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Sample records for functional proteomic robotic

  1. HepatoProteomics: Applying Proteomic Technologies to the Study of Liver Function and Disease

    SciTech Connect

    Diamond, Deborah L.; Proll, Sean; Jacobs, Jon M.; Chan, Eric Y.; Camp, David G.; Smith, Richard D.; Katze, Michael G.

    2006-08-01

    The wealth of human genome sequence information now available, coupled with technological advances in robotics, nanotechnology, mass spectrometry, and information systems, has given rise to a method of scientific inquiry known as functional genomics. By using these technologies to survey gene expression and protein production on a near global scale, the goal of functional genomics is to assign biological function to genes with currently unknown roles in physiology. This approach carries particular appeal in disease research, where it can uncover the function of previously unknown genes and molecular pathways that are directly involved in disease progression. With this knowledge may come improved diagnostic techniques, prognostic capabilities, and novel therapeutic approaches. In this regard, the continuing evolution of proteomic technologies has resulted in an increasingly greater impact of proteome studies in many areas of research and hepatology is no exception. Our laboratory has been extremely active in this area, applying both genomic and proteomic technologies to the analysis of virus-host interactions in several systems, including the study of hepatitis C virus (HCV) infection and HCV-associated liver disease. Since proteomic technologies are foreign to many hepatologists (and to almost everyone else), this article will provide an overview of proteomic methods and technologies and describe how they're being used to study liver function and disease. We use our studies of HCV infection and HCV-associated liver disease to present an operational framework for performing high throughput proteome analysis and extracting biologically meaningful information.

  2. Functional proteomics within the genus Lactobacillus.

    PubMed

    De Angelis, Maria; Calasso, Maria; Cavallo, Noemi; Di Cagno, Raffaella; Gobbetti, Marco

    2016-03-01

    Lactobacillus are mainly used for the manufacture of fermented dairy, sourdough, meat, and vegetable foods or used as probiotics. Under optimal processing conditions, Lactobacillus strains contribute to food functionality through their enzyme portfolio and the release of metabolites. An extensive genomic diversity analysis was conducted to elucidate the core features of the genus Lactobacillus, and to provide a better comprehension of niche adaptation of the strains. However, proteomics is an indispensable "omics" science to elucidate the proteome diversity, and the mechanisms of regulation and adaptation of Lactobacillus strains. This review focuses on the novel and comprehensive knowledge of functional proteomics and metaproteomics of Lactobacillus species. A large list of proteomic case studies of different Lactobacillus species is provided to illustrate the adaptability of the main metabolic pathways (e.g., carbohydrate transport and metabolism, pyruvate metabolism, proteolytic system, amino acid metabolism, and protein synthesis) to various life conditions. These investigations have highlighted that lactobacilli modulate the level of a complex panel of proteins to growth/survive in different ecological niches. In addition to the general regulation and stress response, specific metabolic pathways can be switched on and off, modifying the behavior of the strains.

  3. The proteome: structure, function and evolution.

    PubMed

    Fleming, Keiran; Kelley, Lawrence A; Islam, Suhail A; MacCallum, Robert M; Muller, Arne; Pazos, Florencio; Sternberg, Michael J E

    2006-03-29

    This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family.

  4. A proteomic approach to neuropeptide function elucidation.

    PubMed

    Temmerman, L; Bogaerts, A; Meelkop, E; Cardoen, D; Boerjan, B; Janssen, T; Schoofs, L

    2012-03-01

    Many of the diverse functions of neuropeptides are still elusive. As they are ideally suited to modulate traditional signaling, their added actions are not always detectable under standard laboratory conditions. The search for function assignment to peptide encoding genes can therefore greatly benefit from molecular information. Specific molecular changes resulting from neuropeptide signaling may direct researchers to yet unknown processes or conditions, for which studying these signaling systems may eventually lead to phenotypic confirmation. Here, we applied gel-based proteomics after pdf-1 neuropeptide gene knockout in the model organism Caenorhabditis elegans. It has previously been described that pdf-1 null mutants display a locomotion defect, being slower and making more turns and reversals than wild type worms. The vertebrate functional homolog of PDF-1, vasocative intestinal peptide (VIP), is known to influence a plethora of processes, which have so far not been investigated for pdf-1. Because proteins represent the actual effectors inside an organism, proteomic analysis can guide our view to novel pdf-1 actions in the nematode worm. Our data show that knocking out pdf-1 results in alteration of levels of proteins involved in fat metabolism, stress resistance and development. This indicates a possible conservation of VIP-like actions for pdf-1 in C. elegans.

  5. The disulfide proteome and other reactive cysteine proteomes: analysis and functional significance.

    PubMed

    Lindahl, Marika; Mata-Cabana, Alejandro; Kieselbach, Thomas

    2011-06-15

    Ten years ago, proteomics techniques designed for large-scale investigations of redox-sensitive proteins started to emerge. The proteomes, defined as sets of proteins containing reactive cysteines that undergo oxidative post-translational modifications, have had a particular impact on research concerning the redox regulation of cellular processes. These proteomes, which are hereafter termed "disulfide proteomes," have been studied in nearly all kingdoms of life, including animals, plants, fungi, and bacteria. Disulfide proteomics has been applied to the identification of proteins modified by reactive oxygen and nitrogen species under stress conditions. Other studies involving disulfide proteomics have addressed the functions of thioredoxins and glutaredoxins. Hence, there is a steadily growing number of proteins containing reactive cysteines, which are probable targets for redox regulation. The disulfide proteomes have provided evidence that entire pathways, such as glycolysis, the tricarboxylic acid cycle, and the Calvin-Benson cycle, are controlled by mechanisms involving changes in the cysteine redox state of each enzyme implicated. Synthesis and degradation of proteins are processes highly represented in disulfide proteomes and additional biochemical data have established some mechanisms for their redox regulation. Thus, combined with biochemistry and genetics, disulfide proteomics has a significant potential to contribute to new discoveries on redox regulation and signaling.

  6. Systems proteomics of liver mitochondria function.

    PubMed

    Williams, Evan G; Wu, Yibo; Jha, Pooja; Dubuis, Sébastien; Blattmann, Peter; Argmann, Carmen A; Houten, Sander M; Amariuta, Tiffany; Wolski, Witold; Zamboni, Nicola; Aebersold, Ruedi; Auwerx, Johan

    2016-06-10

    Recent improvements in quantitative proteomics approaches, including Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS), permit reproducible large-scale protein measurements across diverse cohorts. Together with genomics, transcriptomics, and other technologies, transomic data sets can be generated that permit detailed analyses across broad molecular interaction networks. Here, we examine mitochondrial links to liver metabolism through the genome, transcriptome, proteome, and metabolome of 386 individuals in the BXD mouse reference population. Several links were validated between genetic variants toward transcripts, proteins, metabolites, and phenotypes. Among these, sequence variants in Cox7a2l alter its protein's activity, which in turn leads to downstream differences in mitochondrial supercomplex formation. This data set demonstrates that the proteome can now be quantified comprehensively, serving as a key complement to transcriptomics, genomics, and metabolomics--a combination moving us forward in complex trait analysis. PMID:27284200

  7. Systems proteomics of liver mitochondria function.

    PubMed

    Williams, Evan G; Wu, Yibo; Jha, Pooja; Dubuis, Sébastien; Blattmann, Peter; Argmann, Carmen A; Houten, Sander M; Amariuta, Tiffany; Wolski, Witold; Zamboni, Nicola; Aebersold, Ruedi; Auwerx, Johan

    2016-06-10

    Recent improvements in quantitative proteomics approaches, including Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS), permit reproducible large-scale protein measurements across diverse cohorts. Together with genomics, transcriptomics, and other technologies, transomic data sets can be generated that permit detailed analyses across broad molecular interaction networks. Here, we examine mitochondrial links to liver metabolism through the genome, transcriptome, proteome, and metabolome of 386 individuals in the BXD mouse reference population. Several links were validated between genetic variants toward transcripts, proteins, metabolites, and phenotypes. Among these, sequence variants in Cox7a2l alter its protein's activity, which in turn leads to downstream differences in mitochondrial supercomplex formation. This data set demonstrates that the proteome can now be quantified comprehensively, serving as a key complement to transcriptomics, genomics, and metabolomics--a combination moving us forward in complex trait analysis.

  8. The Arabidopsis Cytosolic Ribosomal Proteome: From form to Function

    PubMed Central

    Carroll, Adam J.

    2013-01-01

    The cytosolic ribosomal proteome of Arabidopsis thaliana has been studied intensively by a range of proteomics approaches and is now one of the most well characterized eukaryotic ribosomal proteomes. Plant cytosolic ribosomes are distinguished from other eukaryotic ribosomes by unique proteins, unique post-translational modifications and an abundance of ribosomal proteins for which multiple divergent paralogs are expressed and incorporated. Study of the A. thaliana ribosome has now progressed well beyond a simple cataloging of protein parts and is focused strongly on elucidating the functions of specific ribosomal proteins, their paralogous isoforms and covalent modifications. This review summarises current knowledge concerning the Arabidopsis cytosolic ribosomal proteome and highlights potentially fruitful areas of future research in this fast moving and important area. PMID:23459595

  9. Comparative analyses of nuclear proteome: extending its function

    PubMed Central

    Narula, Kanika; Datta, Asis; Chakraborty, Niranjan; Chakraborty, Subhra

    2013-01-01

    Organeller proteomics is an emerging technology that is critical in determining the cellular signal transduction pathways. Nucleus, the regulatory hub of the eukaryotic cell is a dynamic system and a repository of various macromolecules that serve as modulators of such signaling that dictate cell fate decisions. Nuclear proteins (NPs) are predicted to comprise about 10–20% of the total cellular proteins, suggesting the involvement of the nucleus in a number of diverse functions. Indeed, NPs constitute a highly organized but complex network that plays diverse roles during development and physiological processes. In plants, relatively little is known about the nature of the molecular components and mechanisms involved in coordinating NP synthesis, their action and function. Proteomic study hold promise to understand the molecular basis of nuclear function using an unbiased comparative and differential approach. We identified a few hundred proteins that include classical and non-canonical nuclear components presumably associated with variety of cellular functions impinging on the complexity of nuclear proteome. Here, we review the nuclear proteome based on our own findings, available literature, and databases focusing on detailed comparative analysis of NPs and their functions in order to understand how plant nucleus works. The review also shed light on the current status of plant nuclear proteome and discusses the future prospect. PMID:23637696

  10. Mass-spectrometric exploration of proteome structure and function.

    PubMed

    Aebersold, Ruedi; Mann, Matthias

    2016-01-01

    Numerous biological processes are concurrently and coordinately active in every living cell. Each of them encompasses synthetic, catalytic and regulatory functions that are, almost always, carried out by proteins organized further into higher-order structures and networks. For decades, the structures and functions of selected proteins have been studied using biochemical and biophysical methods. However, the properties and behaviour of the proteome as an integrated system have largely remained elusive. Powerful mass-spectrometry-based technologies now provide unprecedented insights into the composition, structure, function and control of the proteome, shedding light on complex biological processes and phenotypes. PMID:27629641

  11. Mass-spectrometric exploration of proteome structure and function.

    PubMed

    Aebersold, Ruedi; Mann, Matthias

    2016-09-14

    Numerous biological processes are concurrently and coordinately active in every living cell. Each of them encompasses synthetic, catalytic and regulatory functions that are, almost always, carried out by proteins organized further into higher-order structures and networks. For decades, the structures and functions of selected proteins have been studied using biochemical and biophysical methods. However, the properties and behaviour of the proteome as an integrated system have largely remained elusive. Powerful mass-spectrometry-based technologies now provide unprecedented insights into the composition, structure, function and control of the proteome, shedding light on complex biological processes and phenotypes.

  12. High-Throughput Fully Automated Construction of a Multiplex Library of Mutagenized Open Reading Frames for an Insecticidal Peptide Using a Plasmid-Based Functional Proteomic Robotic Workcell with Improved Vacuum System

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Robotic platforms are essential for the production and screening of large numbers of expression-ready plasmid sets used to develop optimized clones and improved microbial strains. Here we demonstrate a plasmid-based integrated workcell that was used to automate the molecular biology protocols inclu...

  13. [FUNCTIONAL DIFFERENTIATION IN BRYOZOAN COLONY: A PROTEOMIC ANALYSIS].

    PubMed

    Kutyumov, V A; Maltseva, A L; Kotenko, N; Ostrovsky, A N

    2016-01-01

    Bryozoans are typical modular organisms. They consist of repetitive structural units, the zooids. Bryozoan colonies grow by zooidal budding, with the distribution pattern of the budding loci underlying the diversity of colony forms. Budding is usually restricted to the zooids at the periphery of the colony, which form a "growing edge" or local terminal growth zones. Non-budding parts of the colony can be functionally subdivided, too. In many species colonies consists of regular, often repetitive zones of feeding and non-feeding modules, associated with a periodical degeneration and regeneration of the polypide, retractile tentacle crown with a gut and the accompanying musculature. So, there is functional differentiation in bryozoan colonies but its mechanisms are unknown. Presumably, budding and/or polypide recycling in different colony parts are induced or inhibited by certain determinants of functional specialization. An effective tool of their identification is the comparison of proteomes of functionally different zones. Here we report the results of proteomic analysis of three bryozoan species from the White Sea, which have a different colony form: Flustrellidra hispida, Terminoflustra membranaceotruncata and Securiflustra securifrons. Using differential two-dimensional electrophoresis (2D-DIGE), we compared proteomes of the growing edge and the zones consisting of feeding and non-feeding zooids in these species. We estimated the overall proteome variability, revealed proteins whose relative abundance gradually changed along the proximal-distal colony axis and suggested that they might be involved in the functional differentiation of the colony.

  14. [FUNCTIONAL DIFFERENTIATION IN BRYOZOAN COLONY: A PROTEOMIC ANALYSIS].

    PubMed

    Kutyumov, V A; Maltseva, A L; Kotenko, N; Ostrovsky, A N

    2016-01-01

    Bryozoans are typical modular organisms. They consist of repetitive structural units, the zooids. Bryozoan colonies grow by zooidal budding, with the distribution pattern of the budding loci underlying the diversity of colony forms. Budding is usually restricted to the zooids at the periphery of the colony, which form a "growing edge" or local terminal growth zones. Non-budding parts of the colony can be functionally subdivided, too. In many species colonies consists of regular, often repetitive zones of feeding and non-feeding modules, associated with a periodical degeneration and regeneration of the polypide, retractile tentacle crown with a gut and the accompanying musculature. So, there is functional differentiation in bryozoan colonies but its mechanisms are unknown. Presumably, budding and/or polypide recycling in different colony parts are induced or inhibited by certain determinants of functional specialization. An effective tool of their identification is the comparison of proteomes of functionally different zones. Here we report the results of proteomic analysis of three bryozoan species from the White Sea, which have a different colony form: Flustrellidra hispida, Terminoflustra membranaceotruncata and Securiflustra securifrons. Using differential two-dimensional electrophoresis (2D-DIGE), we compared proteomes of the growing edge and the zones consisting of feeding and non-feeding zooids in these species. We estimated the overall proteome variability, revealed proteins whose relative abundance gradually changed along the proximal-distal colony axis and suggested that they might be involved in the functional differentiation of the colony. PMID:27220253

  15. Proteomic profiling reveals insights into Triticeae stigma development and function.

    PubMed

    Nazemof, Nazila; Couroux, Philippe; Rampitsch, Christof; Xing, Tim; Robert, Laurian S

    2014-11-01

    To our knowledge, this study represents the first high-throughput characterization of a stigma proteome in the Triticeae. A total of 2184 triticale mature stigma proteins were identified using three different gel-based approaches combined with mass spectrometry. The great majority of these proteins are described in a Triticeae stigma for the first time. These results revealed many proteins likely to play important roles in stigma development and pollen-stigma interactions, as well as protection against biotic and abiotic stresses. Quantitative comparison of the triticale stigma transcriptome and proteome showed poor correlation, highlighting the importance of having both types of analysis. This work makes a significant contribution towards the elucidation of the Triticeae stigma proteome and provides novel insights into its role in stigma development and function. PMID:25170101

  16. Meeting Report: "Proteomics from Discovery to Function:" 6th Annual Meeting of Proteomics Society, India and International Conference-A Milestone for the Indian Proteomics Community.

    PubMed

    Gupta, Shabarni; Reddy, Panga Jaipal; Ray, Sandipan; Atak, Apurva; Gollapalli, Kishore; Jain, Rekha; Shah, Veenita Grover; Ghantasala, Saicharan; Kumar, Saurabh; Pandala, Narendra Goud; Phapale, Prasad; Pandey, Vishnu Kumar; Zingde, Surekha; Srivastava, Sanjeeva

    2015-06-01

    Proteomics is at the epicenter of post-genomics biotechnologies that are currently driving the next generation system science. Moreover, proteomics is a truly global science. The 6(th) Annual Meeting of Proteomics Society, India (PSI) and International Conference on "Proteomics from Discovery to Function" held from December 7-9, 2014, was a transformative endeavor for global proteomics, bringing together the luminaries in the field of proteomics for the very first time in India. This meeting report presents the lessons learned and the highlights of this international scientific conference that was comprised of nine thematic sessions, pre- and post-conference workshops, and an opportunity to cultivate enduring collaborations for proteomics science to benefit both India and global society. The conference had an unforgettable impression on the participants: for the first time, India hosted past and present President and Council members from the Human Proteome Organization (HUPO), along with eminent scientists and young scholars from India and abroad in the field of proteomics at such a large scale, a major highlight of this international event. In all, the PSI 2014 was a milestone conference that has firmly poised the Indian life sciences community as a leading contributor to post-genomics life sciences, thus cultivating crucial trans-generational capacity and inspiration by recognizing the emerging scholars and omics systems scientists who can think and conduct science from cell to society.

  17. Making blind robots see: the synergy between fluorescent dyes and imaging devices in automated proteomics.

    PubMed

    Patton, W F

    2000-05-01

    Proteomics investigations endeavor to provide a global understanding of gene product synthesis rate, degradation rate, functional competence, posttranslational modification, subcellular distribution and physical interactions with other cell components. Protein expression encompasses an enormous dynamic range. Since rare proteins cannot be amplified by any type of PCR method, sensitive detection is critical to proteome projects. Fluorescence methods deliver streamlined detection protocols, superior detection sensitivity, broad linear dynamic range and excellent compatibility with modern microchemical identification methods such as mass spectrometry. Two general approaches to fluorescence detection of proteins are currently practiced: the covalent derivatization of proteins with fluorophores or noncovalent interaction of fluorophores either via the SDS micelle or through direct electrostatic interaction with proteins. One approach for quantifying fluorescence is to use a photomultiplier tube detector combined with a laser light scanner. In addition, fluorescence imaging is performed using a charge-coupled device camera combined with a UV light or xenon arc source. Fluorescent dyes with bimodal excitation spectra may be broadly implemented on a wide range of analytical imaging devices, permitting their widespread application to proteomics studies and incorporation into semiautomated analysis environments.

  18. Current Approaches on Viral Infection: Proteomics and Functional Validations

    PubMed Central

    Zheng, Jie; Tan, Boon Huan; Sugrue, Richard; Tang, Kai

    2012-01-01

    Viruses could manipulate cellular machinery to ensure their continuous survival and thus become parasites of living organisms. Delineation of sophisticated host responses upon virus infection is a challenging task. It lies in identifying the repertoire of host factors actively involved in the viral infectious cycle and characterizing host responses qualitatively and quantitatively during viral pathogenesis. Mass spectrometry based proteomics could be used to efficiently study pathogen-host interactions and virus-hijacked cellular signaling pathways. Moreover, direct host and viral responses upon infection could be further investigated by activity-based functional validation studies. These approaches involve drug inhibition of secretory pathway, immunofluorescence staining, dominant negative mutant of protein target, real-time PCR, small interfering siRNA-mediated knockdown, and molecular cloning studies. In this way, functional validation could gain novel insights into the high-content proteomic dataset in an unbiased and comprehensive way. PMID:23162545

  19. Proteomics

    SciTech Connect

    Hixson, Kim K.; Lopez-Ferrer, Daniel; Robinson, Errol W.; Pasa-Tolic, Ljiljana

    2010-02-01

    Proteomics aims to characterize the spatial distribution and temporal dynamics of proteins in biological systems, the protein response to environmental stimuli, and the differences in protein states between diseased and control biological systems. Mass spectrometry (MS) plays a crucial role in enabling the analysis of proteomes and typically is the method of choice for identifying proteins present in biological systems. Peptide (and consequently protein) identifications are made by comparing measured masses to calculated values obtained from genome data. Several methodologies based on MS have been developed for the analysis of proteomes. The complexity of the biological systems requires that the proteome be separated prior to analysis. Both gel based and liquid chromatography based separations have proven very useful in this regard. Typically, separated proteins are analyzed with MS either intact (top-down proteomics) or are digested into peptides (bottom-up) prior to MS analysis. Additionally, several procedures, with and without stable isotopic labeling, have been introduced to facilitate protein quantitation (e.g. characterize changes in protein abundances between given biological states).

  20. Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology.

    PubMed

    Agrawal, Ganesh Kumar; Rakwal, Randeep

    2011-05-01

    Growing rice is an important socio-economic activity. Rice proteomics has achieved a tremendous progress in establishing techniques to proteomes of almost all tissues, organs, and organelles during the past one decade (year 2000-2010). We have compiled these progresses time to time over this period. The present compilation discusses proteomics research in rice published between 1st April 2008 and 30th July 2010. Progress continues mainly towards protein cataloging deep into the proteome with high-confident protein assignment and some functional significance than ever before by (i) identifying previously unreported/low-abundance proteins, (ii) quantifying relative/absolute values of proteins, (iii) assigning protein responses to biotic/abiotic stresses, (iv) protein localization into organelles, (v) validating previous proteomes and eliminating false-positive proteins, and (vi) discovering potential biomarkers for tissues, organs, organelles, and for screening transgenic plants and food-safety evaluation. The notable achievements in global mapping of phosphorylation sites and identifying several novel secreted proteins into the extracellular space are worth appreciating. Our ever-increasing knowledge on the rice proteomics is beginning to impact the biology of not only rice, but also crops and plants. These major achievements will be discussed in this review keeping in mind newcomers, young, and established scientists in proteomics and plants.

  1. Attitudinal Change in Elderly Citizens Toward Social Robots: The Role of Personality Traits and Beliefs About Robot Functionality.

    PubMed

    Damholdt, Malene F; Nørskov, Marco; Yamazaki, Ryuji; Hakli, Raul; Hansen, Catharina Vesterager; Vestergaard, Christina; Seibt, Johanna

    2015-01-01

    Attitudes toward robots influence the tendency to accept or reject robotic devices. Thus it is important to investigate whether and how attitudes toward robots can change. In this pilot study we investigate attitudinal changes in elderly citizens toward a tele-operated robot in relation to three parameters: (i) the information provided about robot functionality, (ii) the number of encounters, (iii) personality type. Fourteen elderly residents at a rehabilitation center participated. Pre-encounter attitudes toward robots, anthropomorphic thinking, and personality were assessed. Thereafter the participants interacted with a tele-operated robot (Telenoid) during their lunch (c. 30 min.) for up to 3 days. Half of the participants were informed that the robot was tele-operated (IC) whilst the other half were naïve to its functioning (UC). Post-encounter assessments of attitudes toward robots and anthropomorphic thinking were undertaken to assess change. Attitudes toward robots were assessed with a new generic 35-items questionnaire (attitudes toward social robots scale: ASOR-5), offering a differentiated conceptualization of the conditions for social interaction. There was no significant difference between the IC and UC groups in attitude change toward robots though trends were observed. Personality was correlated with some tendencies for attitude changes; Extraversion correlated with positive attitude changes to intimate-personal relatedness with the robot (r = 0.619) and to psychological relatedness (r = 0.581) whilst Neuroticism correlated negatively (r = -0.582) with mental relatedness with the robot. The results tentatively suggest that neither information about functionality nor direct repeated encounters are pivotal in changing attitudes toward robots in elderly citizens. This may reflect a cognitive congruence bias where the robot is experienced in congruence with initial attitudes, or it may support action-based explanations of cognitive dissonance reductions

  2. Attitudinal Change in Elderly Citizens Toward Social Robots: The Role of Personality Traits and Beliefs About Robot Functionality

    PubMed Central

    Damholdt, Malene F.; Nørskov, Marco; Yamazaki, Ryuji; Hakli, Raul; Hansen, Catharina Vesterager; Vestergaard, Christina; Seibt, Johanna

    2015-01-01

    Attitudes toward robots influence the tendency to accept or reject robotic devices. Thus it is important to investigate whether and how attitudes toward robots can change. In this pilot study we investigate attitudinal changes in elderly citizens toward a tele-operated robot in relation to three parameters: (i) the information provided about robot functionality, (ii) the number of encounters, (iii) personality type. Fourteen elderly residents at a rehabilitation center participated. Pre-encounter attitudes toward robots, anthropomorphic thinking, and personality were assessed. Thereafter the participants interacted with a tele-operated robot (Telenoid) during their lunch (c. 30 min.) for up to 3 days. Half of the participants were informed that the robot was tele-operated (IC) whilst the other half were naïve to its functioning (UC). Post-encounter assessments of attitudes toward robots and anthropomorphic thinking were undertaken to assess change. Attitudes toward robots were assessed with a new generic 35-items questionnaire (attitudes toward social robots scale: ASOR-5), offering a differentiated conceptualization of the conditions for social interaction. There was no significant difference between the IC and UC groups in attitude change toward robots though trends were observed. Personality was correlated with some tendencies for attitude changes; Extraversion correlated with positive attitude changes to intimate-personal relatedness with the robot (r = 0.619) and to psychological relatedness (r = 0.581) whilst Neuroticism correlated negatively (r = -0.582) with mental relatedness with the robot. The results tentatively suggest that neither information about functionality nor direct repeated encounters are pivotal in changing attitudes toward robots in elderly citizens. This may reflect a cognitive congruence bias where the robot is experienced in congruence with initial attitudes, or it may support action-based explanations of cognitive dissonance reductions

  3. Attitudinal Change in Elderly Citizens Toward Social Robots: The Role of Personality Traits and Beliefs About Robot Functionality.

    PubMed

    Damholdt, Malene F; Nørskov, Marco; Yamazaki, Ryuji; Hakli, Raul; Hansen, Catharina Vesterager; Vestergaard, Christina; Seibt, Johanna

    2015-01-01

    Attitudes toward robots influence the tendency to accept or reject robotic devices. Thus it is important to investigate whether and how attitudes toward robots can change. In this pilot study we investigate attitudinal changes in elderly citizens toward a tele-operated robot in relation to three parameters: (i) the information provided about robot functionality, (ii) the number of encounters, (iii) personality type. Fourteen elderly residents at a rehabilitation center participated. Pre-encounter attitudes toward robots, anthropomorphic thinking, and personality were assessed. Thereafter the participants interacted with a tele-operated robot (Telenoid) during their lunch (c. 30 min.) for up to 3 days. Half of the participants were informed that the robot was tele-operated (IC) whilst the other half were naïve to its functioning (UC). Post-encounter assessments of attitudes toward robots and anthropomorphic thinking were undertaken to assess change. Attitudes toward robots were assessed with a new generic 35-items questionnaire (attitudes toward social robots scale: ASOR-5), offering a differentiated conceptualization of the conditions for social interaction. There was no significant difference between the IC and UC groups in attitude change toward robots though trends were observed. Personality was correlated with some tendencies for attitude changes; Extraversion correlated with positive attitude changes to intimate-personal relatedness with the robot (r = 0.619) and to psychological relatedness (r = 0.581) whilst Neuroticism correlated negatively (r = -0.582) with mental relatedness with the robot. The results tentatively suggest that neither information about functionality nor direct repeated encounters are pivotal in changing attitudes toward robots in elderly citizens. This may reflect a cognitive congruence bias where the robot is experienced in congruence with initial attitudes, or it may support action-based explanations of cognitive dissonance reductions

  4. Robot-aided assessment of lower extremity functions: a review.

    PubMed

    Maggioni, Serena; Melendez-Calderon, Alejandro; van Asseldonk, Edwin; Klamroth-Marganska, Verena; Lünenburger, Lars; Riener, Robert; van der Kooij, Herman

    2016-01-01

    The assessment of sensorimotor functions is extremely important to understand the health status of a patient and its change over time. Assessments are necessary to plan and adjust the therapy in order to maximize the chances of individual recovery. Nowadays, however, assessments are seldom used in clinical practice due to administrative constraints or to inadequate validity, reliability and responsiveness. In clinical trials, more sensitive and reliable measurement scales could unmask changes in physiological variables that would not be visible with existing clinical scores.In the last decades robotic devices have become available for neurorehabilitation training in clinical centers. Besides training, robotic devices can overcome some of the limitations in traditional clinical assessments by providing more objective, sensitive, reliable and time-efficient measurements. However, it is necessary to understand the clinical needs to be able to develop novel robot-aided assessment methods that can be integrated in clinical practice.This paper aims at providing researchers and developers in the field of robotic neurorehabilitation with a comprehensive review of assessment methods for the lower extremities. Among the ICF domains, we included those related to lower extremities sensorimotor functions and walking; for each chapter we present and discuss existing assessments used in routine clinical practice and contrast those to state-of-the-art instrumented and robot-aided technologies. Based on the shortcomings of current assessments, on the identified clinical needs and on the opportunities offered by robotic devices, we propose future directions for research in rehabilitation robotics. The review and recommendations provided in this paper aim to guide the design of the next generation of robot-aided functional assessments, their validation and their translation to clinical practice. PMID:27485106

  5. Single-cell-type proteomics: toward a holistic understanding of plant function.

    PubMed

    Dai, Shaojun; Chen, Sixue

    2012-12-01

    Multicellular organisms such as plants contain different types of cells with specialized functions. Analyzing the protein characteristics of each type of cell will not only reveal specific cell functions, but also enhance understanding of how an organism works. Most plant proteomics studies have focused on using tissues and organs containing a mixture of different cells. Recent single-cell-type proteomics efforts on pollen grains, guard cells, mesophyll cells, root hairs, and trichomes have shown utility. We expect that high resolution proteomic analyses will reveal novel functions in single cells. This review provides an overview of recent developments in plant single-cell-type proteomics. We discuss application of the approach for understanding important cell functions, and we consider the technical challenges of extending the approach to all plant cell types. Finally, we consider the integration of single-cell-type proteomics with transcriptomics and metabolomics with the goal of providing a holistic understanding of plant function.

  6. Robotics.

    ERIC Educational Resources Information Center

    Waddell, Steve; Doty, Keith L.

    1999-01-01

    "Why Teach Robotics?" (Waddell) suggests that the United States lags behind Europe and Japan in use of robotics in industry and teaching. "Creating a Course in Mobile Robotics" (Doty) outlines course elements of the Intelligent Machines Design Lab. (SK)

  7. The MMACHC proteome: hallmarks of functional cobalamin deficiency in humans.

    PubMed

    Hannibal, Luciana; DiBello, Patricia M; Yu, Michelle; Miller, Abby; Wang, Sihe; Willard, Belinda; Rosenblatt, David S; Jacobsen, Donald W

    2011-07-01

    Cobalamin (Cbl, B(12)) is an essential micronutrient required to fulfill the enzymatic reactions of cytosolic methylcobalamin-dependent methionine synthase and mitochondrial adenosylcobalamin-dependent methylmalonyl-CoA mutase. Mutations in the MMACHC gene (cblC complementation group) disrupt processing of the upper-axial ligand of newly internalized cobalamins, leading to functional deficiency of the vitamin. Patients with cblC disease present with both hyperhomocysteinemia and methylmalonic acidemia, cognitive dysfunction, and megaloblastic anemia. In the present study we show that cultured skin fibroblasts from cblC patients export increased levels of both homocysteine and methylmalonic acid compared to control skin fibroblasts, and that they also have decreased levels of total intracellular folates. This is consistent with the clinical phenotype of functional cobalamin deficiency in vivo. The protein changes that accompany human functional Cbl deficiency are unknown. The proteome of control and cblC fibroblasts was quantitatively examined by two dimensional difference in-gel electrophoresis (2D-DIGE) and liquid chromatography-electrospray ionization-mass spectrometry (LC/ESI/MS). Major changes were observed in the expression levels of proteins involved in cytoskeleton organization and assembly, the neurological system and cell signaling. Pathway analysis of the differentially expressed proteins demonstrated strong associations with neurological disorders, muscular and skeletal disorders, and cardiovascular diseases in the cblC mutant cell lines. Supplementation of the cell cultures with hydroxocobalamin did not restore the cblC proteome to the patterns of expression observed in control cells. These results concur with the observed phenotype of patients with the cblC disorder and their sometimes poor response to treatment with hydroxocobalamin. Our findings could be valuable for designing alternative therapies to alleviate the clinical manifestation of the cbl

  8. Proteomics Analysis Reveals Overlapping Functions of Clustered Protocadherins*

    PubMed Central

    Han, Meng-Hsuan; Lin, Chengyi; Meng, Shuxia; Wang, Xiaozhong

    2010-01-01

    The three tandem-arrayed protocadherin (Pcdh) gene clusters, namely Pcdh-α, Pcdh-β, and Pcdh-γ, play important roles in the development of the vertebrate central nervous system. To gain insight into the molecular action of PCDHs, we performed a systematic proteomics analysis of PCDH-γ-associated protein complexes. We identified a list of 154 non-redundant proteins in the PCDH-γ complexes. This list includes nearly 30 members of clustered Pcdh-α, -β, and -γ families as core components of the complexes and additionally over 120 putative PCDH-associated proteins. We validated a selected subset of PCDH-γ-associated proteins using specific antibodies. Analysis of the identities of PCDH-associated proteins showed that the majority of them overlap with the proteomic profile of postsynaptic density preparations. Further analysis of membrane protein complexes revealed that several validated PCDH-γ-associated proteins exhibit reduced levels in Pcdh-γ-deficient brain tissues. Therefore, PCDH-γs are required for the integrity of the complexes. However, the size of the overall complexes and the abundance of many other proteins remained unchanged, raising a possibility that PCDH-αs and PCDH-βs might compensate for PCDH-γ function in complex formation. As a test of this idea, RNA interference knockdown of both PCDH-αs and PCDH-γs showed that PCDHs have redundant functions in regulating neuronal survival in the chicken spinal cord. Taken together, our data provide evidence that clustered PCDHs coexist in large protein complexes and have overlapping functions during vertebrate neural development. PMID:19843561

  9. Proteomics enhances evolutionary and functional analysis of reproductive proteins.

    PubMed

    Findlay, Geoffrey D; Swanson, Willie J

    2010-01-01

    Reproductive proteins maintain species-specific barriers to fertilization, affect the outcome of sperm competition, mediate reproductive conflicts between the sexes, and potentially contribute to the formation of new species. However, the specific proteins and molecular mechanisms that underlie these processes are understood in only a handful of cases. Advances in genomic and proteomic technologies enable the identification of large suites of reproductive proteins, making it possible to dissect reproductive phenotypes at the molecular level. We first review these technological advances and describe how reproductive proteins are identified in diverse animal taxa. We then discuss the dynamic evolution of reproductive proteins and the potential selective forces that act on them. Finally, we describe molecular and genomic tools for functional analysis and detail how evolutionary data may be used to make predictions about interactions among reproductive proteins.

  10. Speeding up the learning of robot kinematics through function decomposition.

    PubMed

    Ruiz de Angulo, Vicente; Torras, Carme

    2005-11-01

    The main drawback of using neural networks or other example-based learning procedures to approximate the inverse kinematics (IK) of robot arms is the high number of training samples (i.e., robot movements) required to attain an acceptable precision. We propose here a trick, valid for most industrial robots, that greatly reduces the number of movements needed to learn or relearn the IK to a given accuracy. This trick consists in expressing the IK as a composition of learnable functions, each having half the dimensionality of the original mapping. Off-line and on-line training schemes to learn these component functions are also proposed. Experimental results obtained by using nearest neighbors and parameterized self-organizing map, with and without the decomposition, show that the time savings granted by the proposed scheme grow polynomially with the precision required.

  11. Robotic Mirror Therapy System for Functional Recovery of Hemiplegic Arms.

    PubMed

    Beom, Jaewon; Koh, Sukgyu; Nam, Hyung Seok; Kim, Wonshik; Kim, Yoonjae; Seo, Han Gil; Oh, Byung-Mo; Chung, Sun Gun; Kim, Sungwan

    2016-08-15

    Mirror therapy has been performed as effective occupational therapy in a clinical setting for functional recovery of a hemiplegic arm after stroke. It is conducted by eliciting an illusion through use of a mirror as if the hemiplegic arm is moving in real-time while moving the healthy arm. It can facilitate brain neuroplasticity through activation of the sensorimotor cortex. However, conventional mirror therapy has a critical limitation in that the hemiplegic arm is not actually moving. Thus, we developed a real-time 2-axis mirror robot system as a simple add-on module for conventional mirror therapy using a closed feedback mechanism, which enables real-time movement of the hemiplegic arm. We used 3 Attitude and Heading Reference System sensors, 2 brushless DC motors for elbow and wrist joints, and exoskeletal frames. In a feasibility study on 6 healthy subjects, robotic mirror therapy was safe and feasible. We further selected tasks useful for activities of daily living training through feedback from rehabilitation doctors. A chronic stroke patient showed improvement in the Fugl-Meyer assessment scale and elbow flexor spasticity after a 2-week application of the mirror robot system. Robotic mirror therapy may enhance proprioceptive input to the sensory cortex, which is considered to be important in neuroplasticity and functional recovery of hemiplegic arms. The mirror robot system presented herein can be easily developed and utilized effectively to advance occupational therapy.

  12. Robotic Mirror Therapy System for Functional Recovery of Hemiplegic Arms.

    PubMed

    Beom, Jaewon; Koh, Sukgyu; Nam, Hyung Seok; Kim, Wonshik; Kim, Yoonjae; Seo, Han Gil; Oh, Byung-Mo; Chung, Sun Gun; Kim, Sungwan

    2016-01-01

    Mirror therapy has been performed as effective occupational therapy in a clinical setting for functional recovery of a hemiplegic arm after stroke. It is conducted by eliciting an illusion through use of a mirror as if the hemiplegic arm is moving in real-time while moving the healthy arm. It can facilitate brain neuroplasticity through activation of the sensorimotor cortex. However, conventional mirror therapy has a critical limitation in that the hemiplegic arm is not actually moving. Thus, we developed a real-time 2-axis mirror robot system as a simple add-on module for conventional mirror therapy using a closed feedback mechanism, which enables real-time movement of the hemiplegic arm. We used 3 Attitude and Heading Reference System sensors, 2 brushless DC motors for elbow and wrist joints, and exoskeletal frames. In a feasibility study on 6 healthy subjects, robotic mirror therapy was safe and feasible. We further selected tasks useful for activities of daily living training through feedback from rehabilitation doctors. A chronic stroke patient showed improvement in the Fugl-Meyer assessment scale and elbow flexor spasticity after a 2-week application of the mirror robot system. Robotic mirror therapy may enhance proprioceptive input to the sensory cortex, which is considered to be important in neuroplasticity and functional recovery of hemiplegic arms. The mirror robot system presented herein can be easily developed and utilized effectively to advance occupational therapy. PMID:27583794

  13. Alternative Splicing and Subfunctionalization Generates Functional Diversity in Fungal Proteomes

    PubMed Central

    Jiménez-López, Claudia; Lorenz, Michael C.; van Hoof, Ambro

    2013-01-01

    Alternative splicing is commonly used by the Metazoa to generate more than one protein from a gene. However, such diversification of the proteome by alternative splicing is much rarer in fungi. We describe here an ancient fungal alternative splicing event in which these two proteins are generated from a single alternatively spliced ancestral SKI7/HBS1 gene retained in many species in both the Ascomycota and Basidiomycota. While the ability to express two proteins from a single SKI7/HBS1 gene is conserved in many fungi, the exact mechanism by which they achieve this varies. The alternative splicing was lost in Saccharomyces cerevisiae following the whole-genome duplication event as these two genes subfunctionalized into the present functionally distinct HBS1 and SKI7 genes. When expressed in yeast, the single gene from Lachancea kluyveri generates two functionally distinct proteins. Expression of one of these proteins complements hbs1, but not ski7 mutations, while the other protein complements ski7, but not hbs1. This is the first known case of subfunctionalization by loss of alternative splicing in yeast. By coincidence, the ancestral alternatively spliced gene was also duplicated in Schizosaccharomyces pombe with subsequent subfunctionalization and loss of splicing. Similar subfunctionalization by loss of alternative splicing in fungi also explains the presence of two PTC7 genes in the budding yeast Tetrapisispora blattae, suggesting that this is a common mechanism to preserve duplicate alternatively spliced genes. PMID:23516382

  14. Functional proteomic and interactome analysis of proteins associated with beef tenderness in angus cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beef is a source of high quality protein for the human population, and beef tenderness has significant influence on beef palatability, consumer expectation and industry profitability. To further elucidate the factors affecting beef tenderness, functional proteomics and bioinformatics interactome ana...

  15. Proteomic Insight into the Molecular Function of the Vitreous

    PubMed Central

    Skeie, Jessica M.; Roybal, C. Nathaniel; Mahajan, Vinit B.

    2015-01-01

    The human vitreous contains primarily water, but also contains proteins which have yet to be fully characterized. To gain insight into the four vitreous substructures and their potential functions, we isolated and analyzed the vitreous protein profiles of three non-diseased human eyes. The four analyzed substructures were the anterior hyaloid, the vitreous cortex, the vitreous core, and the vitreous base. Proteins were separated by multidimensional liquid chromatography and identified by tandem mass spectrometry. Bioinformatics tools then extracted the expression profiles, signaling pathways, and interactomes unique to each tissue. From each substructure, a mean of 2,062 unique proteins were identified, with many being differentially expressed in a specific substructure: 278 proteins were unique to the anterior hyaloid, 322 to the vitreous cortex, 128 to the vitreous base, and 136 to the vitreous core. When the identified proteins were organized according to relevant functional pathways and networks, key patterns appeared. The blood coagulation pathway and extracellular matrix turnover networks were highly represented. Oxidative stress regulation and energy metabolism proteins were distributed throughout the vitreous. Immune functions were represented by high levels of immunoglobulin, the complement pathway, damage-associated molecular patterns (DAMPs), and evolutionarily conserved antimicrobial proteins. The majority of vitreous proteins detected were intracellular proteins, some of which originate from the retina, including rhodopsin (RHO), phosphodiesterase 6 (PDE6), and glial fibrillary acidic protein (GFAP). This comprehensive analysis uncovers a picture of the vitreous as a biologically active tissue, where proteins localize to distinct substructures to protect the intraocular tissues from infection, oxidative stress, and energy disequilibrium. It also reveals the retina as a potential source of inflammatory mediators. The vitreous proteome catalogues the

  16. Neurocognitive robot-assisted therapy of hand function.

    PubMed

    Metzger, Jean-Claude; Lambercy, Olivier; Califfi, Antonella; Conti, Fabio M; Gassert, Roger

    2014-01-01

    Neurocognitive therapy, according to the Perfetti method, proposes exercises that challenge motor, sensory as well as cognitive functions of neurologically impaired patients. At the level of the hand, neurocognitive exercises typically involve haptic exploration and interaction with objects of various shapes and mechanical properties. Haptic devices are thus an ideal support to provide neurocognitive exercises under well-controlled and reproducible conditions, and to objectively assess patient performance. Here we present three neurocognitive robot-assisted exercises which were implemented on the ReHapticKnob, a high-fidelity two-degrees-of-freedom hand rehabilitation robot. The exercises were evaluated for feasibility and acceptance in a pilot study on five patients suffering from different neurological disorders. Results showed that all patients were able to take part in the neurocognitive robot-assisted therapy, and that the proposed therapy was well accepted by patients, as assessed through subjective questionnaires. Force/torque and position measurements provided insights on the motor strategy employed by the patients during the exploration of virtual object properties, and served as objective assessment of task performance. The fusion of the neurocognitive therapy concept with robot-assisted rehabilitation enriches therapeutic approaches through the focus on haptics, and could provide novel insights on sensorimotor impairment and recovery.

  17. Aging synaptic mitochondria exhibit dynamic proteomic changes while maintaining bioenergetic function.

    PubMed

    Stauch, Kelly L; Purnell, Phillip R; Fox, Howard S

    2014-04-01

    Aging correlates with a progressive impairment of mitochondrial homeostasis and is an influential factor for several forms of neurodegeneration. However, the mechanisms underlying age-related alterations in synaptosomal mitochondria, a neuronal mitochondria population highly susceptible to insults and critical for brain function, remain incompletely understood. Therefore this study investigates the synaptic mitochondrial proteomic and bioenergetic alterations that occur with age. The utilization of a state of the art quantitative proteomics approach allowed for the comparison of protein expression levels in synaptic mitochondria isolated from 5 (mature), 12 (old), and 24 (aged) month old mice. During the process of aging we find that dynamic proteomic alterations occur in synaptic mitochondria. Despite direct (mitochondrial DNA deletions) and indirect (increased antioxidant protein levels) signs of mitochondrial damage in the aged mice, there was an overall maintenance of mitochondrial function. Therefore the synaptic mitochondrial proteomic changes that occur with aging correlate with preservation of synaptic mitochondrial function.

  18. Proteome-wide dataset supporting functional study of tyrosine kinases in breast cancer

    PubMed Central

    Angelopoulos, Nicos; Stebbing, Justin; Xu, Yichen; Giamas, Georgios; Zhang, Hua

    2016-01-01

    Tyrosine kinases (TKs) play an essential role in regulating various cellular activities and dysregulation of TK signaling contributes to oncogenesis. However, less than half of the TKs have been thoroughly studied. Through a combined use of RNAi and stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics, a global functional proteomic landscape of TKs in breast cancer was recently revealed highlighting a comprehensive and highly integrated signaling network regulated by TKs (Stebbing et al., 2015) [1]. We collate the enormous amount of the proteomic data in an open access platform, providing a valuable resource for studying the function of TKs in cancer and benefiting the science community. Here we present a detailed description related to this study (Stebbing et al., 2015) [1] and the raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier PXD002065. PMID:27054188

  19. Biomimetic robotics should be based on functional morphology

    PubMed Central

    Witte, Hartmut; Hoffmann, Helge; Hackert, Rémi; Schilling, Cornelius; Fischer, Martin S; Preuschoft, Holger

    2004-01-01

    Due to technological improvements made during the last decade, bipedal robots today present a surprisingly high level of humanoid skill. Autonomy, with respect to the processing of information, is realized to a relatively high degree. What is mainly lacking in robotics, moving from purely anthropomorphic robots to ‘anthropofunctional’ machines, is energetic autonomy. In a previously published analysis, we showed that closer attention to the functional morphology of human walking could give robotic engineers the experiences of an at least 6 Myr beta test period on minimization of power requirements for biped locomotion. From our point of view, there are two main features that facilitate sustained walking in modern humans. The first main feature is the existence of ‘energetically optimal velocities’ provided by the systematic use of various resonance mechanisms: (a) suspended pendula (involving arms as well as legs in the swing phase of the gait cycle) and matching of the pendular length of the upper and lower limbs; (b) inverted pendula (involving the legs in the stance phase), driven by torsional springs around the ankle joints; and (c) torsional springs in the trunk. The second main feature is compensation for undesirable torques induced by the inertial properties of the swinging extremities: (a) mass distribution in the trunk characterized by maximized mass moments of inertia; (b) lever arms of joint forces at the hip and shoulder, which are inversely proportional to their amplitude; and (c) twisting of the trunk, especially torsion. Our qualitative conclusions are three-fold. (1) Human walking is an interplay between masses, gravity and elasticity, which is modulated by musculature. Rigid body mechanics is insufficient to describe human walking. Thus anthropomorphic robots completely following the rules of rigid body mechanics cannot be functionally humanoid. (2) Humans are vertebrates. Thus, anthropomorphic robots that do not use the trunk for purposes

  20. Heterogeneity in Neutrophil Microparticles Reveals Distinct Proteome and Functional Properties*

    PubMed Central

    Dalli, Jesmond; Montero-Melendez, Trinidad; Norling, Lucy V; Yin, Xiaoke; Hinds, Charles; Haskard, Dorian; Mayr, Manuel; Perretti, Mauro

    2013-01-01

    Altered plasma neutrophil microparticle levels have recently been implicated in a number of vascular and inflammatory diseases, yet our understanding of their actions is very limited. Herein, we investigate the proteome of neutrophil microparticles in order to shed light on their biological actions. Stimulation of human neutrophils, either in suspension or adherent to an endothelial monolayer, led to the production of microparticles containing >400 distinct proteins with only 223 being shared by the two subsets. For instance, postadherent microparticles were enriched in alpha-2 macroglobulin and ceruloplasmin, whereas microparticles produced by neutrophils in suspension were abundant in heat shock 70 kDa protein 1. Annexin A1 and lactotransferrin were expressed in both microparticle subsets. We next determined relative abundance of these proteins in three types of human microparticle samples: healthy volunteer plasma, plasma of septic patients and skin blister exudates finding that these proteins were differentially expressed on neutrophil microparticles from these samples reflecting in part the expression profiles we found in vitro. Functional assessment of the neutrophil microparticles subsets demonstrated that in response to direct stimulation neutrophil microparticles produced reactive oxygen species and leukotriene B4 as well as locomoted toward a chemotactic gradient. Finally, we investigated the actions of the two neutrophil microparticles subsets described herein on target cell responses. Microarray analysis with human primary endothelial cells incubated with either microparticle subset revealed a discrete modulation of endothelial cell gene expression profile. These findings demonstrate that neutrophil microparticles are heterogenous and can deliver packaged information propagating the activation status of the parent cell, potentially exerting novel and fundamental roles both under homeostatic and disease conditions. PMID:23660474

  1. Robotics

    NASA Technical Reports Server (NTRS)

    Ambrose, Robert O.

    2007-01-01

    Lunar robotic functions include: 1. Transport of crew and payloads on the surface of the moon; 2. Offloading payloads from a lunar lander; 3. Handling the deployment of surface systems; with 4. Human commanding of these functions from inside a lunar vehicle, habitat, or extravehicular (space walk), with Earth-based supervision. The systems that will perform these functions may not look like robots from science fiction. In fact, robotic functions may be automated trucks, cranes and winches. Use of this equipment prior to the crew s arrival or in the potentially long periods without crews on the surface, will require that these systems be computer controlled machines. The public release of NASA's Exploration plans at the 2nd Space Exploration Conference (Houston, December 2006) included a lunar outpost with as many as four unique mobility chassis designs. The sequence of lander offloading tasks involved as many as ten payloads, each with a unique set of geometry, mass and interface requirements. This plan was refined during a second phase study concluded in August 2007. Among the many improvements to the exploration plan were a reduction in the number of unique mobility chassis designs and a reduction in unique payload specifications. As the lunar surface system payloads have matured, so have the mobility and offloading functional requirements. While the architecture work continues, the community can expect to see functional requirements in the areas of surface mobility, surface handling, and human-systems interaction as follows: Surface Mobility 1. Transport crew on the lunar surface, accelerating construction tasks, expanding the crew s sphere of influence for scientific exploration, and providing a rapid return to an ascent module in an emergency. The crew transport can be with an un-pressurized rover, a small pressurized rover, or a larger mobile habitat. 2. Transport Extra-Vehicular Activity (EVA) equipment and construction payloads. 3. Transport habitats and

  2. Proteomics of ovarian cancer: functional insights and clinical applications

    DOE PAGES

    Elzek, Mohamed A.; Rodland, Karin D.

    2015-03-04

    In the past decade, there has been an increasing interest in applying proteomics to assist in understanding the pathogenesis of ovarian cancer, elucidating the mechanism of drug resistance, and in the development of biomarkers for early detection of ovarian cancer. Although ovarian cancer is a spectrum of different diseases, the strategies for diagnosis and treatment with surgery and adjuvant therapy are similar across ovarian cancer types, increasing the general applicability of discoveries made through proteomics research. While proteomic experiments face many difficulties which slow the pace of clinical applications, recent advances in proteomic technology contribute significantly to the identification ofmore » aberrant proteins and networks which can serve as targets for biomarker development and individualized therapies. This review provides a summary of the literature on proteomics’ contributions to ovarian cancer research and highlights the current issues, future directions, and challenges. In conclusion, we propose that protein-level characterization of primary lesion in ovarian cancer can decipher the mystery of this disease, improve diagnostic tools, and lead to more effective screening programs.« less

  3. Proteomics of ovarian cancer: functional insights and clinical applications

    SciTech Connect

    Elzek, Mohamed A.; Rodland, Karin D.

    2015-03-04

    In the past decade, there has been an increasing interest in applying proteomics to assist in understanding the pathogenesis of ovarian cancer, elucidating the mechanism of drug resistance, and in the development of biomarkers for early detection of ovarian cancer. Although ovarian cancer is a spectrum of different diseases, the strategies for diagnosis and treatment with surgery and adjuvant therapy are similar across ovarian cancer types, increasing the general applicability of discoveries made through proteomics research. While proteomic experiments face many difficulties which slow the pace of clinical applications, recent advances in proteomic technology contribute significantly to the identification of aberrant proteins and networks which can serve as targets for biomarker development and individualized therapies. This review provides a summary of the literature on proteomics’ contributions to ovarian cancer research and highlights the current issues, future directions, and challenges. In conclusion, we propose that protein-level characterization of primary lesion in ovarian cancer can decipher the mystery of this disease, improve diagnostic tools, and lead to more effective screening programs.

  4. Proteomic analysis uncovers a metabolic phenotype in C. elegans after nhr-40 reduction of function

    SciTech Connect

    Pohludka, Michal; Simeckova, Katerina; Vohanka, Jaroslav; Yilma, Petr; Novak, Petr; Krause, Michael W.; Kostrouchova, Marta; Kostrouch, Zdenek

    2008-09-12

    Caenorhabditis elegans has an unexpectedly large number (284) of genes encoding nuclear hormone receptors, most of which are nematode-specific and are of unknown function. We have exploited comparative two-dimensional chromatography of synchronized cultures of wild type C. elegans larvae and a mutant in nhr-40 to determine if proteomic approaches will provide additional insight into gene function. Chromatofocusing, followed by reversed-phase chromatography and mass spectrometry, identified altered chromatographic patterns for a set of proteins, many of which function in muscle and metabolism. Prompted by the proteomic analysis, we find that the penetrance of the developmental phenotypes in the mutant is enhanced at low temperatures and by food restriction. The combination of our phenotypic and proteomic analysis strongly suggests that NHR-40 provides a link between metabolism and muscle development. Our results highlight the utility of comparative two-dimensional chromatography to provide a relatively rapid method to gain insight into gene function.

  5. Microchip platforms for multiplex single-cell functional proteomics with applications to immunology and cancer research

    PubMed Central

    2013-01-01

    Single-cell functional proteomics assays can connect genomic information to biological function through quantitative and multiplex protein measurements. Tools for single-cell proteomics have developed rapidly over the past 5 years and are providing approaches for directly elucidating phosphoprotein signaling networks in cancer cells or for capturing high-resolution snapshots of immune system function in patients with various disease conditions. We discuss advances in single-cell proteomics platforms, with an emphasis on microchip methods. These methods can provide a direct correlation of morphological, functional and molecular signatures at the single-cell level. We also provide examples of how those platforms are being applied to both fundamental biology and clinical studies, focusing on immune-system monitoring and phosphoprotein signaling networks in cancer. PMID:23998271

  6. Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics.

    PubMed

    Zhu, Heng; Cox, Eric; Qian, Jiang

    2012-12-01

    Functional protein microarrays were developed as a high-throughput tool to overcome the limitations of DNA microarrays and to provide a versatile platform for protein functional analyses. Recent years have witnessed tremendous growth in the use of protein microarrays, particularly functional protein microarrays, to address important questions in the field of clinical proteomics. In this review, we will summarize some of the most innovative and exciting recent applications of protein microarrays in clinical proteomics, including biomarker identification, pathogen-host interactions, and cancer biology. PMID:23027439

  7. Kinematic functions for the 7 DOF robotics research arm

    NASA Technical Reports Server (NTRS)

    Kreutz, K.; Long, M.; Seraji, Homayoun

    1989-01-01

    The Robotics Research Model K-1207 manipulator is a redundant 7R serial link arm with offsets at all joints. To uniquely determine joint angles for a given end-effector configuration, the redundancy is parameterized by a scalar variable which corresponds to the angle between the manipulator elbow plane and the vertical plane. The forward kinematic mappings from joint-space to end-effector configuration and elbow angle, and the augmented Jacobian matrix which gives end-effector and elbow angle rates as a function of joint rates, are also derived.

  8. Applied proteomics: mitochondrial proteins and effect on function.

    PubMed

    Lopez, Mary F; Melov, Simon

    2002-03-01

    The identification of a majority of the polypeptides in mitochondria would be invaluable because they play crucial and diverse roles in many cellular processes and diseases. The endogenous production of reactive oxygen species (ROS) is a major limiter of life as illustrated by studies in which the transgenic overexpression in invertebrates of catalytic antioxidant enzymes results in increased lifespans. Mitochondria have received considerable attention as a principal source---and target---of ROS. Mitochondrial oxidative stress has been implicated in heart disease including myocardial preconditioning, ischemia/reperfusion, and other pathologies. In addition, oxidative stress in the mitochondria is associated with the pathogenesis of Alzheimer's disease, Parkinson's disease, prion diseases, and amyotrophic lateral sclerosis (ALS) as well as aging itself. The rapidly emerging field of proteomics can provide powerful strategies for the characterization of mitochondrial proteins. Current approaches to mitochondrial proteomics include the creation of detailed catalogues of the protein components in a single sample or the identification of differentially expressed proteins in diseased or physiologically altered samples versus a reference control. It is clear that for any proteomics approach prefractionation of complex protein mixtures is essential to facilitate the identification of low-abundance proteins because the dynamic range of protein abundance within cells has been estimated to be as high as 10(7). The opportunities for identification of proteins directly involved in diseases associated with or caused by mitochondrial dysfunction are compelling. Future efforts will focus on linking genomic array information to actual protein levels in mitochondria. PMID:11884366

  9. Identification of multiple metabolic enzymes from mice cochleae tissue using a novel functional proteomics technology.

    PubMed

    Wang, David L; Li, Hui; Liang, Ruqiang; Bao, Jianxin

    2015-01-01

    A new type of technology in proteomics was developed in order to separate a complex protein mixture and analyze protein functions systematically. The technology combines the ability of two-dimensional gel electrophoresis (2-DE) to separate proteins with a protein elution plate (PEP) to recover active proteins for functional analysis and mass spectrometry (MS)-based identification. In order to demonstrate the feasibility of this functional proteomics approach, NADH and NADPH-dependent oxidases, major redox enzyme families, were identified from mice cochlear tissue after a specific drug treatment. By comparing the enzymatic activity between mice that were treated with a drug and a control group significant changes were observed. Using MS, five NADH-dependent oxidases were identified that showed highly altered enzymatic activities due to the drug treatment. In essence, the PEP technology allows for a systematic analysis of a large enzyme family from a complex proteome, providing insights in understanding the mechanism of drug treatment.

  10. Current Progress in Tonoplast Proteomics Reveals Insights into the Function of the Large Central Vacuole

    PubMed Central

    Trentmann, Oliver; Haferkamp, Ilka

    2013-01-01

    Vacuoles of plants fulfill various biologically important functions, like turgor generation and maintenance, detoxification, solute sequestration, or protein storage. Different types of plant vacuoles (lytic versus protein storage) are characterized by different functional properties apparently caused by a different composition/abundance and regulation of transport proteins in the surrounding membrane, the tonoplast. Proteome analyses allow the identification of vacuolar proteins and provide an informative basis for assigning observed transport processes to specific carriers or channels. This review summarizes techniques required for vacuolar proteome analyses, like e.g., isolation of the large central vacuole or tonoplast membrane purification. Moreover, an overview about diverse published vacuolar proteome studies is provided. It becomes evident that qualitative proteomes from different plant species represent just the tip of the iceberg. During the past few years, mass spectrometry achieved immense improvement concerning its accuracy, sensitivity, and application. As a consequence, modern tonoplast proteome approaches are suited for detecting alterations in membrane protein abundance in response to changing environmental/physiological conditions and help to clarify the regulation of tonoplast transport processes. PMID:23459586

  11. Social categorization of social robots: anthropomorphism as a function of robot group membership.

    PubMed

    Eyssel, Friederike; Kuchenbrandt, Dieta

    2012-12-01

    Previous work on social categorization has shown that people often use cues such as a person's gender, age, or ethnicity to categorize and form impressions of others. The present research investigated effects of social category membership on the evaluation of humanoid robots. More specifically, participants rated a humanoid robot that either belonged to their in-group or to a national out-group with regard to anthropomorphism (e.g., mind attribution, warmth), psychological closeness, contact intentions, and design. We predicted that participants would show an in-group bias towards the robot that ostensibly belonged to their in-group--as indicated by its name and location of production. In line with our hypotheses, participants not only rated the in-group robot more favourably--importantly, they also anthropomorphized it more strongly than the out-group robot. Our findings thus document that people even apply social categorization processes and subsequent differential social evaluations to robots.

  12. ProtoBug: functional families from the complete proteomes of insects

    PubMed Central

    Rappoport, Nadav; Linial, Michal

    2015-01-01

    ProtoBug (http://www.protobug.cs.huji.ac.il) is a database and resource of protein families in Arthropod genomes. ProtoBug platform presents the relatedness of complete proteomes from 17 insects as well as a proteome of the crustacean, Daphnia pulex. The represented proteomes from insects include louse, bee, beetle, ants, flies and mosquitoes. Based on an unsupervised clustering method, protein sequences were clustered into a hierarchical tree, called ProtoBug. ProtoBug covers about 300 000 sequences that are partitioned to families. At the default setting, all sequences are partitioned to ∼20 000 families (excluding singletons). From the species perspective, each of the 18 analysed proteomes is composed of 5000–8000 families. In the regime of the advanced operational mode, the ProtoBug provides rich navigation capabilities for touring the hierarchy of the families at any selected resolution. A proteome viewer shows the composition of sequences from any of the 18 analysed proteomes. Using functional annotation from an expert system (Pfam) we assigned domains, families and repeats by 4400 keywords that cover 73% of the sequences. A strict inference protocol is applied for expanding the functional knowledge. Consequently, secured annotations were associated with 81% of the proteins, and with 70% of the families (≥10 proteins each). ProtoBug is a database and webtool with rich visualization and navigation tools. The properties of each family in relation to other families in the ProtoBug tree, and in view of the taxonomy composition are reported. Furthermore, the user can paste its own sequences to find relatedness to any of the ProtoBug families. The database and the navigation tools are the basis for functional discoveries that span 350 million years of evolution of Arthropods. ProtoBug is available with no restriction at: www.protobug.cs.huji.ac.il. Database URL: www.protobug.cs.huji.ac.il. PMID:25911153

  13. High level functions for the intuitive use of an assistive robot.

    PubMed

    Lebec, Olivier; Ben Ghezala, Mohamed Walid; Leynart, Violaine; Laffont, Isabelle; Fattal, Charles; Devilliers, Laurence; Chastagnol, Clement; Martin, Jean-Claude; Mezouar, Youcef; Korrapatti, Hermanth; Dupourqué, Vincent; Leroux, Christophe

    2013-06-01

    This document presents the research project ARMEN (Assistive Robotics to Maintain Elderly People in a Natural environment), aimed at the development of a user friendly robot with advanced functions for assistance to elderly or disabled persons at home. Focus is given to the robot SAM (Smart Autonomous Majordomo) and its new features of navigation, manipulation, object recognition, and knowledge representation developed for the intuitive supervision of the robot. The results of the technical evaluations show the value and potential of these functions for practical applications. The paper also documents the details of the clinical evaluations carried out with elderly and disabled persons in a therapeutic setting to validate the project.

  14. Functional Proteomic Profiling of Phosphodiesterases Using SeraFILE Separations Platform

    PubMed Central

    Oka, Amita R.; Kuruc, Matthew P.; Gujarathi, Ketan M.; Roy, Swapan

    2012-01-01

    Functional proteomic profiling can help identify targets for disease diagnosis and therapy. Available methods are limited by the inability to profile many functional properties measured by enzymes kinetics. The functional proteomic profiling approach proposed here seeks to overcome such limitations. It begins with surface-based proteome separations of tissue/cell-line extracts, using SeraFILE, a proprietary protein separations platform. Enzyme kinetic properties of resulting subproteomes are then characterized, and the data integrated into proteomic profiles. As a model, SeraFILE-derived subproteomes of cyclic nucleotide-hydrolyzing phosphodiesterases (PDEs) from bovine brain homogenate (BBH) and rat brain homogenate (RBH) were characterized for cAMP hydrolysis activity in the presence (challenge condition) and absence of cGMP. Functional profiles of RBH and BBH were compiled from the enzyme activity response to the challenge condition in each of the respective subproteomes. Intersample analysis showed that comparable profiles differed in only a few data points, and that distinctive subproteomes can be generated from comparable tissue samples from different animals. These results demonstrate that the proposed methods provide a means to simplify intersample differences, and to localize proteins attributable to sample-specific responses. It can be potentially applied for disease and nondisease sample comparison in biomarker discovery and drug discovery profiling. PMID:23227336

  15. SOFT ROBOTICS. A 3D-printed, functionally graded soft robot powered by combustion.

    PubMed

    Bartlett, Nicholas W; Tolley, Michael T; Overvelde, Johannes T B; Weaver, James C; Mosadegh, Bobak; Bertoldi, Katia; Whitesides, George M; Wood, Robert J

    2015-07-10

    Roboticists have begun to design biologically inspired robots with soft or partially soft bodies, which have the potential to be more robust and adaptable, and safer for human interaction, than traditional rigid robots. However, key challenges in the design and manufacture of soft robots include the complex fabrication processes and the interfacing of soft and rigid components. We used multimaterial three-dimensional (3D) printing to manufacture a combustion-powered robot whose body transitions from a rigid core to a soft exterior. This stiffness gradient, spanning three orders of magnitude in modulus, enables reliable interfacing between rigid driving components (controller, battery, etc.) and the primarily soft body, and also enhances performance. Powered by the combustion of butane and oxygen, this robot is able to perform untethered jumping.

  16. Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota

    DOE PAGES

    Xiong, Weili; Abraham, Paul E.; Li, Zhou; Pan, Chongle; Robert L. Hettich

    2015-01-01

    We found that the human gastrointestinal (GI) tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome component is not insignificant, but rather provides important functions that are absolutely critical to many aspects of human health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial community proteomics (sometimes referred to as metaproteomics) provides a powerful approach to measure the range and details of human gut microbiota functions and metabolic activities, revealing information about microbiome development and stability especially with regard to human health vs.more » disease states. In most cases, both microbial and human proteins are extracted from fecal samples and then measured by the high performance MS-based proteomics technology. We review the field of human gut microbiome community proteomics, with a focus on the experimental and informatics considerations involved in characterizing systems that range from low complexity defined model gut microbiota in gnotobiotic mice, to the simple gut microbiota in the GI tract of newborn infants, and finally to the complex gut microbiota in adults. Moreover, the current state-of-the-art in experimental and bioinformatics capabilities for community proteomics enable a detailed measurement of the gut microbiota, yielding valuable insights into the broad functional profiles of even complex microbiota. Future developments are likely to expand into improved analysis throughput and coverage depth, as well as post-translational modification characterizations.« less

  17. Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota

    SciTech Connect

    Xiong, Weili; Abraham, Paul E.; Li, Zhou; Pan, Chongle; Robert L. Hettich

    2015-01-01

    We found that the human gastrointestinal (GI) tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome component is not insignificant, but rather provides important functions that are absolutely critical to many aspects of human health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial community proteomics (sometimes referred to as metaproteomics) provides a powerful approach to measure the range and details of human gut microbiota functions and metabolic activities, revealing information about microbiome development and stability especially with regard to human health vs. disease states. In most cases, both microbial and human proteins are extracted from fecal samples and then measured by the high performance MS-based proteomics technology. We review the field of human gut microbiome community proteomics, with a focus on the experimental and informatics considerations involved in characterizing systems that range from low complexity defined model gut microbiota in gnotobiotic mice, to the simple gut microbiota in the GI tract of newborn infants, and finally to the complex gut microbiota in adults. Moreover, the current state-of-the-art in experimental and bioinformatics capabilities for community proteomics enable a detailed measurement of the gut microbiota, yielding valuable insights into the broad functional profiles of even complex microbiota. Future developments are likely to expand into improved analysis throughput and coverage depth, as well as post-translational modification characterizations.

  18. High-Density Lipoprotein Proteomics: Identifying New Drug Targets and Biomarkers by Understanding Functionality

    PubMed Central

    Gordon, Scott; Durairaj, Anita; Lu, Jason L.; Davidson, W. Sean

    2010-01-01

    Recent proteomics studies on human plasma high-density lipoprotein (HDL) have discovered up to 50 individual protein constituents. Many of these have known functions that vary surprisingly from the lipid transport roles commonly thought to mediate HDL’s ability to protect from coronary artery disease. Given newly discovered roles in inflammation, protease inhibition, complement regulation, and innate immunity, many have begun to view HDL as a broad collection of distinct particle subfamilies, each distinguished by unique protein compositions and functions. Herein we review recent applications of high-resolution proteomics to HDL and summarize evidence supporting the idea of HDL functional subspeciation. These studies have set the stage for a more complete understanding of the molecular basis of HDL functional heterogeneity and hold promise for the identification of new biomarkers that can predict disease or evaluate the success of clinical interventions. PMID:20625533

  19. Protein intrinsic disorder within the Potyvirus genus: from proteome-wide analysis to functional annotation.

    PubMed

    Charon, Justine; Theil, Sébastien; Nicaise, Valérie; Michon, Thierry

    2016-02-01

    Within proteins, intrinsically disordered regions (IDRs) are devoid of stable secondary and tertiary structures under physiological conditions and rather exist as dynamic ensembles of inter-converting conformers. Although ubiquitous in all domains of life, the intrinsic disorder content is highly variable in viral genomes. Over the years, functional annotations of disordered regions at the scale of the whole proteome have been conducted for several animal viruses. But to date, similar studies applied to plant viruses are still missing. Based on disorder prediction tools combined with annotation programs and evolutionary studies, we analyzed the intrinsic disorder content in Potyvirus, using a 10-species dataset representative of this genus diversity. In this paper, we revealed that: (i) the Potyvirus proteome displays high disorder content, (ii) disorder is conserved during Potyvirus evolution, suggesting a functional advantage of IDRs, (iii) IDRs evolve faster than ordered regions, and (iv) IDRs may be associated with major biological functions required for the Potyvirus cycle. Notably, the proteins P1, Coat protein (CP) and Viral genome-linked protein (VPg) display a high content of conserved disorder, enriched in specific motifs mimicking eukaryotic functional modules and suggesting strategies of host machinery hijacking. In these three proteins, IDRs are particularly conserved despite their high amino acid polymorphism, indicating a link to adaptive processes. Through this comprehensive study, we further investigate the biological relevance of intrinsic disorder in Potyvirus biology and we propose a functional annotation of potyviral proteome IDRs. PMID:26699268

  20. Protein intrinsic disorder within the Potyvirus genus: from proteome-wide analysis to functional annotation.

    PubMed

    Charon, Justine; Theil, Sébastien; Nicaise, Valérie; Michon, Thierry

    2016-02-01

    Within proteins, intrinsically disordered regions (IDRs) are devoid of stable secondary and tertiary structures under physiological conditions and rather exist as dynamic ensembles of inter-converting conformers. Although ubiquitous in all domains of life, the intrinsic disorder content is highly variable in viral genomes. Over the years, functional annotations of disordered regions at the scale of the whole proteome have been conducted for several animal viruses. But to date, similar studies applied to plant viruses are still missing. Based on disorder prediction tools combined with annotation programs and evolutionary studies, we analyzed the intrinsic disorder content in Potyvirus, using a 10-species dataset representative of this genus diversity. In this paper, we revealed that: (i) the Potyvirus proteome displays high disorder content, (ii) disorder is conserved during Potyvirus evolution, suggesting a functional advantage of IDRs, (iii) IDRs evolve faster than ordered regions, and (iv) IDRs may be associated with major biological functions required for the Potyvirus cycle. Notably, the proteins P1, Coat protein (CP) and Viral genome-linked protein (VPg) display a high content of conserved disorder, enriched in specific motifs mimicking eukaryotic functional modules and suggesting strategies of host machinery hijacking. In these three proteins, IDRs are particularly conserved despite their high amino acid polymorphism, indicating a link to adaptive processes. Through this comprehensive study, we further investigate the biological relevance of intrinsic disorder in Potyvirus biology and we propose a functional annotation of potyviral proteome IDRs.

  1. Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms

    PubMed Central

    Nasir, Arshan; Naeem, Aisha; Khan, Muhammad Jawad; Lopez-Nicora, Horacio D.; Caetano-Anollés, Gustavo

    2011-01-01

    The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of

  2. Integrative proteomic profiling of ovarian cancer cell lines reveals precursor cell associated proteins and functional status

    PubMed Central

    Coscia, F.; Watters, K. M.; Curtis, M.; Eckert, M. A.; Chiang, C. Y.; Tyanova, S.; Montag, A.; Lastra, R. R.; Lengyel, E.; Mann, M.

    2016-01-01

    A cell line representative of human high-grade serous ovarian cancer (HGSOC) should not only resemble its tumour of origin at the molecular level, but also demonstrate functional utility in pre-clinical investigations. Here, we report the integrated proteomic analysis of 26 ovarian cancer cell lines, HGSOC tumours, immortalized ovarian surface epithelial cells and fallopian tube epithelial cells via a single-run mass spectrometric workflow. The in-depth quantification of >10,000 proteins results in three distinct cell line categories: epithelial (group I), clear cell (group II) and mesenchymal (group III). We identify a 67-protein cell line signature, which separates our entire proteomic data set, as well as a confirmatory publicly available CPTAC/TCGA tumour proteome data set, into a predominantly epithelial and mesenchymal HGSOC tumour cluster. This proteomics-based epithelial/mesenchymal stratification of cell lines and human tumours indicates a possible origin of HGSOC either from the fallopian tube or from the ovarian surface epithelium. PMID:27561551

  3. Mass spectrometry-based functional proteomics of poly(ADP-ribose) polymerase-1.

    PubMed

    Pic, Emilie; Gagné, Jean-Philippe; Poirier, Guy G

    2011-12-01

    PARP-1 is an abundant nuclear protein that plays an essential role in the regulation of many genome integrity and chromatin-based processes, such as DNA repair, replication or transcriptional regulation. PARP-1 modulates the function of chromatin and nuclear proteins through several poly(ADP-ribose) (pADPr)-dependent pathways. Aside from the clearly established role of PARP-1 in the maintenance of genome stability, PARP-1 also emerged as an important regulator that links chromatin functions with extranuclear compartments. pADPr signaling has notably been found to be responsible for PARP-1-mediated mitochondrial dysfunction and cell death. Defining the mechanisms that govern the intrinsic functions of PARP-1 is fundamental to the understanding of signaling networks regulated by pADPr. The emergence of mass spectrometry-based proteomics and its broad applications in the study of biological systems represents an outstanding opportunity to widen our knowledge of the functional spectrum of PARP-1. In this article, we summarize various PARP-1 targeted proteomics studies and proteome-wide analyses that shed light on its protein interaction partners, expression levels and post-translational modifications.

  4. Post-translational modification of cardiac proteasomes: functional delineation enabled by proteomics

    PubMed Central

    Scruggs, Sarah B.; Zong, Nobel C.; Wang, Ding; Stefani, Enrico

    2012-01-01

    Proteasomes are ubiquitously expressed multicatalytic complexes that serve as key regulators of protein homeostasis. There are several lines of evidence indicating that proteasomes exist in heterogeneous subpopulations in cardiac muscle, differentiated, in part, by post-translational modifications (PTMs). PTMs regulate numerous facets of proteasome function, including catalytic activities, complex assembly, interactions with associating partners, subcellular localization, substrate preference, and complex turnover. Classical technologies used to identify PTMs on proteasomes have lacked the ability to determine site specificity, quantify stoichiometry, and perform large-scale, multi-PTM analysis. Recent advancements in proteomic technologies have largely overcome these limitations. We present here a discussion on the importance of PTMs in modulating proteasome function in cardiac physiology and pathophysiology, followed by the presentation of a state-of-the-art proteomic workflow for identifying and quantifying PTMs of cardiac proteasomes. PMID:22523251

  5. A Proteomic Approach to Investigating Gene Cluster Expression and Secondary Metabolite Functionality in Aspergillus fumigatus

    PubMed Central

    Owens, Rebecca A.; Hammel, Stephen; Sheridan, Kevin J.; Jones, Gary W.; Doyle, Sean

    2014-01-01

    A combined proteomics and metabolomics approach was utilised to advance the identification and characterisation of secondary metabolites in Aspergillus fumigatus. Here, implementation of a shotgun proteomic strategy led to the identification of non-redundant mycelial proteins (n = 414) from A. fumigatus including proteins typically under-represented in 2-D proteome maps: proteins with multiple transmembrane regions, hydrophobic proteins and proteins with extremes of molecular mass and pI. Indirect identification of secondary metabolite cluster expression was also achieved, with proteins (n = 18) from LaeA-regulated clusters detected, including GliT encoded within the gliotoxin biosynthetic cluster. Biochemical analysis then revealed that gliotoxin significantly attenuates H2O2-induced oxidative stress in A. fumigatus (p>0.0001), confirming observations from proteomics data. A complementary 2-D/LC-MS/MS approach further elucidated significantly increased abundance (p<0.05) of proliferating cell nuclear antigen (PCNA), NADH-quinone oxidoreductase and the gliotoxin oxidoreductase GliT, along with significantly attenuated abundance (p<0.05) of a heat shock protein, an oxidative stress protein and an autolysis-associated chitinase, when gliotoxin and H2O2 were present, compared to H2O2 alone. Moreover, gliotoxin exposure significantly reduced the abundance of selected proteins (p<0.05) involved in de novo purine biosynthesis. Significantly elevated abundance (p<0.05) of a key enzyme, xanthine-guanine phosphoribosyl transferase Xpt1, utilised in purine salvage, was observed in the presence of H2O2 and gliotoxin. This work provides new insights into the A. fumigatus proteome and experimental strategies, plus mechanistic data pertaining to gliotoxin functionality in the organism. PMID:25198175

  6. A novel approach to the study of the functional proteome in breast cancer

    SciTech Connect

    Hennessy, Bryan; Lu, Yiling; Gonzalez-Angulo, Ana Maria; Carey, Mark; Myhre, Simen; Ju, Zhenlin; Coombes, Kevin; Meric-Bernstam, Funda; Bedrosian, Isabelle; Davies, Michael A.; Siwak, Doris; Agarwal, Roshan; Zhang, Fan; Overgaard, Jens; Alsner, Jan; Neve, Richard M.; Kuo, Wen-Lin; Gray, Joe W.; Borresen-Dale, Anne-Lise; Mills, Gordon B.

    2008-10-10

    Factors including intratumoral heterogeneity and variability in tissue handling potentially hamper the application of reverse phase protein arrays (RPPA) to study of the solid tumor functional proteome. To address this, RPPA was applied to quantify protein expression and activation in 233 human breast tumors and 52 breast cancer cell lines. Eighty-two antibodies that recognize kinase and steroid signaling events and their effectors were validated for RPPA because of the importance of these proteins to breast carcinogenesis. Reproducibility in replicate lysates was excellent. Intratumoral protein expression was less variable than intertumoral expression, and prognostic biomarkers retained the ability to accurately predict patient outcomes when analyzed in different tumor sites. Although 21/82 total and phosphoproteins demonstrated time-dependent instability in breast tumors that were placed at room temperature after surgical excision for 24 hours prior to freezing, the functional proteomic 'fingerprint' was robust in most tumors until at least 24 hours before tissue freezing. Correlations between RPPA and immunohistochemistry were statistically significant for assessed proteins but RPPA demonstrated a superior dynamic range and detected, for example, an 866-fold difference in estrogen receptor alpha level across breast tumors. Protein and mRNA levels were concordant (at p {le} 0.05) for 41.3% and 61.1% of assayed targets in breast tumors and cell lines, respectively. Several phosphorylation and cleavage products did not correlate with the corresponding transcript levels. In conclusion, the reproducibility of RPPA, the faithfulness with which proteins and the functional proteomic 'fingerprint' are preserved in different sections derived from primary breast tumors, and the surprising stability of this 'fingerprint' with increasing time to freezing all facilitate the application of RPPA to the accurate study of protein biomarkers in non-microdissected tumor specimens

  7. The Functional Network of the Arabidopsis Plastoglobule Proteome Based on Quantitative Proteomics and Genome-Wide Coexpression Analysis1[C][W][OA

    PubMed Central

    Lundquist, Peter K.; Poliakov, Anton; Bhuiyan, Nazmul H.; Zybailov, Boris; Sun, Qi; van Wijk, Klaas J.

    2012-01-01

    Plastoglobules (PGs) in chloroplasts are thylakoid-associated monolayer lipoprotein particles containing prenyl and neutral lipids and several dozen proteins mostly with unknown functions. An integrated view of the role of the PG is lacking. Here, we better define the PG proteome and provide a conceptual framework for further studies. The PG proteome from Arabidopsis (Arabidopsis thaliana) leaf chloroplasts was determined by mass spectrometry of isolated PGs and quantitative comparison with the proteomes of unfractionated leaves, thylakoids, and stroma. Scanning electron microscopy showed the purity and size distribution of the isolated PGs. Compared with previous PG proteome analyses, we excluded several proteins and identified six new PG proteins, including an M48 metallopeptidase and two Absence of bc1 complex (ABC1) atypical kinases, confirmed by immunoblotting. This refined PG proteome consisted of 30 proteins, including six ABC1 kinases and seven fibrillins together comprising more than 70% of the PG protein mass. Other fibrillins were located predominantly in the stroma or thylakoid and not in PGs; we discovered that this partitioning can be predicted by their isoelectric point and hydrophobicity. A genome-wide coexpression network for the PG genes was then constructed from mRNA expression data. This revealed a modular network with four distinct modules that each contained at least one ABC1K and/or fibrillin gene. Each module showed clear enrichment in specific functions, including chlorophyll degradation/senescence, isoprenoid biosynthesis, plastid proteolysis, and redox regulators and phosphoregulators of electron flow. We propose a new testable model for the PGs, in which sets of genes are associated with specific PG functions. PMID:22274653

  8. Proteomic and functional profiles of a follicle-stimulating hormone positive human nonfunctional pituitary adenoma.

    PubMed

    Wang, Xiaowei; Guo, Tianyao; Peng, Fang; Long, Ying; Mu, Yun; Yang, Haiyan; Ye, Ningrong; Li, Xuejun; Zhan, Xianquan

    2015-06-01

    Nonfunctional pituitary adenoma (NFPA) is highly heterogeneous with different hormone-expressed subtypes in NFPA tissues including follicle-stimulating hormone (FSH) positive, luteinizing hormone-positive, FSH/luteinizing hormone-positive, and negative types. To analyze in-depth the variations in the proteomes among different NFPA subtypes for our long-term goal to clarify molecular mechanisms of NFPA and to detect tumor biomarker for personalized medicine practice, a reference map of proteome of a human FSH-expressed NFPA tissue was described here. 2DE and PDQuest image analysis were used to array each protein. MALDI-TOF PMF and human Swiss-Prot databases with MASCOT search were used to identify each protein. A good 2DE pattern with high level of between-gel reproducibility was attained with an average positional deviation 1.98 ± 0.75 mm in the IEF direction and 1.62 ± 0.68 mm in the SDS-PAGE direction. Approximately 1200 protein spots were 2DE-detected and 192 redundant proteins that were contained in 141 protein spots were PMF-identified, representing 107 nonredundant proteins. Those proteins were located in cytoplasm, nucleus, plasma membrane, extracellular space, and so on, and those functioned in transmembrane receptor, ion channel, transcription/translation regulator, transporter, enzyme, phosphatase, kinase, and so on. Several important pathway networks were characterized from those identified proteins with DAVID and Ingenuity Pathway Analysis systems, including gluconeogenesis and glycolysis, mitochondrial dysfunction, oxidative stress, cell-cycle alteration, MAPKsignaling system, immune response, TP53-signaling, VEGF-signaling, and inflammation signaling pathways. Those resulting data contribute to a functional profile of the proteome of a human FSH-positive NFPA tissue, and will serve as a reference for the heterogeneity analysis of NFPA proteomes. PMID:25809007

  9. Differential proteomics and functional research following gene therapy in a mouse model of Leber congenital amaurosis.

    PubMed

    Zheng, Qinxiang; Ren, Yueping; Tzekov, Radouil; Zhang, Yuanping; Chen, Bo; Hou, Jiangping; Zhao, Chunhui; Zhu, Jiali; Zhang, Ying; Dai, Xufeng; Ma, Shan; Li, Jia; Pang, Jijing; Qu, Jia; Li, Wensheng

    2012-01-01

    Leber congenital amaurosis (LCA) is one of the most severe forms of inherited retinal degeneration and can be caused by mutations in at least 15 different genes. To clarify the proteomic differences in LCA eyes, a cohort of retinal degeneration 12 (rd12) mice, an LCA2 model caused by a mutation in the RPE65 gene, were injected subretinally with an AAV vector (scAAV5-smCBA-hRPE65) in one eye, while the contralateral eye served as a control. Proteomics were compared between untreated rd12 and normal control retinas on P14 and P21, and among treated and untreated rd12 retinas and control retinas on P42. Gene therapy in rd12 mice restored retinal function in treated eyes, which was demonstrated by electroretinography (ERG). Proteomic analysis successfully identified 39 proteins expressed differently among the 3 groups. The expression of 3 proteins involved in regulation of apoptosis and neuroptotection (alpha A crystallin, heat shock protein 70 and peroxiredoxin 6) were investigated further. Immunofluorescence, Western blot and real-time PCR confirmed the quantitative changes in their expression. Furthermore, cell culture studies suggested that peroxiredoxin 6 could act in an antioxidant role in rd12 mice. Our findings support the feasibility of gene therapy in LCA2 patients and support a role for alpha A crystallin, heat shock protein 70 and peroxiredoxin 6 in the pathogenetic mechanisms involved in LCA2 disease process. PMID:22953002

  10. Robotics

    NASA Technical Reports Server (NTRS)

    Rothschild, Lynn J.

    2012-01-01

    Earth's upper atmosphere is an extreme environment: dry, cold, and irradiated. It is unknown whether our aerobiosphere is limited to the transport of life, or there exist organisms that grow and reproduce while airborne (aerophiles); the microenvironments of suspended particles may harbor life at otherwise uninhabited altitudes[2]. The existence of aerophiles would significantly expand the range of planets considered candidates for life by, for example, including the cooler clouds of a hot Venus-like planet. The X project is an effort to engineer a robotic exploration and biosampling payload for a comprehensive survey of Earth's aerobiology. While many one-shot samples have been retrieved from above 15 km, their results are primarily qualitative; variations in method confound comparisons, leaving such major gaps in our knowledge of aerobiology as quantification of populations at different strata and relative species counts[1]. These challenges and X's preliminary solutions are explicated below. X's primary balloon payload is undergoing a series of calibrations before beginning flights in Spring 2012. A suborbital launch is currently planned for Summer 2012. A series of ground samples taken in Winter 2011 is being used to establish baseline counts and identify likely background contaminants.

  11. Global analysis of the rat and human platelet proteome - the molecular blueprint for illustrating multi-functional platelets and cross-species function evolution.

    PubMed

    Yu, Yanbao; Leng, Taohua; Yun, Dong; Liu, Na; Yao, Jun; Dai, Ying; Yang, Pengyuan; Chen, Xian

    2010-07-01

    Emerging evidences indicate that blood platelets function in multiple biological processes including immune response, bone metastasis and liver regeneration in addition to their known roles in hemostasis and thrombosis. Global elucidation of platelet proteome will provide the molecular base of these platelet functions. Here, we set up a high-throughput platform for maximum exploration of the rat/human platelet proteome using integrated proteomic technologies, and then applied to identify the largest number of the proteins expressed in both rat and human platelets. After stringent statistical filtration, a total of 837 unique proteins matched with at least two unique peptides were precisely identified, making it the first comprehensive protein database so far for rat platelets. Meanwhile, quantitative analyses of the thrombin-stimulated platelets offered great insights into the biological functions of platelet proteins and therefore confirmed our global profiling data. A comparative proteomic analysis between rat and human platelets was also conducted, which revealed not only a significant similarity, but also an across-species evolutionary link that the orthologous proteins representing "core proteome", and the "evolutionary proteome" is actually a relatively static proteome.

  12. Microsomal proteomics.

    PubMed

    Wong, Diana M; Adeli, Khosrow

    2009-01-01

    Proteomic profiling of subcellular compartments has many advantages over traditional proteomic approaches using whole cell lysates as it allows for detailed proteome analysis of a specific organelle and corresponding functional characteristics. The microsome is a critical, membranous compartment involved in the synthesis, sorting, and secretion of proteins as well as other metabolic functions. This chapter will describe detailed methods for the isolation of microsomal organelles including the ER, Golgi, and prechylomicron transport vesicle (PCTV), a recently identified vesicular system involved in intestinal lipoprotein assembly and secretion. Particular focus is given to the isolation of microsomes from primary hepatocytes and enterocytes freshly isolated from rodent liver and intestinal tissue, and their proteomic profiling using a combination of two-dimensional gel electrophoresis and mass spectrometry.

  13. Modifications of wheat germ cell-free system for functional proteomics of plant membrane proteins.

    PubMed

    Nozawa, Akira; Tozawa, Yuzuru

    2014-01-01

    Functional proteomics of plant membrane proteins is an important approach to understand the comprehensive architecture of each metabolic pathway in plants. One bottleneck in the characterization of membrane proteins is the difficulty in producing sufficient quantities of functional protein for analysis. Here, we describe three methods for membrane protein production utilizing a wheat germ cell-free protein expression system. Owing to the open nature of cell-free synthesis reaction, protein synthesis can be modified with components necessary to produce functional protein. In this way we have developed modifications to a wheat germ cell-free system for the production of functional membrane proteins. Supplementation of liposomes or detergents allows the synthesis of functional integral membrane proteins. Furthermore, supplementation of myristic acid enables synthesis of N-myristylated peripheral membrane proteins. These modified cell-free synthesis methods facilitate the preparation and subsequent functional analyses of a wide variety of membrane proteins. PMID:24136528

  14. Robot and robot system

    NASA Technical Reports Server (NTRS)

    Behar, Alberto E. (Inventor); Marzwell, Neville I. (Inventor); Wall, Jonathan N. (Inventor); Poole, Michael D. (Inventor)

    2011-01-01

    A robot and robot system that are capable of functioning in a zero-gravity environment are provided. The robot can include a body having a longitudinal axis and having a control unit and a power source. The robot can include a first leg pair including a first leg and a second leg. Each leg of the first leg pair can be pivotally attached to the body and constrained to pivot in a first leg pair plane that is substantially perpendicular to the longitudinal axis of the body.

  15. Functionalization of Tactile Sensation for Robot Based on Haptograph and Modal Decomposition

    NASA Astrophysics Data System (ADS)

    Yokokura, Yuki; Katsura, Seiichiro; Ohishi, Kiyoshi

    In the real world, robots should be able to recognize the environment in order to be of help to humans. A video camera and a laser range finder are devices that can help robots recognize the environment. However, these devices cannot obtain tactile information from environments. Future human-assisting-robots should have the ability to recognize haptic signals, and a disturbance observer can possibly be used to provide the robot with this ability. In this study, a disturbance observer is employed in a mobile robot to functionalize the tactile sensation. This paper proposes a method that involves the use of haptograph and modal decomposition for the haptic recognition of road environments. The haptograph presents a graphic view of the tactile information. It is possible to classify road conditions intuitively. The robot controller is designed by considering the decoupled modal coordinate system, which consists of translational and rotational modes. Modal decomposition is performed by using a quarry matrix. Once the robot is provided with the ability to recognize tactile sensations, its usefulness to humans will increase.

  16. Characterization of Functional Reprogramming during Osteoclast Development Using Quantitative Proteomics and mRNA Profiling*

    PubMed Central

    An, Eunkyung; Narayanan, Manikandan; Manes, Nathan P.; Nita-Lazar, Aleksandra

    2014-01-01

    In addition to forming macrophages and dendritic cells, monocytes in adult peripheral blood retain the ability to develop into osteoclasts, mature bone-resorbing cells. The extensive morphological and functional transformations that occur during osteoclast differentiation require substantial reprogramming of gene and protein expression. Here we employ -omic-scale technologies to examine in detail the molecular changes at discrete developmental stages in this process (precursor cells, intermediate osteoclasts, and multinuclear osteoclasts), quantitatively comparing their transcriptomes and proteomes. The data have been deposited to the ProteomeXchange with identifier PXD000471. Our analysis identified mitochondrial changes, along with several alterations in signaling pathways, as central to the development of mature osteoclasts, while also confirming changes in pathways previously implicated in osteoclast biology. In particular, changes in the expression of proteins involved in metabolism and redirection of energy flow from basic cellular function toward bone resorption appeared to play a key role in the switch from monocytic immune system function to specialized bone-turnover function. These findings provide new insight into the differentiation program involved in the generation of functional osteoclasts. PMID:25044017

  17. Exploring the “dark matter” of a mammalian proteome by protein structure and function modeling

    PubMed Central

    2013-01-01

    Background A growing body of evidence shows that gene products encoded by short open reading frames play key roles in numerous cellular processes. Yet, they are generally overlooked in genome assembly, escaping annotation because small protein-coding genes are difficult to predict computationally. Consequently, there are still a considerable number of small proteins whose functions are yet to be characterized. Results To address this issue, we apply a collection of structural bioinformatics algorithms to infer molecular function of putative small proteins from the mouse proteome. Specifically, we construct 1,743 confident structure models of small proteins, which reveal a significant structural diversity with a noticeably high helical content. A subsequent structure-based function annotation of small protein models exposes 178,745 putative protein-protein interactions with the remaining gene products in the mouse proteome, 1,100 potential binding sites for small organic molecules and 987 metal-binding signatures. Conclusions These results strongly indicate that many small proteins adopt three-dimensional structures and are fully functional, playing important roles in transcriptional regulation, cell signaling and metabolism. Data collected through this work is freely available to the academic community at http://www.brylinski.org/content/databases to support future studies oriented on elucidating the functions of hypothetical small proteins. PMID:24321360

  18. Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules.

    PubMed

    Tikka, Saara; Monogioudi, Evanthia; Gotsopoulos, Athanasios; Soliymani, Rabah; Pezzini, Francesco; Scifo, Enzo; Uusi-Rauva, Kristiina; Tyynelä, Jaana; Baumann, Marc; Jalanko, Anu; Simonati, Alessandro; Lalowski, Maciej

    2016-03-01

    Neuronal ceroid lipofuscinoses (NCL) are the most commonly inherited progressive encephalopathies of childhood. Pathologically, they are characterized by endolysosomal storage with different ultrastructural features and biochemical compositions. The molecular mechanisms causing progressive neurodegeneration and common molecular pathways linking expression of different NCL genes are largely unknown. We analyzed proteome alterations in the brains of a mouse model of human infantile CLN1 disease-palmitoyl-protein thioesterase 1 (Ppt1) gene knockout and its wild-type age-matched counterpart at different stages: pre-symptomatic, symptomatic and advanced. For this purpose, we utilized a combination of laser capture microdissection-based quantitative liquid chromatography tandem mass spectrometry (MS) and matrix-assisted laser desorption/ionization time-of-flight MS imaging to quantify/visualize the changes in protein expression in disease-affected brain thalamus and cerebral cortex tissue slices, respectively. Proteomic profiling of the pre-symptomatic stage thalamus revealed alterations mostly in metabolic processes and inhibition of various neuronal functions, i.e., neuritogenesis. Down-regulation in dynamics associated with growth of plasma projections and cellular protrusions was further corroborated by findings from RNA sequencing of CLN1 patients' fibroblasts. Changes detected at the symptomatic stage included: mitochondrial functions, synaptic vesicle transport, myelin proteome and signaling cascades, such as RhoA signaling. Considerable dysregulation of processes related to mitochondrial cell death, RhoA/Huntington's disease signaling and myelin sheath breakdown were observed at the advanced stage of the disease. The identified changes in protein levels were further substantiated by bioinformatics and network approaches, immunohistochemistry on brain tissues and literature knowledge, thus identifying various functional modules affected in the CLN1 childhood

  19. A robotic system for automation of logistics functions on the Space Station

    NASA Technical Reports Server (NTRS)

    Martin, J. C.; Purves, R. B.; Hosier, R. N.; Krein, B. A.

    1988-01-01

    Spacecraft inventory management is currently performed by the crew and as systems become more complex, increased crew time will be required to perform routine logistics activities. If future spacecraft are to function effectively as research labs and production facilities, the efficient use of crew time as a limited resource for performing mission functions must be employed. The use of automation and robotics technology, such as automated warehouse and materials handling functions, can free the crew from many logistics tasks and provide more efficient use of crew time. Design criteria for a Space Station Automated Logistics Inventory Management System is focused on through the design and demonstration of a mobile two armed terrestrial robot. The system functionally represents a 0 gravity automated inventory management system and the problems associated with operating in such an environment. Features of the system include automated storage and retrieval, item recognition, two armed robotic manipulation, and software control of all inventory item transitions and queries.

  20. Proteomic and functional analyses of a novel porin-like protein in Xanthomonas oryzae pv. oryzae.

    PubMed

    Park, Hye-Jee; Lee, Sang-Won; Han, Sang-Wook

    2014-12-01

    Proteomic analysis is a useful technique for postulating and elucidating protein functions. In the present work, a shotgun proteomic analysis was used to identify functions of the PXO_03968 gene (previously known as the ax21) from Xanthomonas oryzae pv. oryzae (Xoo), a causal agent for bacterial blight disease in rice. Structural prediction performed on the protein sequence encoded by PXO_03968 reveals that it encodes a putative porin-like protein, possessing a β-barrel domain with 10 β-strands and a signal peptide at the N-terminus. We renamed the gene as an omp1X (outer membrane protein 1 in Xoo), generated its knock out mutant (XooΔomp1X), and compared the protein expression level in the mutant to that in the wild type. A total of 106 proteins displayed more than 1.5-fold difference in expression between the mutant and the wild type strains. COG analysis revealed that these proteins are involved in cell motility as well as signal transduction. In addition, phenotypic analysis demonstrated that motility and biofilm formation in XooΔomp1X are lower than the wild type. These results provide new insights into the functions of outer membrane proteins in Gram-negative bacteria.

  1. Revisiting the Identification of Canonical Splice Isoforms through Integration of Functional Genomics and Proteomics Evidence

    PubMed Central

    Li, Hong-Dong; Menon, Rajasree; Omenn, Gilbert S.; Guan, Yuanfang

    2014-01-01

    Canonical isoforms in different databases have been defined as the most prevalent, most conserved, most expressed, longest, or the one with the clearest description of domains or post-translational modifications. In this article, we revisit these definitions of canonical isoforms based on functional genomics and proteomics evidence, focusing on mouse data. We report a novel functional relationship network-based approach for identifying the Highest Connected Isoforms (HCIs). We show that 46% of these HCIs are not the longest transcripts. In addition, this approach revealed many genes that have more than one highly connected isoforms. Averaged across 175 RNA-seq datasets covering diverse tissues and conditions, 65% of the HCIs show higher expression levels than non-highest connected isoforms (NCIs) at the transcript level. At the protein level, these HCIs highly overlap with the expressed splice variants, based on proteomic data from eight different normal tissues. These results suggest that a more confident definition of canonical isoforms can be made through integration of multiple lines of evidence, including highest connected isoforms defined by biological processes and pathways, expression prevalence at the transcript level, and relative or absolute abundance at the protein level. This integrative proteogenomics approach can successfully identify principal isoforms that are responsible for the canonical functions of genes. PMID:25265570

  2. Proteomic Profiling and Functional Characterization of Multiple Post-Translational Modifications of Tubulin.

    PubMed

    Liu, Ningning; Xiong, Yun; Ren, Yiran; Zhang, Linlin; He, Xianfei; Wang, Xincheng; Liu, Min; Li, Dengwen; Shui, Wenqing; Zhou, Jun

    2015-08-01

    Tubulin is known to undergo unique post-translational modifications (PTMs), such as detyrosination and polyglutamylation, particularly in the unstructured carboxy-terminal tails (CTTs). However, more conventional PTMs of tubulin and their roles in the regulation of microtubule properties and functions remain poorly defined. Here, we report the comprehensive profiling of tubulin phosphorylation, acetylation, ubiquitylation, and O-GlcNAcylation in HeLa cells with a proteomic approach. Our tubulin-targeted analysis has identified 80 residues bearing single or multiple conventional PTMs including 24 novel PTM sites not covered in previous global proteomic surveys. By using a series of PTM-deficient or PTM-mimicking mutants, we further find that tubulin phosphorylation and acetylation play important roles in the control of microtubule assembly and stability. In addition, these tubulin PTMs have distinct effects on the retrograde transport of adenoviruses along microtubules. These findings thus enlarge the repertoire of tubulin PTMs and foster our understanding of their versatile roles in the regulation of microtubule dynamics and cellular functions.

  3. Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics

    PubMed Central

    Zhang, Peng; Shen, Yu; Guo, Jin-Song; Li, Chun; Wang, Han; Chen, You-Peng; Yan, Peng; Yang, Ji-Xiang; Fang, Fang

    2015-01-01

    In this work, proteins in extracellular polymeric substances extracted from anaerobic, anoxic and aerobic sludges of wastewater treatment plant (WWTP) were analyzed to probe their origins and functions. Extracellular proteins in WWTP sludges were identified using shotgun proteomics, and 130, 108 and 114 proteins in anaerobic, anoxic and aerobic samples were classified, respectively. Most proteins originated from cell and cell part, and their most major molecular functions were catalytic activity and binding activity. The results exhibited that the main roles of extracellular proteins in activated sludges were multivalence cations and organic molecules binding, as well as in catalysis and degradation. The catalytic activity proteins were more widespread in anaerobic sludge compared with those in anoxic and aerobic sludges. The structure difference between anaerobic and aerobic sludges could be associated with their catalytic activities proteins. The results also put forward a relation between the macro characteristics of activated sludges and micro functions of extracellular proteins in biological wastewater treatment process. PMID:26160685

  4. Construction typification as the tool for optimizing the functioning of a robotized manufacturing system

    NASA Astrophysics Data System (ADS)

    Gwiazda, A.; Banas, W.; Sekala, A.; Foit, K.; Hryniewicz, P.; Kost, G.

    2015-11-01

    Process of workcell designing is limited by different constructional requirements. They are related to technological parameters of manufactured element, to specifications of purchased elements of a workcell and to technical characteristics of a workcell scene. This shows the complexity of the design-constructional process itself. The results of such approach are individually designed workcell suitable to the specific location and specific production cycle. Changing this parameters one must rebuild the whole configuration of a workcell. Taking into consideration this it is important to elaborate the base of typical elements of a robot kinematic chain that could be used as the tool for building Virtual modelling of kinematic chains of industrial robots requires several preparatory phase. Firstly, it is important to create a database element, which will be models of industrial robot arms. These models could be described as functional primitives that represent elements between components of the kinematic pairs and structural members of industrial robots. A database with following elements is created: the base kinematic pairs, the base robot structural elements, the base of the robot work scenes. The first of these databases includes kinematic pairs being the key component of the manipulator actuator modules. Accordingly, as mentioned previously, it includes the first stage rotary pair of fifth stage. This type of kinematic pairs was chosen due to the fact that it occurs most frequently in the structures of industrial robots. Second base consists of structural robot elements therefore it allows for the conversion of schematic structures of kinematic chains in the structural elements of the arm of industrial robots. It contains, inter alia, the structural elements such as base, stiff members - simple or angular units. They allow converting recorded schematic three-dimensional elements. Last database is a database of scenes. It includes elements of both simple and complex

  5. Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.

    PubMed

    Li, Hong-Dong; Menon, Rajasree; Govindarajoo, Brandon; Panwar, Bharat; Zhang, Yang; Omenn, Gilbert S; Guan, Yuanfang

    2015-09-01

    Alternative splicing allows a single gene to produce multiple transcript-level splice isoforms from which the translated proteins may show differences in their expression and function. Identifying the major functional or canonical isoform is important for understanding gene and protein functions. Identification and characterization of splice isoforms is a stated goal of the HUPO Human Proteome Project and of neXtProt. Multiple efforts have catalogued splice isoforms as "dominant", "principal", or "major" isoforms based on expression or evolutionary traits. In contrast, we recently proposed highest connected isoforms (HCIs) as a new class of canonical isoforms that have the strongest interactions in a functional network and revealed their significantly higher (differential) transcript-level expression compared to nonhighest connected isoforms (NCIs) regardless of tissues/cell lines in the mouse. HCIs and their expression behavior in the human remain unexplored. Here we identified HCIs for 6157 multi-isoform genes using a human isoform network that we constructed by integrating a large compendium of heterogeneous genomic data. We present examples for pairs of transcript isoforms of ABCC3, RBM34, ERBB2, and ANXA7. We found that functional networks of isoforms of the same gene can show large differences. Interestingly, differential expression between HCIs and NCIs was also observed in the human on an independent set of 940 RNA-seq samples across multiple tissues, including heart, kidney, and liver. Using proteomic data from normal human retina and placenta, we showed that HCIs are a promising indicator of expressed protein isoforms exemplified by NUDFB6 and M6PR. Furthermore, we found that a significant percentage (20%, p = 0.0003) of human and mouse HCIs are homologues, suggesting their conservation between species. Our identified HCIs expand the repertoire of canonical isoforms and are expected to facilitate studying main protein products, understanding gene

  6. Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.

    PubMed

    Li, Hong-Dong; Menon, Rajasree; Govindarajoo, Brandon; Panwar, Bharat; Zhang, Yang; Omenn, Gilbert S; Guan, Yuanfang

    2015-09-01

    Alternative splicing allows a single gene to produce multiple transcript-level splice isoforms from which the translated proteins may show differences in their expression and function. Identifying the major functional or canonical isoform is important for understanding gene and protein functions. Identification and characterization of splice isoforms is a stated goal of the HUPO Human Proteome Project and of neXtProt. Multiple efforts have catalogued splice isoforms as "dominant", "principal", or "major" isoforms based on expression or evolutionary traits. In contrast, we recently proposed highest connected isoforms (HCIs) as a new class of canonical isoforms that have the strongest interactions in a functional network and revealed their significantly higher (differential) transcript-level expression compared to nonhighest connected isoforms (NCIs) regardless of tissues/cell lines in the mouse. HCIs and their expression behavior in the human remain unexplored. Here we identified HCIs for 6157 multi-isoform genes using a human isoform network that we constructed by integrating a large compendium of heterogeneous genomic data. We present examples for pairs of transcript isoforms of ABCC3, RBM34, ERBB2, and ANXA7. We found that functional networks of isoforms of the same gene can show large differences. Interestingly, differential expression between HCIs and NCIs was also observed in the human on an independent set of 940 RNA-seq samples across multiple tissues, including heart, kidney, and liver. Using proteomic data from normal human retina and placenta, we showed that HCIs are a promising indicator of expressed protein isoforms exemplified by NUDFB6 and M6PR. Furthermore, we found that a significant percentage (20%, p = 0.0003) of human and mouse HCIs are homologues, suggesting their conservation between species. Our identified HCIs expand the repertoire of canonical isoforms and are expected to facilitate studying main protein products, understanding gene

  7. Passive reach and grasp with functional electrical stimulation and robotic arm support.

    PubMed

    Westerveld, Ard J; Schouten, Alfred C; Veltink, Peter H; van der Kooij, Herman

    2014-01-01

    Rehabilitation of arm and hand function is crucial to increase functional independence of stroke subjects. Here, we investigate the technical feasibility of an integrated training system combining robotics and functional electrical stimulation (FES) to support reach and grasp during functional manipulation of objects. To support grasp and release, FES controlled the thumb and fingers using Model Predictive Control (MPC), while a novel 3D robotic manipulator provided reach support. The system's performance was assessed in both stroke and blindfolded healthy subjects, where the subject's passive arm and hand made functional reach, grasp, move and release movements while manipulating objects. The success rate of complete grasp, move and release tasks with different objects ranged from 33% to 87% in healthy subjects. In severe chronic stroke subjects especially the hand opening had a low success rate (<25%) and no complete movements could be made. We demonstrated that our developed integrated training system can move the passive arm and hand for functional pick and place movements. In the current setup, the positioning accuracy of the robot with respect to the object position was critical for the overall performance. The use of a higher virtual stiffness and including feedback of object position in the robot control would likely improve the relative position accuracy. The system has potential for post-stroke rehabilitation, where support could be reduced based on patient performance which is needed to aid motor relearning of reach, grasp and release.

  8. Functional assessment and performance evaluation for assistive robotic manipulators: Literature review

    PubMed Central

    Chung, Cheng-Shiu; Wang, Hongwu; Cooper, Rory A.

    2013-01-01

    Context The user interface development of assistive robotic manipulators can be traced back to the 1960s. Studies include kinematic designs, cost-efficiency, user experience involvements, and performance evaluation. This paper is to review studies conducted with clinical trials using activities of daily living (ADLs) tasks to evaluate performance categorized using the International Classification of Functioning, Disability, and Health (ICF) frameworks, in order to give the scope of current research and provide suggestions for future studies. Methods We conducted a literature search of assistive robotic manipulators from 1970 to 2012 in PubMed, Google Scholar, and University of Pittsburgh Library System – PITTCat. Results Twenty relevant studies were identified. Conclusion Studies were separated into two broad categories: user task preferences and user-interface performance measurements of commercialized and developing assistive robotic manipulators. The outcome measures and ICF codes associated with the performance evaluations are reported. Suggestions for the future studies include (1) standardized ADL tasks for the quantitative and qualitative evaluation of task efficiency and performance to build comparable measures between research groups, (2) studies relevant to the tasks from user priority lists and ICF codes, and (3) appropriate clinical functional assessment tests with consideration of constraints in assistive robotic manipulator user interfaces. In addition, these outcome measures will help physicians and therapists build standardized tools while prescribing and assessing assistive robotic manipulators. PMID:23820143

  9. Altered Skeletal Muscle Mitochondrial Proteome As the Basis of Disruption of Mitochondrial Function in Diabetic Mice.

    PubMed

    Zabielski, Piotr; Lanza, Ian R; Gopala, Srinivas; Heppelmann, Carrie J Holtz; Bergen, H Robert; Dasari, Surendra; Nair, K Sreekumaran

    2016-03-01

    Insulin plays pivotal role in cellular fuel metabolism in skeletal muscle. Despite being the primary site of energy metabolism, the underlying mechanism on how insulin deficiency deranges skeletal muscle mitochondrial physiology remains to be fully understood. Here we report an important link between altered skeletal muscle proteome homeostasis and mitochondrial physiology during insulin deficiency. Deprivation of insulin in streptozotocin-induced diabetic mice decreased mitochondrial ATP production, reduced coupling and phosphorylation efficiency, and increased oxidant emission in skeletal muscle. Proteomic survey revealed that the mitochondrial derangements during insulin deficiency were related to increased mitochondrial protein degradation and decreased protein synthesis, resulting in reduced abundance of proteins involved in mitochondrial respiration and β-oxidation. However, a paradoxical upregulation of proteins involved in cellular uptake of fatty acids triggered an accumulation of incomplete fatty acid oxidation products in skeletal muscle. These data implicate a mismatch of β-oxidation and fatty acid uptake as a mechanism leading to increased oxidative stress in diabetes. This notion was supported by elevated oxidative stress in cultured myotubes exposed to palmitate in the presence of a β-oxidation inhibitor. Together, these results indicate that insulin deficiency alters the balance of proteins involved in fatty acid transport and oxidation in skeletal muscle, leading to impaired mitochondrial function and increased oxidative stress. PMID:26718503

  10. Dermal toxicity elicited by phthalates: evaluation of skin absorption, immunohistology, and functional proteomics.

    PubMed

    Pan, Tai-Long; Wang, Pei-Wen; Aljuffali, Ibrahim A; Hung, Yi-Yun; Lin, Chwan-Fwu; Fang, Jia-You

    2014-03-01

    The toxicity of phthalates is an important concern in the fields of environmental health and toxicology. Dermal exposure via skin care products, soil, and dust is a main route for phthalate delivery. We had explored the effect of topically-applied phthalates on skin absorption and toxicity. Immunohistology, functional proteomics, and Western blotting were employed as methodologies for validating phthalate toxicity. Among 5 phthalates tested, di(2-ethylhexyl)phthalate (DEHP) showed the highest skin reservoir. Only diethyl phthalate (DEP) and dibutyl phthalate (DBP) could penetrate across skin. Strat-M(®) membrane could be used as permeation barrier for predicting phthalate penetration through skin. The accumulation of DEHP in hair follicles was ∼15nmol/cm(2), which was significantly greater than DBP and DEP. DBP induced apoptosis of keratinocytes and fibroblasts via caspase-3 activation. This result was confirmed by downregulation of 14-3-3 and immunohistology of TUNEL. On the other hand, the HSP60 overexpression and immunostaining of COX-2 suggested inflammatory response induced by DEP and DEHP. The proteomic profiling verified the role of calcium homeostasis on skin inflammation. Some proteins investigated in this study can be sensitive biomarkers for dermal toxicity of phthalates. These included HSPs, 14-3-3, and cytokeratin. This work provided novel platforms for examining phthalate toxicity on skin.

  11. Proteome profiling of flax (Linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development.

    PubMed

    Barvkar, Vitthal T; Pardeshi, Varsha C; Kale, Sandip M; Kadoo, Narendra Y; Giri, Ashok P; Gupta, Vidya S

    2012-12-01

    Flax (Linum usitatissimum L.) seeds are an important source of food and feed due to the presence of various health promoting compounds, making it a nutritionally and economically important plant. An in-depth analysis of the proteome of developing flax seed is expected to provide significant information with respect to the regulation and accumulation of such storage compounds. Therefore, a proteomic analysis of seven seed developmental stages (4, 8, 12, 16, 22, 30, and 48 days after anthesis) in a flax variety, NL-97 was carried out using a combination of 1D-SDS-PAGE and LC-MSE methods. A total 1716 proteins were identified and their functional annotation revealed that a majority of them were involved in primary metabolism, protein destination, storage and energy. Three carbon assimilatory pathways appeared to operate in flax seeds. Reverse transcription quantitative PCR of selected 19 genes was carried out to understand their roles during seed development. Besides storage proteins, methionine synthase, RuBisCO and S-adenosylmethionine synthetase were highly expressed transcripts, highlighting their importance in flax seed development. Further, the identified proteins were mapped onto developmental seed specific expressed sequence tag (EST) libraries of flax to obtain transcriptional evidence and 81% of them had detectable expression at the mRNA level. This study provides new insights into the complex seed developmental processes operating in flax.

  12. Dermal toxicity elicited by phthalates: evaluation of skin absorption, immunohistology, and functional proteomics.

    PubMed

    Pan, Tai-Long; Wang, Pei-Wen; Aljuffali, Ibrahim A; Hung, Yi-Yun; Lin, Chwan-Fwu; Fang, Jia-You

    2014-03-01

    The toxicity of phthalates is an important concern in the fields of environmental health and toxicology. Dermal exposure via skin care products, soil, and dust is a main route for phthalate delivery. We had explored the effect of topically-applied phthalates on skin absorption and toxicity. Immunohistology, functional proteomics, and Western blotting were employed as methodologies for validating phthalate toxicity. Among 5 phthalates tested, di(2-ethylhexyl)phthalate (DEHP) showed the highest skin reservoir. Only diethyl phthalate (DEP) and dibutyl phthalate (DBP) could penetrate across skin. Strat-M(®) membrane could be used as permeation barrier for predicting phthalate penetration through skin. The accumulation of DEHP in hair follicles was ∼15nmol/cm(2), which was significantly greater than DBP and DEP. DBP induced apoptosis of keratinocytes and fibroblasts via caspase-3 activation. This result was confirmed by downregulation of 14-3-3 and immunohistology of TUNEL. On the other hand, the HSP60 overexpression and immunostaining of COX-2 suggested inflammatory response induced by DEP and DEHP. The proteomic profiling verified the role of calcium homeostasis on skin inflammation. Some proteins investigated in this study can be sensitive biomarkers for dermal toxicity of phthalates. These included HSPs, 14-3-3, and cytokeratin. This work provided novel platforms for examining phthalate toxicity on skin. PMID:24384410

  13. Individual muscle control using an exoskeleton robot for muscle function testing.

    PubMed

    Ueda, Jun; Ming, Ding; Krishnamoorthy, Vijaya; Shinohara, Minoru; Ogasawara, Tsukasa

    2010-08-01

    Healthy individuals modulate muscle activation patterns according to their intended movement and external environment. Persons with neurological disorders (e.g., stroke and spinal cord injury), however, have problems in movement control due primarily to their inability to modulate their muscle activation pattern in an appropriate manner. A functionality test at the level of individual muscles that investigates the activity of a muscle of interest on various motor tasks may enable muscle-level force grading. To date there is no extant work that focuses on the application of exoskeleton robots to induce specific muscle activation in a systematic manner. This paper proposes a new method, named "individual muscle-force control" using a wearable robot (an exoskeleton robot, or a power-assisting device) to obtain a wider variety of muscle activity data than standard motor tasks, e.g., pushing a handle by hand. A computational algorithm systematically computes control commands to a wearable robot so that a desired muscle activation pattern for target muscle forces is induced. It also computes an adequate amount and direction of a force that a subject needs to exert against a handle by his/her hand. This individual muscle control method enables users (e.g., therapists) to efficiently conduct neuromuscular function tests on target muscles by arbitrarily inducing muscle activation patterns. This paper presents a basic concept, mathematical formulation, and solution of the individual muscle-force control and its implementation to a muscle control system with an exoskeleton-type robot for upper extremity. Simulation and experimental results in healthy individuals justify the use of an exoskeleton robot for future muscle function testing in terms of the variety of muscle activity data.

  14. Protein functional analysis data in support of comparative proteomics of the pathogenic black yeast Exophiala dermatitidis under different temperature conditions.

    PubMed

    Tesei, Donatella; Marzban, Gorji; Marchetti-Deschmann, Martina; Tafer, Hakim; Arcalis, Elsa; Sterflinger, Katja

    2015-12-01

    In the current study a comparative proteomic approach was used to investigate the response of the human pathogen black yeast Exophiala dermatitidis toward temperature treatment. Protein functional analysis - based on cellular process GO terms - was performed on the 32 temperature-responsive identified proteins. The bioinformatics analyses and data presented here provided novel insights into the cellular pathways at the base of the fungus temperature tolerance. A detailed analysis and interpretation of the data can be found in "Proteome of tolerance fine-tuning in the human pathogen black yeast Exophiala dermatitidis" by Tesei et al. (2015) [1]. PMID:26958594

  15. Protein functional analysis data in support of comparative proteomics of the pathogenic black yeast Exophiala dermatitidis under different temperature conditions

    PubMed Central

    Tesei, Donatella; Marzban, Gorji; Marchetti-Deschmann, Martina; Tafer, Hakim; Arcalis, Elsa; Sterflinger, Katja

    2015-01-01

    In the current study a comparative proteomic approach was used to investigate the response of the human pathogen black yeast Exophiala dermatitidis toward temperature treatment. Protein functional analysis – based on cellular process GO terms – was performed on the 32 temperature-responsive identified proteins. The bioinformatics analyses and data presented here provided novel insights into the cellular pathways at the base of the fungus temperature tolerance. A detailed analysis and interpretation of the data can be found in “Proteome of tolerance fine-tuning in the human pathogen black yeast Exophiala dermatitidis” by Tesei et al. (2015) [1]. PMID:26958594

  16. Protein functional analysis data in support of comparative proteomics of the pathogenic black yeast Exophiala dermatitidis under different temperature conditions.

    PubMed

    Tesei, Donatella; Marzban, Gorji; Marchetti-Deschmann, Martina; Tafer, Hakim; Arcalis, Elsa; Sterflinger, Katja

    2015-12-01

    In the current study a comparative proteomic approach was used to investigate the response of the human pathogen black yeast Exophiala dermatitidis toward temperature treatment. Protein functional analysis - based on cellular process GO terms - was performed on the 32 temperature-responsive identified proteins. The bioinformatics analyses and data presented here provided novel insights into the cellular pathways at the base of the fungus temperature tolerance. A detailed analysis and interpretation of the data can be found in "Proteome of tolerance fine-tuning in the human pathogen black yeast Exophiala dermatitidis" by Tesei et al. (2015) [1].

  17. Retraining of interjoint arm coordination after stroke using robot-assisted time-independent functional training.

    PubMed

    Brokaw, Elizabeth B; Murray, Theresa; Nef, Tobias; Lum, Peter S

    2011-01-01

    We have developed a haptic-based approach for retraining of interjoint coordination following stroke called time-independent functional training (TIFT) and implemented this mode in the ARMin III robotic exoskeleton. The ARMin III robot was developed by Drs. Robert Riener and Tobias Nef at the Swiss Federal Institute of Technology Zurich (Eidgenossische Technische Hochschule Zurich, or ETH Zurich), in Zurich, Switzerland. In the TIFT mode, the robot maintains arm movements within the proper kinematic trajectory via haptic walls at each joint. These arm movements focus training of interjoint coordination with highly intuitive real-time feedback of performance; arm movements advance within the trajectory only if their movement coordination is correct. In initial testing, 37 nondisabled subjects received a single session of learning of a complex pattern. Subjects were randomized to TIFT or visual demonstration or moved along with the robot as it moved though the pattern (time-dependent [TD] training). We examined visual demonstration to separate the effects of action observation on motor learning from the effects of the two haptic guidance methods. During these training trials, TIFT subjects reduced error and interaction forces between the robot and arm, while TD subject performance did not change. All groups showed significant learning of the trajectory during unassisted recall trials, but we observed no difference in learning between groups, possibly because this learning task is dominated by vision. Further testing in stroke populations is warranted.

  18. Functional proteomic analysis reveals the involvement of KIAA1199 in breast cancer growth, motility and invasiveness

    PubMed Central

    2014-01-01

    Background KIAA1199 is a recently identified novel gene that is up-regulated in human cancer with poor survival. Our proteomic study on signaling polarity in chemotactic cells revealed KIAA1199 as a novel protein target that may be involved in cellular chemotaxis and motility. In the present study, we examined the functional significance of KIAA1199 expression in breast cancer growth, motility and invasiveness. Methods We validated the previous microarray observation by tissue microarray immunohistochemistry using a TMA slide containing 12 breast tumor tissue cores and 12 corresponding normal tissues. We performed the shRNA-mediated knockdown of KIAA1199 in MDA-MB-231 and HS578T cells to study the role of this protein in cell proliferation, migration and apoptosis in vitro. We studied the effects of KIAA1199 knockdown in vivo in two groups of mice (n = 5). We carried out the SILAC LC-MS/MS based proteomic studies on the involvement of KIAA1199 in breast cancer. Results KIAA1199 mRNA and protein was significantly overexpressed in breast tumor specimens and cell lines as compared with non-neoplastic breast tissues from large-scale microarray and studies of breast cancer cell lines and tumors. To gain deeper insights into the novel role of KIAA1199 in breast cancer, we modulated KIAA1199 expression using shRNA-mediated knockdown in two breast cancer cell lines (MDA-MB-231 and HS578T), expressing higher levels of KIAA1199. The KIAA1199 knockdown cells showed reduced motility and cell proliferation in vitro. Moreover, when the knockdown cells were injected into the mammary fat pads of female athymic nude mice, there was a significant decrease in tumor incidence and growth. In addition, quantitative proteomic analysis revealed that knockdown of KIAA1199 in breast cancer (MDA-MB-231) cells affected a broad range of cellular functions including apoptosis, metabolism and cell motility. Conclusions Our findings indicate that KIAA1199 may play an important role in breast

  19. Proteomics as the final step in the functional metagenomics study of antimicrobial resistance.

    PubMed

    Fouhy, Fiona; Stanton, Catherine; Cotter, Paul D; Hill, Colin; Walsh, Fiona

    2015-01-01

    The majority of clinically applied antimicrobial agents are derived from natural products generated by soil microorganisms and therefore resistance is likely to be ubiquitous in such environments. This is supported by the fact that numerous clinically important resistance mechanisms are encoded within the genomes of such bacteria. Advances in genomic sequencing have enabled the in silico identification of putative resistance genes present in these microorganisms. However, it is not sufficient to rely on the identification of putative resistance genes, we must also determine if the resultant proteins confer a resistant phenotype. This will require an analysis pipeline that extends from the extraction of environmental DNA, to the identification and analysis of potential resistance genes and their resultant proteins and phenotypes. This review focuses on the application of functional metagenomics and proteomics to study antimicrobial resistance in diverse environments. PMID:25784907

  20. FunSys: Software for functional analysis of prokaryotic transcriptome and proteome

    PubMed Central

    de Sá, Pablo; Pinto, Anne; Ramos, Rommel Thiago Jucá; Coimbra, Nilson; Baraúna, Rafael; Dall'Agnol, Hivana; Carneiro, Adriana; Ranieri, Alex; Valadares, Agenor; Azevedo, Vasco; Schneider, Maria Paula; Barh, Debmalya; Silva, Artur

    2012-01-01

    The vast amount of data produced by next-generation sequencing (NGS) has necessitated the development of computational tools to assist in understanding the myriad functions performed by the biological macromolecules involved in heredity. In this work, we developed the FunSys programme, a stand-alone tool with an user friendly interface that enables us to evaluate and correlate differential expression patterns from RNA sequencing and proteomics datasets. The FunSys generates charts and reports based on the results of the analysis of differential expression to aid the interpretation of the results. Availability FunSys and a test dataset are freely available at https://sourceforge.net/projects/funsysufpa/. It requires Sun jdk 6 or higher and MySQL server 5.1 or higher. PMID:22829724

  1. Proteomics as the final step in the functional metagenomics study of antimicrobial resistance.

    PubMed

    Fouhy, Fiona; Stanton, Catherine; Cotter, Paul D; Hill, Colin; Walsh, Fiona

    2015-01-01

    The majority of clinically applied antimicrobial agents are derived from natural products generated by soil microorganisms and therefore resistance is likely to be ubiquitous in such environments. This is supported by the fact that numerous clinically important resistance mechanisms are encoded within the genomes of such bacteria. Advances in genomic sequencing have enabled the in silico identification of putative resistance genes present in these microorganisms. However, it is not sufficient to rely on the identification of putative resistance genes, we must also determine if the resultant proteins confer a resistant phenotype. This will require an analysis pipeline that extends from the extraction of environmental DNA, to the identification and analysis of potential resistance genes and their resultant proteins and phenotypes. This review focuses on the application of functional metagenomics and proteomics to study antimicrobial resistance in diverse environments.

  2. A hardware investigation of robotic SPECT for functional and molecular imaging onboard radiation therapy systems

    PubMed Central

    Yan, Susu; Bowsher, James; Tough, MengHeng; Cheng, Lin; Yin, Fang-Fang

    2014-01-01

    Purpose: To construct a robotic SPECT system and to demonstrate its capability to image a thorax phantom on a radiation therapy flat-top couch, as a step toward onboard functional and molecular imaging in radiation therapy. Methods: A robotic SPECT imaging system was constructed utilizing a gamma camera detector (Digirad 2020tc) and a robot (KUKA KR150 L110 robot). An imaging study was performed with a phantom (PET CT PhantomTM), which includes five spheres of 10, 13, 17, 22, and 28 mm diameters. The phantom was placed on a flat-top couch. SPECT projections were acquired either with a parallel-hole collimator or a single-pinhole collimator, both without background in the phantom and with background at 1/10th the sphere activity concentration. The imaging trajectories of parallel-hole and pinhole collimated detectors spanned 180° and 228°, respectively. The pinhole detector viewed an off-centered spherical common volume which encompassed the 28 and 22 mm spheres. The common volume for parallel-hole system was centered at the phantom which encompassed all five spheres in the phantom. The maneuverability of the robotic system was tested by navigating the detector to trace the phantom and flat-top table while avoiding collision and maintaining the closest possible proximity to the common volume. The robot base and tool coordinates were used for image reconstruction. Results: The robotic SPECT system was able to maneuver parallel-hole and pinhole collimated SPECT detectors in close proximity to the phantom, minimizing impact of the flat-top couch on detector radius of rotation. Without background, all five spheres were visible in the reconstructed parallel-hole image, while four spheres, all except the smallest one, were visible in the reconstructed pinhole image. With background, three spheres of 17, 22, and 28 mm diameters were readily observed with the parallel-hole imaging, and the targeted spheres (22 and 28 mm diameters) were readily observed in the pinhole

  3. A hardware investigation of robotic SPECT for functional and molecular imaging onboard radiation therapy systems

    SciTech Connect

    Yan, Susu Tough, MengHeng; Bowsher, James; Yin, Fang-Fang; Cheng, Lin

    2014-11-01

    Purpose: To construct a robotic SPECT system and to demonstrate its capability to image a thorax phantom on a radiation therapy flat-top couch, as a step toward onboard functional and molecular imaging in radiation therapy. Methods: A robotic SPECT imaging system was constructed utilizing a gamma camera detector (Digirad 2020tc) and a robot (KUKA KR150 L110 robot). An imaging study was performed with a phantom (PET CT Phantom{sup TM}), which includes five spheres of 10, 13, 17, 22, and 28 mm diameters. The phantom was placed on a flat-top couch. SPECT projections were acquired either with a parallel-hole collimator or a single-pinhole collimator, both without background in the phantom and with background at 1/10th the sphere activity concentration. The imaging trajectories of parallel-hole and pinhole collimated detectors spanned 180° and 228°, respectively. The pinhole detector viewed an off-centered spherical common volume which encompassed the 28 and 22 mm spheres. The common volume for parallel-hole system was centered at the phantom which encompassed all five spheres in the phantom. The maneuverability of the robotic system was tested by navigating the detector to trace the phantom and flat-top table while avoiding collision and maintaining the closest possible proximity to the common volume. The robot base and tool coordinates were used for image reconstruction. Results: The robotic SPECT system was able to maneuver parallel-hole and pinhole collimated SPECT detectors in close proximity to the phantom, minimizing impact of the flat-top couch on detector radius of rotation. Without background, all five spheres were visible in the reconstructed parallel-hole image, while four spheres, all except the smallest one, were visible in the reconstructed pinhole image. With background, three spheres of 17, 22, and 28 mm diameters were readily observed with the parallel-hole imaging, and the targeted spheres (22 and 28 mm diameters) were readily observed in the

  4. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis.

    PubMed

    Parsons, Harriet T; Christiansen, Katy; Knierim, Bernhard; Carroll, Andrew; Ito, Jun; Batth, Tanveer S; Smith-Moritz, Andreia M; Morrison, Stephanie; McInerney, Peter; Hadi, Masood Z; Auer, Manfred; Mukhopadhyay, Aindrila; Petzold, Christopher J; Scheller, Henrik V; Loqué, Dominique; Heazlewood, Joshua L

    2012-05-01

    The plant Golgi plays a pivotal role in the biosynthesis of cell wall matrix polysaccharides, protein glycosylation, and vesicle trafficking. Golgi-localized proteins have become prospective targets for reengineering cell wall biosynthetic pathways for the efficient production of biofuels from plant cell walls. However, proteomic characterization of the Golgi has so far been limited, owing to the technical challenges inherent in Golgi purification. In this study, a combination of density centrifugation and surface charge separation techniques have allowed the reproducible isolation of Golgi membranes from Arabidopsis (Arabidopsis thaliana) at sufficiently high purity levels for in-depth proteomic analysis. Quantitative proteomic analysis, immunoblotting, enzyme activity assays, and electron microscopy all confirm high purity levels. A composition analysis indicated that approximately 19% of proteins were likely derived from contaminating compartments and ribosomes. The localization of 13 newly assigned proteins to the Golgi using transient fluorescent markers further validated the proteome. A collection of 371 proteins consistently identified in all replicates has been proposed to represent the Golgi proteome, marking an appreciable advancement in numbers of Golgi-localized proteins. A significant proportion of proteins likely involved in matrix polysaccharide biosynthesis were identified. The potential within this proteome for advances in understanding Golgi processes has been demonstrated by the identification and functional characterization of the first plant Golgi-resident nucleoside diphosphatase, using a yeast complementation assay. Overall, these data show key proteins involved in primary cell wall synthesis and include a mixture of well-characterized and unknown proteins whose biological roles and importance as targets for future research can now be realized. PMID:22430844

  5. Early Poststroke Rehabilitation Using a Robotic Tilt-Table Stepper and Functional Electrical Stimulation

    PubMed Central

    Kuznetsov, Alexey N.; Rybalko, Natalia V.; Daminov, Vadim D.; Luft, Andreas R.

    2013-01-01

    Background. Stroke frequently leaves survivors with hemiparesis. To prevent persistent deficits, rehabilitation may be more effective if started early. Early training is often limited because of orthostatic reactions. Tilt-table stepping robots and functional electrical stimulation (FES) may prevent these reactions. Objective. This controlled convenience sample study compares safety and feasibility of robotic tilt-table training plus FES (ROBO-FES) and robotic tilt-table training (ROBO) against tilt-table training alone (control). A preliminary assessment of efficacy is performed. Methods. Hemiparetic ischemic stroke survivors (age 58.3 ± 1.2 years, 4.6 ± 1.2 days after stroke) were assigned to 30 days of ROBO-FES (n = 38), ROBO (n = 35), or control (n = 31) in addition to conventional physical therapy. Impedance cardiography and transcranial doppler sonography were performed before, during, and after training. Hemiparesis was assessed using the British Medical Research Council (MRC) strength scale. Results. No serious adverse events occurred; 8 patients in the tilt-table group prematurely quit the study because of orthostatic reactions. Blood pressure and CBFV dipped <10% during robot training. In 52% of controls mean arterial pressure decreased by ≥20%. ROBO-FES increased leg strength by 1.97 ± 0.88 points, ROBO by 1.50 ± 0.85 more than control (1.03 ± 0.61, P < 0.05). CBFV increased in both robotic groups more than in controls (P < 0.05). Conclusions. Robotic tilt-table exercise with or without FES is safe and may be more effective in improving leg strength and cerebral blood flow than tilt table alone. PMID:23691432

  6. A Multi-Function Force Sensing Instrument for Variable Admittance Robot Control in Retinal Microsurgery*

    PubMed Central

    He, Xingchi; Balicki, Marcin; Gehlbach, Peter; Handa, James; Taylor, Russell; Iordachita, Iulian

    2014-01-01

    Robotic systems have the potential to assist vitreoretinal surgeons in extremely difficult surgical tasks inside the human eye. In addition to reducing hand tremor and improving tool positioning, a robotic assistant can provide assistive motion guidance using virtual fixtures, and incorporate real-time feedback from intraocular force sensing ophthalmic instruments to present tissue manipulation forces, that are otherwise physically imperceptible to the surgeon. This paper presents the design of an FBG-based, multi-function instrument that is capable of measuring mN-level forces at the instrument tip located inside the eye, and also the sclera contact location on the instrument shaft and the corresponding contact force. The given information is used to augment cooperatively controlled robot behavior with variable admittance control. This effectively creates an adaptive remote center-of-motion (RCM) constraint to minimize eye motion, but also allows the translation of the RCM location if the instrument is not near the retina. In addition, it provides force scaling for sclera force feedback. The calibration and validation of the multi-function force sensing instrument are presented, along with demonstration and performance assessment of the variable admittance robot control on an eye phantom. PMID:25383234

  7. Selective conjugation of proteins by mining active proteomes through click-functionalized magnetic nanoparticles.

    PubMed

    Ilyas, Shaista; Ilyas, Muhammad; van der Hoorn, Renier A L; Mathur, Sanjay

    2013-11-26

    Superparamagnetic iron oxide nanoparticles (SPIONs) coated with azide groups were functionalized at the surface with biotin (biotin@SPIONs) and cysteine protease inhibitor E-64 (E-64@SPIONs) with the purpose of developing nanoparticle-based assays for identifying cysteine proteases in proteomes. Magnetite particles (ca. 6 nm) were synthesized by microwave-assisted thermal decomposition of iron acetylacetonate and subsequently functionalized following a click chemistry protocol to obtain biotin and E-64 labeled particulate systems. Successful surface modification and covalent attachment of functional groups and molecules were confirmed by FT-IR spectroscopy and thermal gravimetric analysis. The ability of the surface-grafted biotin terminal groups to specifically interact with streptavidin (either horseradish peroxidase [(HRP)-luminol-H2O2] or rhodamine) was confirmed by chemiluminescent assay. A quantitative assessment showed a capture limit of 0.55-1.65 μg protein/100 μg particles. Furthermore, E-64@SPIONs were successfully used to specifically label papain-like cysteine proteases from crude plant extracts. Owing to the simplicity and versatility of the technique, together with the superparamagnetic behavior of FeOx-nanoparticles, the results demonstrate that click chemistry on surface anchored azide group is a viable approach toward bioconjugations that can be extended to other nanoparticles surfaces with different functional groups to target specific therapeutic and diagnostic applications. PMID:24143894

  8. Functional proteome of macrophage carried nanoformulated antiretroviral therapy demonstrates enhanced particle carrying capacity.

    PubMed

    Martinez-Skinner, Andrea L; Veerubhotla, Ram S; Liu, Han; Xiong, Huangui; Yu, Fang; McMillan, JoEllyn M; Gendelman, Howard E

    2013-05-01

    Our laboratory developed long-acting nanoformulations of antiretroviral therapy (nanoART) to improve drug compliance, reduce toxicities, and facilitate access of drug to viral reservoirs. These all function to inevitably improve treatment of human immunodeficiency virus (HIV) infection. Formulations are designed to harness the carrying capacities of mononuclear phagocytes (MP; monocytes and macrophages) and to use these cells as Trojan horses for drug delivery. Such a drug distribution system limits ART metabolism and excretion while facilitating access to viral reservoirs. Our prior works demonstrated a high degree of nanoART sequestration in macrophage recycling endosomes with broad and sustained drug tissue biodistribution and depots with limited untoward systemic toxicities. Despite such benefits, the effects of particle carriage on the cells' functional capacities remained poorly understood. Thus, we employed pulsed stable isotope labeling of amino acids in cell culture to elucidate the macrophage proteome and assess any alterations in cellular functions that would affect cell-drug carriage and release kinetics. NanoART-MP interactions resulted in the induction of a broad range of activation-related proteins that can enhance phagocytosis, secretory functions, and cell migration. Notably, we now demonstrate that particle-cell interactions serve to enhance drug loading while facilitating drug tissue depots and transportation. PMID:23544708

  9. Microfluidics-based single-cell functional proteomics for fundamental and applied biomedical applications.

    PubMed

    Yu, Jing; Zhou, Jing; Sutherland, Alex; Wei, Wei; Shin, Young Shik; Xue, Min; Heath, James R

    2014-01-01

    We review an emerging microfluidics-based toolkit for single-cell functional proteomics. Functional proteins include, but are not limited to, the secreted signaling proteins that can reflect the biological behaviors of immune cells or the intracellular phosphoproteins associated with growth factor-stimulated signaling networks. Advantages of the microfluidics platforms are multiple. First, 20 or more functional proteins may be assayed simultaneously from statistical numbers of single cells. Second, cell behaviors (e.g., motility) may be correlated with protein assays. Third, extensions to quantized cell populations can permit measurements of cell-cell interactions. Fourth, rare cells can be functionally identified and then separated for further analysis or culturing. Finally, certain assay types can provide a conduit between biology and the physicochemical laws. We discuss the history and challenges of the field then review design concepts and uses of the microchip platforms that have been reported, with an eye toward biomedical applications. We then look to the future of the field.

  10. Exploration of Panviral Proteome: High-Throughput Cloning and Functional Implications in Virus-host Interactions

    PubMed Central

    Yu, Xiaobo; Bian, Xiaofang; Throop, Andrea; Song, Lusheng; Moral, Lerys Del; Park, Jin; Seiler, Catherine; Fiacco, Michael; Steel, Jason; Hunter, Preston; Saul, Justin; Wang, Jie; Qiu, Ji; Pipas, James M.; LaBaer, Joshua

    2014-01-01

    Throughout the long history of virus-host co-evolution, viruses have developed delicate strategies to facilitate their invasion and replication of their genome, while silencing the host immune responses through various mechanisms. The systematic characterization of viral protein-host interactions would yield invaluable information in the understanding of viral invasion/evasion, diagnosis and therapeutic treatment of a viral infection, and mechanisms of host biology. With more than 2,000 viral genomes sequenced, only a small percent of them are well investigated. The access of these viral open reading frames (ORFs) in a flexible cloning format would greatly facilitate both in vitro and in vivo virus-host interaction studies. However, the overall progress of viral ORF cloning has been slow. To facilitate viral studies, we are releasing the initiation of our panviral proteome collection of 2,035 ORF clones from 830 viral genes in the Gateway® recombinational cloning system. Here, we demonstrate several uses of our viral collection including highly efficient production of viral proteins using human cell-free expression system in vitro, global identification of host targets for rubella virus using Nucleic Acid Programmable Protein Arrays (NAPPA) containing 10,000 unique human proteins, and detection of host serological responses using micro-fluidic multiplexed immunoassays. The studies presented here begin to elucidate host-viral protein interactions with our systemic utilization of viral ORFs, high-throughput cloning, and proteomic technologies. These valuable plasmid resources will be available to the research community to enable continued viral functional studies. PMID:24955142

  11. Detailed Functional and Proteomic Characterization of Fludarabine Resistance in Mantle Cell Lymphoma Cells

    PubMed Central

    Lorkova, Lucie; Scigelova, Michaela; Arrey, Tabiwang Ndipanquang; Vit, Ondrej; Pospisilova, Jana; Doktorova, Eliska; Klanova, Magdalena; Alam, Mahmudul; Vockova, Petra; Maswabi, Bokang

    2015-01-01

    Mantle cell lymphoma (MCL) is a chronically relapsing aggressive type of B-cell non-Hodgkin lymphoma considered incurable by currently used treatment approaches. Fludarabine is a purine analog clinically still widely used in the therapy of relapsed MCL. Molecular mechanisms of fludarabine resistance have not, however, been studied in the setting of MCL so far. We therefore derived fludarabine-resistant MCL cells (Mino/FR) and performed their detailed functional and proteomic characterization compared to the original fludarabine sensitive cells (Mino). We demonstrated that Mino/FR were highly cross-resistant to other antinucleosides (cytarabine, cladribine, gemcitabine) and to an inhibitor of Bruton tyrosine kinase (BTK) ibrutinib. Sensitivity to other types of anti-lymphoma agents was altered only mildly (methotrexate, doxorubicin, bortezomib) or remained unaffacted (cisplatin, bendamustine). The detailed proteomic analysis of Mino/FR compared to Mino cells unveiled over 300 differentially expressed proteins. Mino/FR were characterized by the marked downregulation of deoxycytidine kinase (dCK) and BTK (thus explaining the observed crossresistance to antinucleosides and ibrutinib), but also by the upregulation of several enzymes of de novo nucleotide synthesis, as well as the up-regulation of the numerous proteins of DNA repair and replication. The significant upregulation of the key antiapoptotic protein Bcl-2 in Mino/FR cells was associated with the markedly increased sensitivity of the fludarabine-resistant MCL cells to Bcl-2-specific inhibitor ABT199 compared to fludarabine-sensitive cells. Our data thus demonstrate that a detailed molecular analysis of drug-resistant tumor cells can indeed open a way to personalized therapy of resistant malignancies. PMID:26285204

  12. Robot programming

    SciTech Connect

    Lozano-Perez, T.

    1982-12-01

    The industrial robot's principal advantage over traditional automation is programmability. Robots can perform arbitrary sequences of pre-stored motions or of motions computed as functions of sensory input. This paper reviews requirements for and developments in robot programming systems. The key requirements for robot programming systems examined in the paper are in the areas of sensing, world modeling, motion specification, flow of control, and programming support. Existing and proposed robot programming systems fall into three broad categories: guiding systems in which the user leads a robot through the motions to be performed, robot-level programming systems in which the user writes a computer program specifying motion and sensing, and task-level programming systems in which the user writes a computer program specifying motion and sensing, and task-level programming systems in which the user specifies operations by their desired effect on objects. A representative sample of systems in each of these categories is surveyed in the paper.

  13. Novel aspects of grapevine response to phytoplasma infection investigated by a proteomic and phospho-proteomic approach with data integration into functional networks

    PubMed Central

    2013-01-01

    Background Translational and post-translational protein modifications play a key role in the response of plants to pathogen infection. Among the latter, phosphorylation is critical in modulating protein structure, localization and interaction with other partners. In this work, we used a multiplex staining approach with 2D gels to study quantitative changes in the proteome and phosphoproteome of Flavescence dorée-affected and recovered ‘Barbera’ grapevines, compared to healthy plants. Results We identified 48 proteins that differentially changed in abundance, phosphorylation, or both in response to Flavescence dorée phytoplasma infection. Most of them did not show any significant difference in recovered plants, which, by contrast, were characterized by changes in abundance, phosphorylation, or both for 17 proteins not detected in infected plants. Some enzymes involved in the antioxidant response that were up-regulated in infected plants, such as isocitrate dehydrogenase and glutathione S-transferase, returned to healthy-state levels in recovered plants. Others belonging to the same functional category were even down-regulated in recovered plants (oxidoreductase GLYR1 and ascorbate peroxidase). Our proteomic approach thus agreed with previously published biochemical and RT-qPCR data which reported down-regulation of scavenging enzymes and accumulation of H2O2 in recovered plants, possibly suggesting a role for this molecule in remission from infection. Fifteen differentially phosphorylated proteins (| ratio | > 2, p < 0.05) were identified in infected compared to healthy plants, including proteins involved in photosynthesis, response to stress and the antioxidant system. Many were not differentially phosphorylated in recovered compared to healthy plants, pointing to their specific role in responding to infection, followed by a return to a steady-state phosphorylation level after remission of symptoms. Gene ontology (GO) enrichment and statistical

  14. Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function.

    PubMed

    Sadhukhan, Sushabhan; Liu, Xiaojing; Ryu, Dongryeol; Nelson, Ornella D; Stupinski, John A; Li, Zhi; Chen, Wei; Zhang, Sheng; Weiss, Robert S; Locasale, Jason W; Auwerx, Johan; Lin, Hening

    2016-04-19

    Cellular metabolites, such as acyl-CoA, can modify proteins, leading to protein posttranslational modifications (PTMs). One such PTM is lysine succinylation, which is regulated by sirtuin 5 (SIRT5). Although numerous proteins are modified by lysine succinylation, the physiological significance of lysine succinylation and SIRT5 remains elusive. Here, by profiling acyl-CoA molecules in various mouse tissues, we have discovered that different tissues have different acyl-CoA profiles and that succinyl-CoA is the most abundant acyl-CoA molecule in the heart. This interesting observation has prompted us to examine protein lysine succinylation in different mouse tissues in the presence and absence of SIRT5. Protein lysine succinylation predominantly accumulates in the heart whenSirt5is deleted. Using proteomic studies, we have identified many cardiac proteins regulated by SIRT5. Our data suggest that ECHA, a protein involved in fatty acid oxidation, is a major enzyme that is regulated by SIRT5 and affects heart function.Sirt5knockout (KO) mice have lower ECHA activity, increased long-chain acyl-CoAs, and decreased ATP in the heart under fasting conditions.Sirt5KO mice develop hypertrophic cardiomyopathy, as evident from the increased heart weight relative to body weight, as well as reduced shortening and ejection fractions. These findings establish that regulating heart metabolism and function is a major physiological function of lysine succinylation and SIRT5. PMID:27051063

  15. Functional Proteomics Screen Enables Enrichment of Distinct Cell Types from Human Pancreatic Islets

    PubMed Central

    Sharivkin, Revital; Walker, Michael D.; Soen, Yoav

    2015-01-01

    The current world-wide epidemic of diabetes has prompted attempts to generate new sources of insulin-producing cells for cell replacement therapy. An inherent challenge in many of these strategies is the lack of cell-surface markers permitting isolation and characterization of specific cell types from differentiating stem cell populations. Here we introduce an iterative proteomics procedure allowing tag-free isolation of cell types based on their function. Our method detects and associates specific cell-surface markers with particular cell functionality by coupling cell capture on antibody arrays with immunofluorescent labeling. Using this approach in an iterative manner, we discovered marker combinations capable of enriching for discrete pancreatic cell subtypes from human islets of Langerhans: insulin-producing beta cells (CD9high/CD56+), glucagon-producing alpha cells (CD9- /CD56+) and trypsin-producing acinar cells (CD9- /CD56-). This strategy may assist future beta cell research and the development of diagnostic tools for diabetes. It can also be applied more generally for function-based purification of desired cell types from other limited and heterogeneous biological samples. PMID:25706282

  16. Structural and Functional Proteomic Analysis of a Developing Energy Transducing Membrane

    SciTech Connect

    Niederman, Robert A

    2012-06-04

    While much is known about the light reactions of photosynthesis in purple bacteria, comparatively little information is available on how the requisite integral membrane proteins are assembled, their patterns of cellular localization are established or their apoproteins cooperate with numerous assembly factors in their insertion into the growing intracytoplasmic membrane (ICM). This problem was approached through a detailed structural and functional proteomic analysis of ICM assembly process in the well-characterized purple bacterium Rhodobacter sphaeroides. Proteomic approaches have focused upon identification of membrane proteins temporally expressed during ICM development and spatially localized in both membrane growth initiation sites and in mature ICM vesicles. Protocols were established for ICM induction under reduced aeration and ICM remodeling in cells adapting to low intensity illumination, which permitted isolation, in sucrose density gradients, of ICM growth initiation sites as an upper pigmented band (UPB) and mature ICM vesicles as the main (chromatophore) band. Non-denaturing clear native gel electrophoresis (CNE) of these isolated membrane fractions gave rise to pigmented bands containing the peripheral light-harvesting 2 (LH2) antenna and the reaction center-light-harvesting 1 (RC-LH1) core complex, together with a full array of other ICM proteins, which were subjected to proteomic analysis. Proteomic analysis of the gel bands from chromatophores revealed developmental changes including increasing levels of the LH2 complex as ICM development proceeded, as well as a large array of other associated proteins including high spectral counts for the F1FO ATP synthase subunits, given the inability to detect this coupling factor, as well as the more abundant cytochrome bc1 complex by atomic force microscopy (AFM). Significant levels of general membrane assembly factors were encountered, as well as high counts for RSP6124, a protein of unknown function

  17. The cognitive nature of action - functional links between cognitive psychology, movement science, and robotics.

    PubMed

    Schack, Thomas; Ritter, Helge

    2009-01-01

    This paper examines the cognitive architecture of human action, showing how it is organized over several levels and how it is built up. Basic action concepts (BACs) are identified as major building blocks on a representation level. These BACs are cognitive tools for mastering the functional demands of movement tasks. Results from different lines of research showed that not only the structure formation of mental representations in long-term memory but also chunk formation in working memory are built up on BACs and relate systematically to movement structures. It is concluded that such movement representations might provide the basis for action implementation and action control in skilled voluntary movements in the form of cognitive reference structures. To simulate action implementation we discuss challenges and issues that arise when we try to replicate complex movement abilities in robots. Among the key issues to be addressed is the question how structured representations can arise during skill acquisition and how the underlying processes can be understood sufficiently succinctly to replicate them on robot platforms. Working towards this goal, we translate our findings in studies of motor control in humans into models that can guide the implementation of cognitive robot architectures. Focusing on the issue of manual action control, we illustrate some results in the context of grasping with a five-fingered anthropomorphic robot hand.

  18. Platelet proteomics.

    PubMed

    Zufferey, Anne; Fontana, Pierre; Reny, Jean-Luc; Nolli, Severine; Sanchez, Jean-Charles

    2012-01-01

    Platelets are small cell fragments, produced by megakaryocytes, in the bone marrow. They play an important role in hemostasis and diverse thrombotic disorders. They are therefore primary targets of antithrombotic therapies. They are implicated in several pathophysiological pathways, such as inflammation or wound repair. In blood circulation, platelets are activated by several pathways including subendothelial matrix and thrombin, triggering the formation of the platelet plug. Studying their proteome is a powerful approach to understand their biology and function. However, particular attention must be paid to different experimental parameters, such as platelet quality and purity. Several technologies are involved during the platelet proteome processing, yielding information on protein identification, characterization, localization, and quantification. Recent technical improvements in proteomics combined with inter-disciplinary strategies, such as metabolomic, transcriptomics, and bioinformatics, will help to understand platelets biological mechanisms. Therefore, a comprehensive analysis of the platelet proteome under different environmental conditions may contribute to elucidate complex processes relevant to platelet function regarding bleeding disorders or platelet hyperreactivity and identify new targets for antiplatelet therapy.

  19. Flux Balance Analysis with Objective Function Defined by Proteomics Data-Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine.

    PubMed

    Montezano, Daniel; Meek, Laura; Gupta, Rashmi; Bermudez, Luiz E; Bermudez, José C M

    2015-01-01

    We present a study of the metabolism of the Mycobacterium tuberculosis after exposure to antibiotics using proteomics data and flux balance analysis (FBA). The use of FBA to study prokaryotic organisms is well-established and allows insights into the metabolic pathways chosen by the organisms under different environmental conditions. To apply FBA a specific objective function must be selected that represents the metabolic goal of the organism. FBA estimates the metabolism of the cell by linear programming constrained by the stoichiometry of the reactions in an in silico metabolic model of the organism. It is assumed that the metabolism of the organism works towards the specified objective function. A common objective is the maximization of biomass. However, this goal is not suitable for situations when the bacterium is exposed to antibiotics, as the goal of organisms in these cases is survival and not necessarily optimal growth. In this paper we propose a new approach for defining the FBA objective function in studies when the bacterium is under stress. The function is defined based on protein expression data. The proposed methodology is applied to the case when the bacterium is exposed to the drug mefloquine, but can be easily extended to other organisms, conditions or drugs. We compare our method with an alternative method that uses experimental data for adjusting flux constraints. We perform comparisons in terms of essential enzymes and agreement using enzyme abundances. Results indicate that using proteomics data to define FBA objective functions yields less essential reactions with zero flux and lower error rates in prediction accuracy. With flux variability analysis we observe that overall variability due to alternate optima is reduced with the incorporation of proteomics data. We believe that incorporating proteomics data in the objective function used in FBA may help obtain metabolic flux representations that better support experimentally observed features

  20. Functional proteomics reveal the effect of Salvia miltiorrhiza aqueous extract against vascular atherosclerotic lesions.

    PubMed

    Hung, Yu-Chiang; Wang, Pei-Wen; Pan, Tai-Long

    2010-06-01

    Salvia miltiorrhiza is a Chinese herb widely used for cardiovascular disorder regimens, yet little is known about the cellular mechanisms that contribute to attenuated growth of smooth muscle cells (SMCs) under oxidative stress such as homocysteine (Hcy) treatment. As anticipated, a low dose (0.015 mg/mL) of S.miltiorrhiza aqueous extract (SMAE) significantly inhibited (>60%) the growth of a rat smooth muscle cell line (A10) under Hcy stimulation and the intracellular reactive oxygen species (ROS) concentration obviously decreased after SMAE treatment in terms of reducing p47(phox) translocation and increasing catalase activity. Signaling profile suggests that SMAE inhibited Hcy-induced A10 cell growth via the PKC/MAPK-dependent pathway. Two-dimensional electrophoresis (2-DE) coupled with mass spectrometry revealed statistically significant changes in the intensity of 14 proteins in response to Hcy and Hcy/SMAE. Meanwhile, SMAE attenuated carbonyl-modification of specific cytoskeleton and chaperone proteins leading to cell type transformation. Moreover, a network analysis using MetaCore shed more light on the molecular basis associated with SMAE efficacy. SMAE exerts its protective effect through the scavenging of ROS and subsequent modulation of protein carbonylation to inhibit cell proliferation. These signature networks and functional proteomics highlighted herein may facilitate the evaluation of potential therapeutic targets and elucidate novel mechanisms through which protein functions can be regulated by the redox status.

  1. Changes in the proteome of functional and regressing corpus luteum during pregnancy and lactation in the rat.

    PubMed

    González-Fernández, Raquel; Martínez-Galisteo, Emilia; Gaytán, Francisco; Bárcena, José Antonio; Sánchez-Criado, José Eugenio

    2008-07-01

    The corpus luteum (CL) is an exquisitely regulated transitory endocrine gland necessary for the onset and maintenance of pregnancy in mammals. Most of the data on the mechanisms of CL differentiation at the molecular level come from genomic studies, but direct protein data are scarce. Here we have undertaken a differential expression proteomic approach to identify, in an unbiased way, those proteins whose levels change significantly in the rat CL as it evolves from functionality during pregnancy to regression after parturition. Moreover, we have compared the regressing CL with the newly formed functional CL that coexist during lactation under the same endocrine environment. We have defined a "proteomic signature" of CL functionality, which is constituted by a set of 24 proteins with a few differences between pregnancy and lactation. Most of these markers are new and are involved in microtubule assembly, retinoic acid transport, and Raf kinase signaling cascade; 10 are enzymes that define a ketogenic metabolic landscape, demonstrating, for the first time, the prevalence of de novo cholesterol synthesis in luteal cells. The "proteomic signature of regression," on the other hand, is composed of nine proteins, one of which is 20alpha-hydroxysteroid dehydrogenase and two, ferritin and gamma-actin, are new. The discovery of unpredictable new actors in the differentiation process of CL reported here will contribute to new hypotheses that explain the complex female reproductive function at the protein level. It will also open new doors to research on each identified protein by relating them to cellular differentiation.

  2. New structural and functional defects in polyphosphate deficient bacteria: A cellular and proteomic study

    PubMed Central

    2010-01-01

    Background Inorganic polyphosphate (polyP), a polymer of tens or hundreds of phosphate residues linked by ATP-like bonds, is found in all organisms and performs a wide variety of functions. PolyP is synthesized in bacterial cells by the actions of polyphosphate kinases (PPK1 and PPK2) and degraded by exopolyphosphatase (PPX). Bacterial cells with polyP deficiencies due to knocking out the ppk1 gene are affected in many structural and important cellular functions such as motility, quorum sensing, biofilm formation and virulence among others. The cause of this pleiotropy is not entirely understood. Results The overexpression of exopolyphosphatase in bacteria mimicked some pleitropic defects found in ppk1 mutants. By using this approach we found new structural and functional defects in the polyP-accumulating bacteria Pseudomonas sp. B4, which are most likely due to differences in the polyP-removal strategy. Colony morphology phenotype, lipopolysaccharide (LPS) structure changes and cellular division malfunction were observed. Finally, we used comparative proteomics in order to elucidate the cellular adjustments that occurred during polyP deficiency in this bacterium and found some clues that helped to understand the structural and functional defects observed. Conclusions The results obtained suggest that during polyP deficiency energy metabolism and particularly nucleoside triphosphate (NTP) formation were affected and that bacterial cells overcame this problem by increasing the flux of energy-generating metabolic pathways such as tricarboxilic acid (TCA) cycle, β-oxidation and oxidative phosphorylation and by reducing energy-consuming ones such as active transporters and amino acid biosynthesis. Furthermore, our results suggest that a general stress response also took place in the cell during polyP deficiency. PMID:20067623

  3. Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chromoplasts are unique plastids that accumulate massive amounts of carotenoids. To gain a general and comparative characterization of chromoplast proteins, we performed proteomic analysis of chromoplasts from six carotenoid-rich crops: watermelon, tomato, carrot, orange cauliflower, red papaya, and...

  4. Global Proteomic Analysis of Functional Compartments in Immature Avian Follicles Using Laser Microdissection Coupled to LC-MS/MS

    PubMed Central

    Nepomuceno, Angelito I.; Muddiman, David C.; Petitte, James N.

    2015-01-01

    Laser microdissection (LMD) was utilized for the separation of the yolk, follicular wall and surrounding stromal cells of small white follicles (SWF) obtained from reproductively active domestic fowl. Herein, we provide an in-situ proteomics based approach to studying follicular development through the use of LMD and mass spectrometry. This study resulted in a total of 2,889 proteins identified from the three specific isolated compartments. White yolk from the smallest avian follicles resulted in the identification of 1,984 proteins, while isolated follicular wall and ovarian stroma yielded 2,470 and 2,456 proteins, respectively. GO annotations highlighted the functional differences between the compartments. Among the three compartments examined, the relative abundance of vitellogenins, steroidogenic enzymes, anti-Mullerian hormone, transcription factors, and proteins involved in retinoic acid receptors/retinoic acid synthesis, transcription factors and cell surface receptors such as EGFR and their associated signaling pathways reflected known cellular function of the ovary. This study has provided a global proteome for SWF, white yolk and ovarian stroma of the avian ovary that can be used as a baseline for future studies and verifies that the coupling of LMD with proteomic analysis can be used to evaluate proteins from small, physiologically functional compartments of complex tissue. PMID:26211554

  5. Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response

    SciTech Connect

    Allen, Michael S.; Hurst, Gregory B.; Lu, Tse-Yuan S.; Perry, Leslie M.; Pan, Chongle; Lankford, Patricia K.; Pelletier, Dale A.

    2015-04-08

    Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. In this paper, to begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σRPA4225 (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the -35 and -10 regions with the consensus sequence GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Finally, taken together, these data suggest that ECF σRPA4225 and the three additional genes make up a sigma factor mimicry system in R. palustris.

  6. Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response

    DOE PAGES

    Allen, Michael S.; Hurst, Gregory B.; Lu, Tse-Yuan S.; Perry, Leslie M.; Pan, Chongle; Lankford, Patricia K.; Pelletier, Dale A.

    2015-04-08

    Rhodopseudomonas palustris encodes 16 extracytoplasmic function (ECF) σ factors. In this paper, to begin to investigate the regulatory network of one of these ECF σ factors, the whole proteome of R. palustris CGA010 was quantitatively analyzed by tandem mass spectrometry from cultures episomally expressing the ECF σRPA4225 (ecfT) versus a WT control. Among the proteins with the greatest increase in abundance were catalase KatE, trehalose synthase, a DPS-like protein, and several regulatory proteins. Alignment of the cognate promoter regions driving expression of several upregulated proteins suggested a conserved binding motif in the -35 and -10 regions with the consensus sequencemore » GGAAC-18N-TT. Additionally, the putative anti-σ factor RPA4224, whose gene is contained in the same predicted operon as RPA4225, was identified as interacting directly with the predicted response regulator RPA4223 by mass spectrometry of affinity-isolated protein complexes. Furthermore, another gene (RPA4226) coding for a protein that contains a cytoplasmic histidine kinase domain is located immediately upstream of RPA4225. The genomic organization of orthologs for these four genes is conserved in several other strains of R. palustris as well as in closely related α-Proteobacteria. Finally, taken together, these data suggest that ECF σRPA4225 and the three additional genes make up a sigma factor mimicry system in R. palustris.« less

  7. Proteomics profiling reveals novel proteins and functions of the plant stigma exudate

    PubMed Central

    Rejón, Juan David; Delalande, François; Castro, Antonio Jesús

    2013-01-01

    Proteomic analysis of the stigmatic exudate of Lilium longiflorum and Olea europaea led to the identification of 51 and 57 proteins, respectively, most of which are described for the first time in this secreted fluid. These results indicate that the stigmatic exudate is an extracellular environment metabolically active, participating in at least 80 different biological processes and 97 molecular functions. The stigma exudate showed a markedly catabolic profile and appeared to possess the enzyme machinery necessary to degrade large polysaccharides and lipids secreted by papillae to smaller units, allowing their incorporation into the pollen tube during pollination. It may also regulate pollen-tube growth in the pistil through the selective degradation of tube-wall components. Furthermore, some secreted proteins were involved in pollen-tube adhesion and orientation, as well as in programmed cell death of the papillae cells in response to either compatible pollination or incompatible pollen rejection. Finally, the results also revealed a putative cross-talk between genetic programmes regulating stress/defence and pollination responses in the stigma. PMID:24151302

  8. Discovery metabolite profiling--forging functional connections between the proteome and metabolome.

    PubMed

    Saghatelian, Alan; Cravatt, Benjamin F

    2005-08-19

    Of primary interest for every enzyme is the identification of its physiological substrates. However, the vast structural diversity of endogenous metabolites, coupled with the overlapping activities of numerous enzymes, makes it difficult to deduce the identity of natural substrates for a given enzyme based on in vitro experiments. To address this challenge, we recently introduced an LC-MS based analytical method termed discovery metabolite profiling (DMP) to evaluate the global metabolic effects of enzyme inactivation in vivo. We have applied DMP to study mice lacking the enzyme fatty acid amide hydrolase (FAAH), which degrades the endocannabinoid family of signaling lipids. DMP identified several previously uncharacterized FAAH substrates, including a structurally novel class of brain lipids that represent conjugates of very long chain fatty acids with the amino acid derivative taurine [N-acyl taurines (NATs)]. These findings show that DMP can establish direct connections between the proteome and metabolome and thus offers a powerful strategy to assign physiological functions to enzymes in the post-genomic era.

  9. CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis

    PubMed Central

    Ochoa-Montaño, Bernardo; Mohan, Nishita; Blundell, Tom L.

    2015-01-01

    Tuberculosis kills more than a million people annually and presents increasingly high levels of resistance against current first line drugs. Structural information about Mycobacterium tuberculosis (Mtb) proteins is a valuable asset for the development of novel drugs and for understanding the biology of the bacterium; however, only about 10% of the ∼4000 proteins have had their structures determined experimentally. The CHOPIN database assigns structural domains and generates homology models for 2911 sequences, corresponding to ∼73% of the proteome. A sophisticated pipeline allows multiple models to be created using conformational states characteristic of different oligomeric states and ligand binding, such that the models reflect various functional states of the proteins. Additionally, CHOPIN includes structural analyses of mutations potentially associated with drug resistance. Results are made available at the web interface, which also serves as an automatically updated repository of all published Mtb experimental structures. Its RESTful interface allows direct and flexible access to structures and metadata via intuitive URLs, enabling easy programmatic use of the models. Database URL: http://structure.bioc.cam.ac.uk/chopin PMID:25833954

  10. CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis.

    PubMed

    Ochoa-Montaño, Bernardo; Mohan, Nishita; Blundell, Tom L

    2015-01-01

    Tuberculosis kills more than a million people annually and presents increasingly high levels of resistance against current first line drugs. Structural information about Mycobacterium tuberculosis (Mtb) proteins is a valuable asset for the development of novel drugs and for understanding the biology of the bacterium; however, only about 10% of the ∼4000 proteins have had their structures determined experimentally. The CHOPIN database assigns structural domains and generates homology models for 2911 sequences, corresponding to ∼73% of the proteome. A sophisticated pipeline allows multiple models to be created using conformational states characteristic of different oligomeric states and ligand binding, such that the models reflect various functional states of the proteins. Additionally, CHOPIN includes structural analyses of mutations potentially associated with drug resistance. Results are made available at the web interface, which also serves as an automatically updated repository of all published Mtb experimental structures. Its RESTful interface allows direct and flexible access to structures and metadata via intuitive URLs, enabling easy programmatic use of the models.

  11. Proteomic and functional analyses of Nelumbo nucifera annexins involved in seed thermotolerance and germination vigor.

    PubMed

    Chu, Pu; Chen, Huhui; Zhou, Yuliang; Li, Yin; Ding, Yu; Jiang, Liwen; Tsang, Edward W T; Wu, Keqiang; Huang, Shangzhi

    2012-06-01

    Annexins are multifunctional proteins characterized by their capacity to bind calcium ions and negatively charged lipids. Although there is increasing evidence implicating their importance in plant stress responses, their functions in seeds remain to be further studied. In this study, we identified a heat-induced annexin, NnANN1, from the embryonic axes of sacred lotus (Nelumbo nucifera Gaertn.) using comparative proteomics approach. Moreover, the expression of NnANN1 increased considerably in response to high-temperature treatment. Quantitative real-time PCR (qRT-PCR) revealed that the transcripts of NnANN1 were detected predominantly during seed development and germination in sacred lotus, implicating a role for NnANN1 in plant seeds. Ectopic expression of NnANN1 in Arabidopsis resulted in enhanced tolerance to heat stress in transgenic seeds. In addition, compared to the wild-type seeds, transgenic seeds ectopically expressing NnANN1 exhibited improved resistance to accelerated aging treatment used for assessing seed vigor. Furthermore, transgenic seeds showed enhanced peroxidase activities, accompanied with reduced lipid peroxidation and reduced ROS release levels compared to the wild-type seeds. Taken together, these results indicate that NnANN1 plays an important role in seed thermotolerance and germination vigor.

  12. Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function.

    PubMed

    Worah, Kuntal; Mathan, Till S M; Vu Manh, Thien Phong; Keerthikumar, Shivakumar; Schreibelt, Gerty; Tel, Jurjen; Duiveman-de Boer, Tjitske; Sköld, Annette E; van Spriel, Annemiek B; de Vries, I Jolanda M; Huynen, Martijn A; Wessels, Hans J; Gloerich, Jolein; Dalod, Marc; Lasonder, Edwin; Figdor, Carl G; Buschow, Sonja I

    2016-09-13

    Dendritic cells (DCs) play a key role in orchestrating adaptive immune responses. In human blood, three distinct subsets exist: plasmacytoid DCs (pDCs) and BDCA3+ and CD1c+ myeloid DCs. In addition, a DC-like CD16+ monocyte has been reported. Although RNA-expression profiles have been previously compared, protein expression data may provide a different picture. Here, we exploited label-free quantitative mass spectrometry to compare and identify differences in primary human DC subset proteins. Moreover, we integrated these proteomic data with existing mRNA data to derive robust cell-specific expression signatures with more than 400 differentially expressed proteins between subsets, forming a solid basis for investigation of subset-specific functions. We illustrated this by extracting subset identification markers and by demonstrating that pDCs lack caspase-1 and only express low levels of other inflammasome-related proteins. In accordance, pDCs were incapable of interleukin (IL)-1β secretion in response to ATP. PMID:27626665

  13. Casein kinase 1 proteomics reveal prohibitin 2 function in molecular clock.

    PubMed

    Kategaya, Lorna S; Hilliard, Aisha; Zhang, Louying; Asara, John M; Ptáček, Louis J; Fu, Ying-Hui

    2012-01-01

    Throughout the day, clock proteins synchronize changes in animal physiology (e.g., wakefulness and appetite) with external cues (e.g., daylight and food). In vertebrates, both casein kinase 1 delta and epsilon (CK1δ and CK1ε) regulate these circadian changes by phosphorylating other core clock proteins. In addition, CK1 can regulate circadian-dependent transcription in a non-catalytic manner, however, the mechanism is unknown. Furthermore, the extent of functional redundancy between these closely related kinases is debated. To further advance knowledge about CK1δ and CK1ε mechanisms of action in the biological clock, we first carried out proteomic analysis of both kinases in human cells. Next, we tested interesting candidates in a cell-based circadian readout which resulted in the discovery of PROHIBITIN 2 (PHB2) as a modulator of period length. Decreasing the expression of PHB2 increases circadian-driven transcription, thus revealing PHB2 acts as an inhibitor in the molecular clock. While stable binding of PHB2 to either kinase was not detected, knocking down CK1ε expression increases PHB2 protein levels and, unexpectedly, knocking down CK1δ decreases PHB2 transcript levels. Thus, isolating CK1 protein complexes led to the identification of PHB2 as an inhibitor of circadian transcription. Furthermore, we show that CK1δ and CK1ε differentially regulate the expression of PHB2.

  14. Functional specifications of an integrated proteomics information management and analysis platform.

    PubMed

    Tsiknakis, M; Grangeat, P; Binz, P-A; Potamias, G; Lisacek, F; Gerfault, L; Paulus, C; Manakanatas, D; Kritsotakis, V; Kondylakis, H; Perez, M; Plexousakis, D; Kaforou, S; Kafetzopoulos, D

    2007-01-01

    Detecting proteins in human blood holds the promise of a revolution in cancer diagnosis. Also, the ability to perform laboratory operations on small scales using miniaturized (lab-on-a-chip) devices has many benefits. Designing and fabricating such systems is extremely challenging, but physicists and engineers are beginning to construct such highly integrated and compact labs on chips with exciting functionality. This paper focuses on the presentation of the requirements of the information technology layer in such an integrated platform been developed in the LOCCANDIA project. LOCCANDIA is a Specific Targeted Research project (STREP) funded under the 6th Framework program of the EC. Its ultimate objective is to develop an innovative nano-technology based (lab-on-a-chip) platform for the medical-proeomics field. The paper presents the main engineering aspects, challenges and architecture for creating an Integrated Clinico-Proteomic Environment. The environment will be used to monitor and document the analysis and discovery chain and to allow the physician to interpret the digital spectrogram data delivered by the mass spectrometer, for diagnostic purposes. PMID:18003398

  15. Proteomic analysis of FUS interacting proteins provides insights into FUS function and its role in ALS.

    PubMed

    Kamelgarn, Marisa; Chen, Jing; Kuang, Lisha; Arenas, Alexandra; Zhai, Jianjun; Zhu, Haining; Gal, Jozsef

    2016-10-01

    Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease. Mutations in the Fused in Sarcoma/Translocated in Liposarcoma (FUS/TLS) gene cause a subset of familial ALS cases and are also implicated in sporadic ALS. FUS is typically localized to the nucleus. The ALS-related FUS mutations cause cytoplasmic mis-localization and the formation of stress granule-like structures. Abnormal cytoplasmic FUS localization was also found in a subset of frontotemporal dementia (FTLD) cases without FUS mutations. To better understand the function of FUS, we performed wild-type and mutant FUS pull-downs followed by proteomic identification of the interacting proteins. The FUS interacting partners we identified are involved in multiple pathways, including chromosomal organization, transcription, RNA splicing, RNA transport, localized translation, and stress response. FUS interacted with hnRNPA1 and Matrin-3, RNA binding proteins whose mutations were also reported to cause familial ALS, suggesting that hnRNPA1 and Matrin-3 may play common pathogenic roles with FUS. The FUS interactions displayed varied RNA dependence. Numerous FUS interacting partners that we identified are components of exosomes. We found that FUS itself was present in exosomes, suggesting that the secretion of FUS might contribute to the cell-to-cell spreading of FUS pathology. FUS interacting proteins were sequestered into the cytoplasmic mutant FUS inclusions that could lead to their mis-regulation or loss of function, contributing to ALS pathogenesis. Our results provide insights into the physiological functions of FUS as well as important pathways where mutant FUS can interfere with cellular processes and potentially contribute to the pathogenesis of ALS. PMID:27460707

  16. Functional Status and Inflammation after Preseason Training Program in Professional and Recreational Soccer Players: a Proteomic Approach

    PubMed Central

    Martín-Sánchez, Francisco J.; Villalón, José María; Zamorano-León, José J.; Rosas, Luis Fernández; Proietti, Ricardo; Mateos-Caceres, Petra J.; González-Armengol, Juan J.; Villarroel, Pedro; Macaya, Carlos; López-Farré, Antonio J.

    2011-01-01

    The purpose of the study was to determine if an intensive pre- season training program modifies the inflammatory status in professional soccer players and if this inflammatory profile may be associated with the physical state. We compared plasma protein biomarkers, using proteomics, and the physiological state and cardiac function in 12 professional soccer players and 9 recreational soccer players. Reduced cardiac low frequency [LF] after the pre- season training program previous competition with respect to recreational soccer players was found. No differences were found in cardiac high frequency, cardiac high frequency/low frequency ratio, tension index and oxygen volume consumption. Alpha-1-antitrypsin isotype-3, fibrinogen-gamma isotypes-1, 2 and 3 and vitamin-D-binding protein isotype-1 were reduced in professionals players compared with those in recreational players. However, an increased content of alpha-1-antitrypsin isotype-6 and alpha-1-antichymotrypsin 1 and 4 were found in professional soccer players. Spearman’s analysis showed a positive correlation between LF and fibrinogen-gamma chain isotype 3; but LF was negatively correlated with alpha-antichymotrypsin isotype 4. Professional soccer players submitted to an intensive training showed differences in the content of plasma proteins associated with inflammatory/oxidative stress and thrombosis with respect to recreational soccer players. Proteomics analysis in combination with the analysis of cardiac function assessment may be useful to know more in depth molecular processes associated with sport and intensive exercise. Key points Proteomics allow us to find differences in the plasma protein content in sportsmen. Just after pre-season training program, professional soccer players showed lower content of circulating proteins associated with inflammation compared to recreational soccer players. Proteomic analysis in combination with the analysis of cardiac function may be useful to know more in depth

  17. Predicting Functional Recovery in Chronic Stroke Rehabilitation Using Event-Related Desynchronization-Synchronization during Robot-Assisted Movement.

    PubMed

    Caimmi, Marco; Visani, Elisa; Digiacomo, Fabio; Scano, Alessandro; Chiavenna, Andrea; Gramigna, Cristina; Molinari Tosatti, Lorenzo; Franceschetti, Silvana; Molteni, Franco; Panzica, Ferruccio

    2016-01-01

    Although rehabilitation robotics seems to be a promising therapy in the rehabilitation of the upper limb in stroke patients, consensus is still lacking on its additive effects. Therefore, there is a need for determining the possible success of robotic interventions on selected patients, which in turn determine the necessity for new investigating instruments supporting the treatment decision-making process and customization. The objective of the work presented in this preliminary study was to verify that fully robot assistance would not affect the physiological oscillatory cortical activity related to a functional movement in healthy subjects. Further, the clinical results following the robotic treatment of a chronic stroke patient, who positively reacted to the robotic intervention, were analyzed and discussed. First results show that there is no difference in EEG activation pattern between assisted and no-assisted movement in healthy subjects. Even more importantly, the patient's pretreatment EEG activation pattern in no-assisted movement was completely altered, while it recovered to a quasi-physiological one in robot-assisted movement. The functional improvement following treatment was large. Using pretreatment EEG recording during robot-assisted movement might be a valid approach to assess the potential ability of the patient for recovering. PMID:27057546

  18. Predicting Functional Recovery in Chronic Stroke Rehabilitation Using Event-Related Desynchronization-Synchronization during Robot-Assisted Movement

    PubMed Central

    Gramigna, Cristina; Franceschetti, Silvana

    2016-01-01

    Although rehabilitation robotics seems to be a promising therapy in the rehabilitation of the upper limb in stroke patients, consensus is still lacking on its additive effects. Therefore, there is a need for determining the possible success of robotic interventions on selected patients, which in turn determine the necessity for new investigating instruments supporting the treatment decision-making process and customization. The objective of the work presented in this preliminary study was to verify that fully robot assistance would not affect the physiological oscillatory cortical activity related to a functional movement in healthy subjects. Further, the clinical results following the robotic treatment of a chronic stroke patient, who positively reacted to the robotic intervention, were analyzed and discussed. First results show that there is no difference in EEG activation pattern between assisted and no-assisted movement in healthy subjects. Even more importantly, the patient's pretreatment EEG activation pattern in no-assisted movement was completely altered, while it recovered to a quasi-physiological one in robot-assisted movement. The functional improvement following treatment was large. Using pretreatment EEG recording during robot-assisted movement might be a valid approach to assess the potential ability of the patient for recovering. PMID:27057546

  19. Predicting Functional Recovery in Chronic Stroke Rehabilitation Using Event-Related Desynchronization-Synchronization during Robot-Assisted Movement.

    PubMed

    Caimmi, Marco; Visani, Elisa; Digiacomo, Fabio; Scano, Alessandro; Chiavenna, Andrea; Gramigna, Cristina; Molinari Tosatti, Lorenzo; Franceschetti, Silvana; Molteni, Franco; Panzica, Ferruccio

    2016-01-01

    Although rehabilitation robotics seems to be a promising therapy in the rehabilitation of the upper limb in stroke patients, consensus is still lacking on its additive effects. Therefore, there is a need for determining the possible success of robotic interventions on selected patients, which in turn determine the necessity for new investigating instruments supporting the treatment decision-making process and customization. The objective of the work presented in this preliminary study was to verify that fully robot assistance would not affect the physiological oscillatory cortical activity related to a functional movement in healthy subjects. Further, the clinical results following the robotic treatment of a chronic stroke patient, who positively reacted to the robotic intervention, were analyzed and discussed. First results show that there is no difference in EEG activation pattern between assisted and no-assisted movement in healthy subjects. Even more importantly, the patient's pretreatment EEG activation pattern in no-assisted movement was completely altered, while it recovered to a quasi-physiological one in robot-assisted movement. The functional improvement following treatment was large. Using pretreatment EEG recording during robot-assisted movement might be a valid approach to assess the potential ability of the patient for recovering.

  20. Impact of Obesity on Early Erectile Function Recovery after Robotic Radical Prostatectomy

    PubMed Central

    Jensen, James C.

    2011-01-01

    Background and Objective: Studies are limited regarding the impact of obesity on early erectile functional outcomes after robotic radical prostatectomy. Our goal was to determine this impact using patient-reported validated questionnaires. Methods: International Index of Erectile Function (IIEF-6) scores were prospectively collected with institutional review board approval, for patients who underwent robotic radical prostatectomy with bilateral nerve sparing from February 2007 to October 2009. The data were categorized into nonobese and obese groups and subsequently into 2 subgroups based on risk for postprostatectomy erectile dysfunction. Low risk is preoperative IIEF-6 ≥19 and high risk is IIEF-6 <19. The groups and subgroups were compared using chi-square analysis. Results: Of 190 consecutive patients, 67 were excluded for preoperative severe erectile dysfunction (IIEF-6 <7), or lack of IIEF-6 scores, or both. There were 69 nonobese patients of which 88% were potent preoperatively and 20% regained potency at 12 months postoperatively. Of 54 obese patients, 85% were potent preoperatively and 25% at 12 months. There was no difference in erectile function recovery rates between the groups (P=0.755). In both groups, patients with low risk of postoperative erectile dysfunction had statistically similar postoperative mean IIEF-6 scores at 6 and 12 months (P=0.580 and P=0.389, respectively), and no difference in erectile function recovery rates existed at 12 months (P=0.735). Conclusion: Obesity has no major contribution to the rate of early erectile function recovery after robotic radical prostatectomy. Preoperative erectile function remains the determining factor in postradical prostatectomy erectile dysfunction. PMID:21902939

  1. “Spatial Mapping of the Neurite and Soma Proteomes Reveals a Functional Cdc42/Rac Regulatory Network”

    SciTech Connect

    Pertz, Olivier C.; Wang, Yingchun; Yang, Feng; Wang, Wei; gay, laurie J.; Gritsenko, Marina A.; Clauss, Therese RW; Anderson, David J.; Liu, Tao; Auberry, Kenneth J.; Camp, David G.; Smith, Richard D.; Klemke, Richard L.

    2008-02-12

    Neurite extension and growth cone navigation are guided by extracellular cues that control cytoskeletal rearrangements. However, understanding the complex signaling mechanisms that mediate neuritogenesis has been limited by the inability to biochemically separate the neurite and soma for spatial proteomic and bioinformatic analyses. Here, we apply global proteome profiling in combination with a novel neurite purification methodology for comparative analysis of the soma and neurite proteomes of neuroblastoma cells. The spatial relationship of 4855 proteins were mapped revealing networks of signaling proteins that control integrins, the actin cytoskeleton, and axonal guidance in the extending neurite. Bioinformatics and functional analyses revealed a spatially compartmentalized Rac/Cdc42 signaling network that operates in conjunction with multiple GEFs and GAPs to control neurite formation. Interestingly, RNA interference experiments revealed that the different GEFs and GAPs regulate specialized functions during neurite formation including neurite growth and retraction kinetics, cytoskeletal organization, and cell polarity. Our findings provide insight into the spatial organization of signaling networks that enable neuritogenesis and provide a comprehensive system-wide profile of proteins that mediate this process including those that control Rac and Cdc42 signaling.

  2. Robotic Assessment of Upper Limb Function after Proximal Humeral Fracture: Personal Experience as A Patient and Occupational Therapist.

    PubMed

    Nishimoto, Atsuko; Otaka, Yohei; Kasuga, Shoko; Otaka, Eri; Yamazaki, Kotaro; Ushiba, Junichi; Liu, Meigen

    2016-01-01

    Robotics is an emerging field in rehabilitation medicine. Robots have the potential to complement traditional clinical assessments because they can measure functions more precisely and quantitatively than current clinical assessments. We present a patient with a proximal humeral fracture whose recovery process was evaluated with an exoskeleton robotic device. The patient, a 34-year-old woman, suffered a left proximal humeral fracture while snowboarding. She is an occupational therapist and is the first author of this study. With conservative therapy, fracture union was seen on X-ray at 6 weeks post-injury. At that time, the patient was permitted to move her left upper limb actively within the tolerance of pain. We assessed the function of the injured upper limb at 6, 7, and 12 weeks post-injury with the KINARM exoskeleton robotic device and with conventional clinical measures. The active range of motion and the muscle strength of the left shoulder improved over time. Using robotic assessment, the precise movement profiles, position sense, and functional ability of both arms were quantified and also showed progressive improvement over time. Assessment with a robotic device of the recovery process after proximal humeral fracture allowed quantification of functional impairments that could not be felt subjectively nor identified with conventional clinical assessments. PMID:27665866

  3. Function of global regulator CodY in Bacillus thuringiensis BMB171 by comparative proteomic analysis.

    PubMed

    Qi, Mingxia; Mei, Fei; Wang, Hui; Sun, Ming; Wang, Gejiao; Yu, Ziniu; Je, Yeonho; Li, Mingshun

    2015-02-01

    CodY is a highly conserved protein in low G+C gram-positive bacteria that regulates genes involved in sporulation and stationary-phase adaptation. Bacillus thuringiensis is a grampositive bacterium that forms spores and parasporal crystals during the stationary phase. To our knowledge, the regulatory mechanism of CodY in B. thuringiensis is unknown. To study the function of CodY protein in B. thuringiensis, BMB171codY(-) was constructed in a BMB171 strain. A shuttle vector containing the ORF of cry1Ac10 was transformed into BMB171 and BMB171codY(-), named BMB171cry1Ac and BMB171codY(-)cry1Ac, respectively. Some morphological and physiological changes of codY mutant BMB171codY(-)cry1Ac were observed. A comparative proteomic analysis was conducted for both BMB171codY(-)cry1Ac and BMB171cry1Ac through two-dimensional gel electrophoresis and MALDI-TOF-MS/MS analysis. The results showed that the proteins regulated by CodY are involved in microbial metabolism, including branched-chain amino acid metabolism, carbohydrate metabolism, fatty acid metabolism, and energy metabolism. Furthermore, we found CodY to be involved in sporulation, biosynthesis of poly-β-hydroxybutyrate, growth, genetic competence, and translation. According to the analysis of differentially expressed proteins, and physiological characterization of the codY mutant, we performed bacterial one-hybrid and electrophoretic mobility shift assay experiments and confirmed the direct regulation of genes by CodY, specifically those involved in metabolism of branched-chain amino acids, ribosomal recycling factor FRR, and the late competence protein ComER. Our data establish the foundation for in-depth study of the regulation of CodY in B. thuringiensis, and also offer a potential biocatalyst for functions of CodY in other bacteria.

  4. Silencing of mitochondrial Lon protease deeply impairs mitochondrial proteome and function in colon cancer cells.

    PubMed

    Gibellini, Lara; Pinti, Marcello; Boraldi, Federica; Giorgio, Valentina; Bernardi, Paolo; Bartolomeo, Regina; Nasi, Milena; De Biasi, Sara; Missiroli, Sonia; Carnevale, Gianluca; Losi, Lorena; Tesei, Anna; Pinton, Paolo; Quaglino, Daniela; Cossarizza, Andrea

    2014-12-01

    Lon is a nuclear-encoded, mitochondrial protease that assists protein folding, degrades oxidized/damaged proteins, and participates in maintaining mtDNA levels. Here we show that Lon is up-regulated in several human cancers and that its silencing in RKO colon cancer cells causes profound alterations of mitochondrial proteome and function, and cell death. We silenced Lon in RKO cells by constitutive or inducible expression of Lon shRNA. Lon-silenced cells displayed altered levels of 39 mitochondrial proteins (26% related to stress response, 14.8% to ribosome assembly, 12.7% to oxidative phosphorylation, 8.5% to Krebs cycle, 6.3% to β-oxidation, and 14.7% to crista integrity, ketone body catabolism, and mtDNA maintenance), low levels of mtDNA transcripts, and reduced levels of oxidative phosphorylation complexes (with >90% reduction of complex I). Oxygen consumption rate decreased 7.5-fold in basal conditions, and ATP synthesis dropped from 0.25 ± 0.04 to 0.03 ± 0.001 nmol/mg proteins, in the presence of 2-deoxy-d-glucose. Hydrogen peroxide and mitochondrial superoxide anion levels increased by 3- and 1.3-fold, respectively. Mitochondria appeared fragmented, heterogeneous in size and shape, with dilated cristae, vacuoles, and electrondense inclusions. The triterpenoid 2-cyano-3,12-dioxooleana-1,9,-dien-28-oic acid, a Lon inhibitor, partially mimics Lon silencing. In summary, Lon is essential for maintaining mitochondrial shape and function, and for survival of RKO cells.

  5. Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation.

    PubMed

    Yun, Jiae; Malvankar, Nikhil S; Ueki, Toshiyuki; Lovley, Derek R

    2016-02-01

    Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface.

  6. Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development.

    PubMed

    Wang, Yong-Qiang; Yang, Yong; Fei, Zhangjun; Yuan, Hui; Fish, Tara; Thannhauser, Theodore W; Mazourek, Michael; Kochian, Leon V; Wang, Xiaowu; Li, Li

    2013-02-01

    Chromoplasts are unique plastids that accumulate massive amounts of carotenoids. To gain a general and comparative characterization of chromoplast proteins, this study performed proteomic analysis of chromoplasts from six carotenoid-rich crops: watermelon, tomato, carrot, orange cauliflower, red papaya, and red bell pepper. Stromal and membrane proteins of chromoplasts were separated by 1D gel electrophoresis and analysed using nLC-MS/MS. A total of 953-2262 proteins from chromoplasts of different crop species were identified. Approximately 60% of the identified proteins were predicted to be plastid localized. Functional classification using MapMan bins revealed large numbers of proteins involved in protein metabolism, transport, amino acid metabolism, lipid metabolism, and redox in chromoplasts from all six species. Seventeen core carotenoid metabolic enzymes were identified. Phytoene synthase, phytoene desaturase, ζ-carotene desaturase, 9-cis-epoxycarotenoid dioxygenase, and carotenoid cleavage dioxygenase 1 were found in almost all crops, suggesting relative abundance of them among the carotenoid pathway enzymes. Chromoplasts from different crops contained abundant amounts of ATP synthase and adenine nucleotide translocator, which indicates an important role of ATP production and transport in chromoplast development. Distinctive abundant proteins were observed in chromoplast from different crops, including capsanthin/capsorubin synthase and fibrillins in pepper, superoxide dismutase in watermelon, carrot, and cauliflower, and glutathione-S-transferease in papaya. The comparative analysis of chromoplast proteins among six crop species offers new insights into the general metabolism and function of chromoplasts as well as the uniqueness of chromoplasts in specific crop species. This work provides reference datasets for future experimental study of chromoplast biogenesis, development, and regulation in plants.

  7. Using models of the myocyte for functional interpretation of cardiac proteomic data

    PubMed Central

    Winslow, Raimond L; Cortassa, Sonia; Greenstein, Joseph L

    2005-01-01

    There has been significant progress towards the development of highly integrative computational models of the cardiac myocyte over the past decade. Models now incorporate descriptions of voltage-gated ionic currents and membrane transporters, mechanisms of calcium-induced calcium release and intracellular calcium cycling, mitochondrial ATP production and its coupling to energy-requiring membrane transport processes and mechanisms of force generation. There is an extensive literature documenting both the reconstructive and predictive abilities of these models and there is no question that an interplay between quantitative modelling and experimental investigation has become a central component of modern cardiovascular research. As data regarding the cardiovascular proteome in both health and disease emerge, integrative models of the myocyte are becoming useful tools for interpreting the functional significance of changes in protein expression and post-translational modifications (PTMs). Data of particular importance include information on: (a) changes of expressed protein level, (b) changes of protein PTMs, (c) protein localization, and (d) protein–protein interactions, as it is often possible to incorporate and interpret the functional significance of such findings using computational models. We provide two examples of how models may be used in this fashion. In the first example, we show how information on altered expression of the sarcoplasmic reticulum Ca2+-ATPase, when interpreted through the use of a computational model, has provided key insights into fundamental mechanisms regulating cardiac action potential duration. In the second example, we show how information on the effects of phosphorylation of L-type Ca2+ channels, when interpreted through the use of a model, provides insights on how this post-translational modification alters the properties of excitation–contraction coupling and risk for arrhythmia. PMID:15611013

  8. Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development

    PubMed Central

    Wang, Yong-Qiang; Yang, Yong; Li, Li

    2013-01-01

    Chromoplasts are unique plastids that accumulate massive amounts of carotenoids. To gain a general and comparative characterization of chromoplast proteins, this study performed proteomic analysis of chromoplasts from six carotenoid-rich crops: watermelon, tomato, carrot, orange cauliflower, red papaya, and red bell pepper. Stromal and membrane proteins of chromoplasts were separated by 1D gel electrophoresis and analysed using nLC-MS/MS. A total of 953–2262 proteins from chromoplasts of different crop species were identified. Approximately 60% of the identified proteins were predicted to be plastid localized. Functional classification using MapMan bins revealed large numbers of proteins involved in protein metabolism, transport, amino acid metabolism, lipid metabolism, and redox in chromoplasts from all six species. Seventeen core carotenoid metabolic enzymes were identified. Phytoene synthase, phytoene desaturase, ζ-carotene desaturase, 9-cis-epoxycarotenoid dioxygenase, and carotenoid cleavage dioxygenase 1 were found in almost all crops, suggesting relative abundance of them among the carotenoid pathway enzymes. Chromoplasts from different crops contained abundant amounts of ATP synthase and adenine nucleotide translocator, which indicates an important role of ATP production and transport in chromoplast development. Distinctive abundant proteins were observed in chromoplast from different crops, including capsanthin/capsorubin synthase and fibrillins in pepper, superoxide dismutase in watermelon, carrot, and cauliflower, and glutathione-S-transferease in papaya. The comparative analysis of chromoplast proteins among six crop species offers new insights into the general metabolism and function of chromoplasts as well as the uniqueness of chromoplasts in specific crop species. This work provides reference datasets for future experimental study of chromoplast biogenesis, development, and regulation in plants. PMID:23314817

  9. Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development.

    PubMed

    Wang, Yong-Qiang; Yang, Yong; Fei, Zhangjun; Yuan, Hui; Fish, Tara; Thannhauser, Theodore W; Mazourek, Michael; Kochian, Leon V; Wang, Xiaowu; Li, Li

    2013-02-01

    Chromoplasts are unique plastids that accumulate massive amounts of carotenoids. To gain a general and comparative characterization of chromoplast proteins, this study performed proteomic analysis of chromoplasts from six carotenoid-rich crops: watermelon, tomato, carrot, orange cauliflower, red papaya, and red bell pepper. Stromal and membrane proteins of chromoplasts were separated by 1D gel electrophoresis and analysed using nLC-MS/MS. A total of 953-2262 proteins from chromoplasts of different crop species were identified. Approximately 60% of the identified proteins were predicted to be plastid localized. Functional classification using MapMan bins revealed large numbers of proteins involved in protein metabolism, transport, amino acid metabolism, lipid metabolism, and redox in chromoplasts from all six species. Seventeen core carotenoid metabolic enzymes were identified. Phytoene synthase, phytoene desaturase, ζ-carotene desaturase, 9-cis-epoxycarotenoid dioxygenase, and carotenoid cleavage dioxygenase 1 were found in almost all crops, suggesting relative abundance of them among the carotenoid pathway enzymes. Chromoplasts from different crops contained abundant amounts of ATP synthase and adenine nucleotide translocator, which indicates an important role of ATP production and transport in chromoplast development. Distinctive abundant proteins were observed in chromoplast from different crops, including capsanthin/capsorubin synthase and fibrillins in pepper, superoxide dismutase in watermelon, carrot, and cauliflower, and glutathione-S-transferease in papaya. The comparative analysis of chromoplast proteins among six crop species offers new insights into the general metabolism and function of chromoplasts as well as the uniqueness of chromoplasts in specific crop species. This work provides reference datasets for future experimental study of chromoplast biogenesis, development, and regulation in plants. PMID:23314817

  10. Functional and Quality-of-Life Outcomes of Transoral Robotic Surgery for Carcinoma of Unknown Primary

    PubMed Central

    Durmus, Kasim; Patwa, Hafiz S.; Gokozan, Hamza N.; Kucur, Cuneyt; Teknos, Theodoros N.; Agrawal, Amit; Old, Matthew O.; Ozer, Enver

    2014-01-01

    Objectives/Hypothesis To determine speech, eating, aesthetics, social disruption, and overall quality-of-life outcomes over a year period in patients who underwent transoral robotic surgery as part of carcinoma of unknown primary diagnosis and treatment. Study Design Observational prospective study. Methods Twenty-two patients who underwent transoral robotic surgery for the management of carcinoma of unknown primary were included. Patients prospectively completed the Head and Neck Cancer Inventory during a preoperative visit, and at 3-week, 3-month, 6-month, and 12-month postoperative visits. Patients’ demographic, pathological, and follow-up information were also collected. Results The mean follow-up time was 19.8 months. There were overall declines in all quality of life scores during treatment period, which was followed by a continuous recovery. The scores immediately after transoral robotic surgery (3 weeks) were significantly higher than the scores after conclusion of adjuvant therapy (3 months) in multiple domains (P <.05) and the 6-month scores in speech (P = .02) and eating (P = .008) domains. All scores, except for eating (P = .01) returned to pre-treatment levels at 1 year. Patients with detected primaries displayed similar quality-of-life scores compared to patients with occult primaries. Human papillomavirus status and type of adjuvant treatment had no significant impact on quality of life. Conclusions Transoral robotic surgery is a promising, minimally invasive procedure for the surgical management of carcinoma of unknown primary. Patients maintain high functional and quality-of-life status at 1 year after surgery. PMID:24706455

  11. Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

    SciTech Connect

    Bowsher, James Giles, William; Yin, Fang-Fang; Yan, Susu; Roper, Justin

    2014-01-15

    Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard SPECT. Methods: Computer-aided design (CAD) studies were performed to assess the feasibility of maneuvering a robotic SPECT system about a patient in position for radiation therapy. In order to obtain fast, high-quality SPECT images, a 49-pinhole SPECT camera was designed which provides high sensitivity to photons emitted from an imaging region of interest. This multipinhole system was investigated by computer-simulation studies. Seventeen hot spots 10 and 7 mm in diameter were placed in the breast region of a supine female phantom. Hot spot activity concentration was six times that of background. For the 49-pinhole camera and a reference, more conventional, broad field-of-view (FOV) SPECT system, projection data were computer simulated for 4-min scans and SPECT images were reconstructed. Hot-spot localization was evaluated using a nonprewhitening forced-choice numerical observer. Results: The CAD simulation studies found that robots could maneuver SPECT cameras about patients in position for radiation therapy. In the imaging studies, most hot spots were apparent in the 49-pinhole images. Average localization errors for 10-mm- and 7-mm-diameter hot spots were 0.4 and 1.7 mm, respectively, for the 49-pinhole system, and 3.1 and 5.7 mm, respectively, for the reference broad-FOV system. Conclusions: A robot could maneuver a multipinhole SPECT system about a patient in position for radiation therapy. The system could provide onboard functional and molecular imaging with 4-min

  12. Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

    PubMed Central

    Bowsher, James; Yan, Susu; Roper, Justin; Giles, William; Yin, Fang-Fang

    2014-01-01

    Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard SPECT. Methods: Computer-aided design (CAD) studies were performed to assess the feasibility of maneuvering a robotic SPECT system about a patient in position for radiation therapy. In order to obtain fast, high-quality SPECT images, a 49-pinhole SPECT camera was designed which provides high sensitivity to photons emitted from an imaging region of interest. This multipinhole system was investigated by computer-simulation studies. Seventeen hot spots 10 and 7 mm in diameter were placed in the breast region of a supine female phantom. Hot spot activity concentration was six times that of background. For the 49-pinhole camera and a reference, more conventional, broad field-of-view (FOV) SPECT system, projection data were computer simulated for 4-min scans and SPECT images were reconstructed. Hot-spot localization was evaluated using a nonprewhitening forced-choice numerical observer. Results: The CAD simulation studies found that robots could maneuver SPECT cameras about patients in position for radiation therapy. In the imaging studies, most hot spots were apparent in the 49-pinhole images. Average localization errors for 10-mm- and 7-mm-diameter hot spots were 0.4 and 1.7 mm, respectively, for the 49-pinhole system, and 3.1 and 5.7 mm, respectively, for the reference broad-FOV system. Conclusions: A robot could maneuver a multipinhole SPECT system about a patient in position for radiation therapy. The system could provide onboard functional and molecular imaging with 4-min

  13. Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function.

    PubMed

    Ramakrishnan, Gayatri; Ochoa-Montaño, Bernardo; Raghavender, Upadhyayula S; Mudgal, Richa; Joshi, Adwait G; Chandra, Nagasuma R; Sowdhamini, Ramanathan; Blundell, Tom L; Srinivasan, Narayanaswamy

    2015-01-01

    The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better

  14. Proteomic Assessment of Poultry Spermatozoa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fully characterizing the protein composition of spermatozoa is the first step in utilizing proteomics to delineate the function of sperm proteins. To date, sperm proteome maps have been partially developed for the human, mouse, rat, bull and several invertebrates. Here we report the first proteomic...

  15. Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

    PubMed Central

    Schrimpf, Sabine P; Weiss, Manuel; Reiter, Lukas; Ahrens, Christian H; Jovanovic, Marko; Malmström, Johan; Brunner, Erich; Mohanty, Sonali; Lercher, Martin J; Hunziker, Peter E; Aebersold, Ruedi; von Mering, Christian; Hengartner, Michael O

    2009-01-01

    The nematode Caenorhabditis elegans is a popular model system in genetics, not least because a majority of human disease genes are conserved in C. elegans. To generate a comprehensive inventory of its expressed proteome, we performed extensive shotgun proteomics and identified more than half of all predicted C. elegans proteins. This allowed us to confirm and extend genome annotations, characterize the role of operons in C. elegans, and semiquantitatively infer abundance levels for thousands of proteins. Furthermore, for the first time to our knowledge, we were able to compare two animal proteomes (C. elegans and Drosophila melanogaster). We found that the abundances of orthologous proteins in metazoans correlate remarkably well, better than protein abundance versus transcript abundance within each organism or transcript abundances across organisms; this suggests that changes in transcript abundance may have been partially offset during evolution by opposing changes in protein abundance. PMID:19260763

  16. Extensive dataset of boar seminal plasma proteome displaying putative reproductive functions of identified proteins.

    PubMed

    Perez-Patiño, Cristina; Barranco, Isabel; Parrilla, Inmaculada; Martinez, Emilio A; Rodriguez-Martinez, Heriberto; Roca, Jordi

    2016-09-01

    A complete proteomic profile of seminal plasma (SP) remains challenging, particularly in porcine. The data reports on the analysis of boar SP-proteins by using a combination of SEC, 1-D SDS PAGE and NanoLC-ESI-MS/MS from 33 pooled SP-samples (11 boars, 3 ejaculates/boar). A complete dataset of the 536 SP-proteins identified and validated with confidence ≥95% (Unused Score >1.3) and a false discovery rate (FDR) ≤1%, is provided. In addition, the relative abundance of 432 of them is also shown. Gene ontology annotation of the complete SP-proteome complemented by an extensive description of the putative reproductive role of SP-proteins, providing a valuable source for a better understanding of SP role in the reproductive success. This data article refers to the article entitled "Characterization of the porcine seminal plasma proteome comparing ejaculate portions" (Perez-Patiño et al., 2016) [1]. PMID:27583342

  17. Multifactorial comparative proteomic study of cytochrome P450 2E1 function in chronic alcohol administration.

    PubMed

    Wang, Yuan; Kou, Yan; Wang, Xiaodong; Cederbaum, Arthur; Wang, Rong

    2014-01-01

    With the use of iTRAQ technique, a multifactorial comparative proteomic study can be performed. In this study, to obtain an overview of ethanol, CYP2E1 and gender effects on liver injury and gain more insight into the underlying molecular mechanism, mouse liver proteomes were quantitatively analyzed using iTRAQ under eight conditions including mice of different genders, wild type versus CYP2E1 knockout, and normal versus alcohol diet. A series of statistical and bioinformatic analyses were explored to simplify and clarify multifactorial comparative proteomic data. First, with the Principle Component analysis, six proteins, CYP2E1, FAM25, CA3, BHMT, HIBADH and ECHS1, involved in oxidation reduction, energy and lipid metabolism and amino acid metabolism, were identified as the most differentially expressed gene products across all of the experimental conditions of our chronic alcoholism model. Second, hierarchical clustering analysis showed CYP2E1 knockout played a primary role in the overall differential protein expression compared with ethanol and gender factors. Furthermore, pair-wise multiple comparisons have revealed that the only significant expression difference lied in wild-type and CYP2E1 knockout mice both treated with ethanol. Third, K-mean clustering analysis indicated that the CYP2E1 knockout had the reverse effect on ethanol induced oxidative stress and lipid oxidation. More importantly, IPA analysis of proteomic data inferred that the gene expressions of two upstream regulators, NRF2 and PPARα, regulated by chronic alcohol feeding and CYP2E1 knockout, are involved in ethanol induced oxidative stress and lipid oxidation. The present study provides an effectively comprehensive data analysis strategy to compare multiple biological factors, contributing to biochemical effects of alcohol on the liver. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with data set identifier of PXD000635.

  18. Functional nanoparticle-based proteomic strategies for characterization of pathogenic bacteria.

    PubMed

    Chen, Wei-Jen; Tsai, Pei-Jane; Chen, Yu-Chie

    2008-12-15

    Although matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) can be employed to rapidly characterize pathogenic bacteria, bacterial cultures are generally required to obtain sufficient quantities of the bacterial cells prior to MALDI MS analysis. If this time-consuming step could be eliminated, the length of time required for identification of bacterial strains would be greatly reduced. In this paper, we propose an effective means of rapidly identifying bacteria--one that does not require bacterial culturing--using functional nanoparticle-based proteomic strategies that are characterized by extremely short analysis time. In this approach, we used titania-coated magnetic iron oxide nanoparticles (Fe(3)O(4)@TiO(2) NPs) as affinity probes to concentrate the target bacteria. The magnetic properties of the Fe(3)O(4)@TiO(2) NPs allow the conjugated target species to be rapidly isolated from the sample solutions under a magnetic field. Taking advantage of the absorption of the magnetic Fe(3)O(4) NPs in the microwave region of the electromagnetic spectrum, we performed the tryptic digestion of the captured bacteria under microwave heating for only 1-1.5 min prior to MALDI MS analysis. We identified the resulting biomarker ions by combining their MS/MS analysis results with protein database searches. Using this technique, we identified potential biomarker ions representing five gram-negative bacteria: Escherichia coli O157:H7, uropathogenic E. coli, Shigella sonnei, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Finally, we demonstrated the practical feasibility of using this approach to rapidly characterize bacteria in clinical samples. PMID:19007241

  19. Effects of Lon protease down-regulation on the mitochondrial function and proteome.

    PubMed

    Hamon, Marie-Paule; Bayot, Aurélien; Gareil, Monique; Chavatte, Laurent; Lombès, Anne; Friguet, Bertrand; Bulteau, Anne-Laure

    2014-10-01

    The Lon protease is an ATP-dependent protease of the mitochondrial matrix that contributes to the degradation of abnormal and oxidized proteins in this compartment. It is also involved in the stability and regulation of the mitochondrial genome. The effects of a depletion of this protease on the mitochondrial function and the identification of oxidized target proteins of Lon have been performed using as cellular model HeLa cells in which Lon level expression can be down-regulated. The expression level of proteins playing a role in the stress response was first determined. The amount of ClpP, another protease in charge of protein degradation of the mitochondrial matrix, and the amount of several chaperones have been evaluated. The expression level of respiratory chain subunits was also measured with or without Lon depletion. The mitochondrial compartment morphology was monitored in different stress conditions, and measured using a parameter devoted to the evaluation of the mitochondrial dynamics. None of these investigations showed a significant phenotype resulting from Lon down-regulation A possible impact of Lon depletion on oxidized mitochondrial proteins level was then sought. 1D gel electrophoresis after the derivatization of protein carbonyl groups with 2,4-dinitrophenyl hydrazine (DNPH) revealed an increase in carbonylated proteins more important in mitochondrial extracts than in total cellular extracts. 2D difference gel electrophoresis (DIGE) experiments provide results consistent with these observations with some enlightenments. Performed with fluorescent dyes labelling either proteins or their carbonyl groups, these experiments indicated proteome modifications in cells with Lon down-regulation both at the level of protein expression and at the level of protein oxidation. These variations are noted in proteins acting in different cellular activities, i.e. metabolism, protein quality control and cytoskeleton organization.

  20. Functional nanoparticle-based proteomic strategies for characterization of pathogenic bacteria.

    PubMed

    Chen, Wei-Jen; Tsai, Pei-Jane; Chen, Yu-Chie

    2008-12-15

    Although matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) can be employed to rapidly characterize pathogenic bacteria, bacterial cultures are generally required to obtain sufficient quantities of the bacterial cells prior to MALDI MS analysis. If this time-consuming step could be eliminated, the length of time required for identification of bacterial strains would be greatly reduced. In this paper, we propose an effective means of rapidly identifying bacteria--one that does not require bacterial culturing--using functional nanoparticle-based proteomic strategies that are characterized by extremely short analysis time. In this approach, we used titania-coated magnetic iron oxide nanoparticles (Fe(3)O(4)@TiO(2) NPs) as affinity probes to concentrate the target bacteria. The magnetic properties of the Fe(3)O(4)@TiO(2) NPs allow the conjugated target species to be rapidly isolated from the sample solutions under a magnetic field. Taking advantage of the absorption of the magnetic Fe(3)O(4) NPs in the microwave region of the electromagnetic spectrum, we performed the tryptic digestion of the captured bacteria under microwave heating for only 1-1.5 min prior to MALDI MS analysis. We identified the resulting biomarker ions by combining their MS/MS analysis results with protein database searches. Using this technique, we identified potential biomarker ions representing five gram-negative bacteria: Escherichia coli O157:H7, uropathogenic E. coli, Shigella sonnei, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Finally, we demonstrated the practical feasibility of using this approach to rapidly characterize bacteria in clinical samples.

  1. Central Functions of the Lumenal and Peripheral Thylakoid Proteome of Arabidopsis Determined by Experimentation and Genome-Wide Prediction

    PubMed Central

    Peltier, Jean-Benoît; Emanuelsson, Olof; Kalume, Dário E.; Ytterberg, Jimmy; Friso, Giulia; Rudella, Andrea; Liberles, David A.; Söderberg, Linda; Roepstorff, Peter; von Heijne, Gunnar; van Wijk, Klaas J.

    2002-01-01

    Experimental proteome analysis was combined with a genome-wide prediction screen to characterize the protein content of the thylakoid lumen of Arabidopsis chloroplasts. Soluble thylakoid proteins were separated by two-dimensional electrophoresis and identified by mass spectrometry. The identities of 81 proteins were established, and N termini were sequenced to validate localization prediction. Gene annotation of the identified proteins was corrected by experimental data, and an interesting case of alternative splicing was discovered. Expression of a surprising number of paralogs was detected. Expression of five isomerases of different classes suggests strong (un)folding activity in the thylakoid lumen. These isomerases possibly are connected to a network of peripheral and lumenal proteins involved in antioxidative response, including peroxiredoxins, m-type thioredoxins, and a lumenal ascorbate peroxidase. Characteristics of the experimentally identified lumenal proteins and their orthologs were used for a genome-wide prediction of the lumenal proteome. Lumenal proteins with a typical twin-arginine translocation motif were predicted with good accuracy and sensitivity and included additional isomerases and proteases. Thus, prime functions of the lumenal proteome include assistance in the folding and proteolysis of thylakoid proteins as well as protection against oxidative stress. Many of the predicted lumenal proteins must be present at concentrations at least 10,000-fold lower than proteins of the photosynthetic apparatus. PMID:11826309

  2. Identification of the proteomic variations of invasive relative to non-invasive non-functional pituitary adenomas.

    PubMed

    Zhan, Xianquan; Desiderio, Dominic M; Wang, Xiaowei; Zhan, Xiaohan; Guo, Tianyao; Li, Maoyu; Peng, Fang; Chen, Xiaoyu; Yang, Haiyan; Zhang, Pengfei; Li, Xuejun; Chen, Zhuchu

    2014-08-01

    The incomplete surgery section of invasive non-functional pituitary adenomas (NFPAs) carries the increased risks of complications and requires adjuvant radiotherapy and medications. It is necessary to clarify the molecular mechanisms and markers of invasiveness to guide the management of NFPA patients. The study aimed to proteomic variations of invasive and non-invasive NFPAs and sought the protein markers for invasive NFPAs. Invasive (n = 4) and non-invasive (n = 4) NFPA tissues were analyzed (n = 3-5/each tissue) with 2DE and PDQuest software. Twenty-four high-resolution 2DE gels were quantitatively compared to determine differentially expressed proteins (DEPs) between invasive and non-invasive NFPAs. Approximately 1200 protein spots were detected in each 2DE map, and 103 differential spots (64 upregulated and 39 downregulated) were identified. Among those 103 differential spots, 57 DEPs (30 upregulated and 27 downregulated) were characterized with peptide mass fingerprint and MS/MS. Gene-ontology (GO) and ingenuity pathway analyses of those DEPs revealed pathway networks including mitochondrial dysfunction, oxidative stress, mitogen-activated protein kinase signaling abnormality, TR/RXR activation, proteolysis abnormality, ketogenesis and ketolysis, cyclin-dependent kinase C signaling abnormality, and amyloid processing that were significantly associated with invasive characteristics of invasive NFPA. Those data demonstrate that proteomic variations exist between invasive and non-invasive NFPAs. 2DE-based comparative proteomics is an effective approach to identify proteomic variations and pathway network variations. Those findings will serve as a basis to understand the molecular mechanisms of invasive NFPAs and to discover protein markers to effectively manage patients with invasive NFPAs. PMID:24729304

  3. Proteomics and transcriptomics analyses of Arabidopsis floral buds uncover important functions of ARABIDOPSIS SKP1-LIKE1

    DOE PAGES

    Lu, Dihong; Ni, Weimin; Stanley, Bruce A.; Ma, Hong

    2016-03-03

    The ARABIDOPSIS SKP1-LIKE1 (ASK1) protein functions as a subunit of SKP1-CUL1-F-box (SCF) E3 ubiquitin ligases. Previous genetic studies showed that ASK1 plays important roles in Arabidopsis flower development and male meiosis. However, the molecular impact of ASK1-containing SCF E3 ubiquitin ligases (ASK1-E3s) on the floral proteome and transcriptome is unknown. Here we identified proteins that are potentially regulated by ASK1-E3s by comparing floral bud proteomes of wild-type and the ask1 mutant plants. More than 200 proteins were detected in the ask1 mutant but not in wild-type and >300 were detected at higher levels in the ask1 mutant than in wild-type,more » but their RNA levels were not significantly different between wild-type and ask1 floral buds as shown by transcriptomics analysis, suggesting that they are likely regulated at the protein level by ASK1-E3s. Integrated analyses of floral proteomics and transcriptomics of ask1 and wild-type uncovered several potential aspects of ASK1-E3 functions, including regulation of transcription regulators, kinases, peptidases, and ribosomal proteins, with implications on possible mechanisms of ASK1-E3 functions in floral development. In conclusion, our results suggested that ASK1-E3s play important roles in Arabidopsis protein degradation during flower development. This study opens up new possibilities for further functional studies of these candidate E3 substrates.« less

  4. Development and application of automated systems for plasmid-based functional proteomics to improve syntheitc biology of engineered industrial microbes for high level expression of proteases for biofertilizer production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In addition to microarray technology, which provides a robust method to study protein function in a rapid, economical, and proteome-wide fashion, plasmid-based functional proteomics is an important technology for rapidly obtaining large quantities of protein and determining protein function across a...

  5. Hypoxia and reoxygenation of primary human hepatocytes induce proteome changes of glucose metabolism, oxidative protection and peroxisomal function.

    PubMed

    Strey, Christoph W; Gestrich, Johannes; Beckhaus, Tobias; Marquez-Pinilla, Rosa Maria; Oppermann, Elsie; Mönch, Christian; Lambris, John D; Karas, Michael; Bechstein, Wolf O

    2010-10-01

    Protective hepatocellular responses to a hypoxic challenge are crucial to preserve liver function. The knowledge of affected metabolic functions could help assess and enhance hepatic ischemic tolerance. Here we studied adaptive mechanisms in human hepatocytes after hypoxia and reoxygenation using a proteomic approach. Proteins from primary hepatocytes were extracted after 6 h of hypoxia and 24 h of reoxygenation. The proteome was analyzed by 2D-electrophoresis. Densitometry and mass spectrometry (MALDI-TOF-MS) were used for protein identification. Two hundred and sixty-two spots were differentially analyzed and 33 spots displayed significant differences between hypoxic and normoxic cells. Seventeen proteins were identified by mass spectrometry. After hypoxia and reoxygenation the UTP-glucose-1-phosphate uridyltransferase, phosphoglycerate kinase1, fructose-1,6-bisphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase, fructose-1,6-bisphosphatase, thiosulfat-sulfurtransferase, thioredoxin peroxidase, peroxiredoxin III, and annexin A2 proteins were down-regulated. An increased expression was found for carbamoyl phosphate synthetase I, heat shock 70 kDa protein5, phosphoenolpyruvate carboxy-kinase, catalase isoform2, peroxiredoxin II, glutathione S-transferase, hydroxyacid oxidase1, and F1-ATP synthase, alpha subunit1. Hepatocellular adaptation to hypoxia and reoxygenation involve glucose metabolism, peroxisomal functions, and oxidative stress protection. The identified proteins can serve as possible diagnostic targets to monitor hepatic hypoxic tolerance e.g. in the context of liver surgery and transplantation.

  6. Effects of robot training on bowel function in patients with spinal cord injury.

    PubMed

    Huang, Qiuchen; Yu, Lili; Gu, Rui; Zhou, Yue; Hu, Chunying

    2015-05-01

    [Purpose] The purpose of this study was to compare the effects of body weight-supported treadmill training (BWSTT) and robot-assisted rehabilitation (RAT) on bowel function in patients with spinal cord injury with respect to defecation time and defecation drug dose (enema). [Subjects] Twenty-four patients with spinal cord injury participated in the study. All subjects had an incomplete injury ranging from level T8 to L2. [Methods] The subjects were randomly divided into BWSTT and RAT groups. Walking training was provided to both groups for 20 minutes, four times a week, for one month. The defecation time and enema dose were measured before and after the experiment. [Results] The RAT group showed significant shortening of defecation time and decrease of enema dose. [Conclusion] The results demonstrated that significantly better improvement in bowel function can be achieved with RAT. PMID:26157223

  7. ProGeRF: Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function

    PubMed Central

    Moraes, Walas Jhony Lopes; Rodrigues, Thiago de Souza; Bartholomeu, Daniella Castanheira

    2015-01-01

    Repetitive element sequences are adjacent, repeating patterns, also called motifs, and can be of different lengths; repetitions can involve their exact or approximate copies. They have been widely used as molecular markers in population biology. Given the sizes of sequenced genomes, various bioinformatics tools have been developed for the extraction of repetitive elements from DNA sequences. However, currently available tools do not provide options for identifying repetitive elements in the genome or proteome, displaying a user-friendly web interface, and performing-exhaustive searches. ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences. It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results. ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool. It was developed using the hash table approach to extract perfect and imperfect repetitive regions in a (multi)FASTA file, while allowing a linear time complexity. PMID:25811026

  8. Proteomic and functional characterization of the outer membrane vesicles from the gastric pathogen Helicobacter pylori.

    PubMed

    Mullaney, Erica; Brown, Paul A; Smith, Sinead M; Botting, Catherine H; Yamaoka, Yoshio Y; Terres, Ana M; Kelleher, Dermot P; Windle, Henry J

    2009-07-01

    The gastric pathogen Helicobacter pylori causes a spectrum of gastro-duodenal diseases, which may be mediated in part by the outer membrane vesicles (OMVs) constitutively shed by the pathogen. We aimed to determine the proteome of H. pylori OMV to help evaluate the mechanisms whereby these structures confer their known immuno-modulatory and cytotoxic activities to host cells, as such disease-associated activities are also conferred by the bacterium from which the vesicles are derived. We also evaluated the effect of the OMV on gastric/colonic epithelial cells, duodenal explants and neutrophils. A proteomic analysis of the OMV proteins separated by SDS-PAGE from two strains of H. pylori (J99 and NCTC 11637) was undertaken and 162 OMV-associated proteins were identified in J99 and 91 in NCTC 11637 by LC-MS/MS. The vesicles are rich in membrane proteins, porins, adhesins and several molecules known to modulate chemokine secretion, cell proliferation and other host cellular processes. Further, the OMVs are also vehicles for the carriage of the cytotoxin-associated gene A cytotoxin in addition to the previously documented toxin, vacuolating cytotoxin. Taken together, it is evident from the proteome of H. pylori OMV that these structures are equipped with the molecules required to interact with host cells in a manner not dissimilar from the intact pathogen.

  9. ProGeRF: proteome and genome repeat finder utilizing a fast parallel hash function.

    PubMed

    Lopes, Robson da Silva; Moraes, Walas Jhony Lopes; Rodrigues, Thiago de Souza; Bartholomeu, Daniella Castanheira

    2015-01-01

    Repetitive element sequences are adjacent, repeating patterns, also called motifs, and can be of different lengths; repetitions can involve their exact or approximate copies. They have been widely used as molecular markers in population biology. Given the sizes of sequenced genomes, various bioinformatics tools have been developed for the extraction of repetitive elements from DNA sequences. However, currently available tools do not provide options for identifying repetitive elements in the genome or proteome, displaying a user-friendly web interface, and performing-exhaustive searches. ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences. It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results. ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool. It was developed using the hash table approach to extract perfect and imperfect repetitive regions in a (multi)FASTA file, while allowing a linear time complexity. PMID:25811026

  10. ProGeRF: proteome and genome repeat finder utilizing a fast parallel hash function.

    PubMed

    Lopes, Robson da Silva; Moraes, Walas Jhony Lopes; Rodrigues, Thiago de Souza; Bartholomeu, Daniella Castanheira

    2015-01-01

    Repetitive element sequences are adjacent, repeating patterns, also called motifs, and can be of different lengths; repetitions can involve their exact or approximate copies. They have been widely used as molecular markers in population biology. Given the sizes of sequenced genomes, various bioinformatics tools have been developed for the extraction of repetitive elements from DNA sequences. However, currently available tools do not provide options for identifying repetitive elements in the genome or proteome, displaying a user-friendly web interface, and performing-exhaustive searches. ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences. It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results. ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool. It was developed using the hash table approach to extract perfect and imperfect repetitive regions in a (multi)FASTA file, while allowing a linear time complexity.

  11. Cold stratification and exogenous nitrates entail similar functional proteome adjustments during Arabidopsis seed dormancy release.

    PubMed

    Arc, Erwann; Chibani, Kamel; Grappin, Philippe; Jullien, Marc; Godin, Béatrice; Cueff, Gwendal; Valot, Benoit; Balliau, Thierry; Job, Dominique; Rajjou, Loïc

    2012-11-01

    Despite having very similar initial pools of stored mRNAs and proteins in the dry state, mature Arabidopsis seeds can either proceed toward radicle protrusion or stay in a dormant state upon imbibition. Dormancy breaking, a prerequisite to germination completion, can be induced by different treatments though the underlying mechanisms remain elusive. Thus, we investigated the consequence of such treatments on the seed proteome. Two unrelated dormancy-releasing treatments were applied to dormant seeds, namely, cold stratification and exogenous nitrates, in combination with differential proteomic tools to highlight the specificities of the imbibed dormant state. The results reveal that both treatments lead to highly similar proteome adjustments. In the imbibed dormant state, enzymes involved in reserve mobilization are less accumulated and it appears that several energetically costly processes associated to seed germination and preparation for subsequent seedling establishment are repressed. Our data suggest that dormancy maintenance is associated to an abscisic-acid-dependent recapitulation of the late maturation program resulting in a higher potential to cope with environmental stresses. The comparison of the present results with previously published -omic data sets reinforces and extends the assumption that post-transcriptional, translational, and post-translational regulations are determinant for seed germination.

  12. Soft robotic arm inspired by the octopus: I. From biological functions to artificial requirements.

    PubMed

    Margheri, L; Laschi, C; Mazzolai, B

    2012-06-01

    Octopuses are molluscs that belong to the group Cephalopoda. They lack joints and rigid links, and as a result, their arms possess virtually limitless freedom of movement. These flexible appendages exhibit peculiar biomechanical features such as stiffness control, compliance, and high flexibility and dexterity. Studying the capabilities of the octopus arm is a complex task that presents a challenge for both biologists and roboticists, the latter of whom draw inspiration from the octopus in designing novel technologies within soft robotics. With this idea in mind, in this study, we used new, purposively developed methods of analysing the octopus arm in vivo to create new biologically inspired design concepts. Our measurements showed that the octopus arm can elongate by 70% in tandem with a 23% diameter reduction and exhibits an average pulling force of 40 N. The arm also exhibited a 20% mean shortening at a rate of 17.1 mm s(-1) and a longitudinal stiffening rate as high as 2 N (mm s)(-1). Using histology and ultrasounds, we investigated the functional morphology of the internal tissues, including the sinusoidal arrangement of the nerve cord and the local insertion points of the longitudinal and transverse muscle fibres. The resulting information was used to create novel design principles and specifications that can in turn be used in developing a new soft robotic arm.

  13. Sensorless Interaction Force Control Based on B-Spline Function for Human-Robot Systems

    NASA Astrophysics Data System (ADS)

    Mitsantisuk, Chowarit; Katsura, Seiichiro; Ohishi, Kiyoshi

    In this paper, to provide precise force sensation of human operator, a twin direct-drive motor system with wire rope mechanism has been developed. The human-robot interaction force and the wire rope tension are independently controlled in acceleration dimension by realizing the dual disturbance observer based on modal space design. In the common mode, it is utilized for control of vibration suppression and wire rope tension. In the differential mode, the purity of human external force with compensation of friction force is obtained. This mode is useful for control of the interaction force of human. Furthermore, the human-robot system that has the ability of support of human interaction force is also proposed. The interaction force generation based on B-spline function is applied to automatically adjust the smooth force command corresponding to the adaptive parameters.
    To analyze the human movement stroke, the multi-sensor scheme is applied to fuse both two motor encoders and acceleration sensor signal by using Kalman filter. From the experimental results, the ability to design different level of assistive force makes it well suited to customized training programs due to time and human movement constraints.

  14. Proteomic Analysis of Excretory-Secretory Products of Mesocestoides corti Metacestodes Reveals Potential Suppressors of Dendritic Cell Functions

    PubMed Central

    Vendelova, Emilia; Camargo de Lima, Jeferson; Lorenzatto, Karina Rodrigues; Monteiro, Karina Mariante; Mueller, Thomas; Veepaschit, Jyotishman; Grimm, Clemens; Brehm, Klaus; Hrčková, Gabriela; Lutz, Manfred B.; Ferreira, Henrique B.

    2016-01-01

    Accumulating evidences have assigned a central role to parasite-derived proteins in immunomodulation. Here, we report on the proteomic identification and characterization of immunomodulatory excretory-secretory (ES) products from the metacestode larva (tetrathyridium) of the tapeworm Mesocestoides corti (syn. M. vogae). We demonstrate that ES products but not larval homogenates inhibit the stimuli-driven release of the pro-inflammatory, Th1-inducing cytokine IL-12p70 by murine bone marrow-derived dendritic cells (BMDCs). Within the ES fraction, we biochemically narrowed down the immunosuppressive activity to glycoproteins since active components were lipid-free, but sensitive to heat- and carbohydrate-treatment. Finally, using bioassay-guided chromatographic analyses assisted by comparative proteomics of active and inactive fractions of the ES products, we defined a comprehensive list of candidate proteins released by M. corti tetrathyridia as potential suppressors of DC functions. Our study provides a comprehensive library of somatic and ES products and highlight some candidate parasite factors that might drive the subversion of DC functions to facilitate the persistence of M. corti tetrathyridia in their hosts. PMID:27736880

  15. Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions.

    PubMed

    Pan, Cuiping; Kumar, Chanchal; Bohl, Sebastian; Klingmueller, Ursula; Mann, Matthias

    2009-03-01

    Biological experiments are most often performed with immortalized cell lines because they are readily available and can be expanded without limitation. However, cell lines may differ from the in vivo situation in important aspects. Here we introduce a straightforward methodology to compare cell lines to their cognate primary cells and to derive a comparative functional phenotype. We used SILAC (stable isotope labeling by amino acids in cell culture) for quantitative, mass spectrometry-based comparison of the hepatoma cell line Hepa1-6 with primary hepatocytes. The resulting quantitative proteome of 4,063 proteins had an asymmetric distribution, with many proteins down-regulated in the cell line. Bioinformatic analysis of the quantitative proteomics phenotypes revealed that Hepa1-6 cells were deficient in mitochondria, reflecting re-arrangement of metabolic pathways, drastically up-regulate cell cycle-associated functions and largely shut down drug metabolizing enzymes characteristic for the liver. This quantitative knowledge of changes provides an important basis to adapt cell lines to more closely resemble physiological conditions.

  16. Functional proteomics reveals hepatotoxicity and the molecular mechanisms of different forms of chromium delivered by skin administration.

    PubMed

    Pan, Tai-Long; Wang, Pei-Wen; Chen, Chih-Chieh; Fang, Jia-You; Sintupisut, Nardnisa

    2012-02-01

    Chromium compounds are known to be associated with cytotoxicity and carcinogenicity when applied via the skin. However, there is no perspective research to elucidate the causations between chromium exposure and hepatotoxicity. In the present study, the impact of hexavalent/trivalent chromium on the liver and the underlying pathogenic processes were revealed in the female nude mice model. The liver damage under different treatments was evaluated by histologic examination. Functional proteome tools combined with a network analysis revealed statistically significant candidate protein networks predicted to be changed in the presence of chromium compounds. RNA interference-mediated silencing and immunohistochemistry were used to confirm whether the candidate protein was capable of resulting in hepatotoxicity elicited by chromium. Potassium chromate as the Cr(VI) compound generated greater oxidative stress, apoptosis and hepatotoxicity compared to chromium nitrate [Cr(III)]-treated samples. The most meaningful changes were observed amongst proteins involved in carbohydrate metabolism, endoplasmic reticulum (ER) stress, calcium homeostasis and apoptosis. Furthermore, abrogation of transitional ER ATPase (VCP) led to significant inhibition in hepatic cell viability under Cr(VI) administration, and the expression profiles of cytokeratin were closely correlated with apoptotic degrees of liver tissue. Collectively, our findings suggest that Cr(VI) might induce the accumulation of misfolded proteins and adverse effects leading to cell apoptosis and liver injury. These signature networks represent an approach to discover novel relationships in complex data, and functional proteomics of liver may provide solid evidence of chromium-caused hepatic damage via the skin.

  17. Recovery of hand function with robot-assisted therapy in acute stroke patients: a randomized-controlled trial.

    PubMed

    Sale, Patrizio; Mazzoleni, Stefano; Lombardi, Valentina; Galafate, Daniele; Massimiani, Maria P; Posteraro, Federico; Damiani, Carlo; Franceschini, Marco

    2014-09-01

    In the last few years, not many studies on the use of robot-assisted therapy to recover hand function in acute stroke patients have been carried out. This randomized-controlled observer trial is aimed at evaluating the effects of intensive robot-assisted hand therapy compared with intensive occupational therapy in the early recovery phases after stroke with a 3-month follow-up. Twenty acute stroke patients at their first-ever stroke were enrolled and randomized into two groups. The experimental treatment was performed using the Amadeo Robotic System. Control treatment, instead, was carried out using occupational therapy executed by a trained physiotherapist. All participants received 20 sessions of treatment for 4 consecutive weeks (5 days/week). The following clinical scales, Fugl-Meyer Scale (FM), Medical Research Council Scale for Muscle Strength (hand flexor and extensor muscles) (MRC), Motricity Index (MI) and modified Ashworth Scale for wrist and hand muscles (MAS), were performed at baseline (T0), after 20 sessions (end of treatment) (T1) and at the 3-month follow-up (T2). The Barthel Index was assessed only at T0 and T1. Evidence of a significant improvement was shown by the Friedman test for the FM [experimental group (EG): P=0.0039, control group (CG): P<0.0001], Box and Block Test (EG: P=0.0185, CG: P=0.0086), MI (EG: P<0.0001, CG: P=0.0303) and MRC (EG: P<0.0001, CG: P=0.001) scales. These results provide further support to the generalized therapeutic impact of intensive robot-assisted treatment on hand recovery functions in individuals with acute stroke. The robotic rehabilitation treatment may contribute toward the recovery of hand motor function in acute stroke patients. The positive results obtained through the safe and reliable robotic rehabilitation treatment reinforce the recommendation to extend it to a larger clinical practice.

  18. Implement of the Owner Distinction Function for Healing-Type Pet Robots

    NASA Astrophysics Data System (ADS)

    Nambo, Hidetaka; Kimura, Haruhiko; Hirose, Sadaki

    In recent years, a robotics technology is extremely progressive, and robots are widely applied in many fields. One of the most typical robots is a pet robot. The pet robot is based on an animal pet, such as a dog or a cat. Also, it is known that an animal pet has a healing effect. Therefore, the study to apply pet robots to Animal Assisted Therapy instead of an animal pet has begun to be investigated. We, also, have investigated a method of an owner distinction for pet robot, to emphasize a healing effect of pet robots. In this paper, taking account of implementation into pet robots, a real-time owner distinction method is proposed. In the concrete, the method provides a real-time matching algorithm and an oblivion mechanism. The real-time matching means that a matching and a data acquisition are processed simultaneously. The oblivion mechanism is deleting features of owners in the database of the pet robots. Additionally, the mechanism enables to reduce matching costs or size of database and it enables to follow a change of owners. Furthermore, effectivity and a practicality of the method are evaluated by experiments.

  19. Functional genomics and proteomics in the clinical neurosciences: data mining and bioinformatics.

    PubMed

    Phan, John H; Quo, Chang-Feng; Wang, May D

    2006-01-01

    The goal of this chapter is to introduce some of the available computational methods for expression analysis. Genomic and proteomic experimental techniques are briefly discussed to help the reader understand these methods and results better in context with the biological significance. Furthermore, a case study is presented that will illustrate the use of these analytical methods to extract significant biomarkers from high-throughput microarray data. Genomic and proteomic data analysis is essential for understanding the underlying factors that are involved in human disease. Currently, such experimental data are generally obtained by high-throughput microarray or mass spectrometry technologies among others. The sheer amount of raw data obtained using these methods warrants specialized computational methods for data analysis. Biomarker discovery for neurological diagnosis and prognosis is one such example. By extracting significant genomic and proteomic biomarkers in controlled experiments, we come closer to understanding how biological mechanisms contribute to neural degenerative diseases such as Alzheimers' and how drug treatments interact with the nervous system. In the biomarker discovery process, there are several computational methods that must be carefully considered to accurately analyze genomic or proteomic data. These methods include quality control, clustering, classification, feature ranking, and validation. Data quality control and normalization methods reduce technical variability and ensure that discovered biomarkers are statistically significant. Preprocessing steps must be carefully selected since they may adversely affect the results of the following expression analysis steps, which generally fall into two categories: unsupervised and supervised. Unsupervised or clustering methods can be used to group similar genomic or proteomic profiles and therefore can elucidate relationships within sample groups. These methods can also assign biomarkers to sub

  20. Comparative proteomic study and functional analysis of translationally controlled tumor protein in rice roots under Hg2+ stress.

    PubMed

    Wang, Feijuan; Shang, Yongshen; Yang, Ling; Zhu, Cheng

    2012-01-01

    So far, very little is known about mercury stress-induced intercellular metabolic changes in rice roots at the proteome level. To investigate the response of rice roots to mercury stress, changes in protein expression in rice roots were analyzed using a comparative proteomics approach. Six-leaf stage rice seedlings were treated with 50 micromol/L HgCl2 for 3 hr; 29 protein spots showed a significant changes in abundance under stress when compared with the Hg2+ -tolerant rice mutant and wild type (Zhonghua 11). Furthermore, all these protein spots were identified by mass spectrometry to match 27 diverse protein species. The identified proteins were involved in several processes, including stress response, redox homeostasis, signal transduction, regulation and metabolism; some were found to be cellular structure proteins and a few were unknown. Among the up-regulated proteins, OsTCTP (translationally controlled tumor protein) was chosen to perform hetereologous expression in yeast which was presumed to participate in the Hg2+ tolerance of rice, providing evidence for its role in alleviating Hg2+ damage. Among the many tests, we found that OsTCTP-overexpressed yeast strains were more resistant to Hg2+ than wild-type yeast. Thus, we propose that OsTCTP contributes to Hg2+ resistance. Here we present, for the first time, the functional characterization of OsTCTP in connection with Hg2+ stress in plants.

  1. Application of a proteomic approach to identify proteins associated with primary graft non-function after liver transplantation.

    PubMed

    Kornasiewicz, Oskar; Bojarczuk, Kamil; Bugajski, Marek; Golab, Jakub; Krawczyk, Marek

    2012-10-01

    Primary graft non-function (PNF) is a rare, life-threatening complication of liver transplantation. Increasing use of extended criteria donor pools and high-risk recipients seem to influence the incidence of PNF. Primary failure is associated with high patient morbidity and inferior graft survival. The only available treatment for PNF is emergency hepatic retransplantation, which is also correlated with significant morbidity and mortality. Therefore, researchers are working to identify risk factors of diagnostic value to prevent PNF. The current study attempted to explore liver proteomic patterns in patients with PNF. Using two-dimensional gel electrophoresis and liquid chromatography-mass spectrometry (LC-MS), we compared liver protein homogenates from 3 patients with PNF to those obtained from 6 healthy liver samples to identify potential new biomarkers of PNF. Our comparisons revealed 21 proteins with differential expression (13 upregulated and 8 downregulated). Most of these proteins are involved in energy metabolism, lipid metabolism, peptide cleavage, cell differentiation, and apoptosis. Although none of these proteins appeared more than once in separate analyses, this preliminary study shows that two-dimensional gel electrophoresis and LC-MS may allow identification of characteristic proteins to be used as biomarkers of a life-threatening complication of liver transplantation. Larger-scale analyses could improve patient care by finding suitable prognostic and therapeutic options. These data represent the first global proteomic approach to study PNF.

  2. The developments and achievements of endoscopic surgery, robotic surgery and function-preserving surgery.

    PubMed

    Yoshida, Masashi; Furukawa, Toshiharu; Morikawa, Yasuhide; Kitagawa, Yuko; Kitajima, Masaki

    2010-09-01

    The breakthrough in laparoscopic surgery has been the development of a charge-coupled device camera system and Mouret performing cholecystectomy in 1987. The short-term benefits of laparoscopic surgery are widely accepted and the long-term benefit of less incidence of bowel obstruction can be expected. The important developments have been the articulating instrumentation via new laparoscopic access ports. Since 2007, single-incision laparoscopic surgery has spread all over the world. Not only single-scar but also no-scar operation is a current topic. In 2004, Kalloo reported the flexible transgastric peritoneoscopy as a novel approach to therapeutic interventions. In 2007, Marescaux reported transvaginal cholecystectomy in a patient. The breakthrough in robotic surgery was the development of the da Vinci Surgical System. It was introduced to Keio University Hospital in March 2000. Precision in the surgery will reach a higher level with the use of robotics. In collaboration with the faculty of technology and science, Keio University, the combined master-slave manipulator has been developed. The haptic forceps, which measure the elasticity of organs, have also been developed. The first possible sites of lymphatic metastasis are known as sentinel nodes. Otani reported vagus-sparing segmental gastrectomy under sentinel node navigation. This kind of function-preserving surgery will be performed frequently if the results of the multicenter prospective trial of the dual tracer method are favorable. Indocyanine green fluorescence-guided method using the HyperEye charge-coupled device camera system can be a highly sensitive method without using the radioactive colloid. 'Minimally invasive, function-preserving and precise surgery under sentinel node navigation in community hospital' may be a goal for us. PMID:20736221

  3. Exploratorium: Robots.

    ERIC Educational Resources Information Center

    Brand, Judith, Ed.

    2002-01-01

    This issue of Exploratorium Magazine focuses on the topic robotics. It explains how to make a vibrating robotic bug and features articles on robots. Contents include: (1) "Where Robot Mice and Robot Men Run Round in Robot Towns" (Ray Bradbury); (2) "Robots at Work" (Jake Widman); (3) "Make a Vibrating Robotic Bug" (Modesto Tamez); (4) "The Robot…

  4. Robotic intelligence kernel

    DOEpatents

    Bruemmer, David J.

    2009-11-17

    A robot platform includes perceptors, locomotors, and a system controller. The system controller executes a robot intelligence kernel (RIK) that includes a multi-level architecture and a dynamic autonomy structure. The multi-level architecture includes a robot behavior level for defining robot behaviors, that incorporate robot attributes and a cognitive level for defining conduct modules that blend an adaptive interaction between predefined decision functions and the robot behaviors. The dynamic autonomy structure is configured for modifying a transaction capacity between an operator intervention and a robot initiative and may include multiple levels with at least a teleoperation mode configured to maximize the operator intervention and minimize the robot initiative and an autonomous mode configured to minimize the operator intervention and maximize the robot initiative. Within the RIK at least the cognitive level includes the dynamic autonomy structure.

  5. Cypermethrin-induced nigrostriatal dopaminergic neurodegeneration alters the mitochondrial function: a proteomics study.

    PubMed

    Agrawal, Sonal; Singh, Ashish; Tripathi, Pratibha; Mishra, Manisha; Singh, Pradhyumna Kumar; Singh, Mahendra Pratap

    2015-04-01

    Cypermethrin induces the slow and progressive degeneration of the nigrostriatal dopaminergic neurons in rats. Postnatal preexposure with low doses of cypermethrin is known to enhance the susceptibility of animals upon adulthood reexposure. The study was undertaken to delineate the role of mitochondria in cypermethrin-induced neurodegeneration. Indexes of dopaminergic neurodegeneration, microglial activation, and mitochondrial dysfunction and its proteome profile were assessed in controls and cypermethrin-treated rats. Cypermethrin increased nigral dopaminergic neurodegeneration and microglial activation while reduced mitochondrial membrane potential and complex I activity. Cypermethrin attenuated striatal dopamine content and differentially regulated the expressions of the nine striatal and ten nigral proteins. Western blot analyses showed that cypermethrin also increased c-Jun N-terminal kinase (JNK), caspase-3, tumor suppressor protein (p53), tumor necrosis factor-α (TNF-α), p38 mitogen-activated protein kinase (p38 MAPK), and heme oxygenase-1 (HO-1) expressions and reduced B cell lymphoma-2 protein (Bcl-2) expression. Syndopa and minocycline rescued from cypermethrin induced augmentation in microglial activation and reductions in mitochondrial membrane potential and complex I activity, striatal dopamine content, and degeneration of nigral dopaminergic neurons. Syndopa and minocycline, respectively, modulated the expressions of four and six striatal and four and seven nigral proteins. Furthermore, they reinstated the expressions of JNK, caspase-3, Bcl-2, p53, p38 MAPK, TNF-α, and HO-1. The study demonstrates that cypermethrin induces mitochondrial dysfunction and alters mitochondrial proteome leading to oxidative stress and apoptosis, which regulate the nigrostriatal dopaminergic neurodegeneration.

  6. Differential proteomic analysis of STAT6 knockout mice reveals new regulatory function in liver lipid homeostasis.

    PubMed

    Iff, Joël; Wang, Wei; Sajic, Tatjana; Oudry, Nathalie; Gueneau, Estelle; Hopfgartner, Gérard; Varesio, Emmanuel; Szanto, Ildiko

    2009-10-01

    Increased inflammatory signaling is a key feature of metabolic disorders. In this context, the role of increased pro-inflammatory signals has been extensively studied. By contrast, no efforts have been dedicated to study the contrasting scenario: the attenuation of anti-inflammatory signals and their role in metabolic homeostasis. IL-4 and IL-13 are anti-inflammatory cytokines signaling through the Signal Transducer and Activator of Transcription 6 (STAT6). Our study was aimed at evaluating the lack of STAT6 signaling on liver homeostasis. To this end we analyzed the liver proteome of wild type and STAT6 knock-out mice using 2D nanoscale LC-MS/MS with iTRAQ labeling technique. The coordinated changes in proteins identified by this quantitative proteome analysis indicated disturbed lipid homeostasis and a state of hepatocellular stress. Most significantly, the expression of the liver fatty acid binding protein (FABP1) was increased in the knock-out mice. In line with the elevated FABP1 expression we found latent liver lipid accumulation in the STAT6-deficient mice which was further aggravated when mice were challenged by a high fat diet. In conclusion, our study revealed a so far uncharacterized role for STAT6 in regulating liver lipid homeostasis and demonstrates the importance of anti-inflammatory signaling in the defense against the development of liver steatosis.

  7. Nucleoid-Enriched Proteomes in Developing Plastids and Chloroplasts from Maize Leaves: A New Conceptual Framework for Nucleoid Functions1[C][W][OA

    PubMed Central

    Majeran, Wojciech; Friso, Giulia; Asakura, Yukari; Qu, Xian; Huang, Mingshu; Ponnala, Lalit; Watkins, Kenneth P.; Barkan, Alice; van Wijk, Klaas J.

    2012-01-01

    Plastids contain multiple copies of the plastid chromosome, folded together with proteins and RNA into nucleoids. The degree to which components of the plastid gene expression and protein biogenesis machineries are nucleoid associated, and the factors involved in plastid DNA organization, repair, and replication, are poorly understood. To provide a conceptual framework for nucleoid function, we characterized the proteomes of highly enriched nucleoid fractions of proplastids and mature chloroplasts isolated from the maize (Zea mays) leaf base and tip, respectively, using mass spectrometry. Quantitative comparisons with proteomes of unfractionated proplastids and chloroplasts facilitated the determination of nucleoid-enriched proteins. This nucleoid-enriched proteome included proteins involved in DNA replication, organization, and repair as well as transcription, mRNA processing, splicing, and editing. Many proteins of unknown function, including pentatricopeptide repeat (PPR), tetratricopeptide repeat (TPR), DnaJ, and mitochondrial transcription factor (mTERF) domain proteins, were identified. Strikingly, 70S ribosome and ribosome assembly factors were strongly overrepresented in nucleoid fractions, but protein chaperones were not. Our analysis strongly suggests that mRNA processing, splicing, and editing, as well as ribosome assembly, take place in association with the nucleoid, suggesting that these processes occur cotranscriptionally. The plastid developmental state did not dramatically change the nucleoid-enriched proteome but did quantitatively shift the predominating function from RNA metabolism in undeveloped plastids to translation and homeostasis in chloroplasts. This study extends the known maize plastid proteome by hundreds of proteins, including more than 40 PPR and mTERF domain proteins, and provides a resource for targeted studies on plastid gene expression. Details of protein identification and annotation are provided in the Plant Proteome Database

  8. Assessment of Metabolomic and Proteomic Biomarkers in Detection and Prognosis of Progression of Renal Function in Chronic Kidney Disease

    PubMed Central

    Nkuipou-Kenfack, Esther; Duranton, Flore; Gayrard, Nathalie; Argilés, Àngel; Lundin, Ulrika; Weinberger, Klaus M.; Dakna, Mohammed; Delles, Christian; Mullen, William; Husi, Holger; Klein, Julie; Koeck, Thomas; Zürbig, Petra; Mischak, Harald

    2014-01-01

    Chronic kidney disease (CKD) is part of a number of systemic and renal diseases and may reach epidemic proportions over the next decade. Efforts have been made to improve diagnosis and management of CKD. We hypothesised that combining metabolomic and proteomic approaches could generate a more systemic and complete view of the disease mechanisms. To test this approach, we examined samples from a cohort of 49 patients representing different stages of CKD. Urine samples were analysed for proteomic changes using capillary electrophoresis-mass spectrometry and urine and plasma samples for metabolomic changes using different mass spectrometry-based techniques. The training set included 20 CKD patients selected according to their estimated glomerular filtration rate (eGFR) at mild (59.9±16.5 mL/min/1.73 m2; n = 10) or advanced (8.9±4.5 mL/min/1.73 m2; n = 10) CKD and the remaining 29 patients left for the test set. We identified a panel of 76 statistically significant metabolites and peptides that correlated with CKD in the training set. We combined these biomarkers in different classifiers and then performed correlation analyses with eGFR at baseline and follow-up after 2.8±0.8 years in the test set. A solely plasma metabolite biomarker-based classifier significantly correlated with the loss of kidney function in the test set at baseline and follow-up (ρ = −0.8031; p<0.0001 and ρ = −0.6009; p = 0.0019, respectively). Similarly, a urinary metabolite biomarker-based classifier did reveal significant association to kidney function (ρ = −0.6557; p = 0.0001 and ρ = −0.6574; p = 0.0005). A classifier utilising 46 identified urinary peptide biomarkers performed statistically equivalent to the urinary and plasma metabolite classifier (ρ = −0.7752; p<0.0001 and ρ = −0.8400; p<0.0001). The combination of both urinary proteomic and urinary and plasma metabolic biomarkers did not improve the correlation with eGFR. In

  9. Functional proteomic analysis revealed ground-base ion radiations cannot reflect biological effects of space radiations of rice

    NASA Astrophysics Data System (ADS)

    Wang, Wei; Sun, Yeqing; Zhao, Qian; Han, Lu

    2016-07-01

    Highly ionizing radiation (HZE) in space is considered as main factor causing biological effects. Radiobiological studies during space flights are unrepeatable due to the variable space radiation environment, ground-base ion radiations are usually performed to simulate of the space biological effect. Spaceflights present a low-dose rate (0.1˜~0.3mGy/day) radiation environment inside aerocrafts while ground-base ion radiations present a much higher dose rate (100˜~500mGy/min). Whether ground-base ion radiation can reflect effects of space radiation is worth of evaluation. In this research, we compared the functional proteomic profiles of rice plants between on-ground simulated HZE particle radiation and spaceflight treatments. Three independent ground-base seed ionizing radiation experiments with different cumulative doses (dose range: 2˜~20000mGy) and different liner energy transfer (LET) values (13.3˜~500keV/μμm) and two independent seed spaceflight experiments onboard Chinese 20th satellite and SZ-6 spacecraft were carried out. Alterations in the proteome were analyzed by two-dimensional difference gel electrophoresis (2-D DIGE) with MALDI-TOF/TOF mass spectrometry identifications. 45 and 59 proteins showed significant (p<0.05) and reproducible quantitative differences in ground-base ion radiation and spaceflight experiments respectively. The functions of ground-base radiation and spaceflight proteins were both involved in a wide range of biological processes. Gene Ontology enrichment analysis further revealed that ground-base radiation responsive proteins were mainly involved in removal of superoxide radicals, defense response to stimulus and photosynthesis, while spaceflight responsive proteins mainly participate in nucleoside metabolic process, protein folding and phosphorylation. The results implied that ground-base radiations cannot truly reflect effects of spaceflight radiations, ground-base radiation was a kind of indirect effect to rice causing

  10. Community proteomics provides functional insight into polyhydroxyalkanoate production by a mixed microbial culture cultivated on fermented dairy manure.

    PubMed

    Hanson, Andrea J; Guho, Nicholas M; Paszczynski, Andrzej J; Coats, Erik R

    2016-09-01

    Polyhydroxyalkanoates (PHAs) are bio-based, biodegradable polyesters that can be produced from organic-rich waste streams using mixed microbial cultures (MMCs). To maximize PHA production, MMCs are enriched for bacteria with a high polymer storage capacity through the application of aerobic dynamic feeding (ADF) in a sequencing batch reactor (SBR), which consequently induces a feast-famine metabolic response. Though the feast-famine response is generally understood empirically at a macro-level, the molecular level is less refined. The objective of this study was to investigate the microbial community composition and proteome profile of an enriched MMC cultivated on fermented dairy manure. The enriched MMC exhibited a feast-famine response and was capable of producing up to 40 % (wt. basis) PHA in a fed-batch reactor. High-throughput 16S rRNA gene sequencing revealed a microbial community dominated by Meganema, a known PHA-producing genus not often observed in high abundance in enrichment SBRs. The application of the proteomic methods two-dimensional electrophoresis and LC-MS/MS revealed PHA synthesis, energy generation, and protein synthesis prominently occurring during the feast phase, corroborating bulk solution variable observations and theoretical expectations. During the famine phase, nutrient transport, acyl-CoA metabolism, additional energy generation, and housekeeping functions were more pronounced, informing previously under-determined MMC functionality under famine conditions. During fed-batch PHA production, acetyl-CoA acetyltransferase and PHA granule-bound phasin proteins were in increased abundance relative to the SBR, supporting the higher PHA content observed. Collectively, the results provide unique microbial community structural and functional insight into feast-famine PHA production from waste feedstocks using MMCs. PMID:27147532

  11. IL-15Rα deficiency in skeletal muscle alters respiratory function and the proteome of mitochondrial subpopulations independent of changes to the mitochondrial genome.

    PubMed

    O'Connell, Grant C; Nichols, Cody; Guo, Ge; Croston, Tara L; Thapa, Dharendra; Hollander, John M; Pistilli, Emidio E

    2015-11-01

    Interleukin-15 receptor alpha knockout (IL15RαKO) mice exhibit a greater skeletal muscle mitochondrial density with an altered mitochondrial morphology. However, the mechanism and functional impact of these changes have not been determined. In this study, we characterized the functional, proteomic, and genomic alterations in mitochondrial subpopulations isolated from the skeletal muscles of IL15RαKO mice and B6129 background control mice. State 3 respiration was greater in interfibrillar mitochondria and whole muscle ATP levels were greater in IL15RαKO mice supporting the increases in respiration rate. However, the state 3/state 4 ratio was lower, suggesting some degree of respiratory uncoupling. Proteomic analyses identified several markers independently in mitochondrial subpopulations that are associated with these functional alterations. Next Generation Sequencing of mtDNA revealed a high degree of similarity between the mitochondrial genomes of IL15RαKO mice and controls in terms of copy number, consensus coding and the presence of minor alleles, suggesting that the functional and proteomic alterations we observed occurred independent of alterations to the mitochondrial genome. These data provide additional evidence to implicate IL-15Rα as a regulator of skeletal muscle phenotypes through effects on the mitochondrion, and suggest these effects are driven by alterations to the mitochondrial proteome.

  12. Recent trends in robot-assisted therapy environments to improve real-life functional performance after stroke

    PubMed Central

    Johnson, Michelle J

    2006-01-01

    Upper and lower limb robotic tools for neuro-rehabilitation are effective in reducing motor impairment but they are limited in their ability to improve real world function. There is a need to improve functional outcomes after robot-assisted therapy. Improvements in the effectiveness of these environments may be achieved by incorporating into their design and control strategies important elements key to inducing motor learning and cerebral plasticity such as mass-practice, feedback, task-engagement, and complex problem solving. This special issue presents nine articles. Novel strategies covered in this issue encourage more natural movements through the use of virtual reality and real objects and faster motor learning through the use of error feedback to guide acquisition of natural movements that are salient to real activities. In addition, several articles describe novel systems and techniques that use of custom and commercial games combined with new low-cost robot systems and a humanoid robot to embody the " supervisory presence" of the therapy as possible solutions to exercise compliance in under-supervised environments such as the home. PMID:17176474

  13. A new strategy for gene targeting and functional proteomics using the DT40 cell line

    PubMed Central

    Orlowska, Kinga P.; Klosowska, Kamila; Szczesny, Roman J.; Cysewski, Dominik; Krawczyk, Pawel S.; Dziembowski, Andrzej

    2013-01-01

    DT40 cells derived from chicken B lymphocytes exhibit exceptionally high homologous recombination rates. Therefore, they can be used as a convenient tool and model for gene targeting experiments. However, lack of efficient cloning strategies, protein purification protocols and a well annotated protein database limits the utility of these cells for proteomic studies. Here we describe a fast and inexpensive experimental pipeline for protein localization, quantification and mass spectrometry–based interaction studies using DT40 cells. Our newly designed set of pQuant vectors and a sequence- and ligation-independent cloning (SLIC) strategy allow for simple and efficient generation of gene targeting constructs, facilitating homologous-recombination–based protein tagging on a multi-gene scale. We also report proof of principle results using the key proteins involved in RNA decay, namely EXOSC8, EXOSC9, CNOT7 and UPF1. PMID:23892402

  14. Insights into aging through measurements of the Drosophila proteome as a function of temperature

    PubMed Central

    Robinson, Renã A. S.; Kellie, John F.; Kaufman, Thomas C.; Clemmer, David E.

    2010-01-01

    Drosophila melanogaster is used as a model system to investigate protein changes associated with the aging process under conditions that alter organism lifespan. Changes in the proteome are assessed at various ages in populations of Oregon-R adult males that have mean lifetimes of 47 and 111 days at 28 and 18 °C, respectively. Peptide hits detected from strong-cation-exchange and reversed-phase liquid chromatography coupled to tandem mass spectrometry analysis are employed to examine patterns in relative protein expression. Thirty-three proteins were identified as having similar patterns of expression at both temperatures investigated when scaling the organism age to lifespan. In addition, the proteins ferritin 2 light chain homologue and larval serum protein 1β were identified in relatively high abundance and displayed distinctly different patterns of expression between the two temperatures. Overall, the results support the notion that aspects of the aging process may be preprogrammed at the protein level. PMID:20732347

  15. Can selective arterial clamping with fluorescence imaging preserve kidney function during robotic partial nephrectomy?

    PubMed Central

    McClintock, Tyler R.; Bjurlin, Marc A.; Wysock, James S.; Borofsky, Michael S.; Marien, Tracy P.; Okoro, Chinonyerem; Stifelman, Michael D.

    2015-01-01

    Objectives To compare renal functional outcomes in robotic partial nephrectomy (RPN) with selective arterial clamping guided by near infrared fluorescence (NIRF) imaging to a matched cohort of patients who underwent RPN without selective arterial clamping and NIRF imaging. Methods From April 2011 to December 2012, NIRF imaging-enhanced RPN with selective clamping was utilized in 42 cases. Functional outcomes of successful cases were compared with a cohort of patients, matched by tumor size, preoperative eGFR, functional kidney status, age, sex, body mass index, and American Society of Anesthesiologists score, who underwent RPN without selective clamping and NIRF imaging. Results In matched-pair analysis, selective clamping with NIRF was associated with superior kidney function at discharge, as demonstrated by postoperative eGFR (78.2 vs 68.5 ml/min per 1.73m2; P=0.04), absolute reduction of eGFR (−2.5 vs −14.0 ml/min per 1.73m2; P<0.01) and percent change in eGFR (−1.9% vs −16.8%, P<0.01). Similar trends were noted at three month follow up but these differences became non-significant (P[eGFR]=0.07], P[absolute reduction of eGFR]=0.10, and P[percent change in eGFR]=0.07). In the selective clamping group, a total of four perioperative complications occurred in three patients, all of which were Clavien I-III. Conclusion Utilization of NIRF imaging was associated with improved short-term renal functional outcomes when compared to RPN without selective arterial clamping and NIRF imaging. With this effect attenuated at later follow-up, randomized prospective studies and long-term assessment of kidney-specific functional outcomes are needed to further assess the benefits of this technology. PMID:24909960

  16. Proteomic profiling and functional characterization of early and late shoulder osteoarthritis

    PubMed Central

    2013-01-01

    Introduction The development of effective treatments for osteoarthritis (OA) has been hampered by a poor understanding of OA at the cellular and molecular levels. Emerging as a disease of the 'whole joint’, the importance of the biochemical contribution of various tissues, including synovium, bone and articular cartilage, has become increasingly significant. Bathing the entire joint structure, the proteomic analysis of synovial fluid (SF) from osteoarthritic shoulders offers a valuable 'snapshot’ of the biologic environment throughout disease progression. The purpose of this study was to identify differentially expressed proteins in early and late shoulder osteoarthritic SF in comparison to healthy SF. Methods A quantitative 18O labeling proteomic approach was employed to identify the dysregulated SF proteins in early (n = 5) and late (n = 4) OA patients compared to control individuals (n = 5). In addition, ELISA was used to quantify six pro-inflammatory and two anti-inflammatory cytokines. Results Key results include a greater relative abundance of proteins related to the complement system and the extracellular matrix in SF from both early and late OA. Pathway analyses suggests dysregulation of the acute phase response, liver x receptor/retinoid x receptor (LXR/RXR), complement system and coagulation pathways in both early and late OA. The network related to lipid metabolism was down-regulated in both early and late OA. Inflammatory cytokines including interleukin (IL) 6, IL 8 and IL 18 were up-regulated in early and late OA. Conclusions The results suggest a dysregulation of wound repair pathways in shoulder OA contributing to the presence of a 'chronic wound’ that progresses irreversibly from early to later stages of OA. Protease inhibitors were downregulated in late OA suggesting uncontrolled proteolytic activity occurring in late OA. These results contribute to the theory that protease inhibitors represent promising therapeutic agents which

  17. Proteomics data repositories

    PubMed Central

    Riffle, Michael; Eng, Jimmy K.

    2010-01-01

    The field of proteomics, particularly the application of mass spectrometry analysis to protein samples, is well-established and growing rapidly. Proteomics studies generate large volumes of raw experimental data and inferred biological results. To facilitate the dissemination of these data, centralized data repositories have been developed that make the data and results accessible to proteomics researchers and biologists alike. This review of proteomics data repositories focuses exclusively on freely-available, centralized data resources that disseminate or store experimental mass spectrometry data and results. The resources chosen reflect a current “snapshot” of the state of resources available with an emphasis placed on resources that may be of particular interest to yeast researchers. Resources are described in terms of their intended purpose and the features and functionality provided to users. PMID:19795424

  18. Quantitative Targeted Absolute Proteomics of Transporters and Pharmacoproteomics-Based Reconstruction of P-Glycoprotein Function in Mouse Small Intestine.

    PubMed

    Akazawa, Takanori; Uchida, Yasuo; Tachikawa, Masanori; Ohtsuki, Sumio; Terasaki, Tetsuya

    2016-07-01

    The purpose of this study was to investigate whether a pharmacokinetic model integrating in vitro mdr1a efflux activity (which we previously reported) with in vitro/in vivo differences in protein expression level can reconstruct intestinal mdr1a function. In situ intestinal permeability-surface area product ratio between wild-type and mdr1a/1b (-/-) mice is one of the parameters used to describe intestinal mdr1a function. The reconstructed ratios of six mdr1a substrates (dexamethasone, digoxin, loperamide, quinidine, verapamil, vinblastine) and one nonsubstrate (diazepam) were consistent with the observed values reported by Adachi et al. within 2.1-fold difference. Thus, intestinal mdr1a function can be reconstructed by our pharmacoproteomic modeling approach. Furthermore, we evaluated regional differences in protein expression levels of mouse intestinal transporters. Sixteen (mdr1a, mrp4, bcrp, abcg5, abcg8, glut1, 4f2hc, sglt1, lat2, pept1, mct1, slc22a18, ostβ, villin1, Na(+)/K(+)-ATPase, γ-gtp) out of 46 target molecules were detected by employing our established quantitative targeted absolute proteomics technique. The protein expression amounts of mdr1a and bcrp increased progressively from duodenum to ileum. Sglt1, lat2, and 4f2hc were highly expressed in jejunum and ileum. Mct1 and ostβ were highly expressed in ileum. The quantitative expression profiles established here should be helpful to understand and predict intestinal transporter functions. PMID:27276518

  19. Comparative Proteomic Analysis of Serum from Patients with Systemic Sclerosis and Sclerodermatous GVHD. Evidence of Defective Function of Factor H

    PubMed Central

    Scambi, Cinzia; La Verde, Valentina; De Franceschi, Lucia; Barausse, Giovanni; Poli, Fabio; Benedetti, Fabio; Sorio, Marco; Deriu, Francesca; Roncada, Paola; Bortolami, Oscar; Turrini, Francesco; Caramaschi, Paola; Stranieri, Chiara; Bambara, Lisa M.; Biasi, Domenico

    2010-01-01

    Background Systemic sclerosis (SSc) is an autoimmune disease characterized by immunological and vascular abnormalities. Until now, the cause of SSc remains unclear. Sclerodermatous graft-versus-host disease (ScGVHD) is one of the most severe complications following bone marrow transplantation (BMT) for haematological disorders. Since the first cases, the similarity of ScGVHD to SSc has been reported. However, both diseases could have different etiopathogeneses. The objective of this study was to identify new serum biomarkers involved in SSc and ScGVHD. Methodology Serum was obtained from patients with SSc and ScGVHD, patients without ScGVHD who received BMT for haematological disorders and healthy controls. Bi-dimensional electrophoresis (2D) was carried out to generate maps of serum proteins from patients and controls. The 2D maps underwent image analysis and differently expressed proteins were identified. Immuno-blot analysis and ELISA assay were used to validate the proteomic data. Hemolytic assay with sheep erythrocytes was performed to evaluate the capacity of Factor H (FH) to control complement activation on the cellular surface. FH binding to endothelial cells (ECs) was also analysed in order to assess possible dysfunctions of this protein. Principal Findings Fourteen differentially expressed proteins were identified. We detected pneumococcal antibody cross-reacting with double stranded DNA in serum of all bone marrow transplanted patients with ScGVHD. We documented higher levels of FH in serum of SSc and ScGVHD patients compared healthy controls and increased sheep erythrocytes lysis after incubation with serum of diffuse SSc patients. In addition, we observed that FH binding to ECs was reduced when we used serum from these patients. Conclusions The comparative proteomic analysis of serum from SSc and ScGVHD patients highlighted proteins involved in either promoting or maintaining an inflammatory state. We also found a defective function of Factor H

  20. Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics

    SciTech Connect

    Baas, T.; Baskin, C. R.; Diamond, Deborah L.; Garcia-Sastre, A.; Bielefeldt-Ohmann, H.; Tumpey, T. M.; Thomas, M. J.; Carter, V. S.; Teal, T. H.; Van Hoven, N.; Proll, Sean; Jacobs, Jon M.; Caldwell, Z.; Gritsenko, Marina A.; Hukkanen, R.; Camp, David G.; Smith, Richard D.; Katze, Michael G.

    2006-11-01

    Recent outbreaks of avian influenza in humans have stressed the need for an improved non-human primate model of influenza pathogenesis. In order to develop our macaque model, we expanded our in vivo and functional genomics experiments: We focused on the innate immune response at day 2 post-inoculation and on gene expression in affected lung tissue with viral genetic material present; finally, we sought to identify signature genes for early infection in whole blood. For these purposes, we infected six pigtailed macaques with 107 TCID50 of influenza A/Texas/36/91 virus and three control animals with a sham inoculate. We sacrificed one control and two experimental animals at day 2, 4, and 7 and lung tissue was harvested for pathology, gene expression profiling, and proteomics. Additionally, blood was collected for genomics every other day from each animal until its endpoint. Gross and microscopic pathology, immunohistochemistry, viral gene expression by arrays and/or quantitative real-time RT-PCR confirmed successful yet mild infection in all experimental animals. Genomic experiments were performed using second generation macaque-specific oligonucleotide arrays and high-throughput proteomics revealed host response to infection at the protein level. Our data showed dramatic differences in gene expression within the same influenza-induced lesion based on the presence or absence of viral mRNA. We also identified genes tightly co-regulated in peripheral white blood cells and in lung tissue at day 2 post-inoculation. This latter finding opens the possibility of using gene expression arrays on whole blood to detect infection after exposure but prior to onset of symptoms or shedding.

  1. Incorporating robotic-assisted telerehabilitation in a home program to improve arm function following stroke: a case study

    PubMed Central

    Linder, Susan M.; Reiss, Aimee; Buchanan, Sharon; Sahu, Komal; Rosenfeldt, Anson B.; Clark, Cindy; Wolf, Steven L.; Alberts, Jay L.

    2013-01-01

    Background and Purpose After stroke, many individuals lack resources to receive the intensive rehabilitation thought to improve upper extremity motor function. This case study describes the application of a telerehabilitation intervention using a portable robotic device combined with a home exercise program (HEP) designed to improve upper extremity function. Case Description The participant was a 54 year-old male, 22 weeks following right medullary pyramidal ischemic infarct. At baseline, he exhibited residual paresis of the left upper extremity resulting in impaired motor control consistent with a flexion synergistic pattern, scoring 22/66 on the Fugl-Meyer Motor Assessment (FMA). Intervention The participant completed 85 total hours of training (38 hours of robotic device and 47 hours of HEP) over the 8-week intervention period. Outcomes The participant demonstrated an improvement of 26 points on the Action Research Arm Test, 5 points on the Functional Ability Scale portion of the Wolf Motor Function Test (WMFT), and 20 points on the FMA, all of which surpassed the minimal clinically important difference (MCID). Of the 17 tasks of the WMFT, he demonstrated improvement on 11 of the 15 time-based tasks and both strength measures. The participant reported an overall improvement in his stroke recovery on the Stroke Impact Scale quality of life questionnaire from 40/100 to 65/100. His score on the Center for Epidemiologic Studies Depression Scale improved by 19 points. Discussion This case demonstrates that robotic-assisted therapy paired with a HEP can be successfully delivered within a home environment to a person with stroke. Robotic assisted therapy may be a feasible and efficacious adjunct to a HEP program to elicit substantial improvements in upper extremity motor function especially in those persons with stroke who lack access to stroke rehabilitation centers. Video Abstract available (See Video, Supplemental Digital Content 1.) for more insights from the

  2. Rehabilitation robotics

    PubMed Central

    KREBS, H.I.; VOLPE, B.T.

    2015-01-01

    This chapter focuses on rehabilitation robotics which can be used to augment the clinician’s toolbox in order to deliver meaningful restorative therapy for an aging population, as well as on advances in orthotics to augment an individual’s functional abilities beyond neurorestoration potential. The interest in rehabilitation robotics and orthotics is increasing steadily with marked growth in the last 10 years. This growth is understandable in view of the increased demand for caregivers and rehabilitation services escalating apace with the graying of the population. We will provide an overview on improving function in people with a weak limb due to a neurological disorder who cannot properly control it to interact with the environment (orthotics); we will then focus on tools to assist the clinician in promoting rehabilitation of an individual so that s/he can interact with the environment unassisted (rehabilitation robotics). We will present a few clinical results occurring immediately poststroke as well as during the chronic phase that demonstrate superior gains for the upper extremity when employing rehabilitation robotics instead of usual care. These include the landmark VA-ROBOTICS multisite, randomized clinical study which demonstrates clinical gains for chronic stroke that go beyond usual care at no additional cost. PMID:23312648

  3. Rehabilitation robotics.

    PubMed

    Krebs, H I; Volpe, B T

    2013-01-01

    This chapter focuses on rehabilitation robotics which can be used to augment the clinician's toolbox in order to deliver meaningful restorative therapy for an aging population, as well as on advances in orthotics to augment an individual's functional abilities beyond neurorestoration potential. The interest in rehabilitation robotics and orthotics is increasing steadily with marked growth in the last 10 years. This growth is understandable in view of the increased demand for caregivers and rehabilitation services escalating apace with the graying of the population. We provide an overview on improving function in people with a weak limb due to a neurological disorder who cannot properly control it to interact with the environment (orthotics); we then focus on tools to assist the clinician in promoting rehabilitation of an individual so that s/he can interact with the environment unassisted (rehabilitation robotics). We present a few clinical results occurring immediately poststroke as well as during the chronic phase that demonstrate superior gains for the upper extremity when employing rehabilitation robotics instead of usual care. These include the landmark VA-ROBOTICS multisite, randomized clinical study which demonstrates clinical gains for chronic stroke that go beyond usual care at no additional cost.

  4. Molecular Biologist's Guide to Proteomics

    PubMed Central

    Graves, Paul R.; Haystead, Timothy A. J.

    2002-01-01

    The emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Moreover, only through the study of proteins can posttranslational modifications be determined, which can profoundly affect protein function. Proteomics has been enabled by the accumulation of both DNA and protein sequence databases, improvements in mass spectrometry, and the development of computer algorithms for database searching. In this review, we describe why proteomics is important, how it is conducted, and how it can be applied to complement other existing technologies. We conclude that currently, the most practical application of proteomics is the analysis of target proteins as opposed to entire proteomes. This type of proteomics, referred to as functional proteomics, is always driven by a specific biological question. In this way, protein identification and characterization has a meaningful outcome. We discuss some of the advantages of a functional proteomics approach and provide examples of how different methodologies can be utilized to address a wide variety of biological problems. PMID:11875127

  5. Rapid Discovery of Functional Small Molecule Ligands against Proteomic Targets through Library-Against-Library Screening

    PubMed Central

    2016-01-01

    Identifying “druggable” targets and their corresponding therapeutic agents are two fundamental challenges in drug discovery research. The one-bead-one-compound (OBOC) combinatorial library method has been developed to discover peptides or small molecules that bind to a specific target protein or elicit a specific cellular response. The phage display cDNA expression proteome library method has been employed to identify target proteins that interact with specific compounds. Here, we combined these two high-throughput approaches, efficiently interrogated approximately 1013 possible molecular interactions, and identified 91 small molecule compound beads that interacted strongly with the phage library. Of 19 compounds resynthesized, 4 were cytotoxic against cancer cells; one of these compounds was found to interact with EIF5B and inhibit protein translation. As more binding pairs are confirmed and evaluated, the “library-against-library” screening approach and the resulting small molecule–protein domain interaction database may serve as a valuable tool for basic research and drug development. PMID:27053324

  6. Comparative proteomics reveal diverse functions and dynamic changes of Bombyx mori silk proteins spun from different development stages.

    PubMed

    Dong, Zhaoming; Zhao, Ping; Wang, Chen; Zhang, Yan; Chen, Jianping; Wang, Xin; Lin, Ying; Xia, Qingyou

    2013-11-01

    Silkworms (Bombyx mori) produce massive amounts of silk proteins to make cocoons during the final stages of larval development. Although the major components, fibroin and sericin, have been the focus for a long time, few researchers have realized the complexity of the silk proteome. We collected seven kinds of silk fibers spun by silkworm larvae at different developmental stages: the silks spun by new hatched larvae, second instar day 0 larvae, third instar day 0 larvae, fourth instar day 0 larvae, and fourth instar molting larvae, the scaffold silk used to attach the cocoon to the substrate and the cocoon silk. Analysis by liquid chromatography-tandem mass spectrometry identified 500 proteins from the seven silks. In addition to the expected fibroins, sericins, and some known protease inhibitors, we also identified further protease inhibitors, enzymes, proteins of unknown function, and other proteins. Unsurprisingly, our quantitative results showed fibroins and sericins were the most abundant proteins in all seven silks. Except for fibroins and sericins, protease inhibitors, enzymes, and proteins of unknown function were more abundant than other proteins. We found significant change in silk protein compositions through development, being consistent with their different biological functions and complicated formation.

  7. Genomic and proteomic profiling reveals reduced mitochondrial function and disruption of the neuromuscular junction driving rat sarcopenia.

    PubMed

    Ibebunjo, Chikwendu; Chick, Joel M; Kendall, Tracee; Eash, John K; Li, Christine; Zhang, Yunyu; Vickers, Chad; Wu, Zhidan; Clarke, Brian A; Shi, Jun; Cruz, Joseph; Fournier, Brigitte; Brachat, Sophie; Gutzwiller, Sabine; Ma, QiCheng; Markovits, Judit; Broome, Michelle; Steinkrauss, Michelle; Skuba, Elizabeth; Galarneau, Jean-Rene; Gygi, Steven P; Glass, David J

    2013-01-01

    Molecular mechanisms underlying sarcopenia, the age-related loss of skeletal muscle mass and function, remain unclear. To identify molecular changes that correlated best with sarcopenia and might contribute to its pathogenesis, we determined global gene expression profiles in muscles of rats aged 6, 12, 18, 21, 24, and 27 months. These rats exhibit sarcopenia beginning at 21 months. Correlation of the gene expression versus muscle mass or age changes, and functional annotation analysis identified gene signatures of sarcopenia distinct from gene signatures of aging. Specifically, mitochondrial energy metabolism (e.g., tricarboxylic acid cycle and oxidative phosphorylation) pathway genes were the most downregulated and most significantly correlated with sarcopenia. Also, perturbed were genes/pathways associated with neuromuscular junction patency (providing molecular evidence of sarcopenia-related functional denervation and neuromuscular junction remodeling), protein degradation, and inflammation. Proteomic analysis of samples at 6, 18, and 27 months confirmed the depletion of mitochondrial energy metabolism proteins and neuromuscular junction proteins. Together, these findings suggest that therapeutic approaches that simultaneously stimulate mitochondrogenesis and reduce muscle proteolysis and inflammation have potential for treating sarcopenia.

  8. Establishment of an ectopically expressed and functional PRMT1 for proteomic analysis of arginine-methylated proteins.

    PubMed

    Chang, Yuan-I; Lin, Sheng-Wei; Chiou, Yi-Ying; Sung, Jung-Sung; Cheng, Lee-Chun; Lu, Yu-Ling; Sun, Kuang-Hui; Chang, Keejong; Lin, Chao-Hsiung; Lin, Wey-Jinq

    2010-12-01

    Protein arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), plays crucial roles in a variety of cellular processes. Mammalian PRMT1 exists in a large protein complex in cells, which has been implied in modulating the regulatory and catalytic properties of this enzyme. Establishment of a mammalian comparative approach will help to identify putative substrates of PRMT1 in an authentic condition. Here, we showed that ectopically expressed PRMT1 in mammalian HEK293 cells not only exhibited catalytic properties comparable to the endogenous enzyme but also existed in a functional complex together with endogenous PRMT1 and thus functioned as an endogenous counterpart. In addition, the measured methylation level of cellular proteins using a tritium-labeled methyl donor was accordingly enhanced upon ectopic expression of PRMT1. Subsequent proteomic analysis with such PRMT1-expressing cells allowed us to identify several known and putative methylated proteins. In vitro methylation of selected proteins, eukaryotic translation initiation factor 4A-I and vimentin, by cellular PRMT1 was shown. Together, we have demonstrated the functional equivalence of ectopically expressed PRMT1 in HEK293 cells and its application to systematically identify the substrate proteins in a mammalian cell context. PMID:21080372

  9. Genomic and Proteomic Profiling Reveals Reduced Mitochondrial Function and Disruption of the Neuromuscular Junction Driving Rat Sarcopenia

    PubMed Central

    Ibebunjo, Chikwendu; Chick, Joel M.; Kendall, Tracee; Eash, John K.; Li, Christine; Zhang, Yunyu; Vickers, Chad; Wu, Zhidan; Clarke, Brian A.; Shi, Jun; Cruz, Joseph; Fournier, Brigitte; Brachat, Sophie; Gutzwiller, Sabine; Ma, QiCheng; Markovits, Judit; Broome, Michelle; Steinkrauss, Michelle; Skuba, Elizabeth; Galarneau, Jean-Rene; Gygi, Steven P.

    2013-01-01

    Molecular mechanisms underlying sarcopenia, the age-related loss of skeletal muscle mass and function, remain unclear. To identify molecular changes that correlated best with sarcopenia and might contribute to its pathogenesis, we determined global gene expression profiles in muscles of rats aged 6, 12, 18, 21, 24, and 27 months. These rats exhibit sarcopenia beginning at 21 months. Correlation of the gene expression versus muscle mass or age changes, and functional annotation analysis identified gene signatures of sarcopenia distinct from gene signatures of aging. Specifically, mitochondrial energy metabolism (e.g., tricarboxylic acid cycle and oxidative phosphorylation) pathway genes were the most downregulated and most significantly correlated with sarcopenia. Also, perturbed were genes/pathways associated with neuromuscular junction patency (providing molecular evidence of sarcopenia-related functional denervation and neuromuscular junction remodeling), protein degradation, and inflammation. Proteomic analysis of samples at 6, 18, and 27 months confirmed the depletion of mitochondrial energy metabolism proteins and neuromuscular junction proteins. Together, these findings suggest that therapeutic approaches that simultaneously stimulate mitochondrogenesis and reduce muscle proteolysis and inflammation have potential for treating sarcopenia. PMID:23109432

  10. Industrial robots and robotics

    SciTech Connect

    Kafrissen, S.; Stephens, M.

    1984-01-01

    This book discusses the study of robotics. It provides information of hardware, software, applications and economics. Eleven chapters examine the following: Minicomputers, Microcomputers, and Microprocessors; The Servo-Control System; The Activators; Robot Vision Systems; and Robot Workcell Environments. Twelve appendices supplement the data.

  11. Proteomics Research in Schizophrenia

    PubMed Central

    Davalieva, Katarina; Maleva Kostovska, Ivana; Dwork, Andrew J.

    2016-01-01

    Despite intense scientific efforts, the neuropathology and pathophysiology of schizophrenia are poorly understood. Proteomic studies, by testing large numbers of proteins for associations with disease, may contribute to the understanding of the molecular mechanisms of schizophrenia. They may also indicate the types and locations of cells most likely to harbor pathological alterations. Investigations using proteomic approaches have already provided much information on quantitative and qualitative protein patterns in postmortem brain tissue, peripheral tissues and body fluids. Different proteomic technologies such as 2-D PAGE, 2-D DIGE, SELDI-TOF, shotgun proteomics with label-based (ICAT), and label-free (MSE) quantification have been applied to the study of schizophrenia for the past 15 years. This review summarizes the results, mostly from brain but also from other tissues and bodily fluids, of proteomics studies in schizophrenia. Emphasis is given to proteomics platforms, varying sources of material, proposed candidate biomarkers emerging from comparative proteomics studies, and the specificity of the putative markers in terms of other mental illnesses. We also compare proteins altered in schizophrenia with reports of protein or mRNA sequences that are relatively enriched in specific cell types. While proteomic studies of schizophrenia find abnormalities in the expression of many proteins that are not cell type-specific, there appears to be a disproportionate representation of proteins whose synthesis and localization are highly enriched in one or more brain cell type compared with other types of brain cells. Two of the three proteins most commonly altered in schizophrenia are aldolase C and glial fibrillary acidic protein, astrocytic proteins with entirely different functions, but the studies are approximately evenly divided with regard to the direction of the differences and the concordance or discordance between the two proteins. Alterations of common myelin

  12. Scene analysis for a breadboard Mars robot functioning in an indoor environment

    NASA Technical Reports Server (NTRS)

    Levine, M. D.

    1973-01-01

    The problem is delt with of computer perception in an indoor laboratory environment containing rocks of various sizes. The sensory data processing is required for the NASA/JPL breadboard mobile robot that is a test system for an adaptive variably-autonomous vehicle that will conduct scientific explorations on the surface of Mars. Scene analysis is discussed in terms of object segmentation followed by feature extraction, which results in a representation of the scene in the robot's world model.

  13. Using Functional Electrical Stimulation Mediated by Iterative Learning Control and Robotics to Improve Arm Movement for People With Multiple Sclerosis.

    PubMed

    Sampson, Patrica; Freeman, Chris; Coote, Susan; Demain, Sara; Feys, Peter; Meadmore, Katie; Hughes, Ann-Marie

    2016-02-01

    Few interventions address multiple sclerosis (MS) arm dysfunction but robotics and functional electrical stimulation (FES) appear promising. This paper investigates the feasibility of combining FES with passive robotic support during virtual reality (VR) training tasks to improve upper limb function in people with multiple sclerosis (pwMS). The system assists patients in following a specified trajectory path, employing an advanced model-based paradigm termed iterative learning control (ILC) to adjust the FES to improve accuracy and maximise voluntary effort. Reaching tasks were repeated six times with ILC learning the optimum control action from previous attempts. A convenience sample of five pwMS was recruited from local MS societies, and the intervention comprised 18 one-hour training sessions over 10 weeks. The accuracy of tracking performance without FES and the amount of FES delivered during training were analyzed using regression analysis. Clinical functioning of the arm was documented before and after treatment with standard tests. Statistically significant results following training included: improved accuracy of tracking performance both when assisted and unassisted by FES; reduction in maximum amount of FES needed to assist tracking; and less impairment in the proximal arm that was trained. The system was well tolerated by all participants with no increase in muscle fatigue reported. This study confirms the feasibility of FES combined with passive robot assistance as a potentially effective intervention to improve arm movement and control in pwMS and provides the basis for a follow-up study.

  14. Robotic surgery

    MedlinePlus

    Robot-assisted surgery; Robotic-assisted laparoscopic surgery; Laparoscopic surgery with robotic assistance ... Robotic surgery is similar to laparoscopic surgery. It can be performed through smaller cuts than open surgery. ...

  15. Substrate specificity of clostridial glucosylating toxins and their function on colonocytes analyzed by proteomics techniques.

    PubMed

    Zeiser, Johannes; Gerhard, Ralf; Just, Ingo; Pich, Andreas

    2013-04-01

    Clostridium difficile is the major cause of intestinal infections in hospitals. The major virulence factors are toxin A (TcdA) and toxin B (TcdB), which belong to the group of clostridial glucosylating toxins (CGT) that inactivate small GTPases. After a 24 h incubation period with TcdA or a glucosyltransferase-deficient mutant TcdA (gdTcdA), quantitative changes in the proteome of colonic cells (Caco-2) were analyzed using high-resolution LC-MS/MS and the SILAC technique. The changes in abundance of more than 5100 proteins were quantified. Nearly 800 toxin-responsive proteins were identified that were involved in cell cycle, cell structure, and adhesion as well as metabolic processes. Several proteins localized to mitochondria or involved in lipid metabolism were consistently of higher abundance after TcdA treatment. All changes of protein abundance depended on the glucosyltransferase activity of TcdA. Glucosylation of the known targets of TcdA such as RhoA, RhoC, RhoG was detected by LC-MS/MS. In addition, an almost complete glucosylation of Rap1(A/B), Rap2(A/B/C) and a partial glucosylation of Ral(A/B) and (H/K/N)Ras were detected. The glucosylation pattern of TcdA was compared to that of other CGT like TcdB, the variant TcdB from C. difficile strain VPI 1470 (TcdBF), and lethal toxin from C. sordellii (TcsL). PMID:23387933

  16. Proteomics Analysis with a Nano Random Forest Approach Reveals Novel Functional Interactions Regulated by SMC Complexes on Mitotic Chromosomes*

    PubMed Central

    Ohta, Shinya; Montaño-Gutierrez, Luis F.; de Lima Alves, Flavia; Ogawa, Hiromi; Toramoto, Iyo; Sato, Nobuko; Morrison, Ciaran G.; Takeda, Shunichi; Hudson, Damien F.; Earnshaw, William C.

    2016-01-01

    Packaging of DNA into condensed chromosomes during mitosis is essential for the faithful segregation of the genome into daughter nuclei. Although the structure and composition of mitotic chromosomes have been studied for over 30 years, these aspects are yet to be fully elucidated. Here, we used stable isotope labeling with amino acids in cell culture to compare the proteomes of mitotic chromosomes isolated from cell lines harboring conditional knockouts of members of the condensin (SMC2, CAP-H, CAP-D3), cohesin (Scc1/Rad21), and SMC5/6 (SMC5) complexes. Our analysis revealed that these complexes associate with chromosomes independently of each other, with the SMC5/6 complex showing no significant dependence on any other chromosomal proteins during mitosis. To identify subtle relationships between chromosomal proteins, we employed a nano Random Forest (nanoRF) approach to detect protein complexes and the relationships between them. Our nanoRF results suggested that as few as 113 of 5058 detected chromosomal proteins are functionally linked to chromosome structure and segregation. Furthermore, nanoRF data revealed 23 proteins that were not previously suspected to have functional interactions with complexes playing important roles in mitosis. Subsequent small-interfering-RNA-based validation and localization tracking by green fluorescent protein-tagging highlighted novel candidates that might play significant roles in mitotic progression. PMID:27231315

  17. Differential proteomic analysis of midguts from Nosema ceranae-infected honeybees reveals manipulation of key host functions.

    PubMed

    Vidau, Cyril; Panek, Johan; Texier, Catherine; Biron, David G; Belzunces, Luc P; Le Gall, Morgane; Broussard, Cédric; Delbac, Frédéric; El Alaoui, Hicham

    2014-09-01

    Many invasive pathogens effectively bypass the insect defenses to ensure the completion of their life cycle. Among those, an invasive microsporidian species, Nosema ceranae, can cause nosemosis in honeybees. N. ceranae was first described in the Asian honeybee Apis cerana and is suspected to be involved in Western honeybee (Apis mellifera) declines worldwide. The midgut of honeybees is the first barrier against N. ceranae attacks. To bring proteomics data on honeybee/N. ceranae crosstalk and more precisely to decipher the worker honeybee midgut response after an oral inoculation of N. ceranae (10days post-infection), we used 2D-DIGE (2-Dimensional Differential In-Gel Electrophoresis) combined with mass spectrometry. Forty-five protein spots produced by the infected worker honeybee group were shown to be differentially expressed when compared to the uninfected group; 14 were subsequently identified by mass spectrometry. N. ceranae mainly caused a modulation of proteins involved in three key host biological functions: (i) energy production, (ii) innate immunity (reactive oxygen stress) and (iii) protein regulation. The modulation of these host biological functions suggests that N. ceranae creates a zone of "metabolic habitat modification" in the honeybee midgut favoring its development by enhancing availability of nutrients and reducing the worker honeybee defense.

  18. Isolation of acetylated and free N-terminal peptides from proteomic samples based on tresyl-functionalized microspheres.

    PubMed

    Li, Lanting; Yan, Guoquan; Zhang, Xiangmin

    2015-11-01

    Analysis of protein N-termini is of great importance in helping to figure out important posttranslational modifications (PTMs) occurred in N-termini. Those PTMs include initial methionine removal, proteolytic cleavage, peptide signal processing, or N-terminal acetylation, which are usually neglected by conventional shotgun proteomics strategies. Herein, we develop a protein N-terminal peptides enrichment method based on commercial tresyl-functionalized microspheres (TFM). TFM could specifically immobilize the non-N-terminal peptides (internal peptides) from the supernatant. We demonstrated the isolation by TFM was more fast and efficient than formyl or epoxy-functionalized microspheres. Furthermore, this method could simultaneously isolate not only naturally free but acetylated blocked N-terminus. That facilitates a more comprehensive acquisition of N-terminus. After being verified by three standard proteins, cytochrome C, ribonuclease B and bovine serum albumin, this method was applied to mouse liver protein sample. We identified 122 naturally acetylated N-terminus and 107 free N-terminus in the sample. With the good performance of TFM, this method is efficient and useful for N-termini recovery.

  19. Enabling Proteomics Discovery Through Visual Analysis

    SciTech Connect

    Havre, Susan L.; Singhal, Mudita; Payne, Deborah A.; Lipton, Mary S.; Webb-Robertson, Bobbie-Jo M.

    2005-05-01

    With the completion of the Human Genome Project and the sequencing of large genomes, proteomics is the new big challenge. A proteome is the collection of all the proteins present in an organism at a given moment. Unlike the genome, the proteome is dynamic, changing continuously in response to tens of thousands of intra- and extra-cellular environmental signals. Proteomics is the study of proteomes under different conditions—for example, over time, under different environments, or in different disease states. Because proteins are the key actors in cellular processes and proteomics is the study of not one or two proteins at a time but whole proteomes, proteomics has a key role in revealing the complex processes of cells at a global or systems level. There are several high-throughput proteomics techniques; all generate data faster than the data can currently be analyzed. The tremendous size and complexity of the high-throughput experimental data make it very difficult to process and interpret. The success of proteomics will rely on high-throughput experimental techniques coupled with sophisticated visual analysis and data mining methods. This article presents the motivation for developing visual analysis tools for proteomic data and demonstrates their application to proteomics research with a visualization tool named Peptide Permutation and Protein Prediction, or PQuad. PQuad is a functioning visual analytic tool in operation at the Pacific Northwest National Laboratory for the study of systems biology. PQuad supports the exploration of proteins identified by proteomic techniques in the context of supplemental biological information.

  20. A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes1[OPEN

    PubMed Central

    Malik, Waqas Ahmed; Shen, Zhouxin; Paschold, Anja

    2015-01-01

    A high-resolution proteome and phosphoproteome atlas of four maize (Zea mays) primary root tissues, the cortex, stele, meristematic zone, and elongation zone, was generated. High-performance liquid chromatography coupled with tandem mass spectrometry identified 11,552 distinct nonmodified and 2,852 phosphorylated proteins across the four root tissues. Two gradients reflecting the abundance of functional protein classes along the longitudinal root axis were observed. While the classes RNA, DNA, and protein peaked in the meristematic zone, cell wall, lipid metabolism, stress, transport, and secondary metabolism culminated in the differentiation zone. Functional specialization of tissues is underscored by six of 10 cortex-specific proteins involved in flavonoid biosynthesis. Comparison of this data set with high-resolution seed and leaf proteome studies revealed 13% (1,504/11,552) root-specific proteins. While only 23% of the 1,504 root-specific proteins accumulated in all four root tissues, 61% of all 11,552 identified proteins accumulated in all four root tissues. This suggests a much higher degree of tissue-specific functionalization of root-specific proteins. In summary, these data illustrate the remarkable plasticity of the proteomic landscape of maize primary roots and thus provide a starting point for gaining a better understanding of their tissue-specific functions. PMID:25780097

  1. A high-resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axes.

    PubMed

    Marcon, Caroline; Malik, Waqas Ahmed; Walley, Justin W; Shen, Zhouxin; Paschold, Anja; Smith, Laurie G; Piepho, Hans-Peter; Briggs, Steven P; Hochholdinger, Frank

    2015-05-01

    A high-resolution proteome and phosphoproteome atlas of four maize (Zea mays) primary root tissues, the cortex, stele, meristematic zone, and elongation zone, was generated. High-performance liquid chromatography coupled with tandem mass spectrometry identified 11,552 distinct nonmodified and 2,852 phosphorylated proteins across the four root tissues. Two gradients reflecting the abundance of functional protein classes along the longitudinal root axis were observed. While the classes RNA, DNA, and protein peaked in the meristematic zone, cell wall, lipid metabolism, stress, transport, and secondary metabolism culminated in the differentiation zone. Functional specialization of tissues is underscored by six of 10 cortex-specific proteins involved in flavonoid biosynthesis. Comparison of this data set with high-resolution seed and leaf proteome studies revealed 13% (1,504/11,552) root-specific proteins. While only 23% of the 1,504 root-specific proteins accumulated in all four root tissues, 61% of all 11,552 identified proteins accumulated in all four root tissues. This suggests a much higher degree of tissue-specific functionalization of root-specific proteins. In summary, these data illustrate the remarkable plasticity of the proteomic landscape of maize primary roots and thus provide a starting point for gaining a better understanding of their tissue-specific functions.

  2. Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints

    PubMed Central

    Axe, Douglas D.; Dixon, Brendan W.; Lu, Philip

    2008-01-01

    The study of protein evolution is complicated by the vast size of protein sequence space, the huge number of possible protein folds, and the extraordinary complexity of the causal relationships between protein sequence, structure, and function. Much simpler model constructs may therefore provide an attractive complement to experimental studies in this area. Lattice models, which have long been useful in studies of protein folding, have found increasing use here. However, while these models incorporate actual sequences and structures (albeit non-biological ones), they incorporate no actual functions—relying instead on largely arbitrary structural criteria as a proxy for function. In view of the central importance of function to evolution, and the impossibility of incorporating real functional constraints without real function, it is important that protein-like models be developed around real structure–function relationships. Here we describe such a model and introduce open-source software that implements it. The model is based on the structure–function relationship in written language, where structures are two-dimensional ink paths and functions are the meanings that result when these paths form legible characters. To capture something like the hierarchical complexity of protein structure, we use the traditional characters of Chinese origin. Twenty coplanar vectors, encoded by base triplets, act like amino acids in building the character forms. This vector-world model captures many aspects of real proteins, including life-size sequences, a life-size structural repertoire, a realistic genetic code, secondary, tertiary, and quaternary structure, structural domains and motifs, operon-like genetic structures, and layered functional complexity up to a level resembling bacterial genomes and proteomes. Stylus is a full-featured implementation of the vector world for Unix systems. To demonstrate the utility of Stylus, we generated a sample set of homologous vector

  3. Physiological and iTRAQ-Based Proteomic Analyses Reveal the Function of Spermidine on Improving Drought Tolerance in White Clover.

    PubMed

    Li, Zhou; Zhang, Yan; Xu, Yi; Zhang, Xinquan; Peng, Yan; Ma, Xiao; Huang, Linkai; Yan, Yanhong

    2016-05-01

    Endogenous spermidine interacting with phytohormones may be involved in the regulation of differentially expressed proteins (DEPs) associated with drought tolerance in white clover. Plants treated with or without spermidine (50 μM) were subjected to 20% PEG 6000 nutrient solution to induce drought stress (50% leaf-relative water content). The results showed that increased endogenous spermidine induced by exogenous spermidine altered endogenous phytohormones in association with improved drought tolerance, as demonstrated by the delay in water-deficit development, improved photosynthesis and water use efficiency, and lower oxidative damage. As compared to untreated plants, Spd-treated plants maintained a higher abundance of DEPs under drought stress involved in (1) protein biosynthesis (ribosomal and chaperone proteins); (2) amino acids synthesis; (3) the carbon and energy metabolism; (4) antioxidant and stress defense (ascorbate peroxidase, glutathione peroxidase, and dehydrins); and (5) GA and ABA signaling pathways (gibberellin receptor GID1, ABA-responsive protein 17, and ABA stress ripening protein). Thus, the findings of proteome could explain the Spd-induced physiological effects associated with drought tolerance. The analysis of functional protein-protein networks further proved that the alteration of endogenous spermidine and phytohormones induced the interaction among ribosome, photosynthesis, carbon metabolism, and amino acid biosynthesis. These differences could contribute to improved drought tolerance. PMID:27030016

  4. Proteomic and functional analysis of proline dehydrogenase 1 link proline catabolism to mitochondrial electron transport in Arabidopsis thaliana.

    PubMed

    Cabassa-Hourton, Cécile; Schertl, Peter; Bordenave-Jacquemin, Marianne; Saadallah, Kaouthar; Guivarc'h, Anne; Lebreton, Sandrine; Planchais, Séverine; Klodmann, Jennifer; Eubel, Holger; Crilat, Emilie; Lefebvre-De Vos, Delphine; Ghelis, Thanos; Richard, Luc; Abdelly, Chedly; Carol, Pierre; Braun, Hans-Peter; Savouré, Arnould

    2016-09-01

    Proline accumulates in many plant species in response to environmental stresses. Upon relief from stress, proline is rapidly oxidized in mitochondria by proline dehydrogenase (ProDH) and then by pyrroline-5-carboxylate dehydrogenase (P5CDH). Two ProDH genes have been identified in the genome of the model plant Arabidopsis thaliana To gain a better understanding of ProDH1 functions in mitochondria, proteomic analysis was performed. ProDH1 polypeptides were identified in Arabidopsis mitochondria by immunoblotting gels after 2D blue native (BN)-SDS/PAGE, probing them with an anti-ProDH antibody and analysing protein spots by MS. The 2D gels showed that ProDH1 forms part of a low-molecular-mass (70-140 kDa) complex in the mitochondrial membrane. To evaluate the contribution of each isoform to proline oxidation, mitochondria were isolated from wild-type (WT) and prodh1, prodh2, prodh1prodh2 and p5cdh mutants. ProDH activity was high for genotypes in which ProDH, most likely ProDH1, was strongly induced by proline. Respiratory measurements indicate that ProDH1 has a role in oxidizing excess proline and transferring electrons to the respiratory chain. PMID:27303048

  5. Proteomic and functional analyses reveal a dual molecular mechanism underlying arsenic-induced apoptosis in human multiple myeloma cells.

    PubMed

    Ge, Feng; Lu, Xin-Peng; Zeng, Hui-Lan; He, Quan-Yuan; Xiong, Sheng; Jin, Lin; He, Qing-Yu

    2009-06-01

    Multiple myeloma (MM) is an incurable plasma cell malignancy with a terminal phase marked by increased proliferation and resistance to therapy. Arsenic trioxide (ATO), an antitumor agent with a multifaceted mechanism of action, displayed clinical activity in patients with late-stage multiple myeloma. However, the precise mechanism(s) of action of ATO has not been completely elucidated. In the present study, we used proteomics to analyze the ATO-induced protein alterations in MM cell line U266 and then investigated the molecular pathways responsible for the anticancer actions of ATO. Several clusters of proteins altered in expression in U266 cells upon ATO treatment were identified, including down-regulated signal transduction proteins and ubiquitin/proteasome members, and up-regulated immunity and defense proteins. Significantly regulated 14-3-3zeta and heat shock proteins (HSPs) were selected for further functional studies. Overexpression of 14-3-3zeta in MM cells attenuated ATO-induced cell death, whereas RNAi-based 14-3-3zeta knock-down or the inhibition of HSP90 enhanced tumor cell sensitivity to the ATO induction. These observations implicate 14-3-3zeta and HSP90 as potential molecular targets for drug intervention of multiple myeloma and thus improve our understanding on the mechanisms of antitumor activity of ATO.

  6. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

    PubMed

    Shameer, Khader; Tripathi, Lokesh P; Kalari, Krishna R; Dudley, Joel T; Sowdhamini, Ramanathan

    2016-09-01

    Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics. Ascribing functional roles and/or clinical significances to single nucleotide variants identified from a next-generation sequencing study is an important step in genome interpretation. Experimental characterization of all the observed functional variants is yet impractical; thus, the prediction of functional and/or regulatory impacts of the various mutations using in silico approaches is an important step toward the identification of functionally significant or clinically actionable variants. The relationships between genotypes and the expressed phenotypes are multilayered and biologically complex; such relationships present numerous challenges and at the same time offer various opportunities for the design of in silico variant assessment strategies. Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions. In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants. We discuss the currently available approaches and major challenges from the perspective of protein sequence, structure, function and interactions that require consideration when interpreting the impact of putatively functional variants. We also discuss the relevance of incorporating integrated workflows for predicting the biomedical impact of the functionally important variations encoded in a genome, exome or transcriptome. Finally, we propose a framework to classify variant assessment approaches and strategies for incorporation of variant assessment within electronic health records.

  7. Beer and wort proteomics.

    PubMed

    Iimure, Takashi; Kihara, Makoto; Sato, Kazuhiro

    2014-01-01

    Proteome analysis provides a way to identify proteins related to the quality traits of beer. A number of protein species in beer and wort have been identified by two-dimensional gel electrophoresis combined with enzyme digestion such as trypsin, followed by mass spectrometry analyses and/or liquid chromatography mass/mass spectrometry. In addition, low molecular weight polypeptides in beer have been identified by the combination of non-enzyme digestion and mass analyses. These data sets of various molecular weight polypeptides (i.e., proteomes) provide a platform for analyzing protein functions in beer. Several novel proteins related to beer quality traits such as foam stability and haze formation have been identified by analyzing these proteomes. Some of the proteins have been applied to the development of efficient protein or DNA markers for trait selection in malting barley breeding. In this chapter, recent proteome studies of beer and wort are reviewed, and the methods and protocols of beer and wort proteome analysis are described.

  8. Proteomics in alcohol research.

    PubMed

    Anni, Helen; Israel, Yedy

    2002-01-01

    The proteome is the complete set of proteins in an organism. It is considerably larger and more complex than the genome--the collection of genes that encodes these proteins. Proteomics deals with the qualitative and quantitative study of the proteome under physiological and pathological conditions (e.g., after exposure to alcohol, which causes major changes in numerous proteins of different cell types). To map large proteomes such as the human proteome, proteins from discrete tissues, cells, cell components, or biological fluids are first separated by high-resolution two-dimensional electrophoresis and multidimensional liquid chromatography. Then, individual proteins are identified by mass spectrometry. The huge amount of data acquired using these techniques is analyzed and assembled by fast computers and bioinformatics tools. Using these methods, as well as other technological advances, alcohol researchers can gain a better understanding of how alcohol globally influences protein structure and function, protein-protein interactions, and protein networks. This knowledge ultimately will assist in the early diagnosis and prognosis of alcoholism and the discovery of new drug targets and medications for treatment.

  9. Biophotonics applied to proteomics.

    PubMed

    Faupel, Michel; Bonenfant, Débora; Schindler, Patrick; Bertrand, Eric; Mueller, Dieter; Stoeckli, Markus; Bitsch, Francis; Rohner, Tatiana; Staab, Dieter; Van Oostrum, Jan

    2007-01-01

    Since the completion of the human genome sequencing, our understanding of gene and protein function and their involvement in physiopathological states has increased dramatically, partly due to technological developments in photonics. Photonics is a very active area where new developments occur on a weekly basis, while established tools are adapted to fulfill the needs of other disciplines like genomics and proteomics. Biophotonics emerged at the interface of photonics and biology as a very straightforward and efficient approach to observe and manipulate living systems. In this chapter, we review the current applications of photonics and imaging to proteomics from 2D gels analysis to molecular imaging.

  10. Recent advances in chemical proteomics: exploring the post-translational proteome.

    PubMed

    Tate, Edward W

    2008-11-01

    Identification and quantification of multiple proteins from complex mixtures is a central theme in post-genomic biology. Despite recent progress in high-throughput proteomics, proteomic analysis of post-translationally modified (PTM) proteins remains particularly challenging. This mini-review introduces the emerging field of chemical proteomics and reviews recent advances in chemical proteomic technology that are offering striking new insights into the functional biology of post-translational modification.

  11. Algal Functional Annotation Tool from the DOE-UCLA Institute for Genomics and Proteomics

    DOE Data Explorer

    Lopez, David

    The Algal Functional Annotation Tool is a bioinformatics resource to visualize pathway maps, identify enriched biological terms, or convert gene identifiers to elucidate biological function in silico. These types of analysis have been catered to support lists of gene identifiers, such as those coming from transcriptome gene expression analysis. By analyzing the functional annotation of an interesting set of genes, common biological motifs may be elucidated and a first-pass analysis can point further research in the right direction. Currently, the following databases have been parsed, processed, and added to the tool: 1( Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways Database, 2) MetaCyc Encyclopedia of Metabolic Pathways, 3) Panther Pathways Database, 4) Reactome Pathways Database, 5) Gene Ontology, 6) MapMan Ontology, 7) KOG (Eukaryotic Clusters of Orthologous Groups), 5)Pfam, 6) InterPro.

  12. Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition.

    PubMed

    Mao, Chunhong; Shukla, Maulik; Larrouy-Maumus, Gérald; Dix, Flora L; Kelley, Lawrence A; Sternberg, Michael J; Sobral, Bruno W; de Carvalho, Luiz Pedro S

    2013-01-01

    Hundreds of putative enzymes from Mycobacterium tuberculosis as well as other mycobacteria remain categorized as "conserved hypothetical proteins" or "hypothetical proteins", offering little or no information on their functional role in pathogenic and non-pathogenic processes. In this study we have predicted the fold and 3-D structure of more than 99% of all proteins encoded in the genome of M. tuberculosis H37Rv. Fold-recognition, database search, 3-D modelling was performed using Protein Homology/analogy Recognition Engine V 2.0 (Phyre2). These results are used to tentatively assign potential function for unannotated enzymes and proteins. In summary, fold-recognition and structural homology might be used as a complementary tool in genome annotation efforts and furthermore, it can deliver primary sequence-independent information regarding structure, ligands and even substrate specificity for enzymes that display low primary sequence identity with potential homologues in other species.

  13. LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris

    SciTech Connect

    Zhang, Weiwen; Culley, David E.; Gritsenko, Marina A.; Moore, Ronald J.; Nie, Lei; Scholten, Johannes C.; Petritis, Konstantinos; Strittmatter, Eric F.; Camp, David G.; Smith, Richard D.; Brockman, Fred J.

    2006-11-03

    ABSTRACT In the previous study, the whole-genome gene expression profiles of D. vulgaris in response to oxidative stress and heat shock were determined. The results showed 24-28% of the responsive genes were hypothetical proteins that have not been experimentally characterized or whose function can not be deduced by simple sequence comparison. To further explore the protecting mechanisms employed in D. vulgaris against the oxidative stress and heat shock, attempt was made in this study to infer functions of these hypothetical proteins by phylogenomic profiling along with detailed sequence comparison against various publicly available databases. By this approach we were ableto assign possible functions to 25 responsive hypothetical proteins. The findings included that DVU0725, induced by oxidative stress, may be involved in lipopolysaccharide biosynthesis, implying that the alternation of lipopolysaccharide on cell surface might service as a mechanism against oxidative stress in D. vulgaris. In addition, two responsive proteins, DVU0024 encoding a putative transcriptional regulator and DVU1670 encoding predicted redox protein, were sharing co-evolution atterns with rubrerythrin in Archaeoglobus fulgidus and Clostridium perfringens, respectively, implying that they might be part of the stress response and protective systems in D. vulgaris. The study demonstrated that phylogenomic profiling is a useful tool in interpretation of experimental genomics data, and also provided further insight on cellular response to oxidative stress and heat shock in D. vulgaris.

  14. Translating Proteomic Into Functional Data: An High Mobility Group A1 (HMGA1) Proteomic Signature Has Prognostic Value in Breast Cancer*

    PubMed Central

    Maurizio, Elisa; Wiśniewski, Jacek R.; Ciani, Yari; Amato, Angela; Arnoldo, Laura; Penzo, Carlotta; Pegoraro, Silvia; Giancotti, Vincenzo; Zambelli, Alberto; Piazza, Silvano; Manfioletti, Guidalberto; Sgarra, Riccardo

    2016-01-01

    Cancer is a very heterogeneous disease, and biological variability adds a further level of complexity, thus limiting the ability to identify new genes involved in cancer development. Oncogenes whose expression levels control cell aggressiveness are very useful for developing cellular models that permit differential expression screenings in isogenic contexts. HMGA1 protein has this unique property because it is a master regulator in breast cancer cells that control the transition from a nontumorigenic epithelial-like phenotype toward a highly aggressive mesenchymal-like one. The proteins extracted from HMGA1-silenced and control MDA-MB-231 cells were analyzed using label-free shotgun mass spectrometry. The differentially expressed proteins were cross-referenced with DNA microarray data obtained using the same cellular model and the overlapping genes were filtered for factors linked to poor prognosis in breast cancer gene expression meta-data sets, resulting in an HMGA1 protein signature composed of 21 members (HRS, HMGA1 reduced signature). This signature had a prognostic value (overall survival, relapse-free survival, and distant metastasis-free survival) in breast cancer. qRT-PCR, Western blot, and immunohistochemistry analyses validated the link of three members of this signature (KIFC1, LRRC59, and TRIP13) with HMGA1 expression levels both in vitro and in vivo and wound healing assays demonstrated that these three proteins are involved in modulating tumor cell motility. Combining proteomic and genomic data with the aid of bioinformatic tools, our results highlight the potential involvement in neoplastic transformation of a restricted list of factors with an as-yet-unexplored role in cancer. These factors are druggable targets that could be exploited for the development of new, targeted therapeutic approaches in triple-negative breast cancer. PMID:26527623

  15. Proteomics of extremophiles.

    PubMed

    Burg, Dominic; Ng, Charmaine; Ting, Lily; Cavicchioli, Ricardo

    2011-08-01

    Functional genomic approaches, such as proteomics, greatly enhance the value of genome sequences by providing a global level assessment of which genes are expressed, when genes are expressed and at what cellular levels gene products are synthesized. With over 1000 complete genome sequences of different microorganisms available, and DNA sequencing for environmental samples (metagenomes) producing vast amounts of gene sequence data, there is a real opportunity and a clear need to generate associated functional genomic data to learn about the source microorganisms. In contrast to the technological advances that have led to the accelerated rate and ease at which DNA sequence data can be generated, mass spectrometry based proteomics remains a technically sophisticated and exacting science. In recognition of the need to make proteomics more accessible to a growing number of environmental microbiologists so that the 'functional genomics gap' may be bridged, this review strives to demystify proteomic technologies and describe ways in which they have been applied, and more importantly, can be applied to study the physiology and ecology of extremophiles.

  16. Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach

    PubMed Central

    2014-01-01

    Background Induced resistance (IR) can be part of a sustainable plant protection strategy against important plant diseases. β-aminobutyric acid (BABA) can induce resistance in a wide range of plants against several types of pathogens, including potato infected with Phytophthora infestans. However, the molecular mechanisms behind this are unclear and seem to be dependent on the system studied. To elucidate the defence responses activated by BABA in potato, a genome-wide transcript microarray analysis in combination with label-free quantitative proteomics analysis of the apoplast secretome were performed two days after treatment of the leaf canopy with BABA at two concentrations, 1 and 10 mM. Results Over 5000 transcripts were differentially expressed and over 90 secretome proteins changed in abundance indicating a massive activation of defence mechanisms with 10 mM BABA, the concentration effective against late blight disease. To aid analysis, we present a more comprehensive functional annotation of the microarray probes and gene models by retrieving information from orthologous gene families across 26 sequenced plant genomes. The new annotation provided GO terms to 8616 previously un-annotated probes. Conclusions BABA at 10 mM affected several processes related to plant hormones and amino acid metabolism. A major accumulation of PR proteins was also evident, and in the mevalonate pathway, genes involved in sterol biosynthesis were down-regulated, whereas several enzymes involved in the sesquiterpene phytoalexin biosynthesis were up-regulated. Interestingly, abscisic acid (ABA) responsive genes were not as clearly regulated by BABA in potato as previously reported in Arabidopsis. Together these findings provide candidates and markers for improved resistance in potato, one of the most important crops in the world. PMID:24773703

  17. Proteome complexity and the forces that drive proteome imbalance.

    PubMed

    Harper, J Wade; Bennett, Eric J

    2016-01-01

    The cellular proteome is a complex microcosm of structural and regulatory networks that requires continuous surveillance and modification to meet the dynamic needs of the cell. It is therefore crucial that the protein flux of the cell remains in balance to ensure proper cell function. Genetic alterations that range from chromosome imbalance to oncogene activation can affect the speed, fidelity and capacity of protein biogenesis and degradation systems, which often results in proteome imbalance. An improved understanding of the causes and consequences of proteome imbalance is helping to reveal how these systems can be targeted to treat diseases such as cancer. PMID:27629639

  18. Reinforcement function design and bias for efficient learning in mobile robots

    SciTech Connect

    Touzet, C.; Santos, J.M.

    1998-06-01

    The main paradigm in sub-symbolic learning robot domain is the reinforcement learning method. Various techniques have been developed to deal with the memorization/generalization problem, demonstrating the superior ability of artificial neural network implementations. In this paper, the authors address the issue of designing the reinforcement so as to optimize the exploration part of the learning. They also present and summarize works relative to the use of bias intended to achieve the effective synthesis of the desired behavior. Demonstrative experiments involving a self-organizing map implementation of the Q-learning and real mobile robots (Nomad 200 and Khepera) in a task of obstacle avoidance behavior synthesis are described. 3 figs., 5 tabs.

  19. Divergent metabolome and proteome suggest functional independence of dual phloem transport systems in cucurbits

    PubMed Central

    Zhang, Baichen; Tolstikov, Vladimir; Turnbull, Colin; Hicks, Leslie M.; Fiehn, Oliver

    2010-01-01

    Cucurbitaceous plants (cucurbits) have long been preferred models for studying phloem physiology. However, these species are unusual in that they possess two different phloem systems, one within the main vascular bundles [fascicular phloem (FP)] and another peripheral to the vascular bundles and scattered through stem and petiole cortex tissues [extrafascicular phloem (EFP)]. We have revisited the assumption that the sap released after shoot incision originates from the FP, and also investigated the long-standing question of why the sugar content of this sap is ~30-fold less than predicted for requirements of photosynthate delivery. Video microscopy and phloem labeling experiments unexpectedly reveal that FP very quickly becomes blocked upon cutting, whereas the extrafascicular phloem bleeds for extended periods. Thus, all cucurbit phloem sap studies to date have reported metabolite, protein, and RNA composition and transport in the relatively minor extrafascicular sieve tubes. Using tissue dissection and direct sampling of sieve tube contents, we show that FP in fact does contain up to 1 M sugars, in contrast to low-millimolar levels in the EFP. Moreover, major phloem proteins in sieve tubes of FP differ from those that predominate in the extrafascicular sap, and include several previously uncharacterized proteins with little or no homology to databases. The overall compositional differences of the two phloem systems strongly indicate functional isolation. On this basis, we propose that the fascicular phloem is largely responsible for sugar transport, whereas the extrafascicular phloem may function in signaling, defense, and transport of other metabolites. PMID:20566864

  20. Nanoscale Proteomics

    SciTech Connect

    Shen, Yufeng; Tolic, Nikola; Masselon, Christophe D.; Pasa-Tolic, Liljiana; Camp, David G.; Anderson, Gordon A.; Smith, Richard D.; Lipton, Mary S.

    2004-02-01

    This paper describes efforts to develop a liquid chromatography (LC)/mass spectrometry (MS) technology for ultra-sensitive proteomics studies, i.e. nanoscale proteomics. The approach combines high-efficiency nano-scale LC with advanced MS, including high sensitivity and high resolution Fourier transform ion cyclotron resonance (FTICR) MS, to perform both single-stage MS and tandem MS (MS/MS) proteomic analyses. The technology developed enables large-scale protein identification from nanogram size proteomic samples and characterization of more abundant proteins from sub-picogram size complex samples. Protein identification in such studies using MS is feasible from <75 zeptomole of a protein, and the average proteome measurement throughput is >200 proteins/h and ~3 h/sample. Higher throughput (>1000 proteins/h) and more sensitive detection limits can be obtained using a “accurate mass and time” tag approach developed at our laboratory. These capabilities lay the foundation for studies from single or limited numbers of cells.

  1. Mechanochemically Active Soft Robots.

    PubMed

    Gossweiler, Gregory R; Brown, Cameron L; Hewage, Gihan B; Sapiro-Gheiler, Eitan; Trautman, William J; Welshofer, Garrett W; Craig, Stephen L

    2015-10-14

    The functions of soft robotics are intimately tied to their form-channels and voids defined by an elastomeric superstructure that reversibly stores and releases mechanical energy to change shape, grip objects, and achieve complex motions. Here, we demonstrate that covalent polymer mechanochemistry provides a viable mechanism to convert the same mechanical potential energy used for actuation in soft robots into a mechanochromic, covalent chemical response. A bis-alkene functionalized spiropyran (SP) mechanophore is cured into a molded poly(dimethylsiloxane) (PDMS) soft robot walker and gripper. The stresses and strains necessary for SP activation are compatible with soft robot function. The color change associated with actuation suggests opportunities for not only new color changing or camouflaging strategies, but also the possibility for simultaneous activation of latent chemistry (e.g., release of small molecules, change in mechanical properties, activation of catalysts, etc.) in soft robots. In addition, mechanochromic stress mapping in a functional robotic device might provide a useful design and optimization tool, revealing spatial and temporal force evolution within the robot in a way that might be coupled to autonomous feedback loops that allow the robot to regulate its own activity. The demonstration motivates the simultaneous development of new combinations of mechanophores, materials, and soft, active devices for enhanced functionality.

  2. Mechanochemically Active Soft Robots.

    PubMed

    Gossweiler, Gregory R; Brown, Cameron L; Hewage, Gihan B; Sapiro-Gheiler, Eitan; Trautman, William J; Welshofer, Garrett W; Craig, Stephen L

    2015-10-14

    The functions of soft robotics are intimately tied to their form-channels and voids defined by an elastomeric superstructure that reversibly stores and releases mechanical energy to change shape, grip objects, and achieve complex motions. Here, we demonstrate that covalent polymer mechanochemistry provides a viable mechanism to convert the same mechanical potential energy used for actuation in soft robots into a mechanochromic, covalent chemical response. A bis-alkene functionalized spiropyran (SP) mechanophore is cured into a molded poly(dimethylsiloxane) (PDMS) soft robot walker and gripper. The stresses and strains necessary for SP activation are compatible with soft robot function. The color change associated with actuation suggests opportunities for not only new color changing or camouflaging strategies, but also the possibility for simultaneous activation of latent chemistry (e.g., release of small molecules, change in mechanical properties, activation of catalysts, etc.) in soft robots. In addition, mechanochromic stress mapping in a functional robotic device might provide a useful design and optimization tool, revealing spatial and temporal force evolution within the robot in a way that might be coupled to autonomous feedback loops that allow the robot to regulate its own activity. The demonstration motivates the simultaneous development of new combinations of mechanophores, materials, and soft, active devices for enhanced functionality. PMID:26390078

  3. Towards the molecular dissection of fertilization signaling: Our functional genomic/proteomic strategies.

    PubMed

    Sato, Ken-Ichi; Iwasaki, Tetsushi; Sakakibara, Ken-Ichi; Itakura, Shuji; Fukami, Yasuo

    2002-09-01

    Recent advances in DNA sequencing techniques and automated informatics has led to clarification of all genome sequence of some model organisms in a very short period. The demonstration of the first draft sequence of the human genome has prompted us to elaborate new approaches in biology, pharmacology and medicine. Such new research will focus on high throughput methods to function on collections of genes, and hopefully, on a genome-wide, quantitative modeling of the cell system as a whole. In this review article, we discuss the present status of "post genome sequencing" approaches in line with our strategies for understanding the molecular mechanism of fertilization and activation of development using the African clawed frog, Xenopus laevis, as a model system.

  4. [Robotic surgery: marking time?].

    PubMed

    van der Poel, Henk G; Beerlage, Harry P; Klaver, Sjoerd O

    2013-01-01

    Robot-assisted surgery provides the next step in surgical evolution. Where laparoscopic surgery shortened both hospital stay and recovery, it often prolonged the surgical procedure. Novel laparoscopic instruments such as robotic systems improve visibility and patient outcome. Recent randomized studies show improved functional patient outcome after robot-assisted laparoscopic prostatectomy. Introduction of image-guided surgical technologies is aided by robotic systems. Outside medicine, randomized controlled studies in technological improvements are non-existent. A careful monitoring of study results is mandatory for the introduction of novel technologies in the field of medicine.

  5. Chlamydomonas proteomics.

    PubMed

    Rolland, Norbert; Atteia, Ariane; Decottignies, Paulette; Garin, Jérôme; Hippler, Michael; Kreimer, Georg; Lemaire, Stéphane D; Mittag, Maria; Wagner, Volker

    2009-06-01

    Chlamydomonas reinhardtii is a biflagellate and photosynthetic unicellular alga that has long fascinated scientists because it combines characteristics of both plants and animals. Chlamydomonas offers the simplicity of a unicellular organism that is amenable to genetic screening, molecular, and biochemical approaches, as well as to transformation of its nuclear, plastid, or mitochondrial genomes. Over the past decade, proteomics based studies of Chlamydomonas have provided major research contributions in the areas of photosynthesis, molecular biology, and evolution. This review refers to technical and biological aspects of proteomics studies that have been recently performed on the C. reinhardtii model organism.

  6. Robotics and Industrial Arts.

    ERIC Educational Resources Information Center

    Edmison, Glenn A.; And Others

    Robots are becoming increasingly common in American industry. By l990, they will revolutionize the way industry functions, replacing hundreds of workers and doing hot, dirty jobs better and more quickly than the workers could have done them. Robotics should be taught in high school industrial arts programs as a major curriculum component. The…

  7. Functional and Proteomic Investigations Reveal Major Royal Jelly Protein 1 Associated with Anti-hypertension Activity in Mouse Vascular Smooth Muscle Cells

    PubMed Central

    Fan, Pei; Han, Bin; Feng, Mao; Fang, Yu; Zhang, Lan; Hu, Han; Hao, Yue; Qi, Yuping; Zhang, Xiaozhen; Li, Jianke

    2016-01-01

    Vascular smooth muscle cells (VSMCs) are a major cell type of the arterial wall and their functionality is associated with blood pressure regulation. Although royal jelly (RJ) has reported effects on anti-hypertension, the mechanism of blood pressure regulation by major royal jelly protein 1 (MRJP1), the most abundant RJ protein, is still unknown. The mrjp1 gene was inserted into mouse VSMCs to investigate how MRJP1 influences VSMC functionality by functional and proteomic analysis. The expression of MRJP1 in VSMCs significantly reduced cell contraction, migration, and proliferation, suggesting a potential role in decreasing hypertension via action on VSMCs. These anti-hypertension activities were further observed in the changes of the proteome setting of mouse VSMCs. Among 675 different proteins after MRJP1 expression, 646 were down-regulated and significantly enriched in pathways implicated in VSMC contraction and migration, which suggest MRJP1 lowers VSMC contraction and migration by inhibiting muscle filament movement. The down-regulated proteins also enriched pathways in proliferation, indicating that MRJP1 hinders VSMC proliferation by reducing the supply of energy and genetic material. This is the first report integrating MRJP1 into VSMC, revealing the function and mechanism correlated with anti-hypertensive activity. This offers a therapeutic potential to control hypertension by gene-therapy using bee-products. PMID:27444336

  8. Functional and Proteomic Investigations Reveal Major Royal Jelly Protein 1 Associated with Anti-hypertension Activity in Mouse Vascular Smooth Muscle Cells.

    PubMed

    Fan, Pei; Han, Bin; Feng, Mao; Fang, Yu; Zhang, Lan; Hu, Han; Hao, Yue; Qi, Yuping; Zhang, Xiaozhen; Li, Jianke

    2016-01-01

    Vascular smooth muscle cells (VSMCs) are a major cell type of the arterial wall and their functionality is associated with blood pressure regulation. Although royal jelly (RJ) has reported effects on anti-hypertension, the mechanism of blood pressure regulation by major royal jelly protein 1 (MRJP1), the most abundant RJ protein, is still unknown. The mrjp1 gene was inserted into mouse VSMCs to investigate how MRJP1 influences VSMC functionality by functional and proteomic analysis. The expression of MRJP1 in VSMCs significantly reduced cell contraction, migration, and proliferation, suggesting a potential role in decreasing hypertension via action on VSMCs. These anti-hypertension activities were further observed in the changes of the proteome setting of mouse VSMCs. Among 675 different proteins after MRJP1 expression, 646 were down-regulated and significantly enriched in pathways implicated in VSMC contraction and migration, which suggest MRJP1 lowers VSMC contraction and migration by inhibiting muscle filament movement. The down-regulated proteins also enriched pathways in proliferation, indicating that MRJP1 hinders VSMC proliferation by reducing the supply of energy and genetic material. This is the first report integrating MRJP1 into VSMC, revealing the function and mechanism correlated with anti-hypertensive activity. This offers a therapeutic potential to control hypertension by gene-therapy using bee-products. PMID:27444336

  9. Functional electrical stimulation based on a pelvis support robot for gait rehabilitation of hemiplegic patients after stroke.

    PubMed

    Ye, Jing; Nakashima, Yasutaka; Zhang, Bo; Kobayashi, Yo; Fujie, Masakatsu G

    2014-01-01

    More and more stroke survivors are suffering from physical motor impairments. Current therapeutic interventions have various limits to the efficient recovery of normal motor function of the lower limbs. Therefore, we propose a novel gait rehabilitation system for hemiplegic patients after stroke. It integrates functional electrical stimulation (FES) with a pelvis-supporting robotic system. A corresponding relationship between the gait phase and the active lateral movement of the pelvis is first constructed from experiments on simulated hemiplegic patients. By estimating the gait phase from the lateral motion of the pelvis based on this relationship, the timing of FES sent to the muscles of the lower limbs can be automatically determined during a gait cycle. After experiments on simulated hemiplegic stroke survivors with the FES control algorithm, the proposed algorithm and the gait rehabilitation system are verified to be feasible and promising.

  10. MRH-5 Robot/Student Manual.

    ERIC Educational Resources Information Center

    Fox Valley Technical Coll., Appleton, WI.

    This student manual for the Miller MRH-5 welding robot contains nine modules on how to: safely operate the MRH-5 robot; recognize different types of data; weld a part programming the MRH-5; re-teach an already taught program; weld various joints with the MRH-5 robot; weld a desk plaque with the MRH-5 robot; perform editing functions; check/edit…

  11. Robotic comfort zones

    NASA Astrophysics Data System (ADS)

    Likhachev, Maxim; Arkin, Ronald C.

    2000-10-01

    The paper investigates how the psychological notion of comfort can be useful in the design of robotic systems. A review of the existing study of human comfort, especially regarding its presence in infants, is conducted with the goal being to determine the relevant characteristics for mapping it onto the robotics domain. Focus is place on the identification of the salient features in the environment that affect the comfort level. Factors involved include current state familiarity, working conditions, the amount and location of available resources, etc. As part of our newly developed comfort function theory, the notion of an object as a psychological attachment for a robot is also introduced, as espoused in Bowlby's theory of attachment. The output space of the comfort function and its dependency on the comfort level are analyzed. The results of the derivation of this comfort function are then presented in terms of the impact they have on robotic behavior. Justification for the use of the comfort function are then presented in terms of the impact they have on robotic behavior. Justification for the use of the comfort function in the domain of robotics is presented with relevance for real-world operations. Also, a transformation of the theoretical discussion into a mathematical framework suitable for implementation within a behavior-based control system is presented. The paper concludes with results of simulation studies and real robot experiments using the derived comfort function.

  12. Endosperm and Amyloplast Proteomes of Wheat Grain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advances in proteomics and genomics have improved our understanding of the gluten proteins, a complex and functionally important protein group. Proteomic approaches also have been used to identify other proteins that may play roles in wheat flour functionality, to assign genes for gluten proteins to...

  13. Proteome-wide search for functional motifs altered in tumors: Prediction of nuclear export signals inactivated by cancer-related mutations.

    PubMed

    Prieto, Gorka; Fullaondo, Asier; Rodríguez, Jose A

    2016-01-01

    Large-scale sequencing projects are uncovering a growing number of missense mutations in human tumors. Understanding the phenotypic consequences of these alterations represents a formidable challenge. In silico prediction of functionally relevant amino acid motifs disrupted by cancer mutations could provide insight into the potential impact of a mutation, and guide functional tests. We have previously described Wregex, a tool for the identification of potential functional motifs, such as nuclear export signals (NESs), in proteins. Here, we present an improved version that allows motif prediction to be combined with data from large repositories, such as the Catalogue of Somatic Mutations in Cancer (COSMIC), and to be applied to a whole proteome scale. As an example, we have searched the human proteome for candidate NES motifs that could be altered by cancer-related mutations included in the COSMIC database. A subset of the candidate NESs identified was experimentally tested using an in vivo nuclear export assay. A significant proportion of the selected motifs exhibited nuclear export activity, which was abrogated by the COSMIC mutations. In addition, our search identified a cancer mutation that inactivates the NES of the human deubiquitinase USP21, and leads to the aberrant accumulation of this protein in the nucleus. PMID:27174732

  14. Proteome-wide search for functional motifs altered in tumors: Prediction of nuclear export signals inactivated by cancer-related mutations.

    PubMed

    Prieto, Gorka; Fullaondo, Asier; Rodríguez, Jose A

    2016-05-12

    Large-scale sequencing projects are uncovering a growing number of missense mutations in human tumors. Understanding the phenotypic consequences of these alterations represents a formidable challenge. In silico prediction of functionally relevant amino acid motifs disrupted by cancer mutations could provide insight into the potential impact of a mutation, and guide functional tests. We have previously described Wregex, a tool for the identification of potential functional motifs, such as nuclear export signals (NESs), in proteins. Here, we present an improved version that allows motif prediction to be combined with data from large repositories, such as the Catalogue of Somatic Mutations in Cancer (COSMIC), and to be applied to a whole proteome scale. As an example, we have searched the human proteome for candidate NES motifs that could be altered by cancer-related mutations included in the COSMIC database. A subset of the candidate NESs identified was experimentally tested using an in vivo nuclear export assay. A significant proportion of the selected motifs exhibited nuclear export activity, which was abrogated by the COSMIC mutations. In addition, our search identified a cancer mutation that inactivates the NES of the human deubiquitinase USP21, and leads to the aberrant accumulation of this protein in the nucleus.

  15. Functional Study of miR-27a in Human Hepatic Stellate Cells by Proteomic Analysis: Comprehensive View and a Role in Myogenic Tans-Differentiation

    PubMed Central

    Ji, Yuhua; Zhang, Jinsheng; Wang, Wenwen; Ji, Juling

    2014-01-01

    We previous reported that miR-27a regulates lipid metabolism and cell proliferation during hepatic stellate cells (HSCs) activation. To further explore the biological function and underlying mechanisms of miR-27a in HSCs, global protein expression affected by overexpression of miR-27a in HSCs was analyzed by a cleavable isotope-coded affinity tags (cICAT) based comparative proteomic approach. In the present study, 1267 non-redundant proteins were identified with unique accession numbers (score ≥1.3, i.e. confidence ≥95%), among which 1171 were quantified and 149 proteins (12.72%) were differentially expressed with a differential expression ratio of 1.5. We found that up-regulated proteins by miR-27a mainly participate in cell proliferation and myogenesis, while down-regulated proteins were the key enzymes involved in de novo lipid synthesis. The expression of a group of six miR-27a regulated proteins was validated and the function of one miR-27a regulated protein was further validated. The results not only delineated the underlying mechanism of miR-27a in modulating fat metabolism and cell proliferation, but also revealed a novel role of miR-27a in promoting myogenic tans-differentiation during HSCs activation. This study also exemplified proteomics strategy as a powerful tool for the functional study of miRNA. PMID:25265485

  16. Robotic surgery.

    PubMed

    Oleynikov, Dmitry

    2008-10-01

    This article discusses the developments that led up to robotic surgical systems as well as what is on the horizon for new robotic technology. Topics include how robotics is enabling new types of procedures, including natural orifice endoscopic translumenal surgery in which one cannot reach by hand under any circumstances, and how these developments will drive the next generation of robots. PMID:18790158

  17. A guide to the Proteomics Identifications Database proteomics data repository.

    PubMed

    Vizcaíno, Juan Antonio; Côté, Richard; Reisinger, Florian; Foster, Joseph M; Mueller, Michael; Rameseder, Jonathan; Hermjakob, Henning; Martens, Lennart

    2009-09-01

    The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across-domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy-to-use, platform-independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium.

  18. Assist-as-Needed Robot-Aided Gait Training Improves Walking Function in Individuals Following Stroke.

    PubMed

    Srivastava, Shraddha; Kao, Pei-Chun; Kim, Seok Hun; Stegall, Paul; Zanotto, Damiano; Higginson, Jill S; Agrawal, Sunil K; Scholz, John P

    2015-11-01

    A novel robot-aided assist-as-needed gait training paradigm has been developed recently. This paradigm encourages subjects' active participation during training. Previous pilot studies demonstrated that assist-as-needed robot-aided gait training (RAGT) improves treadmill walking performance post-stroke. However, it is not known if there is an over-ground transfer of the training effects from RAGT on treadmill or long-term retention of the effects. The purpose of the current study was to examine the effects of assist-as-needed RAGT on over-ground walking pattern post-stroke. Nine stroke subjects received RAGT with visual feedback of each subject's instantaneous ankle malleolus position relative to a target template for 15 40-minute sessions. Clinical evaluations and gait analyses were performed before, immediately after, and 6 months post-training. Stroke subjects demonstrated significant improvements and some long-term retention of the improvements in their self-selected over-ground walking speed, Dynamic Gait Index, Timed Up and Go, peak knee flexion angle during swing phase and total hip joint excursion over the whole gait cycle for their affected leg . These preliminary results demonstrate that subjects improved their over-ground walking pattern and some clinical gait measures post-training suggesting that assist-as-needed RAGT including visual feedback may be an effective approach to improve over-ground walking pattern post-stroke.

  19. Proteomic approaches in research of cyanobacterial photosynthesis.

    PubMed

    Battchikova, Natalia; Angeleri, Martina; Aro, Eva-Mari

    2015-10-01

    Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.

  20. Functional analysis of novel Rab GTPases identified in the proteome of purified Legionella-containing vacuoles from macrophages.

    PubMed

    Hoffmann, Christine; Finsel, Ivo; Otto, Andreas; Pfaffinger, Gudrun; Rothmeier, Eva; Hecker, Michael; Becher, Dörte; Hilbi, Hubert

    2014-07-01

    The opportunistic pathogen Legionella pneumophila employs the Icm/Dot type IV secretion system and ∼300 different effector proteins to replicate in macrophages and amoebae in a distinct 'Legionella-containing vacuole' (LCV). LCVs from infected RAW 264.7 macrophages were enriched by immuno-affinity separation and density gradient centrifugation, using an antibody against the L. pneumophila effector SidC, which specifically binds to the phosphoinositide PtdIns(4)P on the pathogen vacuole membrane. The proteome of purified LCVs was determined by mass spectro-metry (data are available via ProteomeXchange with identifier PXD000647). The proteomics analysis revealed more than 1150 host proteins, including 13 small GTPases of the Rab family. Using fluorescence microscopy, 6 novel Rab proteins were confirmed to localize on pathogen vacuoles harbouring wild-type but not ΔicmT mutant L. pneumophila. Individual depletion of 20 GTPases by RNA interference indicated that endocytic GTPases (Rab5a, Rab14 and Rab21) restrict intracellular growth of L. pneumophila, whereas secretory GTPases (Rab8a, Rab10 and Rab32) implicated in Golgi-endosome trafficking promote bacterial replication. Upon silencing of Rab21 or Rab32, fewer LCVs stained positive for Rab4 or Rab9, implicated in secretory or retrograde trafficking respectively. Moreover, depletion of Rab8a, Rab14 or Rab21 significantly decreased the number of SidC-positive LCVs, suggesting that PtdIns(4)P is reduced under these conditions. L. pneumophila proteins identified in purified LCVs included proteins putatively implicated in phosphorus metabolism and as many as 60 Icm/Dot-translocated effectors, which are likely required early during infection. Taken together, the phagocyte and Legionella proteomes of purified LCVs lay the foundation for further hypothesis-driven investigations of the complex process of pathogen vacuole formation.

  1. What Is Cancer Proteomics?

    MedlinePlus

    ... gov The National Institutes of Health Clinical Proteomics Technologies for Cancer Contact Us Intranet Sign Up for ... of proteomics that involves the application of proteomic technologies on clinical specimens such as blood. Cancer, in ...

  2. Metabolic effects of the iodothyronine functional analogue TRC150094 on the liver and skeletal muscle of high-fat diet fed overweight rats: an integrated proteomic study.

    PubMed

    Silvestri, Elena; Glinni, Daniela; Cioffi, Federica; Moreno, Maria; Lombardi, Assunta; de Lange, Pieter; Senese, Rosalba; Ceccarelli, Michele; Salzano, Anna Maria; Scaloni, Andrea; Lanni, Antonia; Goglia, Fernando

    2012-07-01

    A novel functional iodothyronine analogue, TRC150094, which has a much lower potency toward thyroid hormone receptor (α1/β1) activation than triiodothyronine, has been shown to be effective at reducing adiposity in rats simultaneously receiving a high-fat diet (HFD). Here, by combining metabolic, functional and proteomic analysis, we studied how the hepatic and skeletal muscle phenotypes might respond to TRC150094 treatment in HFD-fed overweight rats. Drug treatment increased both the liver and skeletal muscle mitochondrial oxidative capacities without altering mitochondrial efficiency. Coherently, in terms of individual respiratory in-gel activity, blue-native analysis revealed an increased activity of complex V in the liver and of complexes II and V in tibialis muscle in TCR150094-treated animals. Subsequently, the identification of differentially expressed proteins and the analysis of their interrelations gave an integrated view of the phenotypic/metabolic adaptations occurring in the liver and muscle proteomes during drug treatment. TRC150094 significantly altered the expression of several proteins involved in key liver metabolic pathways, including amino acid and nitrogen metabolism, and fructose and mannose metabolism. The canonical pathways most strongly influenced by TRC150094 in tibialis muscle included glycolysis and gluconeogenesis, amino acid, fructose and mannose metabolism, and cell signaling. The phenotypic/metabolic influence of TRC150094 on the liver and skeletal muscle of HFD-fed overweight rats suggests the potential clinical application of this iodothyronine analogue in ameliorating metabolic risk parameters altered by diet regimens.

  3. Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development.

    PubMed

    Li, Ning; Xu, ZhongWei; Zhai, LinHui; Li, YanChang; Fan, FengXu; Zheng, JunJie; Xu, Ping; He, FuChu

    2014-12-01

    Proteomics focuses on the systematic identification and quantification of entire proteomes and interpretation of proteins' biological functions. During the last decade, proteomics in China has grown much faster than other research fields in the life sciences. At the beginning of the second decade of the 21(st) century, the rapid development of high-resolution and high-speed mass spectrometry makes proteomics a powerful tool to study the mechanisms underlying physiological/pathological processes in organisms. This article provides a brief overview of proteomics technology development and representative scientific progress of the Human Liver Proteome Project (HLPP) in China over the past three years.

  4. Architecture for robot intelligence

    NASA Technical Reports Server (NTRS)

    Peters, II, Richard Alan (Inventor)

    2004-01-01

    An architecture for robot intelligence enables a robot to learn new behaviors and create new behavior sequences autonomously and interact with a dynamically changing environment. Sensory information is mapped onto a Sensory Ego-Sphere (SES) that rapidly identifies important changes in the environment and functions much like short term memory. Behaviors are stored in a DBAM that creates an active map from the robot's current state to a goal state and functions much like long term memory. A dream state converts recent activities stored in the SES and creates or modifies behaviors in the DBAM.

  5. Proteomics of the Lysosome

    PubMed Central

    Lübke, Torben; Lobel, Peter; Sleat, David

    2009-01-01

    Defects in lysosomal function have been associated with numerous monogenic human diseases typically classified as lysosomal storage diseases. However, there is increasing evidence that lysosomal proteins are also involved in more widespread human diseases including cancer and Alzheimer disease. Thus, there is a continuing interest in understanding the cellular functions of the lysosome and an emerging approach to this is the identification of its constituent proteins by proteomic analyses. To date, the mammalian lysosome has been shown to contain ~ 60 soluble luminal proteins and ~25 transmembrane proteins. However, recent proteomic studies based upon affinity purification of soluble components or subcellular fractionation to obtain both soluble and membrane components suggest that there may be many more of both classes of protein resident within this organelle than previously appreciated. Discovery of such proteins has important implications for understanding the function and the dynamics of the lysosome but can also lead the way towards the discovery of the genetic basis for human diseases of hitherto unknown etiology. Here, we describe current approaches to lysosomal proteomics and data interpretation and review the new lysosomal proteins that have recently emerged from such studies. PMID:18977398

  6. The proteome of schizophrenia

    PubMed Central

    Nascimento, Juliana M; Martins-de-Souza, Daniel

    2015-01-01

    On observing schizophrenia from a clinical point of view up to its molecular basis, one may conclude that this is likely to be one of the most complex human disorders to be characterized in all aspects. Such complexity is the reflex of an intricate combination of genetic and environmental components that influence brain functions since pre-natal neurodevelopment, passing by brain maturation, up to the onset of disease and disease establishment. The perfect function of tissues, organs, systems, and finally the organism depends heavily on the proper functioning of cells. Several lines of evidence, including genetics, genomics, transcriptomics, neuropathology, and pharmacology, have supported the idea that dysfunctional cells are causative to schizophrenia. Together with the above-mentioned techniques, proteomics have been contributing to understanding the biochemical basis of schizophrenia at the cellular and tissue level through the identification of differentially expressed proteins and consequently their biochemical pathways, mostly in the brain tissue but also in other cells. In addition, mass spectrometry-based proteomics have identified and precisely quantified proteins that may serve as biomarker candidates to prognosis, diagnosis, and medication monitoring in peripheral tissue. Here, we review all data produced by proteomic investigation in the last 5 years using tissue and/or cells from schizophrenic patients, focusing on postmortem brain tissue and peripheral blood serum and plasma. This information has provided integrated pictures of the biochemical systems involved in the pathobiology, and has suggested potential biomarkers, and warrant potential targets to alternative treatment therapies to schizophrenia. PMID:27336025

  7. Humanlike Robots - The Upcoming Revolution in Robotics

    NASA Technical Reports Server (NTRS)

    Bar-Cohen, Yoseph

    2009-01-01

    Humans have always sought to imitate the human appearance, functions and intelligence. Human-like robots, which for many years have been a science fiction, are increasingly becoming an engineering reality resulting from the many advances in biologically inspired technologies. These biomimetic technologies include artificial intelligence, artificial vision and hearing as well as artificial muscles, also known as electroactive polymers (EAP). Robots, such as the vacuum cleaner Rumba and the robotic lawnmower, that don't have human shape, are already finding growing use in homes worldwide. As opposed to other human-made machines and devices, this technology raises also various questions and concerns and they need to be addressed as the technology advances. These include the need to prevent accidents, deliberate harm, or their use in crime. In this paper the state-of-the-art of the ultimate goal of biomimetics, the development of humanlike robots, the potentials and the challenges are reviewed.

  8. Humanlike robots: the upcoming revolution in robotics

    NASA Astrophysics Data System (ADS)

    Bar-Cohen, Yoseph

    2009-08-01

    Humans have always sought to imitate the human appearance, functions and intelligence. Human-like robots, which for many years have been a science fiction, are increasingly becoming an engineering reality resulting from the many advances in biologically inspired technologies. These biomimetic technologies include artificial intelligence, artificial vision and hearing as well as artificial muscles, also known as electroactive polymers (EAP). Robots, such as the vacuum cleaner Rumba and the robotic lawnmower, that don't have human shape, are already finding growing use in homes worldwide. As opposed to other human-made machines and devices, this technology raises also various questions and concerns and they need to be addressed as the technology advances. These include the need to prevent accidents, deliberate harm, or their use in crime. In this paper the state-of-the-art of the ultimate goal of biomimetics, the development of humanlike robots, the potentials and the challenges are reviewed.

  9. Honda humanoid robots development.

    PubMed

    Hirose, Masato; Ogawa, Kenichi

    2007-01-15

    Honda has been doing research on robotics since 1986 with a focus upon bipedal walking technology. The research started with straight and static walking of the first prototype two-legged robot. Now, the continuous transition from walking in a straight line to making a turn has been achieved with the latest humanoid robot ASIMO. ASIMO is the most advanced robot of Honda so far in the mechanism and the control system. ASIMO's configuration allows it to operate freely in the human living space. It could be of practical help to humans with its ability of five-finger arms as well as its walking function. The target of further development of ASIMO is to develop a robot to improve life in human society. Much development work will be continued both mechanically and electronically, staying true to Honda's 'challenging spirit'.

  10. Effects of Robot-assisted Gait Training Combined with Functional Electrical Stimulation on Recovery of Locomotor Mobility in Chronic Stroke Patients: A Randomized Controlled Trial.

    PubMed

    Bae, Young-Hyeon; Ko, Young Jun; Chang, Won Hyuk; Lee, Ju Hyeok; Lee, Kyeong Bong; Park, Yoo Jung; Ha, Hyun Geun; Kim, Yun-Hee

    2014-12-01

    [Purpose] The purpose of the present study was to investigate the effects of robot-assisted gait training combined with functional electrical stimulation on locomotor recovery in patients with chronic stroke. [Subjects] The 20 subjects were randomly assigned into either an experimental group (n = 10) that received a combination of robot-assisted gait training and functional electrical stimulation on the ankle dorsiflexor of the affected side or a control group (n = 10) that received robot-assisted gait training only. [Methods] Both groups received the respective therapies for 30 min/day, 3 days/week for 5 weeks. The outcome was measured using the Modified Motor Assessment Scale (MMAS), Timed Up-and-Go Test (TUG), Berg Balance Scale (BBS), and gait parameters through gait analysis (Vicon 370 motion analysis system, Oxford Metrics Ltd., Oxford, UK). All the variables were measured before and after training. [Results] Step length and maximal knee extension were significantly greater than those before training in the experimental group only. Maximal Knee flexion showed a significant difference between the experimental and control groups. The MMAS, BBS, and TUG scores improved significantly after training compared with before training in both groups. [Conclusion] We suggest that the combination of robot-assisted gait training and functional electrical stimulation encourages patients to actively participate in training because it facilitates locomotor recovery without the risk of adverse effects.

  11. Robotics in medicine

    NASA Astrophysics Data System (ADS)

    Kuznetsov, D. N.; Syryamkin, V. I.

    2015-11-01

    Modern technologies play a very important role in our lives. It is hard to imagine how people can get along without personal computers, and companies - without powerful computer centers. Nowadays, many devices make modern medicine more effective. Medicine is developing constantly, so introduction of robots in this sector is a very promising activity. Advances in technology have influenced medicine greatly. Robotic surgery is now actively developing worldwide. Scientists have been carrying out research and practical attempts to create robotic surgeons for more than 20 years, since the mid-80s of the last century. Robotic assistants play an important role in modern medicine. This industry is new enough and is at the early stage of development; despite this, some developments already have worldwide application; they function successfully and bring invaluable help to employees of medical institutions. Today, doctors can perform operations that seemed impossible a few years ago. Such progress in medicine is due to many factors. First, modern operating rooms are equipped with up-to-date equipment, allowing doctors to make operations more accurately and with less risk to the patient. Second, technology has enabled to improve the quality of doctors' training. Various types of robots exist now: assistants, military robots, space, household and medical, of course. Further, we should make a detailed analysis of existing types of robots and their application. The purpose of the article is to illustrate the most popular types of robots used in medicine.

  12. Automatic robotic arm operations and sampling in near zero gravity environment - functional tests results from Phobos-Grunt mission

    NASA Astrophysics Data System (ADS)

    Kozlova, Tatiana; Karol Seweryn, D..; Grygorczuk, Jerzy; Kozlov, Oleg

    The sample return missions have made a very significant progress to understanding of geology, the extra-terrestrial materials, processes occurring on surface and subsurface level, as well as of interactions between such materials and mechanisms operating there. The various sample return missions in the past (e.g. Apollo missions, Luna missions, Hayabusa mission) have provided scientists with samples of extra-terrestrial materials allowing to discover answers to critical scientific questions concerning the origin and evolution of the Solar System. Several new missions are currently planned: sample return missions, e.g Russian Luna-28, ESA Phootprint and MarcoPolo-R as well as both robotic and manned exploration missions to the Moon and Mars. One of the key challenges in such missions is the reliable sampling process which can be achieved by using many different techniques, e.g. static excavating technique (scoop), core drilling, sampling using dynamic mechanisms (penetrators), brushes and pneumatic systems. The effectiveness of any sampling strategy depends on many factors, including the required sample size, the mechanical and chemical soil properties (cohesive, hard or porous regolith, stones), the environment conditions (gravity, temperature, pressure, radiation). Many sampling mechanism have been studied, designed and built in the past, two techniques to collect regolith samples were chosen for the Phobos-Grunt mission. The proposed system consisted of a robotic arm with a 1,2m reach beyond the lander (IKI RAN); a tubular sampling device designed for collecting both regolith and small rock fragments (IKI RAN); the CHOMIK device (CBK PAN) - the low velocity penetrator with a single-sample container for collecting samples from the rocky surface. The functional tests were essential step in robotic arm, sampling device and CHOMIK device development process in the frame of Phobos-Grunt mission. Three major results were achieved: (i) operation scenario for autonomous

  13. Swarm Robotics

    NASA Astrophysics Data System (ADS)

    Şahin, Erol; Girgin, Sertan; Bayindir, Levent; Turgut, Ali Emre

    Swarm robotics is a novel approach to the coordination of large numbers of robots and has emerged as the application of swarm intelligence to multi-robot systems. Different from other swarm intelligence studies, swarm robotics puts emphases on the physical embodiment of individuals and realistic interactions among the individuals and between the individuals and the environment. In this chapter, we present a brief review of this new approach. We first present its definition, discuss the main motivations behind the approach, as well as its distinguishing characteristics and major coordination mechanisms. Then we present a brief review of swarm robotics research along four axes; namely design, modelling and analysis, robots and problems.

  14. Robotic surgery.

    PubMed

    Stoianovici, D

    2000-09-01

    The industrial revolution demonstrated the capability of robotic systems to facilitate and improve manufacturing. As a result, robotics extended to various other domains, including the delivery of health care. Hence, robots have been developed to assist hospital staff, to facilitate laboratory analyses, to augment patient rehabilitation, and even to advance surgical performance. As robotics lead usefulness and gain wider acceptance among the surgical community, the urologist should become familiar with this new interdisciplinary field and its "URobotics" subset: robotics applied to urology. This article reviews the current applications and experience, issues and debates in surgical robotics, and highlights future directions in the field.

  15. Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome*

    PubMed Central

    Solari, Fiorella A.; Mattheij, Nadine J.A.; Burkhart, Julia M.; Swieringa, Frauke; Collins, Peter W.; Cosemans, Judith M.E.M.; Sickmann, Albert; Heemskerk, Johan W.M.; Zahedi, René P.

    2016-01-01

    The Scott syndrome is a very rare and likely underdiagnosed bleeding disorder associated with mutations in the gene encoding anoctamin-6. Platelets from Scott patients are impaired in various Ca2+-dependent responses, including phosphatidylserine exposure, integrin closure, intracellular protein cleavage, and cytoskeleton-dependent morphological changes. Given the central role of anoctamin-6 in the platelet procoagulant response, we used quantitative proteomics to understand the underlying molecular mechanisms and the complex phenotypic changes in Scott platelets compared with control platelets. Therefore, we applied an iTRAQ-based multi-pronged strategy to quantify changes in (1) the global proteome, (2) the phosphoproteome, and (3) proteolytic events between resting and stimulated Scott and control platelets. Our data indicate a limited number of proteins with decreased (70) or increased (64) expression in Scott platelets, among those we confirmed the absence of anoctamin-6 and the strong up-regulation of aquaporin-1 by parallel reaction monitoring. The quantification of 1566 phosphopeptides revealed major differences between Scott and control platelets after stimulation with thrombin/convulxin or ionomycin. In Scott platelets, phosphorylation levels of proteins regulating cytoskeletal or signaling events were increased. Finally, we quantified 1596 N-terminal peptides in activated Scott and control platelets, 180 of which we identified as calpain-regulated, whereas a distinct set of 23 neo-N termini was caspase-regulated. In Scott platelets, calpain-induced cleavage of cytoskeleton-linked and signaling proteins was downregulated, in accordance with an increased phosphorylation state. Thus, multipronged proteomic profiling of Scott platelets provides detailed insight into their protection against detrimental Ca2+-dependent changes that are normally associated with phosphatidylserine exposure. PMID:27535140

  16. The proteome of human saliva

    NASA Astrophysics Data System (ADS)

    Griffin, Timothy J.

    2013-05-01

    Human saliva holds tremendous potential for transforming disease and health diagnostics given its richness of molecular information and non-invasive collection. Enumerating its molecular constituents is an important first step towards reaching this potential. Among the molecules in saliva, proteins and peptides arguably have the most value: they can directly indicate biochemical functions linked to a health condition/disease state, and they are attractive targets for biomarker assay development. However, cataloging and defining the human salivary proteome is challenging given the dynamic, chemically heterogeneous and complex nature of the system. In addition, the overall human saliva proteome is composed of several "sub-proteomes" which include: intact full length proteins, proteins carrying post-translational modifications (PTMs), low molecular weight peptides, and the metaproteome, derived from protein products from nonhuman organisms (e.g. microbes) present in the oral cavity. Presented here will be a summary of communal efforts to meet the challenge of characterizing the multifaceted saliva proteome, focusing on the use of mass spectrometry as the proteomic technology of choice. Implications of these efforts to characterize the salivary proteome in the context of disease diagnostics will also be discussed.

  17. Proteomic Approach to Reveal the Regulatory Function of Aconitase AcnA in Oxidative Stress Response in the Antibiotic Producer Streptomyces viridochromogenes Tü494

    PubMed Central

    Michta, Ewelina; Ding, Wei; Zhu, Shaochun; Blin, Kai; Ruan, Hongqiang; Wang, Rui; Wohlleben, Wolfgang; Mast, Yvonne

    2014-01-01

    The aconitase AcnA from the phosphinothricin tripeptide producing strain Streptomyces viridochromogenes Tü494 is a bifunctional protein: under iron-sufficiency conditions AcnA functions as an enzyme of the tricarboxylic acid cycle, whereas under iron depletion it is a regulator of iron metabolism and oxidative stress response. As a member of the family of iron regulatory proteins (IRP), AcnA binds to characteristic iron responsive element (IRE) binding motifs and post-transcriptionally controls the expression of respective target genes. A S. viridochromogenes aconitase mutant (MacnA) has previously been shown to be highly sensitive to oxidative stress. In the present paper, we performed a comparative proteomic approach with the S. viridochromogenes wild-type and the MacnA mutant strain under oxidative stress conditions to identify proteins that are under control of the AcnA-mediated regulation. We identified up to 90 differentially expressed proteins in both strains. In silico analysis of the corresponding gene sequences revealed the presence of IRE motifs on some of the respective target mRNAs. From this proteome study we have in vivo evidences for a direct AcnA-mediated regulation upon oxidative stress. PMID:24498397

  18. Activity-Based Proteomic Profiling of Deubiquitinating Enzymes in Salmonella-Infected Macrophages Leads to Identification of Putative Function of UCH-L5 in Inflammasome Regulation.

    PubMed

    Kummari, Evangel; Alugubelly, Navatha; Hsu, Chuan-Yu; Dong, Brittany; Nanduri, Bindu; Edelmann, Mariola J

    2015-01-01

    Although protein ubiquitination has been shown to regulate multiple processes during host response to Salmonella enterica serovar Typhimurium infection, specific functions of host deubiquitinating enzymes remain unknown in this bacterial infection. By using chemical proteomics approach, in which deubiquitinating enzymes were labeled by an active-site probe and analyzed by quantitative proteomics, we identified novel deubiquitinases in chicken macrophages based on their reactivity with the probe. Also, we detected down-regulation of UCH-L3, and USP4 as well as up-regulation of USP5 and UCH-L5 deubiquitinating enzymes in macrophages infected with Salmonella Typhimurium. We showed that decrease in either UCH-L5 activity, or in UCH-L5 protein amount in chicken and human macrophages infected or stimulated with LPS/nigericin, led to decreased IL-1β release. These data point towards a putative role of UCH-L5 in inflammasome regulation during Salmonella infection. Because inflammasome activation is important in innate resistance to these bacteria, one would expect that naturally occurring or therapeutically induced alteration in UCH-L5 activation would influence disease outcome and could represent a target for new therapeutic approaches.

  19. Proteomics: the industrialization of protein chemistry.

    PubMed

    Patterson, S D

    2000-08-01

    Establishing a proteomics platform in the industrial setting initially required implementation of a series of robotic systems to allow a high-throughput approach to analysis and identification of differences observed on 2-D electrophoresis gels. Now, a simpler alternative approach employing chromatography-based systems is emerging for identification of many components of complex mixtures, which can also provide quantitative comparisons through the use of a new labeling methodology.

  20. CASSY Robot

    NASA Astrophysics Data System (ADS)

    Pittman, Anna; Wright, Ann; Rice, Aaron; Shyaka, Claude

    2014-03-01

    The CASSY Robot project involved two square robots coded in RobotC. The goal was to code a robot to do a certain set of tasks autonomously. To begin with, our task was to code the robot so that it would roam a certain area, marked off by black tape. When the robot hit the black tape, it knew to back up and turn around. It was able to do this thanks to the light sensor that was attached to the bottom of the robot. Also, whenever the robot hit an obstacle, it knew to stop, back up, and turn around. This was primarily to prevent the robot from hurting itself if it hit an obstacle. This was accomplished by using touch sensors set up as bumpers. Once that was accomplished, we attached sonar sensors and created code so that one robot was able to find and track the other robot in a sort of intruder/police scenario. The overall goal of this project was to code the robot so that we can test it against a robot coded exactly the same, but using Layered Mode Selection Logic. Professor.

  1. The scientific exploration of saliva in the post-proteomic era: from database back to basic function

    PubMed Central

    Ruhl, Stefan

    2012-01-01

    The proteome of human saliva can be considered as being essentially completed. Diagnostic markers for a number of diseases have been identified among salivary proteins and peptides, taking advantage of saliva as an easy-to-obtain biological fluid. Yet, the majority of disease markers identified so far are serum components and not intrinsic proteins produced by the salivary glands. Furthermore, despite the fact that saliva is essential for protecting the oral integuments and dentition, little progress has been made in finding risk predictors in the salivary proteome for dental caries or periodontal disease. Since salivary proteins, and in particular the attached glycans, play an important role in interactions with the microbial world, the salivary glycoproteome and other post-translational modifications of salivary proteins need to be studied. Risk markers for microbial diseases, including dental caries, are likely to be discovered among the highly glycosylated major protein species in saliva. This review will attempt to raise new ideas and also point to under-researched areas that may hold promise for future applicability in oral diagnostics and prediction of oral disease. PMID:22292826

  2. Does It "Want" or "Was It Programmed to..."? Kindergarten Children's Explanations of an Autonomous Robot's Adaptive Functioning

    ERIC Educational Resources Information Center

    Levy, Sharona T.; Mioduser, David

    2008-01-01

    This study investigates young children's perspectives in explaining a self-regulating mobile robot, as they learn to program its behaviors from rules. We explore their descriptions of a robot in action to determine the nature of their explanatory frameworks: psychological or technological. We have also studied the role of an adult's intervention…

  3. Tandem Analysis of Transcriptome and Proteome Changes after a Single Dose of Corticosteroid: A Systems Approach to Liver Function in Pharmacogenomics

    PubMed Central

    Kamisoglu, Kubra; Sukumaran, Siddharth; Nouri-Nigjeh, Eslam; Tu, Chengjian; Li, Jun; Shen, Xiaomeng; Duan, Xiaotao; Qu, Jun; Almon, Richard R.; DuBois, Debra C.; Jusko, William J.

    2015-01-01

    Abstract Corticosteroids (CS) such as methylprednisolone (MPL) affect almost all liver functions through multiple mechanisms of action, and long-term use results in dysregulation causing diverse side effects. The complexity of involved molecular mechanisms necessitates a systems approach. Integration of information from the transcriptomic and proteomic responses has potential to provide deeper insights into CS actions. The present report describes the tandem analysis of rich time-series transcriptomic and proteomic data in rat liver after a single dose of MPL. Hierarchical clustering of the common genes represented in both mRNA and protein datasets displayed two dominant patterns. One of these patterns exhibited complementary mRNA and protein expression profiles indicating that MPL affected the regulation of these genes at the transcriptional level. Some of the classic pharmacodynamic markers for CS actions, including tyrosine aminotransferase (TAT), were among this group, together with genes encoding urea cycle enzymes and ribosomal proteins. The other pattern was rather unexpected. For this group of genes, MPL had distinctly observable effects at the protein expression level, although a change in the reverse direction occurred at the transcriptional level. These genes were functionally associated with metabolic processes that might be essential to elucidate side effects of MPL on liver, most importantly including modulation of oxidative stress, fatty acid oxidation, and bile acid biosynthesis. Furthermore, profiling of gene and protein expression data was also done independently of one another by a two-way sequential approach. Prominent temporal shifts in expression and relevant cellular functions were described together with the assessment of changes in the complementary side. PMID:25611119

  4. Industrial Robots.

    ERIC Educational Resources Information Center

    Reed, Dean; Harden, Thomas K.

    Robots are mechanical devices that can be programmed to perform some task of manipulation or locomotion under automatic control. This paper discusses: (1) early developments of the robotics industry in the United States; (2) the present structure of the industry; (3) noneconomic factors related to the use of robots; (4) labor considerations…

  5. Basic Robotics.

    ERIC Educational Resources Information Center

    Mullen, Frank

    This curriculum outline consists of instructional materials and information concerning resources for use in teaching a course in robotics. Addressed in the individual sections of the outline are the following topics: the nature of an industrial robot; the parts of an industrial robot (the manipulator, the power structure, and the control system);…

  6. (Robotic hands)

    SciTech Connect

    Mann, R.C.

    1988-09-23

    The traveler attended the International Workshop on Robot Hands at the Palace Hotel in Dubrovnik, Yugoslavia. The traveler presented a lecture on An integrated sensor system for the ORNL mobile robot.'' The traveler obtained important information on current R D efforts in multi-fingered robot hands and object recognition using touch sensing.

  7. Quantifying kinematics of purposeful movements to real, imagined, or absent functional objects: Implications for modelling trajectories for robot-assisted ADL tasks**

    PubMed Central

    Wisneski, Kimberly J; Johnson, Michelle J

    2007-01-01

    Background Robotic therapy is at the forefront of stroke rehabilitation. The Activities of Daily Living Exercise Robot (ADLER) was developed to improve carryover of gains after training by combining the benefits of Activities of Daily Living (ADL) training (motivation and functional task practice with real objects), with the benefits of robot mediated therapy (repeatability and reliability). In combining these two therapy techniques, we seek to develop a new model for trajectory generation that will support functional movements to real objects during robot training. We studied natural movements to real objects and report on how initial reaching movements are affected by real objects and how these movements deviate from the straight line paths predicted by the minimum jerk model, typically used to generate trajectories in robot training environments. We highlight key issues that to be considered in modelling natural trajectories. Methods Movement data was collected as eight normal subjects completed ADLs such as drinking and eating. Three conditions were considered: object absent, imagined, and present. This data was compared to predicted trajectories generated from implementing the minimum jerk model. The deviations in both the plane of the table (XY) and the saggital plane of torso (XZ) were examined for both reaches to a cup and to a spoon. Velocity profiles and curvature were also quantified for all trajectories. Results We hypothesized that movements performed with functional task constraints and objects would deviate from the minimum jerk trajectory model more than those performed under imaginary or object absent conditions. Trajectory deviations from the predicted minimum jerk model for these reaches were shown to depend on three variables: object presence, object orientation, and plane of movement. When subjects completed the cup reach their movements were more curved than for the spoon reach. The object present condition for the cup reach showed more

  8. Left ventricular diastolic function in relation to the urinary proteome: A proof-of-concept study in a general population

    PubMed Central

    Zhang, Zhenyu; Staessen, Jan A.; Thijs, Lutgarde; Gu, Yumei; Liu, Yanping; Jacobs, Lotte; Koeck, Thomas; Zürbig, Petra; Mischak, Harald; Kuznetsova, Tatiana

    2014-01-01

    Background In previous studies, we identified two urinary proteomic classifiers, termed HF1 and HF2, which discriminated subclinical diastolic left ventricular (LV) dysfunction from normal. HF1 and HF2 combine information from 85 and 671 urinary peptides, mainly up- or down-regulated collagen fragments. We sought to validate these classifiers in a population study. Methods In 745 people randomly recruited from a Flemish population (49.8 years; 51.3% women), we measured early and late diastolic peak velocities of mitral inflow (E and A) and mitral annular velocities (e' and a') by conventional and tissue Doppler echocardiography, and the urinary proteome by capillary electrophoresis coupled with mass spectrometry. Results In the analyses adjusted for sex, age, body mass index, blood pressure, heart rate, LV mass index and intake of medications, we expressed effect sizes per 1-SD increment in the classifiers. HF1 was associated with 0.204 cm/s lower e' peak velocity (95% confidence interval, 0.057–0.351; p = 0.007) and 0.145 higher E/e' ratio (0.023–0.268; p = 0.020), while HF2 was associated with a 0.174 higher E/e' ratio (0.046–0.302; p = 0.008). According to published definitions, 67 (9.0%) participants had impaired LV relaxation and 96 (12.9%) had elevated LV filling pressure. The odds of impaired relaxation associated with HF1 was 1.38 (1.01–1.88; p = 0.043) and that of increased LV filling pressure associated with HF2 was 1.38 (1.00–1.90; p = 0.052). Conclusions In a general population, the urinary proteome correlated with diastolic LV dysfunction, proving its utility for early diagnosis of this condition. PMID:25065337

  9. Automated cross-modal mapping in robotic eye/hand systems using plastic radial basis function networks

    NASA Astrophysics Data System (ADS)

    Meng, Qinggang; Lee, M. H.

    2007-03-01

    Advanced autonomous artificial systems will need incremental learning and adaptive abilities similar to those seen in humans. Knowledge from biology, psychology and neuroscience is now inspiring new approaches for systems that have sensory-motor capabilities and operate in complex environments. Eye/hand coordination is an important cross-modal cognitive function, and is also typical of many of the other coordinations that must be involved in the control and operation of embodied intelligent systems. This paper examines a biologically inspired approach for incrementally constructing compact mapping networks for eye/hand coordination. We present a simplified node-decoupled extended Kalman filter for radial basis function networks, and compare this with other learning algorithms. An experimental system consisting of a robot arm and a pan-and-tilt head with a colour camera is used to produce results and test the algorithms in this paper. We also present three approaches for adapting to structural changes during eye/hand coordination tasks, and the robustness of the algorithms under noise are investigated. The learning and adaptation approaches in this paper have similarities with current ideas about neural growth in the brains of humans and animals during tool-use, and infants during early cognitive development.

  10. Toxic metal proteomics: reaction of the mammalian zinc proteome with Cd²⁺.

    PubMed

    Namdarghanbari, Mohammad Ali; Bertling, Joseph; Krezoski, Susan; Petering, David H

    2014-07-01

    The hypothesis was tested that Cd(2+) undergoes measureable reaction with the Zn-proteome through metal ion exchange chemistry. The Zn-proteome of pig kidney LLC-PK1 cells is relatively inert to reaction with competing ligands, including Zinquin acid, EDTA, and apo-metallothionein. Upon reaction of Cd(2+) with the Zn-proteome, Cd(2+) associates with the proteome and near stoichiometric amounts of Zn(2+) become reactive with these chelating agents. The results strongly support the hypothesis that Cd(2+) displaces Zn(2+) from native proteomic binding sites resulting in the formation of a Cd-proteome. Mobilized Zn(2+) becomes adventitiously bound to proteome and available for reaction with added metal binding ligands. Cd-proteome and Zn-metallothionein readily exchange metal ions, raising the possibility that this reaction restores functionality to Cd-proteins. In a parallel experiment, cells were exposed to Cd(2+) and pyrithione briefly to generate substantial proteome-bound Cd(2+). Upon transition to a Cd(2+) free medium, the cells generated new metallothionein protein over time that bound most of the proteomic Cd(2+) as well as additional Zn(2+). PMID:24529759

  11. The International Proteomics Tutorial Programme (IPTP): a teaching tool box for the proteomics community.

    PubMed

    James, Peter

    2011-09-01

    The most critical functions of the various proteomics organisations are the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with their national counterparts are therefore launching the International Proteomics Tutorial Programme to meet these needs. The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan). It involves collaboration between the leading proteomics journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, and Proteomics. The overall level is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. At a later stage the programme may be expanded with a series of more advanced topics focussing on the application of proteomics techniques to biological problem solving. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organisations homepages and at a special website, www.proteomicstutorials.org.

  12. Proteomic profiling revealed the functional networks associated with mitotic catastrophe of HepG2 hepatoma cells induced by 6-bromine-5-hydroxy-4-methoxybenzaldehyde

    SciTech Connect

    Zhang Bo; Huang Bo; Guan Hua; Zhang Shimeng; Xu Qinzhi; He Xingpeng; Liu Xiaodan; Wang Yu; Shang Zengfu; Zhou Pingkun

    2011-05-01

    Mitotic catastrophe, a form of cell death resulting from abnormal mitosis, is a cytotoxic death pathway as well as an appealing mechanistic strategy for the development of anti-cancer drugs. In this study, 6-bromine-5-hydroxy-4-methoxybenzaldehyde was demonstrated to induce DNA double-strand break, multipolar spindles, sustain mitotic arrest and generate multinucleated cells, all of which indicate mitotic catastrophe, in human hepatoma HepG2 cells. We used proteomic profiling to identify the differentially expressed proteins underlying mitotic catastrophe. A total of 137 differentially expressed proteins (76 upregulated and 61 downregulated proteins) were identified. Some of the changed proteins have previously been associated with mitotic catastrophe, such as DNA-PKcs, FoxM1, RCC1, cyclin E, PLK1-pT210, 14-3-3{sigma} and HSP70. Multiple isoforms of 14-3-3, heat-shock proteins and tubulin were upregulated. Analysis of functional significance revealed that the 14-3-3-mediated signaling network was the most significantly enriched for the differentially expressed proteins. The modulated proteins were found to be involved in macromolecule complex assembly, cell death, cell cycle, chromatin remodeling and DNA repair, tubulin and cytoskeletal organization. These findings revealed the overall molecular events and functional signaling networks associated with spindle disruption and mitotic catastrophe. - Graphical abstract: Display Omitted Research highlights: > 6-bromoisovanillin induced spindle disruption and sustained mitotic arrest, consequently resulted in mitotic catastrophe. > Proteomic profiling identified 137 differentially expressed proteins associated mitotic catastrophe. > The 14-3-3-mediated signaling network was the most significantly enriched for the altered proteins. > The macromolecule complex assembly, cell cycle, chromatin remodeling and DNA repair, tubulin organization were also shown involved in mitotic catastrophe.

  13. Proteomic and Functional Analysis of the Cellulase System Expressed by Postia placenta during Brown Rot of Solid Wood▿†

    PubMed Central

    Ryu, Jae San; Shary, Semarjit; Houtman, Carl J.; Panisko, Ellen A.; Korripally, Premsagar; St. John, Franz J.; Crooks, Casey; Siika-aho, Matti; Magnuson, Jon K.; Hammel, Kenneth E.

    2011-01-01

    Brown rot basidiomycetes have an important ecological role in lignocellulose recycling and are notable for their rapid degradation of wood polymers via oxidative and hydrolytic mechanisms. However, most of these fungi apparently lack processive (exo-acting) cellulases, such as cellobiohydrolases, which are generally required for efficient cellulolysis. The recent sequencing of the Postia placenta genome now permits a proteomic approach to this longstanding conundrum. We grew P. placenta on solid aspen wood, extracted proteins from the biodegrading substrate, and analyzed tryptic digests by shotgun liquid chromatography-tandem mass spectrometry. Comparison of the data with the predicted P. placenta proteome revealed the presence of 34 likely glycoside hydrolases, but only four of these—two in glycoside hydrolase family 5, one in family 10, and one in family 12—have sequences that suggested possible activity on cellulose. We expressed these enzymes heterologously and determined that they all exhibited endoglucanase activity on phosphoric acid-swollen cellulose. They also slowly hydrolyzed filter paper, a more crystalline substrate, but the soluble/insoluble reducing sugar ratios they produced classify them as nonprocessive. Computer simulations indicated that these enzymes produced soluble/insoluble ratios on reduced phosphoric acid-swollen cellulose that were higher than expected for random hydrolysis, which suggests that they could possess limited exo activity, but they are at best 10-fold less processive than cellobiohydrolases. It appears likely that P. placenta employs a combination of oxidative mechanisms and endo-acting cellulases to degrade cellulose efficiently in the absence of a significant processive component. PMID:21948841

  14. Proteomic and Functional Analysis of the Cellulase System Expressed by Postia placenta during Brown Rot of Solid Wood

    SciTech Connect

    Ryu, Jae San; Shary, Semarjit; Houtman, Carl J.; Panisko, Ellen A.; Korripally, Premsagar; St John, Franz J.; Crooks, Casey; Siika-aho, Matti; Magnuson, Jon K.; Hammel, Ken

    2011-11-01

    Abstract Brown rot basidiomycetes have an important ecological role in lignocellulose recycling and are notable for their rapid degradation of wood polymers via oxidative and hydrolytic mechanisms. However, most of these fungi apparently lack processive (exo-acting) cellulases, such as cellobiohydrolases, which are generally required for efficient cellulolysis. The recent sequencing of the Postia placenta genome now permits a proteomic approach to this longstanding conundrum. We grew P. placenta on solid aspen wood, extracted proteins from the biodegrading substrate, and analyzed tryptic digests by shotgun liquid chromatography-tandem mass spectrometry. Comparison of the data with the predicted P. placenta proteome revealed the presence of 34 likely glycoside hydrolases, but only four of these-two in glycoside hydrolase family 5, one in family 10, and one in family 12-have sequences that suggested possible activity on cellulose. We expressed these enzymes heterologously and determined that they all exhibited endoglucanase activity on phosphoric acid-swollen cellulose. They also slowly hydrolyzed filter paper, a more crystalline substrate, but the soluble/insoluble reducing sugar ratios they produced classify them as nonprocessive. Computer simulations indicated that these enzymes produced soluble/insoluble ratios on reduced phosphoric acid-swollen cellulose that were higher than expected for random hydrolysis, which suggests that they could possess limited exo activity, but they are at best 10-fold less processive than cellobiohydrolases. It appears likely that P. placenta employs a combination of oxidative mechanisms and endo-acting cellulases to degrade cellulose efficiently in the absence of a significant processive component.

  15. Thoughts turned into high-level commands: Proof-of-concept study of a vision-guided robot arm driven by functional MRI (fMRI) signals.

    PubMed

    Minati, Ludovico; Nigri, Anna; Rosazza, Cristina; Bruzzone, Maria Grazia

    2012-06-01

    Previous studies have demonstrated the possibility of using functional MRI to control a robot arm through a brain-machine interface by directly coupling haemodynamic activity in the sensory-motor cortex to the position of two axes. Here, we extend this work by implementing interaction at a more abstract level, whereby imagined actions deliver structured commands to a robot arm guided by a machine vision system. Rather than extracting signals from a small number of pre-selected regions, the proposed system adaptively determines at individual level how to map representative brain areas to the input nodes of a classifier network. In this initial study, a median action recognition accuracy of 90% was attained on five volunteers performing a game consisting of collecting randomly positioned coloured pawns and placing them into cups. The "pawn" and "cup" instructions were imparted through four mental imaginery tasks, linked to robot arm actions by a state machine. With the current implementation in MatLab language the median action recognition time was 24.3s and the robot execution time was 17.7s. We demonstrate the notion of combining haemodynamic brain-machine interfacing with computer vision to implement interaction at the level of high-level commands rather than individual movements, which may find application in future fMRI approaches relevant to brain-lesioned patients, and provide source code supporting further work on larger command sets and real-time processing.

  16. Structural characterization of the human proteome.

    PubMed

    Müller, Arne; MacCallum, Robert M; Sternberg, Michael J E

    2002-11-01

    This paper reports an analysis of the encoded proteins (the proteome) of the genomes of human, fly, worm, yeast, and representatives of bacteria and archaea in terms of the three-dimensional structures of their globular domains together with a general sequence-based study. We show that 39% of the human proteome can be assigned to known structures. We estimate that for 77% of the proteome, there is some functional annotation, but only 26% of the proteome can be assigned to standard sequence motifs that characterize function. Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. There are substantial differences in the composition of globular domains of transmembrane proteins between the proteomes we have analyzed. Commonly occurring structural superfamilies are identified within the proteome. The frequencies of these superfamilies enable us to estimate that 98% of the human proteome evolved by domain duplication, with four of the 10 most duplicated superfamilies specific for multicellular organisms. The zinc-finger superfamily is massively duplicated in human compared to fly and worm, and occurrence of domains in repeats is more common in metazoa than in single cellular organisms. Structural superfamilies over- and underrepresented in human disease genes have been identified. Data and results can be downloaded and analyzed via web-based applications at http://www.sbg.bio.ic.ac.uk.

  17. Consolidation of proteomics data in the Cancer Proteomics database.

    PubMed

    Arntzen, Magnus Ø; Boddie, Paul; Frick, Rahel; Koehler, Christian J; Thiede, Bernd

    2015-11-01

    Cancer is a class of diseases characterized by abnormal cell growth and one of the major reasons for human deaths. Proteins are involved in the molecular mechanisms leading to cancer, furthermore they are affected by anti-cancer drugs, and protein biomarkers can be used to diagnose certain cancer types. Therefore, it is important to explore the proteomics background of cancer. In this report, we developed the Cancer Proteomics database to re-interrogate published proteome studies investigating cancer. The database is divided in three sections related to cancer processes, cancer types, and anti-cancer drugs. Currently, the Cancer Proteomics database contains 9778 entries of 4118 proteins extracted from 143 scientific articles covering all three sections: cell death (cancer process), prostate cancer (cancer type) and platinum-based anti-cancer drugs including carboplatin, cisplatin, and oxaliplatin (anti-cancer drugs). The detailed information extracted from the literature includes basic information about the articles (e.g., PubMed ID, authors, journal name, publication year), information about the samples (type, study/reference, prognosis factor), and the proteomics workflow (Subcellular fractionation, protein, and peptide separation, mass spectrometry, quantification). Useful annotations such as hyperlinks to UniProt and PubMed were included. In addition, many filtering options were established as well as export functions. The database is freely available at http://cancerproteomics.uio.no.

  18. Robot-assisted "Santosh-Post Graduate Institute tubularized flap pyelovesicostomy" in a solitary functioning kidney with giant hydronephrosis: A minimally invasive salvage procedure

    PubMed Central

    Singh, Shivanshu; Kumar, Navneet

    2016-01-01

    We describe a case of a solitary functioning kidney with giant hydronephrosis secondary to ureteropelvic junction obstruction in a young girl who underwent successful robot-assisted tubularized flap pyelovesicostomy. The aim of this report was to highlight the feasibility and efficacy of this technique in salvaging such renal moieties and to present a brief review of the surgical options available for the management of giant hydronephrosis. PMID:26981597

  19. Improvement in sexual function after robot-assisted radical prostatectomy: A rehabilitation program with involvement of a clinical sexologist

    PubMed Central

    Ströberg, Peter

    2015-01-01

    Introduction To prospectively evaluate if the inclusion of a clinical sexologist in a penile and sexual rehabilitation program improves sexual function one year after prostate cancer surgery. Material and methods Twelve months after da Vinci Radical Prostatectomy (dVRP) for prostate cancer, 28 fully potent (IIEF-5 >21) and sexually active men (ages 47-69 years, mean 61) who, in 2008, were enrolled in a prospectively monitored penile rehabilitation program (reference group) were compared with 79 fully potent (IIEF-5 >21) and sexually active men (ages 45-74 years, mean 61) enrolled in 2009 (study group); whose program differed by the inclusion of evaluation and treatment by a clinical sexologist. Results Twelve months after dVRP, seventeen patients in the reference group (61%) were sexually active with regular penetrating sexual activity compared to sixty-six (84%) in the study group (p = 0.02). These findings were independent of whether they had undergone a nerve sparing or non-nerve sparing procedure. Almost 94% (74 patients) in the study group had at some time been able to perform penetrating sexual activity; 14 patients required additional visits to the clinical sexologist beyond the routine follow-up, 9 for short-term cognitive behavior therapy. Conclusions Inclusion of a clinical sexologist in a penile and sexual rehabilitation program appears to improve the ability to have regular sexual activity with penetrating sex one year after da Vinci Robotic Radical Prostatectomy. PMID:26251748

  20. Mechatronic demonstrator for testing sensors to be used in mobile robotics functioning on the inverted pendulum concept

    NASA Astrophysics Data System (ADS)

    Sandru, L.; Dolga, V.; Moldovan, C.; Savu, D.

    2016-08-01

    As the educational system is evolving, there are a lot of Mechatronic demonstrators used in schools and universities to demonstrate some technical, theoretical principle and analyzing new concept to apply this studied information, build practical hardware parts. The idea of using mobile robots for different applications is very common today. For choosing the best hardware and software configuration for the mobile robot it is necessary to make a documented analysis of the environment in which the mobile robot will perform. In our demonstrator we want to collect information from an optical sensor what can be used to maintain stability in a mobile robot equilibrium reading the reflected light from a surface. After hardware build we make a particularity study to see how optical sensors response in different ambient light and surface. To show some reference point we are collecting data from gyroscopic, accelerometer or rotation sensors.

  1. The role of targeted chemical proteomics in pharmacology

    PubMed Central

    Sutton, Chris W

    2012-01-01

    Traditionally, proteomics is the high-throughput characterization of the global complement of proteins in a biological system using cutting-edge technologies (robotics and mass spectrometry) and bioinformatics tools (Internet-based search engines and databases). As the field of proteomics has matured, a diverse range of strategies have evolved to answer specific problems. Chemical proteomics is one such direction that provides the means to enrich and detect less abundant proteins (the ‘hidden’ proteome) from complex mixtures of wide dynamic range (the ‘deep’ proteome). In pharmacology, chemical proteomics has been utilized to determine the specificity of drugs and their analogues, for anticipated known targets, only to discover other proteins that bind and could account for side effects observed in preclinical and clinical trials. As a consequence, chemical proteomics provides a valuable accessory in refinement of second- and third-generation drug design for treatment of many diseases. However, determining definitive affinity capture of proteins by a drug immobilized on soft gel chromatography matrices has highlighted some of the challenges that remain to be addressed. Examples of the different strategies that have emerged using well-established drugs against pharmaceutically important enzymes, such as protein kinases, metalloproteases, PDEs, cytochrome P450s, etc., indicate the potential opportunity to employ chemical proteomics as an early-stage screening approach in the identification of new targets. PMID:22074351

  2. Lipolytic proteomics.

    PubMed

    Schittmayer, Matthias; Birner-Gruenberger, Ruth

    2012-01-01

    Activity-based proteomics (ABP) employs small molecular probes to specifically label sets of enzymes based on their shared catalytic mechanism. Given that the vast majority of lipases belong to the family of serine hydrolases and share a nucleophilic active-site serine as part of a catalytic triad, activity-based probes are ideal tools to study lipases and lipolysis. Moreover, the ability of ABP to highlight or isolate specific subproteomes results in a massive decrease of sample complexity. Thereby, in-depth analysis of enzymes of interest with mass spectrometry becomes feasible. In this review, we cover probe design, technological developments, and applications of ABP of lipases, as well as give an overview of relevant identified proteins.

  3. Identification of Replication-competent HSV-1 Cgal+ Strain Signaling Targets in Human Hepatoma Cells by Functional Organelle Proteomics*S⃞

    PubMed Central

    Santamaría, Enrique; Mora, María I.; Potel, Corinne; Fernández-Irigoyen, Joaquín; Carro-Roldán, Elvira; Hernández-Alcoceba, Rubén; Prieto, Jesús; Epstein, Alberto L.; Corrales, Fernando J.

    2009-01-01

    In the present work, we have attempted a comprehensive analysis of cytosolic and microsomal proteomes to elucidate the signaling pathways impaired in human hepatoma (Huh7) cells upon herpes simplex virus type 1 (HSV-1; Cgal+) infection. Using a combination of differential in-gel electrophoresis and nano liquid chromatography/tandem mass spectrometry, 18 spots corresponding to 16 unique deregulated cellular proteins were unambiguously identified, which were involved in the regulation of essential processes such as apoptosis, mRNA processing, cellular structure and integrity, signal transduction, and endoplasmic-reticulum-associated degradation pathway. Based on our proteomic data and additional functional studies target proteins were identified indicating a late activation of apoptotic pathways in Huh7 cells upon HSV-1 Cgal+ infection. Additionally to changes on RuvB-like 2 and Bif-1, down-regulation of Erlin-2 suggests stimulation of Ca2+-dependent apoptosis. Moreover, activation of the mitochondrial apoptotic pathway results from a time-dependent multi-factorial impairment as inferred from the stepwise characterization of constitutive pro- and anti-apoptotic factors. Activation of serine-threonine protein phosphatase 2A (PP2A) was also found in Huh7 cells upon HSV-1 Cgal+ infection. In addition, PP2A activation paralleled dephosphorylation and inactivation of downstream mitogen-activated protein (MAP) kinase pathway (MEK½, ERK½) critical to cell survival and activation of proapoptotic Bad by dephosphorylation of Ser-112. Taken together, our results provide novel molecular information that contributes to define in detail the apoptotic mechanisms triggered by HSV-1 Cgal+ in the host cell and lead to the implication of PP2A in the transduction of cell death signals and cell survival pathway arrest. PMID:19098277

  4. New challenges for proteomics technologies: a mini perspective review

    SciTech Connect

    Shen, Yufeng; Pasa-Tolic, Ljiljana; Robinson, Errol W.; Adkins, Joshua N.; Smith, Richard D.

    2014-10-10

    Proteomics technologies have experienced rapid advances over the last decade to identify or quantify thousands of proteins per sample, typically in a few hours, enabling proteomics applications in environmental, biological, medical, and clinical research. A number of publications have reviewed advances in proteomic technologies and applications. This short review focuses first on a discussion of sensitivity in bottom-up (i.e. digested protein) proteomics and approaches for characterization of small cell populations, and secondly on protein separations for top-down (i.e. intact protein) proteomics including discussions of key technical challenges where recent advances are elucidating specific functions of proteins in biological processes.

  5. The proteome browser web portal.

    PubMed

    Goode, Robert J A; Yu, Simon; Kannan, Anitha; Christiansen, Jeffrey H; Beitz, Anthony; Hancock, William S; Nice, Edouard; Smith, A Ian

    2013-01-01

    In 2010, the Human Proteome Organization launched the Human Proteome Project (HPP), aimed at identifying and characterizing the proteome of the human body. To support complete coverage, one arm of the project will take a gene- or chromosomal-centric strategy (C-HPP) aimed at identifying at least one protein product from each protein-coding gene. Despite multiple large international biological databases housing genomic and protein data, there is currently no single system that integrates updated pertinent information from each of these data repositories and assembles the information into a searchable format suitable for the type of global proteomics effort proposed by the C-HPP. We have undertaken the goal of producing a data integration and analysis software system and browser for the C-HPP effort and of making data collections from this resource discoverable through metadata repositories, such as Australian National Data Service's Research Data Australia. Here we present our vision and progress toward the goal of developing a comprehensive data integration and analysis software tool that provides a snapshot of currently available proteomic related knowledge around each gene product, which will ultimately assist in analyzing biological function and the study of human physiology in health and disease.

  6. Biological Soft Robotics.

    PubMed

    Feinberg, Adam W

    2015-01-01

    In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed. PMID:26643022

  7. Robotics and neuroscience.

    PubMed

    Floreano, Dario; Ijspeert, Auke Jan; Schaal, Stefan

    2014-09-22

    In the attempt to build adaptive and intelligent machines, roboticists have looked at neuroscience for more than half a century as a source of inspiration for perception and control. More recently, neuroscientists have resorted to robots for testing hypotheses and validating models of biological nervous systems. Here, we give an overview of the work at the intersection of robotics and neuroscience and highlight the most promising approaches and areas where interactions between the two fields have generated significant new insights. We articulate the work in three sections, invertebrate, vertebrate and primate neuroscience. We argue that robots generate valuable insight into the function of nervous systems, which is intimately linked to behaviour and embodiment, and that brain-inspired algorithms and devices give robots life-like capabilities.

  8. Biological Soft Robotics.

    PubMed

    Feinberg, Adam W

    2015-01-01

    In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.

  9. Microbial proteomics: the quiet revolution

    SciTech Connect

    Seraphin, Bertrand; Hettich, Robert {Bob} L

    2012-01-01

    Technological developments in DNA sequencing and their application to study thousands of microbial genomes or even microbial ecosystems still today often make the headlines of general newspapers and scientific journals. These revolutionary changes are hiding another revolution that is unfolding more quietly in the background: the development of microbial proteomics to study genome expression products. It is important to recognize that while DNA sequencing reveals extensive details about the genomic potential of an organism or community, proteomic measurements reveal the functional gene products that are present and operational under specific environmental conditions, and thus perhaps better characterize the critical biomolecules that execute the life processes (enzymes, signaling, structural factors, etc.).

  10. European and international collaboration in affinity proteomics.

    PubMed

    Stoevesandt, Oda; Taussig, Michael J

    2012-06-15

    In affinity proteomics, specific protein-binding molecules (a.k.a. binders), principally antibodies, are applied as reagents in proteome analysis. In recent years, advances in binder technologies have created the potential for an unprecedented view on protein expression and distribution patterns in plasma, cells and tissues and increasingly on protein function. Particular strengths of affinity proteomics methods include detecting proteins in their natural environments of cell or tissue, high sensitivity and selectivity for detection of low abundance proteins and exploiting binding actions such as functional interference in living cells. To maximise the use and impact of affinity reagents, it will be essential to create comprehensive, standardised binder collections. With this in mind, the EU FP7 programme AFFINOMICS (http://www.affinomics.org), together with the preceding EU programmes ProteomeBinders and AffinityProteome, aims to extend affinity proteomics research by generating a large-scale resource of validated protein-binding molecules for characterisation of the human proteome. Activity is directed at producing binders to about 1000 protein targets, primarily in signal transduction and cancer, by establishing a high throughput, coordinated production pipeline. An important aspect of AFFINOMICS is the development of highly efficient recombinant selection methods, based on phage, cell and ribosome display, capable of producing high quality binders at greater throughput and lower cost than hitherto. The programme also involves development of innovative and sensitive technologies for specific detection of target proteins and their interactions, and deployment of binders in proteomics studies of clinical relevance. The need for such binder generation programmes is now recognised internationally, with parallel initiatives in the USA for cancer (NCI) and transcription factors (NIH) and within the Human Proteome Organisation (HUPO). The papers in this volume of New

  11. Proteomic Insight into Functional Changes of Proteorhodopsin-Containing Bacterial Species Psychroflexus torquis under Different Illumination and Salinity Levels.

    PubMed

    Feng, Shi; Powell, Shane M; Wilson, Richard; Bowman, John P

    2015-09-01

    The extremely psychrophilic proteorhodopsin-containing bacterial species Psychroflexus torquis is considered to be a model sea-ice microorganism, which has adapted to an epiphytic lifestyle. So far, not much is known about proteorhodopsin-based phototrophy and associated life strategies of sea ice bacteria, although it has been previously shown that P. torquis can gain growth advantage from light using a proteorhodopsin proton pump, the activity of which is influenced by environmental salinity. The comprehensive quantitative proteomic study performed here indicated that P. torquis responds to changing salinity and illumination conditions. Proteins in the electron-transfer chain were down-regulated at a suboptimal salinity level, TonB-dependent transporters increased in abundance under supra-optimal salinity and decreased under suboptimal salinity. In addition, several anaplerotic CO2 fixation proteins and three putative light sensing proteins that contain PAS and GAF domains became more abundant under illumination. Furthermore, central metabolic pathways (TCA and glycolysis) were also induced by both salinity stress and illumination. The data suggest that P. torquis responded to changes in both light energy and salinity to modulate membrane and central metabolic proteins that are involved in energy production as well as nutrient uptake and gliding motility processes that would be especially advantageous during the polar summer ice algal bloom.

  12. Proteome Profile of Functional Mitochondria from Human Skeletal Muscle Using One-Dimensional Gel Electrophoresis and HPLC-ESI-MS/MS

    PubMed Central

    Lefort, Natalie; Yi, Zhengping; Bowen, Benjamin; Glancy, Brian; De Filippis, Eleanna A.; Mapes, Rebekka; Hwang, Hyonson; Flynn, Charles R.; Willis, Wayne T.; Civitarese, Anthony; Højlund, Kurt; Mandarino, Lawrence J.

    2009-01-01

    Mitochondria can be isolated from skeletal muscle in a manner that preserves tightly coupled bioenergetic function in vitro. The purpose of this study was to characterize the composition of such preparations using a proteomics approach. Mitochondria isolated from human vastus lateralis biopsies were functional as evidenced by their response to carbohydrate and fat-derived fuels. Using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS, 823 unique proteins were detected, and 487 of these were assigned to the mitochondrion, including the newly characterized SIRT5, MitoNEET and RDH13. Proteins detected included 9 of the 13 mitochondrial DNA-encoded proteins and 86 of 104 electron transport chain (ETC) and ETC-related proteins. In addition, 59 of 78 proteins of the 55S mitoribosome, several TIM and TOM proteins and cell death proteins were present. This study presents an efficient method for future qualitative assessments of proteins from functional isolated mitochondria from small samples of healthy and diseased skeletal muscle. PMID:19567276

  13. An siRNA screen for ATG protein depletion reveals the extent of the unconventional functions of the autophagy proteome in virus replication.

    PubMed

    Mauthe, Mario; Langereis, Martijn; Jung, Jennifer; Zhou, Xingdong; Jones, Alex; Omta, Wienand; Tooze, Sharon A; Stork, Björn; Paludan, Søren Riis; Ahola, Tero; Egan, Dave; Behrends, Christian; Mokry, Michal; de Haan, Cornelis; van Kuppeveld, Frank; Reggiori, Fulvio

    2016-08-29

    Autophagy is a catabolic process regulated by the orchestrated action of the autophagy-related (ATG) proteins. Recent work indicates that some of the ATG proteins also have autophagy-independent roles. Using an unbiased siRNA screen approach, we explored the extent of these unconventional functions of ATG proteins. We determined the effects of the depletion of each ATG proteome component on the replication of six different viruses. Our screen reveals that up to 36% of the ATG proteins significantly alter the replication of at least one virus in an unconventional fashion. Detailed analysis of two candidates revealed an undocumented role for ATG13 and FIP200 in picornavirus replication that is independent of their function in autophagy as part of the ULK complex. The high numbers of unveiled ATG gene-specific and pathogen-specific functions of the ATG proteins calls for caution in the interpretation of data, which rely solely on the depletion of a single ATG protein to specifically ablate autophagy. PMID:27573464

  14. Proteomic identification and functional characterization of MYH9, Hsc70, and DNAJA1 as novel substrates of HDAC6 deacetylase activity.

    PubMed

    Zhang, Linlin; Liu, Shanshan; Liu, Ningning; Zhang, Yong; Liu, Min; Li, Dengwen; Seto, Edward; Yao, Tso-Pang; Shui, Wenqing; Zhou, Jun

    2015-01-01

    Histone deacetylase 6 (HDAC6), a predominantly cytoplasmic protein deacetylase, participates in a wide range of cellular processes through its deacetylase activity. However, the diverse functions of HDAC6 cannot be fully elucidated with its known substrates. In an attempt to explore the substrate diversity of HDAC6, we performed quantitative proteomic analyses to monitor changes in the abundance of protein lysine acetylation in response to HDAC6 deficiency. We identified 107 proteins with elevated acetylation in the liver of HDAC6 knockout mice. Three cytoplasmic proteins, including myosin heavy chain 9 (MYH9), heat shock cognate protein 70 (Hsc70), and dnaJ homolog subfamily A member 1 (DNAJA1), were verified to interact with HDAC6. The acetylation levels of these proteins were negatively regulated by HDAC6 both in the mouse liver and in cultured cells. Functional studies reveal that HDAC6-mediated deacetylation modulates the actin-binding ability of MYH9 and the interaction between Hsc70 and DNAJA1. These findings consolidate the notion that HDAC6 serves as a critical regulator of protein acetylation with the capability of coordinating various cellular functions.

  15. 30 Years of Robotic Surgery.

    PubMed

    Leal Ghezzi, Tiago; Campos Corleta, Oly

    2016-10-01

    The idea of reproducing himself with the use of a mechanical robot structure has been in man's imagination in the last 3000 years. However, the use of robots in medicine has only 30 years of history. The application of robots in surgery originates from the need of modern man to achieve two goals: the telepresence and the performance of repetitive and accurate tasks. The first "robot surgeon" used on a human patient was the PUMA 200 in 1985. In the 1990s, scientists developed the concept of "master-slave" robot, which consisted of a robot with remote manipulators controlled by a surgeon at a surgical workstation. Despite the lack of force and tactile feedback, technical advantages of robotic surgery, such as 3D vision, stable and magnified image, EndoWrist instruments, physiologic tremor filtering, and motion scaling, have been considered fundamental to overcome many of the limitations of the laparoscopic surgery. Since the approval of the da Vinci(®) robot by international agencies, American, European, and Asian surgeons have proved its factibility and safety for the performance of many different robot-assisted surgeries. Comparative studies of robotic and laparoscopic surgical procedures in general surgery have shown similar results with regard to perioperative, oncological, and functional outcomes. However, higher costs and lack of haptic feedback represent the major limitations of current robotic technology to become the standard technique of minimally invasive surgery worldwide. Therefore, the future of robotic surgery involves cost reduction, development of new platforms and technologies, creation and validation of curriculum and virtual simulators, and conduction of randomized clinical trials to determine the best applications of robotics. PMID:27177648

  16. 30 Years of Robotic Surgery.

    PubMed

    Leal Ghezzi, Tiago; Campos Corleta, Oly

    2016-10-01

    The idea of reproducing himself with the use of a mechanical robot structure has been in man's imagination in the last 3000 years. However, the use of robots in medicine has only 30 years of history. The application of robots in surgery originates from the need of modern man to achieve two goals: the telepresence and the performance of repetitive and accurate tasks. The first "robot surgeon" used on a human patient was the PUMA 200 in 1985. In the 1990s, scientists developed the concept of "master-slave" robot, which consisted of a robot with remote manipulators controlled by a surgeon at a surgical workstation. Despite the lack of force and tactile feedback, technical advantages of robotic surgery, such as 3D vision, stable and magnified image, EndoWrist instruments, physiologic tremor filtering, and motion scaling, have been considered fundamental to overcome many of the limitations of the laparoscopic surgery. Since the approval of the da Vinci(®) robot by international agencies, American, European, and Asian surgeons have proved its factibility and safety for the performance of many different robot-assisted surgeries. Comparative studies of robotic and laparoscopic surgical procedures in general surgery have shown similar results with regard to perioperative, oncological, and functional outcomes. However, higher costs and lack of haptic feedback represent the major limitations of current robotic technology to become the standard technique of minimally invasive surgery worldwide. Therefore, the future of robotic surgery involves cost reduction, development of new platforms and technologies, creation and validation of curriculum and virtual simulators, and conduction of randomized clinical trials to determine the best applications of robotics.

  17. Neural Stem Cells (NSCs) and Proteomics*

    PubMed Central

    Shoemaker, Lorelei D.; Kornblum, Harley I.

    2016-01-01

    Neural stem cells (NSCs) can self-renew and give rise to the major cell types of the CNS. Studies of NSCs include the investigation of primary, CNS-derived cells as well as animal and human embryonic stem cell (ESC)-derived and induced pluripotent stem cell (iPSC)-derived sources. NSCs provide a means with which to study normal neural development, neurodegeneration, and neurological disease and are clinically relevant sources for cellular repair to the damaged and diseased CNS. Proteomics studies of NSCs have the potential to delineate molecules and pathways critical for NSC biology and the means by which NSCs can participate in neural repair. In this review, we provide a background to NSC biology, including the means to obtain them and the caveats to these processes. We then focus on advances in the proteomic interrogation of NSCs. This includes the analysis of posttranslational modifications (PTMs); approaches to analyzing different proteomic compartments, such the secretome; as well as approaches to analyzing temporal differences in the proteome to elucidate mechanisms of differentiation. We also discuss some of the methods that will undoubtedly be useful in the investigation of NSCs but which have not yet been applied to the field. While many proteomics studies of NSCs have largely catalogued the proteome or posttranslational modifications of specific cellular states, without delving into specific functions, some have led to understandings of functional processes or identified markers that could not have been identified via other means. Many challenges remain in the field, including the precise identification and standardization of NSCs used for proteomic analyses, as well as how to translate fundamental proteomics studies to functional biology. The next level of investigation will require interdisciplinary approaches, combining the skills of those interested in the biochemistry of proteomics with those interested in modulating NSC function. PMID:26494823

  18. Neural Stem Cells (NSCs) and Proteomics.

    PubMed

    Shoemaker, Lorelei D; Kornblum, Harley I

    2016-02-01

    Neural stem cells (NSCs) can self-renew and give rise to the major cell types of the CNS. Studies of NSCs include the investigation of primary, CNS-derived cells as well as animal and human embryonic stem cell (ESC)-derived and induced pluripotent stem cell (iPSC)-derived sources. NSCs provide a means with which to study normal neural development, neurodegeneration, and neurological disease and are clinically relevant sources for cellular repair to the damaged and diseased CNS. Proteomics studies of NSCs have the potential to delineate molecules and pathways critical for NSC biology and the means by which NSCs can participate in neural repair. In this review, we provide a background to NSC biology, including the means to obtain them and the caveats to these processes. We then focus on advances in the proteomic interrogation of NSCs. This includes the analysis of posttranslational modifications (PTMs); approaches to analyzing different proteomic compartments, such the secretome; as well as approaches to analyzing temporal differences in the proteome to elucidate mechanisms of differentiation. We also discuss some of the methods that will undoubtedly be useful in the investigation of NSCs but which have not yet been applied to the field. While many proteomics studies of NSCs have largely catalogued the proteome or posttranslational modifications of specific cellular states, without delving into specific functions, some have led to understandings of functional processes or identified markers that could not have been identified via other means. Many challenges remain in the field, including the precise identification and standardization of NSCs used for proteomic analyses, as well as how to translate fundamental proteomics studies to functional biology. The next level of investigation will require interdisciplinary approaches, combining the skills of those interested in the biochemistry of proteomics with those interested in modulating NSC function. PMID:26494823

  19. Crossmodal representation of a functional robotic hand arises after extensive training in healthy participants.

    PubMed

    Marini, Francesco; Tagliabue, Chiara F; Sposito, Ambra V; Hernandez-Arieta, Alejandro; Brugger, Peter; Estévez, Natalia; Maravita, Angelo

    2014-01-01

    The way in which humans represent their own bodies is critical in guiding their interactions with the environment. To achieve successful body-space interactions, the body representation is strictly connected with that of the space immediately surrounding it through efficient visuo-tactile crossmodal integration. Such a body-space integrated representation is not fixed, but can be dynamically modulated by the use of external tools. Our study aims to explore the effect of using a complex tool, namely a functional prosthesis, on crossmodal visuo-tactile spatial interactions in healthy participants. By using the crossmodal visuo-tactile congruency paradigm, we found that prolonged training with a mechanical hand capable of distal hand movements and providing sensory feedback induces a pattern of interference, which is not observed after a brief training, between visual stimuli close to the prosthesis and touches on the body. These results suggest that after extensive, but not short, training the functional prosthesis acquires a visuo-tactile crossmodal representation akin to real limbs. This finding adds to previous evidence for the embodiment of functional prostheses in amputees, and shows that their use may also improve the crossmodal combination of somatosensory feedback delivered by the prosthesis with visual stimuli in the space around it, thus effectively augmenting the patients' visuomotor abilities.

  20. Hopping robot

    DOEpatents

    Spletzer, Barry L.; Fischer, Gary J.; Marron, Lisa C.; Martinez, Michael A.; Kuehl, Michael A.; Feddema, John T.

    2001-01-01

    The present invention provides a hopping robot that includes a misfire tolerant linear actuator suitable for long trips, low energy steering and control, reliable low energy righting, miniature low energy fuel control. The present invention provides a robot with hopping mobility, capable of traversing obstacles significant in size relative to the robot and capable of operation on unpredictable terrain over long range. The present invention further provides a hopping robot with misfire-tolerant combustion actuation, and with combustion actuation suitable for use in oxygen-poor environments.

  1. The speciation of the proteome

    PubMed Central

    Jungblut, Peter R; Holzhütter, Hermann G; Apweiler, Rolf; Schlüter, Hartmut

    2008-01-01

    Introduction In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function. Discussion Optimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function. Conclusion To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today. PMID:18638390

  2. World Wide Web Robots: An Overview.

    ERIC Educational Resources Information Center

    Chun, Tham Yoke

    1999-01-01

    Traces the development of World Wide Web Robots and provides an overview of their main functions and workings. The focus is on search robots. Illustrations are drawn from two major search engines: AltaVista and Excite. Concludes with an examination of problems associated with the use of Web Robots and their implications for electronic publishing.…

  3. [Robot-asssisted laparoscopic radical prostatectomy (ralp). Oncological and functional findings after 90 cases].

    PubMed

    Gilberti, C; Schenone, M; Cortese, P; Gallo, F; Gastaldi, E; Ninotta, G

    2009-01-01

    The RALP is the most modern technology available for the treatment of intracapsular prostate cancer (CaP), which can produce a shorter learning curve and better results than the traditional techniques. METHODS. Between March 2005 and March 2008, 90 patients (64.3 ys, range 52-71) with intracapsular CaP underwent RALP at our institute. Before surgery the patients underwent routine examinations and filled in IIEF, IPSS and EORTC-QLQC30/PR 25 questionnaires. Patients were followed up with PSA assay, physical examination and compilation of the questionnaires. Median follow-up was 12.5 months (range 1-35 months). RESULTS. Mean operative time was 230 min. Discharge and catheter removal were at day 7.4 and 8.2, respectively, after surgery. Pathological staging reported pT2 and pT3 in 57 (63%) and 33 patients (37%), respectively. Positive surgical margins were assessed in 30 patients (33%), particularly 8.7% in pT2 tumors. The one-year biochemical disease-free survival rate was 90%. Regarding the functional results, 81 patients (90%) were perfectly continent while a mild and a moderate incontinence were reported in 7 (8%) and 2 (2%) patients, respectively. Mean IPSS score decreased from 8 to 4; among the patients who underwent bilateral nerve sparing RALP and no adjuvant therapy, 31 (70.4%) reported satisfactory sexual intercourses. Concerning postoperative quality of life, mean EORTC-QLQC30/PR 25 questionnaires scores were very similar before and after RALP. CONCLUSIONS. After 90 cases of RALP the oncological and functional results are definitely promising. However, a wider number of patients and a greater follow-up are needed to confirm these data particularly as regards the functional results.

  4. Robotic joint experiments under ultravacuum

    NASA Technical Reports Server (NTRS)

    Borrien, A.; Petitjean, L.

    1988-01-01

    First, various aspects of a robotic joint development program, including gearbox technology, electromechanical components, lubrication, and test results, are discussed. Secondly, a test prototype of the joint allowing simulation of robotic arm dynamic effects is presented. This prototype is tested under vacuum with different types of motors and sensors to characterize the functional parameters: angular position error, mechanical backlash, gearbox efficiency, and lifetime.

  5. Proteomics for Validation of Automated Gene Model Predictions

    SciTech Connect

    Zhou, Kemin; Panisko, Ellen A.; Magnuson, Jon K.; Baker, Scott E.; Grigoriev, Igor V.

    2008-02-14

    High-throughput liquid chromatography mass spectrometry (LC-MS)-based proteomic analysis has emerged as a powerful tool for functional annotation of genome sequences. These analyses complement the bioinformatic and experimental tools used for deriving, verifying, and functionally annotating models of genes and their transcripts. Furthermore, proteomics extends verification and functional annotation to the level of the translation product of the gene model.

  6. Proteomic Analysis of Interaction between a Plant Virus and Its Vector Insect Reveals New Functions of Hemipteran Cuticular Protein.

    PubMed

    Liu, Wenwen; Gray, Stewart; Huo, Yan; Li, Li; Wei, Taiyun; Wang, Xifeng

    2015-08-01

    Numerous viruses can be transmitted by their corresponding vector insects; however, the molecular mechanisms enabling virus transmission by vector insects have been poorly understood, especially the identity of vector components interacting with the virus. Here, we used the yeast two-hybrid system to study proteomic interactions of a plant virus (Rice stripe virus, RSV, genus Tenuivirus) with its vector insect, small brown planthopper (Laodelphax striatellus). Sixty-six proteins of L. striatellus that interacted with the nucleocapsid protein (pc3) of RSV were identified. A virus-insect interaction network, constructed for pc3 and 29 protein homologs of Drosophila melanogaster, suggested that nine proteins might directly interact with pc3. Of the 66 proteins, five (atlasin, a novel cuticular protein, jagunal, NAC domain protein, and vitellogenin) were most likely to be involved in viral movement, replication, and transovarial transmission. This work also provides evidence that the novel cuticular protein, CPR1, from L. striatellus is essential for RSV transmission by its vector insect. CPR1 binds the nucleocapsid protein (pc3) of RSV both in vivo and in vitro and colocalizes with RSV in the hemocytes of L. striatellus. Knockdown of CPR1 transcription using RNA interference resulted in a decrease in the concentration of RSV in the hemolymph, salivary glands and in viral transmission efficiency. These data suggest that CPR1 binds RSV in the insect and stabilizes the viral concentration in the hemolymph, perhaps to protect the virus or to help move the virus to the salivary tissues. Our studies provide direct experimental evidence that viruses can use existing vector proteins to aid their survival in the hemolymph. Identifying these putative vector molecules should lead to a better understanding of the interactions between viruses and vector insects. PMID:26091699

  7. Proteomic Analysis of Interaction between a Plant Virus and Its Vector Insect Reveals New Functions of Hemipteran Cuticular Protein*

    PubMed Central

    Liu, Wenwen; Gray, Stewart; Huo, Yan; Li, Li; Wei, Taiyun; Wang, Xifeng

    2015-01-01

    Numerous viruses can be transmitted by their corresponding vector insects; however, the molecular mechanisms enabling virus transmission by vector insects have been poorly understood, especially the identity of vector components interacting with the virus. Here, we used the yeast two-hybrid system to study proteomic interactions of a plant virus (Rice stripe virus, RSV, genus Tenuivirus) with its vector insect, small brown planthopper (Laodelphax striatellus). Sixty-six proteins of L. striatellus that interacted with the nucleocapsid protein (pc3) of RSV were identified. A virus–insect interaction network, constructed for pc3 and 29 protein homologs of Drosophila melanogaster, suggested that nine proteins might directly interact with pc3. Of the 66 proteins, five (atlasin, a novel cuticular protein, jagunal, NAC domain protein, and vitellogenin) were most likely to be involved in viral movement, replication, and transovarial transmission. This work also provides evidence that the novel cuticular protein, CPR1, from L. striatellus is essential for RSV transmission by its vector insect. CPR1 binds the nucleocapsid protein (pc3) of RSV both in vivo and in vitro and colocalizes with RSV in the hemocytes of L. striatellus. Knockdown of CPR1 transcription using RNA interference resulted in a decrease in the concentration of RSV in the hemolymph, salivary glands and in viral transmission efficiency. These data suggest that CPR1 binds RSV in the insect and stabilizes the viral concentration in the hemolymph, perhaps to protect the virus or to help move the virus to the salivary tissues. Our studies provide direct experimental evidence that viruses can use existing vector proteins to aid their survival in the hemolymph. Identifying these putative vector molecules should lead to a better understanding of the interactions between viruses and vector insects. PMID:26091699

  8. Proteomic profiling of lymphocytes in autoimmunity, inflammation and cancer

    PubMed Central

    2014-01-01

    Lymphocytes play important roles in the balance between body defense and noxious agents involved in a number of diseases, e.g. autoimmune diseases, allergic inflammation and cancer. The proteomic analyses have been applied to identify and validate disease-associated and disease-specific biomarkers for therapeutic strategies of diseases. The proteomic profiles of lymphocytes may provide more information to understand their functions and roles in the development of diseases, although proteomic approaches in lymphocytes are still limited. The present review overviewed the proteomics-based studies on lymphocytes to headlight the proteomic profiles of lymphocytes in diseases, such as autoimmune diseases, allergic inflammation and cancer, with a special focus on lung diseases. We will explore the potential significance of diagnostic biomarkers and therapeutic targets from the current status in proteomic studies of lymphocytes and discuss the value of the currently available proteomic methodologies in the lymphocytes research. PMID:24397796

  9. Robots and Humans: Synergy in Planetary Exploration

    NASA Technical Reports Server (NTRS)

    Landis, Geoffrey A.

    2002-01-01

    How will humans and robots cooperate in future planetary exploration? Are humans and robots fundamentally separate modes of exploration, or can humans and robots work together to synergistically explore the solar system? It is proposed that humans and robots can work together in exploring the planets by use of telerobotic operation to expand the function and usefulness of human explorers, and to extend the range of human exploration to hostile environments.

  10. Robots and humans: synergy in planetary exploration

    NASA Technical Reports Server (NTRS)

    Landis, Geoffrey A.

    2004-01-01

    How will humans and robots cooperate in future planetary exploration? Are humans and robots fundamentally separate modes of exploration, or can humans and robots work together to synergistically explore the solar system? It is proposed that humans and robots can work together in exploring the planets by use of telerobotic operation to expand the function and usefulness of human explorers, and to extend the range of human exploration to hostile environments. Published by Elsevier Ltd.

  11. Robots and Humans: Synergy in Planetary Exploration

    NASA Technical Reports Server (NTRS)

    Landis, Geoffrey A.

    2003-01-01

    How will humans and robots cooperate in future planetary exploration? Are humans and robots fundamentally separate modes of exploration, or can humans and robots work together to synergistically explore the solar system? It is proposed that humans and robots can work together in exploring the planets by use of telerobotic operation to expand the function and usefulness of human explorers, and to extend the range of human exploration to hostile environments.

  12. Proteomics: methodologies and applications in oncology.

    PubMed

    Wouters, Bradly G

    2008-04-01

    Few technological developments have created as much excitement and skepticism as proteomics over their potential to change clinical diagnostic and prognostic procedures. Proteomics concerns itself with the characterization and function of all cellular proteins, the ultimate determinants of cellular function. As such, it represents the end result of all mechanisms of gene regulation and thus offers tremendous potential for characterizing biology. In much the same way as what has occurred with the genome, the scientific community is coming to grips with the fact that the proteome, although enormously complex, is finite. It is conceivable that we will learn the identity of all possible proteins, including all posttranslational modifications. The rate of protein discovery continues to accelerate in large part because of improvements in mass spectrometry-based technologies coupled with improved genomic databases and bioinformatic tools. In addition, there is reason to believe that proteomics is on the verge of moving from a methodology that requires repeated proteome "discovery" to one that can more systematically profile proteomes. This review discusses current proteomic-based technologies and the efforts of scientists to move them into the clinic for use in patients treated with radiotherapy and other modalities.

  13. Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation.

    PubMed

    Colak, Gozde; Pougovkina, Olga; Dai, Lunzhi; Tan, Minjia; Te Brinke, Heleen; Huang, He; Cheng, Zhongyi; Park, Jeongsoon; Wan, Xuelian; Liu, Xiaojing; Yue, Wyatt W; Wanders, Ronald J A; Locasale, Jason W; Lombard, David B; de Boer, Vincent C J; Zhao, Yingming

    2015-11-01

    The protein substrates of sirtuin 5-regulated lysine malonylation (Kmal) remain unknown, hindering its functional analysis. In this study, we carried out proteomic screening, which identified 4042 Kmal sites on 1426 proteins in mouse liver and 4943 Kmal sites on 1822 proteins in human fibroblasts. Increased malonyl-CoA levels in malonyl-CoA decarboxylase (MCD)-deficient cells induces Kmal levels in substrate proteins. We identified 461 Kmal sites showing more than a 2-fold increase in response to MCD deficiency as well as 1452 Kmal sites detected only in MCD-/- fibroblast but not MCD+/+ cells, suggesting a pathogenic role of Kmal in MCD deficiency. Cells with increased lysine malonylation displayed impaired mitochondrial function and fatty acid oxidation, suggesting that lysine malonylation plays a role in pathophysiology of malonic aciduria. Our study establishes an association between Kmal and a genetic disease and offers a rich resource for elucidating the contribution of the Kmal pathway and malonyl-CoA to cellular physiology and human diseases. PMID:26320211

  14. Optimal isolation of mitochondria for proteomic analyses.

    PubMed

    Stimpson, Scott E; Coorssen, Jens R; Myers, Simon J

    2015-04-15

    Considering the key role of mitochondria in cellular (dys)functions, we compared a standard isolation protocol, followed by lysis in urea/detergent buffer, with a commercially available isolation buffer that rapidly yields a mitochondrial protein fraction. The standard protocol yielded significantly better overall resolution and coverage of both the soluble and membrane mitochondrial proteomes; although the kit was faster, it resulted in recovery of only approximately 56% of the detectable proteome. The quality of "omic" analysis depends on sample handling; for large-scale protein studies, well-resolved proteomes are highly dependent on the purity of starting material and the rigor of the extraction protocol. PMID:25596337

  15. Proteomics/genomics and signaling in lymphocytes.

    PubMed

    Wollscheid, Bernd; Watts, Julian D; Aebersold, Ruedi

    2004-06-01

    Recent technological advances in genomics, proteomics and bioinformatics have offered new insights into the molecular mechanisms that underlie lymphocyte signaling and function, and the development of new tools in these areas has opened up new avenues for biological investigation. By adding a quantitative dimension to lymphocyte proteome profiling, molecular machines and spatiotemporal regulatory processes can now be analyzed using such discovery-driven approaches. Biologists employing genomic and proteomic tools are gathering data at increasing speed and their struggle to extract maximal biological information is helped by new software tools that enable the detailed comparison of multiple datasets.

  16. Robotic system

    NASA Technical Reports Server (NTRS)

    Ambrose, Robert O. (Inventor)

    2003-01-01

    A robot having a plurality of interconnected sections is disclosed. Each of the sections includes components which are moveable relative to components of an adjacent section. A plurality of electric motors are operably connected to at least two of said relatively moveable components to effect relative movement. A fitted, removable protective covering surrounds the sections to protect the robot.

  17. Robotics 101

    ERIC Educational Resources Information Center

    Sultan, Alan

    2011-01-01

    Robots are used in all kinds of industrial settings. They are used to rivet bolts to cars, to move items from one conveyor belt to another, to gather information from other planets, and even to perform some very delicate types of surgery. Anyone who has watched a robot perform its tasks cannot help but be impressed by how it works. This article…

  18. Robot Design

    NASA Technical Reports Server (NTRS)

    1988-01-01

    Martin Marietta Aero and Naval Systems has advanced the CAD art to a very high level at its Robotics Laboratory. One of the company's major projects is construction of a huge Field Material Handling Robot for the Army's Human Engineering Lab. Design of FMR, intended to move heavy and dangerous material such as ammunition, was a triumph in CAD Engineering. Separate computer problems modeled the robot's kinematics and dynamics, yielding such parameters as the strength of materials required for each component, the length of the arms, their degree of freedom and power of hydraulic system needed. The Robotics Lab went a step further and added data enabling computer simulation and animation of the robot's total operational capability under various loading and unloading conditions. NASA computer program (IAC), integrated Analysis Capability Engineering Database was used. Program contains a series of modules that can stand alone or be integrated with data from sensors or software tools.

  19. Robotic Surgery

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The Automated Endoscopic System for Optimal Positioning, or AESOP, was developed by Computer Motion, Inc. under a SBIR contract from the Jet Propulsion Lab. AESOP is a robotic endoscopic positioning system used to control the motion of a camera during endoscopic surgery. The camera, which is mounted at the end of a robotic arm, previously had to be held in place by the surgical staff. With AESOP the robotic arm can make more precise and consistent movements. AESOP is also voice controlled by the surgeon. It is hoped that this technology can be used in space repair missions which require precision beyond human dexterity. A new generation of the same technology entitled the ZEUS Robotic Surgical System can make endoscopic procedures even more successful. ZEUS allows the surgeon control various instruments in its robotic arms, allowing for the precision the procedure requires.

  20. Robotic-assisted knee arthroplasty.

    PubMed

    Banerjee, Samik; Cherian, Jeffrey J; Elmallah, Randa K; Jauregui, Julio J; Pierce, Todd P; Mont, Michael A

    2015-01-01

    Robotics in total knee arthroplasty (TKA) has undergone vast improvements. Although some of the systems have fallen out of favor due to safety concerns, there has been recent increased interest for semi-active haptic robotic systems that provide intraoperative tactile feedback to the surgeon. The potential advantages include improvements in radiographic outcomes, reducing the incidence of mechanical axis malalignment of the lower extremity and better tissue balance. Proponents of robotic technology believe that these improvements may lead to superior functional outcomes and implant survivorship. We aim to discuss robotic technology development, outcomes of unicompartmental and total knee arthroplasty and the future outlook. Short-term follow-up studies on robotic-assisted knee arthroplasty suggest that, although some alignment objectives may have been achieved, more studies regarding functional outcomes are needed. Furthermore, studies evaluating the projected cost-benefit analyses of this new technology are needed before widespread adoption. Nevertheless, the short-term results warrant further evaluation. PMID:26365088

  1. [Robot-aided training in rehabilitation].

    PubMed

    Hachisuka, Kenji

    2010-02-01

    Recently, new training techniques that involve the use of robots have been used in the rehabilitation of patients with hemiplegia and paraplegia. Robots used for training the arm include the MIT-MANUS, Arm Trainer, mirror-image motion enabler (MIME) robot, and the assisted rehabilitation and measurement (ARM) Guide. Robots that are used for lower-limb training are the Rehabot, Gait Trainer, Lokomat, LOPES Exoskeleton Robot, and Gait Assist Robot. Robot-aided therapy has enabled the functional training of the arm and the lower limbs in an effective, easy, and comfortable manner. Therefore, with this type of therapy, the patients can repeatedly undergo sufficient and accurate training for a prolonged period. However, evidence of the benefits of robot-aided training has not yet been established.

  2. Wheat proteomics: proteome modulation and abiotic stress acclimation

    PubMed Central

    Komatsu, Setsuko; Kamal, Abu H. M.; Hossain, Zahed

    2014-01-01

    Cellular mechanisms of stress sensing and signaling represent the initial plant responses to adverse conditions. The development of high-throughput “Omics” techniques has initiated a new era of the study of plant molecular strategies for adapting to environmental changes. However, the elucidation of stress adaptation mechanisms in plants requires the accurate isolation and characterization of stress-responsive proteins. Because the functional part of the genome, namely the proteins and their post-translational modifications, are critical for plant stress responses, proteomic studies provide comprehensive information about the fine-tuning of cellular pathways that primarily involved in stress mitigation. This review summarizes the major proteomic findings related to alterations in the wheat proteomic profile in response to abiotic stresses. Moreover, the strengths and weaknesses of different sample preparation techniques, including subcellular protein extraction protocols, are discussed in detail. The continued development of proteomic approaches in combination with rapidly evolving bioinformatics tools and interactive databases will facilitate understanding of the plant mechanisms underlying stress tolerance. PMID:25538718

  3. Identification of metastasis-associated proteins involved in gallbladder carcinoma metastasis by proteomic analysis and functional exploration of chloride intracellular channel 1.

    PubMed

    Wang, Jian-Wei; Peng, Shu-You; Li, Jiang-Tao; Wang, Yong; Zhang, Zhi-Ping; Cheng, Yan; Cheng, De-Qing; Weng, Wei-Hong; Wu, Xiang-Song; Fei, Xiao-Zhou; Quan, Zhi-Wei; Li, Ji-Yu; Li, Song-Gang; Liu, Ying-Bin

    2009-08-18

    Advanced gallbladder cancer has an extremely poor prognosis because of metastasis. Identification of metastasis-related biomarkers is essential to improve patient survival. In the present study, metastasis-associated proteins were identified by comparative proteomic analysis and the metastasis-related function of the candidate protein, chloride intracellular channel 1 (CLIC1), was further elucidated. Two cell lines with high or low metastatic potential (termed GBC-SD18H and GBC-SD18L, respectively), originating from the same parental gallbladder carcinoma GBC-SD cell line, were identified by spontaneous metastasis in vivo and characterized by metastatic phenotypes analysis in vitro. Subsequently, a proteomic approach comprised of two-dimensional gel electrophoresis analysis and mass spectroscopy was used to identify and compare the protein expression patterns between GBC-SD18L and GBC-SD18H. Twenty-six proteins were identified and further verified by one-dimensional Western blotting and semiquantitative reverse transcriptase polymerase chain reaction analysis. It was determined that CLIC1, ezrin, vimentin, annexin A3, WD repeat domain 1, triosephosphate isomerase, C1-tetrahydrofolate synthase, Rho GDP-dissociation inhibitor 1, T-complex protein 1, heterogeneous nuclear ribonucleoprotein K, glutamate dehydrogenase 1, proteasome activator complex subunit 3 and Rab GDP-dissociation inhibitor beta were significantly up-regulated in the highly metastatic GBC-SD18H cell line compared to the poorly metastatic GBC-SD18L cell line. However, phosphoglycerate kinase 1 and programmed cell death protein 8 were significantly down-regulated in the highly metastatic GBC-SD18H cell line compared to GBC-SD18L. Considering that CLIC1 was profuse in highly metastatic GBC-SD18H but scarce in poorly metastatic GBC-SD18L, the association of CLIC1 with metastasis was further elucidated by the overexpression and RNA interference of CLIC1 in GBC-SD18L cells and GBC-SD18H cells, respectively

  4. Proteomic analysis of Chinese hamster ovary cells.

    PubMed

    Baycin-Hizal, Deniz; Tabb, David L; Chaerkady, Raghothama; Chen, Lily; Lewis, Nathan E; Nagarajan, Harish; Sarkaria, Vishaldeep; Kumar, Amit; Wolozny, Daniel; Colao, Joe; Jacobson, Elena; Tian, Yuan; O'Meally, Robert N; Krag, Sharon S; Cole, Robert N; Palsson, Bernhard O; Zhang, Hui; Betenbaugh, Michael

    2012-11-01

    To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multidimensional liquid chromatography, and solid phase extraction of glycopeptides (SPEG). From the 120 different mass spectrometry analyses generating 682,097 MS/MS spectra, 93,548 unique peptide sequences were identified with at most 0.02 false discovery rate (FDR). A total of 6164 grouped proteins were identified from both glycoproteome and proteome analysis, representing an 8-fold increase in the number of proteins currently identified in the CHO proteome. Furthermore, this is the first proteomic study done using the CHO genome exclusively, which provides for more accurate identification of proteins. From this analysis, the CHO codon frequency was determined and found to be distinct from humans, which will facilitate expression of human proteins in CHO cells. Analysis of the combined proteomic and mRNA data sets indicated the enrichment of a number of pathways including protein processing and apoptosis but depletion of proteins involved in steroid hormone and glycosphingolipid metabolism. Five-hundred four of the detected proteins included N-acetylation modifications, and 1292 different proteins were observed to be N-glycosylated. This first large-scale proteomic analysis will enhance the knowledge base about CHO capabilities for recombinant expression and provide information useful in cell engineering efforts aimed at modifying CHO cellular functions. PMID:22971049

  5. The srhSR gene pair from Staphylococcus aureus: genomic and proteomic approaches to the identification and characterization of gene function.

    PubMed

    Throup, J P; Zappacosta, F; Lunsford, R D; Annan, R S; Carr, S A; Lonsdale, J T; Bryant, A P; McDevitt, D; Rosenberg, M; Burnham, M K

    2001-08-28

    Systematic analysis of the entire two-component signal transduction system (TCSTS) gene complement of Staphylococcus aureus revealed the presence of a putative TCSTS (designated SrhSR) which shares considerable homology with the ResDE His-Asp phospho-relay pair of Bacillus subtilis. Disruption of the srhSR gene pair resulted in a dramatic reduction in growth of the srhSR mutant, when cultured under anaerobic conditions, and a 3-log attenuation in growth when analyzed in the murine pyelonephritis model. To further understand the role of SrhSR, differential display two-dimensional gel electrophoresis was used to analyze the cell-free extracts derived from the srhSR mutant and the corresponding wild type. Proteins shown to be differentially regulated were identified by mass spectrometry in combination with protein database searching. An srhSR deletion led to changes in the expression of proteins involved in energy metabolism and other metabolic processes including arginine catabolism, xanthine catabolism, and cell morphology. The impaired growth of the mutant under anaerobic conditions and the dramatic changes in proteins involved in energy metabolism shed light on the mechanisms used by S. aureus to grow anaerobically and indicate that the staphylococcal SrhSR system plays an important role in the regulation of energy transduction in response to changes in oxygen availability. The combination of proteomics, bio-informatics, and microbial genetics employed here represents a powerful set of techniques which can be applied to the study of bacterial gene function.

  6. Quantitative proteomics provides new insights into chicken eggshell matrix protein functions during the primary events of mineralisation and the active calcification phase.

    PubMed

    Marie, Pauline; Labas, Valérie; Brionne, Aurélien; Harichaux, Grégoire; Hennequet-Antier, Christelle; Rodriguez-Navarro, Alejandro B; Nys, Yves; Gautron, Joël

    2015-08-01

    Eggshell is a bioceramic composed of 95% calcium carbonate mineral and 3.5% organic matrix. Its structural organisation is controlled by its organic matrix. We have used quantitative proteomics to study four key stages of shell mineralisation: 1) widespread deposition of amorphous calcium carbonate (ACC), 2) ACC transformation into crystalline calcite aggregates, 3) formation of larger calcite crystal units and 4) development of a columnar structure with preferential calcite crystal orientation. This approach explored the distribution of 216 shell matrix proteins found at the four stages. Variations in abundance according to these calcification events were observed for 175 proteins. A putative function related to the mineralisation process was predicted by bioinformatics for 77 of them and was further characterised. We confirmed the important role of lysozyme, ovotransferrin, ovocleidin-17 and ovocleidin-116 for shell calcification process, characterised major calcium binding proteins (EDIL3, ALB, MFGE8, NUCB2), and described novel proteoglycans core proteins (GPC4, HAPLN3). We suggest that OVAL and OC-17 play a role in the stabilisation of ACC. Finally, we report proteins involved in the regulation of proteins driving the mineralisation. They correspond to numerous molecular chaperones including CLU, PPIB and OCX21, protease and protease inhibitors including OVM and CST3, and regulators of phosphorylation.

  7. When a robot is social: spatial arrangements and multimodal semiotic engagement in the practice of social robotics.

    PubMed

    Alac, Morana; Movellan, Javier; Tanaka, Fumihide

    2011-12-01

    Social roboticists design their robots to function as social agents in interaction with humans and other robots. Although we do not deny that the robot's design features are crucial for attaining this aim, we point to the relevance of spatial organization and coordination between the robot and the humans who interact with it. We recover these interactions through an observational study of a social robotics laboratory and examine them by applying a multimodal interactional analysis to two moments of robotics practice. We describe the vital role of roboticists and of the group of preverbal infants, who are involved in a robot's design activity, and we argue that the robot's social character is intrinsically related to the subtleties of human interactional moves in laboratories of social robotics. This human involvement in the robot's social agency is not simply controlled by individual will. Instead, the human-machine couplings are demanded by the situational dynamics in which the robot is lodged.

  8. Robot visions.

    PubMed

    Castañeda, Claudia; Suchman, Lucy

    2014-06-01

    This article explores the resonating figures of primate, child, and robot in contemporary technoscientific corporealizations of the 'almost human'. We take as our model (in)organism 'Lucy the Robot Orangutan', roboticist Steve Grand's project to create an artificial life form with a mind of its own. One aspect of Lucy's figuration by Grand, we argue, which ties her to Haraway's analysis of the primate, is of the robot as a model for animal, and more specifically (or aspirationally) human, cognition. We follow the trope of 'model organism' as it is under discussion within science and technology studies and as an ironic descriptor for our own interest in Lucy as an entity/project through which to illuminate figurations within robotics more widely. Primate and robot together are forms of natureculture that help to clarify how the categories of animal and machine are entangled, while making explicit investments in their differences from one another, and from the third category of the human. We conclude, again following Haraway, by imagining what other possibilities there might be for figuring humans, robots, and their relations if we escape the reiterative imaginary of the robot as proxy for becoming human. PMID:25051585

  9. Robotic transportation.

    PubMed

    Lob, W S

    1990-09-01

    Mobile robots perform fetch-and-carry tasks autonomously. An intelligent, sensor-equipped mobile robot does not require dedicated pathways or extensive facility modification. In the hospital, mobile robots can be used to carry specimens, pharmaceuticals, meals, etc. between supply centers, patient areas, and laboratories. The HelpMate (Transitions Research Corp.) mobile robot was developed specifically for hospital environments. To reach a desired destination, Help-Mate navigates with an on-board computer that continuously polls a suite of sensors, matches the sensor data against a pre-programmed map of the environment, and issues drive commands and path corrections. A sender operates the robot with a user-friendly menu that prompts for payload insertion and desired destination(s). Upon arrival at its selected destination, the robot prompts the recipient for a security code or physical key and awaits acknowledgement of payload removal. In the future, the integration of HelpMate with robot manipulators, test equipment, and central institutional information systems will open new applications in more localized areas and should help overcome difficulties in filling transport staff positions.

  10. Robot visions.

    PubMed

    Castañeda, Claudia; Suchman, Lucy

    2014-06-01

    This article explores the resonating figures of primate, child, and robot in contemporary technoscientific corporealizations of the 'almost human'. We take as our model (in)organism 'Lucy the Robot Orangutan', roboticist Steve Grand's project to create an artificial life form with a mind of its own. One aspect of Lucy's figuration by Grand, we argue, which ties her to Haraway's analysis of the primate, is of the robot as a model for animal, and more specifically (or aspirationally) human, cognition. We follow the trope of 'model organism' as it is under discussion within science and technology studies and as an ironic descriptor for our own interest in Lucy as an entity/project through which to illuminate figurations within robotics more widely. Primate and robot together are forms of natureculture that help to clarify how the categories of animal and machine are entangled, while making explicit investments in their differences from one another, and from the third category of the human. We conclude, again following Haraway, by imagining what other possibilities there might be for figuring humans, robots, and their relations if we escape the reiterative imaginary of the robot as proxy for becoming human.

  11. Robotic transportation.

    PubMed

    Lob, W S

    1990-09-01

    Mobile robots perform fetch-and-carry tasks autonomously. An intelligent, sensor-equipped mobile robot does not require dedicated pathways or extensive facility modification. In the hospital, mobile robots can be used to carry specimens, pharmaceuticals, meals, etc. between supply centers, patient areas, and laboratories. The HelpMate (Transitions Research Corp.) mobile robot was developed specifically for hospital environments. To reach a desired destination, Help-Mate navigates with an on-board computer that continuously polls a suite of sensors, matches the sensor data against a pre-programmed map of the environment, and issues drive commands and path corrections. A sender operates the robot with a user-friendly menu that prompts for payload insertion and desired destination(s). Upon arrival at its selected destination, the robot prompts the recipient for a security code or physical key and awaits acknowledgement of payload removal. In the future, the integration of HelpMate with robot manipulators, test equipment, and central institutional information systems will open new applications in more localized areas and should help overcome difficulties in filling transport staff positions. PMID:2208684

  12. Periodontal Proteomics: Wonders Never Cease!

    PubMed Central

    Grover, Harpreet Singh; Kapoor, Shalini; Saksena, Neha

    2013-01-01

    Proteins are vital parts of living organisms, as they are integral components of the physiological metabolic pathways of cells. Periodontal tissues comprise multicompartmental groups of interacting cells and matrices that provide continuous support, attachment, proprioception, and physical protection for the teeth. The proteome map, that is, complete catalogue of the matrix and cellular proteins expressed in alveolar bone, cementum, periodontal ligament, and gingiva, is to be explored for more in-depth understanding of periodontium. The ongoing research to understand the signalling pathways that allow cells to divide, differentiate, and die in controlled manner has brought us to the era of proteomics. Proteomics is defined as the study of all proteins including their relative abundance, distribution, posttranslational modifications, functions, and interactions with other macromolecules, in a given cell or organism within a given environment and at a specific stage in the cell cycle. Its application to periodontal science can be used to monitor health status, disease onset, treatment response, and outcome. Proteomics can offer answers to critical, unresolved questions such as the biological basis for the heterogeneity in gingival, alveolar bone, and cemental cell populations. PMID:24490073

  13. [Robotic surgery].

    PubMed

    Sándor, József; Haidegger, Tamás; Kormos, Katalin; Ferencz, Andrea; Csukás, Domokos; Bráth, Endre; Szabó, Györgyi; Wéber, György

    2013-10-01

    Due to the fast spread of laparoscopic cholecystectomy, surgical procedures have been changed essentially. The new techniques applied for both abdominal and thoracic procedures provided the possibility for minimally invasive access with all its advantages. Robots - originally developed for industrial applications - were retrofitted for laparoscopic procedures. The currently prevailing robot-assisted surgery is ergonomically more advantageous for the surgeon, as well as for the patient through the more precise preparative activity thanks to the regained 3D vision. The gradual decrease of costs of robotic surgical systems and development of new generations of minimally invasive devices may lead to substantial changes in routine surgical procedures. PMID:24144815

  14. [Robotic surgery].

    PubMed

    Sándor, József; Haidegger, Tamás; Kormos, Katalin; Ferencz, Andrea; Csukás, Domokos; Bráth, Endre; Szabó, Györgyi; Wéber, György

    2013-10-01

    Due to the fast spread of laparoscopic cholecystectomy, surgical procedures have been changed essentially. The new techniques applied for both abdominal and thoracic procedures provided the possibility for minimally invasive access with all its advantages. Robots - originally developed for industrial applications - were retrofitted for laparoscopic procedures. The currently prevailing robot-assisted surgery is ergonomically more advantageous for the surgeon, as well as for the patient through the more precise preparative activity thanks to the regained 3D vision. The gradual decrease of costs of robotic surgical systems and development of new generations of minimally invasive devices may lead to substantial changes in routine surgical procedures.

  15. Space applications of Automation, Robotics and Machine Intelligence Systems (ARAMIS). Volume 4: Application of ARAMIS capabilities to space project functional elements

    NASA Technical Reports Server (NTRS)

    Miller, R. H.; Minsky, M. L.; Smith, D. B. S.

    1982-01-01

    Applications of automation, robotics, and machine intelligence systems (ARAMIS) to space activities and their related ground support functions are studied, so that informed decisions can be made on which aspects of ARAMIS to develop. The specific tasks which will be required by future space project tasks are identified and the relative merits of these options are evaluated. The ARAMIS options defined and researched span the range from fully human to fully machine, including a number of intermediate options (e.g., humans assisted by computers, and various levels of teleoperation). By including this spectrum, the study searches for the optimum mix of humans and machines for space project tasks.

  16. Functional proteomic analysis reveals sex-dependent differences in structural and energy-producing myocardial proteins in rat model of alcoholic cardiomyopathy

    PubMed Central

    Fogle, Rachel L.; Hollenbeak, Christopher S.; Stanley, Bruce A.; Vary, Thomas C.; Kimball, Scot R.

    2011-01-01

    Long-term ethanol exposure leads to a sexually dimorphic response in both the susceptibility to cardiac pathology (protective effect of the female heart) and the expression of selected myocardial proteins. The purpose of the present study was to use proteomics to examine the effect of chronic alcohol consumption on a broader array of cardiac proteins and how these were affected between the sexes. Male and female rats were maintained for 18 wk on a 40% ethanol-containing diet in which alcohol was provided in drinking water and agar blocks. Differences in the content of specific cardiac proteins in isopycnic centrifugal fractions were determined using mass spectrometry on iTRAQ-labeled tryptic fragments. A random effects model of meta-analysis was developed to combine the results from multiple iTRAQ experiments. Analysis of a network of proteins involved in cardiovascular system development and function showed that troponins were oppositely regulated by alcohol exposure in females (upregulated) vs. males (downregulated), and this effect was validated by Western blot analysis. Pathway analysis also revealed that alcohol-consuming males showed increased expression of proteins involved in various steps of oxidative phosphorylation including complexes I, III, IV, and V, whereas females showed no change or decreased content. One implication from these findings is that females may be protected from the toxic effects of alcohol due to their ability to maintain contractile function, maintain efficiency of force generation, and minimize oxidative stress. However, the alcohol-induced insult may lead to increased production of reactive oxygen species and structural abnormalities in male myocardium. PMID:21245415

  17. Robotic vehicle

    DOEpatents

    Box, W.D.

    1997-02-11

    A robotic vehicle is described for travel through a conduit. The robotic vehicle includes forward and rear housings each having a hub portion, and each being provided with surface engaging mechanisms for selectively engaging the walls of the conduit such that the housings can be selectively held in stationary positions within the conduit. The surface engaging mechanisms of each housing includes a plurality of extendable appendages, each of which is radially extendable relative to the operatively associated hub portion between a retracted position and a radially extended position. The robotic vehicle also includes at least three selectively extendable members extending between the forward and rear housings, for selectively changing the distance between the forward and rear housings to effect movement of the robotic vehicle. 20 figs.

  18. Robotic vehicle

    DOEpatents

    Box, W.D.

    1998-08-11

    A robotic vehicle is described for travel through a conduit. The robotic vehicle includes forward and rear housings each having a hub portion, and each being provided with surface engaging mechanisms for selectively engaging the walls of the conduit such that the housings can be selectively held in stationary positions within the conduit. The surface engaging mechanisms of each housing includes a plurality of extendible appendages, each of which is radially extendible relative to the operatively associated hub portion between a retracted position and a radially extended position. The robotic vehicle also includes at least three selectively extendible members extending between the forward and rear housings, for selectively changing the distance between the forward and rear housings to effect movement of the robotic vehicle. 20 figs.

  19. Robotic vehicle

    SciTech Connect

    Box, W. Donald

    1998-01-01

    A robotic vehicle for travel through a conduit. The robotic vehicle includes forward and rear housings each having a hub portion, and each being provided with surface engaging mechanisms for selectively engaging the walls of the conduit such that the housings can be selectively held in stationary positions within the conduit. The surface engaging mechanisms of each housing includes a plurality of extendable appendages, each of which is radially extendable relative to the operatively associated hub portion between a retracted position and a radially extended position. The robotic vehicle also includes at least three selectively extendable members extending between the forward and rear housings, for selectively changing the distance between the forward and rear housings to effect movement of the robotic vehicle.

  20. Robotic vehicle

    SciTech Connect

    Box, W. Donald

    1997-01-01

    A robotic vehicle for travel through a conduit. The robotic vehicle includes forward and rear housings each having a hub portion, and each being provided with surface engaging mechanisms for selectively engaging the walls of the conduit such that the housings can be selectively held in stationary positions within the conduit. The surface engaging mechanisms of each housing includes a plurality of extendable appendages, each of which is radially extendable relative to the operatively associated hub portion between a retracted position and a radially extended position. The robotic vehicle also includes at least three selectively extendable members extending between the forward and rear housings, for selectively changing the distance between the forward and rear housings to effect movement of the robotic vehicle.

  1. Robotic arm

    DOEpatents

    Kwech, Horst

    1989-04-18

    A robotic arm positionable within a nuclear vessel by access through a small diameter opening and having a mounting tube supported within the vessel and mounting a plurality of arm sections for movement lengthwise of the mounting tube as well as for movement out of a window provided in the wall of the mounting tube. An end effector, such as a grinding head or welding element, at an operating end of the robotic arm, can be located and operated within the nuclear vessel through movement derived from six different axes of motion provided by mounting and drive connections between arm sections of the robotic arm. The movements are achieved by operation of remotely-controllable servo motors, all of which are mounted at a control end of the robotic arm to be outside the nuclear vessel.

  2. Robotic animation

    NASA Astrophysics Data System (ADS)

    Kretch, S. J.

    1982-08-01

    The effectiveness of the robotic systems Place and Animate at McDonnell Douglas is discussed. The systems are designed for CAD/CAM on a kinematic basis. Place allows creation, analysis, and editing of cell descriptions as part of the CAD process, and involves primitive cell configuring prior to eventual integration of the entire robot. Objects are displayed in wire frame form and movement receives an awkwardness rating automatically, indicating the percentage of the real-world joint limit that is being approached. The same program is employed in the Animate process, where verification and debugging of the robot programs proceeds. Clearances, motion limits, and correct responses to commands are checked, allowing decisions on production to be made before any robots are actually built.

  3. Artificial heart for humanoid robot

    NASA Astrophysics Data System (ADS)

    Potnuru, Akshay; Wu, Lianjun; Tadesse, Yonas

    2014-03-01

    A soft robotic device inspired by the pumping action of a biological heart is presented in this study. Developing artificial heart to a humanoid robot enables us to make a better biomedical device for ultimate use in humans. As technology continues to become more advanced, the methods in which we implement high performance and biomimetic artificial organs is getting nearer each day. In this paper, we present the design and development of a soft artificial heart that can be used in a humanoid robot and simulate the functions of a human heart using shape memory alloy technology. The robotic heart is designed to pump a blood-like fluid to parts of the robot such as the face to simulate someone blushing or when someone is angry by the use of elastomeric substrates and certain features for the transport of fluids.

  4. Robotic Surveying

    SciTech Connect

    Suzy Cantor-McKinney; Michael Kruzic

    2007-03-01

    -actuated functions to be controlled by an onboard computer. The computer-controlled Speedrower was developed at Carnegie Mellon University to automate agricultural harvesting. Harvesting tasks require the vehicle to cover a field using minimally overlapping rows at slow speeds in a similar manner to geophysical data acquisition. The Speedrower had demonstrated its ability to perform as it had already logged hundreds of acres of autonomous harvesting. This project is the first use of autonomous robotic technology on a large-scale for geophysical surveying.

  5. Biologically inspired intelligent robots

    NASA Astrophysics Data System (ADS)

    Bar-Cohen, Yoseph; Breazeal, Cynthia

    2003-07-01

    Humans throughout history have always sought to mimic the appearance, mobility, functionality, intelligent operation, and thinking process of biological creatures. This field of biologically inspired technology, having the moniker biomimetics, has evolved from making static copies of human and animals in the form of statues to the emergence of robots that operate with realistic behavior. Imagine a person walking towards you where suddenly you notice something weird about him--he is not real but rather he is a robot. Your reaction would probably be "I can't believe it but this robot looks very real" just as you would react to an artificial flower that is a good imitation. You may even proceed and touch the robot to check if your assessment is correct but, as oppose to the flower case, the robot may be programmed to respond physical and verbally. This science fiction scenario could become a reality as the current trend continues in developing biologically inspired technologies. Technology evolution led to such fields as artificial muscles, artificial intelligence, and artificial vision as well as biomimetic capabilities in materials science, mechanics, electronics, computing science, information technology and many others. This paper will review the state of the art and challenges to biologically-inspired technologies and the role that EAP is expected to play as the technology evolves.

  6. Unexpected features of the dark proteome.

    PubMed

    Perdigão, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth S; Buckley, Michael J; Tabor, Bruce; Signal, Beth; Gloss, Brian S; Hammang, Christopher J; Rost, Burkhard; Schafferhans, Andrea; O'Donoghue, Seán I

    2015-12-29

    We surveyed the "dark" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology. PMID:26578815

  7. Unexpected features of the dark proteome.

    PubMed

    Perdigão, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth S; Buckley, Michael J; Tabor, Bruce; Signal, Beth; Gloss, Brian S; Hammang, Christopher J; Rost, Burkhard; Schafferhans, Andrea; O'Donoghue, Seán I

    2015-12-29

    We surveyed the "dark" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.

  8. Proteomics in the genome engineering era.

    PubMed

    Vandemoortele, Giel; Gevaert, Kris; Eyckerman, Sven

    2016-01-01

    Genome engineering experiments used to be lengthy, inefficient, and often expensive, preventing a widespread adoption of such experiments for the full assessment of endogenous protein functions. With the revolutionary clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 technology, genome engineering became accessible to the broad life sciences community and is now implemented in several research areas. One particular field that can benefit significantly from this evolution is proteomics where a substantial impact on experimental design and general proteome biology can be expected. In this review, we describe the main applications of genome engineering in proteomics, including the use of engineered disease models and endogenous epitope tagging. In addition, we provide an overview on current literature and highlight important considerations when launching genome engineering technologies in proteomics workflows.

  9. [Robotic surgery].

    PubMed

    Moreno-Portillo, Mucio; Valenzuela-Salazar, Carlos; Quiroz-Guadarrama, César David; Pachecho-Gahbler, Carlos; Rojano-Rodríguez, Martín

    2014-12-01

    Medicine has experienced greater scientific and technological advances in the last 50 years than in the rest of human history. The article describes relevant events, revises concepts and advantages and clinical applications, summarizes published clinical results, and presents some personal reflections without giving dogmatic conclusions about robotic surgery. The Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) defines robotic surgery as a surgical procedure using technology to aid the interaction between surgeon and patient. The objective of the surgical robot is to correct human deficiencies and improve surgical skills. The capacity of repeating tasks with precision and reproducibility has been the base of the robot´s success. Robotic technology offers objective and measurable advantages: - Improving maneuverability and physical capacity during surgery. - Correcting bad postural habits and tremor. - Allowing depth perception (3D images). - Magnifying strength and movement limits. - Offering a platform for sensors, cameras, and instruments. Endoscopic surgery transformed conceptually the way of practicing surgery. Nevertheless in the last decade, robotic assisted surgery has become the next paradigm of our era.

  10. [Robotic surgery].

    PubMed

    Moreno-Portillo, Mucio; Valenzuela-Salazar, Carlos; Quiroz-Guadarrama, César David; Pachecho-Gahbler, Carlos; Rojano-Rodríguez, Martín

    2014-12-01

    Medicine has experienced greater scientific and technological advances in the last 50 years than in the rest of human history. The article describes relevant events, revises concepts and advantages and clinical applications, summarizes published clinical results, and presents some personal reflections without giving dogmatic conclusions about robotic surgery. The Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) defines robotic surgery as a surgical procedure using technology to aid the interaction between surgeon and patient. The objective of the surgical robot is to correct human deficiencies and improve surgical skills. The capacity of repeating tasks with precision and reproducibility has been the base of the robot´s success. Robotic technology offers objective and measurable advantages: - Improving maneuverability and physical capacity during surgery. - Correcting bad postural habits and tremor. - Allowing depth perception (3D images). - Magnifying strength and movement limits. - Offering a platform for sensors, cameras, and instruments. Endoscopic surgery transformed conceptually the way of practicing surgery. Nevertheless in the last decade, robotic assisted surgery has become the next paradigm of our era. PMID:25643879

  11. Handbook of industrial robotics

    SciTech Connect

    Nof, S.Y.

    1985-01-01

    This book presents papers on the application of artificial intelligence to robots used in industrial plants. Topics considered include vision systems, elements of industrial robot software, robot teaching, the off-line programming of robots, a structured programming robot language, task-level manipulator programming, expert systems, and the role of the computer in robot intelligence.

  12. Tutorial on robotics

    SciTech Connect

    Lee, C.S.G.; Gonzalez, R.C.; Fu, K.S.

    1986-01-01

    Basic fundamentals in robotics are presented in this tutorial. Topics covered are as follows: robot arm kinematics; robot arm dynamics; planning or manipulator trajectories; servo control for manipulators; force sensing and control; robot vision systems; robot programming languages; and machine intelligence and robot planning.

  13. Optimizing Algorithm Choice for Metaproteomics: Comparing X!Tandem and Proteome Discoverer for Soil Proteomes

    NASA Astrophysics Data System (ADS)

    Diaz, K. S.; Kim, E. H.; Jones, R. M.; de Leon, K. C.; Woodcroft, B. J.; Tyson, G. W.; Rich, V. I.

    2014-12-01

    The growing field of metaproteomics links microbial communities to their expressed functions by using mass spectrometry methods to characterize community proteins. Comparison of mass spectrometry protein search algorithms and their biases is crucial for maximizing the quality and amount of protein identifications in mass spectral data. Available algorithms employ different approaches when mapping mass spectra to peptides against a database. We compared mass spectra from four microbial proteomes derived from high-organic content soils searched with two search algorithms: 1) Sequest HT as packaged within Proteome Discoverer (v.1.4) and 2) X!Tandem as packaged in TransProteomicPipeline (v.4.7.1). Searches used matched metagenomes, and results were filtered to allow identification of high probability proteins. There was little overlap in proteins identified by both algorithms, on average just ~24% of the total. However, when adjusted for spectral abundance, the overlap improved to ~70%. Proteome Discoverer generally outperformed X!Tandem, identifying an average of 12.5% more proteins than X!Tandem, with X!Tandem identifying more proteins only in the first two proteomes. For spectrally-adjusted results, the algorithms were similar, with X!Tandem marginally outperforming Proteome Discoverer by an average of ~4%. We then assessed differences in heat shock proteins (HSP) identification by the two algorithms by BLASTing identified proteins against the Heat Shock Protein Information Resource, because HSP hits typically account for the majority signal in proteomes, due to extraction protocols. Total HSP identifications for each of the 4 proteomes were approximately ~15%, ~11%, ~17%, and ~19%, with ~14% for total HSPs with redundancies removed. Of the ~15% average of proteins from the 4 proteomes identified as HSPs, ~10% of proteins and spectra were identified by both algorithms. On average, Proteome Discoverer identified ~9% more HSPs than X!Tandem.

  14. A visual approach to proteomics.

    PubMed

    Nickell, Stephan; Kofler, Christine; Leis, Andrew P; Baumeister, Wolfgang

    2006-03-01

    Cryo-electron tomography is an emerging imaging technique that has unique potential for molecular cell biology. At the present resolution of 4-5 nm, large supramolecular structures can be studied in unperturbed cellular environments and, in the future, it will become possible to map molecular landscapes inside cells in a more comprehensive manner. 'Visual proteomics' aims to complement and extend mass-spectrometry-based inventories, and to provide a quantitative description of the macromolecular interactions that underlie cellular functions.

  15. Pathway and network analysis in proteomics.

    PubMed

    Wu, Xiaogang; Hasan, Mohammad Al; Chen, Jake Yue

    2014-12-01

    Proteomics is inherently a systems science that studies not only measured protein and their expressions in a cell, but also the interplay of proteins, protein complexes, signaling pathways, and network modules. There is a rapid accumulation of Proteomics data in recent years. However, Proteomics data are highly variable, with results sensitive to data preparation methods, sample condition, instrument types, and analytical methods. To address the challenge in Proteomics data analysis, we review current tools being developed to incorporate biological function and network topological information. We categorize these tools into four types: tools with basic functional information and little topological features (e.g., GO category analysis), tools with rich functional information and little topological features (e.g., GSEA), tools with basic functional information and rich topological features (e.g., Cytoscape), and tools with rich functional information and rich topological features (e.g., PathwayExpress). We first review the potential application of these tools to Proteomics; then we review tools that can achieve automated learning of pathway modules and features, and tools that help perform integrated network visual analytics.

  16. Pathway and Network Analysis in Proteomics

    PubMed Central

    Wu, Xiaogang; Hasan, Mohammad Al; Chen, Jake Yue

    2014-01-01

    Proteomics is inherently a systems science that studies not only measured protein and their expressions in a cell, but also the interplay of proteins, protein complexes, signaling pathways, and network modules. There is a rapid accumulation of Proteomics data in recent years. However, Proteomics data are highly variable, with results being sensitive to data preparation methods, sample condition, instrument types, and analytical method. To address this challenge in Proteomics data analysis, we review common approaches developed to incorporate biological function and network topological information. We categorize existing tools into four categories: tools with basic functional information and little topological features (e.g., GO category analysis), tools with rich functional information and little topological features (e.g., GSEA), tools with basic functional information and rich topological features (e.g., Cytoscape), and tools with rich functional information and rich topological features (e.g., PathwayExpress). We review the general application potential of these tools to Proteomics. In addition, we also review tools that can achieve automated learning of pathway modules and features, and tools that help perform integrated network visual analytics. PMID:24911777

  17. Proteome identification of the silkworm middle silk gland

    PubMed Central

    Li, Jian-ying; Ye, Lu-peng; Che, Jia-qian; Song, Jia; You, Zheng-ying; Wang, Shao-hua; Zhong, Bo-xiong

    2016-01-01

    To investigate the functional differentiation among the anterior (A), middle (M), and posterior (P) regions of silkworm middle silk gland (MSG), their proteomes were characterized by shotgun LC–MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014) [1] via the PRIDE partner repository (Vizcaino, 2013) [2] with the dataset identifier PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP) after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015) [3]. PMID:26937469

  18. Proteome identification of the silkworm middle silk gland.

    PubMed

    Li, Jian-Ying; Ye, Lu-Peng; Che, Jia-Qian; Song, Jia; You, Zheng-Ying; Wang, Shao-Hua; Zhong, Bo-Xiong

    2016-03-01

    To investigate the functional differentiation among the anterior (A), middle (M), and posterior (P) regions of silkworm middle silk gland (MSG), their proteomes were characterized by shotgun LC-MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014) [1] via the PRIDE partner repository (Vizcaino, 2013) [2] with the dataset identifier PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP) after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015) [3]. PMID:26937469

  19. Proteome Based Construction of the Lymphocyte Function-Associated Antigen 1 (LFA-1) Interactome in Human Dendritic Cells

    PubMed Central

    Eich, Christina; Lasonder, Edwin; Cruz, Luis J.; Reinieren-Beeren, Inge; Cambi, Alessandra; Figdor, Carl G.; Buschow, Sonja I.

    2016-01-01

    The β2-integrin lymphocyte function-associated antigen 1 (LFA-1) plays an important role in the migration, adhesion and intercellular communication of dendritic cells (DCs). During the differentiation of human DCs from monocyte precursors, LFA-1 ligand binding capacity is completely lost, even though its expression levels were remained constant. Yet LFA-1-mediated adhesive capacity on DCs can be regained by exposing DCs to the chemokine CCL21, suggesting a high degree of regulation of LFA-1 activity during the course of DC differentiation. The molecular mechanisms underlying this regulation of LFA-1 function in DCs, however, remain elusive. To get more insight we attempted to identify specific LFA-1 binding partners that may play a role in regulating LFA-1 activity in DCs. We used highly sensitive label free quantitative mass-spectrometry to identify proteins co-immunoprecipitated (co-IP) with LFA-1 from ex vivo generated DCs. Among the potential binding partners we identified not only established components of integrin signalling pathways and cytoskeletal proteins, but also several novel LFA-1 binding partners including CD13, galectin-3, thrombospondin-1 and CD44. Further comparison to the LFA-1 interaction partners in monocytes indicated that DC differentiation was accompanied by an overall increase in LFA-1 associated proteins, in particular cytoskeletal, signalling and plasma membrane (PM) proteins. The here presented LFA-1 interactome composed of 78 proteins thus represents a valuable resource of potential regulators of LFA-1 function during the DC lifecycle. PMID:26889827

  20. Proteome Based Construction of the Lymphocyte Function-Associated Antigen 1 (LFA-1) Interactome in Human Dendritic Cells.

    PubMed

    Eich, Christina; Lasonder, Edwin; Cruz, Luis J; Reinieren-Beeren, Inge; Cambi, Alessandra; Figdor, Carl G; Buschow, Sonja I

    2016-01-01

    The β2-integrin lymphocyte function-associated antigen 1 (LFA-1) plays an important role in the migration, adhesion and intercellular communication of dendritic cells (DCs). During the differentiation of human DCs from monocyte precursors, LFA-1 ligand binding capacity is completely lost, even though its expression levels were remained constant. Yet LFA-1-mediated adhesive capacity on DCs can be regained by exposing DCs to the chemokine CCL21, suggesting a high degree of regulation of LFA-1 activity during the course of DC differentiation. The molecular mechanisms underlying this regulation of LFA-1 function in DCs, however, remain elusive. To get more insight we attempted to identify specific LFA-1 binding partners that may play a role in regulating LFA-1 activity in DCs. We used highly sensitive label free quantitative mass-spectrometry to identify proteins co-immunoprecipitated (co-IP) with LFA-1 from ex vivo generated DCs. Among the potential binding partners we identified not only established components of integrin signalling pathways and cytoskeletal proteins, but also several novel LFA-1 binding partners including CD13, galectin-3, thrombospondin-1 and CD44. Further comparison to the LFA-1 interaction partners in monocytes indicated that DC differentiation was accompanied by an overall increase in LFA-1 associated proteins, in particular cytoskeletal, signalling and plasma membrane (PM) proteins. The here presented LFA-1 interactome composed of 78 proteins thus represents a valuable resource of potential regulators of LFA-1 function during the DC lifecycle. PMID:26889827

  1. Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer.

    PubMed

    Lu, Yiling; Ling, Shiyun; Hegde, Apurva M; Byers, Lauren A; Coombes, Kevin; Mills, Gordon B; Akbani, Rehan

    2016-08-01

    The majority of the targeted therapeutic agents in clinical use target proteins and protein function. Although DNA and RNA analyses have been used extensively to identify novel targets and patients likely to benefit from targeted therapies, these are indirect measures of the levels and functions of most therapeutic targets. More importantly, DNA and RNA analysis is ill-suited for determining the pharmacodynamic effects of target inhibition. Assessing changes in protein levels and function is the most efficient way to evaluate the mechanisms underlying sensitivity and resistance to targeted agents. Understanding these mechanisms is necessary to identify patients likely to benefit from treatment and to develop rational drug combinations to prevent or bypass therapeutic resistance. There is an urgent need for a robust approach to assess protein levels and protein function in model systems and across patient samples. While "shot gun" mass spectrometry can provide in-depth analysis of proteins across a limited number of samples, and emerging approaches such as multiple reaction monitoring have the potential to analyze candidate markers, mass spectrometry has not entered into general use because of the high cost, requirement of extensive analysis and support, and relatively large amount of material needed for analysis. Rather, antibody-based technologies, including immunohistochemistry, radioimmunoassays, enzyme-linked immunosorbent assays (ELISAs), and more recently protein arrays, remain the most common approaches for multiplexed protein analysis. Reverse-phase protein array (RPPA) technology has emerged as a robust, sensitive, cost-effective approach to the analysis of large numbers of samples for quantitative assessment of key members of functional pathways that are affected by tumor-targeting therapeutics. The RPPA platform is a powerful approach for identifying and validating targets, classifying tumor subsets, assessing pharmacodynamics, and identifying prognostic

  2. Proteomic profiling of adipose tissue from Zmpste24-/- mice, a model of lipodystrophy and premature aging, reveals major changes in mitochondrial function and vimentin processing.

    PubMed

    Peinado, Juan R; Quirós, Pedro M; Pulido, Marina R; Mariño, Guillermo; Martínez-Chantar, Maria L; Vázquez-Martínez, Rafael; Freije, José M P; López-Otín, Carlos; Malagón, María M

    2011-11-01

    Lipodystrophy is a major disease involving severe alterations of adipose tissue distribution and metabolism. Mutations in genes encoding the nuclear envelope protein lamin A or its processing enzyme, the metalloproteinase Zmpste24, cause diverse human progeroid syndromes that are commonly characterized by a selective loss of adipose tissue. Similarly to humans, mice deficient in Zmpste24 accumulate prelamin A and display phenotypic features of accelerated aging, including lipodystrophy. Herein, we report the proteome and phosphoproteome of adipose tissue as well as serum metabolome in lipodystrophy by using Zmpste24(-/-) mice as experimental model. We show that Zmpste24 deficiency enhanced lipolysis, fatty acid biogenesis and β-oxidation as well as decreased fatty acid re-esterification, thus pointing to an increased partitioning of fatty acid toward β-oxidation and away from storage that likely underlies the observed size reduction of Zmpste24-null adipocytes. Besides the mitochondrial proteins related to lipid metabolism, other protein networks related to mitochondrial function, including those involved in tricarboxylic acid cycle and oxidative phosphorylation, were up-regulated in Zmpste24(-/-) mice. These results, together with the observation of an increased mitochondrial response to oxidative stress, support the relationship between defective prelamin A processing and mitochondrial dysfunction and highlight the relevance of oxidative damage in lipoatrophy and aging. We also show that absence of Zmpste24 profoundly alters the processing of the cytoskeletal protein vimentin and identify a novel protein dysregulated in lipodystrophy, High-Mobility Group Box-1 Protein. Finally, we found several lipid derivates with important roles in energy balance, such as Lysophosphatidylcholine or 2-arachidonoylglycerol, to be dysregulated in Zmpste24(-/-) serum. Together, our findings in Zmpste24(-/-) mice may be useful to unveil the mechanisms underlying adipose tissue

  3. Towards a sustainable modular robot system for planetary exploration

    NASA Astrophysics Data System (ADS)

    Hossain, S. G. M.

    This thesis investigates multiple perspectives of developing an unmanned robotic system suited for planetary terrains. In this case, the unmanned system consists of unit-modular robots. This type of robot has potential to be developed and maintained as a sustainable multi-robot system while located far from direct human intervention. Some characteristics that make this possible are: the cooperation, communication and connectivity among the robot modules, flexibility of individual robot modules, capability of self-healing in the case of a failed module and the ability to generate multiple gaits by means of reconfiguration. To demonstrate the effects of high flexibility of an individual robot module, multiple modules of a four-degree-of-freedom unit-modular robot were developed. The robot was equipped with a novel connector mechanism that made self-healing possible. Also, design strategies included the use of series elastic actuators for better robot-terrain interaction. In addition, various locomotion gaits were generated and explored using the robot modules, which is essential for a modular robot system to achieve robustness and thus successfully navigate and function in a planetary environment. To investigate multi-robot task completion, a biomimetic cooperative load transportation algorithm was developed and simulated. Also, a liquid motion-inspired theory was developed consisting of a large number of robot modules. This can be used to traverse obstacles that inevitably occur in maneuvering over rough terrains such as in a planetary exploration. Keywords: Modular robot, cooperative robots, biomimetics, planetary exploration, sustainability.

  4. Proteomic and Bioinformatic Profile of Primary Human Oral Epithelial Cells

    PubMed Central

    Ghosh, Santosh K.; Yohannes, Elizabeth; Bebek, Gurkan; Weinberg, Aaron; Jiang, Bin; Willard, Belinda; Chance, Mark R.; Kinter, Michael T.; McCormick, Thomas S.

    2012-01-01

    Wounding of the oral mucosa occurs frequently in a highly septic environment. Remarkably, these wounds heal quickly and the oral cavity, for the most part, remains healthy. Deciphering the normal human oral epithelial cell (NHOEC) proteome is critical for understanding the mechanism(s) of protection elicited when the mucosal barrier is intact, as well as when it is breached. Combining 2D gel electrophoresis with shotgun proteomics resulted in identification of 1662 NHOEC proteins. Proteome annotations were performed based on protein classes, molecular functions, disease association and membership in canonical and metabolic signaling pathways. Comparing the NHOEC proteome with a database of innate immunity-relevant interactions (InnateDB) identified 64 common proteins associated with innate immunity. Comparison with published salivary proteomes revealed that 738/1662 NHOEC proteins were common, suggesting that significant numbers of salivary proteins are of epithelial origin. Gene ontology analysis showed similarities in the distributions of NHOEC and saliva proteomes with regard to biological processes, and molecular functions. We also assessed the inter-individual variability of the NHOEC proteome and observed it to be comparable with other primary cells. The baseline proteome described in this study should serve as a resource for proteome studies of the oral mucosa, especially in relation to disease processes. PMID:23035736

  5. Robotics in Remote and Hostile Environments

    NASA Astrophysics Data System (ADS)

    Bellingham, James G.; Rajan, Kanna

    2007-11-01

    In our continuing quest for knowledge, robots are powerful tools for accessing environments too dangerous or too remote for human exploration. Early systems functioned under close human supervision, effectively limited to executing preprogrammed tasks. However, as exploration moves to regions where communication is ineffective or unviable, robots will need to carry out complex tasks without human supervision. To enable such capabilities, robots are being enhanced by advances ranging from new sensor development to automated mission planning software, distributed robotic control, and more efficient power systems. As robotics technology becomes simultaneously more capable and economically viable, individual robots operated at large expense by teams of experts are increasingly supplemented by teams of robots used cooperatively under minimal human supervision.

  6. Some considerations on robotics for environmental friendliness

    SciTech Connect

    Pin, F.G.

    1993-12-01

    This paper presents a series of considerations regarding the use and potential of robotic devices for supporting humans in a variety of tasks, while maintaining, if not improving, environmental friendliness. One of the main considerations brought forward here relates to the type of human-support functions which the robots are, or will be, expected to perform, and from this, a clear differentiation appears between robots designed to replace humans in environments that were engineered in the past for best human functionality, and robots designed to take functions in the future, in environments which could be better engineered for large-scale human-robot synergy. Other considerations discussed involve the ``life-cycle`` cleanliness of robotic systems, including the materials needs for their construction, their operation, their disposal and, more importantly, their energy consumption which will impact the cycle of natural resources utilization. These considerations are discussed using a variety of possible robotic systems applications in contexts varied as manufacturing, energy recovery and production, emergency situations handling, traffic improvement, waste management, agriculture, and space exploration. In all these applications, the operation costs and complexity of the robots seem to vary in inverse proportion to the amount of engineering that is feasible to make the task environment more robot-friendly, but with no seemingly direct impact on the potential for environmental friendliness of the robots.

  7. Medical robotics.

    PubMed

    Ferrigno, Giancarlo; Baroni, Guido; Casolo, Federico; De Momi, Elena; Gini, Giuseppina; Matteucci, Matteo; Pedrocchi, Alessandra

    2011-01-01

    Information and communication technology (ICT) and mechatronics play a basic role in medical robotics and computer-aided therapy. In the last three decades, in fact, ICT technology has strongly entered the health-care field, bringing in new techniques to support therapy and rehabilitation. In this frame, medical robotics is an expansion of the service and professional robotics as well as other technologies, as surgical navigation has been introduced especially in minimally invasive surgery. Localization systems also provide treatments in radiotherapy and radiosurgery with high precision. Virtual or augmented reality plays a role for both surgical training and planning and for safe rehabilitation in the first stage of the recovery from neurological diseases. Also, in the chronic phase of motor diseases, robotics helps with special assistive devices and prostheses. Although, in the past, the actual need and advantage of navigation, localization, and robotics in surgery and therapy has been in doubt, today, the availability of better hardware (e.g., microrobots) and more sophisticated algorithms(e.g., machine learning and other cognitive approaches)has largely increased the field of applications of these technologies,making it more likely that, in the near future, their presence will be dramatically increased, taking advantage of the generational change of the end users and the increasing request of quality in health-care delivery and management.

  8. Robot Serviced Space Facility

    NASA Technical Reports Server (NTRS)

    Purves, Lloyd R. (Inventor)

    1992-01-01

    A robot serviced space facility includes multiple modules which are identical in physical structure, but selectively differing in function. and purpose. Each module includes multiple like attachment points which are identically placed on each module so as to permit interconnection with immediately adjacent modules. Connection is made through like outwardly extending flange assemblies having identical male and female configurations for interconnecting to and locking to a complementary side of another flange. Multiple rows of interconnected modules permit force, fluid, data and power transfer to be accomplished by redundant circuit paths. Redundant modules of critical subsystems are included. Redundancy of modules and of interconnections results in a space complex with any module being removable upon demand, either for module replacement or facility reconfiguration. without eliminating any vital functions of the complex. Module replacement and facility assembly or reconfiguration are accomplished by a computer controlled articulated walker type robotic manipulator arm assembly having two identical end-effectors in the form of male configurations which are identical to those on module flanges and which interconnect to female configurations on other flanges. The robotic arm assembly moves along a connected set or modules by successively disconnecting, moving and reconnecting alternate ends of itself to a succession of flanges in a walking type maneuver. To transport a module, the robot keeps the transported module attached to one of its end-effectors and uses another flange male configuration of the attached module as a substitute end-effector during walking.

  9. High-throughput proteomics

    NASA Astrophysics Data System (ADS)

    Lesley, Scott A.; Nasoff, Marc; Kreusch, Andreas; Spraggon, Glen

    2001-04-01

    Proteomics has become a major focus as researchers attempt to understand the vast amount of genomic information. Protein complexity makes identifying and understanding gene function inherently difficult. The challenge of studying proteins in a global way is driving the development of new technologies for systematic and comprehensive analysis of protein structure and function. We are addressing this challenge through instrumentation and approaches to rapidly express, purify, crystallize, and mutate large numbers of human gene products. Our approach applies the principles of HTS technologies commonly used in pharmaceutical development. Genes are cloned, expressed, and purified in parallel to achieve a throughput potential of hundreds per day. Our instrumentation allows us to produce tens of milligrams of protein from 96 separate clones simultaneously. Purified protein is used for several applications including a high-throughput crystallographic screening approach for structure determination using automated image analysis. To further understand protein function, we are integrating a mutagenesis and screening approach. By combining these key technologies, we hope to provide a fundamental basis for understanding gene function at the protein level.

  10. The Succinated Proteome

    SciTech Connect

    Merkley, Eric D.; Metz, Thomas O.; Smith, Richard D.; Baynes, John; Frizell, Norma

    2014-03-30

    Succination is a chemical modification of cysteine in protein by the Krebs cycle intermediate, fumarate, yielding S-(2-succino)cysteine (2SC). Intracellular fumarate concentration and succination of proteins are increased by hyperpolarization of the inner mitochondrial membrane, in concert with mitochondrial, endoplasmic reticulum (ER) and oxidative stress in adipocytes grown in high glucose medium and in adipose tissue in obesity and diabetes. Increased succination of proteins is also detected in the kidney of a fumarase conditional knock-out mouse which develops renal tumors. Keap1, the gatekeeper of the antioxidant response, was identified as a major succinated protein in renal cancer cells, suggesting that succination may play a role in activation of the antioxidant response. A wide range of proteins is subject to succination, including enzymes, adipokines, cytoskeletal proteins and ER chaperones with functional cysteine residues. There is also significant overlap between succinated and glutathionylated proteins, and with proteins containing cysteine residues that are readily oxidized to the sulfenic (cysteic) acid. Succination of adipocyte proteins is inhibited by uncouplers, which discharge the mitochondrial membrane potential (Δψm) and by ER stress inhibitors. 2SC serves as a biomarker of mitochondrial stress or dysfunction in chronic diseases, such as obesity, diabetes and cancer, and recent studies suggest that succination is a mechanistic link between mitochondrial dysfunction, oxidative and ER stress, and cellular progression toward apoptosis. In this article, we review the history of the succinated proteome and the challenges associated with measuring this non-enzymatic post-translational modification of proteins by proteomics approaches.

  11. Human Saliva Proteome and Transcriptome

    PubMed Central

    Hu, S.; Li, Y.; Wang, J.; Xie, Y.; Tjon, K.; Wolinsky, L.; Loo, R.R.O.; Loo, J.A.; Wong, D.T.

    2007-01-01

    This paper tests the hypothesis that salivary proteins and their counterpart mRNAs co-exist in human whole saliva. Global profiling of human saliva proteomes and transcriptomes by mass spectrometry (MS) and expression microarray technologies, respectively, revealed many similarities between saliva proteins and mRNAs. Of the function-known proteins identified in saliva, from 61 to 70% were also found present as mRNA transcripts. For genes not detected at both protein and mRNA levels, we made further efforts to determine if the counterpart is present. Of 19 selected genes detected only at the protein level, the mRNAs of 13 (68%) genes were found in saliva by RT-PCR. In contrast, of many mRNAs detected only by microarrays, their protein products were found in saliva, as reported previously by other investigators. The saliva transcriptome may provide preliminary insights into the boundary of the saliva proteome. PMID:17122167

  12. Proteomics in evolutionary ecology.

    PubMed

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  13. Generic robot architecture

    DOEpatents

    Bruemmer, David J [Idaho Falls, ID; Few, Douglas A [Idaho Falls, ID

    2010-09-21

    The present invention provides methods, computer readable media, and apparatuses for a generic robot architecture providing a framework that is easily portable to a variety of robot platforms and is configured to provide hardware abstractions, abstractions for generic robot attributes, environment abstractions, and robot behaviors. The generic robot architecture includes a hardware abstraction level and a robot abstraction level. The hardware abstraction level is configured for developing hardware abstractions that define, monitor, and control hardware modules available on a robot platform. The robot abstraction level is configured for defining robot attributes and provides a software framework for building robot behaviors from the robot attributes. Each of the robot attributes includes hardware information from at least one hardware abstraction. In addition, each robot attribute is configured to substantially isolate the robot behaviors from the at least one hardware abstraction.

  14. Proteomic screening of human targets of viral microRNAs reveals functions associated with immune evasion and angiogenesis.

    PubMed

    Gallaher, Amelia M; Das, Sudipto; Xiao, Zhen; Andresson, Thorkell; Kieffer-Kwon, Philippe; Happel, Christine; Ziegelbauer, Joseph

    2013-01-01

    Kaposi's sarcoma (KS) is caused by infection with Kaposi's sarcoma-associated herpesvirus (KSHV). The virus expresses unique microRNAs (miRNAs), but the targets and functions of these miRNAs are not completely understood. In order to identify human targets of viral miRNAs, we measured protein expression changes caused by multiple KSHV miRNAs using pulsed stable labeling with amino acids in cell culture (pSILAC) in primary endothelial cells. This led to the identification of multiple human genes that are repressed at the protein level, but not at the miRNA level. Further analysis also identified that KSHV miRNAs can modulate activity or expression of upstream regulatory factors, resulting in suppressed activation of a protein involved in leukocyte recruitment (ICAM1) following lysophosphatidic acid treatment, as well as up-regulation of a pro-angiogenic protein (HIF1α), and up-regulation of a protein involved in stimulating angiogenesis (HMOX1). This study aids in our understanding of miRNA mechanisms of repression and miRNA contributions to viral pathogenesis.

  15. Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs.

    PubMed

    Welzenbach, Julia; Neuhoff, Christiane; Heidt, Hanna; Cinar, Mehmet Ulas; Looft, Christian; Schellander, Karl; Tholen, Ernst; Große-Brinkhaus, Christine

    2016-01-01

    The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein "phosphoglycerate mutase 2" and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes. PMID:27589727

  16. Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs

    PubMed Central

    Welzenbach, Julia; Neuhoff, Christiane; Heidt, Hanna; Cinar, Mehmet Ulas; Looft, Christian; Schellander, Karl; Tholen, Ernst; Große-Brinkhaus, Christine

    2016-01-01

    The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein “phosphoglycerate mutase 2” and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes. PMID:27589727

  17. Advanced proteomic liquid chromatography

    SciTech Connect

    Xie, Fang; Smith, Richard D.; Shen, Yufeng

    2012-10-26

    Liquid chromatography coupled with mass spectrometry is the predominant platform used to analyze proteomics samples consisting of large numbers of proteins and their proteolytic products (e.g., truncated polypeptides) and spanning a wide range of relative concentrations. This review provides an overview of advanced capillary liquid chromatography techniques and methodologies that greatly improve separation resolving power and proteomics analysis coverage, sensitivity, and throughput.

  18. Robot Swarms

    NASA Technical Reports Server (NTRS)

    Morring, Frank, Jr.

    2005-01-01

    Engineers and interns at this NASA field center are building the prototype of a robotic rover that could go where no wheeled rover has gone before-into the dark cold craters at the lunar poles and across the Moon s rugged highlands-like a walking tetrahedron. With NASA pushing to meet President Bush's new exploration objectives, the robots taking shape here today could be on the Moon in a decade. In the longer term, the concept could lead to shape-shifting robot swarms designed to explore distant planetary surfaces in advance of humans. "If you look at all of NASA s projections of the future, anyone s projections of the space program, they re all rigid-body architecture," says Steven Curtis, principal investigator on the effort. "This is not rigid-body. The whole key here is flexibility and reconfigurability with a capital R."

  19. Robot soccer.

    PubMed

    Sammut, Claude

    2010-11-01

    Robot soccer is a test bed for a variety of robotic and Artificial Intelligence (AI) methods. Its relevance to Cognitive Science is that it confronts the designer with a task that requires the integration of almost all aspects of AI to create an agent that is capable of working in a complex, dynamic environment inhabited by other agents, some of which are cooperative and others competitive. We describe the main elements that make up a robot soccer player and how these players associate to create effective teams. We pay special attention to the architecture of the players. WIREs Cogn Sci 2010 1 824-833 For further resources related to this article, please visit the WIREs website.

  20. Robot Manipulators

    NASA Technical Reports Server (NTRS)

    1988-01-01

    Space Shuttle's Remote Manipulator System (Canadarm) is a 50 foot robot arm used to deploy, retrieve or repair satellites in orbit. Initial spinoff version is designed to remove, inspect and replace large components of Ontario Hydro's CANDU nuclear reactors, which supply 50 percent of Ontario Hydro's total power reduction. CANDU robot is the first of SPAR's Remote Manipulator Systems intended for remote materials handling operations in nuclear servicing, chemical processing, smelting and manufacturing. Inco Limited used remote manipulator for remote control mining equipment to enhance safety and productivity of Inco's hardrock mining operations. System not only improves safety in a hazardous operation that costs more than a score of lives annually, it also increases productivity fourfold. Remote Manipulator System Division is also manufacturing a line of industrial robots and developing additional system for nuclear servicing, mining, defense and space operations.

  1. Robotic Vehicle

    NASA Technical Reports Server (NTRS)

    1994-01-01

    A commercially available ANDROS Mark V-A robot was used by Jet Propulsion Laboratory (JPL) as the departure point in the development of the HAZBOT III, a prototype teleoperated mobile robot designed for response to emergencies. Teleoperated robots contribute significantly to reducing human injury levels by performing tasks too hazardous for humans. ANDROS' manufacturer, REMOTEC, Inc., in turn, adopted some of the JPL concepts, particularly the control panel. HAZBOT III has exceptional mobility, employs solid state electronics and brushless DC motors for safer operation, and is designed so combustible gases cannot penetrate areas containing electronics and motors. Other features include the six-degree-of-freedom manipulator, the 30-pound squeeze force parallel jaw gripper and two video cameras, one for general viewing and navigation and the other for manipulation/grasping.

  2. Invited commentary on comparison of robotics, functional electrical stimulation, and motor learning methods for treatment of persistent upper extremity dysfunction after stroke: a randomized controlled trial.

    PubMed

    Kwakkel, Gert; van Wegen, Erwin E; Meskers, Carel M

    2015-06-01

    In this issue of Archives of Physical Medicine and Rehabilitation, Jessica McCabe and colleagues report findings from their methodologically sound, dose-matched clinical trial in 39 patients beyond 6 months poststroke. In this phase II trial, the effects of 60 treatment sessions, each involving 3.5 hours of intensive practice plus either 1.5 hours of functional electrical stimulation (FES) or a shoulder-arm robotic therapy, were compared with 5 hours of intensive daily practice alone. Although no significant between-group differences were found on the primary outcome measure of Arm Motor Ability Test and the secondary outcome measure of Fugl-Meyer Arm motor score, 10% to 15% within-group therapeutic gains were on the Arm Motor Ability Test and Fugl-Meyer Arm. These gains are clinically meaningful for patients with stroke. However, the underlying mechanisms that drive these improvements remain poorly understood. The approximately $1000 cost reduction per patient calculated for the use of motor learning (ML) methods alone or combined with FES, compared with the combination of ML and shoulder-arm robotics, further emphasizes the need for cost considerations when making clinical decisions about selecting the most appropriate therapy for the upper paretic limb in patients with chronic stroke. PMID:25687763

  3. Invited commentary on comparison of robotics, functional electrical stimulation, and motor learning methods for treatment of persistent upper extremity dysfunction after stroke: a randomized controlled trial.

    PubMed

    Kwakkel, Gert; van Wegen, Erwin E; Meskers, Carel M

    2015-06-01

    In this issue of Archives of Physical Medicine and Rehabilitation, Jessica McCabe and colleagues report findings from their methodologically sound, dose-matched clinical trial in 39 patients beyond 6 months poststroke. In this phase II trial, the effects of 60 treatment sessions, each involving 3.5 hours of intensive practice plus either 1.5 hours of functional electrical stimulation (FES) or a shoulder-arm robotic therapy, were compared with 5 hours of intensive daily practice alone. Although no significant between-group differences were found on the primary outcome measure of Arm Motor Ability Test and the secondary outcome measure of Fugl-Meyer Arm motor score, 10% to 15% within-group therapeutic gains were on the Arm Motor Ability Test and Fugl-Meyer Arm. These gains are clinically meaningful for patients with stroke. However, the underlying mechanisms that drive these improvements remain poorly understood. The approximately $1000 cost reduction per patient calculated for the use of motor learning (ML) methods alone or combined with FES, compared with the combination of ML and shoulder-arm robotics, further emphasizes the need for cost considerations when making clinical decisions about selecting the most appropriate therapy for the upper paretic limb in patients with chronic stroke.

  4. Robot-Aided Neurorehabilitation: A Robot for Wrist Rehabilitation

    PubMed Central

    Krebs, Hermano Igo; Volpe, Bruce T.; Williams, Dustin; Celestino, James; Charles, Steven K.; Lynch, Daniel; Hogan, Neville

    2009-01-01

    In 1991, a novel robot, MIT-MANUS, was introduced to study the potential that robots might assist in and quantify the neuro-rehabilitation of motor function. MIT-MANUS proved an excellent tool for shoulder and elbow rehabilitation in stroke patients, showing in clinical trials a reduction of impairment in movements confined to the exercised joints. This successful proof of principle as to additional targeted and intensive movement treatment prompted a test of robot training examining other limb segments. This paper focuses on a robot for wrist rehabilitation designed to provide three rotational degrees-of-freedom. The first clinical trial of the device will enroll 200 stroke survivors. Ultimately 160 stroke survivors will train with both the proximal shoulder and elbow MIT-MANUS robot, as well as with the novel distal wrist robot, in addition to 40 stroke survivor controls. So far 52 stroke patients have completed the robot training (ongoing protocol). Here, we report on the initial results on 36 of these volunteers. These results demonstrate that further improvement should be expected by adding additional training to other limb segments. PMID:17894265

  5. Autonomous caregiver following robotic wheelchair

    NASA Astrophysics Data System (ADS)

    Ratnam, E. Venkata; Sivaramalingam, Sethurajan; Vignesh, A. Sri; Vasanth, Elanthendral; Joans, S. Mary

    2011-12-01

    In the last decade, a variety of robotic/intelligent wheelchairs have been proposed to meet the need in aging society. Their main research topics are autonomous functions such as moving toward some goals while avoiding obstacles, or user-friendly interfaces. Although it is desirable for wheelchair users to go out alone, caregivers often accompany them. Therefore we have to consider not only autonomous functions and user interfaces but also how to reduce caregivers' load and support their activities in a communication aspect. From this point of view, we have proposed a robotic wheelchair moving with a caregiver side by side based on the MATLAB process. In this project we discussing about robotic wheel chair to follow a caregiver by using a microcontroller, Ultrasonic sensor, keypad, Motor drivers to operate robot. Using camera interfaced with the DM6437 (Davinci Code Processor) image is captured. The captured image are then processed by using image processing technique, the processed image are then converted into voltage levels through MAX 232 level converter and given it to the microcontroller unit serially and ultrasonic sensor to detect the obstacle in front of robot. In this robot we have mode selection switch Automatic and Manual control of robot, we use ultrasonic sensor in automatic mode to find obstacle, in Manual mode to use the keypad to operate wheel chair. In the microcontroller unit, c language coding is predefined, according to this coding the robot which connected to it was controlled. Robot which has several motors is activated by using the motor drivers. Motor drivers are nothing but a switch which ON/OFF the motor according to the control given by the microcontroller unit.

  6. Cooperating mobile robots

    DOEpatents

    Harrington, John J.; Eskridge, Steven E.; Hurtado, John E.; Byrne, Raymond H.

    2004-02-03

    A miniature mobile robot provides a relatively inexpensive mobile robot. A mobile robot for searching an area provides a way for multiple mobile robots in cooperating teams. A robotic system with a team of mobile robots communicating information among each other provides a way to locate a source in cooperation. A mobile robot with a sensor, a communication system, and a processor, provides a way to execute a strategy for searching an area.

  7. Caenorhabditis elegans proteomics comes of age.

    PubMed

    Shim, Yhong-Hee; Paik, Young-Ki

    2010-02-01

    Caenorhabditis elegans, a free-living soil nematode, is an ideal model system for studying various physiological problems relevant to human diseases. Despite its short history, C. elegans proteomics is receiving great attention in multiple research areas, including the genome annotation, major signaling pathways (e.g. TGF-beta and insulin/IGF-1 signaling), verification of RNA interference-mediated gene targeting, aging, disease models, as well as peptidomic analysis of neuropeptides involved in behavior and locomotion. For example, a proteome-wide profiling of developmental and aging processes not only provides basic information necessary for constructing a molecular network, but also identifies important target proteins for chemical modulation. Although C. elegans has a simple body system and neural circuitry, it exhibits very complicated functions ranging from feeding to locomotion. Investigation of these functions through proteomic analysis of various C. elegans neuropeptides, some of which are not found in the predicted genome sequence, would open a new field of peptidomics. Given the importance of nematode infection in plants and mammalian pathogenesis pathways, proteomics could be applied to investigate the molecular mechanisms underlying plant- or animal-nematode pathogenesis and to identify novel antinematodal drugs. Thus, C. elegans proteomics, in combination of other molecular, biological and genetic techniques, would provide a versatile new tool box for the systematic analysis of gene functions throughout the entire life cycle of this nematode. PMID:20029841

  8. Proteomic analyses of soybean root tips during germination.

    PubMed

    Komatsu, Setsuko; Oh, Myeong W; Jang, Hee Y; Kwon, Soo J; Kim, Hye R; Ko, Jung H; Woo, Sun H; Nanjo, Yohei

    2014-01-01

    Plant root systems form complex networks with the surrounding soil environment and are controlled by both internal and external factors. To better understand the function of root tips of soybean during germination, three proteomic techniques were used to analyze the protein profiles of root tip cells. Proteins were extracted from the root tips of 4-day-old soybean seedlings and analyzed using two-dimensional (2D) gel electrophoresis-based proteomics, SDS-gel based proteomics, and gel-free proteomics techniques. A total of 121, 862, and 341 proteins were identified in root tips using the 2D gel-based, SDS gel-based, and gel-free proteomic techniques, respectively. The proteins identified by 2D gel-based proteomic analysis were predominantly localized in the cytoplasm, whereas nuclear-localized proteins were most commonly identified by the SDS gel-based and gel-free proteomics techniques. Of the 862 proteins identified in the SDS gel-based proteomic analysis, 190 were protein synthesis-related proteins. Furthermore, 24 proteins identified using the 2D-gel based proteomic technique shifted between acidic and basic isoelectric points, and 2 proteins, heat shock protein 70.2 and AAA-type ATPase, displayed two different molecular weights at the same isoelectric point. Taken together, these results suggest that a number of proteins related to protein synthesis and modification are activated in the root tips of soybean seedlings during germination.

  9. Hand-held medical robots.

    PubMed

    Payne, Christopher J; Yang, Guang-Zhong

    2014-08-01

    Medical robots have evolved from autonomous systems to tele-operated platforms and mechanically-grounded, cooperatively-controlled robots. Whilst these approaches have seen both commercial and clinical success, uptake of these robots remains moderate because of their high cost, large physical footprint and long setup times. More recently, researchers have moved toward developing hand-held robots that are completely ungrounded and manipulated by surgeons in free space, in a similar manner to how conventional instruments are handled. These devices provide specific functions that assist the surgeon in accomplishing tasks that are otherwise challenging with manual manipulation. Hand-held robots have the advantages of being compact and easily integrated into the normal surgical workflow since there is typically little or no setup time. Hand-held devices can also have a significantly reduced cost to healthcare providers as they do not necessitate the complex, multi degree-of-freedom linkages that grounded robots require. However, the development of such devices is faced with many technical challenges, including miniaturization, cost and sterility, control stability, inertial and gravity compensation and robust instrument tracking. This review presents the emerging technical trends in hand-held medical robots and future development opportunities for promoting their wider clinical uptake.

  10. Robotics and Gaming to Improve Ankle Strength, Motor Control, and Function in Children With Cerebral Palsy — A Case Study Series

    PubMed Central

    Burdea, Grigore C.; Cioi, Daniel; Kale, Angad; Janes, William E.; Ross, Sandy A.; Engsberg, Jack R.

    2014-01-01

    Objective To investigate the feasibility of game-based robotic training of the ankle in children with cerebral palsy (CP). Design Case study, 12 weeks intervention, with no follow-up. Setting University research laboratory. Participants A referred sample of 3 children with cerebral palsy, age 7 to 12, all male were enrolled. Three completed the intervention. Interventions Participants trained on the RA CP system for 36 rehabilitation sessions (12 weeks, 3 times/week), playing two custom virtual reality games. The games were played while participants were seated, and trained one ankle at-a-time for strength, motor control, and coordination. Main Outcome Measures The primary study outcome measures were for impairment (DF/PF torques, DF initial contact angle and gait speed), function (GMFM) and quality of life (Peds QL). Secondary outcome measures relate to game performance (game scores as reflective of ankle motor control and endurance). Results Gait function improved substantially in ankle kinematics, speed and endurance. Overall function (GMFM) indicated improvements that were typical of other ankle strength training programs. Quality of life increased beyond what would be considered a minimal clinical important difference. Game performance improved in both games during the intervention. Conclusions This feasibility study supports the assumption that game-based robotic training of the ankle benefits gait in children with CP. Game technology is appropriate for the age group and was well accepted by the participants. Additional studies are needed however, to quantify the level of benefit and compare the approach presented here to traditional methods of therapy. PMID:22773059

  11. The Escherichia coli Peripheral Inner Membrane Proteome*

    PubMed Central

    Papanastasiou, Malvina; Orfanoudaki, Georgia; Koukaki, Marina; Kountourakis, Nikos; Sardis, Marios Frantzeskos; Aivaliotis, Michalis; Karamanou, Spyridoula; Economou, Anastassios

    2013-01-01

    Biological membranes are essential for cell viability. Their functional characteristics strongly depend on their protein content, which consists of transmembrane (integral) and peripherally associated membrane proteins. Both integral and peripheral inner membrane proteins mediate a plethora of biological processes. Whereas transmembrane proteins have characteristic hydrophobic stretches and can be predicted using bioinformatics approaches, peripheral inner membrane proteins are hydrophilic, exist in equilibria with soluble pools, and carry no discernible membrane targeting signals. We experimentally determined the cytoplasmic peripheral inner membrane proteome of the model organism Escherichia coli using a multidisciplinary approach. Initially, we extensively re-annotated the theoretical proteome regarding subcellular localization using literature searches, manual curation, and multi-combinatorial bioinformatics searches of the available databases. Next we used sequential biochemical fractionations coupled to direct identification of individual proteins and protein complexes using high resolution mass spectrometry. We determined that the proposed cytoplasmic peripheral inner membrane proteome occupies a previously unsuspected ∼19% of the basic E. coli BL21(DE3) proteome, and the detected peripheral inner membrane proteome occupies ∼25% of the estimated expressed proteome of this cell grown in LB medium to mid-log phase. This value might increase when fleeting interactions, not studied here, are taken into account. Several proteins previously regarded as exclusively cytoplasmic bind membranes avidly. Many of these proteins are organized in functional or/and structural oligomeric complexes that bind to the membrane with multiple interactions. Identified proteins cover the full spectrum of biological activities, and more than half of them are essential. Our data suggest that the cytoplasmic proteome displays remarkably dynamic and extensive communication with

  12. [Radical prostatectomy - pro robotic].

    PubMed

    Gillitzer, R

    2012-05-01

    Anatomical radical prostatectomy was introduced in the early 1980s by Walsh and Donker. Elucidation of key anatomical structures led to a significant reduction in the morbidity of this procedure. The strive to achieve similar oncological and functional results to this gold standard open procedure but with further reduction of morbidity through a minimally invasive access led to the establishment of laparoscopic prostatectomy. However, this procedure is complex and difficult and is associated with a long learning curve. The technical advantages of robotically assisted surgery coupled with the intuitive handling of the device led to increased precision and shortening of the learning curve. These main advantages, together with a massive internet presence and aggressive marketing, have resulted in a rapid dissemination of robotic radical prostatectomy and an increasing patient demand. However, superiority of robotic radical prostatectomy in comparison to the other surgical therapeutic options has not yet been proven on a scientific basis. Currently robotic-assisted surgery is an established technique and future technical improvements will certainly further define its role in urological surgery. In the end this technical innovation will have to be balanced against the very high purchase and running costs, which remain the main limitation of this technology.

  13. Beyond Robotics

    ERIC Educational Resources Information Center

    Tally, Beth; Laverdure, Nate

    2006-01-01

    Chantilly High School Academy Robotics Team Number 612 from Chantilly, Virginia, is an award-winning team of high school students actively involved with FIRST (For Inspiration and Recognition of Science and Technology), a multinational nonprofit organization that inspires students to transform culture--making science, math, engineering and…

  14. Robotic Surgery

    ERIC Educational Resources Information Center

    Childress, Vincent W.

    2007-01-01

    The medical field has many uses for automated and remote-controlled technology. For example, if a tissue sample is only handled in the laboratory by a robotic handling system, then it will never come into contact with a human. Such a system not only helps to automate the medical testing process, but it also helps to reduce the chances of…

  15. Development of autonomous eating mechanism for biomimetic robots

    NASA Astrophysics Data System (ADS)

    Jeong, Kil-Woong; Cho, Ik-Jin; Lee, Yun-Jung

    2005-12-01

    Most of the recently developed robots are human friendly robots which imitate animals or humans such as entertainment robot, bio-mimetic robot and humanoid robot. Interest for these robots are being increased because the social trend is focused on health, welfare, and graying. Autonomous eating functionality is most unique and inherent behavior of pets and animals. Most of entertainment robots and pet robots make use of internal-type battery. Entertainment robots and pet robots with internal-type battery are not able to operate during charging the battery. Therefore, if a robot has an autonomous function for eating battery as its feeds, the robot is not only able to operate during recharging energy but also become more human friendly like pets. Here, a new autonomous eating mechanism was introduced for a biomimetic robot, called ELIRO-II(Eating LIzard RObot version 2). The ELIRO-II is able to find a food (a small battery), eat and evacuate by itself. This work describe sub-parts of the developed mechanism such as head-part, mouth-part, and stomach-part. In addition, control system of autonomous eating mechanism is described.

  16. Proteomic Investigations into Hemodialysis Therapy.

    PubMed

    Bonomini, Mario; Sirolli, Vittorio; Pieroni, Luisa; Felaco, Paolo; Amoroso, Luigi; Urbani, Andrea

    2015-01-01

    The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane's performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane's bio(in)compatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research. PMID:26690416

  17. Protein Neighbors and Proximity Proteomics*

    PubMed Central

    Rees, Johanna S.; Li, Xue-Wen; Perrett, Sarah; Lilley, Kathryn S.; Jackson, Antony P.

    2015-01-01

    Within cells, proteins can co-assemble into functionally integrated and spatially restricted multicomponent complexes. Often, the affinities between individual proteins are relatively weak, and proteins within such clusters may interact only indirectly with many of their other protein neighbors. This makes proteomic characterization difficult using methods such as immunoprecipitation or cross-linking. Recently, several groups have described the use of enzyme-catalyzed proximity labeling reagents that covalently tag the neighbors of a targeted protein with a small molecule such as fluorescein or biotin. The modified proteins can then be isolated by standard pulldown methods and identified by mass spectrometry. Here we will describe the techniques as well as their similarities and differences. We discuss their applications both to study protein assemblies and to provide a new way for characterizing organelle proteomes. We stress the importance of proteomic quantitation and independent target validation in such experiments. Furthermore, we suggest that there are biophysical and cell-biological principles that dictate the appropriateness of enzyme-catalyzed proximity labeling methods to address particular biological questions of interest. PMID:26355100

  18. CMPD: cancer mutant proteome database.

    PubMed

    Huang, Po-Jung; Lee, Chi-Ching; Tan, Bertrand Chin-Ming; Yeh, Yuan-Ming; Julie Chu, Lichieh; Chen, Ting-Wen; Chang, Kai-Ping; Lee, Cheng-Yang; Gan, Ruei-Chi; Liu, Hsuan; Tang, Petrus

    2015-01-01

    Whole-exome sequencing, which centres on the protein coding regions of disease/cancer associated genes, represents the most cost-effective method to-date for deciphering the association between genetic alterations and diseases. Large-scale whole exome/genome sequencing projects have been launched by various institutions, such as NCI, Broad Institute and TCGA, to provide a comprehensive catalogue of coding variants in diverse tissue samples and cell lines. Further functional and clinical interrogation of these sequence variations must rely on extensive cross-platforms integration of sequencing information and a proteome database that explicitly and comprehensively archives the corresponding mutated peptide sequences. While such data resource is a critical for the mass spectrometry-based proteomic analysis of exomic variants, no database is currently available for the collection of mutant protein sequences that correspond to recent large-scale genomic data. To address this issue and serve as bridge to integrate genomic and proteomics datasets, CMPD (http://cgbc.cgu.edu.tw/cmpd) collected over 2 millions genetic alterations, which not only facilitates the confirmation and examination of potential cancer biomarkers but also provides an invaluable resource for translational medicine research and opportunities to identify mutated proteins encoded by mutated genes.

  19. CMPD: cancer mutant proteome database

    PubMed Central

    Huang, Po-Jung; Lee, Chi-Ching; Tan, Bertrand Chin-Ming; Yeh, Yuan-Ming; Julie Chu, Lichieh; Chen, Ting-Wen; Chang, Kai-Ping; Lee, Cheng-Yang; Gan, Ruei-Chi; Liu, Hsuan; Tang, Petrus

    2015-01-01

    Whole-exome sequencing, which centres on the protein coding regions of disease/cancer associated genes, represents the most cost-effective method to-date for deciphering the association between genetic alterations and diseases. Large-scale whole exome/genome sequencing projects have been launched by various institutions, such as NCI, Broad Institute and TCGA, to provide a comprehensive catalogue of coding variants in diverse tissue samples and cell lines. Further functional and clinical interrogation of these sequence variations must rely on extensive cross-platforms integration of sequencing information and a proteome database that explicitly and comprehensively archives the corresponding mutated peptide sequences. While such data resource is a critical for the mass spectrometry-based proteomic analysis of exomic variants, no database is currently available for the collection of mutant protein sequences that correspond to recent large-scale genomic data. To address this issue and serve as bridge to integrate genomic and proteomics datasets, CMPD (http://cgbc.cgu.edu.tw/cmpd) collected over 2 millions genetic alterations, which not only facilitates the confirmation and examination of potential cancer biomarkers but also provides an invaluable resource for translational medicine research and opportunities to identify mutated proteins encoded by mutated genes. PMID:25398898

  20. Robotics in near-earth space

    NASA Technical Reports Server (NTRS)

    Card, Michael E.

    1991-01-01

    The areas of space exploration in which robotic devices will play a part are identified, and progress to date in the space agency plans to acquire this capability is briefly reviewed. Roles and functions on orbit for robotic devices include well known activities, such as inspection and maintenance, assembly, docking, berthing, deployment, retrieval, materials handling, orbital replacement unit exchange, and repairs. Missions that could benefit from a robotic capability are discussed.

  1. Upper Extremity Proprioception in Healthy Aging and Stroke Populations, and the Effects of Therapist- and Robot-Based Rehabilitation Therapies on Proprioceptive Function

    PubMed Central

    Hughes, Charmayne Mary Lee; Tommasino, Paolo; Budhota, Aamani; Campolo, Domenico

    2015-01-01

    The world’s population is aging, with the number of people ages 65 or older expected to surpass 1.5 billion people, or 16% of the global total. As people age, there are notable declines in proprioception due to changes in the central and peripheral nervous systems. Moreover, the risk of stroke increases with age, with approximately two-thirds of stroke-related hospitalizations occurring in people over the age of 65. In this literature review, we first summarize behavioral studies investigating proprioceptive deficits in normally aging older adults and stroke patients, and discuss the differences in proprioceptive function between these populations. We then provide a state of the art review the literature regarding therapist- and robot-based rehabilitation of the upper extremity proprioceptive dysfunction in stroke populations and discuss avenues of future research. PMID:25784872

  2. Proteomic profile of dormant Trichophyton Rubrum conidia

    PubMed Central

    Leng, Wenchuan; Liu, Tao; Li, Rui; Yang, Jian; Wei, Candong; Zhang, Wenliang; Jin, Qi

    2008-01-01

    Background Trichophyton rubrum is the most common dermatophyte causing fungal skin infections in humans. Asexual sporulation is an important means of propagation for T. rubrum, and conidia produced by this way are thought to be the primary cause of human infections. Despite their importance in pathogenesis, the conidia of T. rubrum remain understudied. We intend to intensively investigate the proteome of dormant T. rubrum conidia to characterize its molecular and cellular features and to enhance the development of novel therapeutic strategies. Results The proteome of T. rubrum conidia was analyzed by combining shotgun proteomics with sample prefractionation and multiple enzyme digestion. In total, 1026 proteins were identified. All identified proteins were compared to those in the NCBI non-redundant protein database, the eukaryotic orthologous groups database, and the gene ontology database to obtain functional annotation information. Functional classification revealed that the identified proteins covered nearly all major biological processes. Some proteins were spore specific and related to the survival and dispersal of T. rubrum conidia, and many proteins were important to conidial germination and response to environmental conditions. Conclusion Our results suggest that the proteome of T. rubrum conidia is considerably complex, and that the maintenance of conidial dormancy is an intricate and elaborate process. This data set provides the first global framework for the dormant T. rubrum conidia proteome and is a stepping stone on the way to further study of the molecular mechanisms of T. rubrum conidial germination and the maintenance of conidial dormancy. PMID:18578874

  3. Proteomic Findings in Melanoma

    PubMed Central

    Sengupta, Deepanwita; Tackett, Alan J

    2016-01-01

    Although the emergence of proteomics as an independent branch of science is fairly recent, within a short period of time it has contributed substantially in various disciplines. The tool of mass spectrometry has become indispensable in the analysis of complex biological samples. Clinical applications of proteomics include detection of predictive and diagnostic markers, understanding mechanism of action of drugs as well as resistance mechanisms against them and assessment of therapeutic efficacy and toxicity of drugs in patients. Here, we have summarized the major contributions of proteomics towards the study of melanoma, which is a deadly variety of skin cancer with a high mortality rate. PMID:27274624

  4. Human Pituitary Adenoma Proteomics: New Progresses and Perspectives

    PubMed Central

    Zhan, Xianquan; Wang, Xiaowei; Cheng, Tingting

    2016-01-01

    Pituitary adenoma (PA) is a common intracranial neoplasm that impacts on human health through interfering hypothalamus–pituitary–target organ axis systems. The development of proteomics gives great promises in the clarification of molecular mechanisms of a PA and discovery of effective biomarkers for prediction, prevention, early-stage diagnosis, and treatment for a PA. A great progress in the field of PA proteomics has been made in the past 10 years, including (i) the use of laser-capture microdissection, (ii) proteomics analyses of functional PAs (such as prolactinoma), invasive and non-invasive non-functional pituitary adenomas (NFPAs), protein post-translational modifications such as phosphorylation and tyrosine nitration, NFPA heterogeneity, and hormone isoforms, (iii) the use of protein antibody array, (iv) serum proteomics and peptidomics, (v) the integration of proteomics and other omics data, and (vi) the proposal of multi-parameter systematic strategy for a PA. This review will summarize these progresses of proteomics in PAs, point out the existing drawbacks, propose the future research directions, and address the clinical relevance of PA proteomics data, in order to achieve our long-term goal that is use of proteomics to clarify molecular mechanisms, construct molecular networks, and discover effective biomarkers. PMID:27303365

  5. Human Pituitary Adenoma Proteomics: New Progresses and Perspectives.

    PubMed

    Zhan, Xianquan; Wang, Xiaowei; Cheng, Tingting

    2016-01-01

    Pituitary adenoma (PA) is a common intracranial neoplasm that impacts on human health through interfering hypothalamus-pituitary-target organ axis systems. The development of proteomics gives great promises in the clarification of molecular mechanisms of a PA and discovery of effective biomarkers for prediction, prevention, early-stage diagnosis, and treatment for a PA. A great progress in the field of PA proteomics has been made in the past 10 years, including (i) the use of laser-capture microdissection, (ii) proteomics analyses of functional PAs (such as prolactinoma), invasive and non-invasive non-functional pituitary adenomas (NFPAs), protein post-translational modifications such as phosphorylation and tyrosine nitration, NFPA heterogeneity, and hormone isoforms, (iii) the use of protein antibody array, (iv) serum proteomics and peptidomics, (v) the integration of proteomics and other omics data, and (vi) the proposal of multi-parameter systematic strategy for a PA. This review will summarize these progresses of proteomics in PAs, point out the existing drawbacks, propose the future research directions, and address the clinical relevance of PA proteomics data, in order to achieve our long-term goal that is use of proteomics to clarify molecular mechanisms, construct molecular networks, and discover effective biomarkers. PMID:27303365

  6. Development of autonomous grasping and navigating robot

    NASA Astrophysics Data System (ADS)

    Kudoh, Hiroyuki; Fujimoto, Keisuke; Nakayama, Yasuichi

    2015-01-01

    The ability to find and grasp target items in an unknown environment is important for working robots. We developed an autonomous navigating and grasping robot. The operations are locating a requested item, moving to where the item is placed, finding the item on a shelf or table, and picking the item up from the shelf or the table. To achieve these operations, we designed the robot with three functions: an autonomous navigating function that generates a map and a route in an unknown environment, an item position recognizing function, and a grasping function. We tested this robot in an unknown environment. It achieved a series of operations: moving to a destination, recognizing the positions of items on a shelf, picking up an item, placing it on a cart with its hand, and returning to the starting location. The results of this experiment show the applicability of reducing the workforce with robots.

  7. Soldier universal robot controller

    NASA Astrophysics Data System (ADS)

    Hyams, Jeffrey; Batavia, Parag; Liao, Elizabeth; Somerville, Andrew

    2008-04-01

    The Soldier Universal Robot Controller (SURC) is a modular OCU designed for simultaneous control of heterogeneous unmanned vehicles. It has a well defined, published API., defined using XML schemas, that allows other potential users of the system to develop their own modules for rapid integration with SURC. The SURC architecture is broken down into three layers: User Interface, Core Functions, and Transport. The User Interface layer is the front end module which provides the human computer interface for user control of robots. The Core layer is further divided into the following modules: Capabilities, Tactical, Mobility, and World Model. The Capabilities module keeps track of the known robots and provides a list of specifications and services. The Mobility module provides path planning via D*, while the Tactical module provides higher level mission planning (multi-agent/multi-mission) capabilities for collaborative operations. The World Model module is a relational database which stores world model objects. Finally, a Transport module provides translation from the SURC architecture to the robot specific messaging protocols (such as JAUS). This allows fast integration of new robot protocols into an existing SURC implementation to enable a new system to rapidly leverage existing SURC capabilities. The communication between different modules within the SURC architecture is done via XML. This gives developers and users the flexibility to extend existing messages without breaking backwards compatibility. The modularity of SURC offers users and developers alike the capability to create custom modules and plug them into place, as long as they follow the pre defined messaging API for that module.

  8. Facing Up to Robotation.

    ERIC Educational Resources Information Center

    Chamberlin, Leslie J.

    1982-01-01

    Speculates on the effects of introducing robots into American society. Robotization will be used increasingly to reduce labor costs in business and industry. The impact of robotization on leisure time use and education are discussed. (AM)

  9. Tandem mobile robot system

    DOEpatents

    Buttz, James H.; Shirey, David L.; Hayward, David R.

    2003-01-01

    A robotic vehicle system for terrain navigation mobility provides a way to climb stairs, cross crevices, and navigate across difficult terrain by coupling two or more mobile robots with a coupling device and controlling the robots cooperatively in tandem.

  10. Comparison of Renal Function between Robot-Assisted and Open Partial Nephrectomy as Determined by Tc 99m-DTPA Renal Scintigraphy

    PubMed Central

    2016-01-01

    We compared postoperative renal function impairment between patients undergoing robot-assisted partial nephrectomy (RAPN) and those undergoing open partial nephrectomy (OPN) by using Tc-99m diethylenetriaminepentaacetic acid (DTPA) renal scintigraphy. Patients who underwent partial nephrectomy by a single surgeon between 2007 and 2013 were eligible and were matched by propensity score, based on age, tumor size, exophytic properties of tumor, and location relative to the polar lines. Of the 403 patients who underwent partial nephrectomy, 114 (28%) underwent RAPN and 289 (72%) underwent OPN. Mean follow-up duration was 35.2 months. Following propensity matching, there were no significant differences between the two groups in tumor exophytic properties (P = 0.818) or nephrometry score (P = 0.527). Renal ischemic time (24.4 minutes vs. 17.8 minutes, P < 0.001) was significantly longer in the RAPN group than in the OPN group, while the other characteristics were similar. Multivariate analysis showed that greater preoperative renal unit function (P = 0.011) and nephrometry score (P = 0.041) were independently correlated with a reduction in glomerular filtration rate. The operative method did not correlate with renal function impairment (P = 0.704). Postoperative renal function impairment was similar between patients who underwent OPN and those who underwent RAPN, despite RAPN having a longer ischemic time. PMID:27134496

  11. Soft robotics: a bioinspired evolution in robotics.

    PubMed

    Kim, Sangbae; Laschi, Cecilia; Trimmer, Barry

    2013-05-01

    Animals exploit soft structures to move effectively in complex natural environments. These capabilities have inspired robotic engineers to incorporate soft technologies into their designs. The goal is to endow robots with new, bioinspired capabilities that permit adaptive, flexible interactions with unpredictable environments. Here, we review emerging soft-bodied robotic systems, and in particular recent developments inspired by soft-bodied animals. Incorporating soft technologies can potentially reduce the mechanical and algorithmic complexity involved in robot design. Incorporating soft technologies will also expedite the evolution of robots that can safely interact with humans and natural environments. Finally, soft robotics technology can be combined with tissue engineering to create hybrid systems for medical applications.

  12. Soft Robots: Manipulation, Mobility, and Fast Actuation

    NASA Astrophysics Data System (ADS)

    Shepherd, Robert; Ilievski, Filip; Choi, Wonjae; Stokes, Adam; Morin, Stephen; Mazzeo, Aaron; Kramer, Rebecca; Majidi, Carmel; Wood, Rob; Whitesides, George

    2012-02-01

    Material innovation will be a key feature in the next generation of robots. A simple, pneumatically powered actuator composed of only soft-elastomers can perform the function of a complex arrangement of mechanical components and electric motors. This talk will focus on soft-lithography as a simple method to fabricate robots--composed of exclusively soft materials (elastomeric polymers). These robots have sophisticated capabilities: a gripper (with no electrical sensors) can manipulate delicate and irregularly shaped objects and a quadrupedal robot can walk to an obstacle (a gap smaller than its walking height) then shrink its body and squeeze through the gap using an undulatory gait. This talk will also introduce a new method of rapidly actuating soft robots. Using this new method, a robot can be caused to jump more than 30 times its height in under 200 milliseconds.

  13. Advanced proteomic liquid chromatography

    PubMed Central

    Xie, Fang; Smith, Richard D.; Shen, Yufeng

    2012-01-01

    Liquid chromatography coupled with mass spectrometry is the predominant platform used to analyze proteomics samples consisting of large numbers of proteins and their proteolytic products (e.g., truncated polypeptides) and spanning a wide range of relative concentrations. This review provides an overview of advanced capillary liquid chromatography techniques and methodologies that greatly improve separation resolving power and proteomics analysis coverage, sensitivity, and throughput. PMID:22840822

  14. PROTEOMER: A workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics.

    PubMed

    Nebrich, Grit; Herrmann, Marion; Hartl, Daniela; Diedrich, Madeleine; Kreitler, Thomas; Wierling, Christoph; Klose, Joachim; Giavalisco, Patrick; Zabel, Claus; Mao, Lei

    2009-04-01

    In recent years proteomics became increasingly important to functional genomics. Although a large amount of data is generated by high throughput large-scale techniques, a connection of these mostly heterogeneous data from different analytical platforms and of different experiments is limited. Data mining procedures and algorithms are often insufficient to extract meaningful results from large datasets and therefore limit the exploitation of the generated biological information. In our proteomic core facility, which almost exclusively focuses on 2-DE/MS-based proteomics, we developed a proteomic database custom tailored to our needs aiming at connecting MS protein identification information to 2-DE derived protein expression profiles. The tools developed should not only enable an automatic evaluation of single experiments, but also link multiple 2-DE experiments with MS-data on different levels and thereby helping to create a comprehensive network of our proteomics data. Therefore the key feature of our "PROTEOMER" database is its high cross-referencing capacity, enabling integration of a wide range of experimental data. To illustrate the workflow and utility of the system, two practical examples are provided to demonstrate that proper data cross-referencing can transform information into biological knowledge. PMID:19259999

  15. Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

    PubMed Central

    Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L.

    2015-01-01

    Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include mass spectrometry to define protein sequence, protein:protein interactions, and protein post-translational modifications. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative mass spectrometry proteomics. It supports all major operating systems and instrument vendors via open data formats. Here we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of tandem mass spectrometry datasets, as well as some major upcoming features. PMID:25631240

  16. A Robot Hand Testbed Designed for Enhancing Embodiment and Functional Neurorehabilitation of Body Schema in Subjects with Upper Limb Impairment or Loss

    PubMed Central

    Hellman, Randall B.; Chang, Eric; Tanner, Justin; Helms Tillery, Stephen I.; Santos, Veronica J.

    2015-01-01

    Many upper limb amputees experience an incessant, post-amputation “phantom limb pain” and report that their missing limbs feel paralyzed in an uncomfortable posture. One hypothesis is that efferent commands no longer generate expected afferent signals, such as proprioceptive feedback from changes in limb configuration, and that the mismatch of motor commands and visual feedback is interpreted as pain. Non-invasive therapeutic techniques for treating phantom limb pain, such as mirror visual feedback (MVF), rely on visualizations of postural changes. Advances in neural interfaces for artificial sensory feedback now make it possible to combine MVF with a high-tech “rubber hand” illusion, in which subjects develop a sense of embodiment with a fake hand when subjected to congruent visual and somatosensory feedback. We discuss clinical benefits that could arise from the confluence of known concepts such as MVF and the rubber hand illusion, and new technologies such as neural interfaces for sensory feedback and highly sensorized robot hand testbeds, such as the “BairClaw” presented here. Our multi-articulating, anthropomorphic robot testbed can be used to study proprioceptive and tactile sensory stimuli during physical finger–object interactions. Conceived for artificial grasp, manipulation, and haptic exploration, the BairClaw could also be used for future studies on the neurorehabilitation of somatosensory disorders due to upper limb impairment or loss. A remote actuation system enables the modular control of tendon-driven hands. The artificial proprioception system enables direct measurement of joint angles and tendon tensions while temperature, vibration, and skin deformation are provided by a multimodal tactile sensor. The provision of multimodal sensory feedback that is spatiotemporally consistent with commanded actions could lead to benefits such as reduced phantom limb pain, and increased prosthesis use due to improved functionality and reduced

  17. A robot hand testbed designed for enhancing embodiment and functional neurorehabilitation of body schema in subjects with upper limb impairment or loss.

    PubMed

    Hellman, Randall B; Chang, Eric; Tanner, Justin; Helms Tillery, Stephen I; Santos, Veronica J

    2015-01-01

    Many upper limb amputees experience an incessant, post-amputation "phantom limb pain" and report that their missing limbs feel paralyzed in an uncomfortable posture. One hypothesis is that efferent commands no longer generate expected afferent signals, such as proprioceptive feedback from changes in limb configuration, and that the mismatch of motor commands and visual feedback is interpreted as pain. Non-invasive therapeutic techniques for treating phantom limb pain, such as mirror visual feedback (MVF), rely on visualizations of postural changes. Advances in neural interfaces for artificial sensory feedback now make it possible to combine MVF with a high-tech "rubber hand" illusion, in which subjects develop a sense of embodiment with a fake hand when subjected to congruent visual and somatosensory feedback. We discuss clinical benefits that could arise from the confluence of known concepts such as MVF and the rubber hand illusion, and new technologies such as neural interfaces for sensory feedback and highly sensorized robot hand testbeds, such as the "BairClaw" presented here. Our multi-articulating, anthropomorphic robot testbed can be used to study proprioceptive and tactile sensory stimuli during physical finger-object interactions. Conceived for artificial grasp, manipulation, and haptic exploration, the BairClaw could also be used for future studies on the neurorehabilitation of somatosensory disorders due to upper limb impairment or loss. A remote actuation system enables the modular control of tendon-driven hands. The artificial proprioception system enables direct measurement of joint angles and tendon tensions while temperature, vibration, and skin deformation are provided by a multimodal tactile sensor. The provision of multimodal sensory feedback that is spatiotemporally consistent with commanded actions could lead to benefits such as reduced phantom limb pain, and increased prosthesis use due to improved functionality and reduced cognitive burden.

  18. Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

    PubMed

    Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W; Moritz, Robert L

    2015-02-01

    Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost.

  19. Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

    PubMed

    Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W; Moritz, Robert L

    2015-02-01

    Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. PMID:25418363

  20. Processing Shotgun Proteomics Data on the Amazon Cloud with the Trans-Proteomic Pipeline*

    PubMed Central

    Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W.; Moritz, Robert L.

    2015-01-01

    Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. PMID:25418363

  1. Environmental Microbial Community Proteomics: Status, Challenges and Perspectives

    PubMed Central

    Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan; Xie, Zhang-Xian

    2016-01-01

    Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment. PMID:27527164

  2. Environmental Microbial Community Proteomics: Status, Challenges and Perspectives.

    PubMed

    Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan; Xie, Zhang-Xian

    2016-01-01

    Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment. PMID:27527164

  3. A Cell-type-resolved Liver Proteome*

    PubMed Central

    Ding, Chen; Li, Yanyan; Guo, Feifei; Jiang, Ying; Ying, Wantao; Li, Dong; Yang, Dong; Xia, Xia; Liu, Wanlin; Zhao, Yan; He, Yangzhige; Li, Xianyu; Sun, Wei; Liu, Qiongming; Song, Lei; Zhen, Bei; Zhang, Pumin; Qian, Xiaohong; Qin, Jun; He, Fuchu

    2016-01-01

    Parenchymatous organs consist of multiple cell types, primarily defined as parenchymal cells (PCs) and nonparenchymal cells (NPCs). The cellular characteristics of these organs are not well understood. Proteomic studies facilitate the resolution of the molecular details of different cell types in organs. These studies have significantly extended our knowledge about organogenesis and organ cellular composition. Here, we present an atlas of the cell-type-resolved liver proteome. In-depth proteomics identified 6000 to 8000 gene products (GPs) for each cell type and a total of 10,075 GPs for four cell types. This data set revealed features of the cellular composition of the liver: (1) hepatocytes (PCs) express the least GPs, have a unique but highly homogenous proteome pattern, and execute fundamental liver functions; (2) the division of labor among PCs and NPCs follows a model in which PCs make the main components of pathways, but NPCs trigger the pathways; and (3) crosstalk among NPCs and PCs maintains the PC phenotype. This study presents the liver proteome at cell resolution, serving as a research model for dissecting the cell type constitution and organ features at the molecular level. PMID:27562671

  4. PROTEOMICS in aquaculture: applications and trends.

    PubMed

    Rodrigues, Pedro M; Silva, Tomé S; Dias, Jorge; Jessen, Flemming

    2012-07-19

    Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

  5. Nanoscaled Proteomic Analysis

    NASA Astrophysics Data System (ADS)

    Xu, Yan; Jia, Lee

    2013-09-01

    Global proteomics research is currently hampered by the extremely complexity of the proteome and the absence of techniques like the polymerase chain reaction in genomics which enables multiplication of a single protein molecule. Since all the existing analytical technologies cannot overcome the detection limit and the dynamic concentration barrier, development of improved analytical technologies at nanoscale, ideally those that could recognize single protein molecule in the presence of high abundant of others, is a high priority for proteomics. In this chapter, we will show the state-of-the-art of nanoproteomics, i.e., the application of nanotechnologies to proteomics. Various nanomaterials including carbon nanomaterials, magnetic nanoparticles, silica nanoparticles, polymer and copolymer nanoparticles, metal and metal oxide nanoparticles have been used to improve sensitivity, specificity, and repeatability of proteomic analysis especially when the multidimensional separation system coupled with MALDI-TOF-MS is used. Among them, gold nanoparticles (GNPs) and carbon nanotubes (CNTs) are the two most important nanomaterials: while GNPs are frequently utilized for enzyme immobilization, high throughput bioassay, selection of target-peptides and target-protein, CNTs including single-walled carbon nanotubes (SWCNTs) and mutiple-walled carbon nanotubes (MWCNTs) have wide applications to electronic sensor, sensitive immunodetection, nanobiocatalysis, affinity probes, MALDI matrices, protein digestion, peptides enrichment and analysis. In perspectives, a deep understanding of the structures and property of nanomaterials and interdisciplinary applications of nanotechnology to proteomics will certainly be revolutionary and intellectually rewarding.

  6. Unraveling pancreatic islet biology by quantitative proteomics

    SciTech Connect

    Zhou, Jianying; Dann, Geoffrey P.; Liew, Chong W.; Smith, Richard D.; Kulkarni, Rohit N.; Qian, Weijun

    2011-08-01

    The pancreatic islets of Langerhans play a critical role in maintaining blood glucose homeostasis by secreting insulin and several other important peptide hormones. Impaired insulin secretion due to islet dysfunction is linked to the pathogenesis underlying both Type 1 and Type 2 diabetes. Over the past 5 years, emerging proteomic technologies have been applied to dissect the signaling pathways that regulate islet functions and gain an understanding of the mechanisms of islet dysfunction relevant to diabetes. Herein, we briefly review some of the recent quantitative proteomic studies involving pancreatic islets geared towards gaining a better understanding of islet biology relevant to metabolic diseases.

  7. Toward understanding social cues and signals in human-robot interaction: effects of robot gaze and proxemic behavior.

    PubMed

    Fiore, Stephen M; Wiltshire, Travis J; Lobato, Emilio J C; Jentsch, Florian G; Huang, Wesley H; Axelrod, Benjamin

    2013-01-01

    As robots are increasingly deployed in settings requiring social interaction, research is needed to examine the social signals perceived by humans when robots display certain social cues. In this paper, we report a study designed to examine how humans interpret social cues exhibited by robots. We first provide a brief overview of perspectives from social cognition in humans and how these processes are applicable to human-robot interaction (HRI). We then discuss the need to examine the relationship between social cues and signals as a function of the degree to which a robot is perceived as a socially present agent. We describe an experiment in which social cues were manipulated on an iRobot Ava(TM) mobile robotics platform in a hallway navigation scenario. Cues associated with the robot's proxemic behavior were found to significantly affect participant perceptions of the robot's social presence and emotional state while cues associated with the robot's gaze behavior were not found to be significant. Further, regardless of the proxemic behavior, participants attributed more social presence and emotional states to the robot over repeated interactions than when they first interacted with it. Generally, these results indicate the importance for HRI research to consider how social cues expressed by a robot can differentially affect perceptions of the robot's mental states and intentions. The discussion focuses on implications for the design of robotic systems and future directions for research on the relationship between social cues and signals. PMID:24348434

  8. Toward understanding social cues and signals in human-robot interaction: effects of robot gaze and proxemic behavior.

    PubMed

    Fiore, Stephen M; Wiltshire, Travis J; Lobato, Emilio J C; Jentsch, Florian G; Huang, Wesley H; Axelrod, Benjamin

    2013-01-01

    As robots are increasingly deployed in settings requiring social interaction, research is needed to examine the social signals perceived by humans when robots display certain social cues. In this paper, we report a study designed to examine how humans interpret social cues exhibited by robots. We first provide a brief overview of perspectives from social cognition in humans and how these processes are applicable to human-robot interaction (HRI). We then discuss the need to examine the relationship between social cues and signals as a function of the degree to which a robot is perceived as a socially present agent. We describe an experiment in which social cues were manipulated on an iRobot Ava(TM) mobile robotics platform in a hallway navigation scenario. Cues associated with the robot's proxemic behavior were found to significantly affect participant perceptions of the robot's social presence and emotional state while cues associated with the robot's gaze behavior were not found to be significant. Further, regardless of the proxemic behavior, participants attributed more social presence and emotional states to the robot over repeated interactions than when they first interacted with it. Generally, these results indicate the importance for HRI research to consider how social cues expressed by a robot can differentially affect perceptions of the robot's mental states and intentions. The discussion focuses on implications for the design of robotic systems and future directions for research on the relationship between social cues and signals.

  9. Review on design and control aspects of ankle rehabilitation robots.

    PubMed

    Jamwal, Prashant K; Hussain, Shahid; Xie, Sheng Q

    2015-03-01

    Ankle rehabilitation robots can play an important role in improving outcomes of the rehabilitation treatment by assisting therapists and patients in number of ways. Consequently, few robot designs have been proposed by researchers which fall under either of the two categories, namely, wearable robots or platform-based robots. This paper presents a review of both kinds of ankle robots along with a brief analysis of their design, actuation and control approaches. While reviewing these designs it was observed that most of them are undesirably inspired by industrial robot designs. Taking note of the design concerns of current ankle robots, few improvements in the ankle robot designs have also been suggested. Conventional position control or force control approaches, being used in the existing ankle robots, have been reviewed. Apparently, opportunities of improvement also exist in the actuation as well as control of ankle robots. Subsequently, a discussion on most recent research in the development of novel actuators and advanced controllers based on appropriate physical and cognitive human-robot interaction has also been included in this review. Implications for Rehabilitation Ankle joint functions are restricted/impaired as a consequence of stroke or injury during sports or otherwise. Robots can help in reinstating functions faster and can also work as tool for recording rehabilitation data useful for further analysis. Evolution of ankle robots with respect to their design and control aspects has been discussed in the present paper and a novel design with futuristic control approach has been proposed. PMID:24320195

  10. Review on design and control aspects of ankle rehabilitation robots.

    PubMed

    Jamwal, Prashant K; Hussain, Shahid; Xie, Sheng Q

    2015-03-01

    Ankle rehabilitation robots can play an important role in improving outcomes of the rehabilitation treatment by assisting therapists and patients in number of ways. Consequently, few robot designs have been proposed by researchers which fall under either of the two categories, namely, wearable robots or platform-based robots. This paper presents a review of both kinds of ankle robots along with a brief analysis of their design, actuation and control approaches. While reviewing these designs it was observed that most of them are undesirably inspired by industrial robot designs. Taking note of the design concerns of current ankle robots, few improvements in the ankle robot designs have also been suggested. Conventional position control or force control approaches, being used in the existing ankle robots, have been reviewed. Apparently, opportunities of improvement also exist in the actuation as well as control of ankle robots. Subsequently, a discussion on most recent research in the development of novel actuators and advanced controllers based on appropriate physical and cognitive human-robot interaction has also been included in this review. Implications for Rehabilitation Ankle joint functions are restricted/impaired as a consequence of stroke or injury during sports or otherwise. Robots can help in reinstating functions faster and can also work as tool for recording rehabilitation data useful for further analysis. Evolution of ankle robots with respect to their design and control aspects has been discussed in the present paper and a novel design with futuristic control approach has been proposed.

  11. Proteome of Hydra Nematocyst*

    PubMed Central

    Balasubramanian, Prakash G.; Beckmann, Anna; Warnken, Uwe; Schnölzer, Martina; Schüler, Andreas; Bornberg-Bauer, Erich; Holstein, Thomas W.; Özbek, Suat

    2012-01-01

    Stinging cells or nematocytes of jellyfish and other cnidarians represent one of the most poisonous and sophisticated cellular inventions in animal evolution. This ancient cell type is unique in containing a giant secretory vesicle derived from the Golgi apparatus. The organelle structure within the vesicle comprises an elastically stretched capsule (nematocyst) to which a long tubule is attached. During exocytosis, the barbed part of the tubule is accelerated with >5 million g in <700 ns, enabling a harpoon-like discharge (Nüchter, T., Benoit, M., Engel, U., Ozbek, S., and Holstein, T. W. (2006) Curr. Biol. 16, R316–R318). Hitherto, the molecular components responsible for the organelle's biomechanical properties were largely unknown. Here, we describe the proteome of nematocysts from the freshwater polyp Hydra magnipapillata. Our analysis revealed an unexpectedly complex secretome of 410 proteins with venomous and lytic but also adhesive or fibrous properties. In particular, the insoluble fraction of the nematocyst represents a functional extracellular matrix structure of collagenous and elastic nature. This finding suggests an evolutionary scenario in which exocytic vesicles harboring a venomous secretome assembled a sophisticated predatory structure from extracellular matrix motif proteins. PMID:22291027

  12. Complementary Proteomic Analysis of Protein Complexes

    PubMed Central

    Greco, Todd M.; Miteva, Yana; Conlon, Frank L.; Cristea, Ileana M.

    2013-01-01

    Proteomic characterization of protein complexes leverages the versatile platform of liquid chromatography-tandem mass spectrometry to elucidate molecular and cellular signaling processes underlying the dynamic regulation of macromolecular assemblies. Here, we describe a complementary proteomic approach optimized for immunoisolated protein complexes. As the relative complexity, abundance, and physiochemical properties of proteins can vary significantly between samples, we have provided (1) complementary sample preparation workflows, (2) detailed steps for HPLC and mass spectrometric method development, and (3) a bioinformatic workflow that provides confident peptide/protein identification paired with unbiased functional gene ontology analysis. This protocol can also be extended for characterization of larger complexity samples from whole cell or tissue Xenopus proteomes. PMID:22956100

  13. Unexpected features of the dark proteome

    PubMed Central

    Perdigão, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth S.; Buckley, Michael J.; Tabor, Bruce; Signal, Beth; Gloss, Brian S.; Hammang, Christopher J.; Rost, Burkhard; Schafferhans, Andrea

    2015-01-01

    We surveyed the “dark” proteome–that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology. PMID:26578815

  14. Multi-dimensional Liquid Chromatography in Proteomics

    PubMed Central

    Zhang, Xiang; Fang, Aiqin; Riley, Catherine P.; Wang, Mu; Regnier, Fred E.; Buck, Charles

    2010-01-01

    Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. This still-emerging combination of technologies aims to describe and characterize all expressed proteins in a biological system. Because of upper limits on mass detection of mass spectrometers, proteins are usually digested into peptides and the peptides are then separated, identified and quantified from this complex enzymatic digest. The problem in digesting proteins first and then analyzing the peptide cleavage fragments by mass spectrometry is that huge numbers of peptides are generated that overwhelm direct mass spectral analyses. The objective in the liquid chromatography approach to proteomics is to fractionate peptide mixtures to enable and maximize identification and quantification of the component peptides by mass spectrometry. This review will focus on existing multidimensional liquid chromatographic (MDLC) platforms developed for proteomics and their application in combination with other techniques such as stable isotope labeling. We also provide some perspectives on likely future developments. PMID:20363391

  15. The Escherichia coli Proteome: Past, Present, and Future Prospects†

    PubMed Central

    Han, Mee-Jung; Lee, Sang Yup

    2006-01-01

    Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects. PMID:16760308

  16. Robotic concepts for urban operations

    NASA Astrophysics Data System (ADS)

    Digney, Bruce L.; Penzes, Steven G.

    2002-07-01

    While land vehicles in open terrains is currently the primary military operation, it is expected that an increasing number of conflicts will occur in urban setting. Urban robots must operate under mobility, communication, perception and control conditions far more demanding than their open terrain counterparts. The Defense Research Establishment Suffield (DRES) is being tasked to develop robots, unmanned vehicles and supports system to aid the Canadian Forces in urban operations. In preparation for this role DRES personnel were invited to participate in operation Urban Ram, a large urban war game held on the grounds of CFB Griesbach in Edmonton. This paper presents the lessons learned at Urban Ram as to what roles robots could fulfill and the challenges of urban environments that must be overcome. Also presented will be robotic concepts inspired by Urban Ram, specifically discussed will be High Utility Robotics (HUR), which combines geometric shape shifting with function morphing to provide the general purpose, high mobility and broad application robots required for urban environments.

  17. Collaborations in Proteomics Research - Office of Cancer Clinical Proteomics Research

    Cancer.gov

    The National Cancer Institute (NCI), through the Office of Cancer Clinical Proteomics Research (OCCPR), has signed two Memorandums of Understanding (MOUs) in the sharing of proteomics reagents and protocols

  18. Environmental Proteomics: Changes in the Proteome of Marine Organisms in Response to Environmental Stress, Pollutants, Infection, Symbiosis, and Development

    NASA Astrophysics Data System (ADS)

    Tomanek, Lars

    2011-01-01

    Environmental proteomics, the study of changes in the abundance of proteins and their post-translational modifications, has become a powerful tool for generating hypotheses regarding how the environment affects the biology of marine organisms. Proteomics discovers hitherto unknown cellular effects of environmental stressors such as changes in thermal, osmotic, and anaerobic conditions. Proteomic analyses have advanced the characterization of the biological effects of pollutants and identified comprehensive and pollutant-specific sets of biomarkers, especially those highlighting post-translational modifications. Proteomic analyses of infected organisms have highlighted the broader changes occurring during immune responses and how the same pathways are attenuated during the maintenance of symbiotic relationships. Finally, proteomic changes occurring during the early life stages of marine organisms emphasize the importance of signaling events during development in a rapidly changing environment. Changes in proteins functioning in energy metabolism, cytoskeleton, protein stabilization and turnover, oxidative stress, and signaling are common responses to environmental change.

  19. Plant fluid proteomics: Delving into the xylem sap, phloem sap and apoplastic fluid proteomes.

    PubMed

    Rodríguez-Celma, Jorge; Ceballos-Laita, Laura; Grusak, Michael A; Abadía, Javier; López-Millán, Ana-Flor

    2016-08-01

    The phloem sap, xylem sap and apoplastic fluid play key roles in long and short distance transport of signals and nutrients, and act as a barrier against local and systemic pathogen infection. Among other components, these plant fluids contain proteins which are likely to be important players in their functionalities. However, detailed information about their proteomes is only starting to arise due to the difficulties inherent to the collection methods. This review compiles the proteomic information available to date in these three plant fluids, and compares the proteomes obtained in different plant species in order to shed light into conserved functions in each plant fluid. Inter-species comparisons indicate that all these fluids contain the protein machinery for self-maintenance and defense, including proteins related to cell wall metabolism, pathogen defense, proteolysis, and redox response. These analyses also revealed that proteins may play more relevant roles in signaling in the phloem sap and apoplastic fluid than in the xylem sap. A comparison of the proteomes of the three fluids indicates that although functional categories are somewhat similar, proteins involved are likely to be fluid-specific, except for a small group of proteins present in the three fluids, which may have a universal role, especially in cell wall maintenance and defense. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

  20. Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level.

    PubMed

    Bensaddek, Dalila; Narayan, Vikram; Nicolas, Armel; Murillo, Alejandro Brenes; Gartner, Anton; Kenyon, Cynthia J; Lamond, Angus I

    2016-02-01

    Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro-proteomics for the analysis of Caenorhabditis elegans, a eukaryote composed of 959 somatic cells and ∼1500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼3000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (>6 orders of magnitude), including many chromatin-associated factors involved in chromosome structure and gene regulation. We apply the micro-proteomics workflow to measure the global proteome response to heat-shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat-shock, including variable induction of heat-shock proteins. The micro-proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource. PMID:26552604

  1. Micro‐proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level

    PubMed Central

    Bensaddek, Dalila; Narayan, Vikram; Nicolas, Armel; Brenes Murillo, Alejandro; Gartner, Anton; Kenyon, Cynthia J.

    2016-01-01

    Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro‐proteomics for the analysis of Caenorhabditis elegans, a eukaryote composed of 959 somatic cells and ∼1500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼3000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (>6 orders of magnitude), including many chromatin‐associated factors involved in chromosome structure and gene regulation. We apply the micro‐proteomics workflow to measure the global proteome response to heat‐shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat‐shock, including variable induction of heat‐shock proteins. The micro‐proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource. PMID:26552604

  2. Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level.

    PubMed

    Bensaddek, Dalila; Narayan, Vikram; Nicolas, Armel; Murillo, Alejandro Brenes; Gartner, Anton; Kenyon, Cynthia J; Lamond, Angus I

    2016-02-01

    Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro-proteomics for the analysis of Caenorhabditis elegans, a eukaryote composed of 959 somatic cells and ∼1500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼3000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (>6 orders of magnitude), including many chromatin-associated factors involved in chromosome structure and gene regulation. We apply the micro-proteomics workflow to measure the global proteome response to heat-shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat-shock, including variable induction of heat-shock proteins. The micro-proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource.

  3. Proteome-scale identification and characterization of mitochondria targeting proteins of Mycobacterium avium subspecies paratuberculosis: Potential virulence factors modulating host mitochondrial function.

    PubMed

    Rana, Aarti; Kumar, Devender; Rub, Abdur; Akhter, Yusuf

    2015-07-01

    Mycobacterium avium subsp. paratuberculosis is the etiological agent of Johne's Disease among ruminants. During the course of infection, it expresses a number of proteins for its successful persistence inside the host that cause variety of physiological abnormalities in the host. Mitochondrion is one of the attractive targets for pathogenic bacteria. Employing a proteome-wide sequence and structural signature based approach we have identified 46 M. avium subsp. paratuberculosis proteins as potential targets for the host mitochondrial targeting. These may act as virulence factors modulating mitochondrial physiology for bacterial survival and immune evasion inside the host cells.

  4. Proteomics analysis of human oligodendroglioma proteome.

    PubMed

    Khaghani-Razi-Abad, Solmaz; Hashemi, Mehrdad; Pooladi, Mehdi; Entezari, Maliheh; Kazemi, Elham

    2015-09-10

    Proteomics analyses enable the identification and quantitation of proteins. From a purely clinical perspective, the application of proteomics based on innovations, may greatly affect the future management of malignant brain tumors. This optimism is based on four main reasons: diagnosis, prognosis, selection of targeted therapy based on molecular profile of the brain tumor and monitoring therapeutic response, or resistance. We extracted the proteins of tumor and normal brain tissues, and then evaluated the protein purity by Bradford test. In this study, we separated the proteins by two-dimensional (2DG) gel electrophoresis methods. Then spots were analyzed, compared using statistical data and specific software and were identified by pH isoelectric, molecular weights and data banks. The protein profiles were determined using 2D gel electrophoresis and MALDI TOF/TOF mass spectrometry approaches. Simple statistical tests were used to establish a putative hierarchy in which the change in protein level was ranked according to a cut-off point with p<0.05. The 2D gel showed a total of 1328 spots among which 157 spots were under-expressed and 276 spots were overexpressed. Most proteins are subjects to post-translational modifications, where amino acid residues may be chemically modified or conjugated by small proteins like ubiquitin. Proteomics is a powerful way to identifying multiple proteins which are altered following a neuropharmacological intervention in a CNS disease. PMID:26002447

  5. Blood folate status and expression of proteins involved in immune function, inflammation, and coagulation: biochemical and proteomic changes in the plasma of humans in response to long-term synthetic folic acid supplementation.

    PubMed

    Duthie, Susan J; Horgan, Graham; de Roos, Baukje; Rucklidge, Garry; Reid, Martin; Duncan, Gary; Pirie, Lynn; Basten, Graham P; Powers, Hilary J

    2010-04-01

    We used plasma proteomics to identify human proteins responsive to folate status. Plasma was collected from subjects treated with placebo or 1.2 mg of folic acid daily for 12 weeks in a randomized controlled trial. Homocysteine and folate were measured by immunoassay and uracil misincorporation by electrophoresis. The plasma proteome was assessed by 2-D gel electrophoresis, and proteins were identified by LC MS/MS. 5-methylTHF increased 5-fold (P = 0.000003) in response to intervention. Red cell folate doubled (P = 0.013), and lymphocyte folate increased 44% (P = 0.0001). Hcy and uracil dropped 22% (P = 0.0005) and 25% (P = 0.05), respectively. ApoE A-1, alpha-1-antichymotrypsin, antithrombin, and serum amyloid P were downregulated, while albumin, IgM C, and complement C3 were upregulated (P < 0.05). More than 60 proteins were significantly associated with folate pre- and postintervention (P < 0.01). These were categorized into metabolic pathways related to complement fixation (e.g., C1, C3, C4, Factor H, Factor 1, Factor B, clusterin), coagulation (e.g., antithrombin, alpha-1-antitrypsin, kininogen) and mineral transport (e.g., transthyretin, haptoglobin, ceruloplasmin). Low folate status pre- and post-treatment were associated with lower levels of proteins involved in activation and regulation of immune function and coagulation. Supplementation with synthetic folic acid increased expression of these proteins but did not substantially disrupt the balance of these pathways.

  6. Software development to support sensor control of robot arc welding

    NASA Technical Reports Server (NTRS)

    Silas, F. R., Jr.

    1986-01-01

    The development of software for a Digital Equipment Corporation MINC-23 Laboratory Computer to provide functions of a workcell host computer for Space Shuttle Main Engine (SSME) robotic welding is documented. Routines were written to transfer robot programs between the MINC and an Advanced Robotic Cyro 750 welding robot. Other routines provide advanced program editing features while additional software allows communicatin with a remote computer aided design system. Access to special robot functions were provided to allow advanced control of weld seam tracking and process control for future development programs.

  7. Accurate Mass Measurements in Proteomics

    SciTech Connect

    Liu, Tao; Belov, Mikhail E.; Jaitly, Navdeep; Qian, Weijun; Smith, Richard D.

    2007-08-01

    To understand different aspects of life at the molecular level, one would think that ideally all components of specific processes should be individually isolated and studied in details. Reductionist approaches, i.e., studying one biological event at a one-gene or one-protein-at-a-time basis, indeed have made significant contributions to our understanding of many basic facts of biology. However, these individual “building blocks” can not be visualized as a comprehensive “model” of the life of cells, tissues, and organisms, without using more integrative approaches.1,2 For example, the emerging field of “systems biology” aims to quantify all of the components of a biological system to assess their interactions and to integrate diverse types of information obtainable from this system into models that could explain and predict behaviors.3-6 Recent breakthroughs in genomics, proteomics, and bioinformatics are making this daunting task a reality.7-14 Proteomics, the systematic study of the entire complement of proteins expressed by an organism, tissue, or cell under a specific set of conditions at a specific time (i.e., the proteome), has become an essential enabling component of systems biology. While the genome of an organism may be considered static over short timescales, the expression of that genome as the actual gene products (i.e., mRNAs and proteins) is a dynamic event that is constantly changing due to the influence of environmental and physiological conditions. Exclusive monitoring of the transcriptomes can be carried out using high-throughput cDNA microarray analysis,15-17 however the measured mRNA levels do not necessarily correlate strongly with the corresponding abundances of proteins,18-20 The actual amount of functional proteins can be altered significantly and become independent of mRNA levels as a result of post-translational modifications (PTMs),21 alternative splicing,22,23 and protein turnover.24,25 Moreover, the functions of expressed

  8. Robotics in biomedical chromatography and electrophoresis.

    PubMed

    Fouda, H G

    1989-08-11

    The ideal laboratory robot can be viewed as "an indefatigable assistant capable of working continuously for 24 h a day with constant efficiency". The development of a system approaching that promise requires considerable skill and time commitment, a thorough understanding of the capabilities and limitations of the robot and its specialized modules and an intimate knowledge of the functions to be automated. The robot need not emulate every manual step. Effective substitutes for difficult steps must be devised. The future of laboratory robots depends not only on technological advances in other fields, but also on the skill and creativity of chromatographers and other scientists. The robot has been applied to automate numerous biomedical chromatography and electrophoresis methods. The quality of its data can approach, and in some cases exceed, that of manual methods. Maintaining high data quality during continuous operation requires frequent maintenance and validation. Well designed robotic systems can yield substantial increase in the laboratory productivity without a corresponding increase in manpower. They can free skilled personnel from mundane tasks and can enhance the safety of the laboratory environment. The integration of robotics, chromatography systems and laboratory information management systems permits full automation and affords opportunities for unattended method development and for future incorporation of artificial intelligence techniques and the evolution of expert systems. Finally, humanoid attributes aside, robotic utilization in the laboratory should not be an end in itself. The robot is a useful tool that should be utilized only when it is prudent and cost-effective to do so.

  9. Interfacing a haptic robotic system with complex virtual environments to treat impaired upper extremity motor function in children with cerebral palsy

    PubMed Central

    FLUET, GERARD G.; QIU, QINYIN; KELLY, DONNA; PARIKH, HETA D.; RAMIREZ, DIEGO; SALEH, SOHA; ADAMOVICH, SERGEI V.

    2011-01-01

    Objective To investigate the ability of the New Jersey Institute of Technology Robot Assisted Virtual Rehabilitation (NJIT-RAVR) system training to elicit changes in upper extremity (UE) function in children with hemiplegia secondary to cerebral palsy. Methods Nine children (mean age 9 years, three males) participated in three pilots. Subjects trained 1 hour, 3 days a week for 3 weeks. Two groups performed this protocol as their only intervention. The third group also performed 5–6 hours of constraint-induced movement therapy. Results All subjects participated in a short programme of nine, 60-minute training sessions without adverse effects. As a group, subjects demonstrated statistically significant improvements in Melbourne Assessment of Unilateral Upper Limb Function Test, a composite of three timed UE tasks and several measurements of reaching kinematics. Several subjects demonstrated clinically significant improvements in active shoulder abduction and flexion as well as forearm supination. Conclusion Three small pilots of NJIT-RAVR training demonstrated measurable benefit with no complications, warranting further examination. PMID:20828330

  10. Robot environment expert system

    NASA Technical Reports Server (NTRS)

    Potter, J. L.

    1985-01-01

    The Robot Environment Expert System uses a hexidecimal tree data structure to model a complex robot environment where not only the robot arm moves, but also the robot itself and other objects may move. The hextree model allows dynamic updating, collision avoidance and path planning over time, to avoid moving objects.

  11. Proteomics of red and white corolla limbs in petunia reveals a novel function of the anthocyanin regulator ANTHOCYANIN1 in determining flower longevity.

    PubMed

    Prinsi, Bhakti; Negri, Alfredo S; Quattrocchio, Francesca M; Koes, Ronald E; Espen, Luca

    2016-01-10

    The Petunia hybrida ANTHOCYANIN1 (AN1) gene encodes a transcription factor that regulates both the expression of genes involved in anthocyanin synthesis and the acidification of the vacuolar lumen in corolla epidermal cells. In this work, the comparison between the red flowers of the R27 line with the white flowers of the isogenic an1 mutant line W225 showed that the AN1 gene has further pleiotropic effects on flavonoid biosynthesis as well as on distant physiological traits. The proteomic profiling showed that the an1 mutation was associated to changes in accumulation of several proteins, affecting both anthocyanin synthesis and primary metabolism. The flavonoid composition study confirmed that the an1 mutation provoked a broad attenuation of the entire flavonoid pathway, probably by indirect biochemical events. Moreover, proteomic changes and variation of biochemical parameters revealed that the an1 mutation induced a delay in the onset of flower senescence in W225, as supported by the enhanced longevity of the W225 flowers in planta and the loss of sensitivity of cut flowers to sugar. This study suggests that AN1 is possibly involved in the perception and/or transduction of ethylene signal during flower senescence.

  12. Proteomics of red and white corolla limbs in petunia reveals a novel function of the anthocyanin regulator ANTHOCYANIN1 in determining flower longevity.

    PubMed

    Prinsi, Bhakti; Negri, Alfredo S; Quattrocchio, Francesca M; Koes, Ronald E; Espen, Luca

    2016-01-10

    The Petunia hybrida ANTHOCYANIN1 (AN1) gene encodes a transcription factor that regulates both the expression of genes involved in anthocyanin synthesis and the acidification of the vacuolar lumen in corolla epidermal cells. In this work, the comparison between the red flowers of the R27 line with the white flowers of the isogenic an1 mutant line W225 showed that the AN1 gene has further pleiotropic effects on flavonoid biosynthesis as well as on distant physiological traits. The proteomic profiling showed that the an1 mutation was associated to changes in accumulation of several proteins, affecting both anthocyanin synthesis and primary metabolism. The flavonoid composition study confirmed that the an1 mutation provoked a broad attenuation of the entire flavonoid pathway, probably by indirect biochemical events. Moreover, proteomic changes and variation of biochemical parameters revealed that the an1 mutation induced a delay in the onset of flower senescence in W225, as supported by the enhanced longevity of the W225 flowers in planta and the loss of sensitivity of cut flowers to sugar. This study suggests that AN1 is possibly involved in the perception and/or transduction of ethylene signal during flower senescence. PMID:26459403

  13. [Robotic surgery for cancer treatment].

    PubMed

    Oouchida, Kenoki; Ieiri, Satoshi; Kenmotsu, Hajime; Tomikawa, Morimasa; Hashizume, Makoto

    2012-01-01

    Surgical operation is still one of the important options for treatment of many types of cancer. In the present-day treatment of cancer, patients' quality of life is focused on and surgeons need to provide minimally invasive surgery without decreasing the curability of disease. Endoscopic surgery contributed to the prevalence of minimally -invasive surgery. However it has also raised a problem regarding differences in surgical techniques among individual surgeons. Robot-assisted surgery provides some resolutions with 3D vision and increases the freedom of forceps manipulation. Furthermore, 3D visual magnification, scaling function, and the filtering function of surgical robots may make it possible for surgeons to perform microsurgery more delicate than open surgery. Here, we report the present status and the future of the representative surgical robot, and the da Vinci surgical system. PMID:22241345

  14. Robotic Stripping

    NASA Technical Reports Server (NTRS)

    2000-01-01

    UltraStrip Systems, Inc.'s M-200 removes paint from the hulls of ships faster than traditional grit-blasting methods. And, it does so without producing toxic airborne particles common to traditional methods. The M-2000 magnetically attaches itself to the hull of the ship. Its water jets generate 40,000 pounds of pressure per square inch, blasting away paint down to the ships steel substrate. The only by product is water and dried paint chips and these are captured by a vacuum system so no toxic residue can escape. It was built out of a partnership between the Jet Propulsion Laboratory and the National Robotics Engineering Consortium.

  15. The Cysteine Proteome

    PubMed Central

    Go, Young-Mi; Chandler, Joshua D.; Jones, Dean P.

    2015-01-01

    The cysteine (Cys) proteome is a major component of the adaptive interface between the genome and the exposome. The thiol moiety of Cys undergoes a range of biologic modifications enabling biological switching of structure and reactivity. These biological modifications include sulfenylation and disulfide formation, formation of higher oxidation states, S-nitrosylation, persulfidation, metallation, and other modifications. Extensive knowledge about these systems and their compartmentalization now provides a foundation to develop advanced integrative models of Cys proteome regulation. In particular, detailed understanding of redox signaling pathways and sensing networks is becoming available to discriminate network structures. This research focuses attention on the need for atlases of Cys modifications to develop systems biology models. Such atlases will be especially useful for integrative studies linking the Cys proteome to imaging and other omics platforms, providing a basis for improved redox-based therapeutics. Thus, a framework is emerging to place the Cys proteome as a complement to the quantitative proteome in the omics continuum connecting the genome to the exposome. PMID:25843657

  16. Environmental proteomics and metallomics.

    PubMed

    López-Barea, Juan; Gómez-Ariza, José Luis

    2006-04-01

    Monitoring environmental pollution using biomarkers requires detailed knowledge about the markers, and many only allow a partial assessment of pollution. New proteomic methods (environmental proteomics) can identify proteins that, after validation, might be useful as alternative biomarkers, although this approach also has its limitations, derived mainly from their application to non-model organisms. Initial studies using environmental proteomics were carried out in animals exposed to model pollutants, and led to the concept of protein expression signatures. Experiments have been carried out in model organisms (yeast, Arabidopsis, rat cells, or mice) exposed to model contaminants. Over the last few years, proteomics has been applied to organisms from ecosystems with different pollution levels, forming the basis of an environmental branch in proteomics. Another focus is connected with the presence of metals bound to biomolecules, which adds an additional dimension to metal-biomolecule and metalloprotein characterization - the field of metallomics. The metallomic approach considers the metallome: a whole individual metal or metalloid species within a cell or tissue. A metallomic analytical approach (MAA) is proposed as a new tool to study and identify metalloproteins.

  17. Blood-related proteomics.

    PubMed

    Liumbruno, Giancarlo; D'Alessandro, Angelo; Grazzini, Giuliano; Zolla, Lello

    2010-01-01

    Blood-related proteomics is an emerging field, recently gaining momentum. Indeed, a wealth of data is now available and a plethora of groups has contributed to add pieces to the jigsaw puzzle of protein complexity within plasma and blood cells. In this review article we purported to sail across the mare magnum of the actual knowledge in this research endeavour. The main strides in proteomic investigations on red blood cells, platelets, plasma and white blood cells are hereby presented in a chronological order. Moreover, a glance is given at prospective studies which promise to shift the focus of attention from the end product to its provider, the donor, in a sort of Kantian "Copernican revolution". A well-rounded portrait of the usefulness of proteomics in blood-related research is accurately given. In particular, proteomic tools could be adopted to follow the main steps of the blood-banking production processes (a comparison of collection methods, pathogen inactivation techniques, storage protocols). Thus proteomics has been recently transformed from a mere basic-research extremely-expensive toy into a dramatically-sensitive and efficient eye-lens to either delve into the depths of the molecular mechanisms of blood and blood components or to establish quality parameters in the blood-banking production chain totally anew. PMID:19567275

  18. ROBOT TASK SCENE ANALYZER

    SciTech Connect

    William R. Hamel; Steven Everett

    2000-08-01

    Environmental restoration and waste management (ER and WM) challenges in the United States Department of Energy (DOE), and around the world, involve radiation or other hazards which will necessitate the use of remote operations to protect human workers from dangerous exposures. Remote operations carry the implication of greater costs since remote work systems are inherently less productive than contact human work due to the inefficiencies/complexities of teleoperation. To reduce costs and improve quality, much attention has been focused on methods to improve the productivity of combined human operator/remote equipment systems; the achievements to date are modest at best. The most promising avenue in the near term is to supplement conventional remote work systems with robotic planning and control techniques borrowed from manufacturing and other domains where robotic automation has been used. Practical combinations of teleoperation and robotic control will yield telerobotic work systems that outperform currently available remote equipment. It is believed that practical telerobotic systems may increase remote work efficiencies significantly. Increases of 30% to 50% have been conservatively estimated for typical remote operations. It is important to recognize that the basic hardware and software features of most modern remote manipulation systems can readily accommodate the functionality required for telerobotics. Further, several of the additional system ingredients necessary to implement telerobotic control--machine vision, 3D object and workspace modeling, automatic tool path generation and collision-free trajectory planning--are existent.

  19. From protein catalogues towards targeted proteomics approaches in cereal grains.

    PubMed

    Finnie, Christine; Sultan, Abida; Grasser, Klaus D

    2011-07-01

    Due to their importance for human nutrition, the protein content of cereal grains has been a subject of intense study for over a century and cereal grains were not surprisingly one of the earliest subjects for 2D-gel-based proteome analysis. Over the last two decades, countless cereal grain proteomes, mostly derived using 2D-gel based technologies, have been described and hundreds of proteins identified. However, very little is still known about post-translational modifications, subcellular proteomes, and protein-protein interactions in cereal grains. Development of techniques for improved extraction, separation and identification of proteins and peptides is facilitating functional proteomics and analysis of sub-proteomes from small amounts of starting material, such as seed tissues. The combination of proteomics with structural and functional analysis is increasingly applied to target subsets of proteins. These "next-generation" proteomics studies will vastly increase our depth of knowledge about the processes controlling cereal grain development, nutritional and processing characteristics.

  20. IC handling robot

    SciTech Connect

    Law, D.O.

    1986-09-01

    Allied Corporation, Bendix Kansas City Division uses many integrated circuits (ICs) which are 100% tested by receiving inspection prior to installation into the next assemblies. Testing includes functional testing followed by a burn-in cycle then additional functional testing. Before an IC can be functionally tested, it must be inserted into a custom plastic carrier which is placed into a metal magazine that fits the functional tester. The ICs are removed from both tester magazines and carriers prior to being placed into connectors mounted on a printed wiring board for burn-in. Then they are removed from the burn-in board and re-inserted into carriers and magazines for additional functional testing. Each device is handled manually a minimum of 12 times before it is accepted. This project established a robotic workcell which automatically prepares a dual in-line packaged (DIP) integrated circuit for several types of inspection operations performed by Receiving Inspection. Specific activities required to accomplish this goal included definition of the work cell, preparation of the robot and other equipment specifications, installation planning, establishment of programming routines and logic, design of operator safeguards, and development of the work cell concept into an operational unit capable of supporting production.

  1. Proteomics study revealed altered proteome of Dichogaster curgensis upon exposure to fly ash.

    PubMed

    Markad, Vijaykumar L; Adav, Sunil S; Ghole, Vikram S; Sze, Siu Kwan; Kodam, Kisan M

    2016-10-01

    Fly ash is toxic and its escalating use as a soil amendment and disposal by dumping into environment is receiving alarming attention due to its impact on environment. Proteomics technology is being used for environmental studies since proteins respond rapidly when an organism is exposed to a toxicant, and hence soil engineers such as earthworms are used as model organisms to assess the toxic effects of soil toxicants. This study adopted proteomics technology and profiled proteome of earthworm Dichogaster curgensis that was exposed to fly ash, with main aim to elucidate fly ash effects on cellular and metabolic pathways. The functional classification of identified proteins revealed carbohydrate metabolism (14.36%), genetic information processing (15.02%), folding, sorting and degradation (10.83%), replication and repair (3.95%); environmental information processing (2.19%), signal transduction (9.61%), transport and catabolism (17.27%), energy metabolism (6.69%), etc. in the proteome. Proteomics data and functional assays revealed that the exposure of earthworm to fly ash induced protein synthesis, up-regulation of gluconeogenesis, disturbed energy metabolism, oxidative and cellular stress, and mis-folding of proteins. The regulation of ubiquitination, proteasome and modified alkaline comet assay in earthworm coelomocytes suggested DNA-protein cross link affecting chromatin remodeling and protein folding. PMID:27371791

  2. Proteome Dynamics Reveals Pro-Inflammatory Remodeling of Plasma Proteome in a Mouse Model of NAFLD.

    PubMed

    Li, Ling; Bebek, Gurkan; Previs, Stephen F; Smith, Jonathan D; Sadygov, Rovshan G; McCullough, Arthur J; Willard, Belinda; Kasumov, Takhar

    2016-09-01

    Nonalcoholic fatty liver disease (NAFLD) is associated with an increased risk of cardiovascular disease. Because the liver is the major source of circulatory proteins, it is not surprising that hepatic disease could lead to alterations in the plasma proteome, which are therein implicated in atherosclerosis. The current study used low-density lipoprotein receptor-deficient (LDLR(-/-)) mice to examine the impact of Western diet (WD)-induced NAFLD on plasma proteome homeostasis. Using a (2)H2O-metabolic labeling method, we found that a WD led to a proinflammatory distribution of circulatory proteins analyzed in apoB-depleted plasma, which was attributed to an increased production. The fractional turnover rates of short-lived proteins that are implicated in stress-response, lipid metabolism, and transport functions were significantly increased with WD (P < 0.05). Pathway analyses revealed that alterations in plasma proteome dynamics were related to the suppression of hepatic PPARα, which was confirmed based on reduced gene and protein expression of PPARα in mice fed a WD. These changes were associated with ∼4-fold increase (P < 0.0001) in the proinflammatory property of apoB-depleted plasma. In conclusion, the proteome dynamics method reveals proinflammatory remodeling of the plasma proteome relevant to liver disease. The approach used herein may provide a useful metric of in vivo liver function and better enable studies of novel therapies surrounding NAFLD and other diseases. PMID:27439437

  3. Approaching clinical proteomics: current state and future fields of application in cellular proteomics.

    PubMed

    Apweiler, Rolf; Aslanidis, Charalampos; Deufel, Thomas; Gerstner, Andreas; Hansen, Jens; Hochstrasser, Dennis; Kellner, Roland; Kubicek, Markus; Lottspeich, Friedrich; Maser, Edmund; Mewes, Hans-Werner; Meyer, Helmut E; Müllner, Stefan; Mutter, Wolfgang; Neumaier, Michael; Nollau, Peter; Nothwang, Hans G; Ponten, Fredrik; Radbruch, Andreas; Reinert, Knut; Rothe, Gregor; Stockinger, Hannes; Tárnok, Attila; Taussig, Mike J; Thiel, Andreas; Thiery, Joachim; Ueffing, Marius; Valet, Günther; Vandekerckhove, Joel; Wagener, Christoph; Wagner, Oswald; Schmitz, Gerd

    2009-10-01

    Recent developments in proteomics technology offer new opportunities for clinical applications in hospital or specialized laboratories including the identification of novel biomarkers, monitoring of disease, detecting adverse effects of drugs, and environmental hazards. Advanced spectrometry technologies and the development of new protein array formats have brought these analyses to a standard, which now has the potential to be used in clinical diagnostics. Besides standardization of methodologies and distribution of proteomic data into public databases, the nature of the human body fluid proteome with its high dynamic range in protein concentrations, its quantitation problems, and its extreme complexity present enormous challenges. Molecular cell biology (cytomics) with its link to proteomics is a new fast moving scientific field, which addresses functional cell analysis and bioinformatic approaches to search for novel cellular proteomic biomarkers or their release products into body fluids that provide better insight into the enormous biocomplexity of disease processes and are suitable for patient stratification, therapeutic monitoring, and prediction of prognosis. Experience from studies of in vitro diagnostics and especially in clinical chemistry showed that the majority of errors occurs in the preanalytical phase and the setup of the diagnostic strategy. This is also true for clinical proteomics where similar preanalytical variables such as inter- and intra-assay variability due to biological variations or proteolytical activities in the sample will most likely also influence the results of proteomics studies. However, before complex proteomic analysis can be introduced at a broader level into the clinic, standardization of the preanalytical phase including patient preparation, sample collection, sample preparation, sample storage, measurement, and data analysis is another issue which has to be improved. In this report, we discuss the recent advances and

  4. [LEGUME-RHIZOBIUM SYMBIOSIS PROTEOMICS: ACHIEVEMENTS AND PERSPECTIVES].

    PubMed

    Kondratiuk, Iu Iu; Mamenko, P M; Kots, S Ya

    2015-01-01

    The present review contains results of proteomic researches of legume-rhizobium symbiosis. The technical difficulties associated with the methods of obtaining protein extracts from symbiotic structures and ways of overcoming them were discussed. The changes of protein synthesis under formation and functioning of symbiotic structures were shown. Special attention has been given to the importance of proteomic studies of plant-microbe structures in the formation of adaptation strategies under adverse environmental conditions. The technical and conceptual perspectives of legume-rhizobium symbiosis proteomics were shown.

  5. FunRich proteomics software analysis, let the fun begin!

    PubMed

    Benito-Martin, Alberto; Peinado, Héctor

    2015-08-01

    Protein MS analysis is the preferred method for unbiased protein identification. It is normally applied to a large number of both small-scale and high-throughput studies. However, user-friendly computational tools for protein analysis are still needed. In this issue, Mathivanan and colleagues (Proteomics 2015, 15, 2597-2601) report the development of FunRich software, an open-access software that facilitates the analysis of proteomics data, providing tools for functional enrichment and interaction network analysis of genes and proteins. FunRich is a reinterpretation of proteomic software, a standalone tool combining ease of use with customizable databases, free access, and graphical representations.

  6. Spatial and temporal dynamics of the cardiac mitochondrial proteome