garner, Robin; Ferguson, David

    2005-01-01

    Real-time nucleic acid sequence-based amplification (NASBA) using molecular beacon technology (NASBA-beacon) was compared to standard NASBA with postamplification hybridization using electrochemiluminescently labeled probes (NASBA-ECL) for detection of enteroviruses (EV) in 133 cerebrospinal fluid and 27 stool samples. NASBA-ECL and NASBA-beacon were similar in sensitivity, detecting 55 (100%) and 52 (94.5%) EV-positive samples, respectively. There were no false positives. Both NASBA assays w...

  17. Using Triple Helix Forming Peptide Nucleic Acids for Sequence-selective Recognition of Double-stranded RNA

    OpenAIRE

    Hnedzko, Dziyana; Cheruiyot, Samwel K.; Rozners, Eriks

    2014-01-01

    Non-coding RNAs play important roles in regulation of gene expression. Specific recognition and inhibition of these biologically important RNAs that form complex double-helical structures will be highly useful for fundamental studies in biology and practical applications in medicine. This protocol describes a strategy developed in our laboratory for sequence-selective recognition of double-stranded RNA (dsRNA) using triple helix forming peptide nucleic acids (PNAs) that bind in the major grov...

  18. Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids

    OpenAIRE

    Ibarra-Laclette, Enrique; Méndez-Bravo, Alfonso; Pérez-Torres, Claudia Anahí; Albert, Victor A; Mockaitis, Keithanne; Kilaru, Aruna; López-Gómez, Rodolfo; Cervantes-Luevano, Jacob Israel; Herrera-Estrella, Luis

    2015-01-01

    Background Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and developmental processes in avocado is limited due to the lack of transcriptome and genomic information. Results The transcriptomes of seeds, roots, stems, leaves, aerial buds and flowers were determined using different sequencing platforms. Additionally, the transcriptomes of thre...

  19. COV2HTML: a visualization and analysis tool of bacterial next generation sequencing (NGS) data for postgenomics life scientists.

    Science.gov (United States)

    Monot, Marc; Orgeur, Mickael; Camiade, Emilie; Brehier, Clément; Dupuy, Bruno

    2014-03-01

    COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/ . This website is free and open to users without any login requirement.

  20. Fusion protein predicted amino acid sequence of the first US avian pneumovirus isolate and lack of heterogeneity among other US isolates.

    Science.gov (United States)

    Seal, B S; Sellers, H S; Meinersmann, R J

    2000-02-01

    Avian pneumovirus (APV) was first isolated from turkeys in the west-central US following emergence of turkey rhinotracheitis (TRT) during 1996. Subsequently, several APV isolates were obtained from the north-central US. Matrix (M) and fusion (F) protein genes of these isolates were examined for sequence heterogeneity and compared with European APV subtypes A and B. Among US isolates the M gene shared greater than 98% nucleotide sequence identity with only one nonsynonymous change occurring in a single US isolate. Although the F gene among US APV isolates shared 98% nucleotide sequence identity, nine conserved substitutions were detected in the predicted amino acid sequence. The predicted amino acid sequence of the US APV isolate's F protein had 72% sequence identity to the F protein of APV subtype A and 71% sequence identity to the F protein of APV subtype B. This compares with 83% sequence identity between the APV subtype A and B predicted amino acid sequences of the F protein. The US isolates were phylogenetically distinguishable from their European counterparts based on F gene nucleotide or predicted amino acid sequences. Lack of sequence heterogeneity among US APV subtypes indicates these viruses have maintained a relatively stable population since the first outbreak of TRT. Phylogenetic analysis of the F protein among APV isolates supports classification of US isolates as a new APV subtype C.

  1. cDNA-derived amino-acid sequence of a land turtle (Geochelone carbonaria) beta-chain hemoglobin.

    Science.gov (United States)

    Bordin, S; Meza, A N; Saad, S T; Ogo, S H; Costa, F F

    1997-06-01

    The cDNA sequence encoding the turtle Geochelone carbonaria beta-chain was determinated. The isolation of hemoglobin mRNA was based on degenerate primers' PCR in combination with 5'- and 3'-RACE protocol. The full length cDNA is 615 bp with the ATG start codon at position 53 and TGA stop codon at position 495; The AATAAA polyadenylation signal is found at position 599. The deduced polypeptyde contains 146 amino-acid residues. The predicted amino acid sequence shares 83% identity with the beta-globin of a related specie, the aquatic turtle C. p. belli. Otherwise, identity is higher when compared with chicken beta-Hb (80%) than with other reptilian orders (Squamata, 69%, and Crocodilia, 61%). Compared with human HbA, there is 67% identity, and at least three amino acid substitutions could be of some functional significance (Glu43 beta-->Ser, His116 beta-->Thr and His143 beta-->Leu). To our knowledge this represents the first cDNA sequence of a reptile globin gene described. PMID:9238523

  2. Amino acid sequence of the serine-repeat antigen (SERA) of Plasmodium falciparum determined from cloned cDNA.

    Science.gov (United States)

    Bzik, D J; Li, W B; Horii, T; Inselburg, J

    1988-09-01

    We report the isolation of cDNA clones for a Plasmodium falciparum gene that encodes the complete amino acid sequence of a previously identified exported blood stage antigen. The Mr of this antigen protein had been determined by sodium dodecylsulphate-polyacrylamide gel electrophoresis analysis, by different workers, to be 113,000, 126,000, and 140,000. We show, by cDNA nucleotide sequence analysis, that this antigen gene encodes a 989 amino acid protein (111 kDa) that contains a potential signal peptide, but not a membrane anchor domain. In the FCR3 strain the serine content of the protein was 11%, of which 57% of the serine residues were localized within a 201 amino acid sequence that included 35 consecutive serine residues. The protein also contained three possible N-linked glycosylation sites and numerous possible O-linked glycosylation sites. The mRNA was abundant during late trophozoite-schizont parasite stages. We propose to identity this antigen, which had been called p126, by the acronym SERA, serine-repeat antigen, based on its complete structure. The usefulness of the cloned cDNA as a source of a possible malaria vaccine is considered in view of the previously demonstrated ability of the antigen to induce parasite-inhibitory antibodies and a protective immune response in Saimiri monkeys. PMID:2847041

  3. Amino acid sequence and glycosylation of functional unit RtH2-e from Rapana thomasiana (gastropod) hemocyanin.

    Science.gov (United States)

    Stoeva, Stanka; Idakieva, Krasimira; Betzel, Christian; Genov, Nicolay; Voelter, Wolfgang

    2002-03-15

    The complete amino acid sequence of Rapana thomasiana hemocyanin functional unit RtH2-e was determined by direct sequencing and matrix-assisted laser desorption ionization mass spectrometry of peptides obtained by cleavage with EndoLysC proteinase, chymotrypsin, and trypsin. The single-polypeptide chain of RtH2-e consists of 413 amino acid residues and contains two consensus sequences NXS/T (positions 11-19 and 127-129), potential sites for N-glycosylation. Monosaccharide analysis of RtH2-e revealed a carbohydrate content of about 1.1% and the presence of xylose, fucose, mannose, and N-acetylglucosamine, demonstrating that only N-linked carbohydrate chains of high-mannose type seem to be present. On basis of the monosaccharide composition and MALDI-MS analysis of native and PNGase-F-treated chymotryptic glycopeptide fragment of RtH2-e the oligosaccharide Man(5)GlcNAc(2), attached to Asn(127), is suggested. Multiple sequence alignments with other molluscan hemocyanin e functional units revealed an identity of 63% to the cephalopod Octopus dofleini and of 69% to the gastropod Haliotis tuberculata. The present results are discussed in view of the recently determined X-ray structure of the functional unit g of the O. dofleini hemocyanin. PMID:11888200

  4. Cloning, Sequence Analysis, and Expression in Escherichia coli of the Gene Encoding an α-Amino Acid Ester Hydrolase from Acetobacter turbidans

    NARCIS (Netherlands)

    Polderman-Tijmes, Jolanda J.; Jekel, P; de Vries, Erik; van Merode, Annet; Floris, René; Laan, Jan-Metske van der; Sonke, Theo; Janssen, Dick B.

    2002-01-01

    The α-amino acid ester hydrolase from Acetobacter turbidans ATCC 9325 is capable of hydrolyzing and synthesizing β-lactam antibiotics, such as cephalexin and ampicillin. N-terminal amino acid sequencing of the purified α-amino acid ester hydrolase allowed cloning and genetic characterization of the

  5. Complete Genome Sequences of Escherichia coli O157:H7 Strains SRCC 1675 and 28RC, Which Vary in Acid Resistance

    Science.gov (United States)

    Baranzoni, Gian Marco; Reichenberger, Erin R.; Kim, Gwang-Hee; Breidt, Frederick; Kay, Kathryn; Oh, Deog-Hwan

    2016-01-01

    The level of acid resistance among Escherichia coli O157:H7 strains varies, and strains with higher resistance to acid may have a lower infectious dose. The complete genome sequences belonging to two strains of Escherichia coli O157:H7 with different levels of acid resistance are presented here. PMID:27469964

  6. Complete genome sequences of Escherichia coli O157:H7 strains SRCC 1675 and 28RC that vary in acid resistance

    Science.gov (United States)

    The level of acid resistance among Escherichia coli O157:H7 strains varies, and strains with higher resistance to acid may have a lower infectious dose. The complete genome sequences belonging to two strains of Escherichia coli O157:H7 with different levels of acid resistance are presented....

  7. Cloning, sequence analysis, and expression in Escherichia coli of the gene encoding an alpha-amino acid ester hydrolase from Acetobacter turbidans

    NARCIS (Netherlands)

    Polderman-Tijmes, JJ; Jekel, PA; de Vries, EJ; van Merode, Annet; Floris, R; van der Laan, JM; Sonke, T; Janssen, DB

    2002-01-01

    The alpha-amino acid ester hydrolase from Acetobacter turbidans ATCC 9325 is capable of hydrolyzing and synthesizing beta-lactam antibiotics, such as cephalexin and ampicillin. N-terminal amino acid sequencing of the purified alpha-amino acid ester hydrolase allowed cloning and genetic characterizat

  8. Diagnosing Cervical Dysplasia Using Visual Inspection of the Cervix with Acetic Acid in a Woman in Rural Haiti

    Directory of Open Access Journals (Sweden)

    Elizabeth Roger

    2014-11-01

    Full Text Available Cervical cancer remains a significant cause of morbidity and mortality for women in developing countries, despite the fact that inexpensive, simple and effective screening methods are available. Visual inspection of the cervix with acetic acid (VIA can be used as part of a “screen and treat” program to identify precancerous lesions for cryotherapy treatment. This case report details how the VIA screening test was incorporated into the care of a patient presenting to a maternal health clinic in Thomonde, Haiti which was staffed by doctors and medical students from Emory University School of Medicine in collaboration with Haiti Medishare. As demonstrated here, the VIA test requires minimal materials, can be efficiently incorporated into a physical exams, provides immediate results, and is easily demonstrated to and performed by local healthcare providers. The straightforward and sensitive VIA technique is an ideal cervical cancer screening method for resource poor areas.

  9. Visual test for melamine using silver nanoparticles modified with chromotropic acid

    International Nuclear Information System (INIS)

    A simple and low-cost assay for melamine is introduced that is making use of silver nanoparticles (AgNPs) functionalized with chromotropic acid (CTA). The surface of the AgNPs was capped with chromotropic acid which warrants the NPs to remain in stable and dispersed form. The presence of melamine induces the aggregation of the CTA-AgNPs due to the hydrogen bond interaction between CTA and melamine. This is accompanied by a color change from yellow to orange which can be observed with bare eyes. The method allows melamine to be quantified by absorptiometry with a linear response in the concentration range from 0.10 to 1.5 μM (R = 0.9996) and a detection limit of 36 nM which was much lower than the safe limits (20 μM in both the USA and EU, 8 μM for infant formula in China, 1.2 μM in the CAC review for melamine in liquid infant formula). The assay displays high selectivity to melamine over its structural analogs such as cyanuric acid, 2,4,6-trimethyl-1,3,5-triazine, and phloro glucinol owing to the fact that only melamine can act as the hydrogen donor to form hydrogen bonds with the sulfo groups of the CTA-capped AgNPs. The method was successfully applied to the determination of melamine in spiked liquid milk and the average recovery was 99 %. Most amino acids and a high content of calcium do not interfere in this assay. (author)

  10. Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids.

    Science.gov (United States)

    Kim, Ki-Hyun; Nielsen, Peter E; Glazer, Peter M

    2007-01-01

    Sequence-specific DNA-binding molecules such as triple helix-forming oligonucleotides (TFOs) provide a means for inducing site-specific mutagenesis and recombination at chromosomal sites in mammalian cells. However, the utility of TFOs is limited by the requirement for homopurine stretches in the target duplex DNA. Here, we report the use of pseudo-complementary peptide nucleic acids (pcPNAs) for intracellular gene targeting at mixed sequence sites. Due to steric hindrance, pcPNAs are unable to form pcPNA-pcPNA duplexes but can bind to complementary DNA sequences by Watson-Crick pairing via double duplex-invasion complex formation. We show that psoralen-conjugated pcPNAs can deliver site-specific photoadducts and mediate targeted gene modification within both episomal and chromosomal DNA in mammalian cells without detectable off-target effects. Most of the induced psoralen-pcPNA mutations were single-base substitutions and deletions at the predicted pcPNA-binding sites. The pcPNA-directed mutagenesis was found to be dependent on PNA concentration and UVA dose and required matched pairs of pcPNAs. Neither of the individual pcPNAs alone had any effect nor did complementary PNA pairs of the same sequence. These results identify pcPNAs as new tools for site-specific gene modification in mammalian cells without purine sequence restriction, thereby providing a general strategy for designing gene targeting molecules. PMID:17977869

  11. Phylogenetic analysis of evolutionary relationships of the planctomycete division of the domain bacteria based on amino acid sequences of elongation factor Tu.

    Science.gov (United States)

    Jenkins, C; Fuerst, J A

    2001-05-01

    Sequences from the tuf gene coding for the elongation factor EF-Tu were amplified and sequenced from the genomic DNA of Pirellula marina and Isosphaera pallida, two species of bacteria within the order Planctomycetales. A near-complete (1140-bp) sequence was obtained from Pi. marina and a partial (759-bp) sequence was obtained for I. pallida. Alignment of the deduced Pi. marina EF-Tu amino acid sequence against reference sequences demonstrated the presence of a unique 11-amino acid sequence motif not present in any other division of the domain Bacteria. Pi. marina shared the highest percentage amino acid sequence identity with I. pallida but showed only a low percentage identity with other members of the domain Bacteria. This is consistent with the concept of the planctomycetes as a unique division of the Bacteria. Neither primary sequence comparison of EF-Tu nor phylogenetic analysis supports any close relationship between planctomycetes and the chlamydiae, which has previously been postulated on the basis of 16S rRNA. Phylogenetic analysis of aligned EF-Tu amino acid sequences performed using distance, maximum-parsimony, and maximum-likelihood approaches yielded contradictory results with respect to the position of planctomycetes relative to other bacteria. It is hypothesized that long-branch attraction effects due to unequal evolutionary rates and mutational saturation effects may account for some of the contradictions. PMID:11443344

  12. Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage

    Directory of Open Access Journals (Sweden)

    Maugel Timothy K

    2007-07-01

    Full Text Available Abstract Background Bioinformatic analysis of the genome sequence of Neisseria gonorrhoeae revealed the presence of nine probable prophage islands. The distribution, conservation and function of many of these sequences, and their ability to produce bacteriophage particles are unknown. Results Our analysis of the genomic sequence of FA1090 identified five genomic regions (NgoΦ1 – 5 that are related to dsDNA lysogenic phage. The genetic content of the dsDNA prophage sequences were examined in detail and found to contain blocks of genes encoding for proteins homologous to proteins responsible for phage DNA replication, structural proteins and proteins responsible for phage assembly. The DNA sequences from NgoΦ1, NgoΦ2 and NgoΦ3 contain some significant regions of identity. A unique region of NgoΦ2 showed very high similarity with the Pseudomonas aeruginosa generalized transducing phage F116. Comparative analysis at the nucleotide and protein levels suggests that the sequences of NgoΦ1 and NgoΦ2 encode functionally active phages, while NgoΦ3, NgoΦ4 and NgoΦ5 encode incomplete genomes. Expression of the NgoΦ1 and NgoΦ2 repressors in Escherichia coli inhibit the growth of E. coli and the propagation of phage λ. The NgoΦ2 repressor was able to inhibit transcription of N. gonorrhoeae genes and Haemophilus influenzae HP1 phage promoters. The holin gene of NgoΦ1 (identical to that encoded by NgoΦ2, when expressed in E. coli, could serve as substitute for the phage λ s gene. We were able to detect the presence of the DNA derived from NgoΦ1 in the cultures of N. gonorrhoeae. Electron microscopy analysis of culture supernatants revealed the presence of multiple forms of bacteriophage particles. Conclusion These data suggest that the genes similar to dsDNA lysogenic phage present in the gonococcus are generally conserved in this pathogen and that they are able to regulate the expression of other neisserial genes. Since phage particles were

  13. Purification and amino acid sequence of a bacteriocins produced by Lactobacillus salivarius K7 isolated from chicken intestine

    Directory of Open Access Journals (Sweden)

    Kenji Sonomoto

    2006-03-01

    Full Text Available A bacteriocin-producing strain, Lactobacillus K7, was isolated from a chicken intestine. The inhibitory activity was determined by spot-on-lawn technique. Identification of the strain was performed by morphological, biochemical (API 50 CH kit and molecular genetic (16S rDNA basis. Bacteriocin purification processes were carried out by amberlite adsorption, cation exchange and reverse-phase high perform- ance liquid chromatography. N-terminal amino acid sequences were performed by Edman degradation. Molecular mass was determined by electrospray-ionization (ESI mass spectrometry (MS. Lactobacillus K7 showed inhibitory activity against Lactobacillus sakei subsp. sakei JCM 1157T, Leuconostoc mesenteroides subsp. mesenteroides JCM 6124T and Bacillus coagulans JCM 2257T. This strain was identified as Lb. salivarius. The antimicrobial substance was destroyed by proteolytic enzymes, indicating its proteinaceous structure designated as a bacteriocin type. The purification of bacteriocin by amberlite adsorption, cation exchange, and reverse-phase chromatography resulted in only one single active peak, which was designated FK22. Molecular weight of this fraction was 4331.70 Da. By amino acid sequence, this peptide was homology to Abp 118 beta produced by Lb. salivarius UCC118. In addition, Lb. salivarius UCC118 produced 2-peptide bacteriocin, which was Abp 118 alpha and beta. Based on the partial amino acid sequences of Abp 118 beta, specific primers were designed from nucleotide sequences according to data from GenBank. The result showed that the deduced peptide was high homology to 2-peptide bacteriocin, Abp 118 alpha and beta.

  14. Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

    OpenAIRE

    Yan Koon-Kiu; Axelsen Jacob; Maslov Sergei

    2005-01-01

    Abstract Background The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic parameters of these three basic processes is contained in the proteome-wide distribution of sequence identities of pairs of paralogous proteins. Results We introduce a simple mathematical framework based on a stochastic birth-and-death model...

  15. The sequence diversity and expression among genes of the folic acid biosynthesis pathway in industrial Saccharomyces strains.

    Science.gov (United States)

    Goncerzewicz, Anna; Misiewicz, Anna

    2015-01-01

    Folic acid is an important vitamin in human nutrition and its deficiency in pregnant women's diets results in neural tube defects and other neurological damage to the fetus. Additionally, DNA synthesis, cell division and intestinal absorption are inhibited in case of adults. Since this discovery, governments and health organizations worldwide have made recommendations concerning folic acid supplementation of food for women planning to become pregnant. In many countries this has led to the introduction of fortifications, where synthetic folic acid is added to flour. It is known that Saccharomyces strains (brewing and bakers' yeast) are one of the main producers of folic acid and they can be used as a natural source of this vitamin. Proper selection of the most efficient strains may enhance the folate content in bread, fermented vegetables, dairy products and beer by 100% and may be used in the food industry. The objective of this study was to select the optimal producing yeast strain by determining the differences in nucleotide sequences in the FOL2, FOL3 and DFR1 genes of folic acid biosynthesis pathway. The Multitemperature Single Strand Conformation Polymorphism (MSSCP) method and further nucleotide sequencing for selected strains were applied to indicate SNPs in selected gene fragments. The RT qPCR technique was also applied to examine relative expression of the FOL3 gene. Furthermore, this is the first time ever that industrial yeast strains were analysed regarding genes of the folic acid biosynthesis pathway. It was observed that a correlation exists between the folic acid amount produced by industrial yeast strains and changes in the nucleotide sequence of adequate genes. The most significant changes occur in the DFR1 gene, mostly in the first part, which causes major protein structure modifications in KKP 232, KKP 222 and KKP 277 strains. Our study shows that the large amount of SNP contributes to impairment of the selected enzymes and S. cerevisiae and S

  16. The sequence diversity and expression among genes of the folic acid biosynthesis pathway in industrial Saccharomyces strains.

    Science.gov (United States)

    Goncerzewicz, Anna; Misiewicz, Anna

    2015-01-01

    Folic acid is an important vitamin in human nutrition and its deficiency in pregnant women's diets results in neural tube defects and other neurological damage to the fetus. Additionally, DNA synthesis, cell division and intestinal absorption are inhibited in case of adults. Since this discovery, governments and health organizations worldwide have made recommendations concerning folic acid supplementation of food for women planning to become pregnant. In many countries this has led to the introduction of fortifications, where synthetic folic acid is added to flour. It is known that Saccharomyces strains (brewing and bakers' yeast) are one of the main producers of folic acid and they can be used as a natural source of this vitamin. Proper selection of the most efficient strains may enhance the folate content in bread, fermented vegetables, dairy products and beer by 100% and may be used in the food industry. The objective of this study was to select the optimal producing yeast strain by determining the differences in nucleotide sequences in the FOL2, FOL3 and DFR1 genes of folic acid biosynthesis pathway. The Multitemperature Single Strand Conformation Polymorphism (MSSCP) method and further nucleotide sequencing for selected strains were applied to indicate SNPs in selected gene fragments. The RT qPCR technique was also applied to examine relative expression of the FOL3 gene. Furthermore, this is the first time ever that industrial yeast strains were analysed regarding genes of the folic acid biosynthesis pathway. It was observed that a correlation exists between the folic acid amount produced by industrial yeast strains and changes in the nucleotide sequence of adequate genes. The most significant changes occur in the DFR1 gene, mostly in the first part, which causes major protein structure modifications in KKP 232, KKP 222 and KKP 277 strains. Our study shows that the large amount of SNP contributes to impairment of the selected enzymes and S. cerevisiae and S

  17. "De-novo" amino acid sequence elucidation of protein G'e by combined "Top-Down" and "Bottom-Up" mass spectrometry

    Science.gov (United States)

    Yefremova, Yelena; Al-Majdoub, Mahmoud; Opuni, Kwabena F. M.; Koy, Cornelia; Cui, Weidong; Yan, Yuetian; Gross, Michael L.; Glocker, Michael O.

    2015-03-01

    Mass spectrometric de-novo sequencing was applied to review the amino acid sequence of a commercially available recombinant protein Ǵ with great scientific and economic importance. Substantial deviations to the published amino acid sequence (Uniprot Q54181) were found by the presence of 46 additional amino acids at the N-terminus, including a so-called "His-tag" as well as an N-terminal partial α- N-gluconoylation and α- N-phosphogluconoylation, respectively. The unexpected amino acid sequence of the commercial protein G' comprised 241 amino acids and resulted in a molecular mass of 25,998.9 ± 0.2 Da for the unmodified protein. Due to the higher mass that is caused by its extended amino acid sequence compared with the original protein G' (185 amino acids), we named this protein "protein G'e." By means of mass spectrometric peptide mapping, the suggested amino acid sequence, as well as the N-terminal partial α- N-gluconoylations, was confirmed with 100% sequence coverage. After the protein G'e sequence was determined, we were able to determine the expression vector pET-28b from Novagen with the Xho I restriction enzyme cleavage site as the best option that was used for cloning and expressing the recombinant protein G'e in E. coli. A dissociation constant ( K d ) value of 9.4 nM for protein G'e was determined thermophoretically, showing that the N-terminal flanking sequence extension did not cause significant changes in the binding affinity to immunoglobulins.

  18. JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

    Science.gov (United States)

    Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/.

  19. JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

    Science.gov (United States)

    Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/. PMID:26424080

  20. Low molecular weight human pulmonary surfactant protein (SP5): isolation, characterization, and cDNA and amino acid sequences

    International Nuclear Information System (INIS)

    Pulmonary surfactant is a lipid-protein complex that promotes alveolar stability by lowering the surface tension at the air-fluid interface in the peripheral air spaces. A group of hydrophobic surfactant-associated proteins has been shown to be essential for rapid surface film formation by surfactant phospholipids. The authors have purified a hydrophobic surfactant protein of ≅ 5kDa that they term SP5 from bronchopulmonary lavage fluid from a patient with alveolar proteinosis and shown that it promotes rapid surface film formation by simple mixtures of phospholipids. They have derived the full amino acid sequence of human SP5 from the nucleotide sequence of cDNAs identified with oligonucleotide probes based on the NH2-terminal sequence of SP5. SP5 isolated from surfactant is a fragment of a much larger precursor protein (21 kDa). The precursor contains an extremely hydrophobic region of 34 amino acids that comprises most the mature SP5. This hydrophobicity explains the unusual solubility characteristics of SP5 and the fact that it is lipid-associated when isolated from lung

  1. Amino acid sequence of phospholipase A/sub 2/-. cap alpha. from the venom of Crotalus adamanteus

    Energy Technology Data Exchange (ETDEWEB)

    Heinrikson, R.L.; Krueger, E.T.; Keim, P.S.

    1977-07-25

    The complete amino acid sequence of Crotalus adamanteus venom phospholipase A/sub 2/-..cap alpha.. has been determined by analysis of the five tryptic peptides from the citraconylated, reduced, and S-(/sup 14/C)carboxamidomethylated enzyme. Earlier studies provided the information necessary to align the tryptic fragments so that secondary cleavage procedures to establish overlaps were unnecessary. The subunit in the phospholipase A/sub 2/-..cap alpha.. dimer is a single polypeptide chain containing 122 amino acids and seven disulfide bonds. The histidine residue implicated in the active site of mammalian phospholipases is at position 47 in the C. adamanteus enzyme and is located in a domain of the molecule which is highly homologous in sequence with corresponding regions of phospholipases from a variety of venom and pancreatic sources. Comparative sequence analysis has revealed insights with regard to the function and evolution of phospholipases A/sub 2/. Primary structural relationships observed among the snake venom enzymes parallel the phylogenetic classification of the venomous reptiles from which they were derived. It is proposed that phospholipases A/sub 2/ of this general type be divided into two groups depending upon the presence or absence of distinctive structural features elucidated in this study.

  2. Low molecular weight human pulmonary surfactant protein (SP5): isolation, characterization, and cDNA and amino acid sequences

    Energy Technology Data Exchange (ETDEWEB)

    Warr, R.G.; Hawgood, S.; Buckley, D.I.; Crisp, T.M.; Schilling, J.; Benson, B.J.; Ballard, P.L.; Clements, J.A.; White, R.T.

    1987-11-01

    Pulmonary surfactant is a lipid-protein complex that promotes alveolar stability by lowering the surface tension at the air-fluid interface in the peripheral air spaces. A group of hydrophobic surfactant-associated proteins has been shown to be essential for rapid surface film formation by surfactant phospholipids. The authors have purified a hydrophobic surfactant protein of approx. = 5kDa that they term SP5 from bronchopulmonary lavage fluid from a patient with alveolar proteinosis and shown that it promotes rapid surface film formation by simple mixtures of phospholipids. They have derived the full amino acid sequence of human SP5 from the nucleotide sequence of cDNAs identified with oligonucleotide probes based on the NH/sub 2/-terminal sequence of SP5. SP5 isolated from surfactant is a fragment of a much larger precursor protein (21 kDa). The precursor contains an extremely hydrophobic region of 34 amino acids that comprises most the mature SP5. This hydrophobicity explains the unusual solubility characteristics of SP5 and the fact that it is lipid-associated when isolated from lung.

  3. Amino acid sequence and posttranslational modifications of human factor VIIa from plasma and transfected baby hamster kidney cells

    International Nuclear Information System (INIS)

    Blood coagulation factor VII is a vitamin K dependent glycoprotein which in its activated form, factor VIIa, participates in the coagulation process by activating factor X and/or factor IX in the presence of Ca2+ and tissue factor. Three types of potential posttranslational modifications exist in the human factor VIIa molecule, namely, 10 γ-carboxylated, N-terminally located glutamic acid residues, 1 β-hydroxylated aspartic acid residue, and 2 N-glycosylated asparagine residues. In the present study, the amino acid sequence and posttranslational modifications of recombinant factor VIIa as purified from the culture medium of a transfected baby hamster kidney cell line have been compared to human plasma factor VIIa. By use of HPLC, amino acid analysis, peptide mapping, and automated Edman degradation, the protein backbone of recombinant factor VIIa was found to be identical with human factor VIIa. Asparagine residues 145 and 322 were found to be fully N-glycosylated in human plasma factor VIIa. In the recombinant factor VIIa, asparagine residue 322 was fully glycosylated whereas asparagine residue 145 was only partially (approximately 66%) glycosylated. Besides minor differences in the sialic acid and fucose contents, the overall carbohydrate compositions were nearly identical in recombinant factor VIIa and human plasma factor VIIa. These results show that factor VIIa as produced in the transfected baby hamster kidney cells is very similar to human plasma factor VIIa and that this cell line thus might represent an alternative source for human factor VIIa

  4. Characterization of DNA-binding sequences for CcaR in the cephamycin-clavulanic acid supercluster of Streptomyces clavuligerus.

    Science.gov (United States)

    Santamarta, I; López-García, M T; Kurt, A; Nárdiz, N; Alvarez-Álvarez, R; Pérez-Redondo, R; Martín, J F; Liras, P

    2011-08-01

    RT-PCR analysis of the genes in the clavulanic acid cluster revealed three transcriptional polycistronic units that comprised the ceaS2-bls2-pah2-cas2, cyp-fd-orf12-orf13 and oppA2-orf16 genes, whereas oat2, car, oppA1, claR, orf14, gcaS and pbpA were expressed as monocistronic transcripts. Quantitative RT-PCR of Streptomyces clavuligerus ATCC 27064 and the mutant S. clavuligerus ccaR::aph showed that, in the mutant, there was a 1000- to 10,000-fold lower transcript level for the ceaS2 to cas2 polycistronic transcript that encoded CeaS2, the first enzyme of the clavulanic acid pathway that commits arginine to clavulanic acid biosynthesis. Smaller decreases in expression were observed in the ccaR mutant for other genes in the cluster. Two-dimensional electrophoresis and MALDI-TOF analysis confirmed the absence in the mutant strain of proteins CeaS2, Bls2, Pah2 and Car that are required for clavulanic acid biosynthesis, and CefF and IPNS that are required for cephamycin biosynthesis. Gel shift electrophoresis using recombinant r-CcaR protein showed that it bound to the ceaS2 and claR promoter regions in the clavulanic acid cluster, and to the lat, cefF, cefD-cmcI and ccaR promoter regions in the cephamycin C gene cluster. Footprinting experiments indicated that triple heptameric conserved sequences were protected by r-CcaR, and allowed identification of heptameric sequences as CcaR binding sites.

  5. Heterodimeric l-amino acid oxidase enzymes from Egyptian Cerastes cerastes venom: Purification, biochemical characterization and partial amino acid sequencing

    OpenAIRE

    A.E. El Hakim; W.H. Salama; M.B. Hamed; Ali, A. A.; N.M. Ibrahim

    2015-01-01

    Two l-amino acid oxidase enzyme isoforms, Cc-LAAOI and Cc-LAAOII were purified to apparent homogeneity from Cerastes cerastes venom in a sequential two-step chromatographic protocol including; gel filtration and anion exchange chromatography. The native molecular weights of the isoforms were 115 kDa as determined by gel filtration on calibrated Sephacryl S-200 column, while the monomeric molecular weights of the enzymes were, 60, 56 kDa and 60, 53 kDa for LAAOI and LAAOII, respectively. The t...

  6. The nucleotide sequence of HLA-B{sup *}2704 reveals a new amino acid substitution in exon 4 which is also present in HLA-B{sup *}2706

    Energy Technology Data Exchange (ETDEWEB)

    Rudwaleit, M.; Bowness, P.; Wordsworth, P. [John Radcliffe Hospital, Oxford (United Kingdom)

    1996-12-31

    The HLA-B27 subtype HLA-B{sup *}2704 is virtually absent in Caucasians but common in Orientals, where it is associated with ankylosing spondylitis. The amino acid sequence of HLA-B{sup *}2704 has been established by peptide mapping and was shown to differ by two amino acids from HLA-B{sup *}2705, HLA-B{sup *}2704 is characterized by a serine for aspartic acid substitution at position 77 and glutamic acid for valine at position 152. To date, however, no nucleotide sequence confirming these changes at the DNA level has been published. 13 refs., 2 figs.

  7. The shikimate pathway: review of amino acid sequence, function and three-dimensional structures of the enzymes.

    Science.gov (United States)

    Mir, Rafia; Jallu, Shais; Singh, T P

    2015-06-01

    The aromatic compounds such as aromatic amino acids, vitamin K and ubiquinone are important prerequisites for the metabolism of an organism. All organisms can synthesize these aromatic metabolites through shikimate pathway, except for mammals which are dependent on their diet for these compounds. The pathway converts phosphoenolpyruvate and erythrose 4-phosphate to chorismate through seven enzymatically catalyzed steps and chorismate serves as a precursor for the synthesis of variety of aromatic compounds. These enzymes have shown to play a vital role for the viability of microorganisms and thus are suggested to present attractive molecular targets for the design of novel antimicrobial drugs. This review focuses on the seven enzymes of the shikimate pathway, highlighting their primary sequences, functions and three-dimensional structures. The understanding of their active site amino acid maps, functions and three-dimensional structures will provide a framework on which the rational design of antimicrobial drugs would be based. Comparing the full length amino acid sequences and the X-ray crystal structures of these enzymes from bacteria, fungi and plant sources would contribute in designing a specific drug and/or in developing broad-spectrum compounds with efficacy against a variety of pathogens.

  8. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_sequence..._amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  9. The structural analysis of protein sequences based on the quasi-amino acids code

    Institute of Scientific and Technical Information of China (English)

    Zhu Ping; Tang Xu-Qing; Xu Zhen-Yuan

    2009-01-01

    Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Genome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system (∑, +, *) is introduced, where ∑ is the set of 64 codons. According to the characteristics of (∑,+, *), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, +, ×) is a field. Furthermore, the operational results display that the codon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of 'the 64 codon assignments of mRNA to amino acids is probably completely wrong' proposed by Yang (2006 Progress in Modern Biomedicine 6 3).

  10. Performance of visual inspection with acetic acid and human papillomavirus testing for detection of high-grade cervical lesions in HIV positive and HIV negative Tanzanian women

    DEFF Research Database (Denmark)

    Dartell, Myassa Arkam; Rasch, Vibeke; Iftner, Thomas;

    2014-01-01

    The aim of this cross sectional study was to assess type distribution of human papillomavirus (HPV) among HIV positive and HIV negative women who underwent cervical cancer screening, and to examine the ability of visual inspection with acetic acid (VIA), the standard detection method in Tanzania...

  11. Complete amino acid sequence of the major component myoglobin from the goose-beaked whale, Ziphius cavirostris.

    Science.gov (United States)

    Lehman, L D; Jones, B N; Dwulet, F E; Bogardt, R A; Gurd, F R

    1980-10-21

    The complete primary structure of the major component myoglobin from the goose-beaked whale, Ziphius cavirostris, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequencer. Over 80% of the amino acid sequence was established from the three peptides resulting from the cleavage of the apomyoglobin at its two methionine residues with cyanogen bromide along with the four peptides resulting from the cleavage with trypsin of the citraconylated apomyoglobin at its three arginine residues. Further digestion of the central cyanogen bromide peptide with S. aureus strain V8 protease and the 1,2-cyclohexanedione-treated central cyanogen bromide peptide with trypsin enabled the determination of the remainder of the covalent structure. This myoglobin differs from the cetacean myoglobins determined to date at 12 to 17 positions. These large sequence differences reflect the distant taxonomic relationships between the goose-beaked whale and the other species of Cetacea the myoglobin sequences of which have previously been determined.

  12. Amino acid sequences of predicted proteins and their annotation for 95 organism species. - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ID ID of a sequence Cluster ID ID of cluster. gclust_cluster is referenced. Annotation in original... database Annotation at the original website Species Species name Length Amino acid sequen

  13. Construction Strategy for an Internal Amplification Control for Real-Time Diagnostic Assays Using Nucleic Acid Sequence-Based Amplification: Development and Clinical Application

    OpenAIRE

    Rodríguez-Lázaro, David; D'Agostino, Martin; Pla, Maria; Cook, Nigel

    2005-01-01

    An important analytical control in molecular amplification-based methods is an internal amplification control (IAC), which should be included in each reaction mixture. An IAC is a nontarget nucleic acid sequence which is coamplified simultaneously with the target sequence. With negative results for the target nucleic acid, the absence of an IAC signal indicates that amplification has failed. A general strategy for the construction of an IAC for inclusion in molecular beacon-based real-time nu...

  14. Isolation and amino acid sequence of crustacean hyperglycemic hormone precursor-related peptides.

    Science.gov (United States)

    Tensen, C P; Verhoeven, A H; Gaus, G; Janssen, K P; Keller, R; Van Herp, F

    1991-01-01

    The crustacean hyperglycemic hormone (CHH) is synthesized as part of a larger preprohormone in which the sequence of CHH is N-terminally flanked by a peptide for which the name CPRP (CHH precursor-related peptide) is proposed. Both CHH and CPRP are present in the sinus gland, the neurohemal organ of neurosecretory cells located in the eyestalk of decapod crustaceans. This paper describes the isolation and sequence analysis of CPRPs isolated from sinus glands of the crab Carcinus maenas, the crayfish Orconectes limosus and the lobster Homarus americanus. The published sequence of "peptide H" isolated from the land crab, Cardisoma carnifex, has now been recognized as a CPRP in this species. Sequence comparison reveals a high level of identity for the N-terminal region (residues 1-13) between all four peptides, while identity in the C-terminal domain is high between lobster and crayfish CPRP on the one hand, and between both crab species on the other. Conserved N-terminal residues include a putative monobasic processing site at position 11, which suggests that CPRP may be a biosynthetic intermediate from which a potentially bioactive decapeptide can be derived.

  15. Draft Genome Sequence of Ustilago trichophora RK089, a Promising Malic Acid Producer

    Science.gov (United States)

    Zambanini, Thiemo; Buescher, Joerg M.; Meurer, Guido; Blank, Lars M.

    2016-01-01

    The basidiomycetous smut fungus Ustilago trichophora RK089 produces malate from glycerol. De novo genome sequencing revealed a 20.7-Mbp genome (301 gap-closed contigs, 246 scaffolds). A comparison to the genome of Ustilago maydis 521 revealed all essential genes for malate production from glycerol contributing to metabolic engineering for improving malate production. PMID:27469969

  16. Amino Acid Sequence Requirements of the Transmembrane and Cytoplasmic Domains of Influenza Virus Hemagglutinin for Viable Membrane Fusion

    OpenAIRE

    Melikyan, Grigory B.; Lin, Sasa; Roth, Michael G.; Cohen, Fredric S.

    1999-01-01

    The amino acid sequence requirements of the transmembrane (TM) domain and cytoplasmic tail (CT) of the hemagglutinin (HA) of influenza virus in membrane fusion have been investigated. Fusion properties of wild-type HA were compared with those of chimeras consisting of the ectodomain of HA and the TM domain and/or CT of polyimmunoglobulin receptor, a nonviral integral membrane protein. The presence of a CT was not required for fusion. But when a TM domain and CT were present, fusion activity w...

  17. Photophysical characterization of cumarin-doped poly (lactic acid) microparticles and visualization of the biodistribution

    International Nuclear Information System (INIS)

    We prepared fluorescent coumarin dye-doped poly (acrylic acid) microparticles, which are well known as a biodegradable polyester, and the photophysical properties were characterized by scanning electron microscope, atomic force microscope and spectroscopic investigation. Spherical particles with diameters ranging from 0.5 to a few μm were obtained. Based on spectroscopic investigation, the internal environment was close to that of a polar solvent such as methanol, and the dyes were dispersed without aggregation inside the particles. The obtained particles were administered to a mouse through the tail vein, and the biodistribution was then observed after some organs were excited at 1-day and 1-week post-injection. The particles were accumulated in the organs, especially in the lung and spleen. After injection, the particles were trapped temporally in the lung, and then seemed to be transported to other organs by blood circulation. This tendency is similar to the biodistribution of TiO2 microparticles that we have reported previously.

  18. Photophysical characterization of cumarin-doped poly (lactic acid) microparticles and visualization of the biodistribution

    Energy Technology Data Exchange (ETDEWEB)

    Abe, Shigeaki, E-mail: sabe@den.hokudai.ac.j [Department of Biomedical Materials and Engineering, Graduate School of Dental Medicine, Hokkaido University, Kita 13, Nishi 7, Sapporo 060-8586 (Japan); Kiba, Takayuki; Hosokawa, Kiyotada; Nitobe, Satoru; Hirota, Takashi; Kobayashi, Hirohisa [Division of Biotechnology and Macromolecular Chemistry, Graduate School of Hokkaido University, Sapporo 060-8628 (Japan); Akasaka, Tsukasa; Uo, Motohiro; Kuboki, Yoshinori [Department of Biomedical Materials and Engineering, Graduate School of Dental Medicine, Hokkaido University, Kita 13, Nishi 7, Sapporo 060-8586 (Japan); Sato, Shin-Ichiro [Division of Biotechnology and Macromolecular Chemistry, Graduate School of Hokkaido University, Sapporo 060-8628 (Japan); Watari, Fumio [Department of Biomedical Materials and Engineering, Graduate School of Dental Medicine, Hokkaido University, Kita 13, Nishi 7, Sapporo 060-8586 (Japan); Rosca, Iosif D. [Faculty of Engineering and Computer Science, Concordia University, 1455 de Maisonneuve Blvd. W, Montreal, QC H3G 1M8 (Canada)

    2010-08-15

    We prepared fluorescent coumarin dye-doped poly (acrylic acid) microparticles, which are well known as a biodegradable polyester, and the photophysical properties were characterized by scanning electron microscope, atomic force microscope and spectroscopic investigation. Spherical particles with diameters ranging from 0.5 to a few {mu}m were obtained. Based on spectroscopic investigation, the internal environment was close to that of a polar solvent such as methanol, and the dyes were dispersed without aggregation inside the particles. The obtained particles were administered to a mouse through the tail vein, and the biodistribution was then observed after some organs were excited at 1-day and 1-week post-injection. The particles were accumulated in the organs, especially in the lung and spleen. After injection, the particles were trapped temporally in the lung, and then seemed to be transported to other organs by blood circulation. This tendency is similar to the biodistribution of TiO{sub 2} microparticles that we have reported previously.

  19. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles.

    Science.gov (United States)

    Rodrigue, Nicolas; Philippe, Hervé; Lartillot, Nicolas

    2010-03-01

    Modeling the interplay between mutation and selection at the molecular level is key to evolutionary studies. To this end, codon-based evolutionary models have been proposed as pertinent means of studying long-range evolutionary patterns and are widely used. However, these approaches have not yet consolidated results from amino acid level phylogenetic studies showing that selection acting on proteins displays strong site-specific effects, which translate into heterogeneous amino acid propensities across the columns of alignments; related codon-level studies have instead focused on either modeling a single selective context for all codon columns, or a separate selective context for each codon column, with the former strategy deemed too simplistic and the latter deemed overparameterized. Here, we integrate recent developments in nonparametric statistical approaches to propose a probabilistic model that accounts for the heterogeneity of amino acid fitness profiles across the coding positions of a gene. We apply the model to a dozen real protein-coding gene alignments and find it to produce biologically plausible inferences, for instance, as pertaining to site-specific amino acid constraints, as well as distributions of scaled selection coefficients. In their account of mutational features as well as the heterogeneous regimes of selection at the amino acid level, the modeling approaches studied here can form a backdrop for several extensions, accounting for other selective features, for variable population size, or for subtleties of mutational features, all with parameterizations couched within population-genetic theory. PMID:20176949

  20. Prediction of the Occurrence of the ADP-binding βαβ-fold in Proteins, Using an Amino Acid Sequence Fingerprint

    NARCIS (Netherlands)

    Wierenga, Rik K.; Terpstra, Peter; Hol, Wim G.J.

    1986-01-01

    An amino acid sequence "fingerprint” has been derived that can be used to test if a particular sequence will fold into a βαβ-unit with ADP-binding properties. It was deduced from a careful analysis of the known three-dimensional structures of ADP-binding βαβ-folds. This fingerprint is in fact a set

  1. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Energy Technology Data Exchange (ETDEWEB)

    Rhee, Mun Su [University of Florida, Gainesville; Moritz, Brelan E. [University of Florida, Gainesville; Xie, Gary [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Patel, Milind [University of Florida, Gainesville; Ou, Mark [University of Florida, Gainesville; Harbrucker, Roberta [University of Florida, Gainesville; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  2. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Gary [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  3. Convergent evolution of the red- and green-like visual pigment genes in fish, Astyanax fasciatus, and human.

    OpenAIRE

    Yokoyama, R; Yokoyama, S

    1990-01-01

    We have isolated and sequenced genes from the blind cave fish, Astyanax fasciatus, that are homologous to the human red and green visual pigment genes. The data strongly suggest that, like human, these fish have one red-like visual pigment gene and multiple green-like visual pigment genes. By comparing the DNA sequences of the human and fish visual pigment genes and knowing their phylogenetic relationship, one can infer the direction of amino acid substitutions in the red and green visual pig...

  4. Sequence-specific inhibition of duck hepatitis B virus reverse transcription by peptide nucleic acids (PNA)

    DEFF Research Database (Denmark)

    Robaczewska, Magdalena; Narayan, Ramamurthy; Seigneres, Beatrice;

    2005-01-01

    BACKGROUND/AIMS: Peptide nucleic acids (PNAs) appear as promising new antisense agents, that have not yet been examined as hepatitis B virus (HBV) inhibitors. Our aim was to study the ability of PNAs targeting the duck HBV (DHBV) encapsidation signal epsilon to inhibit reverse transcription (RT...

  5. Amino acid sequence of the cold-active alkaline phosphatase from Atlantic cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Asgeirsson, Bjarni; Nielsen, Berit Noesgaard; Højrup, Peter

    2003-01-01

    -linked glycosylation sites were found. The glycan structure was determined as complex biantennary in type with fucose and sialic acid attached, although a trace of complex tri-antennary structure was also observed. A three-dimensional model was obtained by homology modelling using the human placental AP scaffold. Cod...

  6. Complete Genome Sequence of Moraxella osloensis Strain KMC41, a Producer of 4-Methyl-3-Hexenoic Acid, a Major Malodor Compound in Laundry.

    Science.gov (United States)

    Goto, Takatsugu; Hirakawa, Hideki; Morita, Yuji; Tomida, Junko; Sato, Jun; Matsumura, Yuta; Mitani, Asako; Niwano, Yu; Takeuchi, Kohei; Kubota, Hiromi; Kawamura, Yoshiaki

    2016-01-01

    We report the complete genome sequence of Moraxella osloensis strain KMC41, isolated from laundry with malodor. The KMC41 genome comprises a 2,445,556-bp chromosome and three plasmids. A fatty acid desaturase and at least four β-oxidation-related genes putatively associated with 4-methyl-3-hexenoic acid generation were detected in the KMC41 chromosome. PMID:27445387

  7. Identification of a novel HMW glutenin subunit and comparison of its amino acid sequence with those of homologous subunits

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Aegilops tauschii is the donor of the D genome of common wheat (Triticum aestivum). Genetic variation of HMW glutenin subunits encoded by the Glu-1Dt locus of Ae. tauschii has been found to be higher than that specified by the Glu-1D locus in common wheat. In the present note, we report the identification of a novel HMW glutenin subunit, Dy13t, from Ae. tauschii. The newly identified subunit possessed an electrophoretic mobility that was faster than that of the Dy12 subunit of common wheat. The complete ORF of encoding the Dy13t subunit contained 624 codons (excluding the stop codons). The amino acid sequence deduced from the Dy13t gene ORF was the shortest among those of the previously reported subunits derived by the D genome. A further comparison of Dy13t amino acid sequence with those of the subunits characterized from the A, B, D, R genomes of Triticeae showed that the smaller size of the Dy13t subunit was associated with a reduction in the size of its repetitive domain.

  8. EEG changes during sequences of visual and kinesthetic motor imagery Alterações no EEG durante sequencias de imagética motora visual e cinestésica

    Directory of Open Access Journals (Sweden)

    Marcus Vinicius Stecklow

    2010-08-01

    Full Text Available The evoked cerebral electric response when sequences of complex motor imagery (MI task are executed several times is still unclear. This work aims at investigating the existence of habituation in the cortical response, more specifically in the alpha band peak of parietal and occipital areas (10-20 international system electroencephalogram, EEG, protocol. The EEG signals were acquired during sequences of MI of volleyball spike movement in kinesthetic and visual modalities and also at control condition. Thirty right-handed male subjects (18 to 40 years were assigned to either an 'athlete' or a 'non-athlete' group, both containing 15 volunteers. Paired Wilcoxon tests (with α=0.05 indicates that sequential MI of complex tasks promotes cortical changes, mainly in the power vicinity of the alpha peak. This finding is more pronounced along the initial trials and also for the athletes during the modality of kinesthetic motor imagery.A resposta elétrica cerebral evocada quando sequencias de imagética motora (MI de tarefas complexas são executadas seguidamente no tempo permanecem desconhecidas. Este trabalho objetivou investigar a existência de habituação da resposta cortical, mais especificamente na banda do pico de alfa de áreas parietais e occipitais (sistema internacional 10-20, eletroencefalograma, protocolo de EEG. Os sinais de EEG foram adquiridos durante sequências de MI do movimento de ataque do voleibol nas modalidades cinestésica e visual, e também em condição de controle. Trinta voluntários adultos (entre 18 e 40 anos, destros, do gênero masculino foram agrupados como 'atletas' ou 'não-atletas', sendo cada grupo composto de 15 voluntários. Testes pareados de Wilcoxon (com α=0.05 indicaram que a MI sequencial de tarefas complexas promoveram alterações nas respostas corticais, mais especificamente na região ao redor do pico de alfa. Este achado foi mais pronunciado ao longo dos trechos iniciais e também nos atletas durante

  9. Diverse Bacterial PKS Sequences Derived From Okadaic Acid-Producing Dinoflagellates

    Directory of Open Access Journals (Sweden)

    Kathleen S. Rein

    2008-05-01

    Full Text Available Okadaic acid (OA and the related dinophysistoxins are isolated from dinoflagellates of the genus Prorocentrum and Dinophysis. Bacteria of the Roseobacter group have been associated with okadaic acid producing dinoflagellates and have been previously implicated in OA production. Analysis of 16S rRNA libraries reveals that Roseobacter are the most abundant bacteria associated with OA producing dinoflagellates of the genus Prorocentrum and are not found in association with non-toxic dinoflagellates. While some polyketide synthase (PKS genes form a highly supported Prorocentrum clade, most appear to be bacterial, but unrelated to Roseobacter or Alpha-Proteobacterial PKSs or those derived from other Alveolates Karenia brevis or Crytosporidium parvum.

  10. Complete genome sequence of probiotic Bacillus coagulans HM-08: A potential lactic acid producer.

    Science.gov (United States)

    Yao, Guoqiang; Gao, Pengfei; Zhang, Wenyi

    2016-06-20

    Bacillus coagulans HM-08 is a commercialized probiotic strain in China. Its genome contains a 3.62Mb circular chromosome with an average GC content of 46.3%. In silico analysis revealed the presence of one xyl operon as well as several other genes that are correlated to xylose utilization. The genetic information provided here may help to expand its future biotechnology potential in lactic acid production. PMID:27130497

  11. Triose phosphate isomerase from the coelacanth. An approach to the rapid determination of an amino acid sequence with small amounts of material.

    Science.gov (United States)

    Kolb, E; Harris, J I; Bridgen, J

    1974-02-01

    The preparation and purification of cyanogen bromide fragments from [(14)C]carboxymethylated coelacanth triose phosphate isomerase is presented. The automated sequencing of these fragments, the lysine-blocked tryptic peptides derived from them, and also of the intact protein, is described. Combination with results from manual sequence analysis has given the 247-residue amino acid sequence of coelacanth triose phosphate isomerase in 4 months, by using 100mg of enzyme. (Two small adjacent peptides were placed by homology with the rabbit enzyme.) Comparison of this sequence with that of the rabbit muscle enzyme shows that 207 (84%) of the residues are identical. This slow rate of evolutionary change (corresponding to two amino acid substitutions per 100 residues per 100 million years) is similar to that found for glyceraldehyde 3-phosphate dehydrogenase. The reliability of sequence information obtained by automated methods is discussed.

  12. Inferences from protein and nucleic acid sequences - Early molecular evolution, divergence of kingdoms and rates of change

    Science.gov (United States)

    Dayhoff, M. O.; Barker, W. C.; Mclaughlin, P. J.

    1974-01-01

    Description of new sensitive, objective methods for establishing the probable common ancestry of very distantly related sequences and the quantitative evolutionary change which has taken place. These methods are applied to four families of proteins and nucleic acids and evolutionary trees will be derived where possible. Of the three families containing duplications of genetic material, two are nucleic acids: transfer RNA and 5S ribosomal RNA. Both of these structures are functional in the synthesis of coded proteins, and prototypes must have been present in the cell at the inception of the fundamental coding process that all living things share. There are many types of tRNA which recognize the various nucleotide triplets and the 20 amino acids. These types are thought to have arisen as a result of many gene duplications. Relationships among these types are discussed. The 5S ribosomal RNA, presently functional in both eukaryotes and prokaryotes, is very likely descended from an early form incorporating almost a complete duplication of genetic material. The amount of evolution in the various lines can again be compared. The other two families containing duplications are proteins; ferredoxin and cytochrome c.

  13. Mass Spectrometry Analysis Coupled with de novo Sequencing Reveals Amino Acid Substitutions in Nucleocapsid Protein from Influenza A Virus

    Directory of Open Access Journals (Sweden)

    Zijian Li

    2014-02-01

    Full Text Available Amino acid substitutions in influenza A virus are the main reasons for both antigenic shift and virulence change, which result from non-synonymous mutations in the viral genome. Nucleocapsid protein (NP, one of the major structural proteins of influenza virus, is responsible for regulation of viral RNA synthesis and replication. In this report we used LC-MS/MS to analyze tryptic digestion of nucleocapsid protein of influenza virus (A/Puerto Rico/8/1934 H1N1, which was isolated and purified by SDS poly-acrylamide gel electrophoresis. Thus, LC-MS/MS analyses, coupled with manual de novo sequencing, allowed the determination of three substituted amino acid residues R452K, T423A and N430T in two tryptic peptides. The obtained results provided experimental evidence that amino acid substitutions resulted from non-synonymous gene mutations could be directly characterized by mass spectrometry in proteins of RNA viruses such as influenza A virus.

  14. FASMA: A Service to Format and Analyze Sequences in Multiple Alignments

    Institute of Scientific and Technical Information of China (English)

    Susan; Costantini; Giovanni; Colonna; Angelo; M.; Facchiano

    2007-01-01

    Multiple sequence alignments are successfully applied in many studies for under- standing the structural and functional relations among single nucleic acids and pro- tein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http: //bioinformatica.isa.cnr.it /FASMA /.

  15. Evolution of early life inferred from protein and ribonucleic acid sequences

    Science.gov (United States)

    Dayhoff, M. O.; Schwartz, R. M.

    1978-01-01

    The chemical structures of ferredoxin, 5S ribosomal RNA, and c-type cytochrome sequences have been employed to construct a phylogenetic tree which connects all major photosynthesizing organisms: the three types of bacteria, blue-green algae, and chloroplasts. Anaerobic and aerobic bacteria, eukaryotic cytoplasmic components and mitochondria are also included in the phylogenetic tree. Anaerobic nonphotosynthesizing bacteria similar to Clostridium were the earliest organisms, arising more than 3.2 billion years ago. Bacterial photosynthesis evolved nearly 3.0 billion years ago, while oxygen-evolving photosynthesis, originating in the blue-green algal line, came into being about 2.0 billion years ago. The phylogenetic tree supports the symbiotic theory of the origin of eukaryotes.

  16. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome.

    Science.gov (United States)

    Kumar, Ashutosh; Singh, Himanshu N; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)-microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker "retinoic acid" in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5'-AGGTCA-3') in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and embryological

  17. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome.

    Science.gov (United States)

    Kumar, Ashutosh; Singh, Himanshu N; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)-microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker "retinoic acid" in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5'-AGGTCA-3') in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and embryological

  18. Visual detection of trace copper ions based on copper-catalyzed reaction of ascorbic acid with oxygen

    Science.gov (United States)

    Hou, Xin Yan; Chen, Shu; Shun, Lian Ju; Zhao, Yi Ni; Zhang, Zhi Wu; Long, Yun Fei; Zhu, Li

    2015-10-01

    A visual detection method for trace Cu2+ in aqueous solutions using triangular silver nanoplates (abbreviated as TAgNPs) as the probe was developed. The method is based on that TAgNPs could be corroded in sodium thiosulfate (Na2S2O3) solutions. The absorption spectrum of TAgNPs solution changed when it is corroded by Na2S2O3. The reaction of oxygen with ascorbic acid (Vc) in the presence of a low concentration of Cu2+ generates hydrogen peroxide that reacts with Na2S2O3, which leads the concentration of Na2S2O3 in the solution to be decreased. Therefore, the reaction between TAgNPs and the reacted mixture of Na2S2O3/Vc/Cu2+ was prevented efficiently. When the Na2S2O3 concentration and reaction time are constant, the decrease in the concentration of Na2S2O3 is directly proportional to the Cu2+ concentration. Thus, morphology, color, and maximum absorption wavelength of TAgNPs changed with the change of Cu2+ concentration. The changed maximum absorption wavelength of TAgNPs (Δλ) is proportional to Cu2+ concentration in the range from 7.5 × 10-9 to 5.0 × 10-7 M with a correlation coefficient of r = 0.9956. Moreover, color change of TAgNP solution was observed clearly over a Cu2+ concentration range from 7.5 × 10-8 to 5.0 × 10-7 M. This method has been used to detect the Cu2+ content of a human hair sample, and the result is in agreement with that obtained by the atomic absorption spectroscopy (AAS) method.

  19. Nucleic acid sequences encoding D1 and D1/D2 domains of human coxsackievirus and adenovirus receptor (CAR)

    Science.gov (United States)

    Freimuth, Paul I.

    2010-04-06

    The invention provides recombinant human CAR (coxsackievirus and adenovirus receptor) polypeptides which bind adenovirus. Specifically, polypeptides corresponding to adenovirus binding domain D1 and the entire extracellular domain of human CAR protein comprising D1 and D2 are provided. In another aspect, the invention provides nucleic acid sequences encoding these domains and expression vectors for producing the domains and bacterial cells containing such vectors. The invention also includes an isolated fusion protein comprised of the D1 polypeptide fused to a polypeptide which facilitates folding of D1 when expressed in bacteria. The functional D1 domain finds application in a therapeutic method for treating a patient infected with a CAR D1-binding virus, and also in a method for identifying an antiviral compound which interferes with viral attachment. The invention also provides a method for specifically targeting a cell for infection by a virus which binds to D1.

  20. The effects of maternal supplementation of polyunsaturated Fatty acids on visual, neurobehavioural, and developmental outcomes of the child: a systematic review of the randomized trials.

    Science.gov (United States)

    Lo, Andrea; Sienna, Julianna; Mamak, Eva; Djokanovic, Nada; Westall, Carol; Koren, Gideon

    2012-01-01

    Polyunsaturated fatty acid (PUFA) use in pregnancy has been promoted as beneficial for visual and neurobehavioural development in the fetus. However, no systematic review of the randomized trials has been conducted. The objective of this review was to evaluate potential advantages of this regiment by reviewing all randomized trials in pregnancy. Methods. Systematic review of randomized controlled studies comparing cognitive and visual achievements among infants whose mothers were treated and untreated with PUFA during gestation. Results. Nine studies met the inclusion criteria, three focusing on visual and six on neurobehavioural development. Due to differing outcome measurements in the infants, the studies could not be combined into a formal meta-analysis. Synthesizing the existing data, for both visual and neurobehavioural development, most studies could not show sustained benefits to infant cognition or visual development. Conclusion. At the present time a recommendation to change practice and supplement all expecting mothers with PUFA to improve offspring vision or neurobehavioural function is not supported by existing evidence.

  1. The Effects of Maternal Supplementation of Polyunsaturated Fatty Acids on Visual, Neurobehavioural, and Developmental Outcomes of the Child: A Systematic Review of the Randomized Trials

    Directory of Open Access Journals (Sweden)

    Andrea Lo

    2012-01-01

    Full Text Available Polyunsaturated fatty acid (PUFA use in pregnancy has been promoted as beneficial for visual and neurobehavioural development in the fetus. However, no systematic review of the randomized trials has been conducted. The objective of this review was to evaluate potential advantages of this regiment by reviewing all randomized trials in pregnancy. Methods. Systematic review of randomized controlled studies comparing cognitive and visual achievements among infants whose mothers were treated and untreated with PUFA during gestation. Results. Nine studies met the inclusion criteria, three focusing on visual and six on neurobehavioural development. Due to differing outcome measurements in the infants, the studies could not be combined into a formal meta-analysis. Synthesizing the existing data, for both visual and neurobehavioural development, most studies could not show sustained benefits to infant cognition or visual development. Conclusion. At the present time a recommendation to change practice and supplement all expecting mothers with PUFA to improve offspring vision or neurobehavioural function is not supported by existing evidence.

  2. Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

    Directory of Open Access Journals (Sweden)

    Leitner Dietmar

    2005-04-01

    Full Text Available Abstract Background A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. For the analysis of the data sets different statistical methods such as the calculation of the Chou-Fasman parameters and occurrence matrices were used. Furthermore we analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation. Results One of the main results of the statistical investigations is the ranking of the secondary structure and sequence information with respect to the prediction of the Xaa-Pro peptide bond conformation. We observed a significant impact of secondary structure information on the occurrence of the Xaa-Pro peptide bond conformation, while the sequence information of amino acids neighboring proline is of little predictive value for the conformation of this bond. Conclusion In this work, we present an extensive analysis of the occurrence of the cis and trans proline conformation in proteins. Based on the data set, we derived patterns and rules for a possible prediction of the proline conformation. Upon adoption of the Chou-Fasman parameters, we are able to derive statistically relevant correlations between the secondary structure of amino acid fragments and the Xaa-Pro peptide bond conformation.

  3. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

    Directory of Open Access Journals (Sweden)

    Selvaraj S

    2011-10-01

    Full Text Available Abstract Background Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology. Methods We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such as binding propensity, neighboring residues in the vicinity of binding sites, conservation score and conformational switching. Results We observed that the binding propensities of amino acid residues are specific for protein-protein complexes. Further, typical dipeptides and tripeptides showed high preference for binding, which is unique to protein-protein complexes. Most of the binding site residues are highly conserved among homologous sequences. Our analysis showed that 7% of residues changed their conformations upon protein-protein complex formation and it is 9.2% and 6.6% in the binding and non-binding sites, respectively. Specifically, the residues Glu, Lys, Leu and Ser changed their conformation from coil to helix/strand and from helix to coil/strand. Leu, Ser, Thr and Val prefer to change their conformation from strand to coil/helix. Conclusions The results obtained in this study will be helpful for understanding and predicting the binding sites in protein-protein complexes.

  4. Scanning mutagenesis of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex

    Directory of Open Access Journals (Sweden)

    Nagib eAhsan

    2012-07-01

    Full Text Available The mitochondrial pyruvate dehydrogenase complex is regulated by reversible seryl-phosphorylation of the E1α subunit by a dedicated, intrinsic kinase. The phospho-complex is reactivated when dephosphorylated by an intrinsic PP2C-type protein phosphatase. Both the position of the phosphorylated Ser-residue and the sequences of the flanking amino acids are highly conserved. We have used the synthetic peptide-based kinase client assay plus recombinant pyruvate dehydrogenase E1α and E1α-kinase to perform scanning mutagenesis of the residues flanking the site of phosphorylation. Consistent with the results from phylogenetic analysis of the flanking sequences, the direct peptide-based kinase assays tolerated very few changes. Even conservative changes such as Leu, Ile, or Val for Met, or Glu for Asp, gave very marked reductions in phosphorylation. Overall the results indicate that regulation of the mitochondrial pyruvate dehydrogenase complex by reversible phosphorylation is an extreme example of multiple, interdependent instances of co-evolution.

  5. Maternal fish oil supplementation in lactation: Effect on visual acuity and n-3 fatty acid content of infant erythrocytes

    DEFF Research Database (Denmark)

    Lauritzen, L.; Jørgensen, M.H.; Mikkelsen, T.B.;

    2004-01-01

    Studies on formula-fed infants indicate a beneficial effect of dietary DHA on visual acuity. Cross-sectional studies have shown an association between breast-milk DHA levels and visual acuity in breast-fed infants. The objective in this study was to evaluate the biochemical and functional effects...... content of milk samples (0, 2, and 4 mon postnatal) and of infant red blood cell (RBC) membranes (4 mon postnatal), and infant visual acuity (measured by swept visual evoked potential at 2 and 4 mon of age). FO supplementation gave rise to a threefold increase in the DHA content of the 4-mon milk samples...... (P visual acuity was not significantly different in the randomized groups but was positively associated at 4 mon with infant RBC-DHA (P = 0.004, multiple regression). We...

  6. Amino Acid Sequence and Structural Comparison of BACE1 and BACE2 Using Evolutionary Trace Method

    Directory of Open Access Journals (Sweden)

    Hoda Mirsafian

    2014-01-01

    Full Text Available Beta-amyloid precursor protein cleavage enzyme 1 (BACE1 and beta-amyloid precursor protein cleavage enzyme 2 (BACE2, members of aspartyl protease family, are close homologues and have high similarity in their protein crystal structures. However, their enzymatic properties differ leading to disparate clinical consequences. In order to identify the residues that are responsible for such differences, we used evolutionary trace (ET method to compare the amino acid conservation patterns of BACE1 and BACE2 in several mammalian species. We found that, in BACE1 and BACE2 structures, most of the ligand binding sites are conserved which indicate their enzymatic property of aspartyl protease family members. The other conserved residues are more or less randomly localized in other parts of the structures. Four group-specific residues were identified at the ligand binding site of BACE1 and BACE2. We postulated that these residues would be essential for selectivity of BACE1 and BACE2 biological functions and could be sites of interest for the design of selective inhibitors targeting either BACE1 or BACE2.

  7. Thimet oligopeptidase: similarity to 'soluble angiotensin II-binding protein' and some corrections to the published amino acid sequence of the rat testis enzyme.

    Science.gov (United States)

    McKie, N; Dando, P M; Rawlings, N D; Barrett, A J

    1993-01-01

    The deduced amino acid sequence of pig liver soluble angiotensin II-binding protein [Sugiura, Hagiwara and Hirose (1992) J. Biol. Chem. 267, 18067-18072] is similar over most of its length to that reported for rat testis thimet oligopeptidase (EC 3.4.24.15) by Pierotti, Dong, Glucksman, Orlowski and Roberts [(1990) (Biochemistry 29, 10323-10329]. We have found that homogeneous rat testis thimet oligopeptidase binds angiotensin II with the same distinctive characteristics as the pig liver protein. Analysis of the nucleotide sequences reported for the two proteins pointed to the likelihood that sequencing errors had caused two segments of the amino acid sequence of the rat protein to be translated out of frame, and re-sequencing of selected parts of the clone (kindly provided by the previous authors) confirmed this. The revised deduced amino acid sequence of rat thimet oligopeptidase contains 687 residues, representing a protein of 78,308 Da, and is more closely related to those of the pig liver protein and other known homologues of thimet oligopeptidase than that described previously. Images Figure 1 PMID:8216239

  8. Generation of deviation parameters for amino acid singlets, doublets and triplets from three-dimensional structures of proteins and its implications for secondary structure prediction from amino acid sequences

    Indian Academy of Sciences (India)

    S A Mugilan; K Veluraja

    2000-03-01

    We present a new method, secondary structure prediction by deviation parameter (SSPDP) for predicting the secondary structure of proteins from amino acid sequence. Deviation parameters (DP) for amino acid singlets, doublets and triplets were computed with respect to secondary structural elements of proteins based on the dictionary of secondary structure prediction (DSSP)-generated secondary structure for 408 selected non-homologous proteins. To the amino acid triplets which are not found in the selected dataset, a DP value of zero is assigned with respect to the secondary structural elements of proteins. The total number of parameters generated is 15,432, in the possible parameters of 25,260. Deviation parameter is complete with respect to amino acid singlets, doublets, and partially complete with respect to amino acid triplets. These generated parameters were used to predict secondary structural elements from amino acid sequence. The secondary structure predicted by our method (SSPDP) was compared with that of single sequence (NNPREDICT) and multiple sequence (PHD) methods. The average value of the percentage of prediction accuracy for α-helix by SSPDP, NNPREDICT and PHD methods was found to be 57%, 44% and 69% respectively for the proteins in the selected dataset. For -strand the prediction accuracy is found to be 69%, 21% and 53% respectively by SSPDP, NNPREDICT and PHD methods. This clearly indicates that the secondary structure prediction by our method is as good as PHD method but much better than NNPREDICT method.

  9. Complete Genome Sequence of the d-Amino Acid Catabolism Bacterium Phaeobacter sp. Strain JL2886, Isolated from Deep Seawater of the South China Sea.

    Science.gov (United States)

    Fu, Yingnan; Wang, Rui; Zhang, Zilian; Jiao, Nianzhi

    2016-01-01

    Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can catabolize d-amino acids. Here, we report the complete genome sequence of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%. A total of 3,913 protein-coding genes and 10 genes related to d-amino acid catabolism were obtained. PMID:27587825

  10. Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach.

    Science.gov (United States)

    Adamala, Katarzyna; Anella, Fabrizio; Wieczorek, Rafal; Stano, Pasquale; Chiarabelli, Cristiano; Luisi, Pier Luigi

    2014-01-01

    In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From the chemical viewpoint, macromolecules are formed by chemical pathways leading to the condensation of building blocks (amino acids, or nucleotides) in long-chain copolymers (proteins and nucleic acids, respectively). The second difficulty deals with a conceptual problem, namely with the emergence of specific sequences among a vast array of possible ones, the huge "sequence space", leading to the question "why these macromolecules, and not the others?" We have recently addressed these questions by using a chemical synthetic biology approach. In particular, we have tested the catalytic activity of small peptides, like Ser-His, with respect to peptide- and nucleotides-condensation, as a realistic model of primitive organocatalysis. We have also set up a strategy for exploring the sequence space of random proteins and RNAs (the so-called "never born biopolymer" project) with respect to the production of folded structures. Being still far from solved, the main aspects of these "open questions" are discussed here, by commenting on recent results obtained in our groups and by providing a unifying view on the problem and possible solutions. In particular, we propose a general scenario for macromolecule formation via fragment-condensation, as a scheme for the emergence of specific sequences based on molecular growth and selection.

  11. Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly- -D-Glutamic Acid Anthrax Capsule

    KAUST Repository

    Stabler, R. A.

    2013-01-24

    A mixed culture of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8 degraded poly-γ-d-glutamic acid; when the 2 strains were cultured separately, no hydrolytic activity was apparent. Here we report the draft genome sequences of both soil isolates.

  12. 37 CFR 1.824 - Form and format for nucleotide and/or amino acid sequence submissions in computer readable form.

    Science.gov (United States)

    2010-07-01

    ... nucleotide and/or amino acid sequence submissions in computer readable form. 1.824 Section 1.824 Patents... PRACTICE IN PATENT CASES Biotechnology Invention Disclosures Application Disclosures Containing Nucleotide... submissions in computer readable form. (a) The computer readable form required by § 1.821(e) shall meet...

  13. Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines

    NARCIS (Netherlands)

    Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.; Lucas, Patrick M.

    2013-01-01

    Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which mi

  14. Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach

    NARCIS (Netherlands)

    Adamala, K.; Anella, F.M.; Wieczorek, R.; Stano, P.; Chiarabelli, C.; Luisi, P.L.

    2014-01-01

    In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From the c

  15. Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach

    DEFF Research Database (Denmark)

    Adamala, K.; Anella, F.; Wieczorek, R.;

    2014-01-01

    In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From...

  16. Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines

    OpenAIRE

    Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.; Lucas, Patrick M

    2013-01-01

    Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which might shed light onto the enzymatic machineries that are involved in its production of biogenic amines.

  17. Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the Poly-γ-d-Glutamic Acid Anthrax Capsule.

    Science.gov (United States)

    Stabler, Richard A; Negus, David; Pain, Arnab; Taylor, Peter W

    2013-01-01

    A mixed culture of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8 degraded poly-γ-d-glutamic acid; when the 2 strains were cultured separately, no hydrolytic activity was apparent. Here we report the draft genome sequences of both soil isolates.

  18. Identities among actin-encoding cDNAs of the Nile tilapia (Oreochromis niloticus and other eukaryote species revealed by nucleotide and amino acid sequence analyses

    Directory of Open Access Journals (Sweden)

    Andréia B. Poletto

    2008-01-01

    Full Text Available Actin-encoding cDNAs of Nile tilapia (Oreochromis niloticus were isolated by RT-PCR using total RNA samples of different tissues and further characterized by nucleotide sequencing and in silico amino acid (aa sequence analysis. Comparisons among the actin gene sequences of O. niloticus and those of other species evidenced that the isolated genes present a high similarity to other fish and other vertebrate actin genes. The highest nucleotide resemblance was observed between O. niloticus and O. mossambicus a-actin and b-actin genes. Analysis of the predicted aa sequences revealed two distinct types of cytoplasmic actins, one cardiac muscle actin type and one skeletal muscle actin type that were expressed in different tissues of Nile tilapia. The evolutionary relationships between the Nile tilapia actin genes and diverse other organisms is discussed.

  19. PreFRP: Prediction and visualization of fluctuation residues in proteins

    Science.gov (United States)

    Saravanan, Konda Mani; Senthil, Renganathan

    2016-01-01

    Aim: The PreFRP web server extracts sequence and basic information of a protein structure and groups amino acid residues in a protein into three important types such as high, moderate, and weak fluctuating residues. Materials and Methods: The server takes a protein data bank file or an amino acid sequence as input and prints the probability of amino acid residues to fluctuate. The server also provides a link to Jmol, a molecular visualization program to visualize the high, moderate, and weak fluctuating residues in three different colors. Results: Prediction and visualization of fluctuating amino acid residues in proteins may help to understand the complex three-dimensional structure of proteins and may further help in docking and mutation experiments. Availability: The web server is freely accessible through the web page of the author's institution http://www.mpi.edu.in/prefrp/link.html.

  20. Evolution of alpha-lactalbumins. The complete amino acid sequence of the alpha-lactalbumin from a marsupial (Macropus rufogriseus) and corrections to regions of sequence in bovine and goat alpha-lactalbumins.

    Science.gov (United States)

    Shewale, J G; Sinha, S K; Brew, K

    1984-04-25

    alpha-Lactalbumin was purified from a whey protein fraction of the milk of the red-necked wallaby (Macropus rufogriseus). The complete amino acid sequence was determined from the results of automatic sequenator analyses of the intact protein, the three cyanogen bromide fragments, and of peptides generated from the larger, COOH-terminal CNBr fragment by digestion with trypsin or staphylococcal protease. This is the first sequence to be determined of an alpha-lactalbumin from a marsupial and differs from known eutherian alpha-lactalbumins in size and locations of deletions in alignments with the homologous type c lysozymes, as well as in having amino acid substitutions at 8 sites that are invariant in known eutherian proteins. Some corrections are also reported for two regions of sequence in both bovine and goat alpha-lactalbumins. The new and previously published information on alpha-lactalbumin sequences is analyzed in relation to the evolutionary history of the alpha-lactalbumin line as well as the relationship of structure to function in these proteins. PMID:6715332

  1. Identification of Protein-Protein Interactions via a Novel Matrix-Based Sequence Representation Model with Amino Acid Contact Information.

    Science.gov (United States)

    Ding, Yijie; Tang, Jijun; Guo, Fei

    2016-01-01

    Identification of protein-protein interactions (PPIs) is a difficult and important problem in biology. Since experimental methods for predicting PPIs are both expensive and time-consuming, many computational methods have been developed to predict PPIs and interaction networks, which can be used to complement experimental approaches. However, these methods have limitations to overcome. They need a large number of homology proteins or literature to be applied in their method. In this paper, we propose a novel matrix-based protein sequence representation approach to predict PPIs, using an ensemble learning method for classification. We construct the matrix of Amino Acid Contact (AAC), based on the statistical analysis of residue-pairing frequencies in a database of 6323 protein-protein complexes. We first represent the protein sequence as a Substitution Matrix Representation (SMR) matrix. Then, the feature vector is extracted by applying algorithms of Histogram of Oriented Gradient (HOG) and Singular Value Decomposition (SVD) on the SMR matrix. Finally, we feed the feature vector into a Random Forest (RF) for judging interaction pairs and non-interaction pairs. Our method is applied to several PPI datasets to evaluate its performance. On the S . c e r e v i s i a e dataset, our method achieves 94 . 83 % accuracy and 92 . 40 % sensitivity. Compared with existing methods, and the accuracy of our method is increased by 0 . 11 percentage points. On the H . p y l o r i dataset, our method achieves 89 . 06 % accuracy and 88 . 15 % sensitivity, the accuracy of our method is increased by 0 . 76 % . On the H u m a n PPI dataset, our method achieves 97 . 60 % accuracy and 96 . 37 % sensitivity, and the accuracy of our method is increased by 1 . 30 % . In addition, we test our method on a very important PPI network, and it achieves 92 . 71 % accuracy. In the Wnt-related network, the accuracy of our method is increased by 16 . 67 % . The source code and all datasets are available

  2. Sequence-specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid-DNA) in capillary and microfluidic electrophoretic separations.

    Science.gov (United States)

    Wagler, Patrick; Minero, Gabriel Antonio S; Tangen, Uwe; de Vries, Jan Willem; Prusty, Deepak; Kwak, Minseok; Herrmann, Andreas; McCaskill, John S

    2015-10-01

    Reversible noncovalent but sequence-dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite-modified oligonucleotides has enabled sequence-specific mobility assays for DNA in gel electrophoresis: sequences binding to the immobilized DNA are delayed in their migration. Such a system has been used for example to construct complex DNA filters facilitating DNA computations. However, these gels are formed irreversibly and the choice of immobilized sequences is made once off during fabrication. In this work, we demonstrate the reversible self-assembly of gels combined with amphiphilic DNA molecules, which exhibit hydrophobic hydrocarbon chains attached to the nucleobase. This amphiphilic DNA, which we term lipid-DNA, is synthesized in advance and is blended into a block copolymer gel to induce sequence-dependent DNA retention during electrophoresis. Furthermore, we demonstrate and characterize the programmable mobility shift of matching DNA in such reversible gels both in thin films and microchannels using microelectrode arrays. Such sequence selective separation may be employed to select nucleic acid sequences of similar length from a mixture via local electronics, a basic functionality that can be employed in novel electronic chemical cell designs and other DNA information-processing systems. PMID:26095642

  3. Identification of multiple lipid genes with modifications in expression and sequence associated with the evolution of hydroxy fatty acid accumulation in Physaria fendleri.

    Science.gov (United States)

    Horn, Patrick J; Liu, Jinjie; Cocuron, Jean-Christophe; McGlew, Kathleen; Thrower, Nicholas A; Larson, Matt; Lu, Chaofu; Alonso, Ana P; Ohlrogge, John

    2016-05-01

    Two Brassicaceae species, Physaria fendleri and Camelina sativa, are genetically very closely related to each other and to Arabidopsis thaliana. Physaria fendleri seeds contain over 50% hydroxy fatty acids (HFAs), while Camelina sativa and Arabidopsis do not accumulate HFAs. To better understand how plants evolved new biochemical pathways with the capacity to accumulate high levels of unusual fatty acids, transcript expression and protein sequences of developing seeds of Physaria fendleri, wild-type Camelina sativa, and Camelina sativa expressing a castor bean (Ricinus communis) hydroxylase were analyzed. A number of potential evolutionary adaptations within lipid metabolism that probably enhance HFA production and accumulation in Physaria fendleri, and, in their absence, limit accumulation in transgenic tissues were revealed. These adaptations occurred in at least 20 genes within several lipid pathways from the onset of fatty acid synthesis and its regulation to the assembly of triacylglycerols. Lipid genes of Physaria fendleri appear to have co-evolved through modulation of transcriptional abundances and alterations within protein sequences. Only a handful of genes showed evidence for sequence adaptation through gene duplication. Collectively, these evolutionary changes probably occurred to minimize deleterious effects of high HFA amounts and/or to enhance accumulation for physiological advantage. These results shed light on the evolution of pathways for novel fatty acid production in seeds, help explain some of the current limitations to accumulation of HFAs in transgenic plants, and may provide improved strategies for future engineering of their production.

  4. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE Consensus Sequence Repeats in the Viral Genome.

    Directory of Open Access Journals (Sweden)

    Ashutosh Kumar

    2016-08-01

    Full Text Available Owing to the reports of microcephaly as a consistent outcome in the foetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV - microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favour of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1 sequence homology between ZIKV genome and the response element of an early neural tube developmental marker ‘retinoic acid’ in human DNA and (2 comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE consensus sequence (5′–AGGTCA–3′ in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly and other viruses available in National Institute of Health genetic sequence database (GenBank for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause foetal brain defects (for which maternal-foetal transmission during developing stage may be required. The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although bioinformatic

  5. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome

    Science.gov (United States)

    Kumar, Ashutosh; Singh, Himanshu N.; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A.

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)—microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker “retinoic acid” in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5′–AGGTCA–3′) in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and

  6. Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17(T) (=DSM 44213T) producing (S,S)-N,N'-ethylenediaminedisuccinic acid.

    Science.gov (United States)

    Stegmann, Evi; Albersmeier, Andreas; Spohn, Marius; Gert, Helena; Weber, Tilmann; Wohlleben, Wolfgang; Kalinowski, Jörn; Rückert, Christian

    2014-11-10

    We report the complete genome sequence of Amycolatopsis japonica MG417-CF17(T) (=DSM 44213(T)) which was identified as the producer of (S,S)-N,N'-ethylenediaminedisuccinic acid during a screening for phospholipase C inhibitors. The genome of A. japonica MG417-CF17(T) consists of two replicons: the chromosome (8,961,318 bp, 68.89% G+C content) and the plasmid pAmyja1 (92,539 bp, 68.23% G+C content), encoding a total of 8422 protein coding genes. Analysis of the sequence data revealed 30 clusters encoding the biosynthesis of secondary metabolites. PMID:25193710

  7. Ruthenium Hydride/Brønsted Acid-Catalyzed Tandem Isomerization/N-Acyliminium Cyclization Sequence for the Synthesis of Tetrahydro-β-carbolines

    DEFF Research Database (Denmark)

    Hansen, Casper Lykke; Clausen, Janie Regitse Waël; Ohm, Ragnhild Gaard;

    2013-01-01

    This paper describes an efficient tandem sequence for the synthesis of 1,2,3,4-tetrahydro-β-carbolines (THBCs) relying on a ruthenium hydride/Brønsted acid- catalyzed isomerization of allylic amides to N-acyliminium ion intermediates which are trapped by a tethered indolenucleophile. The methodol...... the Suzuki cross-coupling reaction to the isomerization/N-acyliminium cyclization sequence. Finally, diastereo- and enantioselective versions of the title reaction have been examined using substrate control (with dr >15: 1) and asymmetric catalysis (ee up to 57%), respectively...

  8. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  9. Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines

    OpenAIRE

    Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.; Lucas, Patrick M

    2013-01-01

    Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which might shed light onto the enzymatic machineries that are involved in its production of biogenic amines.

  10. Data for amino acid alignment of Japanese stingray melanocortin receptors with other gnathostome melanocortin receptor sequences, and the ligand selectivity of Japanese stingray melanocortin receptors

    Directory of Open Access Journals (Sweden)

    Akiyoshi Takahashi

    2016-06-01

    Full Text Available This article contains structure and pharmacological characteristics of melanocortin receptors (MCRs related to research published in “Characterization of melanocortin receptors from stingray Dasyatis akajei, a cartilaginous fish” (Takahashi et al., 2016 [1]. The amino acid sequences of the stingray, D. akajei, MC1R, MC2R, MC3R, MC4R, and MC5R were aligned with the corresponding melanocortin receptor sequences from the elephant shark, Callorhinchus milii, the dogfish, Squalus acanthias, the goldfish, Carassius auratus, and the mouse, Mus musculus. These alignments provide the basis for phylogenetic analysis of these gnathostome melanocortin receptor sequences. In addition, the Japanese stingray melanocortin receptors were separately expressed in Chinese Hamster Ovary cells, and stimulated with stingray ACTH, α-MSH, β-MSH, γ-MSH, δ-MSH, and β-endorphin. The dose response curves reveal the order of ligand selectivity for each stingray MCR.

  11. Cloning, DNA sequencing and heterologous expression of the gene for thermostable N-acylamino acid racemase from Amycolatopsis sp. TS-1-60 in Escherichia coli.

    Science.gov (United States)

    Tokuyama, S; Hatano, K

    1995-03-01

    The gene encoding the novel enzyme N-acylamino acid racemase (AAR) was cloned in recombinant phage lambda-4 from the DNA library of Amycolatopsis sp. TS-1-60, a rare actinomycete, using antiserum against the enzyme. The cloned gene was subcloned and transformed in Escherichia coli JM105 using pUC118 as a vector. The AAR gene consists of an open-reading frame of 1104 nucleotides, which specifies a 368-amino-acid protein with a molecular mass of 39411Da. The molecular mass deduced from the AAR gene is in good agreement with the subunit molecular mass (40kDa) of AAR from Amycolatopsis sp. TS-1-60. The guanosine plus cytosine content of the AAR gene was about 70%. Although the AAR gene uses the unusual initiation codon GTG, the gene was expressed in Escherichia coli using the lac promoter of pUC118. The amount of the enzyme produced by the transformant was 16 times that produced by Amycolatopsis sp. TS-1-60. When the unusual initiation codon GTG was changed to ATG, the enzyme productivity of the transformant increased to more than 37 times that of Amycolatopsis sp. TS-1-60. In the comparison of the DNA sequence and the deduced amino acid sequence of AAR with those of known racemases and epimerases in data bases, no significant sequence homology was found. However, AAR resembles mandelate racemase in that requires metal ions for enzyme activity.(ABSTRACT TRUNCATED AT 250 WORDS)

  12. Separation of small molecular peptides with the same amino acid composition but different sequences by high performance liquid chromatography-electrospray ionization-mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Peptidomics has emerged as a new discipline in recent years. Mass spectrometry (MS) is the most universal and efficient tool for structure identification of proteins and peptides. However,there is a limitation for the identification of peptides with the same amino acid composition but different se-quences because these peptides have identical mass spectra of molecular ions. This paper presents a high performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) method for the separation of small molecular peptides with the same amino acid composition but dif-ferent sequences. Two tripeptides of Gly-Ser-Phe and Gly-Phe-Ser were used as a model sample. The separation behavior has been investigated and the separation conditions have been optimized. Under the optimum conditions,good repeatability was achieved. The developed method could provide a helpful reference for the separation of other peptides with the same amino acid composition but different sequences in the study of proteomics and peptidomics.

  13. Amino acid sequence of the alpha subunit and computer modelling of the alpha and beta subunits of echicetin from the venom of Echis carinatus (saw-scaled viper).

    Science.gov (United States)

    Polgár, J; Magnenat, E M; Peitsch, M C; Wells, T N; Saqi, M S; Clemetson, K J

    1997-04-15

    Echicetin, a heterodimeric protein from the venom of Echis carinatus, binds to platelet glycoprotein Ib (GPIb) and so inhibits platelet aggregation or agglutination induced by various platelet agonists acting via GPIb. The amino acid sequence of the beta subunit of echicetin has been reported and found to belong to the recently identified snake venom subclass of the C-type lectin protein family. Echicetin alpha and beta subunits were purified. N-terminal sequence analysis provided direct evidence that the protein purified was echicetin. The paper presents the complete amino acid sequence of the alpha subunit and computer models of the alpha and beta subunits. The sequence of alpha echicetin is highly similar to the alpha and beta chains of various heterodimeric and homodimeric C-type lectins. Neither of the fully reduced and alkylated alpha or beta subunits of echicetin inhibited the platelet agglutination induced by von Willebrand factor-ristocetin or alpha-thrombin. Earlier reports about the inhibitory activity of reduced and alkylated echicetin beta subunit might have been due to partial reduction of the protein. PMID:9163349

  14. Detection and identification of human Plasmodium species with real-time quantitative nucleic acid sequence-based amplification

    Directory of Open Access Journals (Sweden)

    Kager Piet A

    2006-10-01

    Full Text Available Abstract Background Decisions concerning malaria treatment depend on species identification causing disease. Microscopy is most frequently used, but at low parasitaemia (Plasmodium antigen detection do often not allow for species discrimination as microscopy does, but also become insensitive at Methods This paper reports the development of a sensitive and specific real-time Quantitative Nucleic Acid Sequence Based Amplification (real-time QT-NASBA assays, based on the small-subunit 18S rRNA gene, to identify the four human Plasmodium species. Results The lower detection limit of the assay is 100 – 1000 molecules in vitro RNA for all species, which corresponds to 0.01 – 0.1 parasite per diagnostic sample (i.e. 50 μl of processed blood. The real-time QT-NASBA was further evaluated using 79 clinical samples from malaria patients: i.e. 11 Plasmodium. falciparum, 37 Plasmodium vivax, seven Plasmodium malariae, four Plasmodium ovale and 20 mixed infections. The initial diagnosis of 69 out of the 79 samples was confirmed with the developed real-time QT-NASBA. Re-analysis of seven available original slides resolved five mismatches. Three of those were initially identified as P. malariae mono-infection, but after re-reading the slides P. falciparum was found, confirming the real-time QT-NASBA result. The other two slides were of poor quality not allowing true species identification. The remaining five discordant results could not be explained by microscopy, but may be due to extreme low numbers of parasites present in the samples. In addition, 12 Plasmodium berghei isolates from mice and 20 blood samples from healthy donors did not show any reaction in the assay. Conclusion Real-time QT-NASBA is a very sensitive and specific technique with a detection limit of 0.1 Plasmodium parasite per diagnostic sample (50 μl of blood and can be used for the detection, identification and quantitative measurement of low parasitaemia of Plasmodium species, thus

  15. In vivo targeted magnetic resonance imaging and visualized photodynamic therapy in deep-tissue cancers using folic acid-functionalized superparamagnetic-upconversion nanocomposites

    Science.gov (United States)

    Zeng, Leyong; Luo, Lijia; Pan, Yuanwei; Luo, Song; Lu, Guangming; Wu, Aiguo

    2015-05-01

    Multifunctional nanoprobes used in magnetic resonance imaging (MRI) and photodynamic therapy (PDT) also have potential applications in diagnosis and visualized therapy of cancers, and hence it is important to investigate the active-targeting ability and in vivo reliability of these nanoprobes. In this work, folic acid (FA)-targeted, photosensitizer (PS)-loaded Fe3O4@NaYF4:Yb/Er (FA-NPs-PS) nanocomposites were synthesized for in vivo T2-weighted MRI and visualized PDT of cancers by modeling MCF-7 tumor-bearing nude mice. By measuring the upconversion luminescence (UCL) and fluorescence emission spectra, the as-prepared FA-NPs-PS nanocomposites showed near-infrared (NIR)-triggered PDT performance due to the production of a singlet oxygen species. Moreover, by tracing PS fluorescence in MCF-7, HeLa cells and in MCF-7 tumors, the FA-targeted nanocomposites demonstrated good targeting ability both in vitro and in vivo. Under the irradiation of a 980 nm laser, the viabilities of MCF-7 and HeLa cells incubated with FA-NPs-PS nanocomposites could decrease to about 18.4% and 30.7%, respectively, and the inhibition of MCF-7 tumors could reach about 94.9%. The transverse MR relaxivity of 63.79 mM-1 s-1 (r2 value) and in vivo MR imaging of MCF-7 tumors indicated an excellent T2-weighted MR performance. This work demonstrated that FA-targeted MRI/PDT nanoprobes are effective for in vivo diagnosis and visualized therapy of breast cancers.Multifunctional nanoprobes used in magnetic resonance imaging (MRI) and photodynamic therapy (PDT) also have potential applications in diagnosis and visualized therapy of cancers, and hence it is important to investigate the active-targeting ability and in vivo reliability of these nanoprobes. In this work, folic acid (FA)-targeted, photosensitizer (PS)-loaded Fe3O4@NaYF4:Yb/Er (FA-NPs-PS) nanocomposites were synthesized for in vivo T2-weighted MRI and visualized PDT of cancers by modeling MCF-7 tumor-bearing nude mice. By measuring the

  16. Genomics Analogy Model for Educators (GAME): Fuzzy DNA Model to Enable the Learning of Gene Sequencing by Visually-Impaired and Blind Students

    Science.gov (United States)

    Butler, Charles; Bello, Julia; York, Alan; Orvis, Kathryn; Pittendrigh, Barry R.

    2008-01-01

    Much of the general population is aware of terms such as biotechnology, genetic engineering, and genomics. However, there is a lack of understanding concerning these fields among many secondary school students. Few teaching models exist to explain concepts behind genomics and even less are available for teaching the visually impaired and blind.…

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

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  18. Assignment of fatty acid-beta-oxidizing syntrophic bacteria to Syntrophomonadaceae fam. nov. on the basis of 16S rRNA sequence analyses

    Science.gov (United States)

    Zhao, H.; Yang, D.; Woese, C. R.; Bryant, M. P.

    1993-01-01

    After enrichment from Chinese rural anaerobic digestor sludge, anaerobic, sporing and nonsporing, saturated fatty acid-beta-oxidizing syntrophic bacteria were isolated as cocultures with H2- and formate-utilizing Methanospirillum hungatei or Desulfovibrio sp. strain G-11. The syntrophs degraded C4 to C8 saturated fatty acids, including isobutyrate and 2-methylbutyrate. They were adapted to grow on crotonate and were isolated as pure cultures. The crotonate-grown pure cultures alone did not grow on butyrate in either the presence or the absence of some common electron acceptors. However, when they were reconstituted with M. hungatei, growth on butyrate again occurred. In contrast, crotonate-grown Clostridium kluyveri and Clostridium sticklandii, as well as Clostridium sporogenes, failed to grow on butyrate when these organisms were cocultured with M. hungatei. The crotonate-grown pure subcultures of the syntrophs described above were subjected to 16S rRNA sequence analysis. Several previously documented fatty acid-beta-oxidizing syntrophs grown in pure cultures with crotonate were also subjected to comparative sequence analyses. The sequence analyses revealed that the new sporing and nonsporing isolates and other syntrophs that we sequenced, which had either gram-negative or gram-positive cell wall ultrastructure, all belonged to the phylogenetically gram-positive phylum. They were not closely related to any of the previously known subdivisions in the gram-positive phylum with which they were compared, but were closely related to each other, forming a new subdivision in the phylum. We recommend that this group be designated Syntrophomonadaceae fam. nov.; a description is given.

  19. Amino acid sequence and carbohydrate-binding analysis of the N-acetyl-D-galactosamine-specific C-type lectin, CEL-I, from the Holothuroidea, Cucumaria echinata.

    Science.gov (United States)

    Hatakeyama, Tomomitsu; Matsuo, Noriaki; Shiba, Kouhei; Nishinohara, Shoichi; Yamasaki, Nobuyuki; Sugawara, Hajime; Aoyagi, Haruhiko

    2002-01-01

    CEL-I is one of the Ca2+-dependent lectins that has been isolated from the sea cucumber, Cucumaria echinata. This protein is composed of two identical subunits held by a single disulfide bond. The complete amino acid sequence of CEL-I was determined by sequencing the peptides produced by proteolytic fragmentation of S-pyridylethylated CEL-I. A subunit of CEL-I is composed of 140 amino acid residues. Two intrachain (Cys3-Cys14 and Cys31-Cys135) and one interchain (Cys36) disulfide bonds were also identified from an analysis of the cystine-containing peptides obtained from the intact protein. The similarity between the sequence of CEL-I and that of other C-type lectins was low, while the C-terminal region, including the putative Ca2+ and carbohydrate-binding sites, was relatively well conserved. When the carbohydrate-binding activity was examined by a solid-phase microplate assay, CEL-I showed much higher affinity for N-acetyl-D-galactosamine than for other galactose-related carbohydrates. The association constant of CEL-I for p-nitrophenyl N-acetyl-beta-D-galactosaminide (NP-GalNAc) was determined to be 2.3 x 10(4) M(-1), and the maximum number of bound NP-GalNAc was estimated to be 1.6 by an equilibrium dialysis experiment. PMID:11866098

  20. A comparative study of 2',3'-cyclic-nucleotide 3'-phosphodiesterase in vertebrates: cDNA cloning and amino acid sequences for chicken and bullfrog enzymes.

    Science.gov (United States)

    Kasama-Yoshida, H; Tohyama, Y; Kurihara, T; Sakuma, M; Kojima, H; Tamai, Y

    1997-10-01

    In mammalian brain, two 2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) isoforms, CNP1 and CNP2, are translated, respectively, from the two mRNAs, which have been transcribed and processed by alternative use of the two transcription start points and by differential splicing. In the present study, the cDNAs encoding chicken CNP2 and bullfrog CNP1, respectively, were isolated, and the amino acid sequences of chicken CNP2 and bullfrog CNP1 were deduced. Western blot analysis showed that chicken brain contains a major CNP2-type protein together with a minor unidentified isoform, and bullfrog brain contains only a CNP1-type protein. All available amino acid sequences of vertebrate 2',3'-cyclic-nucleotide 3'-phosphodiesterases were aligned and compared. Three conserved motif sequences were noted: (a) an ATP-binding site near the amino terminus, (b) an isoprenylation site at the carboxyl terminus, and (c) a probable catalytic site resembling the active site of beta-ketoacyl synthase (EC 2.3.1.41). The second and the third motifs are conserved also in goldfish RICH (regeneration-induced 2',3'-cyclic-nucleotide 3'-phosphodiesterase homologue), which has been shown recently to have 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity. The third motif (probably catalytic site) was assigned for the first time in the present report. PMID:9326261

  1. The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements.

    Directory of Open Access Journals (Sweden)

    Jie Feng

    Full Text Available Natrinema sp. J7-2 is an extreme haloarchaeon capable of growing on synthetic media without amino acid supplements. Here we report the complete genome sequence of Natrinema sp. J7-2 which is composed of a 3,697,626-bp chromosome and a 95,989-bp plasmid pJ7-I. This is the first complete genome sequence of a member of the genus Natrinema. We demonstrate that Natrinema sp. J7-2 can use gluconate, glycerol, or acetate as the sole carbon source and that its genome encodes complete metabolic pathways for assimilating these substrates. The biosynthetic pathways for all 20 amino acids have been reconstructed, and we discuss a possible evolutionary relationship between the haloarchaeal arginine synthetic pathway and the bacterial lysine synthetic pathway. The genome harbors the genes for assimilation of ammonium and nitrite, but not nitrate, and has a denitrification pathway to reduce nitrite to N(2O. Comparative genomic analysis suggests that most sequenced haloarchaea employ the TrkAH system, rather than the Kdp system, to actively uptake potassium. The genomic analysis also reveals that one of the three CRISPR loci in the Natrinema sp. J7-2 chromosome is located in an integrative genetic element and is probably propagated via horizontal gene transfer (HGT. Finally, our phylogenetic analysis of haloarchaeal genomes provides clues about evolutionary relationships of haloarchaea.

  2. Comparison of nucleic acid hybridization and nucleic acid amplification using conserved sequences from the 5' noncoding region for detection of bovine viral diarrhea virus.

    OpenAIRE

    Ridpath, J F; Bolin, S R; Katz, J

    1993-01-01

    Primers and probes derived from conserved sequences located in the 5' noncoding region of pestiviruses were evaluated for detection of bovine viral diarrhea virus. With these reagents, hybridization and polymerase chain reaction tests detected 62 of 90 and 90 of 90 bovine viral diarrhea virus isolates, respectively. A quick lysis method for preparing RNA for use in polymerase chain reaction amplification also was evaluated.

  3. Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis.

    Science.gov (United States)

    Neshat, Armin; Mentz, Almut; Rückert, Christian; Kalinowski, Jörn

    2014-11-20

    The Gram-positive bacterium Corynebacterium glutamicum belongs to the order Corynebacteriales and is used as a producer of amino acids at industrial scales. Due to its economic importance, gene expression and particularly the regulation of amino acid biosynthesis has been investigated extensively. Applying the high-resolution technique of transcriptome sequencing (RNA-seq), recently a vast amount of data has been generated that was used to comprehensively analyze the C. glutamicum transcriptome. By analyzing RNA-seq data from a small RNA cDNA library of C. glutamicum, short transcripts in the known transcriptional attenuators sites of the trp operon, the ilvBNC operon and the leuA gene were verified. Furthermore, whole transcriptome RNA-seq data were used to elucidate the transcriptional organization of these three amino acid biosynthesis operons. In addition, we discovered and analyzed the novel attenuator aroR, located upstream of the aroF gene (cg1129). The DAHP synthase encoded by aroF catalyzes the first step in aromatic amino acid synthesis. The AroR leader peptide contains the amino acid sequence motif F-Y-F, indicating a regulatory effect by phenylalanine and tyrosine. Analysis by real-time RT-PCR suggests that the attenuator regulates the transcription of aroF in dependence of the cellular amount of tRNA loaded with phenylalanine when comparing a phenylalanine-auxotrophic C. glutamicum mutant fed with limiting and excess amounts of a phenylalanine-containing dipeptide. Additionally, the very interesting finding was made that all analyzed attenuators are leaderless transcripts. PMID:24910972

  4. 最大子图序列平滑的飞控图层无缝融合技术%Seamless Fusion Technology of Flight Control Visual Layers Based on Maximum Sub-graph Sequence Smooth Method

    Institute of Scientific and Technical Information of China (English)

    姜军; 卓嘎; 王朝霞; 陈延利

    2014-01-01

    Seamless integration of multi-layer technology is the most difficult thing for three-dimensional visual simulation, the seamless integration points requires for fusion with multiple visual layers effectively smooth, reaching the depth of the layer embedded purposes. In the traditional three-dimensional visual layer fusion method, the fuzzy RGB color pixel inter-polation function method is used,the high-order odd curve fitting is taken as the objective function to deploy and achieve the edge of the center pixel fusion, this method has good effect for a layer of smaller differences, but when the layers are quite different, the results is poor. A three-dimensional flight control visual layers seamless fusion technology based on maximum sub-graph sequence smooth method is proposed, the maximum sub-graph sequence of layers is deducted, the fu-sion sequences is transferred into maximum sub-graph smoothers, the flash wave of door forecast is used in different layers, the smoothing correction method is used for a sequence of smooth curves deviate from the point of correction, and the seam-less smooth result is output. The effective three-dimensional visual simulation layer of flight is taken as experiment, and the results show that with the proposed method, the layer fusion result is better than traditional methods, it has good applica-tion value in the integration layer for the three-dimensional visual simulation.%多图层无缝融合技术是三维视景仿真中的难点,无缝融合中要求对多个视景图层的融合点进行有效平滑,达到图层深度嵌入的目的。传统的三维飞控图层无缝融合方法采用基于RGB颜色模糊调配与像素点函数内插方法实现,以高阶奇次曲线拟合为目标函数,内插形成图层融合过渡带,此方法对于图层差异较小的融合有较好效果,当图层差异较大时,效果不佳。提出一种基于最大子图序列平滑的三维飞控图层无缝融合技术,对不同

  5. Unifying bacteria from decaying wood with various ubiquitous Gibbsiella species as G. acetica sp. nov. based on nucleotide sequence similarities and their acetic acid secretion.

    Science.gov (United States)

    Geider, Klaus; Gernold, Marina; Jock, Susanne; Wensing, Annette; Völksch, Beate; Gross, Jürgen; Spiteller, Dieter

    2015-12-01

    Bacteria were isolated from necrotic apple and pear tree tissue and from dead wood in Germany and Austria as well as from pear tree exudate in China. They were selected for growth at 37 °C, screened for levan production and then characterized as Gram-negative, facultatively anaerobic rods. Nucleotide sequences from 16S rRNA genes, the housekeeping genes dnaJ, gyrB, recA and rpoB alignments, BLAST searches and phenotypic data confirmed by MALDI-TOF analysis showed that these bacteria belong to the genus Gibbsiella and resembled strains isolated from diseased oaks in Britain and Spain. Gibbsiella-specific PCR primers were designed from the proline isomerase and the levansucrase genes. Acid secretion was investigated by screening for halo formation on calcium carbonate agar and the compound identified by NMR as acetic acid. Its production by Gibbsiella spp. strains was also determined in culture supernatants by GC/MS analysis after derivatization with pentafluorobenzyl bromide. Some strains were differentiated by the PFGE patterns of SpeI digests and by sequence analyses of the lsc and the ppiD genes, and the Chinese Gibbsiella strain was most divergent. The newly investigated bacteria as well as Gibbsiella querinecans, Gibbsiella dentisursi and Gibbsiella papilionis, isolated in Britain, Spain, Korea and Japan, are taxonomically related Enterobacteriaceae, tolerate and secrete acetic acid. We therefore propose to unify them in the species Gibbsiella acetica sp. nov. PMID:26071988

  6. Ascorbic acid surface modified TiO₂-thin layers as a fully integrated analysis system for visual simultaneous detection of organophosphorus pesticides.

    Science.gov (United States)

    Li, Shunxing; Liang, Wenjie; Zheng, Fengying; Lin, Xiaofeng; Cai, Jiabai

    2014-11-01

    TiO₂ photocatalysis and colorimetric detection are coupled with thin layer chromatography (TLC) for the first time to develop a fully integrated analysis system. Titania@polystyrene hybrid microspheres were surface modified with ascorbic acid, denoted AA-TiO₂@PS, and used as the stationary phase for TLC. Because the affinity between AA-TiO₂@PS and organophosphorus pesticides (OPs) was different for different species of OPs (including chlopyrifos, malathion, parathion, parathion-methyl, and methamidophos), OPs could be separated simultaneously by the mobile phase in 12.0 min with different Rf values. After surface modification, the UV-vis wavelength response range of AA-TiO₂@PS was expanded to 650 nm. Under visible-light irradiation, all of the OPs could be photodegraded to PO₄(3-) in 25.0 min. Based on the chromogenic reaction between PO₄(3-) and chromogenic agents (ammonium molybdate and ascorbic acid), OPs were quantified from color intensity images using a scanner in conjunction with image processing software. So, AA-TiO₂@PS was respectively used as the stationary phase of TLC for efficient separation of OPs, as a photocatalyst for species transformation of phosphorus, and as a colorimetric probe for on-field simultaneous visual detection of OPs in natural water. Linear calibration curves for each OP ranged from 19.3 nmol P L(-1) to 2.30 μmol P L(-1). This integrated analysis system was simple, inexpensive, easy to operate, and sensitive.

  7. FiveS rRNA sequences and fatty acid profiles of colourless sulfur-oxidising bacteria

    Digital Repository Service at National Institute of Oceanography (India)

    LokaBharathi, P.A.; Ortiz-conde, B.A.; Nair, S.; Chandramohan, D.; Colwell, R.R.

    of these organisms have defied identification by API (Appareils et Procedes d'Identification) and biology systems. Hence, computer-aided MIS (Microbial Identification System) has been used to define their relatedness through fatty acid profiles. To characterize...

  8. Comparison of amino acid sequences of the trypsin inhibitors from taro (Colocasia esculenta), giant taro (Alocasia macrorrhiza) and giant swamp taro (Cyrtosperma chamissonis).

    Science.gov (United States)

    Peng, L; Bradbury, J H; Hammer, B C; Shaw, D C

    1993-09-01

    The amino acid sequences of the trypsin inhibitors from taro Colocasia esculenta var. esculenta and giant swamp taro Cyrtosperma chamissonis have been determined and are compared with the protein sequence of the trypsin/chymotrypsin inhibitor from giant taro Alocasia macrorrhiza. Both inhibitors display polymorphism and there is evidence of two components in the giant swamp taro. The positional identity between the proteins is highest at 73-75% for the comparison of the giant taro (GT) with the polymorphic forms of the taro (T) inhibitors and lowest at 56-58% for the pairs of taro and giant swamp taro (GST) proteins. The comparisons show that the inhibitors from T and GT are more related to each other than to GST, which supports their taxonomic classification into different tribes. Location of the P1 site for the trypsin inhibitors of aroids is different from that of other Kunitz-type inhibitors and could be at Leu56.

  9. Development of an electrochemical DNA biosensor for detection of specific Mycobacterium tuberculosis sequence based on poly(L-glutamic acid) modified electrode

    Indian Academy of Sciences (India)

    MERVE YESIL; SONER DONMEZ; FATMA ARSLAN

    2016-11-01

    An electrochemical DNA biosensor was developed by avidin-biotin interaction of a biotinylated probe and avidin-attached, poly(L-glutamic) acid coated pencil graphite electrode (PGA/PGE) for detection of specific Mycobacterium tuberculosis DNA sequence. The discrimination of fully complementary hybridization and mismatch hybridization was carried out by electrochemical reduction current of Meldola’s Blue (MDB) in square wave voltammetry (SWV). The calibration graph of the DNA biosensor was linear between 1.5–12.5 nM and the detection limit was calculated as 1.3 nM. The proposed biosensor successfully discriminated short andlong oligonucleotides related to DNA sequence of Mycobacterium tuberculosis in optimal condition.

  10. Amino acid sequence of toxin XI of the scorpion Buthus occitanus tunetanus. Evidence of a mutation having an important effect upon neurotoxic activity.

    Science.gov (United States)

    Sampieri, F; Habersetzer-Rochat, C; Martin, M F; Kopeyan, C; Rochat, H

    1987-02-01

    The complete amino acid sequence of toxin XI of the North African scorpion Buthus occitanus tunetanus has been elucidated by automatic sequencing of the reduced and alkylated toxin and of the peptides obtained after tryptic cleavage restricted to arginyl bonds. This toxin is structurally homologous to toxin II of Androctonus australis Hector, the most active among the alpha-toxins, but is far less potent, both in vivo and in vitro. This work points out 12 mutations, many of which are conservative. Nevertheless, the most striking difference is the replacement of the lysine residue at position 58, known to be important in the activity of AaH toxin II, by a valine residue. Thus, it seems that the presence of a positive charge at this location facilitates the interactions between the receptor on the sodium channel and the alpha-type toxins.

  11. "Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography.

    Science.gov (United States)

    Nakamura, Akihiko; Ishida, Takuya; Kusaka, Katsuhiro; Yamada, Taro; Fushinobu, Shinya; Tanaka, Ichiro; Kaneko, Satoshi; Ohta, Kazunori; Tanaka, Hiroaki; Inaka, Koji; Higuchi, Yoshiki; Niimura, Nobuo; Samejima, Masahiro; Igarashi, Kiyohiko

    2015-08-01

    Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions. PMID:26601228

  12. Dietary structured triacylglycerols containing docosahexaenoic acid given from birth affect visual and auditory performance and tissue fatty acid profiles of rats

    DEFF Research Database (Denmark)

    Christensen, M. M.; Lund, S. P.; Simonsen, L.;

    1998-01-01

    structured oil, 22:6(n-3) was located in the sn-2 position, whereas it was equally distributed among the three positions in the triacylglycerol molecule in the randomized oil. A reference group was fed rat milk before weaning and nonpurified diet after weaning. After 12 wk, the fevers of 22:6(n-3) in brain...... and liver phospholipids were higher in the groups fed the experimental diets than in the reference group. The specific structured oil resulted in the highest level of 22:6(n-3) in the brain, whereas the level of 22:6(n-3) was highest in the liver of the group fed randomized oil, indicating differences...... the level of 22:6(n-3), in the retina phospholipids were not affected by the three different diets apart from a lower level of 20:4(n-6) in rats fed the experimental diets, indicating a strong tendency to maintain a high level of 22:6(n-3) in the retina. The changes in the fatty acid profiles did not...

  13. Comparative study of effectiveness of Pap smear versus visual inspection with acetic acid and visual inspection with Lugol′s iodine for mass screening of premalignant and malignant lesion of cervix

    Directory of Open Access Journals (Sweden)

    Shuchi Consul

    2012-01-01

    Full Text Available Background and Objective: Cancer of the cervix is a leading cause of morbidity and mortality among women worldwide. Therefore, to curb the disease, there is a need to develop a screening test that has good sensitivity and specificity. The present study is aimed to compare the effectiveness of the Pap smear, visual inspection with acetic acid (VIA and visual inspection with Lugol′s iodine (VILI for mass screening of premalignant and malignant lesions of the cervix; to evaluate the usefulness of VIA and VILI as an adjunct to improve sensitivity of cervical cytology; and to evaluate the role of VILI as a parallel screening method with VIA to enhance its test performance. Design and Setting: This was a prospective, analytical study in which 210 patients of the reproductive age group attending the gynecology OPD were enrolled. Patients and Methods: Patients were first subjected to Pap smear followed by VIA, VILI, colposcopy and biopsy for confirmation of lesion, if needed. Data was obtained and statistically analyzed. Results: Of the 210 patients, 34 (16.27% had positive Pap test, 29 (13.87% had positive VIA and 24 (11.43% had positive VILI and 31 (14.75% showed features of cervical intraepithelial neoplasia (CIN on colposcopy. Of the total of 48 patients in whom either of the screening tests was positive and had undergone cervical biopsy, one had CIN-3, three had CIN-2, 12 had CIN-1, three had carcinoma in situ CIS and 29 reported normal. In our study, 40 patients were picked up as positive by combination of these tests, of which 19 (47.50% had CIN on biopsy. Conclusion: Our study showed that VIA and VILI had sensitivity comparable to Pap smear and can thus be a suitable potential alternative/adjunctive screening test not only in a resource-poor setting but in well-equipped centers also. And, use of a combination of tests (Pap+VIA+VILI had 100% sensitivity but at cost of low specificity and more false-positive results.

  14. Amino acid sequence requirements in the hinge of human immunoglobulin A1 (IgA1) for cleavage by streptococcal IgA1 proteases

    DEFF Research Database (Denmark)

    Batten, MR; Senior, BW; Kilian, Mogens;

    2003-01-01

    The amino acid sequence requirements in the hinge of human immunoglobulin A1 (IgA1) for cleavage by IgA1 proteases of different species of Streptococcus were investigated. Recombinant IgA1 antibodies were generated with point mutations at proline 227 and threonine 228, the residues lying on either...... that proteases from different strains may have different amino acid requirements for cleavage. Remarkably, some streptococcal proteases appeared able to cleave the hinge at a distant alternative site if substitution prevented efficient cleavage of the original site. Hence, this study has identified key residues...... required for the recognition of the IgA1 hinge as a substrate by streptococcal IgA1 proteases, and it marks a preliminary step towards development of specific enzyme inhibitors....

  15. Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne (L.)).

    Science.gov (United States)

    Hegarty, Matthew; Yadav, Rattan; Lee, Michael; Armstead, Ian; Sanderson, Ruth; Scollan, Nigel; Powell, Wayne; Skøt, Leif

    2013-06-01

    Perennial ryegrass (Lolium perenne L.) is the most important forage crop in temperate livestock agriculture. Its nutritional quality has significant impact on the quality of meat and milk for human consumption. Evidence suggests that higher energy content in forage can assist in reducing greenhouse gas emissions from ruminants. Increasing the fatty acid content (especially α-linolenic acid, an omega-3 fatty acid) may thus contribute to better forage, but little is known about the genetic basis of variation for this trait. To this end, quantitative trait loci (QTLs) were identified associated with major fatty acid content in perennial ryegrass using a population derived from a cross between the heterozygous and outbreeding high-sugar grass variety AberMagic and an older variety, Aurora. A genetic map with 434 restriction-associated DNA (RAD) and SSR markers was generated. Significant QTLs for the content of palmitic (C16:0) on linkage groups (LGs) 2 and 7; stearic (C18:0) on LGs 3, 4 and 7; linoleic (C18:2n-6) on LGs 2 and 5; and α-linolenic acids (C18:3n-3) on LG 1 were identified. Two candidate genes (a lipase and a beta-ketoacyl CoA synthase), both associated with C16:0, and separately with C18:2n-6 and C18:0 contents, were identified. The physical positions of these genes in rice and their genetic positions in perennial ryegrass were consistent with established syntenic relationships between these two species. Validation of these associations is required, but the utility of RAD markers for rapid generation of genetic maps and QTL analysis has been demonstrated for fatty acid composition in a global forage crop. PMID:23331642

  16. A case study on the genetic origin of the high oleic acid trait through FAD2-1 DNA sequence variation in safflower (Carthamus tinctorius L.

    Directory of Open Access Journals (Sweden)

    Sara eRapson

    2015-09-01

    Full Text Available The safflower (Carthamus tinctorius L. is considered a strongly domesticated species with a long history of cultivation. The hybridization of safflower with its wild relatives has played an important role in the evolution of cultivars and is of particular interest with regards to their production of high quality edible oils. Original safflower varieties were all rich in linoleic acid, while varieties rich in oleic acid have risen to prominence in recent decades. The high oleic acid trait is controlled by a partially recessive allele ol at a single locus OL. The ol allele was found to be a defective microsomal oleate desaturase FAD2-1. Here we present DNA sequence data and DNA Southern blot analysis suggesting that there has been an ancient hybridization and introgression of the FAD2-1 gene into C. tinctorius from its wild relative C. palaestinus. It is from this gene that FAD2-1Δ was derived more recently. Identification and characterization of the genetic origin and diversity of FAD2-1 could aid safflower breeders in reducing population size and generations required for the development of new high oleic acid varieties by using perfect molecular marker-assisted selection.

  17. Research on Nucleic Acid Sequence Design Methods for DNA Computing%DNA计算中核酸序列设计方法比较研究

    Institute of Scientific and Technical Information of China (English)

    张凯; 耿修堂; 肖建华; 赵东明

    2008-01-01

    DNA computing maps the instances of a reality problem onto specific nucleic acid mol-ecules and protocols so that the result contains the answers to the problem's instances to enable successful extraction.Good DNA sequences prevent unwanted hybridization errors during the computation and enable easy retrieval the answers in the extraction phase.At first,the paper in-troduces two typical nucleic acid sequence methods,free energy based method and Hamming dis-tance based method,and analyzes the influence of constraints on the quality of DNA sequences.In addition,the paper has compared the integrity and computational cost of two methods for ex-cluding the non-specific hybridization sequence.At last,the paper analyzes the efficiency of two nucleic acid sequence design methods.Through the comparison we can see that the Hamming dis-tance based DNA sequence design method can only approximately estimate the thermodynamic stability of DNA hybridization,and can not be a perfect substitute for the minimum free energy method.Further analysis shows that when only consider the free energy of Watson-crick base pairs,the calculation of free energy will be equal to the Hamming distance method.So,if the precision satisfied the requirement of experiment,Hamming distance based DNA sequence design method,not only can effectively distinguish between specific and non-specific hybridization,and effectively reduce the amount of calculation,improve the efficiency of the DNA sequence designing.%DNA计算是将现实问题进行编码,映射到DNA分子上,然后通过分子生物实验产生出代表问题解的DNA分子.最后通过检测技术提取出该DNA分子.高质量的DNA编码可以尽可能避免或减少计算过程中出现的错误,并使检测阶段易于提取出代表问题解的DNA分子.文中对基于汉明距离和基于自由能的DNA核酸编码方法进行研究,分析了两类方法的约束条件对DNA编码质量的影响,比较了两类方法排除非特异性

  18. Visualizing Data Streams

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Pak C.; Foote, Harlan P.; Adams, Daniel R.; Cowley, Wendy E.; Leung, Lai R.; Thomas, James J.

    2004-12-01

    We introduce two dynamic visualization techniques using multi-dimensional scaling to analyze transient data streams such as newswires and remote sensing imagery. While the time-sensitive nature of these data streams requires immediate attention in many applications, the unpredictable and unbounded characteristics of this information can potentially overwhelm many scaling algorithms that require a full re-computation for every update. We present an adaptive visualization technique based on data stratification to ingest stream information adaptively when influx rate exceeds processing rate. We also describe an incremental visualization technique based on data fusion to project new information directly onto a visualization subspace spanned by the singular vectors of the previously processed neighboring data. The ultimate goal is to leverage the value of legacy and new information and minimize re-processing of the entire dataset in full resolution. We demonstrate these dynamic visualization results using a newswire corpus and a remote sensing imagery sequence.

  19. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

    OpenAIRE

    Selvaraj S; Jayaram B; Saranya N; Gromiha M; Fukui Kazuhiko

    2011-01-01

    Abstract Background Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology. Methods We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such...

  20. A study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition

    Directory of Open Access Journals (Sweden)

    Hiromi Daiyasu

    2005-01-01

    Full Text Available Cellular membrane lipids, of which phospholipids are the major constituents, form one of the characteristic features that distinguish Archaea from other organisms. In this study, we focused on the steps in archaeal phospholipid synthetic pathways that generate polar lipids such as archaetidylserine, archaetidylglycerol, and archaetidylinositol. Only archaetidylserine synthase (ASS, from Methanothermobacter thermautotrophicus, has been experimentally identified. Other enzymes have not been fully examined. Through database searching, we detected many archaeal hypothetical proteins that show sequence similarity to members of the CDP alcohol phosphatidyltransferase family, such as phosphatidylserine synthase (PSS, phosphatidylglycerol synthase (PGS and phosphatidylinositol synthase (PIS derived from Bacteria and Eukarya. The archaeal hypothetical proteins were classified into two groups, based on the sequence similarity. Members of the first group, including ASS from M. thermautotrophicus, were closely related to PSS. The rough agreement between PSS homologue distribution within Archaea and the experimentally identified distribution of archaetidylserine suggested that the hypothetical proteins are ASSs. We found that an open reading frame (ORF tends to be adjacent to that of ASS in the genome, and that the order of the two ORFs is conserved. The sequence similarity of phosphatidylserine decarboxylase to the product of the ORF next to the ASS gene, together with the genomic context conservation, suggests that the ORF encodes archaetidylserine decarboxylase, which may transform archaetidylserine to archaetidylethanolamine. The second group of archaeal hypothetical proteins was related to PGS and PIS. The members of this group were subjected to molecular phylogenetic analysis, together with PGSs and PISs and it was found that they formed two distinct clusters in the molecular phylogenetic tree. The distribution of members of each cluster within Archaea

  1. Draft genome sequence of extremely acidophilic bacterium Acidithiobacillus ferrooxidans DLC-5 isolated from acid mine drainage in Northeast China

    Directory of Open Access Journals (Sweden)

    Peng Chen

    2015-12-01

    Full Text Available Acidithiobacillus ferrooxidans type strain DLC-5, isolated from Wudalianchi in Heihe of Heilongjiang Province, China. Here, we present the draft genome of strain DLC-5 which contains 4,232,149 bp in 2745 contigs with 57.628% GC content and includes 32,719 protein-coding genes and 64 tRNA-encoding genes. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. JNNH00000000.1.

  2. Usefulness of Endoscopic Imaging to Visualize Regional Alterations in Acid Secretion of Noncancerous Gastric Mucosa after Helicobacter pylori Eradication

    Science.gov (United States)

    Iijima, Katsunori; Abe, Yasuhiko; Koike, Tomoyuki; Takahashi, Yasushi; Ara, Nobuyuki; Shimosegawa, Tooru

    2016-01-01

    Purpose Endoscopic diagnosis of gastric cancer (GC) that emerges after eradication of Helicobacter pylori may be affected by unique morphological changes. Using comprehensive endoscopic imaging, which can reveal biological alterations in gastric mucosa after eradication, previous studies demonstrated that Congo red chromoendoscopy (CRE) might clearly show an acid non-secretory area (ANA) with malignant potential, while autofluorescence imaging (AFI) without drug injection or dyeing may achieve early detection or prediction of GC. We aimed to determine whether AFI might be an alternative to CRE for identification of high-risk areas of gastric carcinogenesis after eradication. Materials and Methods We included 27 sequential patients with metachronous GC detected during endoscopic surveillance for a mean of 82.8 months after curative endoscopic resection for primary GC and eradication. After their H. pylori infection status was evaluated by clinical interviews and 13C-urea breath tests, the consistency in the extension of corpus atrophy (e.g., open-type or closed-type atrophy) between AFI and CRE was investigated as a primary endpoint. Results Inconsistencies in atrophic extension between AFI and CRE were observed in 6 of 27 patients, although CRE revealed all GC cases in the ANA. Interobserver and intraobserver agreements in the evaluation of atrophic extension by AFI were significantly less than those for CRE. Conclusions We demonstrated that AFI findings might be less reliable for the evaluation of gastric mucosa with malignant potential after eradication than CRE findings. Therefore, special attention should be paid when we clinically evaluate AFI findings of background gastric mucosa after eradication (University Hospital Medical Information Network Center registration number: UMIN000020849). PMID:27752392

  3. Whole-Exome Sequencing in a South American Cohort Links ALDH1A3, FOXN1 and Retinoic Acid Regulation Pathways to Autism Spectrum Disorders.

    Science.gov (United States)

    Moreno-Ramos, Oscar A; Olivares, Ana María; Haider, Neena B; de Autismo, Liga Colombiana; Lattig, María Claudia

    2015-01-01

    Autism spectrum disorders (ASDs) are a range of complex neurodevelopmental conditions principally characterized by dysfunctions linked to mental development. Previous studies have shown that there are more than 1000 genes likely involved in ASD, expressed mainly in brain and highly interconnected among them. We applied whole exome sequencing in Colombian-South American trios. Two missense novel SNVs were found in the same child: ALDH1A3 (RefSeq NM_000693: c.1514T>C (p.I505T)) and FOXN1 (RefSeq NM_003593: c.146C>T (p.S49L)). Gene expression studies reveal that Aldh1a3 and Foxn1 are expressed in ~E13.5 mouse embryonic brain, as well as in adult piriform cortex (PC; ~P30). Conserved Retinoic Acid Response Elements (RAREs) upstream of human ALDH1A3 and FOXN1 and in mouse Aldh1a3 and Foxn1 genes were revealed using bioinformatic approximation. Chromatin immunoprecipitation (ChIP) assay using Retinoid Acid Receptor B (Rarb) as the immunoprecipitation target suggests RA regulation of Aldh1a3 and Foxn1 in mice. Our results frame a possible link of RA regulation in brain to ASD etiology, and a feasible non-additive effect of two apparently unrelated variants in ALDH1A3 and FOXN1 recognizing that every result given by next generation sequencing should be cautiously analyzed, as it might be an incidental finding. PMID:26352270

  4. Whole-Exome Sequencing in a South American Cohort Links ALDH1A3, FOXN1 and Retinoic Acid Regulation Pathways to Autism Spectrum Disorders.

    Science.gov (United States)

    Moreno-Ramos, Oscar A; Olivares, Ana María; Haider, Neena B; de Autismo, Liga Colombiana; Lattig, María Claudia

    2015-01-01

    Autism spectrum disorders (ASDs) are a range of complex neurodevelopmental conditions principally characterized by dysfunctions linked to mental development. Previous studies have shown that there are more than 1000 genes likely involved in ASD, expressed mainly in brain and highly interconnected among them. We applied whole exome sequencing in Colombian-South American trios. Two missense novel SNVs were found in the same child: ALDH1A3 (RefSeq NM_000693: c.1514T>C (p.I505T)) and FOXN1 (RefSeq NM_003593: c.146C>T (p.S49L)). Gene expression studies reveal that Aldh1a3 and Foxn1 are expressed in ~E13.5 mouse embryonic brain, as well as in adult piriform cortex (PC; ~P30). Conserved Retinoic Acid Response Elements (RAREs) upstream of human ALDH1A3 and FOXN1 and in mouse Aldh1a3 and Foxn1 genes were revealed using bioinformatic approximation. Chromatin immunoprecipitation (ChIP) assay using Retinoid Acid Receptor B (Rarb) as the immunoprecipitation target suggests RA regulation of Aldh1a3 and Foxn1 in mice. Our results frame a possible link of RA regulation in brain to ASD etiology, and a feasible non-additive effect of two apparently unrelated variants in ALDH1A3 and FOXN1 recognizing that every result given by next generation sequencing should be cautiously analyzed, as it might be an incidental finding.

  5. Purification, N-terminal amino acid sequence, and some properties of Cu, Zn-superoxide dismutase from Japanese flounder (Paralichthys olivaceus) hepato-pancreas.

    Science.gov (United States)

    Osatomi, K; Masuda, Y; Hara, K; Ishihara, T

    2001-04-01

    Cu, Zn-superoxide dismutase (SOD) has been purified to homogeneity from Japanese flounder Paralichthys olivaceus hepato-pancreas. The purification of the enzyme was carried out by an ethanol/chloroform treatment and acetone precipitation, and then followed by column chromatographies on Q-Sepharose, S-Sepharose and Ultrogel AcA 54. On SDS-PAGE, the purified enzyme gave a single protein band with molecular mass of 17.8 kDa under reducing conditions, and showed approximately equal proportions of 17.8 and 36 kDa molecular mass under non-reducing conditions. Three bands were obtained when the purified enzyme was subjected to native-PAGE, both on protein and activity staining, but the electrophoretic mobility of the purified enzyme differed from that of bovine erythrocyte Cu, Zn-SOD. Isoelectric point values of 5.9, 6.0 and 6.2, respectively, were obtained for the three components. The N-terminal amino acid sequence of the purified enzyme was determined for 25 amino acid residues, and the sequence was compared with other Cu, Zn-SODs. The N-terminal alanine residue was unacetylated, as in the case of swordfish SOD. Above 60 degrees C, the thermostability of the enzyme was much lower than that of bovine Cu, Zn-SOD. PMID:11290457

  6. Ascorbic acid surface modified TiO2-thin layers as a fully integrated analysis system for visual simultaneous detection of organophosphorus pesticides

    Science.gov (United States)

    Li, Shunxing; Liang, Wenjie; Zheng, Fengying; Lin, Xiaofeng; Cai, Jiabai

    2014-11-01

    TiO2 photocatalysis and colorimetric detection are coupled with thin layer chromatography (TLC) for the first time to develop a fully integrated analysis system. Titania@polystyrene hybrid microspheres were surface modified with ascorbic acid, denoted AA-TiO2@PS, and used as the stationary phase for TLC. Because the affinity between AA-TiO2@PS and organophosphorus pesticides (OPs) was different for different species of OPs (including chlopyrifos, malathion, parathion, parathion-methyl, and methamidophos), OPs could be separated simultaneously by the mobile phase in 12.0 min with different Rf values. After surface modification, the UV-vis wavelength response range of AA-TiO2@PS was expanded to 650 nm. Under visible-light irradiation, all of the OPs could be photodegraded to PO43- in 25.0 min. Based on the chromogenic reaction between PO43- and chromogenic agents (ammonium molybdate and ascorbic acid), OPs were quantified from color intensity images using a scanner in conjunction with image processing software. So, AA-TiO2@PS was respectively used as the stationary phase of TLC for efficient separation of OPs, as a photocatalyst for species transformation of phosphorus, and as a colorimetric probe for on-field simultaneous visual detection of OPs in natural water. Linear calibration curves for each OP ranged from 19.3 nmol P L-1 to 2.30 μmol P L-1. This integrated analysis system was simple, inexpensive, easy to operate, and sensitive.TiO2 photocatalysis and colorimetric detection are coupled with thin layer chromatography (TLC) for the first time to develop a fully integrated analysis system. Titania@polystyrene hybrid microspheres were surface modified with ascorbic acid, denoted AA-TiO2@PS, and used as the stationary phase for TLC. Because the affinity between AA-TiO2@PS and organophosphorus pesticides (OPs) was different for different species of OPs (including chlopyrifos, malathion, parathion, parathion-methyl, and methamidophos), OPs could be separated

  7. Visual agnosia.

    Science.gov (United States)

    Álvarez, R; Masjuan, J

    2016-03-01

    Visual agnosia is defined as an impairment of object recognition, in the absence of visual acuity or cognitive dysfunction that would explain this impairment. This condition is caused by lesions in the visual association cortex, sparing primary visual cortex. There are 2 main pathways that process visual information: the ventral stream, tasked with object recognition, and the dorsal stream, in charge of locating objects in space. Visual agnosia can therefore be divided into 2 major groups depending on which of the two streams is damaged. The aim of this article is to conduct a narrative review of the various visual agnosia syndromes, including recent developments in a number of these syndromes.

  8. CSTX-9, a toxic peptide from the spider Cupiennius salei: amino acid sequence, disulphide bridge pattern and comparison with other spider toxins containing the cystine knot structure.

    Science.gov (United States)

    Schalle, J; Kämpfer, U; Schürch, S; Kuhn-Nentwig, L; Haeberli, S; Nentwig, W

    2001-09-01

    CSTX-9 (68 residues, 7530.9 Da) is one of the most abundant toxic polypeptides in the venom of the wandering spider Cupiennius salei. The amino acid sequence was determined by Edman degradation using reduced and alkylated CSTX-9 and peptides generated by cleavages with endoproteinase Asp-N and trypsin, respectively. Sequence comparison with CSTX-1, the most abundant and the most toxic polypeptide in the crude spider venom, revealed a high degree of similarity (53% identity). By means of limited proteolysis with immobilised trypsin and RP-HPLC, the cystine-containing peptides of CSTX-9 were isolated and the disulphide bridges were assigned by amino acid analysis, Edman degradation and nanospray tandem mass spectrometry. The four disulphide bonds present in CSTX-9 are arranged in the following pattern: 1-4, 2-5, 3-8 and 6-7 (Cys6-Cys21, Cys13-Cys30, Cys20-Cys48, Cys32-Cys46). Sequence comparison of CSTX-1 with CSTX-9 clearly indicates the same disulphide bridge pattern, which is also found in other spider polypeptide toxins, e.g. agatoxins (omega-AGA-IVA, omega-AGA-IVB, mu-AGA-I and mu-AGA-VI) from Agelenopsis aperta, SNX-325 from Segestria florentina and curtatoxins (CT-I, CT-II and CT-III) from Hololena curta. CSTX-1/CSTX-9 belong to the family of ion channel toxins containing the inhibitor cystine knot structural motif. CSTX-9, lacking the lysine-rich C-terminal tail of CSTX-1, exhibits a ninefold lower toxicity to Drosophila melanogaster than CSTX-1. This is in accordance with previous observations of CSTX-2a and CSTX-2b, two truncated forms of CSTX-1 which, like CSTX-9, also lack the C-terminal lysine-rich tail. PMID:11693532

  9. FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences [v1; ref status: indexed, http://f1000r.es/2u2

    Directory of Open Access Journals (Sweden)

    Leyla Garcia

    2014-02-01

    Full Text Available Summary: FeatureViewer is a BioJS component that lays out, maps, orients, and renders position-based annotations for protein sequences. This component is highly flexible and customizable, allowing the presentation of annotations by rows, all centered, or distributed in non-overlapping tracks. It uses either lines or shapes for sites and rectangles for regions. The result is a powerful visualization tool that can be easily integrated into web applications as well as documents as it provides an export-to-image functionality. Availability: https://github.com/biojs/biojs/blob/master/src/main/javascript/Biojs.FeatureViewer.js; http://dx.doi.org/10.5281/zenodo.7719

  10. cDNA and deduced amino acid sequence of human pulmonary surfactant-associated proteolipid SPL(Phe).

    OpenAIRE

    Glasser, S W; Korfhagen, T R; Weaver, T.; Pilot-Matias, T; Fox, J L; Whitsett, J A

    1987-01-01

    Hydrophobic surfactant-associated protein of Mr 6000-14,000 was isolated from ether/ethanol or chloroform/methanol extracts of mammalian pulmonary surfactant. Automated Edman degradation in a gas-phase sequencer showed the major N-terminus of the human low molecular weight protein to be Phe-Pro-Ile-Pro-Leu-Pro-Tyr-Cys-Trp-Leu-Cys-Arg-Ala-Leu-. Because of the N-terminal phenylalanine, the surfactant protein was designated SPL(Phe). Antiserum generated against hydrophobic surfactant protein(s) ...

  11. Acetic acid bacteria from biofilm of strawberry vinegar visualized by microscopy and detected by complementing culture-dependent and culture-independent techniques.

    Science.gov (United States)

    Valera, Maria José; Torija, Maria Jesús; Mas, Albert; Mateo, Estibaliz

    2015-04-01

    Acetic acid bacteria (AAB) usually develop biofilm on the air-liquid interface of the vinegar elaborated by traditional method. This is the first study in which the AAB microbiota present in a biofilm of vinegar obtained by traditional method was detected by pyrosequencing. Direct genomic DNA extraction from biofilm was set up to obtain suitable quality of DNA to apply in culture-independent molecular techniques. The set of primers and TaqMan--MGB probe designed in this study to enumerate the total AAB population by Real Time--PCR detected between 8 × 10(5) and 1.2 × 10(6) cells/g in the biofilm. Pyrosequencing approach reached up to 10 AAB genera identification. The combination of culture-dependent and culture-independent molecular techniques provided a broader view of AAB microbiota from the strawberry biofilm, which was dominated by Ameyamaea, Gluconacetobacter, and Komagataeibacter genera. Culture-dependent techniques allowed isolating only one genotype, which was assigned into the Ameyamaea genus and which required more analysis for a correct species identification. Furthermore, biofilm visualization by laser confocal microscope and scanning electronic microscope showed different dispositions and cell morphologies in the strawberry vinegar biofilm compared with a grape vinegar biofilm. PMID:25475315

  12. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  13. Visual art and visual perception

    NARCIS (Netherlands)

    Koenderink, Jan J.

    2015-01-01

    Visual art and visual perception ‘Visual art’ has become a minor cul-de-sac orthogonal to THE ART of the museum directors and billionaire collectors. THE ART is conceptual, instead of visual. Among its cherished items are the tins of artist’s shit (Piero Manzoni, 1961, Merda d’Artista) “worth their

  14. Explosive Field Visualization Based on Image Fusion

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wen-yao; JIANG Ling-shuang

    2009-01-01

    m the composite sequence. Experimental results show that the new images integrate the advantages of sources, effectively improve the visualization, and disclose more information about explosive field.

  15. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles (Del Mar, CA); Koster, Hubert (La Jolla, CA)

    2010-09-28

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  16. A New Approach to Sequence Analysis Exemplified by Identification of cis-Elements in Abscisic Acid Inducible Promoters

    DEFF Research Database (Denmark)

    Busk, Peter Kamp; Hallin, Peter Fischer; Salomon, Jesper;

    Identification of cis-regulatory elements in DNA promoters by computational approaches are a great help in genome-wide elucidation of signal transduction, transcriptional regulation and gene expression. However, to accomplish this has proven a difficult problem in computational genomics in part due...... the sequences of known cis-elements for promoter prediction4. This is a computational alternative to genome-wide DNA array analysis of gene expression and can be used to confirm the importance of known promoter elements on a genome level. Unfortunately, this approach does not yield information about new cis...... to the redundant nature of cis-regulatory elements1. Moreover, promoter context and chromatin structure have an important influence on the function of cis-elements and does further complicate the identification of functional cis-elements2,3. A related computational approach to promoter studies is to use...

  17. Flow visualization

    CERN Document Server

    Merzkirch, Wolfgang

    1974-01-01

    Flow Visualization describes the most widely used methods for visualizing flows. Flow visualization evaluates certain properties of a flow field directly accessible to visual perception. Organized into five chapters, this book first presents the methods that create a visible flow pattern that could be investigated by visual inspection, such as simple dye and density-sensitive visualization methods. It then deals with the application of electron beams and streaming birefringence. Optical methods for compressible flows, hydraulic analogy, and high-speed photography are discussed in other cha

  18. 醋酸加碘染色肉眼观察法筛查宫颈癌的影响因素%Effect factors of visual inspection with acetic acid and iodine staining in screening of cervical cancer

    Institute of Scientific and Technical Information of China (English)

    樊婷婷; 赵树旺; 崔丽阳; 李洁; 岳天孚; 张丽琴; 魏丽惠; 乔友林

    2011-01-01

    Objective: To explore the effect factors of visual inspection with acetic acid and iodine staining in screening of cervical cancer.Methods: 2003 women who received cervical cancer screening voluntarily were surveyed by a questionnaire, visual inspection with acetic acid and iodine staining was used in the study, pathological diagnosis was applied to confirm the screening results, the effect factors of visual inspection with acetic acid and iodine staining in screening of cervical cancer were analyzed.Results: Experienced doctors had positive impact on the screening results of cervical cancer by visual inspection with acetic acid and iodine staining (β < 0, OR < 1, P < 0.05 ); not taking part in cervical cancer screening within the past 3 years and cervical inflammation had negative impact on the screening results of cervical cancer by visual inspection with acetic acid and iodine staining (β >0, OR > 1, P <0.05 ).The effects of pregnancy times, delivery modes, parturition times, action time of acetic acid and placement of IUD or not had no obvious impact on the screening results of cervical cancer by visual inspection with acetic acid and iodine staining (P > 0.05 ).Conclusion: When using visual inspection with acetic acid and iodine staining in screening of cervical cancer, the rate of missed diagnosis and false positive rate should be reduced for the women with cervical inflammation; technical training for doctors needs strengthening; women should be encouraged to take part in cervical cancer screening regularly; visual inspection with acetic acid and iodine staining is not recommended for postmenopausal women.%目的:探讨醋酸加碘染色肉眼观察法(VIA-VILI)筛查宫颈癌的影响因素.方法:对2003例自愿参加宫颈癌筛查的妇女进行问卷调查,采用VIA-VILI方法筛查宫颈癌,并应用病理诊断对筛查结果进行确认,分析可能影响VIA-VILI方法筛查结果的因素.结果:有经验医师对VIA-VILI方法的

  19. Visualization of Concurrent Program Executions

    Science.gov (United States)

    Artho, Cyrille; Havelund, Klaus; Honiden, Shinichi

    2007-01-01

    Various program analysis techniques are efficient at discovering failures and properties. However, it is often difficult to evaluate results, such as program traces. This calls for abstraction and visualization tools. We propose an approach based on UML sequence diagrams, addressing shortcomings of such diagrams for concurrency. The resulting visualization is expressive and provides all the necessary information at a glance.

  20. Soluble forms of tumor necrosis factor receptors (TNF-Rs). The cDNA for the type I TNF-R, cloned using amino acid sequence data of its soluble form, encodes both the cell surface and a soluble form of the receptor

    DEFF Research Database (Denmark)

    Nophar, Y; Kemper, O; Brakebusch, C;

    1990-01-01

    in the extracellular domains of the nerve growth factor receptor and the B lymphocytes surface antigen CDw40. The amino acid composition and size of the extracellular domain of the type I TNF-R closely resemble those of TBPI. The COOH-terminal amino acid sequence of the four cysteine rich repeats within...... the extracellular domain of the type I TNF-R matches the COOH-terminal sequence of TBPI. Amino acid sequences in the extracellular domain also fully match other sequences found in TBPI. On the other hand, amino acid sequences in the soluble form of the type II TNF-R (TBPII), while indicating a marked homology...

  1. Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland.

    Science.gov (United States)

    Susanti, Dwi; Johnson, Eric F; Lapidus, Alla; Han, James; Reddy, T B K; Pilay, Manoj; Ivanova, Natalia N; Markowitz, Victor M; Woyke, Tanja; Kyrpides, Nikos C; Mukhopadhyay, Biswarup

    2016-01-01

    This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H2S. A metabolic construction derived from the draft genome identified putative pathways for peptide degradation and sulfur respiration in this archaeon. Existence of several hydrogenase genes in the genome supported previous findings that H2 is produced during the growth of D. mobilis in the absence of sulfur. Interestingly, genes encoding glucose transport and utilization systems also exist in the D. mobilis genome though this archaeon does not utilize carbohydrate for growth. The draft genome of D. mobilis provides an additional mean for comparative genomic analysis of desulfurococci. In addition, our analysis on the Average Nucleotide Identity between D. mobilis and Desulfurococcus mucosus suggested that these two desulfurococci are two different strains of the same species.

  2. Identification and Characterization of Second-Generation Invader Locked Nucleic Acids (LNAs) for Mixed-Sequence Recognition of Double-Stranded DNA

    DEFF Research Database (Denmark)

    Sau, Sujay P; Madsen, Andreas S; Podbevsek, Peter;

    2013-01-01

    , but substantial efforts are currently devoted to the development of alternative strategies that overcome the limitations observed with the classic approaches. In 2005, we introduced Invader locked nucleic acids (LNAs), i.e., double-stranded probes that are activated for mixed-sequence recognition of dsDNA through...... modification with "+1 interstrand zippers" of 2'-N-(pyren-1-yl)methyl-2'-amino-α-l-LNA monomers. Despite promising preliminary results, progress has been slow because of the synthetic complexity of the building blocks. Here we describe a study that led to the identification of two simpler classes of Invader...... monomers. We compare the thermal denaturation characteristics of double-stranded probes featuring different interstrand zippers of pyrene-functionalized monomers based on 2'-amino-α-l-LNA, 2'-N-methyl-2'-amino-DNA, and RNA scaffolds. Insights from fluorescence spectroscopy, molecular modeling, and NMR...

  3. Visual inspection with acetic acid (via screening program: 7 years experience in early detection of cervical cancer and pre-cancers in rural South India

    Directory of Open Access Journals (Sweden)

    Usha Rani Poli

    2015-01-01

    Full Text Available Cervical cancer continues to be a major public health problem in India in the absence of wide spread organised cervical screening programs. Visual inspection of the cervix with acetic acid (VIA is an effective, inexpensive screening test that can be combined with simple treatment procedures for early cervical lesions, provided by trained health workers. We report 7 years experience in early detection of cervical cancer and pre-cancers using the VIA test in a community-based program in rural Andhra Pradesh, India where there are no existing organised cervical screening programs. Materials and Methods: Eligible women aged between 26 and 60 were opportunistically screened by trained health wor kers using the VIA test. Women who tested positive were further evaluated and those with cervical lesions were treated either by cryotherapy in the screening clinic or referred to a higher center. Results: A total of 18,869 women were screened by a single round of VIA testing with a positive rate of 10.75%. Biopsy proven high-grade squamous intraepithelials (HSILs were 90 (0.48% and low-grade squamous intraepithelials (LSILs were 43 (0.28%. The overall prevalence of cervical intraepithelial neoplasia (CIN 2+ lesion rate is 1.05%. A total of 312 (1.65% cryotherapies were done and 49 women underwent hysterectomy. Conclusions: VIA by trained female health workers is a safe, acceptable, and effective test that can save lives from cervical cancer even in remote areas with few resources. These results have important implications for efficient service delivery in cervical screening programs in low-resourced settings.

  4. Study to assess the acceptability and feasibility of cervical cancer screening using visual inspection with acetic acid and treatment of precancerous lesions using cryotherapy in low resource settings

    Directory of Open Access Journals (Sweden)

    Tosha M. Sheth

    2014-06-01

    Full Text Available Background: Objective of current study was to assess the acceptability and feasibility of cervical cancer screening using VIA, and treatment of precancerous lesions using cryotherapy in low resource settings Methods: 526 women from three primary health centers of Shinor taluka (population based approach and 250 women of Medical College, Vadodara (facility based approach were sensitized and screened for cervical cancer. Visual Inspection with Acetic acid (VIA was performed as the screening test. In the population based approach, VIA positive women were referred to a Community Health Centre (CHC for colposcopy and biopsy. Ablative treatment in the form of cryotherapy was offered. Patients requiring higher forms of treatment were referred to medical college, Vadodara. In the facility based approach, VIA positive women underwent colposcopy. Guided biopsy was performed in those with positive lesions on colposcopy. Cryotherapy was offered in the same sitting. Those not suitable for cryotherapy were offered loop electrosurgical excision procedure. Women found to have invasive cancer were offered definitive management. Results: VIA positivity rate was 18.8% in the population based approach and 27.2% in the facility based approach.58.8% women in the population based approach and 77.77% women in the facility based approach were treated with cryotherapy on the same day as screening and none reported any severe side effects. Dropout rate in the community approach was 32.32% whereas in the facility it was 0.4%. Conclusions: VIA and cryotherapy procedures were well tolerated by all screened women. This project has shown that the and ldquo;screen and treat and rdquo; approach can be successfully implemented in the existing health setup. [Int J Reprod Contracept Obstet Gynecol 2014; 3(3.000: 615-621

  5. Traffic Visualization

    DEFF Research Database (Denmark)

    Picozzi, Matteo; Verdezoto, Nervo; Pouke, Matti;

    2013-01-01

    In this paper, we present a space-time visualization to provide city's decision-makers the ability to analyse and uncover important "city events" in an understandable manner for city planning activities. An interactive Web mashup visualization is presented that integrates several visualization te...

  6. RNA sequencing identifies upregulated kyphoscoliosis peptidase and phosphatidic acid signaling pathways in muscle hypertrophy generated by transgenic expression of myostatin propeptide.

    Science.gov (United States)

    Miao, Yuanxin; Yang, Jinzeng; Xu, Zhong; Jing, Lu; Zhao, Shuhong; Li, Xinyun

    2015-01-01

    Myostatin (MSTN), a member of the transforming growth factor-β superfamily, plays a crucial negative role in muscle growth. MSTN mutations or inhibitions can dramatically increase muscle mass in most mammal species. Previously, we generated a transgenic mouse model of muscle hypertrophy via the transgenic expression of the MSTN N-terminal propeptide cDNA under the control of the skeletal muscle-specific MLC1 promoter. Here, we compare the mRNA profiles between transgenic mice and wild-type littermate controls with a high-throughput RNA sequencing method. The results show that 132 genes were significantly differentially expressed between transgenic mice and wild-type control mice; 97 of these genes were up-regulated, and 35 genes were down-regulated in the skeletal muscle. Several genes that had not been reported to be involved in muscle hypertrophy were identified, including up-regulated myosin binding protein H (mybph), and zinc metallopeptidase STE24 (Zmpste24). In addition, kyphoscoliosis peptidase (Ky), which plays a vital role in muscle growth, was also up-regulated in the transgenic mice. Interestingly, a pathway analysis based on grouping the differentially expressed genes uncovered that cardiomyopathy-related pathways and phosphatidic acid (PA) pathways (Dgki, Dgkz, Plcd4) were up-regulated. Increased PA signaling may increase mTOR signaling, resulting in skeletal muscle growth. The findings of the RNA sequencing analysis help to understand the molecular mechanisms of muscle hypertrophy caused by MSTN inhibition. PMID:25860951

  7. RNA Sequencing Identifies Upregulated Kyphoscoliosis Peptidase and Phosphatidic Acid Signaling Pathways in Muscle Hypertrophy Generated by Transgenic Expression of Myostatin Propeptide

    Directory of Open Access Journals (Sweden)

    Yuanxin Miao

    2015-04-01

    Full Text Available Myostatin (MSTN, a member of the transforming growth factor-β superfamily, plays a crucial negative role in muscle growth. MSTN mutations or inhibitions can dramatically increase muscle mass in most mammal species. Previously, we generated a transgenic mouse model of muscle hypertrophy via the transgenic expression of the MSTN N-terminal propeptide cDNA under the control of the skeletal muscle-specific MLC1 promoter. Here, we compare the mRNA profiles between transgenic mice and wild-type littermate controls with a high-throughput RNA sequencing method. The results show that 132 genes were significantly differentially expressed between transgenic mice and wild-type control mice; 97 of these genes were up-regulated, and 35 genes were down-regulated in the skeletal muscle. Several genes that had not been reported to be involved in muscle hypertrophy were identified, including up-regulated myosin binding protein H (mybph, and zinc metallopeptidase STE24 (Zmpste24. In addition, kyphoscoliosis peptidase (Ky, which plays a vital role in muscle growth, was also up-regulated in the transgenic mice. Interestingly, a pathway analysis based on grouping the differentially expressed genes uncovered that cardiomyopathy-related pathways and phosphatidic acid (PA pathways (Dgki, Dgkz, Plcd4 were up-regulated. Increased PA signaling may increase mTOR signaling, resulting in skeletal muscle growth. The findings of the RNA sequencing analysis help to understand the molecular mechanisms of muscle hypertrophy caused by MSTN inhibition.

  8. RNA sequencing identifies upregulated kyphoscoliosis peptidase and phosphatidic acid signaling pathways in muscle hypertrophy generated by transgenic expression of myostatin propeptide.

    Science.gov (United States)

    Miao, Yuanxin; Yang, Jinzeng; Xu, Zhong; Jing, Lu; Zhao, Shuhong; Li, Xinyun

    2015-04-09

    Myostatin (MSTN), a member of the transforming growth factor-β superfamily, plays a crucial negative role in muscle growth. MSTN mutations or inhibitions can dramatically increase muscle mass in most mammal species. Previously, we generated a transgenic mouse model of muscle hypertrophy via the transgenic expression of the MSTN N-terminal propeptide cDNA under the control of the skeletal muscle-specific MLC1 promoter. Here, we compare the mRNA profiles between transgenic mice and wild-type littermate controls with a high-throughput RNA sequencing method. The results show that 132 genes were significantly differentially expressed between transgenic mice and wild-type control mice; 97 of these genes were up-regulated, and 35 genes were down-regulated in the skeletal muscle. Several genes that had not been reported to be involved in muscle hypertrophy were identified, including up-regulated myosin binding protein H (mybph), and zinc metallopeptidase STE24 (Zmpste24). In addition, kyphoscoliosis peptidase (Ky), which plays a vital role in muscle growth, was also up-regulated in the transgenic mice. Interestingly, a pathway analysis based on grouping the differentially expressed genes uncovered that cardiomyopathy-related pathways and phosphatidic acid (PA) pathways (Dgki, Dgkz, Plcd4) were up-regulated. Increased PA signaling may increase mTOR signaling, resulting in skeletal muscle growth. The findings of the RNA sequencing analysis help to understand the molecular mechanisms of muscle hypertrophy caused by MSTN inhibition.

  9. Uses of Phage Display in Agriculture: Sequence Analysis and Comparative Modeling of Late Embryogenesis Abundant Client Proteins Suggest Protein-Nucleic Acid Binding Functionality

    Directory of Open Access Journals (Sweden)

    Rekha Kushwaha

    2013-01-01

    Full Text Available A group of intrinsically disordered, hydrophilic proteins—Late Embryogenesis Abundant (LEA proteins—has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.

  10. Evaluation of crop residues on potassium kinetics in an acid soil and potassium use efficiency in potato-garlic sequence using tracer 86Rb

    International Nuclear Information System (INIS)

    Greenhouse and laboratory studies were conducted on an acid soil in order to evaluate the role of two crop residues i.e. paddy and wheat along with farmyard manure on potassium kinetics and its availability in the potato-garlic sequence using tracer 86Rb. Under rapid equilibrium, application of crop residues of paddy, wheat straw and FYM were able to enhance soil pH and organic carbon content. In addition, their application helped in enhancing soil K availability indices like water soluble, available and non-exchangeable -K. This was further augmented by the Q/I studies using 86Rb where application of organic residues helped in lowering the potassium buffering capacity of the soil. Greenhouse study supplemented the results obtained from laboratory study where application of crop residues/FYM were able to improve the potato yield significantly and maintained higher concentration of K in potato leaf at early growth stages. A significant correlation was obtained between leaf K and haulms-K with that of 86Rb activities in potato leaf at 35 days and 86Rb absorbed in the haulms, respectively. Residues/ FYM and PK application to potato left sufficient residual effect on succeeding garlic crop. In potato-garlic sequence, K recovery was highest with FYM while N and P recoveries were higher with wheat residues. The nutrient recoveries with PK application followed law of diminishing returns. (author)

  11. Purification, characterization and N-terminal amino acid sequence of a new major allergen from European chestnut pollen--Cas s 1.

    Science.gov (United States)

    Kos, T; Hoffmann-Sommergruber, K; Ferreira, F; Hirschwehr, R; Ahorn, H; Horak, F; Jager, S; Sperr, W; Kraft, D; Scheiner, O

    1993-11-15

    Pollens from trees of the order Fagales (e.g. birch, alder, hazel, and hornbeam) all contain one major allergen--the main cause for tree pollen allergy. So far the major allergens from birch (Bet v 1), alder (Aln g 1), hazel (Cor a 1), and hornbeam (Car b 1) have been characterized, showing high sequence similarity with each other (1-4). We present the molecular and immunologic characterization of Cas s 1, the major allergen from the European chestnut (Castanea sativa). From aqueous pollen extracts from European chestnut a protein was purified to homogeneity and was subjected to further investigation. The protein revealed a Mr of 22 kDa and was shown to represent the major allergen of the European chestnut (immunoblotting, histamine release) and designated Cas s 1. Despite a marked difference in Mr, Cas s 1 shows significant amino acid sequence similarity at the N-terminus and is antigenically closely related to the major birch pollen allergen Bet v 1 (17 kDa), as shown by binding to the anti-Bet v 1 monoclonal antibody BIP-1 and by IgE-inhibition tests using recombinant Bet v 1.

  12. Identification and sequence analysis of pWcMBF8-1, a bacteriocin-encoding plasmid from the lactic acid bacterium Weissella confusa.

    Science.gov (United States)

    Malik, Amarila; Sumayyah, Sumayyah; Yeh, Chia-Wen; Heng, Nicholas C K

    2016-04-01

    Members of the Gram-positive lactic acid bacteria (LAB) are well-known for their beneficial properties as starter cultures and probiotics. Many LAB species produce ribosomally synthesized proteinaceous antibiotics (bacteriocins). Weissella confusa MBF8-1 is a strain isolated from a fermented soybean product that not only produces useful exopolysaccharides but also exhibits bacteriocin activity, which we call weissellicin MBF. Here, we show that bacteriocin production by W. confusa MBF8-1 is specified by a large plasmid, pWcMBF8-1. Plasmid pWcMBF8-1 (GenBank accession number KR350502), which was identified from the W. confusa MBF8-1 draft genome sequence, is 17 643 bp in length with a G + C content of 34.8% and contains 25 open reading frames (ORFs). Six ORFs constitute the weissellicin MBF locus, encoding three putative double-glycine-motif peptides (Bac1, Bac2, Bac3), an ABC transporter complex (BacTE) and a putative immunity protein (BacI). Two ORFs encode plasmid partitioning and mobilization proteins, suggesting that pWcMBF8-1 is transferable to other hosts. To the best of our knowledge, plasmid pWcMBF8-1 not only represents the first large Weissella plasmid to be sequenced but also the first to be associated with bacteriocin production in W. confusa. PMID:26976853

  13. cDNA and deduced amino acid sequence of human pulmonary surfactant-associated proteolipid SPL(Phe)

    Energy Technology Data Exchange (ETDEWEB)

    Glasser, S.W.; Korfhagen, T.R.; Weaver, T.; Pilot-Matias, T.; Fox, J.L.; Whitsett, J.A.

    1987-06-01

    Hydrophobic surfactant-associated protein of M/sub r/ 6000-14,000 was isolated from either/ethanol or chloroform/methanol extracts of mammalian pulmonary surfactant. Automated Edman degradation in a gas-phase sequencer showed the major N-terminus of the human low molecular weight protein to be Phe-Pro-Ile-Pro-Leu-Pro-Try-Cys-Trp-Leu-Cys-Arg-Ala-Leu-. Because of the N-terminal phenylalanine, the surfactant protein was designated SPL(Phe). Antiserum generated against hydrophobic surfactant protein(s) from bovine pulmonary surfactant recognized protein of M/sub r/ 6000-14,000 in immunoblot analysis and was used to screen a lambdagt11 expression library constructed from adult human lung poly(A)/sup +/ RNA. This resulted in identification of a 1.4-kilobase cDNA clone that was shown to encode the N-terminus of the surfactant polypeptide SPL(Phe) (Phe-Pro-Ile-Pro-Leu-Pro-) within an open reading frame for a larger protein. Expression of a fused ..beta..-galactosidase-SPL (Phe) gene in Escherichia coli yielded an immunoreactive M/sub r/ 34,000 fusion peptide. Hybrid-arrested translation with the cDNA and immunoprecipitation of (/sup 35/S)methionine-labeled in vitro translation products of human poly(A)/sup +/ RNA with a surfactant polyclonal antibody resulted in identification of a M/sub r/ 40,000 precursor protein. Blot hybridization analysis of electrophoretically fractionated RNA from human lung detected a 2.0-kilobase RNA that was more abundant in adult lung than in fetal lung. These proteins, and specifically SPL(Phe), may therefore be useful for synthesis of replacement surfactants for treatment of hyaline membrane disease in newborn infants or of other surfactant-deficient states.

  14. Production of bio-hydrogen by mesophilic anaerobic fermentation in an acid-phase sequencing batch reactor.

    Science.gov (United States)

    Cheong, Dae-Yeol; Hansen, Conly L; Stevens, David K

    2007-02-15

    The pH and hydraulic retention time (HRT) of an anaerobic sequencing batch reactor (ASBR) were varied to optimize the conversion of carbohydrate-rich synthetic wastewater into bio-hydrogen. A full factorial design using evolutionary operation (EVOP) was used to determine the effect of the factors and to find the optimum condition of each factor required for high hydrogen production rate. Experimental results from 20 runs indicate that a maximum hydrogen production rate of 4,460-5,540 mL/L/day under the volumetric organic loading rate (VOLR) of 75 g-COD/L/day obtained at an observed design point of HRT = 8 h and pH = 5.7. The hydrogen production rate was strongly dependent on the HRT, and the effect was statistically significant (P 0.05) was found for the pH on the hydrogen production rate. When the ASBR conditions were set for a maximum hydrogen production rate, the hydrogen production yield and specific hydrogen production rate were 60-74 mL/g-COD and 330-360 mL/g-VSS/day, respectively. The hydrogen composition was 43-51%, and no methanogenesis was observed. Acetate, propionate, butyrate, valerate, caproate, and ethanol were major liquid intermediate metabolites during runs of this ASBR. The dominant fermentative types were butyrate-acetate or ethanol-acetate, representing the typical anaerobic pathway of Clostridium species. This hydrogen-producing ASBR had a higher hydrogen production rate, compared with that produced using continuous-flow stirred tank reactors (CSTRs). This study suggests that the hydrogen-producing ASBR is a promising bio-system for prolonged and stable hydrogen production.

  15. cDNA and deduced amino acid sequence of human pulmonary surfactant-associated proteolipid SPL(Phe)

    International Nuclear Information System (INIS)

    Hydrophobic surfactant-associated protein of M/sub r/ 6000-14,000 was isolated from either/ethanol or chloroform/methanol extracts of mammalian pulmonary surfactant. Automated Edman degradation in a gas-phase sequencer showed the major N-terminus of the human low molecular weight protein to be Phe-Pro-Ile-Pro-Leu-Pro-Try-Cys-Trp-Leu-Cys-Arg-Ala-Leu-. Because of the N-terminal phenylalanine, the surfactant protein was designated SPL(Phe). Antiserum generated against hydrophobic surfactant protein(s) from bovine pulmonary surfactant recognized protein of M/sub r/ 6000-14,000 in immunoblot analysis and was used to screen a λgt11 expression library constructed from adult human lung poly(A)+ RNA. This resulted in identification of a 1.4-kilobase cDNA clone that was shown to encode the N-terminus of the surfactant polypeptide SPL(Phe) (Phe-Pro-Ile-Pro-Leu-Pro-) within an open reading frame for a larger protein. Expression of a fused β-galactosidase-SPL (Phe) gene in Escherichia coli yielded an immunoreactive M/sub r/ 34,000 fusion peptide. Hybrid-arrested translation with the cDNA and immunoprecipitation of [35S]methionine-labeled in vitro translation products of human poly(A)+ RNA with a surfactant polyclonal antibody resulted in identification of a M/sub r/ 40,000 precursor protein. Blot hybridization analysis of electrophoretically fractionated RNA from human lung detected a 2.0-kilobase RNA that was more abundant in adult lung than in fetal lung. These proteins, and specifically SPL(Phe), may therefore be useful for synthesis of replacement surfactants for treatment of hyaline membrane disease in newborn infants or of other surfactant-deficient states

  16. Purification and partial amino acid sequences of a new presynaplic toxin and a cytotoxin from venom of pit veper Agkistrodon blomhoffii brevicaudus

    Institute of Scientific and Technical Information of China (English)

    吉永华; 陆丽芳; 徐科; Hiroyuki Hattori; Susumu Terakawa

    1995-01-01

    The technique of the reverse-phase performance liquid chromatography (RP-HPLC) was employed to separate and purify the toxic proteins from the venom of Agkistrodon blomhoffii brevicaudus collected in China 3 toxic proteins marked as AgTx-1, AgTx-2 and AgTx-3 consisting of about 122 amino acid residues were screened The toxicities (LD50,) of the AgTx-1, AgTx-2 and AgTx-3 were 0.075, 0.51 and 6.6 mg per kg weight of mice respectively. Toxicological experiment in the chick biventer cervicis nerve-muscle preparation showed that the acetylcholine (Ach) sensitivity of the preparation was unchanged after the total failure of the indirect contraction caused by AgTx-1 and AgTx-2. suggesting that they were presynaptic blockers, namely β-type of snake toxins. However, the amplitude of indirect contraction of the preparation was gradually reduced due to its incomplete relaxation caused by AgTx-3, indicating that it should belong to the category of cytotoxins. The partial amino acid sequences of 3 toxins have been

  17. Data visualization

    CERN Document Server

    Azzam, Tarek

    2013-01-01

    Do you communicate data and information to stakeholders? In Part 1, we introduce recent developments in the quantitative and qualitative data visualization field and provide a historical perspective on data visualization, its potential role in evaluation practice, and future directions. Part 2 delivers concrete suggestions for optimally using data visualization in evaluation, as well as suggestions for best practices in data visualization design. It focuses on specific quantitative and qualitative data visualization approaches that include data dashboards, graphic recording, and geographic information systems (GIS). Readers will get a step-by-step process for designing an effective data dashboard system for programs and organizations, and various suggestions to improve their utility.

  18. Amino acid sequence requirements in the hinge of human immunoglobulin A1 (IgA1) for cleavage by streptococcal IgA1 proteases.

    Science.gov (United States)

    Batten, Margaret R; Senior, Bernard W; Kilian, Mogens; Woof, Jenny M

    2003-03-01

    The amino acid sequence requirements in the hinge of human immunoglobulin A1 (IgA1) for cleavage by IgA1 proteases of different species of Streptococcus were investigated. Recombinant IgA1 antibodies were generated with point mutations at proline 227 and threonine 228, the residues lying on either side of the peptide bond at which all streptococcal IgA1 proteases cleave wild-type human IgA1. The amino acid substitutions produced no major effect upon the structure of the mutant IgA1 antibodies or their functional ability to bind to Fcalpha receptors. However, the substitutions had a substantial effect upon sensitivity to cleavage with some streptococcal IgA1 proteases, with, in some cases, a single point mutation rendering the antibody resistant to a particular IgA1 protease. This effect was least marked with the IgA1 protease from Streptococcus pneumoniae, which showed no absolute requirement for either proline or threonine at residues 227 to 228. By contrast, the IgA1 proteases of Streptococcus oralis, Streptococcus sanguis, and Streptococcus mitis had an absolute requirement for proline at 227 but not for threonine at 228, which could be replaced by valine. There was evidence in S. mitis that proteases from different strains may have different amino acid requirements for cleavage. Remarkably, some streptococcal proteases appeared able to cleave the hinge at a distant alternative site if substitution prevented efficient cleavage of the original site. Hence, this study has identified key residues required for the recognition of the IgA1 hinge as a substrate by streptococcal IgA1 proteases, and it marks a preliminary step towards development of specific enzyme inhibitors. PMID:12595464

  19. Visual Language in Visual Communication

    OpenAIRE

    Jia Wang

    2009-01-01

    In visual communication the design information is mainly communicated by visual language, the correct use of which is the standard of evaluation of a graphic design composition. Therefore it is necessary to understand and percept visual language properly. It will be helpful for viewers to percept the desired information from the designer as well as the significance within the work.

  20. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  1. Nucleotide and Predicted Amino Acid Sequence-Based Analysis of the Avian Metapneumovirus Type C Cell Attachment Glycoprotein Gene: Phylogenetic Analysis and Molecular Epidemiology of U.S. Pneumoviruses

    Science.gov (United States)

    Alvarez, Rene; Lwamba, Humphrey M.; Kapczynski, Darrell R.; Njenga, M. Kariuki; Seal, Bruce S.

    2003-01-01

    A serologically distinct avian metapneumovirus (aMPV) was isolated in the United States after an outbreak of turkey rhinotracheitis (TRT) in February 1997. The newly recognized U.S. virus was subsequently demonstrated to be genetically distinct from European subtypes and was designated aMPV serotype C (aMPV/C). We have determined the nucleotide sequence of the gene encoding the cell attachment glycoprotein (G) of aMPV/C (Colorado strain and three Minnesota isolates) and predicted amino acid sequence by sequencing cloned cDNAs synthesized from intracellular RNA of aMPV/C-infected cells. The nucleotide sequence comprised 1,321 nucleotides with only one predicted open reading frame encoding a protein of 435 amino acids, with a predicted Mr of 48,840. The structural characteristics of the predicted G protein of aMPV/C were similar to those of the human respiratory syncytial virus (hRSV) attachment G protein, including two mucin-like regions (heparin-binding domains) flanking both sides of a CX3C chemokine motif present in a conserved hydrophobic pocket. Comparison of the deduced G-protein amino acid sequence of aMPV/C with those of aMPV serotypes A, B, and D, as well as hRSV revealed overall predicted amino acid sequence identities ranging from 4 to 16.5%, suggesting a distant relationship. However, G-protein sequence identities ranged from 72 to 97% when aMPV/C was compared to other members within the aMPV/C subtype or 21% for the recently identified human MPV (hMPV) G protein. Ratios of nonsynonymous to synonymous nucleotide changes were greater than one in the G gene when comparing the more recent Minnesota isolates to the original Colorado isolate. Epidemiologically, this indicates positive selection among U.S. isolates since the first outbreak of TRT in the United States. PMID:12682171

  2. Visualization Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Evaluates and improves the operational effectiveness of existing and emerging electronic warfare systems. By analyzing and visualizing simulation results...

  3. On the activation of bovine plasma factor XIII. Amino acid sequence of the peptide released by thrombin and the terminal residues of the subunit polypeptides.

    Science.gov (United States)

    Nakamura, S; Iwanaga, S; Suzuki, T

    1975-12-01

    A blood coagulation factor, Factor XIII, was highly purified from bovine fresh plasma by a method similar to those used for human plasma Factor XIII. The isolated Factor XIII consisted of two subunit polypeptides, a and b chains, with molecular weights of 79,000 +/- 2,000 and 75,000 +/- 2,000, respectively. In the conversion of Factor XIII to the active enzyme, Factor XIIIa, by bovine thrombin [EC 3.4.21.5], a peptide was liberated. This peptide, designated tentatively as "activation peptide," was isolated by gel-filtration on a Sephadex G-75 column. It contained a total of 37 amino acid residues with a masked N-terminal residue and C-terminal arginine. The whole amino acid sequence of "Activation peptide" was established by the dansyl-Edman method and standard enzymatic techniques, and the masked N-terminal residue was identified as N-acetylserine by using a rat liver acylamino acid-releasing enzyme. This enzyme specifically cleaved the N-acetylserylglutamyl peptide bond serine and the remaining peptide, which was now reactive to 1-dimethylamino-naphthalene-5-sulfonyl chloride. A comparison of the sequences of human and bovine "Activation peptide" revealed five amino acids replacements, Ser-3 to Thr; Gly-5 to Arg; Ile-14 to Val; Thr-18 to Asn, and Pro-26 to Leu. Another difference was the deletion of Leu-34 in the human peptide. Adsorption chromatography on a hydroxylapatite column in the presence of 0.1% sodium dodecyl sulfate was developed as a preparative procedure for the resolution of the two subunit polypeptides, a or a' chain and b chain, constituting the protein molecule of Factor XIII or Factor XIIIa. End group analyses on the isolated pure chains revealed that the structural change of Factor XIII during activation with thrombin occurs only in the N-terminal portion of the a chain, not in the N-terminal end of the b chain or in the C-terminal ends of the a and b chains. From these results, it was concluded that the activation of bovine plasma Factor XIII

  4. 醋酸碘染色肉眼观察联合阴道镜检查在农村宫颈癌筛查中的应用价值%Application Value of Visual Inspection with Acetic Acid and Visual Inspec-tion with Lugol's Iodine Combined with Colposcopy in Cervical Cancer Screening in Rural Area

    Institute of Scientific and Technical Information of China (English)

    李惠彬; 张红; 王益林

    2014-01-01

    目的:探讨醋酸碘染色肉眼观察联合阴道镜检查在农村宫颈癌筛查中的临床应用价值。方法采用醋酸肉眼观察法、碘染色肉眼观察法、阴道镜检查,记录患者各项检查结果,给予统计学分析后得出结论。结果1000例健康体检的农村女性人群中,经VIA检测阳性率最高(7.80%),阴道镜检测阳性率最低(0.60%),对比差异有统计学意义(P<0.05)。结论进行醋酸肉眼观察法及碘染色肉眼观察法确定疑似宫颈癌患者,之后行阴道镜活检确诊,可为医师提供准确诊断依据。%Objective To investigate the application value of visual inspection with acetic acid, visual inspection with Lugol's iodine combined with colposcopy in cervical cancer screening in rural area. Methods Visual inspection with acetic acid, visual inspection with Lugol's iodine and colposcopy were used. The results of examination of the patients were recorded, and the conclusion was obtained by statistical analysis. Results Of the 1000 cases of rural females underwent health examination, the positive rate of VIA detection was the highest (7.80%), the positive rate of colposcopy test was the lowest (0.60%), the results were statistically significant (P<0.05). Conclusion Using visual inspection with acetic acid and visual inspection with Lugol's iodine to determine the patients with suspected cervical cancer, then using colposcopy biopsy to diagnose the patients, can provide an accurate diagnosis basis for physicians.

  5. Genome Sequences of the High-Acetic Acid-Resistant Bacteria Gluconacetobacter europaeus LMG 18890T and G. europaeus LMG 18494 (Reference Strains), G. europaeus 5P3, and Gluconacetobacter oboediens 174Bp2 (Isolated from Vinegar) ▿

    OpenAIRE

    Andrés-Barrao, Cristina; Falquet, Laurent; Sandra P Calderon-Copete; Descombes, Patrick; Ortega Pérez, Ruben; Barja, François

    2011-01-01

    Bacteria of the genus Gluconacetobacter are usually involved in the industrial production of vinegars with high acetic acid concentrations. We describe here the genome sequence of three Gluconacetobacter europaeus strains, a very common bacterial species from industrial fermentors, as well as of a Gluconacetobacter oboediens strain.

  6. Visual art and visual perception

    OpenAIRE

    Koenderink, Jan J.

    2015-01-01

    Visual art and visual perception ‘Visual art’ has become a minor cul-de-sac orthogonal to THE ART of the museum directors and billionaire collectors. THE ART is conceptual, instead of visual. Among its cherished items are the tins of artist’s shit (Piero Manzoni, 1961, Merda d’Artista) “worth their weight in gold”. I perceive a metabletic (van den Berg, 1956) parallel to philosophy transforming itself into speculative logic games, and psychology going cognitive by freeing itself from phenomen...

  7. Domain structures and molecular evolution of class I and class II major histocompatibility gene complex (MHC) products deduced from amino acid and nucleotide sequence homologies

    Science.gov (United States)

    Ohnishi, Koji

    1984-12-01

    Domain structures of class I and class II MHC products were analyzed from a viewpoint of amino acid and nucleotide sequence homologies. Alignment statistics revealed that class I (transplantation) antigen H chains consist of four mutually homologous domains, and that class II (HLA-DR) antigen β and α chains are both composed of three mutually homologous ones. The N-terminal three and two domains of class I and class II (both β and α) gene products, respectively, all of which being ˜90 residues long, were concluded to be homologous to β2-microglobulin (β2M). The membraneembedded C-terminal shorter domains of these MHC products were also found to be homologous to one another and to the third domain of class I H chains. Class I H chains were found to be more closely related to class II α chains than to class II β chains. Based on these findings, an exon duplication history from a common ancestral gene encoding a β2M-like primodial protein of one-domain-length up to the contemporary MHC products was proposed.

  8. PhTX-II a Basic Myotoxic Phospholipase A2 from Porthidium hyoprora Snake Venom, Pharmacological Characterization and Amino Acid Sequence by Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Salomón Huancahuire-Vega

    2014-10-01

    Full Text Available A monomeric basic PLA2 (PhTX-II of 14149.08 Da molecular weight was purified to homogeneity from Porthidium hyoprora venom. Amino acid sequence by in tandem mass spectrometry revealed that PhTX-II belongs to Asp49 PLA2 enzyme class and displays conserved domains as the catalytic network, Ca2+-binding loop and the hydrophobic channel of access to the catalytic site, reflected in the high catalytic activity displayed by the enzyme. Moreover, PhTX-II PLA2 showed an allosteric behavior and its enzymatic activity was dependent on Ca2+. Examination of PhTX-II PLA2 by CD spectroscopy indicated a high content of alpha-helical structures, similar to the known structure of secreted phospholipase IIA group suggesting a similar folding. PhTX-II PLA2 causes neuromuscular blockade in avian neuromuscular preparations with a significant direct action on skeletal muscle function, as well as, induced local edema and myotoxicity, in mice. The treatment of PhTX-II by BPB resulted in complete loss of their catalytic activity that was accompanied by loss of their edematogenic effect. On the other hand, enzymatic activity of PhTX-II contributes to this neuromuscular blockade and local myotoxicity is dependent not only on enzymatic activity. These results show that PhTX-II is a myotoxic Asp49 PLA2 that contributes with toxic actions caused by P. hyoprora venom.

  9. Indole acetic acid production by fluorescent Pseudomonas spp. from the rhizosphere of Plectranthus amboinicus (Lour.) Spreng. and their variation in extragenic repetitive DNA sequences.

    Science.gov (United States)

    Sethia, Bedhya; Mustafa, Mariam; Manohar, Sneha; Patil, Savita V; Jayamohan, Nellickal Subramanian; Kumudini, Belur Satyan

    2015-06-01

    Fluorescent Pseudomonas (FP) is a heterogenous group of growth promoting rhizobacteria that regulate plant growth by releasing secondary metabolic compounds viz., indole acetic acid (IAA), siderophores, ammonia and hydrogen cyanide. In the present study, IAA producing FPs from the rhizosphere of Plectranthus amboinicus were characterized morphologically, biochemically and at the molecular level. Molecular identification of the isolates were carried out using Pseudomonas specific primers. The effect of varying time (24, 48, 72 and 96 h), Trp concentrations (100, 200, 300, 400 and 500 μg x ml(-1)), temperature (10, 26, 37 and 50 ± 2 degrees C) and pH (6, 7 and 8) on IAA production by 10 best isolates were studied. Results showed higher IAA production at 72 h incubation, at 300 μg x ml(-1) Trp concentration, temperature 26 ± 2 degrees C and pH 7. TLC with acidified ethyl acetate extract showed that the IAA produced has a similar Rf value to that of the standard IAA. Results of TLC were confirmed by HPLC analysis. Genetic diversity of the isolates was also studied using 40 RAPD and 4 Rep primers. Genetic diversity parameters such as dominance, Shannon index and Simpson index were calculated. Out of 40 RAPD primers tested, 9 (2 OP-D series and 7 OP-E series) were shortlisted for further analysis. Studies using RAPD, ERIC, BOX, REP and GTG5 primers revealed that isolates exhibit significant diversity in repetitive DNA sequences irrespective of the rhizosphere. PMID:26155673

  10. Triplex formation at single-stranded nucleic acid target sites of unrestricted sequence by two added strands of oligonucleotides: A proposed model

    Energy Technology Data Exchange (ETDEWEB)

    Trapane, T.L.; Ts' o, P.O.P. (John Hopkins Univ., Baltimore, MD (United States))

    1994-11-16

    By using the standard purine nucleosides, guanosine and adenosine, and the pyrimidine C-nucleosides, pseudoisocytidine and pseudouridine, as complements on a probe strand, it is possible to construct a regular Watson-Crick helix with a single-stranded target sequence having any arrangement of the four naturally-occurring bases found in nucleic acids. The major groove of this helix will have a unique configuration of hydrogen-bonding sites on the probe strand for each of these four base pairs. By using this duplex as a framework, an ensemble of recognition patterns composed of base triads may be constructed. In these patterns, either a homopyrimidine or homopurine third strand binds in the major groove of the duplex formed by the target and probe strands. Ten distinct geometries, or motifs, are shown, each one consisting of four isomorphic base triads built upon recognition of C, G, A, or U(T) residues in the target strand. In order to maintain specific hydrogen bonding and to construct isomorphous triads, the use of several nonstandard bases is proposed. 33 refs., 9 figs., 3 tabs.

  11. Towards Dense Visual SLAM

    OpenAIRE

    Pietzsch, Tobias

    2011-01-01

    Visual Simultaneous Localisation and Mapping (SLAM) is concerned with simultaneously estimating the pose of a camera and a map of the environment from a sequence of images. Traditionally, sparse maps comprising isolated point features have been employed, which facilitate robust localisation but are not well suited to advanced applications. In this thesis, we present map representations that allow a more dense description of the environment. In one approach, planar features are used to repr...

  12. Visual Education

    DEFF Research Database (Denmark)

    Buhl, Mie; Flensborg, Ingelise

    2010-01-01

    The intrinsic breadth of various types of images creates new possibilities and challenges for visual education. The digital media have moved the boundaries between images and other kinds of modalities (e.g. writing, speech and sound) and have augmented the possibilities for integrating the functi......The intrinsic breadth of various types of images creates new possibilities and challenges for visual education. The digital media have moved the boundaries between images and other kinds of modalities (e.g. writing, speech and sound) and have augmented the possibilities for integrating...... to emerge in the interlocutory space of a global visual repertoire and diverse local interpretations. The two perspectives represent challenges for future visual education which require visual competences, not only within the arts but also within the subjects of natural sciences, social sciences, languages...

  13. Estimation of visual motion in image sequences

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    1994-01-01

    with a priori knowledge. We have surveyed a series of attempts to extract motion invariants. Specifically we have illustrate the use of local Fourier phase. The Fourier phase is shown to define the local shape of the signal, thus accurately localizing an event. Different strategies for local measurement...

  14. The Conversion of L-Phenylalanine to ("S")-2-Hydroxy-3-Phenylpropanoic Acid: A Simple, Visual Example of a Stereospecific S[subscript N]2 Reaction

    Science.gov (United States)

    Van Draanen, Nanine A.; Hengst, Stephanie

    2010-01-01

    We report a simple, inexpensive, visual, and environmentally friendly S[subscript N]2 reaction appropriate for the second-year organic chemistry laboratory that illustrates stereospecificity, dependence of water solubility on the state of ionization, optical activity, and effect of diastereotopic protons in [superscript 1]H NMR spectroscopy. The…

  15. Visual cognition

    Energy Technology Data Exchange (ETDEWEB)

    Pinker, S.

    1985-01-01

    This book consists of essays covering issues in visual cognition presenting experimental techniques from cognitive psychology, methods of modeling cognitive processes on computers from artificial intelligence, and methods of studying brain organization from neuropsychology. Topics considered include: parts of recognition; visual routines; upward direction; mental rotation, and discrimination of left and right turns in maps; individual differences in mental imagery, computational analysis and the neurological basis of mental imagery: componental analysis.

  16. A unique insertion of low complexity amino acid sequence underlies protein-protein interaction in human malaria parasite orotate phosphoribosyltransferase and orotidine 5'-monophosphate decarboxylase

    Institute of Scientific and Technical Information of China (English)

    Waranya Imprasittichai; Sittiruk Roytrakul; Sudaratana R Krungkrai; Jerapan Krungkrai

    2014-01-01

    Objective:To investigate the multienzyme complex formation of human malaria parasite Plasmodium falciparum(P. falciparum) orotate phosphoribosyltransferase(OPRT) and orotidine 5'-monophosphate decarboxylase(OMPDC), the fifth and sixth enzyme of the de novo pyrimidine biosynthetic pathway.Previously, we have clearly established that the two enzymes in the malaria parasite exist physically as a heterotetrameric(OPRT)2(OMPDC)2 complex containing two subunits each ofOPRT andOMPDC, and that the complex have catalytic kinetic advantages over the monofunctional enzyme.Methods:Both enzymes were cloned and expressed as recombinant proteins.The protein-protein interaction in the enzyme complex was identified using bifunctional chemical cross-linker, liquid chromatography-mass spectrometric analysis and homology modeling.Results:The unique insertions of low complexity region at the α2 and α5 helices of the parasiteOMPDC, characterized by single amino acid repeat sequence which was not found in homologous proteins from other organisms, was located on theOPRT-OMPDC interface.The structural models for the protein-protein interaction of the heterotetrameric(OPRT)2(OMPDC)2 multienzyme complex were proposed.Conclusions:Based on the proteomic data and structural modeling, it is surmised that the human malaria parasite low complexity region is responsible for theOPRT-OMPDC interaction.The structural complex of the parasite enzymes, thus, represents an efficient functional kinetic advantage, which in line with co-localization principles of evolutional origin, and allosteric control in protein-protein-interactions.

  17. Quantitative thermodynamic predication of interactions between nucleic acid and non-nucleic acid species using Microsoft excel.

    Science.gov (United States)

    Zou, Jiaqi; Li, Na

    2013-09-01

    Proper design of nucleic acid sequences is crucial for many applications. We have previously established a thermodynamics-based quantitative model to help design aptamer-based nucleic acid probes by predicting equilibrium concentrations of all interacting species. To facilitate customization of this thermodynamic model for different applications, here we present a generic and easy-to-use platform to implement the algorithm of the model with Microsoft(®) Excel formulas and VBA (Visual Basic for Applications) macros. Two Excel spreadsheets have been developed: one for the applications involving only nucleic acid species, the other for the applications involving both nucleic acid and non-nucleic acid species. The spreadsheets take the nucleic acid sequences and the initial concentrations of all species as input, guide the user to retrieve the necessary thermodynamic constants, and finally calculate equilibrium concentrations for all species in various bound and unbound conformations. The validity of both spreadsheets has been verified by comparing the modeling results with the experimental results on nucleic acid sequences reported in the literature. This Excel-based platform described here will allow biomedical researchers to rationalize the sequence design of nucleic acid probes using the thermodynamics-based modeling even without relevant theoretical and computational skills. PMID:23849929

  18. Quantitative thermodynamic predication of interactions between nucleic acid and non-nucleic acid species using Microsoft excel.

    Science.gov (United States)

    Zou, Jiaqi; Li, Na

    2013-09-01

    Proper design of nucleic acid sequences is crucial for many applications. We have previously established a thermodynamics-based quantitative model to help design aptamer-based nucleic acid probes by predicting equilibrium concentrations of all interacting species. To facilitate customization of this thermodynamic model for different applications, here we present a generic and easy-to-use platform to implement the algorithm of the model with Microsoft(®) Excel formulas and VBA (Visual Basic for Applications) macros. Two Excel spreadsheets have been developed: one for the applications involving only nucleic acid species, the other for the applications involving both nucleic acid and non-nucleic acid species. The spreadsheets take the nucleic acid sequences and the initial concentrations of all species as input, guide the user to retrieve the necessary thermodynamic constants, and finally calculate equilibrium concentrations for all species in various bound and unbound conformations. The validity of both spreadsheets has been verified by comparing the modeling results with the experimental results on nucleic acid sequences reported in the literature. This Excel-based platform described here will allow biomedical researchers to rationalize the sequence design of nucleic acid probes using the thermodynamics-based modeling even without relevant theoretical and computational skills.

  19. Cloning of NruI and Sbo13I restriction and modification sstems in E. coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferases

    Directory of Open Access Journals (Sweden)

    Benner Jack

    2010-05-01

    Full Text Available Abstract Background NruI and Sbo13I are restriction enzyme isoschizomers with the same recognition sequence 5' TCG↓CGA 3' (cleavage as indicated↓. Here we report the cloning of NruI and Sbo13I restriction-modification (R-M systems in E. coli. The NruI restriction endonuclease gene (nruIR was cloned by PCR and inverse PCR using primers designed from the N-terminal amino acid sequence. The NruI methylase gene (nruIM was derived by inverse PCR walking. Results The amino acid sequences of NruI endonuclease and methylase are very similar to the Sbo13I R-M system which has been cloned and expressed in E. coli by phage selection of a plasmid DNA library. Dot blot analysis using rabbit polyclonal antibodies to N6mA- or N4mC-modified DNA indicated that M.NruI is possibly a N6mA-type amino-methyltransferase that most likely modifies the external A in the 5' TCGCGA 3' sequence. M.Sbo13I, however, is implicated as a probable N4mC-type methylase since plasmid carrying sbo13IM gene is not restricted by Mrr endonuclease and Sbo13I digestion is not blocked by Dam methylation of the overlapping site. The amino acid sequence of M.NruI and M.Sbo13I did not show significant sequence similarity to many known amino-methyltransferases in the α, β, and γ groups, except to a few putative methylases in sequenced microbial genomes. Conclusions The order of the conserved amino acid motifs (blocks in M.NruI/M.Sbo13I is similar to the γ. group amino-methyltranferases, but with two distinct features: In motif IV, the sequence is DPPY instead of NPPY; there are two additional conserved motifs, IVa and Xa as extension of motifs IV and X, in this family of enzymes. We propose that M.NruI and M.Sbo13I form a subgroup in the γ group of amino-methyltransferases.

  20. 高灵敏可视化核酸试纸条法快速检测 HBV DNA%Development of a sensitive, visual nucleic acid dipstick assay for rapid detection of hepatitis B virus DNA

    Institute of Scientific and Technical Information of China (English)

    杨贤; 黄欢; 殷竹君; 武海萍; 周国华

    2011-01-01

    目的:本研究旨在建立一种基于试纸条的快速、灵敏及可视化检测乙型肝炎病毒核酸的方法.方法:利用聚合酶链反应扩增乙肝病毒的保守区,其中上、下游引物的5'端分别修饰异硫氰酸荧光素和生物素.核酸试纸条上的胶体金以及检测线处分别标记有链霉亲和素以及抗荧光素抗体.将扩增产物与展开液混合后点样,10min 后即可用肉眼判读结果.在优化了展开液成分、上样体积以及上样浓度之后,对该方法的灵敏度进行了评价.最后收集15例阴性样本及33例HBsAg 阳性样本,按血清标志物结果进行分类后使用核酸试纸条进行检测,并与实时荧光PCR的结果进行了比较.结果:试纸条检测乙肝病毒核酸的灵敏度为250eopies/mL.在临床样本的测定中,该方法与实时荧光定量PCR的特异性均为100%.且两种方法检测不同血清标志物类型的阳性检出率无差异.结论:核酸试纸条技术能够用于乙肝病毒核酸的可视化检测,与实时荧光PCR相比检测速度快,具有较好的灵敏度和特异性,适合流行病学调查以及在基层医院体检使用.%Objective: We aimed to develop a nucleic acid dipstick assay (NADA) for rapid and visual detection of Hepatitis B virus (HBV) with a high specificity and sensitivity. Methods: PCR amplification of HBV conserved sequences was carried out by a pair of primers labeled with FITC and biotin at the 5' end respectively. The gold nanoparticles and test zones in the dipstick were modified with anti-fluorescein and strepavidin respectively. PCR products mixed with developing buffer were applied to the sample-loading area of the dipstick and the detection result can be observed 10 min afterward with naked eyes. As the buffer migrates along the strip by capillary action, the PCR products were captured at the test zones by immobilized anti-fiuorescein and detected by strepavidin-funtcionalized gold uanoparticles, thus generating

  1. Amino Acid sequence analysis of the two major outer Capsid Proteins (VP7 and VP4 from human-derived canine G3P[3] Rotavirus Strain Detected in Brazil

    Directory of Open Access Journals (Sweden)

    Adriana Luchs

    2013-12-01

    Full Text Available Introduction: A close look at the rotavirus group A (RVA genotypes in Brazil revealed the detection of a rare G3P[3] strain close related to canine strains. The aim of this study was to add to the already known genetic analysis by the description of the G3P[3] (IAL-R2638 strain amino acid characteristics. Methods: Amino acid sequence analysis and protein based trees were conducted using BioEdit and MEGA 4.0. Results: The VP7 and VP4 protein of the IAL-R2638 strain displayed the highest amino acid identity to the canine-derived human strain HCR3A (99.2%, and to the canine strain RV52/96 (96.4%, respectively. IAL-R2638 strain did not possess an extra VP7 N-linked glycosylation site at amino acid 238 recently described for some G3 strains, as well as RotaTeqTM G3 vaccine strain. The topology exhibited by phylogenetic trees in previous analysis were maintained in the present amino acid-based trees, reinforcing a stable relationship between G3P[3] strains. Conclusions: Amino acid analysis data were consistent with the previous sequence of data obtained for the IAL-R2638 strain, supporting its possible canine origin. Theoretically, RotaTeqTM vaccine could efficiently protect against G3P[3] infections based on the lack of the extra VP7 N-linked glycosylation site at amino acid 238. Phylogenetic analysis hypothesizes that all features undergo evolution independently of each other; however, unfavorable effects of nucleotide substitutions may be compensated by substitutions in other positions. The present study raises the question as to whether the amino acid-based trees could be applied as an approach to the study of RVA evolution, avoiding incorrect phylogenetic reconstructions.

  2. Loop Sequence Context Influences the Formation and Stability of the i-Motif for DNA Oligomers of Sequence (CCCXXX)4, where X = A and/or T, under Slightly Acidic Conditions.

    Science.gov (United States)

    McKim, Mikeal; Buxton, Alexander; Johnson, Courtney; Metz, Amanda; Sheardy, Richard D

    2016-08-11

    The structure and stability of DNA is highly dependent upon the sequence context of the bases (A, G, C, and T) and the environment under which the DNA is prepared (e.g., buffer, temperature, pH, ionic strength). Understanding the factors that influence structure and stability of the i-motif conformation can lead to the design of DNA sequences with highly tunable properties. We have been investigating the influence of pH and temperature on the conformations and stabilities for all permutations of the DNA sequence (CCCXXX)4, where X = A and/or T, using spectroscopic approaches. All oligomers undergo transitions from single-stranded structures at pH 7.0 to i-motif conformations at pH 5.0 as evidenced by circular dichroism (CD) studies. These folded structures possess stacked C:CH(+) base pairs joined by loops of 5'-XXX-3'. Although the pH at the midpoint of the transition (pHmp) varies slightly with loop sequence, the linkage between pH and log K for the proton induced transition is highly loop sequence dependent. All oligomers also undergo the thermally induced i-motif to single-strand transition at pH 5.0 as the temperature is increased from 25 to 95 °C. The temperature at the midpoint of this transition (Tm) is also highly dependent on loop sequence context effects. For seven of eight possible permutations, the pH induced, and thermally induced transitions appear to be highly cooperative and two state. Analysis of the CD optical melting profiles via a van't Hoff approach reveals sequence-dependent thermodynamic parameters for the unfolding as well. Together, these data reveal that the i-motif conformation exhibits exquisite sensitivity to loop sequence context with respect to formation and stability. PMID:27438583

  3. Visual comparison for information visualization

    KAUST Repository

    Gleicher, M.

    2011-09-07

    Data analysis often involves the comparison of complex objects. With the ever increasing amounts and complexity of data, the demand for systems to help with these comparisons is also growing. Increasingly, information visualization tools support such comparisons explicitly, beyond simply allowing a viewer to examine each object individually. In this paper, we argue that the design of information visualizations of complex objects can, and should, be studied in general, that is independently of what those objects are. As a first step in developing this general understanding of comparison, we propose a general taxonomy of visual designs for comparison that groups designs into three basic categories, which can be combined. To clarify the taxonomy and validate its completeness, we provide a survey of work in information visualization related to comparison. Although we find a great diversity of systems and approaches, we see that all designs are assembled from the building blocks of juxtaposition, superposition and explicit encodings. This initial exploration shows the power of our model, and suggests future challenges in developing a general understanding of comparative visualization and facilitating the development of more comparative visualization tools. © The Author(s) 2011.

  4. Visual cognition

    Energy Technology Data Exchange (ETDEWEB)

    Pinker, S.

    1985-01-01

    This collection of research papers on visual cognition first appeared as a special issue of Cognition: International Journal of Cognitive Science. The study of visual cognition has seen enormous progress in the past decade, bringing important advances in our understanding of shape perception, visual imagery, and mental maps. Many of these discoveries are the result of converging investigations in different areas, such as cognitive and perceptual psychology, artificial intelligence, and neuropsychology. This volume is intended to highlight a sample of work at the cutting edge of this research area for the benefit of students and researchers in a variety of disciplines. The tutorial introduction that begins the volume is designed to help the nonspecialist reader bridge the gap between the contemporary research reported here and earlier textbook introductions or literature reviews.

  5. Localization of an O-glycosylated site in the recombinant barley alpha-amylase 1 produced in yeast and correction of the amino acid sequence using matrix-assisted laser desorption/ionization mass spectrometry of peptide mixtures

    DEFF Research Database (Denmark)

    Andersen, Jens S.; Søgaard, M; Svensson, B;

    1994-01-01

    , and analyzed directly by MALDI-MS. Based on the three mass spectrometric peptide maps, an error in the sequence deduced from cDNA, resulting in a mass difference of 28 Da, was located to a sequence stretch of 5 amino acid residues; furthermore, a dihexose substituent was identified on Thr410. Subsequent Edman...... degradation of two selected peptides isolated from the endoproteinase Lys-C digest corrected the sequence to be Val instead of Ala in position 284 and confirmed the O-glycosylation. These results demonstrate that the direct peptide mixture analysis by MALDI-MS is a rapid and sensitive method for protein......Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of peptide mixtures was used to characterize recombinant barley alpha-amylase 1, produced in yeast. Three peptide mixtures were generated by cleavage with CNBr, digestion with endoproteinase Lys-C and Asp-N, respectively...

  6. Molecular cloning of the α-subunit of human prolyl 4-hydroxylase: The complete cDNA-derived amino acid sequence and evidence for alternative splicing of RNA transcripts

    International Nuclear Information System (INIS)

    Prolyl 4-hydroxylase an α2β2 tetramer, catalyzes the formation of 4-hydroxyproline in collagens by the hydroxylation of proline residues in peptide linkages. The authors report here on the isolation of cDNA clones encoding the α-subunit of the enzyme from human tumor HT-1080, placenta, and fibroblast cDNA libraries. Eight overlapping clones covering almost all of the corresponding 3,000-nucleotide mRNA, including all the coding sequences, were characterized. These clones encode a polypeptide of 517 amino acid residues and a signal peptide of 17 amino acids. Previous characterization of cDNA clones for the β-subunit of prolyl 4-hydroxylase has indicated that its C terminus has the amino acid sequence Lys-Asp-Gly-Leu, which, it has been suggested, is necessary for the retention of a polypeptide within the lumen of the endoplasmic reticulum. The α-subunit does not have this C-terminal sequence, and thus one function of the β-subunit in the prolyl 4-hydroxylase tetramer appears to be to retain the enzyme within this cell organelle. Southern blot analyses of human genomic DNA with a cDNA probe for the α-subunit suggested the presence of only one gene encoding the two types of mRNA, which appear to result from mutually exclusive alternative splicing of primary transcripts of one gene

  7. Assessment of Epstein-Barr virus nucleic acids in gastric but not in breast cancer by next-generation sequencing of pooled Mexican samples

    Science.gov (United States)

    Fuentes-Pananá, Ezequiel M; Larios-Serrato, Violeta; Méndez-Tenorio, Alfonso; Morales-Sánchez, Abigail; Arias, Carlos F; Torres, Javier

    2016-01-01

    Gastric (GC) and breast (BrC) cancer are two of the most common and deadly tumours. Different lines of evidence suggest a possible causative role of viral infections for both GC and BrC. Wide genome sequencing (WGS) technologies allow searching for viral agents in tissues of patients with cancer. These technologies have already contributed to establish virus-cancer associations as well as to discovery new tumour viruses. The objective of this study was to document possible associations of viral infection with GC and BrC in Mexican patients. In order to gain idea about cost effective conditions of experimental sequencing, we first carried out an in silico simulation of WGS. The next-generation-platform IlluminaGallx was then used to sequence GC and BrC tumour samples. While we did not find viral sequences in tissues from BrC patients, multiple reads matching Epstein-Barr virus (EBV) sequences were found in GC tissues. An end-point polymerase chain reaction confirmed an enrichment of EBV sequences in one of the GC samples sequenced, validating the next-generation sequencing-bioinformatics pipeline. PMID:26910355

  8. Sequence-specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid-DNA) in capillary and microfluidic electrophoretic separations

    NARCIS (Netherlands)

    Wagler, Patrick; Minero, Gabriel Antonio S.; Tangen, Uwe; de Vries, Jan Willem; Prusty, Deepak; Kwak, Minseok; Herrmann, Andreas; McCaskill, John S.

    2015-01-01

    Reversible noncovalent but sequence-dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite-modified oligonucleotides has enabled sequence-specific mobility assays for DN

  9. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  10. Visualizing inequality

    Science.gov (United States)

    Eliazar, Iddo

    2016-07-01

    The study of socioeconomic inequality is of substantial importance, scientific and general alike. The graphic visualization of inequality is commonly conveyed by Lorenz curves. While Lorenz curves are a highly effective statistical tool for quantifying the distribution of wealth in human societies, they are less effective a tool for the visual depiction of socioeconomic inequality. This paper introduces an alternative to Lorenz curves-the hill curves. On the one hand, the hill curves are a potent scientific tool: they provide detailed scans of the rich-poor gaps in human societies under consideration, and are capable of accommodating infinitely many degrees of freedom. On the other hand, the hill curves are a powerful infographic tool: they visualize inequality in a most vivid and tangible way, with no quantitative skills that are required in order to grasp the visualization. The application of hill curves extends far beyond socioeconomic inequality. Indeed, the hill curves are highly effective 'hyperspectral' measures of statistical variability that are applicable in the context of size distributions at large. This paper establishes the notion of hill curves, analyzes them, and describes their application in the context of general size distributions.

  11. Cleavage of nucleic acids

    Science.gov (United States)

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    2000-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  12. The gene clone and sequence analysis of FAD2 from different erucic acid content rapeseed lines%不同芥酸含量油菜品系FAD2基因克隆测序分析

    Institute of Scientific and Technical Information of China (English)

    陈光尧; 王国槐; 张振乾; 官春云; 陈社员

    2011-01-01

    对高芥酸品系M13、60Coy辐照得到的高芥酸油菜突变体H27和低芥酸品系742的FAD2基因克隆并测序.结果发现,FAD2基因存在两个拷贝FAD2.1(1155bp)、FAD2.2(1140bp).H27的FAD2.1与M13序列相同.但FAD2.2核苷酸序列中M13在409位点A(腺嘌呤)变成了T(鸟嘌呤),导致密码子由AGA变换为TGA(终止密码子),使H27中的FAD2.2基因的功能丧失,这可能是芥酸含量的提高原因.%In order to better understand the molecular mechanism of erucic acid mutation, the FAD2 genes of high erucic acid M13 strain, high-erucic acid rapeseed mutant H27 by 60Coγ irradiation and low erucic acid strain 742 were sequenced by our laboratory. The results showed that there were two copies of FAD2 gene FAD2. 1 ( 1155bp) , FAD2. 2 (1140bp) .Compared with the FAD2. 1 and FAD2. 2 gene sequences of H27 and M13 , both of them had the same FAD2. 1 nucleotide sequence and the different FAD2. 2 nucleotide sequence. The FAD2. 2 nucleotide sequence of M13 in the 409 point A ( adenine) was replaced by T ( guanine) in H27 , then the AGA codon transformed into TGA ( stop codon) , which resulted in FAD2. 2 gene some function loss. It might be the reason why H27 had higher erucic acid content than M13.

  13. Learning Sequence Neighbourhood Metrics

    CERN Document Server

    Bayer, Justin; van der Smagt, Patrick

    2011-01-01

    Recurrent neural networks (RNNs) in combination with a pooling operator and the neighbourhood components analysis (NCA) objective function are able to detect the characterizing dynamics of sequences and embed them into a fixed-length vector space of arbitrary dimensionality. Subsequently, the resulting features are meaningful and can be used for visualization or nearest neighbour classification in linear time. This kind of metric learning for sequential data enables the use of algorithms tailored towards fixed length vector spaces such as R^n.

  14. DNAVis: interactive visualization of comparative genome annotations

    NARCIS (Netherlands)

    Fiers, M.W.E.J.; Wetering, van de H.; Peeters, T.H.J.M.; Wijk, van J.J.; Nap, J.P.H.

    2006-01-01

    The software package DNAVis offers a fast, interactive and real-time visualization of DNA sequences and their comparative genome annotations. DNAVis implements advanced methods of information visualization such as linked views, perspective walls and semantic zooming, in addition to the display of he

  15. Draft Genome Sequence of D-Branched-Chain Amino Acid Producer Lactobacillus otakiensis JCM 15040T, Isolated from a Traditional Japanese Pickle.

    Science.gov (United States)

    Doi, Katsumi; Mori, Kazuki; Mutaguchi, Yuta; Tashiro, Kosuke; Fujino, Yasuhiro; Ohmori, Taketo; Kuhara, Satoru; Ohshima, Toshihisa

    2013-01-01

    Lactobacillus otakiensis strain JCM 15040(T) was isolated from an unsalted pickling solution used in the production of sunki, a traditional Japanese pickle. Here, we prepared a draft genome sequence for this strain consisting of 40 contigs containing a total of 2,347,132 bp, 2,310 predicted coding sequences, and a G+C content of 42.4%. PMID:23929467

  16. Detection of Differences in the Nucleotide and Amino Acid Sequences of Diphtheria Toxin from Corynebacterium diphtheriae and Corynebacterium ulcerans Causing Extrapharyngeal Infections

    OpenAIRE

    Sing, Andreas; Hogardt, Michael; Bierschenk, Suse; Heesemann, Jürgen

    2003-01-01

    While Corynebacterium ulcerans can mimic classical diphtheria, extrapharyngeal infections are extremely rare. Sequencing of the diphtheria toxin (DT)-encoding tox gene of two C. ulcerans isolates from extrapharyngeal infections revealed differences from C. diphtheriae DT sequences, mainly in the translocation and receptor-binding domains. C. ulcerans supernatants were much less potent than supernatant from C. diphtheriae. A C. ulcerans DT-specific PCR is described below.

  17. Visual Pigments, Ocular Filters and the Evolution of Snake Vision.

    Science.gov (United States)

    Simões, Bruno F; Sampaio, Filipa L; Douglas, Ronald H; Kodandaramaiah, Ullasa; Casewell, Nicholas R; Harrison, Robert A; Hart, Nathan S; Partridge, Julian C; Hunt, David M; Gower, David J

    2016-10-01

    Much of what is known about the molecular evolution of vertebrate vision comes from studies of mammals, birds and fish. Reptiles (especially snakes) have barely been sampled in previous studies despite their exceptional diversity of retinal photoreceptor complements. Here, we analyze opsin gene sequences and ocular media transmission for up to 69 species to investigate snake visual evolution. Most snakes express three visual opsin genes (rh1, sws1, and lws). These opsin genes (especially rh1 and sws1) have undergone much evolutionary change, including modifications of amino acid residues at sites of known importance for spectral tuning, with several tuning site combinations unknown elsewhere among vertebrates. These changes are particularly common among dipsadine and colubrine "higher" snakes. All three opsin genes are inferred to be under purifying selection, though dN/dS varies with respect to some lineages, ecologies, and retinal anatomy. Positive selection was inferred at multiple sites in all three opsins, these being concentrated in transmembrane domains and thus likely to have a substantial effect on spectral tuning and other aspects of opsin function. Snake lenses vary substantially in their spectral transmission. Snakes active at night and some of those active by day have very transmissive lenses, whereas some primarily diurnal species cut out shorter wavelengths (including UVA). In terms of retinal anatomy, lens transmission, visual pigment spectral tuning and opsin gene evolution the visual system of snakes is exceptionally diverse compared with all other extant tetrapod orders.

  18. Molecular level understanding of resistance to nalidixic acid in Salmonella enteric serovar typhimurium associates with the S83F sequence type.

    Science.gov (United States)

    Preethi, B; Ramanathan, K

    2016-01-01

    Nalidixic acid is an antibiotic drug used for treatment of Salmonellosis, a gastrointestinal infection. DNA gyrase subunit A (GyrA) of Salmonella typhimurium is the drug target for nalidixic acid. Resistance of GyrA to nalidixic acid, because of a point mutation in S. typhimurium, was recently reported. Substitution of Phe in place of Ser at locus 83 in GyrA of S. typhimurium has been experimentally associated with nalidixic acid resistance. Despite recent efforts, the mechanism of this resistance is not well understood. In this investigation we used computational techniques to address this shortcoming. Our results showed that contact with residue Arg 91 is certainly important for efficient binding of nalidixic acid to the target protein, and that mutation of this residue results in 180° rotation of the antibiotic in its binding pocket, around its own long axis. It is hoped these findings may enable development of new antibiotics against resistant forms of Salmonella. PMID:26329667

  19. Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE – binding linear epitopes of allergens

    Directory of Open Access Journals (Sweden)

    Peijnenburg Ad ACM

    2002-12-01

    Full Text Available Abstract Background Transgenic proteins expressed by genetically modified food crops are evaluated for their potential allergenic properties prior to marketing, among others by identification of short identical amino acid sequences that occur both in the transgenic protein and allergenic proteins. A strategy is proposed, in which the positive outcomes of the sequence comparison with a minimal length of six amino acids are further screened for the presence of potential linear IgE-epitopes. This double track approach involves the use of literature data on IgE-epitopes and an antigenicity prediction algorithm. Results Thirty-three transgenic proteins have been screened for identities of at least six contiguous amino acids shared with allergenic proteins. Twenty-two transgenic proteins showed positive results of six- or seven-contiguous amino acids length. Only a limited number of identical stretches shared by transgenic proteins (papaya ringspot virus coat protein, acetolactate synthase GH50, and glyphosate oxidoreductase and allergenic proteins could be identified as (part of potential linear epitopes. Conclusion Many transgenic proteins have identical stretches of six or seven amino acids in common with allergenic proteins. Most identical stretches are likely to be false positives. As shown in this study, identical stretches can be further screened for relevance by comparison with linear IgE-binding epitopes described in literature. In the absence of literature data on epitopes, antigenicity prediction by computer aids to select potential antibody binding sites that will need verification of IgE binding by sera binding tests. Finally, the positive outcomes of this approach warrant further clinical testing for potential allergenicity.

  20. Cloning of an Erwinia herbicola gene necessary for gluconic acid production and enhanced mineral phosphate solubilization in Escherichia coli HB101: nucleotide sequence and probable involvement in biosynthesis of the coenzyme pyrroloquinoline quinone.

    Science.gov (United States)

    Liu, S T; Lee, L Y; Tai, C Y; Hung, C H; Chang, Y S; Wolfram, J H; Rogers, R; Goldstein, A H

    1992-09-01

    Escherichia coli is capable of synthesizing the apo-glucose dehydrogenase enzyme (GDH) but not the cofactor pyrroloquinoline quinone (PQQ), which is essential for formation of the holoenzyme. Therefore, in the absence of exogenous PQQ, E. coli does not produce gluconic acid. Evidence is presented to show that the expression of an Erwinia herbicola gene in E. coli HB101(pMCG898) resulted in the production of gluconic acid, which, in turn, implied PQQ biosynthesis. Transposon mutagenesis showed that the essential gene or locus was within a 1.8-kb region of a 4.5-kb insert of the plasmid pMCG898. This 1.8-kb region contained only one apparent open reading frame. In this paper, we present the nucleotide sequence of this open reading frame, a 1,134-bp DNA fragment coding for a protein with an M(r) of 42,160. The deduced sequence of this protein had a high degree of homology with that of gene III (M(r), 43,600) of a PQQ synthase gene complex from Acinetobacter calcoaceticus previously identified by Goosen et al. (J. Bacteriol. 171:447-455, 1989). In minicell analysis, pMCG898 encoded a protein with an M(r) of 41,000. These data indicate that E. coli HB101(pMCG898) produced the GDH-PQQ holoenzyme, which, in turn, catalyzed the oxidation of glucose to gluconic acid in the periplasmic space. As a result of the gluconic acid production, E. coli HB101(pMCG898) showed an enhanced mineral phosphate-solubilizing phenotype due to acid dissolution of the hydroxyapatite substrate.

  1. Abalone (Haliotis tuberculata) hemocyanin type 1 (HtH1). Organization of the approximately 400 kDa subunit, and amino acid sequence of its functional units f, g and h.

    Science.gov (United States)

    Keller, H; Lieb Bp6; Altenhein, B; Gebauer, D; Richter, S; Stricker, S; Markl, J

    1999-08-01

    We have identified two separate hemocyanin types (HtH1 and HtH2) in the European abalone Haliotis tuberculata. HtH1/HtH2 hybrid molecules were not found. By selective dissociation of HtH2 we isolated HtH1 which, as revealed by electron microscopy and SDS/PAGE, is present as didecamers of a approximately 400 kDa subunit. Immunologically, HtH1 and HtH2 correspond to keyhole limpet hemocyanin (KLH)1 and KLH2, respectively, the two well-studied hemocyanin types of the closely related marine gastropod Megathura crenulata. On the basis of limited proteolytic cleavage, two-dimensional immunoelectrophoresis, SDS/PAGE and N-terminal sequencing, we identified eight different 40-60 kDa functional units in HtH1, termed HtH1-a to HtH1-h, and determined their linear arrangement within the elongated subunit. From Haliotis mantle tissue, rich in hemocyanin-producing pore cells, we isolated mRNA and constructed a cDNA library. By expression screening with HtH-specific rabbit antibodies, a cDNA clone was isolated and sequenced which codes for the three C-terminal functional units f, g and h of HtH1. Their sequences were aligned to those available from other molluscs, notably to functional unit f and functional unit g from the cephalopod Octopus dofleini. HtH1-f, which is the first sequenced functional unit of type f from a gastropod hemocyanin, corresponds to functional unit f from Octopus. Also functional unit g from Haliotis and Octopus correspond to each other. HtH1-h is a gastropod hemocyanin functional unit type which is absent in cephalopods and has not been sequenced previously. It exhibits a unique tail extension of approximately 95 amino acids, which is lacking in functional units a to g and aligns with a published peptide sequence of 48 amino acids from functional unit h of Helix pomatia hemocyanin. The new Haliotis sequences are discussed with respect to their counterparts in Octopus, the 15 A three-dimensional reconstruction of the KLH1 didecamer from electron

  2. Inhibition of the visual cycle in vivo by 13-cis retinoic acid protects from light damage and provides a mechanism for night blindness in isotretinoin therapy

    OpenAIRE

    Sieving, Paul A.; Chaudhry, Prem; Kondo, Mineo; Provenzano, Matthew; Wu, David; Carlson, Thomas J.; Bush, Ronald A.; Thompson, Debra A.

    2001-01-01

    Isotretinoin (13-cis retinoic acid) is frequently prescribed for severe acne [Peck, G. L., Olsen, T. G., Yoder, F. W., Strauss, J. S., Downing, D. T., Pandya, M., Butkus, D. & Arnaud-Battandier, J. (1979) N. Engl. J. Med. 300, 329–333] but can impair night vision [Fraunfelder, F. T., LaBraico, J. M. & Meyer, S. M. (1985) Am. J. Ophthalmol. 100, 534–537] shortly after the beginning of therapy [Shulman, S. R. (1989) Am. J. Public Health 79, 1565–1568]. As rod ...

  3. Local amino acid sequence patterns dominate the heterogeneous phenotype for the collagen connective tissue disease Osteogenesis Imperfecta resulting from Gly mutations.

    Science.gov (United States)

    Xiao, Jianxi; Yang, Zhangfu; Sun, Xiuxia; Addabbo, Rayna; Baum, Jean

    2015-10-01

    Osteogenesis Imperfecta (OI), a hereditary connective tissue disease in collagen that arises from a single Gly → X mutation in the collagen chain, varies widely in phenotype from perinatal lethal to mild. It is unclear why there is such a large variation in the severity of the disease considering the repeating (Gly-X-Y)n sequence and the uniform rod-like structure of collagen. We systematically evaluate the effect of local (Gly-X-Y)n sequence around the mutation site on OI phenotype using integrated bio-statistical approaches, including odds ratio analysis and decision tree modeling. We show that different Gly → X mutations have different local sequence patterns that are correlated with lethal and nonlethal phenotypes providing a mechanism for understanding the sensitivity of local context in defining lethal and non-lethal OI. A number of important trends about which factors are related to OI phenotypes are revealed by the bio-statistical analyses; most striking is the complementary relationship between the placement of Pro residues and small residues and their correlation to OI phenotype. When Pro is present or small flexible residues are absent nearby a mutation site, the OI case tends to be lethal; when Pro is present or small flexible residues are absent further away from the mutation site, the OI case tends to be nonlethal. The analysis also reveals the dominant role of local sequence around mutation sites in the Major Ligand Binding Regions that are primarily responsible for collagen binding to its receptors and shows that non-lethal mutations are highly predicted by local sequence considerations alone whereas lethal mutations are not as easily predicted and may be a result of more complex interactions. Understanding the sequence determinants of OI mutations will enhance genetic counseling and help establish which steps in the collagen hierarchy to target for drug therapy.

  4. 多位点序列分型技术以及在乳酸菌分类鉴定中的应用%Multi-locus sequence typing technology and its application in Lactic acid bacteria identification

    Institute of Scientific and Technical Information of China (English)

    徐海燕; 张和平

    2013-01-01

    Multi-locus sequence typing (MLST) is a molecular typing method based on the DNA partial nucleotide sequencing of multiple housekeeping genes,the differences of alleles at each loci were defined by the allelic profile or sequence type,it is an effective tool for analysis genetic relationship among strains.MLST schemes have been developed for a variety of bacterial research,in this paper,the method of MLST and its application on classification and identification of Lactic acid bacteria are introduced.%多位点序列分型(Multi-Locus Sequence Typing,MLST)技术是通过测定同种细菌管家基因(housekeeping gene)的序列,来确定等位基因的差异,进而比较分析菌株之间进化关系的一种分子分型方法.该方法在细菌生物学基础研究方面已经发挥了重要的作用,本文主要阐述MLST技术的方法和其在乳酸菌分类鉴定中的应用.

  5. Deduced amino acid sequence of the small hydrophobic protein of US avian pneumovirus has greater identity with that of human metapneumovirus than those of non-US avian pneumoviruses.

    Science.gov (United States)

    Yunus, Abdul S; Govindarajan, Dhanasekaran; Huang, Zhuhui; Samal, Siba K

    2003-05-01

    We report here the nucleotide and deduced amino acid (aa) sequences of the small hydrophobic (SH) gene of the avian pneumovirus strain Colorado (APV/CO). The SH gene of APV/CO is 628 nucleotides in length from gene-start to gene-end. The longest ORF of the SH gene encoded a protein of 177 aas in length. Comparison of the deduced aa sequence of the SH protein of APV/CO with the corresponding published sequences of other members of genera metapneumovirus showed 28% identity with the newly discovered human metapneumovirus (hMPV), but no discernable identity with the APV subgroup A or B. Collectively, this data supports the hypothesis that: (i) APV/CO is distinct from European APV subgroups and belongs to the novel subgroup APV/C (APV/US); (ii) APV/CO is more closely related to hMPV, a mammalian metapneumovirus, than to either APV subgroup A or B. The SH gene of APV/CO was cloned using a genomic walk strategy which initiated cDNA synthesis from genomic RNA that traversed the genes in the order 3'-M-F-M2-SH-G-5', thus confirming that gene-order of APV/CO conforms in the genus Metapneumovirus. We also provide the sequences of transcription-signals and the M-F, F-M2, M2-SH and SH-G intergenic regions of APV/CO.

  6. Visual analysis of extraction process of ursolic acid with supercritical carbon dioxide%超临界二氧化碳萃取熊果酸工艺的可视化分析

    Institute of Scientific and Technical Information of China (English)

    孙益民; 汤宏; 陶伟; 卞国琛; 孙若琼; 江飚

    2011-01-01

    采用超临界二氧化碳流体技术萃取枇杷叶中熊果酸进行了较为系统的研究。选择萃取压力、萃取温度、萃取时间及分离温度4个影响因素,运用多因素多水平法安排试验,以高效液相色谱测定熊果酸的含量。选择萃取物中熊果酸含量为试验指标,用自主提出的多因素多水平试验可视化分析方法对多维空间试验数据进行分析。找出最佳工艺范围为:萃取压力为22~30MPa,分离温度为33~37℃,萃取时间为75~80min,萃取温度影响较为复杂,可以在20~38℃内进一步试验选优确定。研究证明多因素多水平可视化分析法对于多维空间多水平试验结果分析正确,应用成功。%Extracting ursolic acid from Folium Eriobotryae with supercritical carbon dioxide technology was systematically investigated.Four factors(extracting pressure,extracting temperature,extracting time and separating temperature) were chosen as influencing ones and the multifactor and multilevel method was applied to arrange the experiments.The content of ursolic acid was determined with HPLC method.The experimental target was the content of ursolic acid in the extracted products.This paper used the multifactor and multilevel visual analysis method(m2VA) proposed by our research group to analyze experimental data in multi-dimension space.Finally the best extracting process parameters were found:extracting pressure is 22~30 MPa,separating temperature 33~37 ℃,extracting time 75~80 min.Generally,extracting temperature is more complex and it could be selective in the range of 30~38 ℃ by the further test.The study proved that the multifactor and multilevel visual analysis method(m2VA) shows correctness and practice well in analysis of experimental data in multi-dimension space.

  7. Three-dimensional-fast imaging employing steady-state acquisition and T2-weighted fast spin-echo magnetic resonance sequences on visualization of cranial nerves Ⅲ-Ⅻ

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Because of the small diameter and complex anatomic course of the cranial nerves except for the optic nerve,mgeminal nerve,facial nerve,and cochlear and vestibular nerve,other cranial nerves are difficult to be visualized in magnetic resonance imaging (MRI) scanning with conventional thickness (5-10 mm).

  8. Genome Sequence of "Candidatus Microthrix parvicella" Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant

    OpenAIRE

    Muller, Emilie; Pinel, Nicolás; Gillece, John D.; Schupp, James M.; Lance B Price; Engelthaler, David M.; Levantesi, Caterina; Tandoi, Valter; Luong, Kkai; Baliga, Nitin S.; Korlach, Jonas; Keim, Paul S.; Wilmes, Paul

    2012-01-01

    “Candidatus Microthrix” bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for foaming and bulking. Here, we report the first draft genome sequence of a strain from this genus: “Candidatus Microthrix parvicella” strain Bio17-1.

  9. Electrochemical deoxyribonucleic acid biosensor based on electrodeposited graphene and nickel oxide nanoparticle modified electrode for the detection of salmonella enteritidis gene sequence.

    Science.gov (United States)

    Sun, Wei; Wang, Xiuli; Lu, Yongxi; Gong, Shixing; Qi, Xiaowei; Lei, Bingxin; Sun, Zhenfan; Li, Guangjiu

    2015-04-01

    In this paper a new electrochemical DNA biosensor was prepared by using graphene (GR) and nickel oxide (NiO) nanocomposite modified carbon ionic liquid electrode (CILE) as the substrate electrode. GR and NiO nanoparticles were electrodeposited on the CILE surface step-by-step to get the nanocomposite. Due to the strong affinity of NiO with phosphate groups of ssDNA, oligonucleotide probe with a terminal 5'-phosphate group could be attached on the surface of NiO/GR/CILE, which could further hybridize with the target ssDNA sequence. Methylene blue (MB) was used as the electrochemical indicator for monitoring the hybridization reaction. Under the optimal conditions the reduction peak current of MB was proportional to the concentration of salmonella enteritidis gene sequence in the range from 1.0×10(-13) to 1.0×10(-6)molL(-1) with a detection limit as 3.12×10(-14)molL(-1). This electrochemical DNA sensor exhibited good discrimination ability to one-base and three-base mismatched ssDNA sequences, and the polymerase chain reaction amplification product of salmonella enteritidis gene sequences were further detected with satisfactory results.

  10. Studies on deoxyribonucleic acids and related compounds. V. Synthesis of pentadecanucleotide duplex containing the ideal Pribnow sequence of promoter by the phosphotriester method using a new phosphorylating reagent.

    OpenAIRE

    Ohtsuka, E; Taniyama, Y; Marumoto, R; Sato, H.; Hirosaki, H; Ikehara, M

    1982-01-01

    A phosphorylating reagent o-chlorophenyl phosphoro-p-anisi-dochloridate was synthesized to phosphorylate the 3'-hydroxyl group of N, 5'-protected deoxynucleosides. These nucleotides served as 3'-terminal units for the synthesis of oligonucleotide blocks. By condensation of these oligonucleotide blocks the partially complementary deoxypentadecanucleotides dAGCTTATAATGC-TCG and dAGCTCGAGCATTATA, which contained the ideal Pribnow sequence TATAATG, were synthesized.

  11. Measurement of the amino acid sequence for the fusion protein FP3 with LC-MS/MS%LC-MS/MS法对融合蛋白FP3的氨基酸全序列测定

    Institute of Scientific and Technical Information of China (English)

    李响; 高向东; 陶磊; 裴德宁; 郭莹; 饶春明; 王军志

    2012-01-01

    The amino acid sequence of the fusion protein FP3 was measured by two types of LC-MS/MS and its primary structure was confirmed. After reduction and alkylation, the protein was digested with trypsin and glycosyl groups in glycopeptide were removed by PNGase F. The mixed peptides were separated by LC, then Q-TOF and Ion trap tandem mass spectrometry were used to measure b, y fragment ions of each peptide to analyze the amino acid sequence of fusion protein FP3. Seventy-six percent of full amino acid sequence of the fusion protein FP3 was measured by LC-ESI-Q-TOF with the remaining 24% completed by LC-ESI-Trap. As LC-MS and tandem mass spectrometry are rapid, sensitive, accurate to measure the protein ammo acid sequence, they are important approach to structure analysis and identification of recombinant protein.%运用液质联用、两种串联质谱对融合蛋白FP3的氨基酸全序列测定,确证其一级结构.将样品还原烷基化后,通过胰蛋白酶酶解蛋白,PNGase F去除多肽混合物中糖肽的糖基化,将去糖后的总肽用于液质联用系统,通过液相分离后,运用Q-TOF和线性离子阱两种串联质谱测定各个肽段的b,y碎片离子,分析测定融合蛋白FP3的氨基酸全序列.通过LC-ESI-Q-TOF完成了融合蛋白FP3的76%氨基酸序列测定,通过LC-ESI-Trap完成余下24%氨基酸序列测定.液质联用、串联质谱法测定蛋白质氨基酸序列快速、灵敏、准确,是对重组蛋白结构分析和确证的重要手段.

  12. Development of Electrochemical Biosensorfor Sequence-Specific Deoxyribonucleic Acid%特定序列脱氧核糖核酸电化学生物传感器进展

    Institute of Scientific and Technical Information of China (English)

    杨丽菊; 彭图治

    2001-01-01

    对当今电分析化学中的研究热点之一——脱氧核糖核酸(DNA)的电化学生物传感技术的最新进展进行了综述,评述了其发展前景。%This is a review of electrochemical biosensor for sequence-specific deoxyribonucleic acid (DNA) with 51 references. Resent Progress in designation of the sensor, immobilization of DNA, indicator of hybridizatio, applications and some new concepts of the sensor are discussed in detail.

  13. Turtle Graphics of Morphic Sequences

    Science.gov (United States)

    Zantema, Hans

    2016-02-01

    The simplest infinite sequences that are not ultimately periodic are pure morphic sequences: fixed points of particular morphisms mapping single symbols to strings of symbols. A basic way to visualize a sequence is by a turtle curve: for every alphabet symbol fix an angle, and then consecutively for all sequence elements draw a unit segment and turn the drawing direction by the corresponding angle. This paper investigates turtle curves of pure morphic sequences. In particular, criteria are given for turtle curves being finite (consisting of finitely many segments), and for being fractal or self-similar: it contains an up-scaled copy of itself. Also space-filling turtle curves are considered, and a turtle curve that is dense in the plane. As a particular result we give an exact relationship between the Koch curve and a turtle curve for the Thue-Morse sequence, where until now for such a result only approximations were known.

  14. Sequence diversity and functional conformity

    OpenAIRE

    de Lange, Orlando

    2015-01-01

    At least four phylogenetically distinct groups of bacteria encode repeat proteins with the common ability to bind specific DNA sequences with a unique but conserved code. Each repeat binds a single DNA base, and specificity is determined by the amino acid residue at position 13 of each repeat. Repeats are typically 33-35 amino acids long. Comparing repeat sequences across all groups reveals that only three positions are hyper-conserved. Repeats are in most cases functionally compatible such t...

  15. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  16. Visualization rhetoric: framing effects in narrative visualization.

    Science.gov (United States)

    Hullman, Jessica; Diakopoulos, Nicholas

    2011-12-01

    Narrative visualizations combine conventions of communicative and exploratory information visualization to convey an intended story. We demonstrate visualization rhetoric as an analytical framework for understanding how design techniques that prioritize particular interpretations in visualizations that "tell a story" can significantly affect end-user interpretation. We draw a parallel between narrative visualization interpretation and evidence from framing studies in political messaging, decision-making, and literary studies. Devices for understanding the rhetorical nature of narrative information visualizations are presented, informed by the rigorous application of concepts from critical theory, semiotics, journalism, and political theory. We draw attention to how design tactics represent additions or omissions of information at various levels-the data, visual representation, textual annotations, and interactivity-and how visualizations denote and connote phenomena with reference to unstated viewing conventions and codes. Classes of rhetorical techniques identified via a systematic analysis of recent narrative visualizations are presented, and characterized according to their rhetorical contribution to the visualization. We describe how designers and researchers can benefit from the potentially positive aspects of visualization rhetoric in designing engaging, layered narrative visualizations and how our framework can shed light on how a visualization design prioritizes specific interpretations. We identify areas where future inquiry into visualization rhetoric can improve understanding of visualization interpretation. PMID:22034342

  17. Visualization rhetoric: framing effects in narrative visualization.

    Science.gov (United States)

    Hullman, Jessica; Diakopoulos, Nicholas

    2011-12-01

    Narrative visualizations combine conventions of communicative and exploratory information visualization to convey an intended story. We demonstrate visualization rhetoric as an analytical framework for understanding how design techniques that prioritize particular interpretations in visualizations that "tell a story" can significantly affect end-user interpretation. We draw a parallel between narrative visualization interpretation and evidence from framing studies in political messaging, decision-making, and literary studies. Devices for understanding the rhetorical nature of narrative information visualizations are presented, informed by the rigorous application of concepts from critical theory, semiotics, journalism, and political theory. We draw attention to how design tactics represent additions or omissions of information at various levels-the data, visual representation, textual annotations, and interactivity-and how visualizations denote and connote phenomena with reference to unstated viewing conventions and codes. Classes of rhetorical techniques identified via a systematic analysis of recent narrative visualizations are presented, and characterized according to their rhetorical contribution to the visualization. We describe how designers and researchers can benefit from the potentially positive aspects of visualization rhetoric in designing engaging, layered narrative visualizations and how our framework can shed light on how a visualization design prioritizes specific interpretations. We identify areas where future inquiry into visualization rhetoric can improve understanding of visualization interpretation.

  18. OPEN QUESTIONS IN ORIGIN OF LIFE: EXPERIMENTAL STUDIES ON THE ORIGIN OF NUCLEIC ACIDS AND PROTEINS WITH SPECIFIC AND FUNCTIONAL SEQUENCES BY A CHEMICAL SYNTHETIC BIOLOGY APPROACH

    Directory of Open Access Journals (Sweden)

    Katarzyna Adamala

    2014-02-01

    We have recently addressed these questions by using a chemical synthetic biology approach. In particular, we have tested the catalytic activity of small peptides, like Ser-His, with respect to peptide- and nucleotides-condensation, as a realistic model of primitive organocatalysis. We have also set up a strategy for exploring the sequence space of random proteins and RNAs (the so-called “never born biopolymer” project with respect to the production of folded structures. Being still far from solved, the main aspects of these “open questions” are discussed here, by commenting on recent results obtained in our groups and by providing a unifying view on the problem and possible solutions. In particular, we propose a general scenario for macromolecule formation via fragment-condensation, as a scheme for the emergence of specific sequences based on molecular growth and selection.

  19. The amino acid sequence of a 20 kDa bifunctional subtilisin/alpha-amylase inhibitor from bran [correction of brain] of rice (Oryza sativa L.) seeds.

    Science.gov (United States)

    Ohtsubo, K; Richardson, M

    1992-08-31

    A 20 kDa bifunctional inhibitor of the microbial proteinase, subtilisin, and the alpha-amylase from the larvae of the red flour beetle (Tribolium castaneum) was purified from bran of rice seeds by saline extraction, precipitation with ammonium sulphate, ion-exchange chromatography on DEAE-Cellulose and Toyopearl CM-650, and preparative HPLC on Vydac C18. The complete primary structure was determined by automatic degradation of the intact, reduced and S-alkylated protein, and by manual DABITC/PITC micro-sequencing of peptides obtained from the protein following separate enzymic digestions with trypsin, pepsin, chymotrypsin, elastase and the protease from S. aureus V8. The protein sequence, which contained 176 residues, showed strong homology with similar bifunctional inhibitors previously isolated from wheat and barley which are related to the Kunitz family of proteinase inhibitors from legume seeds. PMID:1511747

  20. Nanoelectronic three-dimensional (3D) nanotip sensing array for real-time, sensitive, label-free sequence specific detection of nucleic acids.

    Science.gov (United States)

    Esfandyarpour, Rahim; Yang, Lu; Koochak, Zahra; Harris, James S; Davis, Ronald W

    2016-02-01

    The improvements in our ability to sequence and genotype DNA have opened up numerous avenues in the understanding of human biology and medicine with various applications, especially in medical diagnostics. But the realization of a label free, real time, high-throughput and low cost biosensing platforms to detect molecular interactions with a high level of sensitivity has been yet stunted due to two factors: one, slow binding kinetics caused by the lack of probe molecules on the sensors and two, limited mass transport due to the planar structure (two-dimensional) of the current biosensors. Here we present a novel three-dimensional (3D), highly sensitive, real-time, inexpensive and label-free nanotip array as a rapid and direct platform to sequence-specific DNA screening. Our nanotip sensors are designed to have a nano sized thin film as their sensing area (~ 20 nm), sandwiched between two sensing electrodes. The tip is then conjugated to a DNA oligonucleotide complementary to the sequence of interest, which is electrochemically detected in real-time via impedance changes upon the formation of a double-stranded helix at the sensor interface. This 3D configuration is specifically designed to improve the biomolecular hit rate and the detection speed. We demonstrate that our nanotip array effectively detects oligonucleotides in a sequence-specific and highly sensitive manner, yielding concentration-dependent impedance change measurements with a target concentration as low as 10 pM and discrimination against even a single mismatch. Notably, our nanotip sensors achieve this accurate, sensitive detection without relying on signal indicators or enhancing molecules like fluorophores. It can also easily be scaled for highly multiplxed detection with up to 5000 sensors/square centimeter, and integrated into microfluidic devices. The versatile, rapid, and sensitive performance of the nanotip array makes it an excellent candidate for point-of-care diagnostics, and high

  1. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome

    OpenAIRE

    Kumar, Ashutosh; Singh, Himanshu N.; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A.

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)—microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIK...

  2. Amino acid sequence requirements in the human IgA1 hinge for cleavage by streptococcal IgA1 proteases

    DEFF Research Database (Denmark)

    Senior, BW; Batten, MR; Kilian, Mogens;

    2002-01-01

    All the IgA1 proteases of the different pathogenic species of Streptococcus cleave the hinge of the alpha chain of human IgA1 only at one proline-threonine peptide bond. In order to study the importance of these amino acids for cleavage, several hinge mutant recombinant IgA1 antibodies were...

  3. Promoter sequence of 3-phosphoglycerate kinase gene 2 of lactic acid-producing fungus rhizopus oryzae and a method of expressing a gene of interest in fungal species

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Johnway [Richland, WA; Skeen, Rodney S [Pendleton, OR

    2003-03-04

    The present invention provides the promoter clone discovery of phosphoglycerate kinase gene 2 of a lactic acid-producing filamentous fungal strain, Rhizopus oryzae. The isolated promoter can constitutively regulate gene expression under various carbohydrate conditions. In addition, the present invention also provides a design of an integration vector for the transformation of a foreign gene in Rhizopus oryzae.

  4. Promoter sequence of 3-phosphoglycerate kinase gene 1 of lactic acid-producing fungus rhizopus oryzae and a method of expressing a gene of interest in fungal species

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Johnway [Richland, WA; Skeen, Rodney S [Pendleton, OR

    2002-10-15

    The present invention provides the promoter clone discovery of phosphoglycerate kinase gene 1 of a lactic acid-producing filamentous fungal strain, Rhizopus oryzae. The isolated promoter can constitutively regulate gene expression under various carbohydrate conditions. In addition, the present invention also provides a design of an integration vector for the transformation of a foreign gene in Rhizopus oryzae.

  5. Mechanism analysis of acid tolerance response of bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing.

    Directory of Open Access Journals (Sweden)

    Junhua Jin

    Full Text Available To analyze the mechanism of the acid tolerance response (ATR in Bifidobacterium longum subsp. longum BBMN68, we optimized the acid-adaptation condition to stimulate ATR effectively and analyzed the change of gene expression profile after acid-adaptation using high-throughput RNA-Seq. After acid-adaptation at pH 4.5 for 2 hours, the survival rate of BBMN68 at lethal pH 3.5 for 120 min was increased by 70 fold and the expression of 293 genes were upregulated by more than 2 fold, and 245 genes were downregulated by more than 2 fold. Gene expression profiling of ATR in BBMN68 suggested that, when the bacteria faced acid stress, the cells strengthened the integrity of cell wall and changed the permeability of membrane to keep the H(+ from entering. Once the H(+ entered the cytoplasm, the cells showed four main responses: First, the F(0F(1-ATPase system was initiated to discharge H(+. Second, the ability to produce NH(3 by cysteine-cystathionine-cycle was strengthened to neutralize excess H(+. Third, the cells started NER-UVR and NER-VSR systems to minimize the damage to DNA and upregulated HtpX, IbpA, and γ-glutamylcysteine production to protect proteins against damage. Fourth, the cells initiated global response signals ((pppGpp, polyP, and Sec-SRP to bring the whole cell into a state of response to the stress. The cells also secreted the quorum sensing signal (AI-2 to communicate between intraspecies cells by the cellular signal system, such as two-component systems, to improve the overall survival rate. Besides, the cells varied the pathways of producing energy by shifting to BCAA metabolism and enhanced the ability to utilize sugar to supply sufficient energy for the operation of the mechanism mentioned above. Based on these reults, it was inferred that, during industrial applications, the acid resistance of bifidobacteria could be improved by adding BCAA, γ-glutamylcysteine, cysteine, and cystathionine into the acid-stress environment.

  6. Controlled processing during sequencing.

    Science.gov (United States)

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region's activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  7. Controlled processing during sequencing

    Directory of Open Access Journals (Sweden)

    Malathi eThothathiri

    2015-10-01

    Full Text Available Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6 in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex (ACC. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  8. Lateral flow devices for nucleic acid analysis exploiting quantum dots as reporters

    Energy Technology Data Exchange (ETDEWEB)

    Sapountzi, Eleni A.; Tragoulias, Sotirios S.; Kalogianni, Despina P. [Department of Chemistry, University of Patras, GR-26504 Patras (Greece); Ioannou, Penelope C. [Department of Chemistry, University of Athens, GR-15771 Athens (Greece); Christopoulos, Theodore K., E-mail: tchrist@upatras.gr [Department of Chemistry, University of Patras, GR-26504 Patras (Greece); Institute of Chemical Engineering and High Temperature Processes, Foundation of Research and Technology Hellas, GR-26504 Patras (Greece)

    2015-03-15

    Highlights: • Dipstick tests for DNA hybridization assays and genotyping of single-nucleotide polymorphisms. • Use of quantum dots as reporters. • Visual detection without the need for expensive instrumentation. • Simplicity and low-cost of the assays. - Abstract: There is a growing interest in the development of biosensors in the form of simple lateral flow devices that enable visual detection of nucleic acid sequences while eliminating several steps required for pipetting, incubation and washing out the excess of reactants. In this work, we present the first dipstick-type nucleic acid biosensors based on quantum dots (QDs) as reporters. The biosensors enable sequence confirmation of the target DNA by hybridization and simple visual detection of the emitted fluorescence under a UV lamp. The ‘diagnostic’ membrane of the biosensor contains a test zone (TZ) and a control zone (CZ). The CZ always fluoresces in order to confirm the proper function of the biosensor. Fluorescence is emitted from the TZ, only when the specific nucleic acid sequence is present. We have developed two general types of QD-based nucleic acid biosensors, namely, Type I and Type II, in which the TZ consists of either immobilized streptavidin (Type I) or immobilized oligodeoxynucleotides (Type II). The control zone consists of immobilized biotinylated albumin. No purification steps are required prior to the application of the DNA sample on the strip. The QD-based nucleic acid biosensors performed accurately and reproducibly when applied to (a) the visual detection of PCR amplification products and (b) visual genotyping of single nucleotide polymorphisms (SNPs) in human genomic DNA from clinical samples. As low as 1.5 fmol of double-stranded DNA were clearly detected by naked eye and the dynamic range extended to 200 fmol. The %CV were estimated to be 4.3–8.2.

  9. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria;

    2009-01-01

    and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...

  10. Myeloid neoplasm demonstrating a STAT5B-RARA rearrangement and genetic alterations associated with all-trans retinoic acid resistance identified by a custom next-generation sequencing assay.

    Science.gov (United States)

    Kluk, Michael J; Abo, Ryan P; Brown, Ronald D; Kuo, Frank C; Dal Cin, Paola; Pozdnyakova, Olga; Morgan, Elizabeth A; Lindeman, Neal I; DeAngelo, Daniel J; Aster, Jon C

    2015-10-01

    We describe the case of a patient presenting with several weeks of symptoms related to pancytopenia associated with a maturation arrest at the late promyelocyte/early myelocyte stage of granulocyte differentiation. A diagnosis of acute promyelocytic leukemia was considered, but the morphologic features were atypical for this entity and conventional tests for the presence of a PML-RARA fusion gene were negative. Additional analysis using a custom next-generation sequencing assay revealed a rearrangement producing a STAT5B-RARA fusion gene, which was confirmed by reverse transcription polymerase chain reaction (RT-PCR) and supplementary cytogenetic studies, allowing the diagnosis of a morphologically atypical form of acute promyelocytic leukemia to be made. Analysis of the sequencing data permitted characterization of both chromosomal breakpoints and revealed two additional alterations, a small deletion in RARA exon 9 and a RARA R276W substitution, that have been linked to resistance to all-trans retinoic acid. This case highlights how next-generation sequencing can augment currently standard testing to establish diagnoses in difficult cases, and in doing so help guide selection of therapy. PMID:27148563

  11. Molecular characterization of crustacean visual pigments and the evolution of pancrustacean opsins.

    Science.gov (United States)

    Porter, Megan L; Cronin, Thomas W; McClellan, David A; Crandall, Keith A

    2007-01-01

    Investigations of opsin evolution outside of vertebrate systems have long been focused on insect visual pigments, whereas other groups have received little attention. Furthermore, few studies have explicitly investigated the selective influences across all the currently characterized arthropod opsins. In this study, we contribute to the knowledge of crustacean opsins by sequencing 1 opsin gene each from 6 previously uncharacterized crustacean species (Euphausia superba, Homarus gammarus, Archaeomysis grebnitzkii, Holmesimysis costata, Mysis diluviana, and Neomysis americana). Visual pigment spectral absorbances were measured using microspectrophotometry for species not previously characterized (A. grebnitzkii=496 nm, H. costata=512 nm, M. diluviana=501 nm, and N. americana=520 nm). These novel crustacean opsin sequences were included in a phylogenetic analysis with previously characterized arthropod opsin sequences to determine the evolutionary placement relative to the well-established insect spectral clades (long-/middle-/short-wavelength sensitive). Phylogenetic analyses indicate these novel crustacean opsins form a monophyletic clade with previously characterized crayfish opsin sequences and form a sister group to insect middle-/long-wavelength-sensitive opsins. The reconstructed opsin phylogeny and the corresponding spectral data for each sequence were used to investigate selective influences within arthropod, and mainly "pancrustacean," opsin evolution using standard dN/dS ratio methods and more sensitive techniques investigating the amino acid property changes resulting from nonsynonymous replacements in a historical (i.e., phylogenetic) context. Although the conservative dN/dS methods did not detect any selection, 4 amino acid properties (coil tendencies, compressibility, power to be at the middle of an alpha-helix, and refractive index) were found to be influenced by destabilizing positive selection. Ten amino acid sites relating to these properties were

  12. Guanine nucleotide-binding proteins that enhance choleragen ADP-ribosyltransferase activity: nucleotide and deduced amino acid sequence of an ADP-ribosylation factor cDNA.

    OpenAIRE

    Price, S R; Nightingale, M.; Tsai, S C; Williamson, K. C.; Adamik, R; H. C. Chen; Moss, J; M. Vaughan

    1988-01-01

    Three (two soluble and one membrane) guanine nucleotide-binding proteins (G proteins) that enhance ADP-ribosylation of the Gs alpha stimulatory subunit of the adenylyl cyclase (EC 4.6.1.1) complex by choleragen have recently been purified from bovine brain. To further define the structure and function of these ADP-ribosylation factors (ARFs), we isolated a cDNA clone (lambda ARF2B) from a bovine retinal library by screening with a mixed heptadecanucleotide probe whose sequence was based on th...

  13. Visual time series analysis

    DEFF Research Database (Denmark)

    Fischer, Paul; Hilbert, Astrid

    2012-01-01

    We introduce a platform which supplies an easy-to-handle, interactive, extendable, and fast analysis tool for time series analysis. In contrast to other software suits like Maple, Matlab, or R, which use a command-line-like interface and where the user has to memorize/look-up the appropriate...... commands, our application is select-and-click-driven. It allows to derive many different sequences of deviations for a given time series and to visualize them in different ways in order to judge their expressive power and to reuse the procedure found. For many transformations or model-ts, the user may...... choose between manual and automated parameter selection. The user can dene new transformations and add them to the system. The application contains efficient implementations of advanced and recent techniques for time series analysis including techniques related to extreme value analysis and filtering...

  14. Why Teach Visual Culture?

    Science.gov (United States)

    Passmore, Kaye

    2007-01-01

    Visual culture is a hot topic in art education right now as some teachers are dedicated to teaching it and others are adamant that it has no place in a traditional art class. Visual culture, the author asserts, can include just about anything that is visually represented. Although people often think of visual culture as contemporary visuals such…

  15. Existing and emerging detection technologies for DNA (Deoxyribonucleic Acid) finger printing, sequencing, bio- and analytical chips: a multidisciplinary development unifying molecular biology, chemical and electronics engineering.

    Science.gov (United States)

    Kumar Khanna, Vinod

    2007-01-01

    The current status and research trends of detection techniques for DNA-based analysis such as DNA finger printing, sequencing, biochips and allied fields are examined. An overview of main detectors is presented vis-à-vis these DNA operations. The biochip method is explained, the role of micro- and nanoelectronic technologies in biochip realization is highlighted, various optical and electrical detection principles employed in biochips are indicated, and the operational mechanisms of these detection devices are described. Although a diversity of biochips for diagnostic and therapeutic applications has been demonstrated in research laboratories worldwide, only some of these chips have entered the clinical market, and more chips are awaiting commercialization. The necessity of tagging is eliminated in refractive-index change based devices, but the basic flaw of indirect nature of most detection methodologies can only be overcome by generic and/or reagentless DNA sensors such as the conductance-based approach and the DNA-single electron transistor (DNA-SET) structure. Devices of the electrical detection-based category are expected to pave the pathway for the next-generation DNA chips. The review provides a comprehensive coverage of the detection technologies for DNA finger printing, sequencing and related techniques, encompassing a variety of methods from the primitive art to the state-of-the-art scenario as well as promising methods for the future.

  16. Complementary DNA and derived amino acid sequence of the β subunit of human complement protein C8: identification of a close structural and ancestral relationship to the α subunit and C9

    International Nuclear Information System (INIS)

    A cDNA clone encoding the β subunit (M/sub r/ 64,000) of the eighth component of complement (C8) has been isolated from a human liver cDNA library. This clone has a cDNA insert of 1.95 kilobases (kb) and contains the entire β sequence [1608 base pairs (bp)]. Analysis of total cellular RNA isolated from the hepatoma cell line HepG2 revealed the mRNA for β to be ∼ 2.5 kb. This is similar to the message size for the α subunit of C8 and confirms the existence of different mRNAs for α and β. This finding supports genetic evidence that α and β are encoded at different loci. Analysis of the derived amino acid sequence revealed several membrane surface seeking segments that may facilitate β interaction with target membranes during complement-mediated cytolysis. Determined of the carbohydrate composition indicated 1 or 2 asparagine-linked but no O-linked oligosaccharide chains. Comparison of the β sequence to that reported earlier and to that of human C9 revealed a striking homology between all three proteins. For β and α, the overall homology is 33% on the basis of identity and 53% when conserved substitutions are allowed. For β and C9, the values are 26% and 475, respectively. All three have a large internal domain that is nearly cysteine free and N- and C-termini that are cysteine-rich and homologous to the low-density lipoprotein receptor repeat and epidermal growth factor type sequences, respectively. The overall homology and similarities in size and structural organization are indicative of a close ancestral relationship. It is concluded that α, β and C9 are members of a family of structurally related proteins that are capable of interacting to produce a hydrophilic to amphiphilic transition and membrane association

  17. Thermoresponsive physical hydrogels of poly(lactic acid)/poly(ethylene glycol) stereoblock copolymers tuned by stereostructure and hydrophobic block sequence.

    Science.gov (United States)

    Mao, Hailiang; Shan, Guorong; Bao, Yongzhong; Wu, Zi Liang; Pan, Pengju

    2016-05-18

    CBABC-type poly(lactic acid) (PLA)/poly(ethylene glycol) (PEG) pentablock copolymers composed of a central PEG block (A) and enantiomeric poly(l-lactic acid) (PLLA, B), poly(d-lactic acid) (PDLA, C) blocks were synthesized. Such pentablock copolymers form physical hydrogels at high concentrations in an aqueous solution, which stem from the aggregation and physical bridging of copolymer micelles. These gels are thermoresponsive and turn into sols upon heating. Physical gelation, gel-to-sol transition, crystalline state, microstructure, rheological behavior, biodegradation, and drug release behavior of PLA/PEG pentablock copolymers and their gels were investigated; they were also compared with PLA-PEG-PLA triblock copolymers containing the isotactic PLLA or atactic poly(d,l-lactide) (PDLLA) endblocks and PLLA-PEG-PLLA/PDLA-PEG-PDLA enantiomeric mixtures. PLA hydrophobic domains in pentablock copolymer gels changed from a homocrystalline to stereocomplexed structure as the PLLA/PDLA block length ratio approached 1/1. The gel of symmetric pentablock copolymer exhibited a wider gelation region, higher gel-to-sol transition temperature, higher hydrophobic domain crystallinity, larger intermicellar distance, higher storage modulus, and slower degradation and drug release rate compared to those of the asymmetric PLA/PEG pentablock copolymers or triblock copolymers. SAXS results indicated that the PLLA/PDLA blocks stereocomplexation in pentablock copolymers facilitated the intermicellar aggregation and bridging. Cylindrical ordered structures were observed in all the gels formed from the PLA/PEG pentablock and triblock copolymers. The stereocomplexation degree and intermicellar distance of the pentablock copolymer gels increased with heating. PMID:27121732

  18. HMMEditor: a visual editing tool for profile hidden Markov model

    Directory of Open Access Journals (Sweden)

    Cheng Jianlin

    2008-03-01

    Full Text Available Abstract Background Profile Hidden Markov Model (HMM is a powerful statistical model to represent a family of DNA, RNA, and protein sequences. Profile HMM has been widely used in bioinformatics research such as sequence alignment, gene structure prediction, motif identification, protein structure prediction, and biological database search. However, few comprehensive, visual editing tools for profile HMM are publicly available. Results We develop a visual editor for profile Hidden Markov Models (HMMEditor. HMMEditor can visualize the profile HMM architecture, transition probabilities, and emission probabilities. Moreover, it provides functions to edit and save HMM and parameters. Furthermore, HMMEditor allows users to align a sequence against the profile HMM and to visualize the corresponding Viterbi path. Conclusion HMMEditor provides a set of unique functions to visualize and edit a profile HMM. It is a useful tool for biological sequence analysis and modeling. Both HMMEditor software and web service are freely available.

  19. Amino acid sequence requirements in the human IgA1 hinge for cleavage by streptococcal IgA1 proteases.

    Science.gov (United States)

    Senior, B W; Batten, M R; Kilian, M; Woof, J M

    2002-08-01

    All the IgA1 proteases of the different pathogenic species of Streptococcus cleave the hinge of the alpha chain of human IgA1 only at one proline-threonine peptide bond. In order to study the importance of these amino acids for cleavage, several hinge mutant recombinant IgA1 antibodies were constructed. The mutations were found to be without major effect upon the structure or functional abilities of the antibodies. However, they had a major effect upon their sensitivity to cleavage by some of the IgA1 proteases. PMID:12196126

  20. Combination of acid labile detergent and C18 Empore™ disks for improved identification and sequence coverage of in-gel digested proteins.

    Science.gov (United States)

    Koehn, Henning; Lau, Benjamin; Clerens, Stefan; Plowman, Jeffrey E; Dyer, Jolon M; Ramli, Umi Salamah; Deb-Choudhury, Santanu

    2011-04-01

    A protocol for improved extraction of peptides from in-gel protein digests, using a combination of the acid labile surfactant, sodium deoxycholate (SDC) and C18 Empore™ membranes, is presented. This approach results in better mass spectrum quality, higher numbers of identified peptide peaks and improved identification scores compared to standard tryptic digestion protocols, or protocols using only SDC or only C18 Empore™ disks. The advantages of the new protocol are demonstrated for two different types of samples: Merino wool intermediate filament proteins and Elaeis guineensis (oil palm) mesocarp proteins. PMID:21327873

  1. Data Visualization and Infographics

    OpenAIRE

    Prepared by Mathematica Policy Research

    2014-01-01

    Data visualization translates complex ideas and concepts into a simple visual context. Patterns, trends, and relationships that might go undetected in text are conveyed at a glance in effective data visualization.

  2. A Computer Program to Visualize Gravitational Lenses

    CERN Document Server

    Frutos-Alfaro, F

    2002-01-01

    Gravitational lenses are presently playing an important role in astrophysics. By means of these lenses the parameters of the deflector such as its mass, ellipticity, etc. and Hubble's constant can be determined. Using C, Xforms, Mesa and Imlib a computer program to visualize this lens effect has been developed. This program has been applied to generate sequences of images of a source object and its corresponding images. It has also been used to visually test different models of gravitational lenses.

  3. The molecular basis for the green-blue sensitivity shift in the rod visual pigments of the European eel.

    Science.gov (United States)

    Archer, S; Hope, A; Partridge, J C

    1995-12-22

    When the European eel matures sexually and migrates back to deep sea breeding grounds the visual pigments in its rod photoreceptors change from being maximally sensitive to green light to being maximally sensitive to blue light. In part, this change in sensitivity is due to a change in the opsin component of the visual pigment molecule. We used hormone injection to induce these developmental changes in a group of eels and from these animals an opsin coding region was cloned and sequenced using cDNA made from retinal mRNA. From the retinae of hormone-injected eels and those not injected with hormones, distinct opsin mRNAs were isolated. These mRNAs encode two rod opsin proteins that are very similar but have significant amino acid substitutions in key positions that are likely to be involved in spectral tuning of the eel green and blue sensitive rod visual pigment molecules. PMID:8587887

  4. Sequence-specific {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments for intestinal fatty-acid-binding protein complexed with palmitate (15.4 kDA)

    Energy Technology Data Exchange (ETDEWEB)

    Hodsdon, M.E.; Toner, J.J.; Cistola, D.P. [Washington Univ. School of Medicine, St. Louis, MO (United States)

    1994-12-01

    Intestinal fatty-acid-binding protein (I-FABP) belongs to a family of soluble, cytoplasmic proteins that are thought to function in the intracellular transport and trafficking of polar lipids. Individual members of this protein family have distinct specificities and affinities for fatty acids, cholesterol, bile salts, and retinoids. We are comparing several retinol- and fatty-acid-binding proteins from intestine in order to define the factors that control molecular recognition in this family of proteins. We have established sequential resonance assignments for uniformly {sup 13}C/{sup 15}N-enriched I-FABP complexed with perdeuterated palmitate at pH7.2 and 37{degrees}C. The assignment strategy was similar to that introduced for calmodulin. We employed seven three-dimensional NMR experiments to establish scalar couplings between backbone and sidechain atoms. Backbone atoms were correlated using triple-resonance HNCO, HNCA, TOCSY-HMQC, HCACO, and HCA(CO)N experiments. Sidechain atoms were correlated using CC-TOCSY, HCCH-TOCSY, and TOCSY-HMQC. The correlations of peaks between three-dimensional spectra were established in a computer-assisted manner using NMR COMPASS (Molecular Simulations, Inc.) Using this approach, {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments have been established for 120 of the 131 residues of I-FABP. For 18 residues, amide {sup 1}H and {sup 15}N resonances were unobservable, apparently because of the rapid exchange of amide protons with bulk water at pH 7.2. The missing amide protons correspond to distinct amino acid patterns in the protein sequence, which will be discussed. During the assignment process, several sources of ambiguity in spin correlations were observed. To overcome this ambiguity, the additional inter-residue correlations often observed in the HNCA experiment were used as cross-checks for the sequential backbone assignments.

  5. Lateralized visual behavior in bottlenose dolphins (Tursiops truncatus) performing audio-visual tasks: the right visual field advantage.

    Science.gov (United States)

    Delfour, F; Marten, K

    2006-01-10

    Analyzing cerebral asymmetries in various species helps in understanding brain organization. The left and right sides of the brain (lateralization) are involved in different cognitive and sensory functions. This study focuses on dolphin visual lateralization as expressed by spontaneous eye preference when performing a complex cognitive task; we examine lateralization when processing different visual stimuli displayed on an underwater touch-screen (two-dimensional figures, three-dimensional figures and dolphin/human video sequences). Three female bottlenose dolphins (Tursiops truncatus) were submitted to a 2-, 3- or 4-, choice visual/auditory discrimination problem, without any food reward: the subjects had to correctly match visual and acoustic stimuli together. In order to visualize and to touch the underwater target, the dolphins had to come close to the touch-screen and to position themselves using monocular vision (left or right eye) and/or binocular naso-ventral vision. The results showed an ability to associate simple visual forms and auditory information using an underwater touch-screen. Moreover, the subjects showed a spontaneous tendency to use monocular vision. Contrary to previous findings, our results did not clearly demonstrate right eye preference in spontaneous choice. However, the individuals' scores of correct answers were correlated with right eye vision, demonstrating the advantage of this visual field in visual information processing and suggesting a left hemispheric dominance. We also demonstrated that the nature of the presented visual stimulus does not seem to have any influence on the animals' monocular vision choice. PMID:16246503

  6. Novel algorithms for protein sequence analysis

    NARCIS (Netherlands)

    Ye, Kai

    2008-01-01

    Each protein is characterized by its unique sequential order of amino acids, the so-called protein sequence. Biology”s paradigm is that this order of amino acids determines the protein”s architecture and function. In this thesis, we introduce novel algorithms to analyze protein sequences. Chapter 1

  7. Covariance of charged amino acids at positions 322 and 440 of HIV-1 Env contributes to coreceptor specificity of subtype B viruses, and can be used to improve the performance of V3 sequence-based coreceptor usage prediction algorithms.

    Directory of Open Access Journals (Sweden)

    Kieran Cashin

    Full Text Available The ability to determine coreceptor usage of patient-derived human immunodeficiency virus type 1 (HIV-1 strains is clinically important, particularly for the administration of the CCR5 antagonist maraviroc. The envelope glycoprotein (Env determinants of coreceptor specificity lie primarily within the gp120 V3 loop region, although other Env determinants have been shown to influence gp120-coreceptor interactions. Here, we determined whether conserved amino acid alterations outside the V3 loop that contribute to coreceptor usage exist, and whether these alterations improve the performance of V3 sequence-based coreceptor usage prediction algorithms. We demonstrate a significant covariant association between charged amino acids at position 322 in V3 and position 440 in the C4 Env region that contributes to the specificity of HIV-1 subtype B strains for CCR5 or CXCR4. Specifically, positively charged Lys/Arg at position 322 and negatively charged Asp/Glu at position 440 occurred more frequently in CXCR4-using viruses, whereas negatively charged Asp/Glu at position 322 and positively charged Arg at position 440 occurred more frequently in R5 strains. In the context of CD4-bound gp120, structural models suggest that covariation of amino acids at Env positions 322 and 440 has the potential to alter electrostatic interactions that are formed between gp120 and charged amino acids in the CCR5 N-terminus. We further demonstrate that inclusion of a "440 rule" can improve the sensitivity of several V3 sequence-based genotypic algorithms for predicting coreceptor usage of subtype B HIV-1 strains, without compromising specificity, and significantly improves the AUROC of the geno2pheno algorithm when set to its recommended false positive rate of 5.75%. Together, our results provide further mechanistic insights into the intra-molecular interactions within Env that contribute to coreceptor specificity of subtype B HIV-1 strains, and demonstrate that incorporation

  8. Effect of temperature and solvent composition on acid dissociation equilibria, I: Sequenced {sup s}{sub s}pK{sub a} determination of compounds commonly used as buffers in high performance liquid chromatography coupled to mass spectroscopy detection

    Energy Technology Data Exchange (ETDEWEB)

    Padro, Juan M.; Acquaviva, Agustin; Tascon, Marcos [Laboratorio de Separaciones Analiticas, Division Quimica Analitica, Universidad Nacional de La Plata y CIDEPINT, 47 y 115, (1900) La Plata (Argentina); Gagliardi, Leonardo G., E-mail: leogagliardi@quimica.unlp.edu.ar [Laboratorio de Separaciones Analiticas, Division Quimica Analitica, Universidad Nacional de La Plata y CIDEPINT, 47 y 115, (1900) La Plata (Argentina); Castells, Cecilia B., E-mail: castells@isis.unlp.edu.ar [Laboratorio de Separaciones Analiticas, Division Quimica Analitica, Universidad Nacional de La Plata y CIDEPINT, 47 y 115, (1900) La Plata (Argentina)

    2012-05-06

    Highlights: Black-Right-Pointing-Pointer We developed a rapid potentiometric method for sequential pK{sub a} determinations. Black-Right-Pointing-Pointer We measured pK{sub a} of buffers from 0 to 90% (v/v) acetonitrile/water and from 20 to 60 Degree-Sign C. Black-Right-Pointing-Pointer Sequences of 42 pK{sub a}-data spanned over a wide solvent composition range needed 2 h. Black-Right-Pointing-Pointer We measured pK{sub a} of formic acid and triethylamine/HCl in up to 90% (v/v) acetonitrile. Black-Right-Pointing-Pointer The high-throughput method was applied to obtain pK{sub a} of two common buffers in LC/MS. - Abstract: A new automated and rapid potentiometric method for determining the effect of organic-solvent composition on pK{sub a} has been developed. It is based on the measurements of pH values of buffer solutions of variable solvent compositions using a combined glass electrode. Additions of small volumes of one precisely thermostated solution into another, both containing exactly the same analytical concentrations of the buffer components, can produce continuous changes in the solvent composition. Two sequences of potential measurements, one of increasing and the other of decreasing solvent content, are sufficient to obtain the pK{sub a} values of the acidic compound within the complete solvent-composition range in about 2 h. The experimental design, procedures, and calculations needed to convert the measured pH into the thermodynamic pK{sub a} values are thoroughly discussed. This rapid and automated method allows the systematic study of the effect of solvent compositions and temperatures on the pK{sub a}. It has been applied to study the dissociation constants of two monoprotic acids: formic acid and triethylamine:HCl in acetonitrile/water mixtures within the range from 0 to 90% (v/v) at temperatures between 20 Degree-Sign C and 60 Degree-Sign C. These volatile compounds are frequently used to control the pH of the mobile phase in HPLC, especially in

  9. Conceptual Change and Science Achievement Related to a Lesson Sequence on Acids and Bases Among African American Alternative High School Students: A Teacher's Practical Arguments and the Voice of the "Other"

    Science.gov (United States)

    Wood, Lynda Charese

    The study of teaching and learning during the period of translating ideals of reform into classroom practice enables us to understand student-teacher-researcher symbiotic learning. In line with this assumption, the purpose of this study is threefold:(1) observe effects of the Common Knowledge Construction Model (CKCM), a conceptual change inquiry model of teaching and learning, on African American students' conceptual change and achievement; (2) observe the shift in teacher's practical arguments; and (3) narrate the voice of "the Other" about teacher professional learning. This study uses retrospective data from a mixed-method approach consisting of Phenomenography, practical arguments and story-telling. Data sources include audio-recordings of a chemistry teacher's individual interviews of her students' prior- and post-intervention conceptions of acids and bases; results of Acid-Base Achievement Test (ABA-T); video-recordings of a chemistry teacher's enactment of CKCM acid-base lesson sequence; audio-recordings of teacher-researcher reflective discourse using classroom video-clips; teacher interviews; and teacher and researcher personal reflective journals. Students' conceptual changes reflect change in the number of categories of description; shift in language use from everyday talk to chemical talk; and development of a hierarchy of chemical knowledge. ABA-T results indicated 17 students in the experimental group achieved significantly higher scores than 22 students in the control group taught by traditional teaching methods. The teacher-researcher reflective discourse about enactment of the CKCM acid-base lesson sequence reveals three major shifts in teacher practical arguments: teacher inadequate preparedness to adequate preparedness; lack of confidence to gain in confidence; and surface learning to deep learning. The developing story uncovers several aspects about teaching and learning of African American students: teacher caring for the uncared; cultivating

  10. Invasive cleavage of nucleic acids

    Science.gov (United States)

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  11. Induction of severe experimental autoimmune neuritis with a synthetic peptide corresponding to the 53-78 amino acid sequence of the myelin P2 protein.

    Science.gov (United States)

    Rostami, A; Gregorian, S K; Brown, M J; Pleasure, D E

    1990-12-01

    We generated a synthetic peptide (SP-26), corresponding to the amino acid residues 53-78 of bovine P2 protein, which induced severe clinical and pathological characteristics of experimental autoimmune neuritis (EAN) in Lewis rats. Lymph node cell populations from SP-26-immunized rats elicited a proliferative response to the peptide and to the P2 protein. After 16 cycles of antigen stimulation with the peptide, the SP-26 T cell line shows a decreased response to P2, but not to SP-26. Fluorescence-activated cell sorter (FACS) analysis of a SP-26 T cell line indicated the majority of cells to be of CD4+ CD8-. This report demonstrates that the synthetic peptide SP-26 can induce severe EAN in Lewis rats in a dose-dependent manner. Furthermore, specific T cell lines reactive to SP-26 can be generated from the lymph nodes of SP-26-immunized rats. PMID:1699975

  12. 石蒜核糖体蛋白L21的基因克隆及氨基酸序列分析%Gene cloning and amino acid sequence analysis of ribosomal protein L21 from Lycoris radiata

    Institute of Scientific and Technical Information of China (English)

    佟金凤; 汪仁; 李晓丹; 江玉梅; 彭峰; 夏冰

    2011-01-01

    根据已知核糖体蛋白L21( RPL21)基因的保守序列设计1对引物,采用PCR技术从石蒜[Lycoris radiata (L'Hér.) Herb.]叶片全长cDNA文库中筛选出阳性克隆.通过测序和分析,获得1条石蒜RPL21基因全长cDNA 序列,命名为LrRPL21,GenBank登录号为FJ972626;序列全长709 bp,编码1条具有164个氨基酸残基的多肽.采用多种分析程序对石蒜RPL21的理化性质以及氨基酸序列的同源性进行了分析比较.结果显示:石蒜RPL21的预测分子量为18 628,理论等电点为10.36,分子式为C833 H1348 N254S4,总平均疏水性指数为-0.668,为亲水性蛋白;石蒜RPL21与其他8种植物RPL21的氨基酸序列同源性百分率均较高,达到85%~95%;根据系统树可推测其与油棕(Elaeis guineensis Jacq.) RPL21的进化关系最近.%A pair of primers were designed according to the known conserved sequence of ribosomal protein L21 (RPL21) gene, and the positive clone was selected from full length Cdna library of Lycoris radiata (L'Her.) Herb, leaf by PCR technology. By means of sequencing and analyzing, a full length Cdna sequence of L. Radiata RPL21 gene was obtained, which was named LrRPL2\\ and its Gen Bank accession number was FJ972626. The full length of LrRPL21 is 709 bp, which encodes a polypeptide being composed of 164 ami no acid residues. Physicochemical property and amino acid sequence homology of L. Radiata RPL21 were analyzed and compared by some analysis programs. The results show that the putative molecular weight and theoretical isoelectric point of L. Radiata RPL21 are 18 628 and 10. 36, respectively, the molecular formula is C833H 1348N254S4, and the grand average index of hydrophobicity is -0. 668, which is a hydrophilic protein. Homologous percentage of amino acid sequence of RPL21 between L. Radiata and other eight species is higher with a percentage of 85%-95%. And according to phylogenetic tree, it can be conjectured that the evolutionary relationship of RPL21 between

  13. Establishment of the Nucleic Acid Sequence-based Amplification Method for Detecting Vibio Alginolyticus%溶藻弧菌的依赖于核酸序列恒温扩增检测方法的建立

    Institute of Scientific and Technical Information of China (English)

    秦胜利; 王建广

    2012-01-01

    A new method, based on Nucleic Acid Sequence-based Amplification (NAS-BA) to detect Vibio alginolyticus of samples, was established. A highly specific set of primers was synthesized to target the hsp60 gene of Vibio alginolyticus so as to establish Nucleic Acid Sequence-based Amplification method. Specificity and sensitivity were tested. The results showed that the sensitivity of NASBA was 6. 9×102cfu ? mL-1 which was higher than the result of PCR method. Detecting Vibio alginolyticus with NASBA was more specific and sensitive than PCR method and has lower instrumental requirement. So,there is a broad prospect.%采用自行建立和优化的依赖于核酸序列恒温扩增(NASBA)检测体系,对溶藻弧菌进行检测.采用溶藻弧菌的hsp60基因为目的片段设计特异性引物,建成可快速检测溶藻弧菌的NASBA检测法,并进行了特异性和灵敏度试验.结果表明:所建立起的NASBA检测方法,灵敏度为6.9× 102 cfu·mL-1,高于普通PCR方法.溶藻弧菌的依赖于核酸序列恒温扩增检测方法具有较高灵敏度和和良好特异性,并且对仪器要求更低,用普通恒温设备即可进行反应,具有广阔的推广前景.

  14. Deep Hierarchies in the Primate Visual Cortex

    DEFF Research Database (Denmark)

    Krüger, Norbert; Jannsen, Per; Kalkan, S.;

    2013-01-01

    of the processing hierarchies present in the primate visual system considering recent discoveries in neurophysiology. The hierarchal processing in the primate visual system is characterized by a sequence of different levels of processing (in the order of ten) that constitute a deep hierarchy in contrast to the flat...... vision architectures predominantly used in today's mainstream computer vision. We hope that the functional description of the deep hierarchies realized in the primate visual system provides valuable insights for the design of computer vision algorithms, fostering increasingly productive interaction...

  15. The H-Index of `An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database'

    Science.gov (United States)

    Washburn, Michael P.

    2015-11-01

    Over 20 years ago a remarkable paper was published in the Journal of American Society for Mass Spectrometry. This paper from Jimmy Eng, Ashley McCormack, and John Yates described the use of protein databases to drive the interpretation of tandem mass spectra of peptides. This paper now has over 3660 citations and continues to average more than 260 per year over the last decade. This is an amazing scientific achievement. The reason for this is the paper was a cutting edge development at the moment in time when genomes of organisms were being sequenced, protein and peptide mass spectrometry was growing into the field of proteomics, and the power of computing was growing quickly in accordance with Moore's law. This work by the Yates lab grew in importance as genomics, proteomics, and computation all advanced and eventually resulted in the widely used SEQUEST algorithm and platform for the analysis of tandem mass spectrometry data. This commentary provides an analysis of the impact of this paper by analyzing the citations it has generated and the impact of these citing papers.

  16. Photoaffinity analogues of methotrexate as folate antagonist binding probes. 1. Photoaffinity labeling of murine L1210 dihydrofolate reductase and amino acid sequence of the binding region

    International Nuclear Information System (INIS)

    N/sup α/-(4-Amino-4-deoxy-10-methylpteroyl)-N/sup epsilon/-(4-azido-5-[125I]iodosalicylyl)-L-lysine, a photoaffinity analogue of methotrexate, is only 2-fold less potent than methotrexate in the inhibition of murine L1210 dihydrofolate reductase. Irradiation of the enzyme in the presence of an equimolar concentration of the 125I-labeled analogue ultimately leads to an 8% incorporation of the photoprobe. A 100-fold molar excess of methotrexate essentially blocks this incorporation. Cyanogen bromide digestion of the labeled enzyme, followed by high-pressure liquid chromatography purification of the generated peptides, indicates that greater than 85% of the total radioactivity is incorporated into a single cyanogen bromide peptide. Sequence analysis revealed this peptide to be residues 53-111, with a majority of the radioactivity centered around residues 63-65 (Lys-Asn-Arg). These data demonstrate that the photoaffinity analogue specifically binds to dihydrofolate reductase and covalently modifies the enzyme following irradiation and is therefore a photolabeling agent useful for probing the inhibitor binding domain of the enzyme

  17. Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

    Science.gov (United States)

    Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

    2016-06-01

    As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. PMID:27025952

  18. Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

    Science.gov (United States)

    Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

    2016-06-01

    As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/.

  19. Visuals for Information.

    Science.gov (United States)

    Pettersson, Rune

    This report focuses on the visual component of verbo-visual literacy, a communications concept involving the production, transmission, and perception of verbal and visual images. Five current problem areas in verbal-visual research are introduced and discussed: (1) communication (communication models, media consumption, new media, the information…

  20. 内蒙古少数民族地区宫颈癌的筛查方法研究%The value of HPV testing combining with acetic acid, iodine visual inspection in cervical cancer screening

    Institute of Scientific and Technical Information of China (English)

    贾震; 王少明; 段仙芝

    2012-01-01

    目的 探讨内蒙古少数民族聚居区宫颈癌及癌前病变适宜的筛查方法.方法 2009年4月-8月对内蒙古自治区鄂尔多斯、兴安盟、通辽三个地区的2 958名年龄30~59岁的已婚妇女进行了宫颈癌筛查.取宫颈脱落细胞,做人乳头瘤病毒( HPV - HC2)检测;同时用醋酸着色及碘着色(VIA/VILI)肉眼观察的方法进行筛查.对HPV- HC2阳性或VIA/VILI肉眼观察异常或两者均异常者,行阴道镜检查,在可疑处取宫颈组织活检,必要时行颈管诊刮术(ECC);送组织病理学检查确诊.结果 内蒙古鄂尔多斯、通辽、兴安盟三地区HPV总感染率为17.36%,中度及以上宫颈上皮内瘤样病变(≥CIN2)和宫颈癌的检出率为0.9%;应用HPV- HC2筛出阳性者最后确诊≥CIN2者27例,而用VIA/VILI仅确诊13例,漏诊14例.结论 HPV检测结合醋酸、碘肉眼观察是宫颈癌筛查的有效方法.在内蒙等经济发展不均衡地区,可尝试采用HPV检测进行初筛,对HPV阳性患者用VIA+ VILI或者细胞学筛查的方法进行分流的筛查策略,降低漏诊率,也相对降低HPV阳性患者阴道镜的转诊率.%Objective To evaluate the financial burden of cervical cancer and cervical intraepithelial neoplasia (CIN) in minorities of Inner Mongolia, and to investigate the appropriate screening measure for the areas. Methods In 2009, 2 958 married women of 30~59 yrs from three areas of Inner Mongolia Autonomous Region were underwent cervical cancer screening. Each subject was requested to collect the cervical exfoliated cells for human papillo-ma virus (HPV) detection (HC2), and then was screened by visual inspection with acetic acid (VIA) and Lugol's iodine (VILI) for the visual inspection of the cervix. Direct biopsies under colposcopy were taken if any abnormalities were found by V1A+VILI or HPV positive, endocervical curettage (ECC) was conducted if necessary. Women with positive HPV test results were called back in two weeks, and

  1. Genomic Phenotyping by Barcode Sequencing Broadly Distinguishes between Alkylating Agents, Oxidizing Agents, and Non-Genotoxic Agents, and Reveals a Role for Aromatic Amino Acids in Cellular Recovery after Quinone Exposure

    Science.gov (United States)

    Svensson, J. Peter; Quirós Pesudo, Laia; McRee, Siobhan K.; Adeleye, Yeyejide; Carmichael, Paul; Samson, Leona D.

    2013-01-01

    Toxicity screening of compounds provides a means to identify compounds harmful for human health and the environment. Here, we further develop the technique of genomic phenotyping to improve throughput while maintaining specificity. We exposed cells to eight different compounds that rely on different modes of action: four genotoxic alkylating (methyl methanesulfonate (MMS), N-Methyl-N-nitrosourea (MNU), N,N′-bis(2-chloroethyl)-N-nitroso-urea (BCNU), N-ethylnitrosourea (ENU)), two oxidizing (2-methylnaphthalene-1,4-dione (menadione, MEN), benzene-1,4-diol (hydroquinone, HYQ)), and two non-genotoxic (methyl carbamate (MC) and dimethyl sulfoxide (DMSO)) compounds. A library of S. cerevisiae 4,852 deletion strains, each identifiable by a unique genetic ‘barcode’, were grown in competition; at different time points the ratio between the strains was assessed by quantitative high throughput ‘barcode’ sequencing. The method was validated by comparison to previous genomic phenotyping studies and 90% of the strains identified as MMS-sensitive here were also identified as MMS-sensitive in a much lower throughput solid agar screen. The data provide profiles of proteins and pathways needed for recovery after both genotoxic and non-genotoxic compounds. In addition, a novel role for aromatic amino acids in the recovery after treatment with oxidizing agents was suggested. The role of aromatic acids was further validated; the quinone subgroup of oxidizing agents were extremely toxic in cells where tryptophan biosynthesis was compromised. PMID:24040048

  2. Nonlinear analysis of sequence repeats of multi-domain proteins

    International Nuclear Information System (INIS)

    Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences

  3. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_seque...nce_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  4. [Sequencing babies?].

    Science.gov (United States)

    Jordan, Bertrand

    2015-10-01

    An extension of newborn screening to genome sequencing is now feasible but raises a number of scientific, organisational and ethical issues. This is being explored in discussions and in several funded trials, in order to maximize benefits and avoid some identified risks. As some companies are already offering such a service, this is quite an urgent matter. PMID:26481033

  5. The sequence of the CA-SP1 junction accounts for the differential sensitivity of HIV-1 and SIV to the small molecule maturation inhibitor 3-O-{3',3'-dimethylsuccinyl}-betulinic acid

    Directory of Open Access Journals (Sweden)

    Aiken Christopher

    2004-06-01

    Full Text Available Abstract Background Despite the effectiveness of currently available antiretroviral therapies in the treatment of HIV-1 infection, a continuing need exists for novel compounds that can be used in combination with existing drugs to slow the emergence of drug-resistant viruses. We previously reported that the small molecule 3-O-{3',3'-dimethylsuccinyl}-betulinic acid (DSB specifically inhibits HIV-1 replication by delaying the processing of the CA-SP1 junction in Pr55Gag. By contrast, SIVmac239 replicates efficiently in the presence of high concentrations of DSB. To determine whether sequence differences in the CA-SP1 junction can fully account for the differential sensitivity of HIV-1 and SIV to DSB, we engineered mutations in this region of two viruses and tested their sensitivity to DSB in replication assays using activated human primary CD4+ T cells. Results Substitution of the P2 and P1 residues of HIV-1 by the corresponding amino acids of SIV resulted in strong resistance to DSB, but the mutant virus replicated with reduced efficiency. Conversely, replication of an SIV mutant containing three amino acid substitutions in the CA-SP1 cleavage site was highly sensitive to DSB, and the mutations resulted in delayed cleavage of the CA-SP1 junction in the presence of the drug. Conclusions These results demonstrate that the CA-SP1 junction in Pr55Gag represents the primary viral target of DSB. They further suggest that the therapeutic application of DSB will be accompanied by emergence of mutant viruses that are highly resistant to the drug but which exhibit reduced fitness relative to wild type HIV-1.

  6. Custom Visualization without Real Programming

    DEFF Research Database (Denmark)

    Pantazos, Kostas

    Information Visualization tools have simplified visualization development. Some tools help simple users construct standard visualizations; others help programmers develop custom visualizations. This thesis contributes to the field of Information Visualization and End-User Development. The first c...

  7. Analysis of various sequence-specific triplexes by electron and atomic force microscopies.

    OpenAIRE

    Cherny, D I; Fourcade, A; Svinarchuk, F; Nielsen, P E; Malvy, C; Delain, E

    1998-01-01

    Sequence-specific interactions of 20-mer G,A-containing triple helix-forming oligonucleotides (TFOs) and bis-PNAs (peptide nucleic acids) with double-stranded DNA was visualized by electron (EM) and atomic force (AFM) microscopies. Triplexes formed by biotinylated TFOs are easily detected by both EM and AFM in which streptavidin is a marker. AFM images of the unlabeled triplex within a long plasmid DNA show a approximately 0.4-nm height increment of the double helix within the target site pos...

  8. Universal visualization platform

    Science.gov (United States)

    Gee, Alexander G.; Li, Hongli; Yu, Min; Smrtic, Mary Beth; Cvek, Urska; Goodell, Howie; Gupta, Vivek; Lawrence, Christine; Zhou, Jainping; Chiang, Chih-Hung; Grinstein, Georges G.

    2005-03-01

    Although there are a number of visualization systems to choose from when analyzing data, only a few of these allow for the integration of other visualization and analysis techniques. There are even fewer visualization toolkits and frameworks from which one can develop ones own visualization applications. Even within the research community, scientists either use what they can from the available tools or start from scratch to define a program in which they are able to develop new or modified visualization techniques and analysis algorithms. Presented here is a new general-purpose platform for constructing numerous visualization and analysis applications. The focus of this system is the design and experimentation of new techniques, and where the sharing of and integration with other tools becomes second nature. Moreover, this platform supports multiple large data sets, and the recording and visualizing of user sessions. Here we introduce the Universal Visualization Platform (UVP) as a modern data visualization and analysis system.

  9. Declarative Visualization Queries

    Science.gov (United States)

    Pinheiro da Silva, P.; Del Rio, N.; Leptoukh, G. G.

    2011-12-01

    In an ideal interaction with machines, scientists may prefer to write declarative queries saying "what" they want from a machine than to write code stating "how" the machine is going to address the user request. For example, in relational database, users have long relied on specifying queries using Structured Query Language (SQL), a declarative language to request data results from a database management system. In the context of visualizations, we see that users are still writing code based on complex visualization toolkit APIs. With the goal of improving the scientists' experience of using visualization technology, we have applied this query-answering pattern to a visualization setting, where scientists specify what visualizations they want generated using a declarative SQL-like notation. A knowledge enhanced management system ingests the query and knows the following: (1) know how to translate the query into visualization pipelines; and (2) how to execute the visualization pipelines to generate the requested visualization. We define visualization queries as declarative requests for visualizations specified in an SQL like language. Visualization queries specify what category of visualization to generate (e.g., volumes, contours, surfaces) as well as associated display attributes (e.g., color and opacity), without any regards for implementation, thus allowing scientists to remain partially unaware of a wide range of visualization toolkit (e.g., Generic Mapping Tools and Visualization Toolkit) specific implementation details. Implementation details are only a concern for our knowledge-based visualization management system, which uses both the information specified in the query and knowledge about visualization toolkit functions to construct visualization pipelines. Knowledge about the use of visualization toolkits includes what data formats the toolkit operates on, what formats they output, and what views they can generate. Visualization knowledge, which is not

  10. Visualization analysis and design

    CERN Document Server

    Munzner, Tamara

    2015-01-01

    Visualization Analysis and Design provides a systematic, comprehensive framework for thinking about visualization in terms of principles and design choices. The book features a unified approach encompassing information visualization techniques for abstract data, scientific visualization techniques for spatial data, and visual analytics techniques for interweaving data transformation and analysis with interactive visual exploration. It emphasizes the careful validation of effectiveness and the consideration of function before form. The book breaks down visualization design according to three questions: what data users need to see, why users need to carry out their tasks, and how the visual representations proposed can be constructed and manipulated. It walks readers through the use of space and color to visually encode data in a view, the trade-offs between changing a single view and using multiple linked views, and the ways to reduce the amount of data shown in each view. The book concludes with six case stu...

  11. [Gastric Acid].

    Science.gov (United States)

    Ruíz Chávez, R

    1996-01-01

    Gastric acid, a product of parietal cells secretion, full fills multiple biological roles which are absolutely necessary to keep corporal homeostasis. The production of the acid depends upon an effector cellular process represented in the first step by histamine, acetilcholine and gastrin, first messengers of the process. These interact with specific receptors than in sequence activate second messengers -cAMP and the calcium-calmodulin system- which afterwards activate a kinase. An specific protein is then phosphorilated by this enzyme, being the crucial factor that starts the production of acid. Finally, a proton bomb, extrudes the acid towards the gastric lumen. The secretion process mentioned above, is progressive lyactivated in three steps, two of which are stimulators -cephalic and gastric phases- and the other one inhibitor or intestinal phase. These stages are started by mental and neurological phenomena -thought, sight, smell or memory-; by food, drugs or other ingested substances; and by products of digestion. Changes in regulation of acid secretion, in the structure of gastro-duodenal mucosal barrier by a wide spectrum of factors and agents including food, drugs and H. pylori, are the basis of acid-peptic disease, entity in which gastric acid plays a fundamental role. From the therapeutic point of view, so at the theoretical as at the practical levels, t is possible to interfere with the secretion of acid by neutralization of some of the steps of the effector cellular process. An adequate knowledge of the basics related to gastric acid, allows to create strategies for the clinical handling of associated pathology, specifically in relation to peptic acid disease in all of the known clinical forms. PMID:12165790

  12. Visual tracking: detecting and mapping occlusion and camouflage using process-behaviour charts

    OpenAIRE

    Chandesa, Tissa

    2013-01-01

    Visual tracking aims to identify a target object in each frame of an image sequence. It presents an important scientific problem since the human visual system is capable of tracking moving objects in a wide variety of situations. Artificial visual tracking systems also find practical application in areas such as visual surveillance, robotics, biomedical image analysis, medicine and the media. However, automatic visual tracking algorithms suffer from two common problems: occlusion and camoufla...

  13. Interaction for visualization

    CERN Document Server

    Tominski, Christian

    2015-01-01

    Visualization has become a valuable means for data exploration and analysis. Interactive visualization combines expressive graphical representations and effective user interaction. Although interaction is an important component of visualization approaches, much of the visualization literature tends to pay more attention to the graphical representation than to interaction.The goal of this work is to strengthen the interaction side of visualization. Based on a brief review of general aspects of interaction, we develop an interaction-oriented view on visualization. This view comprises five key as

  14. Visualizing ensembles in structural biology.

    Science.gov (United States)

    Melvin, Ryan L; Salsbury, Freddie R

    2016-06-01

    Displaying a single representative conformation of a biopolymer rather than an ensemble of states mistakenly conveys a static nature rather than the actual dynamic personality of biopolymers. However, there are few apparent options due to the fixed nature of print media. Here we suggest a standardized methodology for visually indicating the distribution width, standard deviation and uncertainty of ensembles of states with little loss of the visual simplicity of displaying a single representative conformation. Of particular note is that the visualization method employed clearly distinguishes between isotropic and anisotropic motion of polymer subunits. We also apply this method to ligand binding, suggesting a way to indicate the expected error in many high throughput docking programs when visualizing the structural spread of the output. We provide several examples in the context of nucleic acids and proteins with particular insights gained via this method. Such examples include investigating a therapeutic polymer of FdUMP (5-fluoro-2-deoxyuridine-5-O-monophosphate) - a topoisomerase-1 (Top1), apoptosis-inducing poison - and nucleotide-binding proteins responsible for ATP hydrolysis from Bacillus subtilis. We also discuss how these methods can be extended to any macromolecular data set with an underlying distribution, including experimental data such as NMR structures. PMID:27179343

  15. Visualizing ensembles in structural biology.

    Science.gov (United States)

    Melvin, Ryan L; Salsbury, Freddie R

    2016-06-01

    Displaying a single representative conformation of a biopolymer rather than an ensemble of states mistakenly conveys a static nature rather than the actual dynamic personality of biopolymers. However, there are few apparent options due to the fixed nature of print media. Here we suggest a standardized methodology for visually indicating the distribution width, standard deviation and uncertainty of ensembles of states with little loss of the visual simplicity of displaying a single representative conformation. Of particular note is that the visualization method employed clearly distinguishes between isotropic and anisotropic motion of polymer subunits. We also apply this method to ligand binding, suggesting a way to indicate the expected error in many high throughput docking programs when visualizing the structural spread of the output. We provide several examples in the context of nucleic acids and proteins with particular insights gained via this method. Such examples include investigating a therapeutic polymer of FdUMP (5-fluoro-2-deoxyuridine-5-O-monophosphate) - a topoisomerase-1 (Top1), apoptosis-inducing poison - and nucleotide-binding proteins responsible for ATP hydrolysis from Bacillus subtilis. We also discuss how these methods can be extended to any macromolecular data set with an underlying distribution, including experimental data such as NMR structures.

  16. Cloning and sequencing of the bovine gastrin gene

    DEFF Research Database (Denmark)

    Lund, T; Rehfeld, J F; Olsen, Jørgen

    1989-01-01

    In order to deduce the primary structure of bovine preprogastrin we therefore sequenced a gastrin DNA clone isolated from a bovine liver cosmid library. Bovine preprogastrin comprises 104 amino acids and consists of a signal peptide, a 37 amino acid spacer-sequence, the gastrin-34 sequence followed...

  17. Volume visualization of multiple alignment of genomic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Nameeta; Weber, Gunther H.; Dillard, Scott E.; Hamann, Bernd

    2004-05-01

    Genomes of hundreds of species have been sequenced to date and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. We present a technique to arrange 1D data in 3D space to allow us to apply state-of-the-art interactive volume visualization techniques for data exploration. We provide results for aligned DNA sequence data and compare it with traditional 1D line plots. Our technique, coupled with 1D line plots, results in effective multiresolution visualization of very large aligned sequence data sets.

  18. Implementation of cervical cancer screening using visual inspection with acetic acid in rural Mozambique: successes and challenges using HIV care and treatment programme investments in Zambézia Province

    Directory of Open Access Journals (Sweden)

    Alberto J Baptista

    2012-06-01

    Full Text Available Background: In order to maximize the benefits of HIV care and treatment investments in sub-Saharan Africa, programs can broaden to target other diseases amenable to screening and efficient management. We nested cervical cancer screening into family planning clinics at select sites also receiving PEPFAR support for antiretroviral therapy (ART rollout. This was done using visual inspection with acetic acid (VIA by maternal child health nurses. We report on achievements and obstacles in the first year of the program in rural Mozambique. Methods: VIA was taught to clinic nurses and hospital physicians, with a regular clinical feedback loop for quality evaluation and retraining. Cryotherapy using carbon dioxide as the refrigerant was provided at clinics; loop electrosurgical excision procedure (LEEP and surgery were provided at the provincial hospital for serious cases. No pathology services were available. Results: Nurses screened 4651 women using VIA in Zambézia Province in year one of the program, more than double the Ministry of Health service target. VIA was judged positive for squamous intraepithelial lesions in 8% (n=380 of the women (9% if age ≥30 years (n=3154 and 7% if age <30 years (n=1497; p=0.02. Of the 380 VIA-positive women, 4% (n=16 had lesions (0.3% of 4651 total screened requiring referral to Quelimane Provincial Hospital. Fourteen (88% of these 16 women were seen at the hospital, but records were inadequate to judge outcomes. Of women screened, 2714 (58% either had knowledge of their HIV status prior to VIA or were subsequently sent for HIV testing, of which 583 (21% were HIV positive. Conclusions: Screening and clinical services were successfully provided on a large scale for the first time ever in these rural clinics. However, health manpower shortages, equipment problems, poor paper record systems and a limited ability to follow-up patients inhibited the quality of the cervical cancer screening services. Using prior HIV

  19. Visualization of Social Networks

    NARCIS (Netherlands)

    Boertjes, E.M.; Kotterink, B.; Jager, E.J.

    2011-01-01

    Current visualizations of social networks are mostly some form of node-link diagram. Depending on the type of social network, this can be some treevisualization with a strict hierarchical structure or a more generic network visualization.

  20. Visual attention capacity

    DEFF Research Database (Denmark)

    Habekost, Thomas; Starrfelt, Randi

    2009-01-01

    Psychophysical studies have identified two distinct limitations of visual attention capacity: processing speed and apprehension span. Using a simple test, these cognitive factors can be analyzed by Bundesen's Theory of Visual Attention (TVA). The method has strong specificity and sensitivity...