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Sample records for functional proteomic robotic

  1. Automation, parallelism, and robotics for proteomics.

    PubMed

    Alterovitz, Gil; Liu, Jonathan; Chow, Jijun; Ramoni, Marco F

    2006-07-01

    The speed of the human genome project (Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C. et al., Nature 2001, 409, 860-921) was made possible, in part, by developments in automation of sequencing technologies. Before these technologies, sequencing was a laborious, expensive, and personnel-intensive task. Similarly, automation and robotics are changing the field of proteomics today. Proteomics is defined as the effort to understand and characterize proteins in the categories of structure, function and interaction (Englbrecht, C. C., Facius, A., Comb. Chem. High Throughput Screen. 2005, 8, 705-715). As such, this field nicely lends itself to automation technologies since these methods often require large economies of scale in order to achieve cost and time-saving benefits. This article describes some of the technologies and methods being applied in proteomics in order to facilitate automation within the field as well as in linking proteomics-based information with other related research areas.

  2. 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.

  3. 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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. The power of functional proteomics

    PubMed Central

    Wagner, Volker; Kreimer, Georg

    2008-01-01

    One of the key modifications of proteins that can affect protein functions, activities, stabilities, localizations and interactions, represents phosphorylation. For functional phosphoproteomics, phosphopeptides are enriched from isolated sub-cellular fractions of interest and analyzed by liquid chromatography-electrospray ionization-mass spectrometry. Such an approach was recently applied to the eyespot apparatus of the green flagellate alga Chlamydomonas reinhardtii, which represents a primordial visual system. Thereby, 32 phosphoproteins of known eyespot proteins along with 52 precise in vivo phosphorylation sites were identified. They include enzymes of carotenoid and fatty acid metabolism, (putative) light signaling components and proteins with unknown function. Strikingly, the two unique green algal photoreceptors, channelrhodopsin-1 and -2 were found to be phosphorylated in the cytoplasmic loop next to their seven transmembrane regions in a similar distance as observed in vertebrate rhodopsins. PMID:19513232

  5. The proteome: structure, function and evolution

    PubMed Central

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

    2006-01-01

    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. PMID:16524832

  6. Proteomic approaches to dissect platelet function: half the story

    PubMed Central

    Gnatenko, Dmitri V.; Perrotta, Peter L.; Bahou, Wadie F.

    2006-01-01

    Platelets play critical roles in diverse hemostatic and pathologic disorders and are broadly implicated in various biological processes that include inflammation, wound healing, and thrombosis. Recent progress in high-throughput mRNA and protein profiling techniques has advanced our understanding of the biological functions of platelets. Platelet proteomics has been adopted to decode the complex processes that underlie platelet function by identifying novel platelet-expressed proteins, dissecting mechanisms of signal or metabolic pathways, and analyzing functional changes of the platelet proteome in normal and pathologic states. The integration of transcriptomics and proteomics, coupled with progress in bioinformatics, provides novel tools for dissecting platelet biology. In this review, we focus on current advances in platelet proteomic studies, with emphasis on the importance of parallel transcriptomic studies to optimally dissect platelet function. Applications of these global profiling approaches to investigate platelet genetic diseases and platelet-related disorders are also addressed. PMID:16926286

  7. Soft robotic sleeve supports heart function.

    PubMed

    Roche, Ellen T; Horvath, Markus A; Wamala, Isaac; Alazmani, Ali; Song, Sang-Eun; Whyte, William; Machaidze, Zurab; Payne, Christopher J; Weaver, James C; Fishbein, Gregory; Kuebler, Joseph; Vasilyev, Nikolay V; Mooney, David J; Pigula, Frank A; Walsh, Conor J

    2017-01-18

    There is much interest in form-fitting, low-modulus, implantable devices or soft robots that can mimic or assist in complex biological functions such as the contraction of heart muscle. We present a soft robotic sleeve that is implanted around the heart and actively compresses and twists to act as a cardiac ventricular assist device. The sleeve does not contact blood, obviating the need for anticoagulation therapy or blood thinners, and reduces complications with current ventricular assist devices, such as clotting and infection. Our approach used a biologically inspired design to orient individual contracting elements or actuators in a layered helical and circumferential fashion, mimicking the orientation of the outer two muscle layers of the mammalian heart. The resulting implantable soft robot mimicked the form and function of the native heart, with a stiffness value of the same order of magnitude as that of the heart tissue. We demonstrated feasibility of this soft sleeve device for supporting heart function in a porcine model of acute heart failure. The soft robotic sleeve can be customized to patient-specific needs and may have the potential to act as a bridge to transplant for patients with heart failure. Copyright © 2017, American Association for the Advancement of Science.

  8. Comparing function and structure between entire proteomes

    PubMed Central

    Liu, Jinfeng; Rost, Burkhard

    2001-01-01

    More than 30 organisms have been sequenced entirely. Here, we applied a variety of simple bioinformatics tools to analyze 29 proteomes for representatives from all three kingdoms: eukaryotes, prokaryotes, and archaebacteria. We confirmed that eukaryotes have relatively more long proteins than prokaryotes and archaes, and that the overall amino acid composition is similar among the three. We predicted that ∼15%–30% of all proteins contained transmembrane helices. We could not find a correlation between the content of membrane proteins and the complexity of the organism. In particular, we did not find significantly higher percentages of helical membrane proteins in eukaryotes than in prokaryotes or archae. However, we found more proteins with seven transmembrane helices in eukaryotes and more with six and 12 transmembrane helices in prokaryotes. We found twice as many coiled-coil proteins in eukaryotes (10%) as in prokaryotes and archaes (4%–5%), and we predicted ∼15%–25% of all proteins to be secreted by most eukaryotes and prokaryotes. Every tenth protein had no known homolog in current databases, and 30%–40% of the proteins fell into structural families with >100 members. A classification by cellular function verified that eukaryotes have a higher proportion of proteins for communication with the environment. Finally, we found at least one homolog of experimentally known structure for ∼20%–45% of all proteins; the regions with structural homology covered 20%–30% of all residues. These numbers may or may not suggest that there are 1200–2600 folds in the universe of protein structures. All predictions are available at http://cubic.bioc.columbia.edu/genomes. PMID:11567088

  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. Comparative analyses of nuclear proteome: extending its function.

    PubMed

    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.

  11. Bead Based Proteome Enrichment Enhances Features of the Protein Elution Plate (PEP) for Functional Proteomic Profiling

    PubMed Central

    Wang, Xing; Davies, Michael; Roy, Swapan; Kuruc, Matthew

    2015-01-01

    A novel functional proteomics technology called PEP(Protein Elution Plate) was developed to separate complex proteomes from natural sources and analyze protein functions systematically. The technology takes advantage of the powerful resolution of two-dimensional gel electrophoresis (2-D Gels). The modification of electrophoretic conditions in combination with a high-resolution protein elution plate supports the recovery of functionally active proteins. As 2DE(2-Dimensional Electrophoresis) resolution can be limited by protein load, we investigated the use of bead based enrichment technologies, called AlbuVoid™ and KinaSorb™ to determine their effect on the proteomic features which can be generated from the PEP platform. Using a variety of substrates and enzyme activity assays, we report on the benefits of combining bead based enrichment to improve the signal report and the features generated for Hexokinase, Protein Kinase, Protease, and Alkaline Phosphatase activities. As a result, the PEP technology allows systematic analysis of large enzyme families and can build a comprehensive picture of protein function from a complex proteome, providing biological insights that could otherwise not be observed if only protein abundances were analyzed. PMID:28248280

  12. Cancer heterogeneity determined by functional proteomics.

    PubMed

    Szász, A Marcell; Győrffy, Balázs; Marko-Varga, György

    2016-08-26

    Current manuscript gives a synopsis of tumor heterogeneity related to patient samples analyzed by proteomics, protein expression analysis and imaging mass spectrometry. First, we discuss the pathophysiologocal background of cancer biology as a multifactorial and challenging diseases. Disease pathology forms the basis for protein target selection. Therefore, histopathological diagnostics and grading of tumors is highlighted. Pathology is the cornerstone of state-of-the-art diagnostics of tumors today both by establishing dignity and - when needed - describing molecular properties of the cancers. Drug development by the pharmaceutical industry utilizes proteomics studies to pinpoint the most relevant targets. Molecular studies profiling affinity-interactions of the protein(s) with targeted small drug molecules to reach efficacy and optimal patient safety are today requested by the FDA and other agencies for new drug development. An understading of basic mechanisms, controlling drug action and drug binding is central, as a new era of personalized medicine becomes an important milestone solution for the healthcare sector as well as the Pharma and Biotech industry. Development of further diagnostic, prognostic and predictive tests will aid current and future treatment of cancer patients. In the paper we present current status of Proteomics that we believe requires attention in order to collectively advance forward in the fight against cancer, addressing the burning opportunities and challenges.

  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. 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. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  15. 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.

  16. Plant organelle proteomics: collaborating for optimal cell function.

    PubMed

    Agrawal, Ganesh Kumar; Bourguignon, Jacques; Rolland, Norbert; Ephritikhine, Geneviève; Ferro, Myriam; Jaquinod, Michel; Alexiou, Konstantinos G; Chardot, Thierry; Chakraborty, Niranjan; Jolivet, Pascale; Doonan, John H; Rakwal, Randeep

    2011-01-01

    Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in

  17. Association between the seminal plasma proteome and sperm functional traits.

    PubMed

    Intasqui, Paula; Camargo, Mariana; Antoniassi, Mariana Pereira; Cedenho, Agnaldo Pereira; Carvalho, Valdemir Melechco; Cardozo, Karina Helena Morais; Zylbersztejn, Daniel Suslik; Bertolla, Ricardo Pimenta

    2016-03-01

    To analyze the seminal plasma proteome and biological functions associated with sperm functional alterations. Cross-sectional study. University andrology and research laboratories. A total of 156 normozoospermic men. Sperm mitochondrial activity, acrosome integrity, and DNA fragmentation were evaluated in a semen aliquot. Remaining semen was centrifuged, and seminal plasma was utilized for proteomic analysis (liquid chromatography-tandem mass spectrometry). Patients were divided into percentiles (15%) to form the following groups: substudy 1, high (control, n = 26) and low (study, n = 23) sperm mitochondrial activity; substudy 2, high (control, n = 23) and low (study, n = 22) sperm acrosome integrity; and substudy 3, low (control, n = 22) and high (study, n = 22) sperm DNA fragmentation. Groups were compared using univariate and multivariate analyses. Differentially expressed proteins were used for functional enrichment analysis. Seminal plasma proteome and postgenomic pathways are associated with several sperm functional traits. In total, 506, 493, and 464 proteins were observed in substudies 1, 2, and 3, respectively. Enriched functions in substudy 1 were intramolecular oxidoreductase activity, aminoglycans catabolism, endopeptidases inhibition, lysosomes, and acute-phase response (study group). In substudy 2, main enriched functions were phospholipase inhibition, arachidonic acid metabolism, exocytosis, regulation of acute inflammation, response to hydrogen peroxide, and lysosomal transport (study group). In substudy 3, enriched functions were prostaglandin biosynthesis and fatty acid binding (study group). We proposed eight, six, and eight seminal biomarkers for substudies 1, 2, and 3, respectively. Seminal plasma proteome reflects sperm mitochondrial activity reduction, acrosome damage, and DNA fragmentation, with several postgenomic functions related to these alterations. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc

  18. Robotic approaches for rehabilitation of hand function after stroke.

    PubMed

    Lum, Peter S; Godfrey, Sasha B; Brokaw, Elizabeth B; Holley, Rahsaan J; Nichols, Diane

    2012-11-01

    The goal of this review was to discuss the impairments in hand function after stroke and present previous work on robot-assisted approaches to movement neurorehabilitation. Robotic devices offer a unique training environment that may enhance outcomes beyond what is possible with conventional means. Robots apply forces to the hand, allowing completion of movements while preventing inappropriate movement patterns. Evidence from the literature is emerging that certain characteristics of the human-robot interaction are preferable. In light of this evidence, the robotic hand devices that have undergone clinical testing are reviewed, highlighting the authors' work in this area. Finally, suggestions for future work are offered. The ability to deliver therapy doses far higher than what has been previously tested is a potentially key advantage of robotic devices that needs further exploration. In particular, more efforts are needed to develop highly motivating home-based devices, which can increase access to high doses of assisted movement therapy.

  19. Proteomic profiling of high risk medulloblastoma reveals functional biology

    PubMed Central

    Staal, Jerome A.; Lau, Ling San; Zhang, Huizhen; Ingram, Wendy J.; Hallahan, Andrew R.; Northcott, Paul A.; Pfister, Stefan M.; Wechsler-Reya, Robert J.; Rusert, Jessica M.; Taylor, Michael D.; Cho, Yoon-Jae; Packer, Roger J.; Brown, Kristy J.; Rood, Brian R.

    2015-01-01

    Genomic characterization of medulloblastoma has improved molecular risk classification but struggles to define functional biological processes, particularly for the most aggressive subgroups. We present here a novel proteomic approach to this problem using a reference library of stable isotope labeled medulloblastoma-specific proteins as a spike-in standard for accurate quantification of the tumor proteome. Utilizing high-resolution mass spectrometry, we quantified the tumor proteome of group 3 medulloblastoma cells and demonstrate that high-risk MYC amplified tumors can be segregated based on protein expression patterns. We cross-validated the differentially expressed protein candidates using an independent transcriptomic data set and further confirmed them in a separate cohort of medulloblastoma tissue samples to identify the most robust proteogenomic differences. Interestingly, highly expressed proteins associated with MYC-amplified tumors were significantly related to glycolytic metabolic pathways via alternative splicing of pyruvate kinase (PKM) by heterogeneous ribonucleoproteins (HNRNPs). Furthermore, when maintained under hypoxic conditions, these MYC-amplified tumors demonstrated increased viability compared to non-amplified tumors within the same subgroup. Taken together, these findings highlight the power of proteomics as an integrative platform to help prioritize genetic and molecular drivers of cancer biology and behavior. PMID:25970789

  20. Proteomic profiling of high risk medulloblastoma reveals functional biology.

    PubMed

    Staal, Jerome A; Lau, Ling San; Zhang, Huizhen; Ingram, Wendy J; Hallahan, Andrew R; Northcott, Paul A; Pfister, Stefan M; Wechsler-Reya, Robert J; Rusert, Jessica M; Taylor, Michael D; Cho, Yoon-Jae; Packer, Roger J; Brown, Kristy J; Rood, Brian R

    2015-06-10

    Genomic characterization of medulloblastoma has improved molecular risk classification but struggles to define functional biological processes, particularly for the most aggressive subgroups. We present here a novel proteomic approach to this problem using a reference library of stable isotope labeled medulloblastoma-specific proteins as a spike-in standard for accurate quantification of the tumor proteome. Utilizing high-resolution mass spectrometry, we quantified the tumor proteome of group 3 medulloblastoma cells and demonstrate that high-risk MYC amplified tumors can be segregated based on protein expression patterns. We cross-validated the differentially expressed protein candidates using an independent transcriptomic data set and further confirmed them in a separate cohort of medulloblastoma tissue samples to identify the most robust proteogenomic differences. Interestingly, highly expressed proteins associated with MYC-amplified tumors were significantly related to glycolytic metabolic pathways via alternative splicing of pyruvate kinase (PKM) by heterogeneous ribonucleoproteins (HNRNPs). Furthermore, when maintained under hypoxic conditions, these MYC-amplified tumors demonstrated increased viability compared to non-amplified tumors within the same subgroup. Taken together, these findings highlight the power of proteomics as an integrative platform to help prioritize genetic and molecular drivers of cancer biology and behavior.

  1. Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

    PubMed

    Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

    2017-06-23

    The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

  2. 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. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Characterization of Robotic Tail Orientation as a Function of Platform Position for Surf-Zone Robots

    DTIC Science & Technology

    2009-06-01

    34 x Figure 29. Robot Pitch and Tail Angle..............................................................................35 Figure 30. Dynamic...greater vertical reach for its legs and prevents high centering off the obstacle during a climb by bending the front half of its body down. 2. Early...body flexion function of the DAGSI Whegs™ by acting as a foot during climbing, preventing the robot from high -centering and falling back off of

  4. 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

  5. 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

  6. Temporal changes in milk proteomes reveal developing milk functions.

    PubMed

    Gao, Xinliu; McMahon, Robert J; Woo, Jessica G; Davidson, Barbara S; Morrow, Ardythe L; Zhang, Qiang

    2012-07-06

    Human milk proteins provide essential nutrition for growth and development, and support a number of vital developmental processes in the neonate. A complete understanding of the possible functions of human milk proteins has been limited by incomplete knowledge of the human milk proteome. In this report, we have analyzed the proteomes of whey from human transitional and mature milk using ion-exchange and SDS-PAGE based protein fractionation methods. With a larger-than-normal sample loading approach, we are able to largely extend human milk proteome to 976 proteins. Among them, 152 proteins are found to render significant regulatory changes between transitional milk and mature milk. We further found that immunoglobulins sIgA and IgM are more abundant in transitional milk, whereas IgG is more abundant in mature milk, suggesting a transformation in defense mechanism from newborns to young infants. Additionally, we report a more comprehensive view of a complement system and associated regulatory apparatus in human milk, demonstrating the presence and function of a system similar to that found in the circulation but prevailed by alternative pathway in complement activation. Proteins involved in various aspects of carbohydrate metabolism are also described, revealing either a transition in milk functionality to accommodate carbohydrate-rich secretions as lactation progresses, or a potentially novel way of looking at the metabolic state of the mammary tissue. Lately, a number of extracellular matrix (ECM) proteins are found to be in higher abundance in transitional milk and may be relevant to the development of infants' gastrointestinal tract in early life. In contrast, the ECM protein fibronectin and several of the actin cytoskeleton proteins that it regulates are more abundant in mature milk, which may indicate the important functional role for milk in regulating reactive oxygen species.

  7. Quantitative reactivity profiling predicts functional cysteines in proteomes

    PubMed Central

    Weerapana, Eranthie; Wang, Chu; Simon, Gabriel M.; Richter, Florian; Khare, Sagar; Dillon, Myles B.D.; Bachovchin, Daniel A.; Mowen, Kerri; Baker, David; Cravatt, Benjamin F.

    2010-01-01

    Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here, we describe a proteomics method to quantitatively profile the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyperreactivity was a rare feature among cysteines and found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyperreactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and involved in iron-sulfur protein biogenesis. Finally, we demonstrate that quantitative reactivity profiling can also form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs. PMID:21085121

  8. 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

    2016-08-02

    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.

  9. Medulloblastoma Exosome Proteomics Yield Functional Roles for Extracellular Vesicles

    PubMed Central

    Epple, Laura M.; Griffiths, Steve G.; Dechkovskaia, Anjelika M.; Dusto, Nathaniel L.; White, Jason; Ouellette, Rodney J.; Anchordoquy, Thomas J.; Bemis, Lynne T.; Graner, Michael W.

    2012-01-01

    Medulloblastomas are the most prevalent malignant pediatric brain tumors. Survival for these patients has remained largely the same for approximately 20 years, and our therapies for these cancers cause significant health, cognitive, behavioral and developmental sequelae for those who survive the tumor and their treatments. We obviously need a better understanding of the biology of these tumors, particularly with regard to their migratory/invasive behaviors, their proliferative propensity, and their abilities to deflect immune responses. Exosomes, virus-sized membrane vesicles released extracellularly from cells after formation in, and transit thru, the endosomal pathway, may play roles in medulloblastoma pathogenesis but are as yet unstudied in this disease. Here we characterized exosomes from a medulloblastoma cell line with biochemical and proteomic analyses, and included characterization of patient serum exosomes. Further scrutiny of the proteomic data suggested functional properties of the exosomes that are relevant to medulloblastoma tumor biology, including their roles as proliferation stimulants, their activities as attractants for tumor cell migration, and their immune modulatory impacts on lymphocytes. Aspects of this held true for exosomes from other medulloblastoma cell lines as well. Additionally, pathway analyses suggested a possible role for the transcription factor hepatocyte nuclear factor 4 alpha (HNF4A); however, inhibition of the protein’s activity actually increased D283MED cell proliferation/clonogenecity, suggesting that HNF4A may act as a tumor suppressor in this cell line. Our work demonstrates that relevant functional properties of exosomes may be derived from appropriate proteomic analyses, which translate into mechanisms of tumor pathophysiology harbored in these extracellular vesicles. PMID:22848702

  10. Adapting a Robot Hand to Specialized Functions

    NASA Technical Reports Server (NTRS)

    Clark, Keith H.

    1987-01-01

    Adaptor enables mechanical and electrical connections made easily between special-purpose end effector and arm of robot or remote mainpulator. Use in prosthetic devices also contemplatd. With adaptor, hand changed quickly from device designed to grasp objects of various sizes and shapes to device intended to do specific task efficiently.

  11. Adapting a Robot Hand to Specialized Functions

    NASA Technical Reports Server (NTRS)

    Clark, Keith H.

    1987-01-01

    Adaptor enables mechanical and electrical connections made easily between special-purpose end effector and arm of robot or remote mainpulator. Use in prosthetic devices also contemplatd. With adaptor, hand changed quickly from device designed to grasp objects of various sizes and shapes to device intended to do specific task efficiently.

  12. Comprehensive Proteomic Analysis of Human Milk-derived Extracellular Vesicles Unveils a Novel Functional Proteome Distinct from Other Milk Components.

    PubMed

    van Herwijnen, Martijn J C; Zonneveld, Marijke I; Goerdayal, Soenita; Nolte-'t Hoen, Esther N M; Garssen, Johan; Stahl, Bernd; Maarten Altelaar, A F; Redegeld, Frank A; Wauben, Marca H M

    2016-11-01

    Breast milk contains several macromolecular components with distinctive functions, whereby milk fat globules and casein micelles mainly provide nutrition to the newborn, and whey contains molecules that can stimulate the newborn's developing immune system and gastrointestinal tract. Although extracellular vesicles (EV) have been identified in breast milk, their physiological function and composition has not been addressed in detail. EV are submicron sized vehicles released by cells for intercellular communication via selectively incorporated lipids, nucleic acids, and proteins. Because of the difficulty in separating EV from other milk components, an in-depth analysis of the proteome of human milk-derived EV is lacking. In this study, an extensive LC-MS/MS proteomic analysis was performed of EV that had been purified from breast milk of seven individual donors using a recently established, optimized density-gradient-based EV isolation protocol. A total of 1963 proteins were identified in milk-derived EV, including EV-associated proteins like CD9, Annexin A5, and Flotillin-1, with a remarkable overlap between the different donors. Interestingly, 198 of the identified proteins are not present in the human EV database Vesiclepedia, indicating that milk-derived EV harbor proteins not yet identified in EV of different origin. Similarly, the proteome of milk-derived EV was compared with that of other milk components. For this, data from 38 published milk proteomic studies were combined in order to construct the total milk proteome, which consists of 2698 unique proteins. Remarkably, 633 proteins identified in milk-derived EV have not yet been identified in human milk to date. Interestingly, these novel proteins include proteins involved in regulation of cell growth and controlling inflammatory signaling pathways, suggesting that milk-derived EVs could support the newborn's developing gastrointestinal tract and immune system. Overall, this study provides an expansion of

  13. 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)

  14. 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)

  15. Single-cell-type Proteomics: Toward a Holistic Understanding of Plant Function*

    PubMed Central

    Dai, Shaojun; Chen, Sixue

    2012-01-01

    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. PMID:22982375

  16. 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.

  17. Active robotic training improves locomotor function in a stroke survivor.

    PubMed

    Krishnan, Chandramouli; Ranganathan, Rajiv; Kantak, Shailesh S; Dhaher, Yasin Y; Rymer, William Z

    2012-08-20

    Clinical outcomes after robotic training are often not superior to conventional therapy. One key factor responsible for this is the use of control strategies that provide substantial guidance. This strategy not only leads to a reduction in volitional physical effort, but also interferes with motor relearning. We tested the feasibility of a novel training approach (active robotic training) using a powered gait orthosis (Lokomat) in mitigating post-stroke gait impairments of a 52-year-old male stroke survivor. This gait training paradigm combined patient-cooperative robot-aided walking with a target-tracking task. The training lasted for 4-weeks (12 visits, 3 × per week). The subject's neuromotor performance and recovery were evaluated using biomechanical, neuromuscular and clinical measures recorded at various time-points (pre-training, post-training, and 6-weeks after training). Active robotic training resulted in considerable increase in target-tracking accuracy and reduction in the kinematic variability of ankle trajectory during robot-aided treadmill walking. These improvements also transferred to overground walking as characterized by larger propulsive forces and more symmetric ground reaction forces (GRFs). Training also resulted in improvements in muscle coordination, which resembled patterns observed in healthy controls. These changes were accompanied by a reduction in motor cortical excitability (MCE) of the vastus medialis, medial hamstrings, and gluteus medius muscles during treadmill walking. Importantly, active robotic training resulted in substantial improvements in several standard clinical and functional parameters. These improvements persisted during the follow-up evaluation at 6 weeks. The results indicate that active robotic training appears to be a promising way of facilitating gait and physical function in moderately impaired stroke survivors.

  18. 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.

  19. 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.

  20. The application of proteomic approaches to the study of mammalian spermatogenesis and sperm function.

    PubMed

    Macleod, Graham; Varmuza, Susannah

    2013-11-01

    Spermatogenesis is the process by which terminally differentiated sperm are produced from male germline stem cells. This complex developmental process requires the coordination of both somatic and germ cells through phases of proliferation, meiosis, and morphological differentiation, to produce the cell responsible for the delivery of the paternal genome. With infertility affecting ~ 15% of all couples, furthering our understanding of spermatogenesis and sperm function is vital for improving the diagnosis and treatment of male factor infertility. The emerging use of proteomic technologies has played an instrumental role in our understanding of spermatogenesis by providing information regarding the genes involved. This article reviews existing proteomic literature regarding spermatogenesis and sperm function, including the proteomic characterization of spermatogenic cell types, subcellular proteomics, post-translational modifications, interactomes, and clinical studies. Future directions in the application of proteomics to the study of spermatogenesis and sperm function are also discussed.

  1. Project management system for structural and functional proteomics: Sesame.

    PubMed

    Zolnai, Zsolt; Lee, Peter T; Li, Jing; Chapman, Michael R; Newman, Craig S; Phillips, George N; Rayment, Ivan; Ulrich, Eldon L; Volkman, Brian F; Markley, John L

    2003-01-01

    A computing infrastructure (Sesame) has been designed to manage and link individual steps in complex projects. Sesame is being developed to support a large-scale structural proteomics pilot project. When complete, the system is expected to manage all steps from target selection to data-bank deposition and report writing. We report here on the design criteria of the Sesame system and on results demonstrating successful achievement of the basic goals of its architecture. The Sesame software package, which follows the client/server paradigm, consists of a framework, which supports secure interactions among the three tiers of the system (the client, server, and database tiers), and application modules that carry out specific tasks. The framework utilizes industry standards. The client tier is written in Java2 and can be accessed anywhere through the Internet. All the development on the server tier is also carried out in Java2 so as to accommodate a wide variety of computer platforms. The database tier employs a commercial database management system. Each Sesame application module consists of a simple user interface in the client tier, corresponding objects in the server tier, and relevant data stored in the centralized database. For security, access to stored data is controlled by access privileges. The system facilitates both local and remote collaborations. Because users interact with the system using Java Web Start or through a web browser, access is limited only by the availability of an Internet connection. We describe several Sesame modules that have been developed to the point where they are being utilized routinely to support steps involved in structural and functional proteomics. This software is available to parties interested in using it and assisting to guide its further development.

  2. Functional Complexity of the Axonal Growth Cone: A Proteomic Analysis

    PubMed Central

    Estrada-Bernal, Adriana; Sanford, Staci D.; Sosa, Lucas J.; Simon, Glenn C.; Hansen, Kirk C.; Pfenninger, Karl H.

    2012-01-01

    The growth cone, the tip of the emerging neurite, plays a crucial role in establishing the wiring of the developing nervous system. We performed an extensive proteomic analysis of axonal growth cones isolated from the brains of fetal Sprague-Dawley rats. Approximately 2000 proteins were identified at ≥99% confidence level. Using informatics, including functional annotation cluster and KEGG pathway analysis, we found great diversity of proteins involved in axonal pathfinding, cytoskeletal remodeling, vesicular traffic and carbohydrate metabolism, as expected. We also found a large and complex array of proteins involved in translation, protein folding, posttranslational processing, and proteasome/ubiquitination-dependent degradation. Immunofluorescence studies performed on hippocampal neurons in culture confirmed the presence in the axonal growth cone of proteins representative of these processes. These analyses also provide evidence for rough endoplasmic reticulum and reveal a reticular structure equipped with Golgi-like functions in the axonal growth cone. Furthermore, Western blot revealed the growth cone enrichment, relative to fetal brain homogenate, of some of the proteins involved in protein synthesis, folding and catabolism. Our study provides a resource for further research and amplifies the relatively recently developed concept that the axonal growth cone is equipped with proteins capable of performing a highly diverse range of functions. PMID:22384089

  3. A computational interactome and functional annotation for the human proteome

    PubMed Central

    Garzón, José Ignacio; Deng, Lei; Murray, Diana; Shapira, Sagi; Petrey, Donald; Honig, Barry

    2016-01-01

    We present a database, PrePPI (Predicting Protein-Protein Interactions), of more than 1.35 million predicted protein-protein interactions (PPIs). Of these at least 127,000 are expected to constitute direct physical interactions although the actual number may be much larger (~500,000). The current PrePPI, which contains predicted interactions for about 85% of the human proteome, is related to an earlier version but is based on additional sources of interaction evidence and is far larger in scope. The use of structural relationships allows PrePPI to infer numerous previously unreported interactions. PrePPI has been subjected to a series of validation tests including reproducing known interactions, recapitulating multi-protein complexes, analysis of disease associated SNPs, and identifying functional relationships between interacting proteins. We show, using Gene Set Enrichment Analysis (GSEA), that predicted interaction partners can be used to annotate a protein’s function. We provide annotations for most human proteins, including many annotated as having unknown function. DOI: http://dx.doi.org/10.7554/eLife.18715.001 PMID:27770567

  4. Reducing robotic guidance during robot-assisted gait training improves gait function: a case report on a stroke survivor.

    PubMed

    Krishnan, Chandramouli; Kotsapouikis, Despina; Dhaher, Yasin Y; Rymer, William Z

    2013-06-01

    To test the feasibility of patient-cooperative robotic gait training for improving locomotor function of a chronic stroke survivor with severe lower-extremity motor impairments. Single-subject crossover design. Performed in a controlled laboratory setting. A 62-year-old man with right temporal lobe ischemic stroke was recruited for this study. The baseline lower-extremity Fugl-Meyer score of the subject was 10 on a scale of 34, which represented severe impairment in the paretic leg. However, the subject had a good ambulation level (community walker with the aid of a stick cane and ankle-foot orthosis) and showed no signs of sensory or cognitive impairments. The subject underwent 12 sessions (3 times per week for 4wk) of conventional robotic training with the Lokomat, where the robot provided full assistance to leg movements while walking, followed by 12 sessions (3 times per week for 4wk) of patient-cooperative robotic control training, where the robot provided minimal guidance to leg movements during walking. Clinical outcomes were evaluated before the start of the intervention, immediately after 4 weeks of conventional robotic training, and immediately after 4 weeks of cooperative control robotic training. These included: (1) self-selected and fast walking speed, (2) 6-minute walk test, (3) Timed Up & Go test, and (4) lower-extremity Fugl-Meyer score. Results showed that clinical outcomes changed minimally after full guidance robotic training, but improved considerably after 4 weeks of reduced guidance robotic training. The findings from this case study suggest that cooperative control robotic training is superior to conventional robotic training and is a feasible option to restoring locomotor function in ambulatory stroke survivors with severe motor impairments. A larger trial is needed to verify the efficacy of this advanced robotic control strategy in facilitating gait recovery after stroke. Copyright © 2013 American Congress of Rehabilitation Medicine

  5. Locomotor Sub-functions for Control of Assistive Wearable Robots.

    PubMed

    Sharbafi, Maziar A; Seyfarth, Andre; Zhao, Guoping

    2017-01-01

    A primary goal of comparative biomechanics is to understand the fundamental physics of locomotion within an evolutionary context. Such an understanding of legged locomotion results in a transition from copying nature to borrowing strategies for interacting with the physical world regarding design and control of bio-inspired legged robots or robotic assistive devices. Inspired from nature, legged locomotion can be composed of three locomotor sub-functions, which are intrinsically interrelated: Stance: redirecting the center of mass by exerting forces on the ground. Swing: cycling the legs between ground contacts. Balance: maintaining body posture. With these three sub-functions, one can understand, design and control legged locomotory systems with formulating them in simpler separated tasks. Coordination between locomotor sub-functions in a harmonized manner appears then as an additional problem when considering legged locomotion. However, biological locomotion shows that appropriate design and control of each sub-function simplifies coordination. It means that only limited exchange of sensory information between the different locomotor sub-function controllers is required enabling the envisioned modular architecture of the locomotion control system. In this paper, we present different studies on implementing different locomotor sub-function controllers on models, robots, and an exoskeleton in addition to demonstrating their abilities in explaining humans' control strategies.

  6. Locomotor Sub-functions for Control of Assistive Wearable Robots

    PubMed Central

    Sharbafi, Maziar A.; Seyfarth, Andre; Zhao, Guoping

    2017-01-01

    A primary goal of comparative biomechanics is to understand the fundamental physics of locomotion within an evolutionary context. Such an understanding of legged locomotion results in a transition from copying nature to borrowing strategies for interacting with the physical world regarding design and control of bio-inspired legged robots or robotic assistive devices. Inspired from nature, legged locomotion can be composed of three locomotor sub-functions, which are intrinsically interrelated: Stance: redirecting the center of mass by exerting forces on the ground. Swing: cycling the legs between ground contacts. Balance: maintaining body posture. With these three sub-functions, one can understand, design and control legged locomotory systems with formulating them in simpler separated tasks. Coordination between locomotor sub-functions in a harmonized manner appears then as an additional problem when considering legged locomotion. However, biological locomotion shows that appropriate design and control of each sub-function simplifies coordination. It means that only limited exchange of sensory information between the different locomotor sub-function controllers is required enabling the envisioned modular architecture of the locomotion control system. In this paper, we present different studies on implementing different locomotor sub-function controllers on models, robots, and an exoskeleton in addition to demonstrating their abilities in explaining humans' control strategies. PMID:28928650

  7. Robotics

    SciTech Connect

    Scheide, A.W.

    1983-11-01

    This article reviews some of the technical areas and history associated with robotics, provides information relative to the formation of a Robotics Industry Committee within the Industry Applications Society (IAS), and describes how all activities relating to robotics will be coordinated within the IEEE. Industrial robots are being used for material handling, processes such as coating and arc welding, and some mechanical and electronics assembly. An industrial robot is defined as a programmable, multifunctional manipulator designed to move material, parts, tools, or specialized devices through variable programmed motions for a variety of tasks. The initial focus of the Robotics Industry Committee will be on the application of robotics systems to the various industries that are represented within the IAS.

  8. Robotic Characterization of Ipsilesional Motor Function in Subacute Stroke.

    PubMed

    Semrau, Jennifer A; Herter, Troy M; Kenzie, Jeffrey M; Findlater, Sonja E; Scott, Stephen H; Dukelow, Sean P

    2017-06-01

    Poststroke impairments of the ipsilesional arm are often discussed, but rarely receive focused rehabilitation. Ipsilesional deficits may affect daily function and although many studies have investigated them in chronic stroke, few characterizations have been made in the subacute phase. Furthermore, most studies have quantified ipsilesional deficits using clinical measures that can fail to detect subtle, but important deficits in motor function. We aimed to quantify reaching deficits of the contra- and ipsilesional limbs in the subacute phase poststroke. A total of 227 subjects with first-time, unilateral stroke completed a unilateral assessment of motor function (visually guided reaching) using a KINARM robot. Subjects completed the task with both the ipsi- and contralesional arms. Subjects were assessed on a variety of traditional clinical measures (Functional Independence Measure, Chedoke-McMaster Stroke Assessment, Purdue Pegboard, Behavioral Inattention Test) to compare with robotic measures of motor function. Ipsilesional deficits were common and occurred in 37% (n = 84) of subjects. Impairments of the ipsilesional and contralesional arm were weakly to moderately correlated on robotic measures. Magnitude of impairment of the contralesional arm was similar for subjects with and without ipsilesional deficits. Furthermore, we found that a higher percentage of subjects with right-hemisphere stroke had ipsilesional deficits and more subjects with left-hemisphere subcortical strokes did not have ipsilesional deficits. Magnitude of contralesional impairment and lesion location may be poor predictors of individuals with ipsilesional impairments after stroke. Careful characterization of ipsilesional deficits could identify individuals who may benefit from rehabilitation of the less affected arm.

  9. Prospective cohort study of bowel function after robotic sacrocolpopexy.

    PubMed

    Lewis, Christa; Salamon, Charbel; Priestley, Jennifer L; Gurshumov, Emil; Culligan, Patrick

    2014-01-01

    This study aimed to determine bowel function changes 12 months after robotic sacrocolpopexy. We performed a single-center prospective cohort study evaluating bowel function 12 months after robotic sacrocolpopexy between 2007 and 2011. Bowel function symptoms were measured by the Colorectal-Anal Distress Inventory, Short Form 8 (CRADI-8). Specific impacts on quality of life with regard to bowel function were evaluated using the Colorectal-Anal Impact Questionnaire, Short Form 7 (CRAIQ-7). "Splinting to defecate" was defined as any positive response to question 4 of the Pelvic Floor Distress Inventory-20 which reads, "do you ever have to push on the vagina or around the rectum to have or complete a bowel movement?." Lastly, patients were grouped according to perineorrhaphy versus no perineorrhaphy and bowel function scores were examined. Of 423 consecutive patients who underwent robotic sacrocolpopexy at our institution, 393 (93%) completed a 12-month follow-up. Mean CRADI-8 scores at baseline and 12 months were 21.1 (20) and 7.3 (11), respectively (P < 0.0001). Mean CRAIQ-7 scores at baseline and 12 months were 11.1 (20) and 2.4 (9), respectively (P < 0.0001). Preoperatively, 152 patients reported a need to splint the vagina or perineum to complete a bowel movement. At 12 months, 70% reported complete resolution of "splinting." Con comitant perineorrhaphy was performed on 87 patients and there were no differences in 12-month CRADI-8 or CRAIQ-7 scores between groups. Robotic sacrocolpopexy was associated with significant improvements in bowel function as measured by CRADI-8 as well as improvements in impact on quality of life as measured by CRAIQ-7.

  10. Comparative Proteomics of Mouse Tears and Saliva: Evidence from Large Protein Families for Functional Adaptation

    PubMed Central

    Karn, Robert C.; Laukaitis, Christina M.

    2015-01-01

    We produced a tear proteome of the genome mouse, C57BL/6, that contained 139 different protein identifications: 110 from a two-dimensional (2D) gel with subsequent trypsin digestion, 19 from a one-dimensional (1D) gel with subsequent trypsin digestion and ten from a 1D gel with subsequent Asp-N digestion. We compared this tear proteome with a C57BL/6 mouse saliva proteome produced previously. Sixteen of the 139 tear proteins are shared between the two proteomes, including six proteins that combat microbial growth. Among the 123 other tear proteins, were members of four large protein families that have no counterparts in humans: Androgen-binding proteins (ABPs) with different members expressed in the two proteomes, Exocrine secreted peptides (ESPs) expressed exclusively in the tear proteome, major urinary proteins (MUPs) expressed in one or both proteomes and the mouse-specific Kallikreins (subfamily b KLKs) expressed exclusively in the saliva proteome. All four families have members with suggested roles in mouse communication, which may influence some aspect of reproductive behavior. We discuss this in the context of functional adaptation involving tear and saliva proteins in the secretions of mouse lacrimal and salivary glands, respectively.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  12. 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.

  13. Validity of Robot-Based Assessments of Upper Extremity Function.

    PubMed

    McKenzie, Alison; Dodakian, Lucy; See, Jill; Le, Vu; Quinlan, Erin Burke; Bridgford, Claire; Head, Daniel; Han, Vy L; Cramer, Steven C

    2017-10-01

    To examine the validity of 5 robot-based assessments of arm motor function poststroke. Cross-sectional study. Outpatient clinical research center. Volunteer sample of participants (N=40; age, >18y; 3-6mo poststroke) with arm motor deficits that had reached a stable plateau. Not applicable. Clinical standards included the arm motor domain of the Fugl-Meyer Assessment (FMA) and 5 secondary motor outcomes: hand/wrist subsection of the arm motor domain of the FMA, Action Research Arm Test, Box and Block test (BBT), hand motor subscale of the Stroke Impact Scale Version 2.0, and Barthel Index. Robot-based assessments included wrist targeting, finger targeting, finger movement speed, reaction time, and a robotic version of the BBT. Anatomical measures included percent injury to the corticospinal tract (CST) and extent of injury of the hand region of the primary motor cortex obtained from magnetic resonance imaging. Participants had moderate to severe impairment (arm motor domain of the FMA scores, 35.6±14.4; range, 13.5-60). Performance on the robot-based tests, including speed (r=.82; P<.0001), wrist targeting (r=.72; P<.0001), and finger targeting (r=.67; P<.0001), correlated significantly with the arm motor domain of the FMA scores. Wrist targeting (r=.57-.82) and finger targeting (r=.49-.68) correlated significantly with all 5 secondary motor outcomes and with percent CST injury. The robotic version of the BBT correlated significantly with the clinical BBT but was less prone to floor effects. Robot-based assessments were comparable to the arm motor domain of the FMA score in relation to percent CST injury and superior in relation to extent of injury to the hand region of the primary motor cortex. The present findings support using a battery of robot-based methods for assessing the upper extremity motor function in participants with chronic stroke. Copyright © 2017 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  14. Effect of a human-type communication robot on cognitive function in elderly women living alone.

    PubMed

    Tanaka, Masaaki; Ishii, Akira; Yamano, Emi; Ogikubo, Hiroki; Okazaki, Masatsugu; Kamimura, Kazuro; Konishi, Yasuharu; Emoto, Shigeru; Watanabe, Yasuyoshi

    2012-09-01

    Considering the high prevalence of dementia, it would be of great value to develop effective tools to improve cognitive function. We examined the effects of a human-type communication robot on cognitive function in elderly women living alone. In this study, 34 healthy elderly female volunteers living alone were randomized to living with either a communication robot or a control robot at home for 8 weeks. The shape, voice, and motion features of the communication robot resemble those of a 3-year-old boy, while the control robot was not designed to talk or nod. Before living with the robot and 4 and 8 weeks after living with the robot, experiments were conducted to evaluate a variety of cognitive functions as well as saliva cortisol, sleep, and subjective fatigue, motivation, and healing. The Mini-Mental State Examination score, judgement, and verbal memory function were improved after living with the communication robot; those functions were not altered with the control robot. In addition, the saliva cortisol level was decreased, nocturnal sleeping hours tended to increase, and difficulty in maintaining sleep tended to decrease with the communication robot, although alterations were not shown with the control. The proportions of the participants in whom effects on attenuation of fatigue, enhancement of motivation, and healing could be recognized were higher in the communication robot group relative to the control group. This study demonstrates that living with a human-type communication robot may be effective for improving cognitive functions in elderly women living alone.

  15. Functional Module Search in Protein Networks based on Semantic Similarity Improves the Analysis of Proteomics Data*

    PubMed Central

    Boyanova, Desislava; Nilla, Santosh; Klau, Gunnar W.; Dandekar, Thomas; Müller, Tobias; Dittrich, Marcus

    2014-01-01

    The continuously evolving field of proteomics produces increasing amounts of data while improving the quality of protein identifications. Albeit quantitative measurements are becoming more popular, many proteomic studies are still based on non-quantitative methods for protein identification. These studies result in potentially large sets of identified proteins, where the biological interpretation of proteins can be challenging. Systems biology develops innovative network-based methods, which allow an integrated analysis of these data. Here we present a novel approach, which combines prior knowledge of protein-protein interactions (PPI) with proteomics data using functional similarity measurements of interacting proteins. This integrated network analysis exactly identifies network modules with a maximal consistent functional similarity reflecting biological processes of the investigated cells. We validated our approach on small (H9N2 virus-infected gastric cells) and large (blood constituents) proteomic data sets. Using this novel algorithm, we identified characteristic functional modules in virus-infected cells, comprising key signaling proteins (e.g. the stress-related kinase RAF1) and demonstrate that this method allows a module-based functional characterization of cell types. Analysis of a large proteome data set of blood constituents resulted in clear separation of blood cells according to their developmental origin. A detailed investigation of the T-cell proteome further illustrates how the algorithm partitions large networks into functional subnetworks each representing specific cellular functions. These results demonstrate that the integrated network approach not only allows a detailed analysis of proteome networks but also yields a functional decomposition of complex proteomic data sets and thereby provides deeper insights into the underlying cellular processes of the investigated system. PMID:24807868

  16. Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data.

    PubMed

    Boyanova, Desislava; Nilla, Santosh; Klau, Gunnar W; Dandekar, Thomas; Müller, Tobias; Dittrich, Marcus

    2014-07-01

    The continuously evolving field of proteomics produces increasing amounts of data while improving the quality of protein identifications. Albeit quantitative measurements are becoming more popular, many proteomic studies are still based on non-quantitative methods for protein identification. These studies result in potentially large sets of identified proteins, where the biological interpretation of proteins can be challenging. Systems biology develops innovative network-based methods, which allow an integrated analysis of these data. Here we present a novel approach, which combines prior knowledge of protein-protein interactions (PPI) with proteomics data using functional similarity measurements of interacting proteins. This integrated network analysis exactly identifies network modules with a maximal consistent functional similarity reflecting biological processes of the investigated cells. We validated our approach on small (H9N2 virus-infected gastric cells) and large (blood constituents) proteomic data sets. Using this novel algorithm, we identified characteristic functional modules in virus-infected cells, comprising key signaling proteins (e.g. the stress-related kinase RAF1) and demonstrate that this method allows a module-based functional characterization of cell types. Analysis of a large proteome data set of blood constituents resulted in clear separation of blood cells according to their developmental origin. A detailed investigation of the T-cell proteome further illustrates how the algorithm partitions large networks into functional subnetworks each representing specific cellular functions. These results demonstrate that the integrated network approach not only allows a detailed analysis of proteome networks but also yields a functional decomposition of complex proteomic data sets and thereby provides deeper insights into the underlying cellular processes of the investigated system.

  17. 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

  18. 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.

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

    PubMed Central

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

    2014-01-01

    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. PMID:24827396

  20. 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

  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. 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

  3. Functional proteomics of barley and barley chloroplasts – strategies, methods and perspectives

    PubMed Central

    Petersen, Jørgen; Rogowska-Wrzesinska, Adelina; Jensen, Ole N.

    2013-01-01

    Barley (Hordeum vulgare) is an important cereal grain that is used in a range of products for animal and human consumption. Crop yield and seed quality has been optimized during decades by plant breeding programs supported by biotechnology and molecular biology techniques. The recently completed whole-genome sequencing of barley revealed approximately 26,100 open reading frames, which provides a foundation for detailed molecular studies of barley by functional genomics and proteomics approaches. Such studies will provide further insights into the mechanisms of, for example, drought and stress tolerance, micronutrient utilization, and photosynthesis in barley. In the present review we present the current state of proteomics research for investigations of barley chloroplasts, i.e., the organelle that contain the photosynthetic apparatus in the plant. We describe several different proteomics strategies and discuss their applications in characterization of the barley chloroplast as well as future perspectives for functional proteomics in barley research. PMID:23515231

  4. A functional system architecture for fully autonomous robot

    NASA Astrophysics Data System (ADS)

    Kalaycioglu, S.

    The Mobile Servicing System (MSS) Autonomous Robotics Program intends to define and plan the development of technologies required to provide a supervised autonomous operation capability for the Special Purpose Dexterous Manipulator (SPDM) on the MSS. The operational functions for the SPDM to perform the required tasks, both in fully autonomous or supervised modes, are identified. Functional decomposition is performed using a graphics oriented methodology called Structural Analysis Design Technique. This process defines the functional architecture of the system, the types of data required to support its functionality, and the control processes that need to be emplaced. On the basis of the functional decomposition, a technology breakdown structure is also developed. A preliminary estimate of the status and maturity of each relevant technology is made, based on this technology breakdown. The developed functional hierarchy is found to be very effective for a robotic system with any level of autonomy. Moreover, this hierarchy can easily be applied to an existing very low level autonomous system and can provide a smooth transition towards a higher degree of autonomy. The effectiveness of the developed functional hierarchy will also play a very significant role both in the system design as well as in the development of the control hierarchy.

  5. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

    SciTech Connect

    Wang, Jing; Ma, Zihao; Carr, Steven A.; Mertins, Philipp; Zhang, Hui; Zhang, Zhen; Chan, Daniel W.; Ellis, Matthew J. C.; Townsend, R. Reid; Smith, Richard D.; McDermott, Jason E.; Chen, Xian; Paulovich, Amanda G.; Boja, Emily S.; Mesri, Mehdi; Kinsinger, Christopher R.; Rodriguez, Henry; Rodland, Karin D.; Liebler, Daniel C.; Zhang, Bing

    2016-11-11

    Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies

  6. Potential biomarkers of human salivary function: a modified proteomic approach

    PubMed Central

    Rudney, J.D.; Staikov, R.K.; Johnson, J.D.

    2009-01-01

    Summary Objective In previous studies, we defined groups of subjects with opposite salivary function. Group membership was associated with clinically-relevant outcomes. High aggregation-adherence (HAA) groups showed lower levels of caries, supragingival plaque, total streptococci, and Tannerella forsythensis than low high aggregation-adherence (LAA) groups. In this study, we used a proteomic approach to search for biomarkers which could be useful as risk indicators for those outcomes. Design Clarified resting whole saliva from each of 41 HAA and LAA subjects was separated by preparative isoelectric focusing. Fractions showing the most distinctive protein profiles were pooled into four sets (pI 3–3.5, pI 4–4.7, pI 5.7–7.7, pI 10–11.5). Each pool then was compared by SDS-PAGE. Image analysis software was used to quantify matched bands. Partial least squares analysis (PLS) was used to determine which of the 65 bands from all four pools were the best predictors of group membership, caries, total plaque, total streptococci, and T. forsythensis counts. Those bands were identified by mass spectroscopy (MSMS). Results Two bands consistently were strong predictors in separate PLS analyses of each outcome variable. In follow-up univariate analyses, those bands showed the strongest significant differences between the HAA and LAA groups. They also showed significant inverse correlations with caries and all the microbiological variables. MSMS identified those bands as statherin, and a truncated cystatin S missing the first eight N-terminal amino acids. Conclusions Levels of statherin and truncated cystatin S may be potential risk indicators for the development of caries and other oral diseases. PMID:18804197

  7. Functional profiling of the Tritrichomonas foetus transcriptome and proteome.

    PubMed

    Huang, Kuo-Yang; Shin, Jyh-Wei; Huang, Po-Jung; Ku, Fu-Man; Lin, Wei-Chen; Lin, Rose; Hsu, Wei-Min; Tang, Petrus

    2013-01-01

    Tritrichomonas foetus is a potent veterinary pathogen, causing bovine and feline trichomoniasis. The principal clinical manifestation of infection in cattle is inflammation of the genital tract and infertility. In feline, the parasite causes large-bowel disease resulting in chronic diarrhea. In contrast to other well-studied protozoan, genetic data regarding the molecular characterization and expression in T. foetus is far less understood. In this study, the first large-scale T. foetus expressed sequence tag (TfEST) project was conducted on 5064 randomly selected EST clones from a non-normalized unidirectional Tf30924 cDNA library. Assembling of 5064 single-pass sequences from the 5' end resulted in 713 contigs and 1961 singlets. BLAST search revealed that 53.52% of the unigenes showed significant similarity to known sequences or protein motifs/domains. Functional classifications indicated that most of the unigenes are involved in translation, ribosomal structure and ribosome biogenesis. The average GC content of the T. foetus transcriptome is 40.93%. Intriguingly, only 31.29% of the unigenes contain the classical AAUAAA polyadenylation signal sequence at the 3'-UTR region. Furthermore, a panel of potential chemotherapeutic targets was also identified for the first time in T. foetus. The protein expression levels were verified by using two-dimensional electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. A total of 68 highly abundant protein spots were successfully identified in the reference 2-DE map based on our T. foetus-specific protein database. The EST dataset and the reference 2-DE map established in the present study will provide a foundation for future whole genome sequencing project and comparative transcriptomic/proteomic analyses to provide potential drug targets against T. foetus infection.

  8. 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.

  9. 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

  10. Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

    PubMed

    Pal, Lipika R; Guda, Chittibabu

    2006-11-07

    The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome.

  11. 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.

  12. 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.

  13. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

    PubMed

    Nabieva, Elena; Jim, Kam; Agarwal, Amit; Chazelle, Bernard; Singh, Mona

    2005-06-01

    Determining protein function is one of the most important problems in the post-genomic era. For the typical proteome, there are no functional annotations for one-third or more of its proteins. Recent high-throughput experiments have determined proteome-scale protein physical interaction maps for several organisms. These physical interactions are complemented by an abundance of data about other types of functional relationships between proteins, including genetic interactions, knowledge about co-expression and shared evolutionary history. Taken together, these pairwise linkages can be used to build whole-proteome protein interaction maps. We develop a network-flow based algorithm, FunctionalFlow, that exploits the underlying structure of protein interaction maps in order to predict protein function. In cross-validation testing on the yeast proteome, we show that FunctionalFlow has improved performance over previous methods in predicting the function of proteins with few (or no) annotated protein neighbors. By comparing several methods that use protein interaction maps to predict protein function, we demonstrate that FunctionalFlow performs well because it takes advantage of both network topology and some measure of locality. Finally, we show that performance can be improved substantially as we consider multiple data sources and use them to create weighted interaction networks. http://compbio.cs.princeton.edu/function

  14. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction.

    PubMed

    Wang, Jing; Ma, Zihao; Carr, Steven A; Mertins, Philipp; Zhang, Hui; Zhang, Zhen; Chan, Daniel W; Ellis, Matthew J C; Townsend, R Reid; Smith, Richard D; McDermott, Jason E; Chen, Xian; Paulovich, Amanda G; Boja, Emily S; Mesri, Mehdi; Kinsinger, Christopher R; Rodriguez, Henry; Rodland, Karin D; Liebler, Daniel C; Zhang, Bing

    2017-01-01

    Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies. © 2017 by

  15. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction*

    PubMed Central

    Wang, Jing; Ma, Zihao; Carr, Steven A.; Mertins, Philipp; Zhang, Hui; Zhang, Zhen; Chan, Daniel W.; Ellis, Matthew J. C.; Townsend, R. Reid; Smith, Richard D.; McDermott, Jason E.; Chen, Xian; Paulovich, Amanda G.; Boja, Emily S.; Mesri, Mehdi; Kinsinger, Christopher R.; Rodriguez, Henry; Rodland, Karin D.; Liebler, Daniel C.; Zhang, Bing

    2017-01-01

    Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies. PMID

  16. Cell wall proteomics contributes to explore the functional proteins of Brachypodium distachyon grains.

    PubMed

    Fang, Xianping; Chen, Wenyue; Ma, Huasheng

    2015-07-01

    The plant cell wall is the first barrier in response to external stimuli and cell wall proteins (CWPs) can play an important role in the modulation of plant growth and development. In the past 10 years, the plant cell wall proteomics has increasingly become a very active research filed, which provides a broader understanding of CWPs for people. The cell wall proteome of Arabidopsis, rice, and other model plants has begun to take shape, and proteomic technology has become an effective way to identify the candidate functional CWPs in large scale. The challenging work of Francin-Allami et al. (Proteomics 2015, 15, 2296-2306) is a vital step toward building the most extensive cell wall proteome of a monocot species. They identified 299 cell wall proteins in Brachypodium distachyon grains, and also compared the grain cell wall proteome with those of B. distachyon culms and leaves, which provides a new perspective for further explaining the plant cell wall structures and remodeling mechanism.

  17. Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations.

    PubMed

    Caffrey, Brian E; Williams, Tom A; Jiang, Xiaowei; Toft, Christina; Hokamp, Karsten; Fares, Mario A

    2012-01-01

    Functional divergence is the process by which new genes and functions originate through the modification of existing ones. Both genetic and environmental factors influence the evolution of new functions, including gene duplication or changes in the ecological requirements of an organism. Novel functions emerge at the expense of ancestral ones and are generally accompanied by changes in the selective forces at constrained protein regions. We present software capable of analyzing whole proteomes, identifying putative amino acid replacements leading to functional change in each protein and performing statistical tests on all tabulated data. We apply this method to 750 complete bacterial proteomes to identify high-level patterns of functional divergence and link these patterns to ecological adaptations. Proteome-wide analyses of functional divergence in bacteria with different ecologies reveal a separation between proteins involved in information processing (Ribosome biogenesis etc.) and those which are dependent on the environment (energy metabolism, defense etc.). We show that the evolution of pathogenic and symbiotic bacteria is constrained by their association with the host, and also identify unusual events of functional divergence even in well-studied bacteria such as Escherichia coli. We present a description of the roles of phylogeny and ecology in functional divergence at the level of entire proteomes in bacteria.

  18. Effect of a human-type communication robot on cognitive function in elderly women living alone

    PubMed Central

    Tanaka, Masaaki; Ishii, Akira; Yamano, Emi; Ogikubo, Hiroki; Okazaki, Masatsugu; Kamimura, Kazuro; Konishi, Yasuharu; Emoto, Shigeru; Watanabe, Yasuyoshi

    2012-01-01

    Summary Background Considering the high prevalence of dementia, it would be of great value to develop effective tools to improve cognitive function. We examined the effects of a human-type communication robot on cognitive function in elderly women living alone. Material/Methods In this study, 34 healthy elderly female volunteers living alone were randomized to living with either a communication robot or a control robot at home for 8 weeks. The shape, voice, and motion features of the communication robot resemble those of a 3-year-old boy, while the control robot was not designed to talk or nod. Before living with the robot and 4 and 8 weeks after living with the robot, experiments were conducted to evaluate a variety of cognitive functions as well as saliva cortisol, sleep, and subjective fatigue, motivation, and healing. Results The Mini-Mental State Examination score, judgement, and verbal memory function were improved after living with the communication robot; those functions were not altered with the control robot. In addition, the saliva cortisol level was decreased, nocturnal sleeping hours tended to increase, and difficulty in maintaining sleep tended to decrease with the communication robot, although alterations were not shown with the control. The proportions of the participants in whom effects on attenuation of fatigue, enhancement of motivation, and healing could be recognized were higher in the communication robot group relative to the control group. Conclusions This study demonstrates that living with a human-type communication robot may be effective for improving cognitive functions in elderly women living alone. PMID:22936190

  19. Functionalized magnetic nanoparticles for sample preparation in proteomics and peptidomics analysis.

    PubMed

    Li, Yan; Zhang, Xiangmin; Deng, Chunhui

    2013-11-07

    Sample preparation is a fundamental step in the proteomics and peptidomics workflow. Due to their good biocompatibility, superparamagnetic property, and high binding capacity, magnetic nanoparticles (MNPs) functionalized with different active moieties have been widely applied in recent years in various sample preparation procedures in proteomics and peptidomics analysis. The magnetic cores of the MNPs facilitate elegant handling using only magnetic devices and their small diameters are advantageous for increasing the sensitivity when using subsequent mass spectrometry (MS) analysis or gel electrophoresis. This review mainly focuses on overviewing present advances in the preparation and application of functionalized magnetic nanoparticles for sample preparation in proteomics and peptidomics analysis, including protein digestion, enrichment of low-abundance peptides/proteins and specific enrichment of peptides/proteins with post-translational modifications, such as phosphorylation and glycosylation.

  20. 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.

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

    PubMed

    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

  2. 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

  3. 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. Copyright © 2015, American Association for the Advancement of Science.

  4. Exhaustive proteome mining for functional MHC-I ligands.

    PubMed

    Koch, Christian P; Perna, Anna M; Weissmüller, Sabrina; Bauer, Stefanie; Pillong, Max; Baleeiro, Renato B; Reutlinger, Michael; Folkers, Gerd; Walden, Peter; Wrede, Paul; Hiss, Jan A; Waibler, Zoe; Schneider, Gisbert

    2013-09-20

    We present the development and application of a new machine-learning approach to exhaustively and reliably identify major histocompatibility complex class I (MHC-I) ligands among all 20(8) octapeptides and in genome-derived proteomes of Mus musculus , influenza A H3N8, and vesicular stomatitis virus (VSV). Focusing on murine H-2K(b), we identified potent octapeptides exhibiting direct MHC-I binding and stabilization on the surface of TAP-deficient RMA-S cells. Computationally identified VSV-derived peptides induced CD8(+) T-cell proliferation after VSV-infection of mice. The study demonstrates that high-level machine-learning models provide a unique access to rationally designed peptides and a promising approach toward "reverse vaccinology".

  5. Functional Proteomic Analysis of Lipid Raft Kinase Complexes

    DTIC Science & Technology

    2009-08-01

    NADPH -- cytochrome P450 reductase Non-raft 6 95/677 + 3.0 1.5 2.0 3 1 3.0 3 2 1.5 584 + IPI00015018 PPA1 Inorganic pyrophosphatase Non-raft 2 38/289...Freeman M.R. Proteome-scale characterization of human S-acylated proteins in lipid raft-enriched and non-raft membrane domains. Molecular & Cellular...IPI00013847 UQCRC1 Ubiquinol- cytochrome -c reductase complex core protein I,mitochondrial precursor Non-raft 2 24/480 – 0.5 1.0 0.5 1 2 0.5 0 0 0.0 891

  6. Bioinformatics as a tool for assessing the quality of sub-cellular proteomic strategies and inferring functions of proteins: plant cell wall proteomics as a test case.

    PubMed

    Clemente, Hélène San; Pont-Lezica, Rafael; Jamet, Elisabeth

    2009-02-18

    Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological questions. The aim of the work was to get a new tool for improving the quality of proteomics of sub-cellular compartments. Starting from the analysis of problems found in databases, we designed a new Arabidopsis database named ProtAnnDB (http://www.polebio.scsv.ups-tlse.fr/ProtAnnDB/). It collects in one page predictions of sub-cellular localization and of functional domains made by available software. Using this database allows not only improvement of interpretation of proteomic data (top-down analysis), but also of procedures to isolate sub-cellular compartments (bottom-up quality control).

  7. Research of the master-slave robot surgical system with the function of force feedback.

    PubMed

    Shi, Yunyong; Zhou, Chaozheng; Xie, Le; Chen, Yongjun; Jiang, Jun; Zhang, Zhenfeng; Deng, Ze

    2017-05-17

    Surgical robots lack force feedback, which may lead to operation errors. In order to improve surgical outcomes, this research developed a new master-slave surgical robot, which was designed with an integrated force sensor. The new structure designed for the master-slave robot employs a force feedback mechanism. A six-dimensional force sensor was mounted on the tip of the slave robot's actuator. Sliding model control was adopted to control the slave robot. According to the movement of the master system manipulated by the surgeon, the slave's movement and the force feedback function were validated. The motion was completed, the standard deviation was calculated, and the force data were detected. Hence, force feedback was realized in the experiment. The surgical robot can help surgeons to complete trajectory motions with haptic sensation. Copyright © 2017 John Wiley & Sons, Ltd.

  8. GENERAL: Collision avoidance for a mobile robot based on radial basis function hybrid force control technique

    NASA Astrophysics Data System (ADS)

    Wen, Shu-Huan

    2009-10-01

    Collision avoidance is always difficult in the planning path for a mobile robot. In this paper, the virtual force field between a mobile robot and an obstacle is formed and regulated to maintain a desired distance by hybrid force control algorithm. Since uncertainties from robot dynamics and obstacle degrade the performance of a collision avoidance task, intelligent control is used to compensate for the uncertainties. A radial basis function (RBF) neural network is used to regulate the force field of an accurate distance between a robot and an obstacle in this paper and then simulation studies are conducted to confirm that the proposed algorithm is effective.

  9. Human-Robot Teams Informed by Human Performance Moderator Functions

    DTIC Science & Technology

    2012-08-29

    Active RFID reader which interfaced with the robot via the robot’s RS232 serial port . The GAO RFID reader was used to sense 433 MHz active RFID tags...for Areas 1 and 2 and was created in the Cooperative Robotic Organization Simulator4 ( CROS ). CROS is a multithreaded, grid-based environment for...simulating multiagent systems designed around the Organizational Model for Adaptive Complex Systems (OMACS) [19]. CROS supports grid-based environments

  10. 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; ...

    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

  11. Microchip-based single-cell functional proteomics for biomedical applications.

    PubMed

    Lu, Yao; Yang, Liu; Wei, Wei; Shi, Qihui

    2017-03-29

    Cellular heterogeneity has been widely recognized but only recently have single cell tools become available that allow characterizing heterogeneity at the genomic and proteomic levels. We review the technological advances in microchip-based toolkits for single-cell functional proteomics. Each of these tools has distinct advantages and limitations, and a few have advanced toward being applied to address biological or clinical problems that traditional population-based methods fail to address. High-throughput single-cell proteomic assays generate high-dimensional data sets that contain new information and thus require developing new analytical frameworks to extract new biology. In this review article, we highlight a few biological and clinical applications in which microchip-based single-cell proteomic tools provide unique advantages. The examples include resolving functional heterogeneity and dynamics of immune cells, dissecting cell-cell interaction by creating a well-controlled on-chip microenvironment, capturing high-resolution snapshots of immune system functions in patients for better immunotherapy and elucidating phosphoprotein signaling networks in cancer cells for guiding effective molecularly targeted therapies.

  12. 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.

  13. Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level

    PubMed Central

    Pal, Lipika R; Guda, Chittibabu

    2006-01-01

    Background The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. Results This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. Conclusion This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome. PMID:17090320

  14. Functional proteomics of light-harvesting complex proteins under varying light-conditions in diatoms.

    PubMed

    Büchel, Claudia; Wilhelm, Christian; Wagner, Volker; Mittag, Maria

    2017-10-01

    Comparative proteome analysis of subcellular compartments like thylakoid membranes and their associated supercomplexes can deliver important in-vivo information on the molecular basis of physiological functions which go far beyond to that what can be learnt from transcriptional-based gene expression studies. For instance, the finding that light intensity influences mainly the relative stoichiometry of subunits could be obtained only by high resolution proteome analysis. The high sensitivity of LC-ESI-MS/MS based proteome analysis allows the determination of proteins in very small subfractions along with their non-labeled semi quantitative analysis. This provides insights in the protein-protein interactions of supercomplexes that are the operative units in intact cells. Here, we have focused on functional proteome approaches for the identification of microalgal light-harvesting complex proteins in chloroplasts and the eyespot in general and in detail for those of diatoms that are exposed to varying light conditions. Copyright © 2017 Elsevier GmbH. All rights reserved.

  15. Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex

    PubMed Central

    2013-01-01

    Background Daphnia pulex (Water flea) is the first fully sequenced crustacean genome. The crustaceans and insects have diverged from a common ancestor. It is a model organism for studying the molecular makeup for coping with the environmental challenges. In the complete proteome, there are 30,550 putative proteins. However, about 10,000 of them have no known homologues. Currently, the UniProtoKB reports on 95% of the Daphnia's proteins as putative and uncharacterized proteins. Results We have applied ProtoNet, an unsupervised hierarchical protein clustering method that covers about 10 million sequences, for automatic annotation of the Daphnia's proteome. 98.7% (26,625) of the Daphnia full-length proteins were successfully mapped to 13,880 ProtoNet stable clusters, and only 1.3% remained unmapped. We compared the properties of the Daphnia's protein families with those of the mouse and the fruitfly proteomes. Functional annotations were successfully assigned for 86% of the proteins. Most proteins (61%) were mapped to only 2953 clusters that contain Daphnia's duplicated genes. We focused on the functionality of maximally amplified paralogs. Cuticle structure components and a variety of ion channels protein families were associated with a maximal level of gene amplification. We focused on gene amplification as a leading strategy of the Daphnia in coping with environmental toxicity. Conclusions Automatic inference is achieved through mapping of sequences to the protein family tree of ProtoNet 6.0. Applying a careful inference protocol resulted in functional assignments for over 86% of the complete proteome. We conclude that the scaffold of ProtoNet can be used as an alignment-free protocol for large-scale annotation task of uncharacterized proteomes. PMID:23514195

  16. Robotic assessment of upper limb motor function after stroke.

    PubMed

    Balasubramanian, Sivakumar; Colombo, Roberto; Sterpi, Irma; Sanguineti, Vittorio; Burdet, Etienne

    2012-11-01

    Traditional assessment of a stroke subject's motor ability, carried out by a therapist who observes and rates the subject's motor behavior using ordinal measurements scales, is subjective, time consuming and lacks sensitivity. Rehabilitation robots, which have been the subject of intense inquiry over the last decade, are equipped with sensors that are used to develop objective measures of motor behaviors in a semiautomated way during therapy. This article reviews the current contributions of robot-assisted motor assessment of the upper limb. It summarizes the various measures related to movement performance, the models of motor recovery in stroke subjects and the relationship of robotic measures to standard clinical measures. It analyses the possibilities offered by current robotic assessment techniques and the aspects to address to make robotic assessment a mainstream motor assessment method.

  17. Urogenital function in robotic vs laparoscopic rectal cancer surgery: a comparative study.

    PubMed

    Panteleimonitis, Sofoklis; Ahmed, Jamil; Ramachandra, Meghana; Farooq, Muhammad; Harper, Mick; Parvaiz, Amjad

    2017-02-01

    Urological and sexual dysfunction are recognised risks of rectal cancer surgery; however, there is limited evidence regarding urogenital function comparing robotic to laparoscopic techniques. The aim of this study was to assess the urogenital functional outcomes of patients undergoing laparoscopic and robotic rectal cancer surgery. Urological and sexual functions were assessed using gender-specific validated standardised questionnaires. Questionnaires were sent a minimum of 6 months after surgery, and patients were asked to report their urogenital function pre- and post-operatively, allowing changes in urogenital function to be identified. Questionnaires were sent to 158 patients (89 laparoscopy, 69 robotic) of whom 126 (80 %) responded. Seventy-eight (49 male, 29 female) of the responders underwent laparoscopic and 48 (35 male, 13 female) robotic surgery. Male patients in the robotic group deteriorated less across all components of sexual function and in five components of urological function. Composite male urological and sexual function score changes from baseline were better in the robotic cohort (p < 0.001). In females, there was no difference between the two groups in any of the components of urological or sexual function. However, composite female urological function score change from baseline was better in the robotic group (p = 0.003). Robotic rectal cancer surgery might offer better post-operative urological and sexual outcomes compared to laparoscopic surgery in male patients and better urological outcomes in females. Larger scale, prospective randomised control studies including urodynamic assessment of urogenital function are required to validate these results.

  18. Functional Proteomics of Arabidopsis thaliana Guard Cells Uncovers New Stomatal Signaling Pathways[W][OA

    PubMed Central

    Zhao, Zhixin; Zhang, Wei; Stanley, Bruce A.; Assmann, Sarah M.

    2008-01-01

    We isolated a total of 3 × 108 guard cell protoplasts from 22,000 Arabidopsis thaliana plants and identified 1734 unique proteins using three complementary proteomic methods: protein spot identification from broad and narrow pH range two-dimensional (2D) gels, and 2D liquid chromatography–matrix assisted laser desorption/ionization multidimensional protein identification technology. This extensive single-cell-type proteome includes 336 proteins not previously represented in transcriptome analyses of guard cells and 52 proteins classified as signaling proteins by Gene Ontology analysis, of which only two have been previously assessed in the context of guard cell function. THIOGLUCOSIDE GLUCOHYDROLASE1 (TGG1), a myrosinase that catalyzes the production of toxic isothiocyanates from glucosinolates, showed striking abundance in the guard cell proteome. tgg1 mutants were hyposensitive to abscisic acid (ABA) inhibition of guard cell inward K+ channels and stomatal opening, revealing that the glucosinolate-myrosinase system, previously identified as a defense against biotic invaders, is required for key ABA responses of guard cells. Our results also suggest a mechanism whereby exposure to abiotic stresses may enhance plant defense against subsequent biotic stressors and exemplify how enhanced knowledge of the signaling networks of a specific cell type can be gained by proteomics approaches. PMID:19114538

  19. 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

  20. The Proteomic Investigation of Chromatin Functional Domains Reveals Novel Synergisms among Distinct Heterochromatin Components*

    PubMed Central

    Soldi, Monica; Bonaldi, Tiziana

    2013-01-01

    Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation. Until now the characterization of the proteomic component of chromatin domains has been held back by the challenge of enriching distinguishable, homogeneous regions for subsequent mass spectrometry analysis. Here we describe a modified protocol for chromatin immunoprecipitation combined with quantitative proteomics based on stable isotope labeling by amino acids in cell culture to identify known and novel histone modifications, variants, and complexes that specifically associate with silent and active chromatin domains. Our chromatin proteomics strategy revealed unique functional interactions among various chromatin modifiers, suggesting new regulatory pathways, such as a heterochromatin-specific modulation of DNA damage response involving H2A.X and WICH, both enriched in silent domains. Chromatin proteomics expands the arsenal of tools for deciphering how all the distinct protein components act together to enforce a given region-specific chromatin status. PMID:23319141

  1. Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions.

    PubMed

    von Zychlinski, Anne; Kleffmann, Torsten; Krishnamurthy, Nandini; Sjölander, Kimmen; Baginsky, Sacha; Gruissem, Wilhelm

    2005-08-01

    We report an extensive proteome analysis of rice etioplasts, which were highly purified from dark-grown leaves by a novel protocol using Nycodenz density gradient centrifugation. Comparative protein profiling of different cell compartments from leaf tissue demonstrated the purity of the etioplast preparation by the absence of diagnostic marker proteins of other cell compartments. Systematic analysis of the etioplast proteome identified 240 unique proteins that provide new insights into heterotrophic plant metabolism and control of gene expression. They include several new proteins that were not previously known to localize to plastids. The etioplast proteins were compared with proteomes from Arabidopsis chloroplasts and plastid from tobacco Bright Yellow 2 cells. Together with computational structure analyses of proteins without functional annotations, this comparative proteome analysis revealed novel etioplast-specific proteins. These include components of the plastid gene expression machinery such as two RNA helicases, an RNase II-like hydrolytic exonuclease, and a site 2 protease-like metalloprotease all of which were not known previously to localize to the plastid and are indicative for so far unknown regulatory mechanisms of plastid gene expression. All etioplast protein identifications and related data were integrated into a data base that is freely available upon request.

  2. High-Throughput Cloning and Expression Library Creation for Functional Proteomics

    PubMed Central

    Festa, Fernanda; Steel, Jason; Bian, Xiaofang; Labaer, Joshua

    2013-01-01

    The study of protein function usually requires the use of a cloned version of the gene for protein expression and functional assays. This strategy is particular important when the information available regarding function is limited. The functional characterization of the thousands of newly identified proteins revealed by genomics requires faster methods than traditional single gene experiments, creating the need for fast, flexible and reliable cloning systems. These collections of open reading frame (ORF) clones can be coupled with high-throughput proteomics platforms, such as protein microarrays and cell-based assays, to answer biological questions. In this tutorial we provide the background for DNA cloning, discuss the major high-throughput cloning systems (Gateway® Technology, Flexi® Vector Systems, and Creator™ DNA Cloning System) and compare them side-by-side. We also report an example of high-throughput cloning study and its application in functional proteomics. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP12). Details can be found at http://www.proteomicstutorials.org. PMID:23457047

  3. 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.

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

    PubMed

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

    2011-11-08

    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

  5. 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

  6. 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.

  7. Towards an ankle neuroprosthesis for hybrid robotics: Concepts and current sources for functional electrical stimulation.

    PubMed

    Casco, S; Fuster, I; Galeano, R; Moreno, J C; Pons, J L; Brunetti, F

    2017-07-01

    Hybrid rehabilitation robotics combine neuro-prosthetic devices (close-loop functional electrical stimulation systems) and traditional robotic structures and actuators to explore better therapies and promote a more efficient motor function recovery or compensation. Although hybrid robotics and ankle neuroprostheses (NPs) have been widely developed over the last years, there are just few studies on the use of NPs to electrically control both ankle flexion and extension to promote ankle recovery and improved gait patterns in paretic limbs. The aim of this work is to develop an ankle NP specifically designed to work in the field of hybrid robotics. This article presents early steps towards this goal and makes a brief review about motor NPs and Functional Electrical Stimulation (FES) principles and most common devices used to aid the ankle functioning during the gait cycle. It also shows a current sources analysis done in this framework, in order to choose the best one for this intended application.

  8. 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

  9. Bioinspired, Mobile Robots With High Stability, Functionality and Low Cost

    DTIC Science & Technology

    2014-02-19

    robots. The views, opinions and/or findings contained in this report are those of the author( s ) and should not contrued as an official Department...of the Army position, policy or decision, unless so designated by other documentation. 9. SPONSORING/MONITORING AGENCY NAME( S ) AND ADDRESS (ES) U.S...Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 soft robots, actuators, pneunet, locomotion, flexible, combustion REPORT

  10. 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

  11. Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights

    PubMed Central

    Kumar, Amitha Sampath; Sowpati, Divya Tej; Mishra, Rakesh K.

    2016-01-01

    Microsatellites or simple sequence repeats (SSR) are abundant, highly diverse stretches of short DNA repeats present in all genomes. Tandem mono/tri/hexanucleotide repeats in the coding regions contribute to single amino acids repeats (SAARs) in the proteome. While SSRs in the coding region always result in amino acid repeats, a majority of SAARs arise due to a combination of various codons representing the same amino acid and not as a consequence of SSR events. Certain amino acids are abundant in repeat regions indicating a positive selection pressure behind the accumulation of SAARs. By analysing 22 proteomes including the human proteome, we explored the functional and structural relationship of amino acid repeats in an evolutionary context. Only ~15% of repeats are present in any known functional domain, while ~74% of repeats are present in the disordered regions, suggesting that SAARs add to the functionality of proteins by providing flexibility, stability and act as linker elements between domains. Comparison of SAAR containing proteins across species reveals that while shorter repeats are conserved among orthologs, proteins with longer repeats, >15 amino acids, are unique to the respective organism. Lysine repeats are well conserved among orthologs with respect to their length and number of occurrences in a protein. Other amino acids such as glutamic acid, proline, serine and alanine repeats are generally conserved among the orthologs with varying repeat lengths. These findings suggest that SAARs have accumulated in the proteome under positive selection pressure and that they provide flexibility for optimal folding of functional/structural domains of proteins. The insights gained from our observations can help in effective designing and engineering of proteins with novel features. PMID:27893794

  12. Critical analysis of the literature investigating urogenital function preservation following robotic rectal cancer surgery.

    PubMed

    Panteleimonitis, Sofoklis; Ahmed, Jamil; Harper, Mick; Parvaiz, Amjad

    2016-11-27

    To analyses the current literature regarding the urogenital functional outcomes of patients receiving robotic rectal cancer surgery. A comprehensive literature search of electronic databases was performed in October 2015. The following search terms were applied: "rectal cancer" or "colorectal cancer" and robot* or "da Vinci" and sexual or urolog* or urinary or erect* or ejaculat* or impot* or incontinence. All original studies examining the urological and/or sexual outcomes of male and/or female patients receiving robotic rectal cancer surgery were included. Reference lists of all retrieved articles were manually searched for further relevant articles. Abstracts were independently searched by two authors. Fifteen original studies fulfilled the inclusion criteria. A total of 1338 patients were included; 818 received robotic, 498 laparoscopic and 22 open rectal cancer surgery. Only 726 (54%) patients had their urogenital function assessed via means of validated functional questionnaires. From the included studies, three found that robotic rectal cancer surgery leads to quicker recovery of male urological function and five of male sexual function as compared to laparoscopic surgery. It is unclear whether robotic surgery offers favourable urogenital outcomes in the long run for males. In female patients only two studies assessed urological and three sexual function independently to that of males. In these studies there was no difference identified between patients receiving robotic and laparoscopic rectal cancer surgery. However, in females the presented evidence was very limited making it impossible to draw any substantial conclusions. There seems to be a trend towards earlier recovery of male urogenital function following robotic surgery. To evaluate this further, larger well designed studies are required.

  13. Critical analysis of the literature investigating urogenital function preservation following robotic rectal cancer surgery

    PubMed Central

    Panteleimonitis, Sofoklis; Ahmed, Jamil; Harper, Mick; Parvaiz, Amjad

    2016-01-01

    AIM To analyses the current literature regarding the urogenital functional outcomes of patients receiving robotic rectal cancer surgery. METHODS A comprehensive literature search of electronic databases was performed in October 2015. The following search terms were applied: “rectal cancer” or “colorectal cancer” and robot* or “da Vinci” and sexual or urolog* or urinary or erect* or ejaculat* or impot* or incontinence. All original studies examining the urological and/or sexual outcomes of male and/or female patients receiving robotic rectal cancer surgery were included. Reference lists of all retrieved articles were manually searched for further relevant articles. Abstracts were independently searched by two authors. RESULTS Fifteen original studies fulfilled the inclusion criteria. A total of 1338 patients were included; 818 received robotic, 498 laparoscopic and 22 open rectal cancer surgery. Only 726 (54%) patients had their urogenital function assessed via means of validated functional questionnaires. From the included studies, three found that robotic rectal cancer surgery leads to quicker recovery of male urological function and five of male sexual function as compared to laparoscopic surgery. It is unclear whether robotic surgery offers favourable urogenital outcomes in the long run for males. In female patients only two studies assessed urological and three sexual function independently to that of males. In these studies there was no difference identified between patients receiving robotic and laparoscopic rectal cancer surgery. However, in females the presented evidence was very limited making it impossible to draw any substantial conclusions. CONCLUSION There seems to be a trend towards earlier recovery of male urogenital function following robotic surgery. To evaluate this further, larger well designed studies are required. PMID:27933136

  14. Male urinary and sexual function after robotic pelvic autonomic nerve-preserving surgery for rectal cancer.

    PubMed

    Wang, Gang; Wang, Zhiming; Jiang, Zhiwei; Liu, Jiang; Zhao, Jian; Li, Jieshou

    2017-03-01

    Urinary and sexual dysfunction is the potential complication of rectal cancer surgery. The aim of this study was to evaluate the urinary and sexual function in male patients with robotic surgery for rectal cancer. This prospective study included 137 of the 336 male patients who underwent surgery for rectal cancer. Urinary and male sexual function was studied by means of a questionnaire based on the International Prostatic Symptom Score and International Index of Erectile Function. All data were collected before surgery and 12 months after surgery. Patients who underwent robotic surgery had significantly decreased incidence of partial or complete erectile dysfunction and sexual dysfunction than patients with laparoscopic surgery. The pre- and post-operative total IPSS scores in patients with robotic surgery were significantly less than that with laparoscopic surgeries. Robotic surgery shows distinct advantages in protecting the pelvic autonomic nerves and relieving post-operative sexual dysfunction. Copyright © 2016 John Wiley & Sons, Ltd.

  15. The effect of fluoride on the structure, function, and proteome of a renal epithelial cell monolayer.

    PubMed

    Antonio, Ligia S; Jeggle, Pia; MacVinish, Lesley J; Bartram, James C; Miller, Henry; Jarvis, Gavin E; Levy, Flávia M; Santesso, Mariana R; Leite, Aline L; Oliveira, Rodrigo C; Buzalaf, Marília A R; Edwardson, J Michael

    2017-04-01

    High concentrations of fluoride in the body may cause toxic effects. Here, we investigated the effects of fluoride on the structure, function, and proteome of a cortical collecting duct epithelium in vitro. Kidney tubule cells (M-1) were chosen because the concentration of fluoride in the kidney is 4-5-fold higher than that in plasma. Mouse M-1 cell monolayers were incubated in fluoride-containing media, and the amiloride-sensitive short-circuit current and transepithelial resistance were measured. The Young's modulus of the epithelium was determined using atomic force microscopy, and the effect of fluoride on epithelial structure was assessed using scanning and transmission electron microscopy, and immunofluorescence. Differences in the expression of membrane proteins were evaluated using proteomics and bioinformatics. Fluoride exposure reduced both transepithelial Na(+) transport and resistance. The IC50 for fluoride was ∼300 µM for both effects, and the half-times for the decays of ion transport and resistance were 8.4 h and 3.6 days, respectively. Fluoride treatment did not affect the sensitivity of Na(+) transport to amiloride. The Young's modulus of the epithelium was also unaffected by fluoride; however, the functional effects of fluoride were accompanied by marked structural effects. Proteomic analysis revealed changes in expression of a number of proteins, and particularly mitochondrial proteins. Treatment with fluoride had profound effects on the structure, function and proteome of a model cortical collecting duct epithelium. Significantly, however, these effects were produced only at concentrations considerably higher than those likely to be encountered in vivo. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 1455-1467, 2017. © 2016 Wiley Periodicals, Inc.

  16. Evolutionary Trace Annotation of Protein Function in the Structural Proteome

    PubMed Central

    Erdin, Serkan; Ward, R. Matthew; Venner, Eric

    2010-01-01

    By design, structural genomics (SG) solves many structures that cannot be assigned function based on homology to known proteins. Alternative function annotation methods are therefore needed and this study focuses on function prediction with three-dimensional (3D) templates: small structural motifs built of just a few functionally critical residues. Although experimentally proven functional residues are scarce, we show here that Evolutionary Trace (ET) rankings of residue importance are sufficient to build 3D templates, match them, and then assign Gene Ontology (GO) functions in enzymes and non-enzymes alike. In a high specificity mode, this Evolutionary Trace Annotation (ETA) method covered half (53%) of the 2384 annotated SG protein controls. Three-quarters (76%) of predictions were both correct and complete. The positive predictive value for all GO depths (all-depth PPV) was 84%, and it rose to 94% over GO depths 1– 3 (depth 3 PPV). In a high sensitivity mode coverage rose significantly (84%) while accuracy fell moderately: 68% of predictions were both correct and complete, all-depth PPV was 75%, and depth 3 PPV was 86%. These data concur with prior mutational experiments showing that ET rank information identifies key functional determinants in proteins. In practice, ETA predicted functions in 42% of 3461 un-annotated SG proteins. In 529 cases—including 280 non-enzymes and 21 for metal ion ligands—the expected accuracy is 84% at any GO depth and 94% down to GO depth 3, while for the remaining 931 the expected accuracies are 60% and 71%, respectively. Thus local structural comparisons of evolutionarily important residues can help decipher protein functions to known reliability levels and without prior assumption on functional mechanisms. ETA is available at http://mammoth.bcm.tmc.edu/eta. PMID:20036248

  17. Does robotics improve minimally invasive rectal surgery? Functional and oncological implications.

    PubMed

    Guerra, Francesco; Pesi, Benedetta; Amore Bonapasta, Stefano; Perna, Federico; Di Marino, Michele; Annecchiarico, Mario; Coratti, Andrea

    2016-02-01

    Robot-assisted surgery has been reported to be a safe and effective alternative to conventional laparoscopy for the treatment of rectal cancer in a minimally invasive manner. Nevertheless, substantial data concerning functional outcomes and long-term oncological adequacy is still lacking. We aimed to assess the current role of robotics in rectal surgery focusing on patients' functional and oncological outcomes. A comprehensive review was conducted to search articles published in English up to 11 September 2015 concerning functional and/or oncological outcomes of patients who received robot-assisted rectal surgery. All relevant papers were evaluated on functional implications such as postoperative sexual and urinary dysfunction and oncological outcomes. Robotics showed a general trend towards lower rates of sexual and urinary postoperative dysfunction and earlier recovery compared with laparoscopy. The rates of 3-year local recurrence, disease-free survival and overall survival of robotic-assisted rectal surgery compared favourably with those of laparoscopy. This study fails to provide solid evidence to draw definitive conclusions on whether robotic systems could be useful in ameliorating the outcomes of minimally invasive surgery for rectal cancer. However, the available data suggest potential advantages over conventional laparoscopy with reference to functional outcomes. © 2016 Chinese Medical Association Shanghai Branch, Chinese Society of Gastroenterology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine and John Wiley & Sons Australia, Ltd.

  18. 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.

  19. A novel cable-driven robotic training improves locomotor function in individuals post-stroke.

    PubMed

    Wu, Ming; Landry, Jill M; Yen, Sheng-Che; Schmit, Brian D; Hornby, T George; Rafferty, Miriam

    2011-01-01

    A novel cable-driven robotic gait training system has been tested to improve the locomotor function in individuals post stroke. Seven subjects with chronic stroke were recruited to participate in this 6 weeks robot-assisted treadmill training paradigm. A controlled assistance force was applied to the paretic leg at the ankle through a cable-driven robotic system. The force was applied from late stance to mid-swing during treadmill training. Body weight support was provided as necessary to prevent knee buckling or toe drag. Subjects were trained 3 times a week for 6 weeks. Overground gait speed, 6 minute walking distance, and balance were evaluated at pre, post 6 weeks robotic training, and at 8 weeks follow up. Significant improvements in gait speed and 6 minute walking distance were obtained following robotic treadmill training through a cable-driven robotic system. Results from this study indicate that it is feasible to improve the locomotor function in individuals post stroke through a flexible cable-driven robot.

  20. 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.

  1. Proteomic and functional consequences of hexokinase deficiency in glucose-repressible Kluyveromyces lactis.

    PubMed

    Mates, Nadia; Kettner, Karina; Heidenreich, Falk; Pursche, Theresia; Migotti, Rebekka; Kahlert, Günther; Kuhlisch, Eberhard; Breunig, Karin D; Schellenberger, Wolfgang; Dittmar, Gunnar; Hoflack, Bernard; Kriegel, Thomas M

    2014-03-01

    The analysis of glucose signaling in the Crabtree-positive eukaryotic model organism Saccharomyces cerevisiae has disclosed a dual role of its hexokinase ScHxk2, which acts as a glycolytic enzyme and key signal transducer adapting central metabolism to glucose availability. In order to identify evolutionarily conserved characteristics of hexokinase structure and function, the cellular response of the Crabtree-negative yeast Kluyveromyces lactis to rag5 null mutation and concomitant deficiency of its unique hexokinase KlHxk1 was analyzed by means of difference gel electrophoresis. In total, 2,851 fluorescent spots containing different protein species were detected in the master gel representing all of the K. lactis proteins that were solubilized from glucose-grown KlHxk1 wild-type and mutant cells. Mass spectrometric peptide analysis identified 45 individual hexokinase-dependent proteins related to carbohydrate, short-chain fatty acid and tricarboxylic acid metabolism as well as to amino acid and protein turnover, but also to general stress response and chromatin remodeling, which occurred as a consequence of KlHxk1 deficiency at a minimum 3-fold enhanced or reduced level in the mutant proteome. In addition, three proteins exhibiting homology to 2-methylcitrate cycle enzymes of S. cerevisiae were detected at increased concentrations, suggesting a stimulation of pyruvate formation from amino acids and/or fatty acids. Experimental validation of the difference gel electrophoresis approach by post-lysis dimethyl labeling largely confirmed the abundance changes detected in the mutant proteome via the former method. Taking into consideration the high proportion of identified hexokinase-dependent proteins exhibiting increased proteomic levels, KlHxk1 is likely to have a repressive function in a multitude of metabolic pathways. The proteomic alterations detected in the mutant classify KlHxk1 as a multifunctional enzyme and support the view of evolutionary conservation of

  2. Effect of Robot-Assisted and Unassisted Exercise on Functional Reaching in Chronic Hemiparesis

    DTIC Science & Technology

    2001-10-25

    EFFECT OF ROBOT-ASSISTED AND UNASSISTED EXERCISE ON FUNCTIONAL REACHING IN CHRONIC HEMIPARESIS L. E. Kahn1,2, M. L. Zygman1, W. Z. Rymer1,2, D...Abstract – A common therapeutic approach for the rehabilitation of patients with hemiparesis involves repetitive voluntary movements with manual...of subjects with chronic hemiparesis (N = 7) performed the same repetitive exercises without the aid of the robotic device. Each group performed 24

  3. Assessing and inducing neuroplasticity with transcranial magnetic stimulation and robotics for motor function.

    PubMed

    O'Malley, Marcia K; Ro, Tony; Levin, Harvey S

    2006-12-01

    To describe 2 new ways of assessing and inducing neuroplasticity in the human brain--transcranial magnetic stimulation (TMS) and robotics--and to investigate and promote the recovery of motor function after brain damage. We identified recent articles and books directly bearing on TMS and robotics. Articles using these tools for purposes other than rehabilitation were excluded. From these studies, we emphasize the methodologic and technical details of these tools as applicable for assessing and inducing plasticity. Because both tools have only recently been used for rehabilitation, the majority of the articles selected for this review have been published only within the last 10 years. We used the PubMed and Compendex databases to find relevant peer-reviewed studies for this review. The studies were required to be relevant to rehabilitation and to use TMS or robotics methodologies. Guidelines were applied via independent extraction by multiple observers. Despite the limited amount of research using these procedures for assessing and inducing neuroplasticity, there is growing evidence that both TMS and robotics can be very effective, inexpensive, and convenient ways for assessing and inducing rehabilitation. Although TMS has primarily been used as an assessment tool for motor function, an increasing number of studies are using TMS as a tool to directly induce plasticity and improve motor function. Similarly, robotic devices have been used for rehabilitation because of their suitability for delivery of highly repeatable training. New directions in robotics-assisted rehabilitation are taking advantage of novel measurements that can be acquired via the devices, enabling unique methods of assessment of motor recovery. As refinements in technology and advances in our knowledge continue, TMS and robotics should play an increasing role in assessing and promoting the recovery of function. Ongoing and future studies combining TMS and robotics within the same populations may

  4. Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences.

    PubMed

    Bright, L A; Mujahid, N; Nanduri, B; McCarthy, F M; Costa, L R R; Burgess, S C; Swiderski, C E

    2011-08-01

    The equine genome sequence enables the use of high-throughput genomic technologies in equine research, but accurate identification of expressed gene products and interpreting their biological relevance require additional structural and functional genome annotation. Here, we employ the equine genome sequence to identify predicted and known proteins using proteomics and model these proteins into biological pathways, identifying 582 proteins in normal cell-free equine bronchoalveolar lavage fluid (BALF). We improved structural and functional annotation by directly confirming the in vivo expression of 558 (96%) proteins, which were computationally predicted previously, and adding Gene Ontology (GO) annotations for 174 proteins, 108 of which lacked functional annotation. Bronchoalveolar lavage is commonly used to investigate equine respiratory disease, leading us to model the associated proteome and its biological functions. Modelling of protein functions using Ingenuity Pathway Analysis identified carbohydrate metabolism, cell-to-cell signalling, cellular function, inflammatory response, organ morphology, lipid metabolism and cellular movement as key biological processes in normal equine BALF. Comparative modelling of protein functions in normal cell-free bronchoalveolar lavage proteomes from horse, human, and mouse, performed by grouping GO terms sharing common ancestor terms, confirms conservation of functions across species. Ninety-one of 92 human GO categories and 105 of 109 mouse GO categories were conserved in the horse. Our approach confirms the utility of the equine genome sequence to characterize protein networks without antibodies or mRNA quantification, highlights the need for continued structural and functional annotation of the equine genome and provides a framework for equine researchers to aid in the annotation effort.

  5. 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.

  6. Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes.

    PubMed

    Chi, An; Valencia, Julio C; Hu, Zhang-Zhi; Watabe, Hidenori; Yamaguchi, Hiroshi; Mangini, Nancy J; Huang, Hongzhan; Canfield, Victor A; Cheng, Keith C; Yang, Feng; Abe, Riichiro; Yamagishi, Shoichi; Shabanowitz, Jeffrey; Hearing, Vincent J; Wu, Cathy; Appella, Ettore; Hunt, Donald F

    2006-11-01

    Melanin, which is responsible for virtually all visible skin, hair, and eye pigmentation in humans, is synthesized, deposited, and distributed in subcellular organelles termed melanosomes. A comprehensive determination of the protein composition of this organelle has been obstructed by the melanin present. Here, we report a novel method of removing melanin that includes in-solution digestion and immobilized metal affinity chromatography (IMAC). Together with in-gel digestion, this method has allowed us to characterize melanosome proteomes at various developmental stages by tandem mass spectrometry. Comparative profiling and functional characterization of the melanosome proteomes identified approximately 1500 proteins in melanosomes of all stages, with approximately 600 in any given stage. These proteins include 16 homologous to mouse coat color genes and many associated with human pigmentary diseases. Approximately 100 proteins shared by melanosomes from pigmented and nonpigmented melanocytes define the essential melanosome proteome. Proteins validated by confirming their intracellular localization include PEDF (pigment-epithelium derived factor) and SLC24A5 (sodium/potassium/calcium exchanger 5, NCKX5). The sharing of proteins between melanosomes and other lysosome-related organelles suggests a common evolutionary origin. This work represents a model for the study of the biogenesis of lysosome-related organelles.

  7. 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.

  8. Acute toxicity of functionalized single wall carbon nanotubes: A biochemical, histopathologic and proteomics approach.

    PubMed

    Ahmadi, Homa; Ramezani, Mohammad; Yazdian-Robati, Rezvan; Behnam, Behzad; Razavi Azarkhiavi, Kamal; Hashem Nia, Azadeh; Mokhtarzadeh, Ahad; Matbou Riahi, Maryam; Razavi, Bibi Marjan; Abnous, Khalil

    2017-09-25

    Recently carbon nanotubes (CNTs) showed promising potentials in different biomedical applications but their safe use in humans and probable toxicities are still challenging. The aim of this study was to determine the acute toxicity of functionalized single walled carbon nanotubes (SWCNTs). In this project, PEGylated and Tween functionalized SWCNTs were prepared. BALB/c mice were randomly divided into nine groups, including PEGylated SWCNTs (75,150μg/mouse) and PEG, Tween80 suspended SWCNTs, Tween 80 and a control group (intact mice). One or 7 days after intravenous injection, the mice were killed and serum and livers were collected. The oxidative stress markers, biochemical and histopathological changes were studied. Subsequently, proteomics approach was used to investigate the alterations of protein expression profiles in the liver. Results showed that there were not any significant differences in malondealdehyde (MDA), glutathione (GSH) levels and biochemical enzymes (ALT and AST) between groups, while the histopathological observations of livers showed some injuries. The results of proteomics analysis revealed indolethylamine N-Methyltransferase (INMT), glycine N-Methyltransferase (GNMT), selenium binding protein (Selenbp), thioredoxin peroxidase (TPx), TNF receptor associated protein 1(Trap1), peroxiredoxin-6 (Prdx6), electron transport flavoprotein (Etf-α), regucalcin (Rgn) and ATP5b proteins were differentially expressed in functionalized SWCNTs groups. Western blot analyses confirmed that the changes in Prdx6 were consistent with 2-DE gel analysis. In summary, acute toxicological study on two functionalized SWCNTs did not show any significant toxicity at selected doses. Proteomics analysis also showed that following exposure to functionalized SWCNTs, the expression of some proteins with antioxidant activity and detoxifying properties were increased in liver tissue. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. 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.

  10. Impact of functional genomics and proteomics on radionuclide imaging.

    PubMed

    Haberkorn, Uwe; Altmann, Annette; Mier, Walter; Eisenhut, Michael

    2004-01-01

    The assessment of gene function following the completion of human genome sequencing may be performed using radionuclide imaging procedures. These procedures are needed for the evaluation of genetically manipulated animals or newly designed biomolecules, which requires a thorough understanding of physiology, biochemistry, and pharmacology. The experimental approaches will involve many new technologies, including in vivo imaging with single photon emission computed tomography and positron emission tomography. Nuclear medicine procedures may be applied for the determination of gene function and regulation using established and new tracers, or using in vivo reporter genes, such as genes encoding enzymes, receptors, antigens, or transporters. Visualization of in vivo reporter gene expression can be performed using radiolabeled substrates, antibodies, or ligands. Combinations of specific promoters and in vivo reporter genes may deliver information about the regulation of the corresponding genes. Furthermore, protein-protein interactions and activation of signal transduction pathways may be visualized noninvasively. The role of radiolabeled antisense molecules for the analysis of messenger ribonucleic acid (RNA) content has to be investigated. However, possible applications are therapeutic intervention using triplex oligonucleotides with therapeutic isotopes, which can be brought near to specific deoxyribonucleic acid sequences to induce deoxyribonucleic acid strand breaks at selected loci. Imaging of labeled siRNA makes sense if these are used for therapeutic purposes to assess the delivery of these new drugs to their target tissue. Pharmacogenomics will identify new surrogate markers for therapy monitoring, which may represent potential new tracers for imaging. Drug distribution studies for new therapeutic biomolecules are needed at least during preclinical stages of drug development. New treatment modalities, such as gene therapy with suicide genes, will need

  11. 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

  12. 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

  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

    Direct liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins extracted from Desulfovibrio vulgaris cells. While our previous study provided a proteomic overview of the cellular metabolism based on proteins with known functions (Zhang et al., 2006a, Proteomics, 6: 4286-4299), this study describes the global detection and functional inference for hypothetical D. vulgaris proteins. Across six growth conditions, 15,841 tryptic peptides were identified with high confidence. Using a criterion of peptide identification from at least two out of three independent LC-MS/MS analyses per protein, 176 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins. These proteins ranged from 6.0 to 153 kDa, and had calculated pI values ranging from 3.7 to 11.5. Based on homology search results (with E value <= 0.01 as a cutoff), 159 proteins were defined as conserved hypothetical proteins, and 17 proteins were unique to the D. vulgaris genome. Functional inference of the conserved hypothetical proteins was performed by a combination of several non-homology based methods: genomic context analysis, phylogenomic profiling, and analysis of a combination of experimental information including peptide detection in cells grown under specific culture conditions and cellular location of the proteins. Using this approach we were able to assign possible functions to 27 conserved hypothetical proteins. This study demonstrated that a combination of proteomics and bioinformatics methodologies can provide verification for the authenticity of hypothetical proteins and improve annotation for the D. vulgaris genome.

  14. Postoperative functional voice changes after conventional open or robotic thyroidectomy: a prospective trial.

    PubMed

    Lee, Jeonghun; Na, Kuk Young; Kim, Ra Mi; Oh, Yeonju; Lee, Ji Hyun; Lee, Jandee; Lee, Jin-Seok; Kim, Chul-Ho; Soh, Euy-Young; Chung, Woong Youn

    2012-09-01

    To use objective and subjective voice function analysis to compare outcomes in patients who had undergone conventional open thyroidectomy or robotic thyroidectomy. The study involved 88 consecutive patients who underwent thyroid surgery between May 2009 and December 2009; 46 patients underwent a conventional open thyroidectomy, and 42 underwent a robotic thyroidectomy. Auditory perceptual evaluation was used to make subjective assessments of voice function, and videolaryngostroboscopy, acoustic voice analysis with aerodynamic study, electroglottography, and voice range profile were used to make objective assessments. Each assessment was made before surgery, and at 1 week and 3 months after surgery. The conventional open and robotic thyroidectomy groups were similar in terms of age, gender ratio, and disease profile. We found that 18 (20.5%) of the 88 patients showed some level of voice dysfunction at 1 week after surgery; that the dysfunction resolved by 3 months after surgery in all cases; and that it was not permanent according to postoperative videolaryngostroboscopy. The conventional open and robotic thyroidectomy groups were found to have similar levels of dysfunction at 1 week after surgery, except for jitter, which was greater in the robotic group. For both groups, any such dysfunction spontaneously resolved by 3 months after surgery, and there were no significant differences between the groups in terms of any voice function parameter. Voice dysfunction was present after both open and robotic thyroidectomy (without any evident laryngeal nerve injury). However, function subsequently normalized to preoperative levels at 3 months after surgery in both groups. Voice function outcomes after robotic thyroidectomy are similar to those after conventional open thyroidectomy.

  15. 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.

  16. Saturated Nussbaum Function Based Approach for Robotic Systems With Unknown Actuator Dynamics.

    PubMed

    Chen, Ci; Liu, Zhi; Zhang, Yun; Chen, C L Philip; Xie, Shengli

    2016-10-01

    This paper presents a saturated Nussbaum function based approach for robotic systems with unknown actuator dynamics. To eliminate the effect of the control shock from the traditional Nussbaum function, a new type of the saturated Nussbaum function is developed with the idea of time-elongation. Moreover, by exploiting properties of the proposed Nussbaum function, a promising theorem is established to deal with unknown multiple actuator nonlinearities. In what follows, the proposed theorem is integrated with the adaptive control technique such that the stability analysis of the robotic system is completed. It thus guarantees that the state of the robotic system asymptotically converges to the desired trajectory. Finally, comparative studies are carried out to validate the effectiveness and the superiority of the proposed approach.

  17. 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.

  18. Intentional Movement Performance Ability (IMPA): a method for robot-aided quantitative assessment of motor function.

    PubMed

    Shin, Sung Yul; Kim, Jung Yoon; Lee, Sanghyeop; Lee, Junwon; Kim, Seung-Jong; Kim, ChangHwan

    2013-06-01

    The purpose of this paper is to propose a new assessment method for evaluating motor function of the patients who are suffering from physical weakness after stroke, incomplete spinal cord injury (iSCI) or other diseases. In this work, we use a robotic device to obtain the information of interaction occur between patient and robot, and use it as a measure for assessing the patients. The Intentional Movement Performance Ability (IMPA) is defined by the root mean square of the interactive torque, while the subject performs given periodic movement with the robot. IMPA is proposed to quantitatively determine the level of subject's impaired motor function. The method is indirectly tested by asking the healthy subjects to lift a barbell to disturb their motor function. The experimental result shows that the IMPA has a potential for providing a proper information of the subject's motor function level.

  19. Functional Outcomes and Complications of Robot-Assisted Free Flap Oropharyngeal Reconstruction.

    PubMed

    Tsai, Yueh-Chi; Liu, Shih-An; Lai, Chih-Sheng; Chen, Yen-Wei; Lu, Chen-Te; Yen, Jung-Hsing; Chen, I-Chen

    2017-03-01

    Robotic surgical systems provide a clear, magnified 3-dimensional visualization as well as precise, stable instrumental movement, thereby minimizing technical difficulties that may be encountered in the surgical treatment of oropharyngeal tumors. This study assessed the outcomes of robotic-assisted free flap oropharyngeal reconstruction compared with those of conventional free flap reconstruction. A retrospective review of 47 patients who underwent reconstructive operations using a free radial forearm fasciocutaneous flap for oropharyngeal defects was conducted over a 20-month period (May 2013-December 2014). Complications were evaluated for a robot-assisted reconstruction group and a conventional reconstruction group; postoperative complication rates and revision rates were further evaluated. The Functional Intraoral Glasgow Scale (FIGS) was adopted for functional outcome assessment. This study recruited 47 people who underwent reconstructive operations using a free radial forearm fasciocutaneous flap for oropharyngeal defects (14 robot-assisted and 33 conventional reconstructions). The mean postoperative FIGS score was 10.29 ± 2.02 in the robot-assisted group (P = 0.010) and 8.42 ± 2.29 in the conventional group at 1 month postoperatively. The mean postoperative FIGS score was 12.57 ± 1.91 in the robot-assisted group (P = 0.005) and 9.91 ± 3.09 in the conventional group at 3 months postoperatively. Complication rates between the robot-assisted and conventional groups were similar for flap failure (P = 0.531), partial necrosis, wound infection, hematoma or seroma formation (P = 0.893), wound dehiscence, and fistula formation (P = 0.515). The number of flap revision operations requiring additional surgery (P = 0.627) was comparable between the cohorts. There is no significant difference in complications or revision rates between the robot-assisted and conventional oropharyngeal reconstructions. The functional postoperative outcomes of robot

  20. Functional proteomic analyses of Bothrops atrox venom reveals phenotypes associated with habitat variation in the Amazon.

    PubMed

    Sousa, Leijiane F; Portes-Junior, José A; Nicolau, Carolina A; Bernardoni, Juliana L; Nishiyama-Jr, Milton Y; Amazonas, Diana R; Freitas-de-Sousa, Luciana A; Mourão, Rosa Hv; Chalkidis, Hipócrates M; Valente, Richard H; Moura-da-Silva, Ana M

    2017-04-21

    Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA2s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA2s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats. In this report, we compared isoforms present in venoms from snakes collected at different Amazonian habitats. By means of a species venom gland transcriptome and the in silico functional prediction of each isoform, we were able to predict the principal venom activities in vitro and in animal models. We also showed remarkable differences in the venom pools from snakes collected at the floodplain (várzea habitat) compared to other habitats. Not only was this venom less hemorrhagic and more procoagulant, when compared to the venom pools from the other three habitats studied, but also this enhanced procoagulant activity was not efficiently

  1. Erectile function post robotic radical prostatectomy: technical tips to improve outcomes?

    PubMed

    Goonewardene, S S; Persad, R; Gillatt, D

    2016-09-01

    Robotic surgery is becoming more and more commonplace. At the same time, so are complications, especially related to erectile function. The population being diagnosed with cancer is younger, with more aggressive cancers and higher expectations for good erectile function postoperatively. We conduct a retrospective analysis of literature over 20 years for Embase and Medline. Search terms used include (Robotic) AND (prostatectomy) AND (erectile function). There are a variety of multifactorial causes, resulting in worsening ED post-robotic radical prostatectomy; however, there are a number of treatments that can support this. There is much we can do to help prevent patients getting postoperative erectile dysfunction post-radical surgery. However, part of this is management of realistic patient expectations.

  2. Chemistry-based functional proteomics to identify novel deubiquitylating enzymes involved in viral infection.

    PubMed

    Lei, Yunlong; Xie, Ke; Huang, Kai; Wu, Hong; Huang, Canhua

    2012-05-01

    Ubiquitylation is a reversible post-translational modification pathway that regulates a variety of cellular processes including protein degradation and trafficking, intracellular localization, DNA repair, immune response and cellcycle progression. Deubiquitylating enzymes (DUBs) can remove the ubiquitin from the modified proteins and reverse the ubiquitylation-induced biological processes; hence it isn't hard to understand that viral pathogens take advantage of the host cell ubiquitin system through disturbing DUBs, for infection and replication. Although accumulated virus-related DUBs have been defined, but how viruses regulate their expression and activities is poor understand because of limitation of technologies. Recently, chemistry-based functional proteomics, which can not only monitor the alteration of abundance but also changes in activity of enzymes, was used to study the function of DUBs involved in virus infection and held much promise. Theses works suggest that chemistry-based functional proteomics is a potent strategy for high throughput screening of virus-related DUBs and exploring their roles in virus infection.

  3. Sma3s: A universal tool for easy functional annotation of proteomes and transcriptomes.

    PubMed

    Casimiro-Soriguer, Carlos S; Muñoz-Mérida, Antonio; Pérez-Pulido, Antonio J

    2017-06-01

    The current cheapening of next-generation sequencing has led to an enormous growth in the number of sequenced genomes and transcriptomes, allowing wet labs to get the sequences from their organisms of study. To make the most of these data, one of the first things that should be done is the functional annotation of the protein-coding genes. But it used to be a slow and tedious step that can involve the characterization of thousands of sequences. Sma3s is an accurate computational tool for annotating proteins in an unattended way. Now, we have developed a completely new version, which includes functionalities that will be of utility for fundamental and applied science. Currently, the results provide functional categories such as biological processes, which become useful for both characterizing particular sequence datasets and comparing results from different projects. But one of the most important implemented innovations is that it has now low computational requirements, and the complete annotation of a simple proteome or transcriptome usually takes around 24 hours in a personal computer. Sma3s has been tested with a large amount of complete proteomes and transcriptomes, and it has demonstrated its potential in health science and other specific projects. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. An insight into fusion technology aiding efficient recombinant protein production for functional proteomics.

    PubMed

    Yadav, Dinesh K; Yadav, Neelam; Yadav, Sarika; Haque, Shafiul; Tuteja, Narendra

    2016-12-15

    Advancements in peptide fusion technologies to maximize the protein production has taken a big leap to fulfill the demands of post-genomics era targeting elucidation of structure/function of the proteome and its therapeutic applications, by over-expression in heterologous expression systems. Despite being most preferred protein expression system armed with variety of cardinal fusion tags, expression of the functionally active recombinant protein in E. coli remains plagued. The present review critically analyses the aptness of well-characterized fusion tags utilized for over-expression of recombinant proteins with improved solubility and their compatibility with downstream purification procedures. The combinatorial tandem affinity strategies have shown to provide more versatile options. Solubility decreasing fusion tags have proved to facilitate the overproduction of antimicrobial peptides. Efficient removal of fusion tags prior to final usage is of utmost importance and has been summarized discussing the efficiency of various enzymatic and chemical methods of tag removal. Unfortunately, no single fusion tag works as a magic bullet to completely fulfill the requirements of protein expression and purification in active form. The information provided might help in selection and development of a successful protocol for efficient recombinant protein production for functional proteomics. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Comparative proteomics reveal fundamental structural and functional differences between the two progeny phenotypes of a baculovirus.

    PubMed

    Hou, Dianhai; Zhang, Leike; Deng, Fei; Fang, Wei; Wang, Ranran; Liu, Xijia; Guo, Lin; Rayner, Simon; Chen, Xinwen; Wang, Hualin; Hu, Zhihong

    2013-01-01

    The replication of lepidopteran baculoviruses is characterized by the production of two progeny phenotypes: the occlusion-derived virus (ODV), which establishes infection in midgut cells, and the budded virus (BV), which disseminates infection to different tissues within a susceptible host. To understand the structural, and hence functional, differences between BV and ODV, we employed multiple proteomic methods to reveal the protein compositions and posttranslational modifications of the two phenotypes of Helicoverpa armigera nucleopolyhedrovirus. In addition, Western blotting and quantitative mass spectrometry were used to identify the localization of proteins in the envelope or nucleocapsid fractions. Comparative protein portfolios of BV and ODV showing the distribution of 54 proteins, encompassing the 21 proteins shared by BV and ODV, the 12 BV-specific proteins, and the 21 ODV-specific proteins, were obtained. Among the 11 ODV-specific envelope proteins, 8 either are essential for or contribute to oral infection. Twenty-three phosphorylated and 6 N-glycosylated viral proteins were also identified. While the proteins that are shared by the two phenotypes appear to be important for nucleocapsid assembly and trafficking, the structural and functional differences between the two phenotypes are evidently characterized by the envelope proteins and posttranslational modifications. This comparative proteomics study provides new insight into how BV and ODV are formed and why they function differently.

  6. The human DNA ends proteome uncovers an unexpected entanglement of functional pathways.

    PubMed

    Berthelot, Vivien; Mouta-Cardoso, Gildas; Hégarat, Nadia; Guillonneau, François; François, Jean-Christophe; Giovannangeli, Carine; Praseuth, Danièle; Rusconi, Filippo

    2016-06-02

    DNA ends get exposed in cells upon either normal or dysfunctional cellular processes or molecular events. Telomeres need to be protected by the shelterin complex to avoid junctions occurring between chromosomes while failing topoisomerases or clustered DNA damage processing may produce double-strand breaks, thus requiring swift repair to avoid cell death. The rigorous study of the great many proteins involved in the maintenance of DNA integrity is a challenging task because of the innumerous unspecific electrostatic and/or hydrophobic DNA-protein interactions that arise due to the chemical nature of DNA. We devised a technique that discriminates the proteins recruited specifically at DNA ends from those that bind to DNA because of a generic affinity for the double helix. Our study shows that the DNA ends proteome comprises proteins of an unexpectedly wide functional spectrum, ranging from DNA repair to ribosome biogenesis and cytoskeleton, including novel proteins of undocumented function. A global mapping of the identified proteome on published DNA repair protein networks demonstrated the excellent specificity and functional coverage of our purification technique. Finally, the native nucleoproteic complexes that assembled specifically onto DNA ends were shown to be endowed with a highly efficient DNA repair activity.

  7. 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

  8. Proteomic and Functional Consequences of Hexokinase Deficiency in Glucose-repressible Kluyveromyces lactis

    PubMed Central

    Mates, Nadia; Kettner, Karina; Heidenreich, Falk; Pursche, Theresia; Migotti, Rebekka; Kahlert, Günther; Kuhlisch, Eberhard; Breunig, Karin D.; Schellenberger, Wolfgang; Dittmar, Gunnar; Hoflack, Bernard; Kriegel, Thomas M.

    2014-01-01

    The analysis of glucose signaling in the Crabtree-positive eukaryotic model organism Saccharomyces cerevisiae has disclosed a dual role of its hexokinase ScHxk2, which acts as a glycolytic enzyme and key signal transducer adapting central metabolism to glucose availability. In order to identify evolutionarily conserved characteristics of hexokinase structure and function, the cellular response of the Crabtree-negative yeast Kluyveromyces lactis to rag5 null mutation and concomitant deficiency of its unique hexokinase KlHxk1 was analyzed by means of difference gel electrophoresis. In total, 2,851 fluorescent spots containing different protein species were detected in the master gel representing all of the K. lactis proteins that were solubilized from glucose-grown KlHxk1 wild-type and mutant cells. Mass spectrometric peptide analysis identified 45 individual hexokinase-dependent proteins related to carbohydrate, short-chain fatty acid and tricarboxylic acid metabolism as well as to amino acid and protein turnover, but also to general stress response and chromatin remodeling, which occurred as a consequence of KlHxk1 deficiency at a minimum 3-fold enhanced or reduced level in the mutant proteome. In addition, three proteins exhibiting homology to 2-methylcitrate cycle enzymes of S. cerevisiae were detected at increased concentrations, suggesting a stimulation of pyruvate formation from amino acids and/or fatty acids. Experimental validation of the difference gel electrophoresis approach by post-lysis dimethyl labeling largely confirmed the abundance changes detected in the mutant proteome via the former method. Taking into consideration the high proportion of identified hexokinase-dependent proteins exhibiting increased proteomic levels, KlHxk1 is likely to have a repressive function in a multitude of metabolic pathways. The proteomic alterations detected in the mutant classify KlHxk1 as a multifunctional enzyme and support the view of evolutionary conservation of

  9. PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease

    PubMed Central

    Schlüter, Agatha; Fourcade, Stéphane; Domènech-Estévez, Enric; Gabaldón, Toni; Huerta-Cepas, Jaime; Berthommier, Guillaume; Ripp, Raymond; Wanders, Ronald J. A.; Poch, Olivier; Pujol, Aurora

    2007-01-01

    Peroxisomes are essential organelles of eukaryotic origin, ubiquitously distributed in cells and organisms, playing key roles in lipid and antioxidant metabolism. Loss or malfunction of peroxisomes causes more than 20 fatal inherited conditions. We have created a peroxisomal database () that includes the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae, by gathering, updating and integrating the available genetic and functional information on peroxisomal genes. PeroxisomeDB is structured in interrelated sections ‘Genes’, ‘Functions’, ‘Metabolic pathways’ and ‘Diseases’, that include hyperlinks to selected features of NCBI, ENSEMBL and UCSC databases. We have designed graphical depictions of the main peroxisomal metabolic routes and have included updated flow charts for diagnosis. Precomputed BLAST, PSI-BLAST, multiple sequence alignment (MUSCLE) and phylogenetic trees are provided to assist in direct multispecies comparison to study evolutionary conserved functions and pathways. Highlights of the PeroxisomeDB include new tools developed for facilitating (i) identification of novel peroxisomal proteins, by means of identifying proteins carrying peroxisome targeting signal (PTS) motifs, (ii) detection of peroxisomes in silico, particularly useful for screening the deluge of newly sequenced genomes. PeroxisomeDB should contribute to the systematic characterization of the peroxisomal proteome and facilitate system biology approaches on the organelle. PMID:17135190

  10. 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

    2015-08-07

    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.

  11. Bayesian Analysis of Mass Spectrometry Proteomics Data using Wavelet Based Functional Mixed Models

    PubMed Central

    Morris, Jeffrey S.; Brown, Philip J.; Herrick, Richard C.; Baggerly, Keith A.; Coombes, Kevin R.

    2008-01-01

    In this paper, we analyze MALDI-TOF mass spectrometry proteomic data using Bayesian wavelet-based functional mixed models. By modeling mass spectra as functions, this approach avoids reliance on peak detection methods. The flexibility of this framework in modeling non-parametric fixed and random effect functions enables it to model the effects of multiple factors simultaneously, allowing one to perform inference on multiple factors of interest using the same model fit, while adjusting for clinical or experimental covariates that may affect both the intensities and locations of peaks in the spectra. From the model output, we identify spectral regions that are differentially expressed across experimental conditions, while controlling the Bayesian FDR, in a way that takes both statistical and clinical significance into account. We apply this method to two cancer studies. PMID:17888041

  12. 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.

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

    PubMed

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

    2013-07-01

    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. We conducted a literature search of assistive robotic manipulators from 1970 to 2012 in PubMed, Google Scholar, and University of Pittsburgh Library System - PITTCat. Twenty relevant studies were identified. 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.

  14. A Wearable Hip Assist Robot Can Improve Gait Function and Cardiopulmonary Metabolic Efficiency in Elderly Adults.

    PubMed

    Lee, Hwang-Jae; Lee, Suhyun; Chang, Won Hyuk; Seo, Keehong; Shim, Youngbo; Choi, Byung-Ok; Ryu, Gyu-Ha; Kim, Yun-Hee

    2017-09-01

    The aims of this paper were to investigate the effectiveness of a newly developed wearable hip assist robot, that uses an active assist algorithm to improve gait function, muscle effort, and cardiopulmonary metabolic efficiency in elderly adults. Thirty elderly adults (15 males/ 15 females) participated in thispaper. The experimental protocol consisted of overground gait at comfortable speed under three different conditions: free gait without robot assistance, robot-assisted gait with zero torque (RAG-Z), and full RAG. Under all conditions, muscle effort was analyzed using a 12-channel surface electromyography system. Spatio-temporal data were collected at 120 Hz using a 3-D motion capture system with six infrared cameras. Metabolic cost parameters were collected as oxygen consumption per unit (ml/min/kg) and aerobic energy expenditure (Kcal/min). In the RAG condition, participants demonstrated improved gait function, decreased muscle effort, and reduced metabolic cost. Although the hip assist robot only provides assistance at the hip joint, our results demonstrated a clear reduction in knee and ankle muscle activity in addition to decreased hip flexor and extensor activity. Our findings suggest that this robot has the potential to improve stabilization of the trunk during walking in elderly adults.

  15. 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

  16. Restoring ADL function after wrist surgery in children with cerebral palsy: a novel Bilateral robot system design.

    PubMed

    Holley, D; Theriault, A; Kamara, S; Anewenter, V; Hughes, D; Johnson, M J

    2013-06-01

    Cerebral palsy is a leading cause of disability in children and reducing its effects on arm function will improve quality of life. Our goal is to train children with CP after wrist tendon transfer surgery using a robotic therapy system consisting of two robot arms and wrist robots. The therapeutic goal is to determine if the robot training combined with surgery intervention improved functional outcomes significantly more than surgery alone. To accomplish this long-term goal we have developed a Bilateral ADL Exercise Robot, BiADLER aimed at training children with CP in reach to grasp coordination on ADLs. Specifically, the robot will provide active training using an assist-as-needed. This paper presents the design concepts.

  17. Tracking control of two-wheel driven mobile robot using compound sine function neural networks

    NASA Astrophysics Data System (ADS)

    Ye, Jun

    2013-06-01

    The purpose of this paper is to propose a compound sine function neural network (NN) with continuous learning algorithm for the velocity and orientation angle tracking control of a mobile robot. Herein, two NN controllers embedded in the closed-loop control system are capable of on-line continuous learning and do not require any knowledge of the dynamics model. The neuron function of the hidden layer in the three-layer feed-forward network structure is on the basis of combining a sine function with a unipolar sigmoid function. In the NN algorithm, the weight values are only adjusted between the nodes in hidden layer and the output nodes, while the weight values between the input layer and the hidden layer are one, that is, constant, without the weight adjustment. The developed NN controllers have simple algorithm and fast learning convergence. Therefore, the proposed NN controllers can be suitable for the real-time tracking control of the mobile robots. The simulation results show that the proposed NN controller has better control performance in the tracking control of the mobile robot. The compound sine function NN provides a new way to solve tracking control problems for a mobile robot.

  18. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant

    SciTech Connect

    Brooks, Brandon; Mueller, R. S.; Young, Jacque C.; Morowitz, Michael J.; Robert L. Hettich; Banfield, Jillian F.

    2015-07-01

    While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13 21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains of Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential.

  19. 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.

  20. Erectile Function and Oncologic Outcomes Following Open Retropubic and Robot-assisted Radical Prostatectomy: Results from the LAParoscopic Prostatectomy Robot Open Trial.

    PubMed

    Sooriakumaran, Prasanna; Pini, Giovannalberto; Nyberg, Tommy; Derogar, Maryam; Carlsson, Stefan; Stranne, Johan; Bjartell, Anders; Hugosson, Jonas; Steineck, Gunnar; Wiklund, Peter N

    2017-09-04

    Whether surgeons perform better utilising a robot-assisted laparoscopic technique compared with an open approach during prostate cancer surgery is debatable. To report erectile function and early oncologic outcomes for both surgical modalities, stratified by prostate cancer risk grouping. In a prospective nonrandomised trial, we recruited 2545 men with prostate cancer from seven open (n=753) and seven robot-assisted (n=1792) Swedish centres (2008-2011). Clinometrically-validated questionnaire-based patient-reported erectile function was collected before, 3 mo, 12 mo, and 24 mo after surgery. Surgeon-reported degree of neurovascular-bundle preservation, pathologist-reported positive surgical margin (PSM) rates, and 2-yr prostate-specific antigen-relapse rates were measured. Among 1702 preoperatively potent men, we found enhanced erectile function recovery for low/intermediate-risk patients in the robot-assisted group at 3 mo. For patients with high-risk tumours, point estimates for erectile function recovery at 24 mo favoured the open surgery group. The degree of neurovascular bundle preservation and erectile function recovery were greater correlated for robot-assisted surgery. In pT2 tumours, 10% versus 17% PSM rates were observed for open and robot-assisted surgery, respectively; corresponding rates for pT3 tumours were 48% and 33%. These differences were associated with biochemical recurrence in pT3 but not pT2 disease. The study is limited by its nonrandomised design and relatively short follow-up. Earlier recovery of erectile function in the robot-assisted surgery group in lower-risk patients is counterbalanced by lower PSM rates for open surgeons in organ-confined disease; thus, both open and robotic surgeons need to consider this trade-off when determining the plane of surgical dissection. Robot-assisted surgery also facilitates easier identification of nerve preservation planes during radical prostatectomy as well as wider dissection for pT3 cases. For

  1. Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover.

    PubMed

    Cambridge, Sidney B; Gnad, Florian; Nguyen, Chuong; Bermejo, Justo Lorenzo; Krüger, Marcus; Mann, Matthias

    2011-12-02

    The turnover of each protein in the mammalian proteome is a functionally important characteristic. Here, we employed high-resolution mass spectrometry to quantify protein dynamics in nondividing mammalian cells. The ratio of externally supplied versus endogenous amino acids to de novo protein synthesis was about 17:1. Using subsaturating SILAC labeling, we obtained accurate turnover rates of 4106 proteins in HeLa and 3528 proteins in C2C12 cells. Comparison of these human and mouse cell lines revealed a highly significant turnover correlation of protein orthologs and thus high species conservation. Functionally, we observed statistically significant trends for the turnover of phosphoproteins and gene ontology categories that showed extensive covariation between mouse and human. Likewise, the members of some protein complexes, such as the proteasome, have highly similar turnover rates. The high species conservation and the low complex variances thus imply great regulatory fine-tuning of protein turnover.

  2. 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

    2012-12-07

    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.

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

    PubMed Central

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

    2016-01-01

    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

  4. Modulation of mitochondrial proteome and improved mitochondrial function by biventricular pacing of dyssynchronous failing hearts.

    PubMed

    Agnetti, Giulio; Kaludercic, Nina; Kane, Lesley A; Elliott, Steven T; Guo, Yurong; Chakir, Khalid; Samantapudi, Daya; Paolocci, Nazareno; Tomaselli, Gordon F; Kass, David A; Van Eyk, Jennifer E

    2010-02-01

    Cardiac resynchronization therapy (CRT) improves chamber mechanoenergetics and morbidity and mortality of patients manifesting heart failure with ventricular dyssynchrony; however, little is known about the molecular changes underlying CRT benefits. We hypothesized that mitochondria may play an important role because of their involvement in energy production. Mitochondria isolated from the left ventricle in a canine model of dyssynchronous or resynchronized (CRT) heart failure were analyzed by a classical, gel-based, proteomic approach. Two-dimensional gel electrophoresis revealed that 31 mitochondrial proteins where changed when controlling the false discovery rate at 30%. Key enzymes in anaplerotic pathways, such as pyruvate carboxylation and branched-chain amino acid oxidation, were increased. These concerted changes, along with others, suggested that CRT may increase the pool of Krebs cycle intermediates and fuel oxidative phosphorylation. Nearly 50% of observed changes pertained to subunits of the respiratory chain. ATP synthase-beta subunit of complex V was less degraded, and its phosphorylation modulated by CRT was associated with increased formation (2-fold, P=0.004) and specific activity (+20%, P=0.05) of the mature complex. The importance of these modifications was supported by coordinated changes in mitochondrial chaperones and proteases. CRT increased the mitochondrial respiratory control index with tightened coupling when isolated mitochondria were reexposed to substrates for both complex I (glutamate and malate) and complex II (succinate), an effect likely related to ATP synthase subunit modifications and complex quantity and activity. CRT potently affects both the mitochondrial proteome and the performance associated with improved cardiac function.

  5. 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.

  6. Autonomous function of wheelchair-mounted robotic manipulators to perform daily activities.

    PubMed

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

    2013-06-01

    Autonomous functions for wheelchair-mounted robotic manipulators (WMRMs) allow a user to focus more on the outcome from the task - for example, eating or drinking, instead of moving robot joints through user interfaces. In this paper, we introduce a novel personal assistive robotic system based on a position-based visual servoing (PBVS) approach. The system was evaluated with a complete drinking task, which included recognizing the location of the drink, picking up the drink from a start location, conveying the drink to the proximity of the user's mouth without spilling, and placing the drink back on the table. For a drink located in front of the wheelchair, the success rate was nearly 100%. Overall, the total time of completing drinking task is within 40 seconds.

  7. Robotic resistance treadmill training improves locomotor function in human spinal cord injury: a pilot study.

    PubMed

    Wu, Ming; Landry, Jill M; Schmit, Brian D; Hornby, T George; Yen, Sheng-Che

    2012-05-01

    To determine whether cable-driven robotic resistance treadmill training can improve locomotor function in humans with incomplete spinal cord injury (SCI). Repeated assessment of the same patients with crossover design. Research units of rehabilitation hospitals in Chicago. Patients with chronic incomplete SCI (N=10) were recruited to participate in this study. Subjects were randomly assigned to 1 of 2 groups. One group received 4 weeks of assistance training followed by 4 weeks of resistance training, while the other group received 4 weeks of resistance training followed by 4 weeks of assistance training. Locomotor training was provided by using a cable-driven robotic locomotor training system, which is highly backdrivable and compliant, allowing patients the freedom to voluntarily move their legs in a natural gait pattern during body weight supported treadmill training (BWSTT), while providing controlled assistance/resistance forces to the leg during the swing phase of gait. Primary outcome measures were evaluated for each participant before training and after 4 and 8 weeks of training. Primary measures were self-selected and fast overground walking velocity and 6-minute walking distance. Secondary measures included clinical assessments of balance, muscle tone, and strength. A significant improvement in walking speed and balance in humans with SCI was observed after robotic treadmill training using the cable-driven robotic locomotor trainer. There was no significant difference in walking functional gains after resistance versus assistance training, although resistance training was more effective for higher functioning patients. Cable-driven robotic resistance training may be used as an adjunct to BWSTT for improving overground walking function in humans with incomplete SCI, particularly for those patients with relatively high function. Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  8. 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

  9. 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

  10. Proteomic profiling reveals dopaminergic regulation of progenitor cell functions of goldfish radial glial cells in vitro.

    PubMed

    Xing, Lei; Martyniuk, Christopher J; Esau, Crystal; Da Fonte, Dillon F; Trudeau, Vance L

    2016-07-20

    Radial glial cells (RGCs) are stem-like cells found in the developing and adult central nervous system. They function as both a scaffold to guide neuron migration and as progenitor cells that support neurogenesis. Our previous study revealed a close anatomical relationship between dopamine neurons and RGCs in the telencephalon of female goldfish. In this study, label-free proteomics was used to identify the proteins in a primary RGC culture and to determine the proteome response to the selective dopamine D1 receptor agonist SKF 38393 (10μM), in order to better understand dopaminergic regulation of RGCs. A total of 689 unique proteins were identified in the RGCs and these were classified into biological and pathological pathways. Proteins such as nucleolin (6.9-fold) and ependymin related protein 1 (4.9-fold) were increased in abundance while proteins triosephosphate isomerase (10-fold) and phosphoglycerate dehydrogenase (5-fold) were decreased in abundance. Pathway analysis revealed that proteins that consistently changed in abundance across biological replicates were related to small molecules such as ATP, lipids and steroids, hormones, glucose, cyclic AMP and Ca(2+). Sub-network enrichment analysis suggested that estrogen receptor signaling, among other transcription factors, is regulated by D1 receptor activation. This suggests that these signaling pathways are correlated to dopaminergic regulation of radial glial cell functions. Most proteins down-regulated by SKF 38393 were involved in cell cycle/proliferation, growth, death, and survival, which suggests that dopamine inhibits the progenitor-related processes of radial glial cells. Examples of differently expressed proteins including triosephosphate isomerase, nucleolin, phosphoglycerate dehydrogenase and capping protein (actin filament) muscle Z-line beta were validated by qPCR and western blot, which were consistent with MS/MS data in the direction of change. This is the first study to characterize the RGC

  11. In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database.

    PubMed

    Friso, Giulia; Giacomelli, Lisa; Ytterberg, A Jimmy; Peltier, Jean-Benoit; Rudella, Andrea; Sun, Qi; Wijk, Klaas J van

    2004-02-01

    An extensive analysis of the Arabidopsis thaliana peripheral and integral thylakoid membrane proteome was performed by sequential extractions with salt, detergent, and organic solvents, followed by multidimensional protein separation steps (reverse-phase HPLC and one- and two-dimensional electrophoresis gels), different enzymatic and nonenzymatic protein cleavage techniques, mass spectrometry, and bioinformatics. Altogether, 154 proteins were identified, of which 76 (49%) were alpha-helical integral membrane proteins. Twenty-seven new proteins without known function but with predicted chloroplast transit peptides were identified, of which 17 (63%) are integral membrane proteins. These new proteins, likely important in thylakoid biogenesis, include two rubredoxins, a potential metallochaperone, and a new DnaJ-like protein. The data were integrated with our analysis of the lumenal-enriched proteome. We identified 83 out of 100 known proteins of the thylakoid localized photosynthetic apparatus, including several new paralogues and some 20 proteins involved in protein insertion, assembly, folding, or proteolysis. An additional 16 proteins are involved in translation, demonstrating that the thylakoid membrane surface is an important site for protein synthesis. The high coverage of the photosynthetic apparatus and the identification of known hydrophobic proteins with low expression levels, such as cpSecE, Ohp1, and Ohp2, indicate an excellent dynamic resolution of the analysis. The sequential extraction process proved very helpful to validate transmembrane prediction. Our data also were cross-correlated to chloroplast subproteome analyses by other laboratories. All data are deposited in a new curated plastid proteome database (PPDB) with multiple search functions (http://cbsusrv01.tc.cornell.edu/users/ppdb/). This PPDB will serve as an expandable resource for the plant community.

  12. 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

  13. 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

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

    PubMed Central

    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

  15. Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

    PubMed Central

    Ezkurdia, Iakes; del Pozo, Angela; Frankish, Adam; Rodriguez, Jose Manuel; Harrow, Jennifer; Ashman, Keith; Valencia, Alfonso; Tress, Michael L.

    2012-01-01

    Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of “novel” and “putative” protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is

  16. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

    PubMed

    Ezkurdia, Iakes; del Pozo, Angela; Frankish, Adam; Rodriguez, Jose Manuel; Harrow, Jennifer; Ashman, Keith; Valencia, Alfonso; Tress, Michael L

    2012-09-01

    Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of "novel" and "putative" protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and

  17. Understanding high-density lipoprotein function in disease: recent advances in proteomics unravel the complexity of its composition and biology.

    PubMed

    Birner-Gruenberger, Ruth; Schittmayer, Matthias; Holzer, Michael; Marsche, Gunther

    2014-10-01

    Although the epidemiology of high-density lipoprotein (HDL) cholesterol and cardiovascular risk has been consistent, pharmacologic interventions to increase HDL-cholesterol by delaying HDL catabolism did not translate into reduction in cardiovascular risk. HDL particles are small, protein-rich when compared to other plasma lipoprotein classes. Latest progresses in proteomics technology have dramatically increased our understanding of proteins carried by HDL. In addition to proteins with well-established functions in lipid transport, iron transport proteins, members of the complement pathway, and proteins involved in immune function and acute phase response were repeatedly identified on HDL particles. With the unraveling of the complexity of the HDL proteome, different laboratories have started to monitor its changes in various disease states. In addition, dynamic aspects of HDL subgroups are being discovered. These recent studies clearly illustrate the promise of HDL proteomics for deriving new biomarkers for disease diagnosis and to measure the effectiveness of current and future treatment regimens. This review summarizes recent advances in proteomics and lipidomics helping to understand HDL function in health and disease. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. Proteomic analysis of the postsynaptic density implicates synaptic function and energy pathways in bipolar disorder

    PubMed Central

    Föcking, M; Dicker, P; Lopez, L M; Hryniewiecka, M; Wynne, K; English, J A; Cagney, G; Cotter, D R

    2016-01-01

    The postsynaptic density (PSD) contains a complex set of proteins of known relevance to neuropsychiatric disorders such as schizophrenia and bipolar disorder. We enriched for this anatomical structure in the anterior cingulate cortex of 16 bipolar disorder samples and 20 controls from the Stanley Medical Research Institute. Unbiased shotgun proteomics incorporating label-free quantitation was used to identify differentially expressed proteins. Quantitative investigation of the PSD identified 2033 proteins, among which 288 were found to be differentially expressed. Validation of expression changes of DNM1, DTNA, NDUFV2, SEPT11 and SSBP was performed by western blotting. Bioinformatics analysis of the differentially expressed proteins implicated metabolic pathways including mitochondrial function, the tricarboxylic acid cycle, oxidative phosphorylation, protein translation and calcium signaling. The data implicate PSD-associated proteins, and specifically mitochondrial function in bipolar disorder. They relate synaptic function in bipolar disorder and the energy pathways that underpin it. Overall, our findings add to a growing literature linking the PSD and mitochondrial function in psychiatric disorders generally, and suggest that mitochondrial function associated with the PSD is particularly important in bipolar disorder. PMID:27898073

  19. Locally optimal control under unknown dynamics with learnt cost function: application to industrial robot positioning

    NASA Astrophysics Data System (ADS)

    Guérin, Joris; Gibaru, Olivier; Thiery, Stéphane; Nyiri, Eric

    2017-01-01

    Recent methods of Reinforcement Learning have enabled to solve difficult, high dimensional, robotic tasks under unknown dynamics using iterative Linear Quadratic Gaussian control theory. These algorithms are based on building a local time-varying linear model of the dynamics from data gathered through interaction with the environment. In such tasks, the cost function is often expressed directly in terms of the state and control variables so that it can be locally quadratized to run the algorithm. If the cost is expressed in terms of other variables, a model is required to compute the cost function from the variables manipulated. We propose a method to learn the cost function directly from the data, in the same way as for the dynamics. This way, the cost function can be defined in terms of any measurable quantity and thus can be chosen more appropriately for the task to be carried out. With our method, any sensor information can be used to design the cost function. We demonstrate the efficiency of this method through simulating, with the V-REP software, the learning of a Cartesian positioning task on several industrial robots with different characteristics. The robots are controlled in joint space and no model is provided a priori. Our results are compared with another model free technique, consisting in writing the cost function as a state variable.

  20. Pelvic floor function before and after robotic sacrocolpopexy: one-year outcomes.

    PubMed

    Geller, Elizabeth J; Parnell, Brent A; Dunivan, Gena C

    2011-01-01

    Estimate pelvic floor function and support 1 year after robotic sacrocolpopexy. Prospective cohort analysis of women undergoing robotic sacrocolpopexy for correction of advanced pelvic organ prolapse (Canadian Task Force Classification III). Primary outcome was pelvic floor function. Secondary outcomes included anatomic support and long-term surgical failures and complications. One university hospital in the southeastern United States. Primarily postmenopausal women (mean age 60) with advanced pelvic organ prolapse. All subjects underwent robotic sacrocolpopexy during the study period. Subjects then underwent 1-year postoperative assessment of pelvic floor function via validated condition-specific quality of life questionnaires and assessment of pelvic floor support, long-term surgical failures, and complications via physical examination. From November 2007 to April 2009, there were 28 subjects, 25 of whom (89.3%) were evaluated. Mean time since surgery was 14.8 months. Pelvic floor function remained significantly improved over preoperative baseline: PFDI-20 (117 vs 38, p <.001), PFIQ-7 (60 vs 10, p = .001), with stable high sexual function: PISQ-12 (34 vs. 36, p = .17), and improved pelvic support on POP-Q: Ba (+3 vs -2, p = .001), Bp (+0.5 vs -1, p = .092), C (+2.25 vs -8, p = .001). Anatomic cure for vault prolapse was 100% at 1 year. There were two mesh exposures and two subsequent prolapse surgeries. Robotic sacrocolpopexy demonstrates durable improvement in pelvic floor function and support, with high sexual function and reasonable failure and complication rates 1 year after surgery. Copyright © 2011 AAGL. Published by Elsevier Inc. All rights reserved.

  1. Robot-Assisted Reach Training for Improving Upper Extremity Function of Chronic Stroke.

    PubMed

    Cho, Ki Hun; Song, Won-Kyung

    2015-10-01

    Stroke, as a major risk factor for chronic impairment of upper limb function, can severely restrict the activities of daily living. Recently, robotic devices have been used to enhance the functional upper extremity movement of stroke patients. The purpose of the current study was to assess whether a robot-assisted reach training program using a whole arm manipulator (WAM) could improve upper extremity kinematic performance and functional movement for chronic stroke patients. Using a single-group design, this study followed 10 people with chronic stroke (6 men, 61.5 years; Mini-Mental State Examination score: 27.0; onset duration: 8.9 years). WAM with seven degrees of freedom for the shoulder, elbow, and wrist joints was used during robot-assisted reach exercises. Subjects participated in the training program for 40 minutes per day, 2 times a week, for 4 weeks. The main outcome measures were upper extremity kinematic performance (movement velocity) for three directions and functional movement (Action Research Arm Test). Upper extremity kinematic performance and functional movement measures were performed three times: at baseline, during intervention (at 2 weeks), and post intervention. Upper extremity kinematic performance and functional movement showed improvement after two weeks (P < 0.05) and four weeks (P < 0.05) of training compared to baseline. The findings of the current study demonstrated the positive effects of short-term robot-assisted reach training on upper extremity kinematic performance as well as functional movement in individuals with chronic stroke. In addition, the findings of the current study may provide valuable information for subsequent randomized controlled trials.

  2. Effects of robotic therapy on upper-extremity function in children with cerebral palsy: A systematic review.

    PubMed

    Chen, Yu-Ping; Howard, Ayanna M

    2016-01-01

    To systematically examine the effects of robotic therapy on upper extremity (UE) function in children with cerebral palsy (CP). A systematic literature search was conducted in Pubmed, CINAHL, Cochrane, PsychInfo, TRIP, and Web of Science up to July 2013. Studies of children with CP, using robotic therapy and measures of UE were included. Nine articles using three different robotic systems were included. Of these, seven were case studies. Overall, robotic therapy showed the potential effects as all studies reported at least one positive outcome: a moderate effect in improving reaching duration, smoothness, or decreased muscle tone, and a small to large effect in standardized clinical assessment (e.g. Fugl-Meyer). This review confirms the potential for robotic therapy to improve UE function in children with CP. However, the paucity of group design studies summons the need for more rigorous research before conclusive recommendations can be made.

  3. 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.

  4. 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.

  5. 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.

  6. Functional and proteomic analysis of Ceratonova shasta (Cnidaria: Myxozoa) polar capsules reveals adaptations to parasitism.

    PubMed

    Piriatinskiy, Gadi; Atkinson, Stephen D; Park, Sinwook; Morgenstern, David; Brekhman, Vera; Yossifon, Gilad; Bartholomew, Jerri L; Lotan, Tamar

    2017-08-21

    Myxozoa is a diverse, speciose group of microscopic parasites, recently placed within the phylum Cnidaria. Myxozoans are highly reduced in size and complexity relative to free-living cnidarians, yet they have retained specialized organelles known as polar capsules, akin to the nematocyst stinging capsules of free-living species. Whereas in free-living cnidarians the stinging capsules are used for prey capture or defense, in myxozoans they have the essential function of initiating the host infection process. To explore the evolutionary adaptation of polar capsules to parasitism, we used as a model organism Ceratonova shasta, which causes lethal disease in salmonids. Here, we report the first isolation of C. shasta myxospore polar capsules using a tailored dielectrophoresis-based microfluidic chip. Using electron microscopy and functional analysis we demonstrated that C. shasta tubules have no openings and are likely used to anchor the spore to the host. Proteomic analysis of C. shasta polar capsules suggested that they have retained typical structural and housekeeping proteins found in nematocysts of jellyfish, sea anemones and Hydra, but have lost the most important functional group in nematocysts, namely toxins. Our findings support the hypothesis that polar capsules and nematocysts are homologous organelles, which have adapted to their distinct functions.

  7. Microfluidics-Based Single-Cell Functional Proteomics for Fundamental and Applied Biomedical Applications

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

  8. FUNCTIONAL PROTEOME OF MACROPHAGE CARRIED NANOFORMULATED ANTIRETROVIRAL THERAPY DEMONSTRATES ENHANCED PARTICLE CARRYING CAPACITY

    PubMed Central

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

    2013-01-01

    Our laboratory has pioneered the development of long-acting nanoformulations of antiretroviral therapy (nanoART). NanoART serves to improve drug compliance, toxicities, and access to viral reservoirs. These all function to 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. Functional proteomics of nonalcoholic steatohepatitis: Mitochondrial proteins as targets of S-adenosylmethionine

    PubMed Central

    Santamaría, Enrique; Avila, Matías A.; Latasa, M. Ujue; Rubio, Angel; Martín-Duce, Antonio; Lu, Shelly C.; Mato, José M.; Corrales, Fernando J.

    2003-01-01

    Recent work shows that S-adenosylmethionine (AdoMet) helps maintain normal liver function as chronic hepatic deficiency results in spontaneous development of steatohepatitis and hepatocellular carcinoma. The mechanisms by which these nontraditional functions of AdoMet occur are unknown. Here, we use knockout mice deficient in hepatic AdoMet synthesis (MAT1A−/−) to study the proteome of the liver during the development of steatohepatitis. One hundred and seventeen protein spots, differentially expressed during the development of steatohepatitis, were selected and identified by peptide mass fingerprinting. Among them, 12 proteins were found to be affected from birth, when MAT1A−/− expression is switched on in WT mouse liver, to the rise of histological lesions, which occurs at ≈8 months. Of the 12 proteins, 4 [prohibitin 1 (PHB1), cytochrome c oxidase I and II, and ATPase β-subunit] have known roles in mitochondrial function. We show that the alteration in expression of PHB1 correlates with a loss of mitochondrial function. Experiments in isolated rat hepatocytes indicate that AdoMet regulates PHB1 content, thus suggesting ways by which steatohepatitis may be induced. Importantly, we found the expression of these mitochondrial proteins was abnormal in ob/ob mice and obese patients who are at risk for nonalcoholic steatohepatitis. PMID:12631701

  10. Extreme evolutionary conservation of functionally important regions in H1N1 influenza proteome.

    PubMed

    Warren, Samantha; Wan, Xiu-Feng; Conant, Gavin; Korkin, Dmitry

    2013-01-01

    The H1N1 subtype of influenza A virus has caused two of the four documented pandemics and is responsible for seasonal epidemic outbreaks, presenting a continuous threat to public health. Co-circulating antigenically divergent influenza strains significantly complicates vaccine development and use. Here, by combining evolutionary, structural, functional, and population information about the H1N1 proteome, we seek to answer two questions: (1) do residues on the protein surfaces evolve faster than the protein core residues consistently across all proteins that constitute the influenza proteome? and (2) in spite of the rapid evolution of surface residues in influenza proteins, are there any protein regions on the protein surface that do not evolve? To answer these questions, we first built phylogenetically-aware models of the patterns of surface and interior substitutions. Employing these models, we found a single coherent pattern of faster evolution on the protein surfaces that characterizes all influenza proteins. The pattern is consistent with the events of inter-species reassortment, the worldwide introduction of the flu vaccine in the early 80's, as well as the differences caused by the geographic origins of the virus. Next, we developed an automated computational pipeline to comprehensively detect regions of the protein surface residues that were 100% conserved over multiple years and in multiple host species. We identified conserved regions on the surface of 10 influenza proteins spread across all avian, swine, and human strains; with the exception of a small group of isolated strains that affected the conservation of three proteins. Surprisingly, these regions were also unaffected by genetic variation in the pandemic 2009 H1N1 viral population data obtained from deep sequencing experiments. Finally, the conserved regions were intrinsically related to the intra-viral macromolecular interaction interfaces. Our study may provide further insights towards the

  11. Anti-platelet effects of olive oil extract: in vitro functional and proteomic studies.

    PubMed

    de Roos, Baukje; Zhang, Xuguang; Rodriguez Gutierrez, Guillermo; Wood, Sharon; Rucklidge, Garry J; Reid, Martin D; Duncan, Gary J; Cantlay, Louise L; Duthie, Garry G; O'Kennedy, Niamh

    2011-10-01

    Platelets play a key role in haemostasis and wound healing, contributing to formation of vascular plugs. They are also involved in formation of atherosclerosic plaques. Some traditional diets, like the Mediterranean diet, are associated with a lower risk of cardiovascular disease. Components in these diets may have anti-platelet functions contributing to their health benefits. We studied the effects of alperujo extract, an olive oil production waste product containing the majority of polyphenols found in olive fruits, through measurement of effects on platelet aggregation and activation in isolated human platelets, and through identification of changes in the platelet proteome. Alperujo extract (40 mg/L) significantly decreased in vitro ADP- (p = 0.002) and TRAP- (p = 0.02) induced platelet activation as measured by the flow cytometry using the antibody for p-selectin (CD62p), but it did not affect the conformation of the fibrinogen receptor as measured by flow cytometry using the antibodies for anti-fibrinogen, CD42a and CD42b. Alperujo extract (100 mg/L) inhibited both collagen- and TRAP-induced platelet aggregation by 5% (p < 0.05), and a combination of hydroxytyrosol and 3,4-dihydroxyphenylglycol were, at least partly, responsible for this effect. Proteomic analysis identified nine proteins that were differentially regulated by the alperujo extract upon ADP-induced platelet aggregation. These proteins represent important mechanisms that may underlie the anti-platelet effects of this extract: regulation of platelet structure and aggregation, coagulation and apoptosis, and signalling by integrin αIIb/β3. Alperujo extract may protect against platelet activation, platelet adhesion and possibly have anti-inflammatory properties.

  12. Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome

    PubMed Central

    Warren, Samantha; Wan, Xiu-Feng; Conant, Gavin; Korkin, Dmitry

    2013-01-01

    The H1N1 subtype of influenza A virus has caused two of the four documented pandemics and is responsible for seasonal epidemic outbreaks, presenting a continuous threat to public health. Co-circulating antigenically divergent influenza strains significantly complicates vaccine development and use. Here, by combining evolutionary, structural, functional, and population information about the H1N1 proteome, we seek to answer two questions: (1) do residues on the protein surfaces evolve faster than the protein core residues consistently across all proteins that constitute the influenza proteome? and (2) in spite of the rapid evolution of surface residues in influenza proteins, are there any protein regions on the protein surface that do not evolve? To answer these questions, we first built phylogenetically-aware models of the patterns of surface and interior substitutions. Employing these models, we found a single coherent pattern of faster evolution on the protein surfaces that characterizes all influenza proteins. The pattern is consistent with the events of inter-species reassortment, the worldwide introduction of the flu vaccine in the early 80’s, as well as the differences caused by the geographic origins of the virus. Next, we developed an automated computational pipeline to comprehensively detect regions of the protein surface residues that were 100% conserved over multiple years and in multiple host species. We identified conserved regions on the surface of 10 influenza proteins spread across all avian, swine, and human strains; with the exception of a small group of isolated strains that affected the conservation of three proteins. Surprisingly, these regions were also unaffected by genetic variation in the pandemic 2009 H1N1 viral population data obtained from deep sequencing experiments. Finally, the conserved regions were intrinsically related to the intra-viral macromolecular interaction interfaces. Our study may provide further insights towards the

  13. Incorporating robotic-assisted telerehabilitation in a home program to improve arm function following stroke.

    PubMed

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

    2013-09-01

    After stroke, many individuals lack resources to receive the intensive rehabilitation that is 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. The participant was a 54-year-old man, 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 of 66 on the Fugl-Meyer Assessment. The participant completed 85 total hours of training (38 hours of robotic device and 47 hours of HEP) over the 8-week intervention period. 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, and 20 points on the Fugl-Meyer Assessment, all of which surpassed the minimal clinically important difference. Of the 17 tasks of the Wolf Motor Function Test, he demonstrated improvement on 11 of the 15 time-based tasks and both strength measures. The participant reported an overall improvement in his recovery from stroke on the Stroke Impact Scale quality-of-life questionnaire from 40 of 100 to 65 of 100. His score on the Center for Epidemiologic Studies Depression Scale improved by 19 points. This case demonstrates that robotic-assisted therapy paired with an 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 an HEP program to elicit substantial improvements in upper extremity motor function, especially in those persons with stroke who lack access to stroke rehabilitation centers.

  14. The cortical activation pattern by a rehabilitation robotic hand: a functional NIRS study

    PubMed Central

    Chang, Pyung-Hun; Lee, Seung-Hee; Gu, Gwang Min; Lee, Seung-Hyun; Jin, Sang-Hyun; Yeo, Sang Seok; Seo, Jeong Pyo; Jang, Sung Ho

    2014-01-01

    Introduction: Clarification of the relationship between external stimuli and brain response has been an important topic in neuroscience and brain rehabilitation. In the current study, using functional near infrared spectroscopy (fNIRS), we attempted to investigate cortical activation patterns generated during execution of a rehabilitation robotic hand. Methods: Ten normal subjects were recruited for this study. Passive movements of the right fingers were performed using a rehabilitation robotic hand at a frequency of 0.5 Hz. We measured values of oxy-hemoglobin (HbO), deoxy-hemoglobin (HbR) and total-hemoglobin (HbT) in five regions of interest: the primary sensory-motor cortex (SM1), hand somatotopy of the contralateral SM1, supplementary motor area (SMA), premotor cortex (PMC), and prefrontal cortex (PFC). Results: HbO and HbT values indicated significant activation in the left SM1, left SMA, left PMC, and left PFC during execution of the rehabilitation robotic hand (uncorrected, p < 0.01). By contrast, HbR value indicated significant activation only in the hand somatotopic area of the left SM1 (uncorrected, p < 0.01). Conclusions: Our results appear to indicate that execution of the rehabilitation robotic hand could induce cortical activation. PMID:24570660

  15. Pull-down combined with proteomic strategy reveals functional diversity of synaptotagmin I.

    PubMed

    Guo, Tianyao; Duan, Zhigui; Chen, Jia; Xie, Chunliang; Wang, Ying; Chen, Ping; Wang, Xianchun

    2017-01-01

    Synaptotagmin I (Syt I) is most abundant in the brain and is involved in multiple cellular processes. Its two C2 domains, C2A and C2B, are the main functional regions. Our present study employed a pull-down combined with proteomic strategy to identify the C2 domain-interacting proteins to comprehensively understand the biological roles of the C2 domains and thus the functional diversity of Syt I. A total of 135 non-redundant proteins interacting with the C2 domains of Syt I were identified. Out of them, 32 and 64 proteins only bound to C2A or C2B domains, respectively, and 39 proteins bound to both of them. Compared with C2A, C2B could bind to many more proteins particularly those involved in synaptic transmission and metabolic regulation. Functional analysis indicated that Syt I may exert impacts by interacting with other proteins on multiple cellular processes, including vesicular membrane trafficking, synaptic transmission, metabolic regulation, catalysis, transmembrane transport and structure formation, etc. These results demonstrate that the functional diversity of Syt I is higher than previously expected, that its two domains may mediate the same and different cellular processes cooperatively or independently, and that C2B domain may play even more important roles than C2A in the functioning of Syt I. This work not only further deepened our understanding of the functional diversity of Syt I and the functional differences between its two C2 domains, but also provided important clues for the further related researches.

  16. Pull-down combined with proteomic strategy reveals functional diversity of synaptotagmin I

    PubMed Central

    Guo, Tianyao; Duan, Zhigui; Chen, Jia; Xie, Chunliang; Wang, Ying; Chen, Ping

    2017-01-01

    Synaptotagmin I (Syt I) is most abundant in the brain and is involved in multiple cellular processes. Its two C2 domains, C2A and C2B, are the main functional regions. Our present study employed a pull-down combined with proteomic strategy to identify the C2 domain-interacting proteins to comprehensively understand the biological roles of the C2 domains and thus the functional diversity of Syt I. A total of 135 non-redundant proteins interacting with the C2 domains of Syt I were identified. Out of them, 32 and 64 proteins only bound to C2A or C2B domains, respectively, and 39 proteins bound to both of them. Compared with C2A, C2B could bind to many more proteins particularly those involved in synaptic transmission and metabolic regulation. Functional analysis indicated that Syt I may exert impacts by interacting with other proteins on multiple cellular processes, including vesicular membrane trafficking, synaptic transmission, metabolic regulation, catalysis, transmembrane transport and structure formation, etc. These results demonstrate that the functional diversity of Syt I is higher than previously expected, that its two domains may mediate the same and different cellular processes cooperatively or independently, and that C2B domain may play even more important roles than C2A in the functioning of Syt I. This work not only further deepened our understanding of the functional diversity of Syt I and the functional differences between its two C2 domains, but also provided important clues for the further related researches. PMID:28194317

  17. Proteome analysis of functionally differentiated bovine (Bos indicus) mammary epithelial cells isolated from milk.

    PubMed

    Janjanam, Jagadeesh; Jamwal, Manu; Singh, Surender; Kumar, Saravanan; Panigrahi, Aswini K; Hariprasad, Gururao; Jena, Manoj K; Anand, Vijay; Kumar, Sudarshan; Kaushik, Jai K; Dang, Ajay K; Mukesh, Manishi; Mishra, Bishnu P; Srinivasan, Alagiri; Reddy, Vanga S; Mohanty, Ashok K

    2013-11-01

    Mammary gland is made up of a branching network of ducts that end in alveoli. Terminally differentiated mammary epithelial cells (MECs) constitute the innermost layer of aveoli. They are milk-secreting cuboidal cells that secrete milk proteins during lactation. Little is known about the expression profile of proteins in the metabolically active MECs during lactation or their functional role in the lactation process. In the present investigation, we have reported the proteome map of MECs in lactating cows using 2DE MALDI-TOF/TOF MS and 1D-Gel-LC-MS/MS. MECs were isolated from milk using immunomagnetic beads and confirmed by RT-PCR and Western blotting. The 1D-Gel-LC-MS/MS and 2DE-MS/MS based approaches led to identification of 431 and 134 proteins, respectively, with a total of 497 unique proteins. Proteins identified in this study were clustered into functional groups using bioinformatics tools. Pathway analysis of the identified proteins revealed 28 pathways (p < 0.05) providing evidence for involvement of various proteins in lactation function. This study further provides experimental evidence for the presence of many proteins that have been predicted in annotated bovine genome. The data generated further provide a set of bovine MEC-specific proteins that will help the researchers to understand the molecular events taking place during lactation.

  18. 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

  19. Functionalization of hybrid monolithic columns via thiol-ene click reaction for proteomics analysis.

    PubMed

    Liu, Zhongshan; Liu, Jing; Liu, Zheyi; Wang, Hongwei; Ou, Junjie; Ye, Mingliang; Zou, Hanfa

    2017-05-19

    The vinyl-functionalized hybrid monolithic columns (75 and 150μm i.d.) were prepared via sol-gel chemistry of tetramethoxysilane (TMOS) and vinyltrimethoxysilane (VTMS). The content of accessible vinyl groups was further improved after the monolithic column was post-treated with vinyldimethylethoxysilane (VDMES). The surface properties of monolithic columns were tailored via thiol-ene click reaction by using 1-octadecanethiol, sodium 3-mercapto-1-propanesulfonate and 2,2'-(ethylenedioxy)diethanethiol/vinylphosphonic acid, respectively. The preparing octadecyl-functionalized monolithic columns were adopted for proteomics analysis in cLC-MS/MS. A 37-cm-long×75-μm-i.d. monolithic column could identify 3918 unique peptides and 1067 unique proteins in the tryptic digest of proteins from HeLa cells. When a 90-cm-long×75-μm-i.d. monolithic column was used, the numbers of unique peptides and proteins were increased by 82% and 32%, respectively. Furthermore, strong cation exchange (SCX) monolithic columns (4cm in length×150μm i.d.) were also prepared and coupled with the 37-cm-long×75-μm-i.d. octadecyl-functionalized monolithic column for two-dimensional SCX-RPLC-MS/MS analysis, which could identify 17114 unique peptides and 3211 unique proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    PubMed Central

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

    2016-01-01

    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 when Sirt5 is 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. Sirt5 knockout (KO) mice have lower ECHA activity, increased long-chain acyl-CoAs, and decreased ATP in the heart under fasting conditions. Sirt5 KO 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

  1. Combined transcranial direct current stimulation and robotic upper limb therapy improves upper limb function in an adult with cerebral palsy.

    PubMed

    Friel, Kathleen M; Lee, Peter; Soles, Lindsey V; Smorenburg, Ana R P; Kuo, Hsing-Ching; Gupta, Disha; Edwards, Dylan J

    2017-01-01

    Robotic therapy can improve upper limb function in hemiparesis. Excitatory transcranial direct current stimulation (tDCS) can prime brain motor circuits before therapy. We tested safety and efficacy of tDCS plus robotic therapy in an adult with unilateral spastic cerebral palsy (USCP). In each of 36 sessions, anodal tDCS (2 mA, 20 min) was applied over the motor map of the affected hand. Immediately after tDCS, the participant completed robotic therapy, using the shoulder, elbow, and wrist (MIT Manus). The participant sat in a padded chair with affected arm abducted, forearm supported, and hand grasping the robot handle. The participant controlled the robot arm with his affected arm to move a cursor from the center of a circle to each of eight targets (960 movements). Motor function was tested before, after, and six months after therapy with the Wolf Motor Function Test (WMFT) and Fugl-Meyer (FM). Reaching accuracy on the robot task improved significantly after therapy. The WMFT and FM improved clinically meaningful amounts after therapy. The motor map of the affected hand expanded after therapy. Improvements were maintained six months after therapy. Combined tDCS and robotics safely improved upper limb function in an adult with USCP.

  2. Effects of robotic-aided rehabilitation on recovery of upper extremity function in chronic stroke: a single case study.

    PubMed

    Flinn, Nancy A; Smith, Jennifer L; Tripp, Christopher J; White, Matthew W

    2009-01-01

    The objective of the study was to examine the results of robotic therapy in a single client. A 48-year-old female client 15 months post-stroke, with right hemiparesis, received robotic therapy as an outpatient in a large Midwestern rehabilitation hospital. Robotic therapy was provided three times a week for 6 weeks. Robotic therapy consisted of goal-directed, robotic-aided reaching tasks to exercise the hemiparetic shoulder and elbow. No other therapeutic intervention for the affected upper extremity was provided during the study or 3 months follow-up period. The outcome measures included the Fugl-Meyer, graded Wolf motor function test (GWMFT), motor activity log, active range of motion and Canadian occupational performance measure. The participant made gains in active movement; performance; and satisfaction of functional tasks, GWMFT and functional use. Limitations involved in this study relate to the generalizability of the sample size, effect of medications, expense of robotic technologies and the impact of aphasia. Future research should incorporate functional use training along with robotic therapy.

  3. Enhancing functional electrical stimulation for emerging rehabilitation robotics in the framework of HYPER project.

    PubMed

    Brunetti, F; Garay, Á; Moreno, J C; Pons, J L

    2011-01-01

    This paper presents the development of a novel functional electrical stimulation (FES) system. New approaches in emerging rehabilitation robotics propose the use of residual muscular activity or limbs movements during the rehabilitation process of neuromotor. More ambitious projects propose the use of FES systems to restore or compensate motor capabilities by controlling existing muscles or subject limbs. These emerging approaches require more sophisticated FES devices in terms of channels, signals controls and portability. In the framework of HYPER project, such devices are being developed to support the main objective of the project: the development of neurorobots and neuroprosthetics to restore functional motor capabilities in patients who suffered cerebrovascular accidents or spinal cord injury. The presented portable FES system includes novel elec-trostimulator circuits and improved channel switching capacities to enable emerging approaches in rehabilitation robotics. © 2011 IEEE

  4. 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

  5. The proteomics of lipid droplets: structure, dynamics, and functions of the organelle conserved from bacteria to humans

    PubMed Central

    Yang, Li; Ding, Yunfeng; Chen, Yong; Zhang, Shuyan; Huo, Chaoxing; Wang, Yang; Yu, Jinhai; Zhang, Peng; Na, Huimin; Zhang, Huina; Ma, Yanbin; Liu, Pingsheng

    2012-01-01

    Lipid droplets are cellular organelles that consists of a neutral lipid core covered by a monolayer of phospholipids and many proteins. They are thought to function in the storage, transport, and metabolism of lipids, in signaling, and as a specialized microenvironment for metabolism in most types of cells from prokaryotic to eukaryotic organisms. Lipid droplets have received a lot of attention in the last 10 years as they are linked to the progression of many metabolic diseases and hold great potential for the development of neutral lipid-derived products, such as biofuels, food supplements, hormones, and medicines. Proteomic analysis of lipid droplets has yielded a comprehensive catalog of lipid droplet proteins, shedding light on the function of this organelle and providing evidence that its function is conserved from bacteria to man. This review summarizes many of the proteomic studies on lipid droplets from a wide range of organisms, providing an evolutionary perspective on this organelle. PMID:22534641

  6. Effect of Robot-Assisted Game Training on Upper Extremity Function in Stroke Patients

    PubMed Central

    2017-01-01

    Objective To determine the effects of combining robot-assisted game training with conventional upper extremity rehabilitation training (RCT) on motor and daily functions in comparison with conventional upper extremity rehabilitation training (OCT) in stroke patients. Methods Subjects were eligible if they were able to perform the robot-assisted game training and were divided randomly into a RCT and an OCT group. The RCT group performed one daily session of 30 minutes of robot-assisted game training with a rehabilitation robot, plus one daily session of 30 minutes of conventional rehabilitation training, 5 days a week for 2 weeks. The OCT group performed two daily sessions of 30 minutes of conventional rehabilitation training. The effects of training were measured by a Manual Function Test (MFT), Manual Muscle Test (MMT), Korean version of the Modified Barthel Index (K-MBI) and a questionnaire about satisfaction with training. These measurements were taken before and after the 2-week training. Results Both groups contained 25 subjects. After training, both groups showed significant improvements in motor and daily functions measured by MFT, MMT, and K-MBI compared to the baseline. Both groups demonstrated similar training effects, except motor power of wrist flexion. Patients in the RCT group were more satisfied than those in the OCT group. Conclusion There were no significant differences in changes in most of the motor and daily functions between the two types of training. However, patients in the RCT group were more satisfied than those in the OCT group. Therefore, RCT could be a useful upper extremity rehabilitation training method. PMID:28971037

  7. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant

    PubMed Central

    Brooks, Brandon; Mueller, Ryan S.; Young, Jacque C.; Morowitz, Michael J.; Hettich, Robert L.; Banfield, Jillian F.

    2015-01-01

    While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13–21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains of Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential. PMID:26191049

  8. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant

    DOE PAGES

    Brooks, Brandon; Mueller, R. S.; Young, Jacque C.; ...

    2015-07-01

    While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13 21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains ofmore » Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential.« less

  9. Plasma input function determination for PET using a commercial laboratory robot.

    PubMed

    Alexoff, D L; Shea, C; Fowler, J S; King, P; Gatley, S J; Schlyer, D J; Wolf, A P

    1995-10-01

    A commercial laboratory robot system (Zymate PyTechnology II Laboratory Automation System) was interfaced to standard and custom laboratory equipment and programmed to perform rapid radiochemical assays necessary for plasma input function determination in quantitative PET studies in humans and baboons. A Zymark XP robot arm was used to carry out two assays: (1) the determination of total plasma radioactivity concentrations in a series of small-volume whole blood samples and (2) the determination of unchanged (parent) radiotracer in plasma using only solid phase extraction methods. Steady state robotic throughput for determination of total plasma radioactivity in whole blood samples (0.350 mL) is 14.3 samples/h, which includes automated centrifugation, pipetting, weighing and radioactivity counting. Robotic throughput for the assay of parent radiotracer in plasma is 4-6 samples/h depending on the radiotracer. Percents of total radioactivities present as parent radiotracers at 60 min, postinjection of 25 +/- 5.0 (N = 25), 26 +/- 6.8 (N = 68), 13 +/- 4.4 (N = 30), 32 +/- 7.2 (N = 18), 16 +/- 4.9 (N = 20), were obtained for carbon-11 labeled benztropine, raclopride, methylphenidate, SR 46349B (trans, 4-[(3Z)3-(2-dimethylamino-ethyl) oxyimino-3 (2-fluorophenyl)propen-1-yl]phenol), and cocaine respectively in baboon plasma and 84 +/- 6.4 (N = 9), 18 +/- 11 (N = 10), 74 +/- 5.7 (N = 118) and 16 +/- 3.7 (N = 18) for carbon-11 labeled benztropine, deprenyl, raclopride, and methylphenidate respectively in human plasma. The automated system has been used for more than 4 years for all plasma analyses for 7 different C-11 labeled compounds used routinely in our laboratory. The robotic radiotracer assay runs unattended and includes automated cleanup procedures that eliminates all human contact with plasma-contaminated containers.

  10. The human sperm proteome 2.0: An integrated resource for studying sperm functions at the level of posttranslational modification.

    PubMed

    Wang, Ying; Wan, Jinyuan; Ling, Xiufeng; Liu, Mingxi; Zhou, Tao

    2016-10-01

    Various types of PTMs play important roles in the regulation of sperm proteins. However, most large-scale proteomic studies only focused on a single type of modification due to the limitation of enrichment methods. To investigate the complex composition of modified sperm proteins, we constructed the human sperm proteome 2.0 that integrated lysine acetylated, phosphorylated, N-linked glycosylated, and protein N-terminal acetylated proteins from previously published proteomic datasets. A total of 6069 modified sites on 2132 proteins were annotated. Functional enrichment analyses showed that different types of modified sperm proteins displayed different functional distributions. We found that acetylated, phosphorylated, and glycosylated proteins are more directly involved in sperm functions. While N-termnial acetylated proteins and nonmodified proteins appear to be more associated with the basic cellular functions. Thus, it is efficient to search for fertility-associated biomarkers in acetylated, phosphorylated, and glycosylated proteins. We also predicted modification cross-talks within the same proteins or between different proteins that provided potential hotspot targets for understanding the regulation of sperm functions via multiple modifications.

  11. [Effects of rehabilitation robot for lower-limb on motor function in hemiplegic patients after stroke].

    PubMed

    Wu, Hua; Gu, Xu-dong; Fu, Jian-ming; Yao, Yun-hai; Li, Jian-hua; Xu, Zhi-sheng

    2012-10-09

    To explore the effects of rehabilitation robot for lower-limb on motor function in hemiplegic patients after stroke. Forty-eight hemiplegic patients were divided randomly into treatment (n = 24) and control (n = 24) group. The neuro-facilitation technique was applied for both groups. But the treatment group had also rehabilitation robot for lower-limb training of 10 - 20 min/d, 6 d/week for 8 weeks. All patients were assessed with the Fugl-Meyer lower limb (FMA), 10 m maximum walking speed (MWS), function ambulation category (FAC) classification and the modified Barthel index (MBI)at the time of beginning and 8 weeks later. Prior to intervention, no significant differences in any parameter existed between two groups. Eight weeks later, all assessment scores of FMA (25.7 ± 3.5), MWS (52 ± 16), FAC (4.3 ± 1.4) and MBI (82 + 17) were significantly better in the treatment group than those FMA (22.8 ± 3.7), MWS (40 ± 17), FAC (3.4 ± 1.3) and MBI (72 ± 14) in the control group. The application of rehabilitation robot for lower-limb may markedly improve the motor function of lower limb, walking ability and activity of daily living.

  12. A damper driven robotic end-point manipulator for functional rehabilitation exercises after stroke.

    PubMed

    Westerveld, Ard J; Aalderink, Bernard Johan; Hagedoorn, Wouter; Buijze, Martijn; Schouten, Alfred C; Kooij, Herman van der

    2014-10-01

    Stroke survivors may benefit from robotic assistance for relearning of functional movements. Current assistive devices are either passive, limited to only two dimensions or very powerful. However, for reach training, weight compensation and a little assistance with limited power is sufficient. We designed and evaluated a novel three-dimensional robotic manipulator, which is able to support the arm weight and assist functional reaching movements. Key points of the design are a damper-based drive train, giving an inherently safe system and its compact and lightweight design. The system is force actuated with a bandwidth of up to 2.3 Hz, which is sufficient for functional arm movements. Maximal assistive forces are 15 N for the up/down and forward/backward directions and 10 N for the left/right direction. Force tracking errors are smaller than 1.5 N for all axes and the total weight of the robot is 25 kg. Furthermore, the device has shown its benefit for increasing reaching distance in a single-case study with a stroke subject. The newly developed system has the technical ability to assist the arm during movement, which is a prerequisite for successful training of stroke survivors. Therapeutic effects of the applied assistance need to be further evaluated. However, with its inherent safety and ease of use, this newly developed system even has the potential for home-based therapeutic training after stroke.

  13. Redox proteomics identification of oxidatively modified myocardial proteins in human heart failure: implications for protein function.

    PubMed

    Brioschi, Maura; Polvani, Gianluca; Fratto, Pasquale; Parolari, Alessandro; Agostoni, Piergiuseppe; Tremoli, Elena; Banfi, Cristina

    2012-01-01

    Increased oxidative stress in a failing heart may contribute to the pathogenesis of heart failure (HF). The aim of this study was to identify the oxidised proteins in the myocardium of HF patients and analyse the consequences of oxidation on protein function. The carbonylated proteins in left ventricular tissue from failing (n = 14) and non-failing human hearts (n = 13) were measured by immunoassay and identified by proteomics. HL-1 cardiomyocytes were incubated in the presence of stimuli relevant for HF in order to assess the generation of reactive oxygen species (ROS), the induction of protein carbonylation, and its consequences on protein function. The levels of carbonylated proteins were significantly higher in the HF patients than in the controls (p<0.01). We identified two proteins that mainly underwent carbonylation: M-type creatine kinase (M-CK), whose activity is impaired, and, to a lesser extent, α-cardiac actin. Exposure of cardiomyocytes to angiotensin II and norepinephrine led to ROS generation and M-CK carbonylation with loss of its enzymatic activity. Our findings indicate that protein carbonylation is increased in the myocardium during HF and that these oxidative changes may help to explain the decreased CK activity and consequent defects in energy metabolism observed in HF.

  14. Redox Proteomics Identification of Oxidatively Modified Myocardial Proteins in Human Heart Failure: Implications for Protein Function

    PubMed Central

    Brioschi, Maura; Polvani, Gianluca; Fratto, Pasquale; Parolari, Alessandro; Agostoni, Piergiuseppe; Tremoli, Elena; Banfi, Cristina

    2012-01-01

    Increased oxidative stress in a failing heart may contribute to the pathogenesis of heart failure (HF). The aim of this study was to identify the oxidised proteins in the myocardium of HF patients and analyse the consequences of oxidation on protein function. The carbonylated proteins in left ventricular tissue from failing (n = 14) and non-failing human hearts (n = 13) were measured by immunoassay and identified by proteomics. HL-1 cardiomyocytes were incubated in the presence of stimuli relevant for HF in order to assess the generation of reactive oxygen species (ROS), the induction of protein carbonylation, and its consequences on protein function. The levels of carbonylated proteins were significantly higher in the HF patients than in the controls (p<0.01). We identified two proteins that mainly underwent carbonylation: M-type creatine kinase (M-CK), whose activity is impaired, and, to a lesser extent, α-cardiac actin. Exposure of cardiomyocytes to angiotensin II and norepinephrine led to ROS generation and M-CK carbonylation with loss of its enzymatic activity. Our findings indicate that protein carbonylation is increased in the myocardium during HF and that these oxidative changes may help to explain the decreased CK activity and consequent defects in energy metabolism observed in HF. PMID:22606238

  15. 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.

  16. Proteomic Landscape of Tissue-Specific Cyclin E Functions in Vivo

    PubMed Central

    Odajima, Junko; Jung, Piotr; Ndassa-Colday, Yasmine; Ficaro, Scott; Geng, Yan; Marco, Eugenio; Michowski, Wojciech; Wang, Yaoyu E.; DeCaprio, James A.; Litovchick, Larisa; Marto, Jarrod; Sicinski, Piotr

    2016-01-01

    E-type cyclins (cyclins E1 and E2) are components of the cell cycle machinery that has been conserved from yeast to humans. The major function of E-type cyclins is to drive cell division. It is unknown whether in addition to their ‘core’ cell cycle functions, E-type cyclins also perform unique tissue-specific roles. Here, we applied high-throughput mass spectrometric analyses of mouse organs to define the repertoire of cyclin E protein partners in vivo. We found that cyclin E interacts with distinct sets of proteins in different compartments. These cyclin E interactors are highly enriched for phosphorylation targets of cyclin E and its catalytic partner, the cyclin-dependent kinase 2 (Cdk2). Among cyclin E interactors we identified several novel tissue-specific substrates of cyclin E-Cdk2 kinase. In proliferating compartments, cyclin E-Cdk2 phosphorylates Lin proteins within the DREAM complex. In the testes, cyclin E-Cdk2 phosphorylates Mybl1 and Dmrtc2, two meiotic transcription factors that represent key regulators of spermatogenesis. In embryonic and adult brains cyclin E interacts with proteins involved in neurogenesis, while in adult brains also with proteins regulating microtubule-based processes and microtubule cytoskeleton. We also used quantitative proteomics to demonstrate re-wiring of the cyclin E interactome upon ablation of Cdk2. This approach can be used to study how protein interactome changes during development or in any pathological state such as aging or cancer. PMID:27828963

  17. A versatile gene trap to visualize and interrogate the function of the vertebrate proteome

    PubMed Central

    Trinh, Le A.; Hochgreb, Tatiana; Graham, Matthew; Wu, David; Ruf-Zamojski, Frederique; Jayasena, Chathurani S.; Saxena, Ankur; Hawk, Rasheeda; Gonzalez-Serricchio, Aidyl; Dixson, Alana; Chow, Elly; Gonzales, Constanza; Leung, Ho-Yin; Solomon, Ilana; Bronner-Fraser, Marianne; Megason, Sean G.; Fraser, Scott E.

    2011-01-01

    We report a multifunctional gene-trapping approach, which generates full-length Citrine fusions with endogenous proteins and conditional mutants from a single integration event of the FlipTrap vector. We identified 170 FlipTrap zebrafish lines with diverse tissue-specific expression patterns and distinct subcellular localizations of fusion proteins generated by the integration of an internal citrine exon. Cre-mediated conditional mutagenesis is enabled by heterotypic lox sites that delete Citrine and “flip” in its place mCherry with a polyadenylation signal, resulting in a truncated fusion protein. Inducing recombination with Cerulean-Cre results in fusion proteins that often mislocalize, exhibit mutant phenotypes, and dramatically knock down wild-type transcript levels. FRT sites in the vector enable targeted genetic manipulation of the trapped loci in the presence of Flp recombinase. Thus, the FlipTrap captures the functional proteome, enabling the visualization of full-length fluorescent fusion proteins and interrogation of function by conditional mutagenesis and targeted genetic manipulation. PMID:22056673

  18. A clinically feasible multiplex proteomic immunoassay as a novel functional diagnostic for pancreatic ductal adenocarcinoma

    PubMed Central

    Lim, Kian-Huat; Langley, Emma; Gao, Feng; Luo, Jingqin; Li, Lin; Meyer, Gary; Kim, Phillip; Singh, Sharat; Kushnir, Vladamir M.; Early, Dayna S.; Mullady, Daniel K.; Edmundowicz, Steven A.; Wani, Sachin; Murad, Faris M.; Cao, Dengfeng; Azar, Riad R.; Wang-Gillam, Andrea

    2017-01-01

    To date, targeted therapy for pancreatic ductal adenocarcinoma (PDAC) remains largely unsuccessful in the clinic. Current genomics-based technologies are unable to reflect the quantitative, dynamic signaling changes in the tumor, and require larger tumor samples that are difficult to obtain in PDAC patients. Therefore, a highly sensitive functional tool that can reliably and comprehensively inform intra-tumoral signaling events is direly needed to guide treatment decision. We tested the utility of a highly sensitive proteomics-based functional diagnostic platform, Collaborative Enzyme Enhanced Reactive-immunoassay (CEERTM), on fine-needle aspiration (FNA) samples obtained from 102 patients with radiographically-evident pancreatic tumors. Two FNA passes were collected from each patient, hybridized to customized chips coated with an array of capture antibodies, and detected using two enzyme-conjugated antibodies which emit quantifiable signals. We demonstrate that this technique is highly sensitive in detecting total and phosphorylated forms of multiple signaling molecules in FNA specimens, with reasonable correlation of marker intensities between two different FNA passes. Notably, signals of several markers were significantly higher in PDAC compared to non-cancerous samples. In PDAC samples, we found high total c-Met signal to be associated with poor survival, and confirmed this finding using an independent PDAC tissue microarray. PMID:28445954

  19. Functional annotation of proteomic data from chicken heterophils and macrophages induced by carbon nanotube exposure.

    PubMed

    Li, Yun-Ze; Cheng, Chung-Shi; Chen, Chao-Jung; Li, Zi-Lin; Lin, Yao-Tung; Chen, Shuen-Ei; Huang, San-Yuan

    2014-05-12

    With the expanding applications of carbon nanotubes (CNT) in biomedicine and agriculture, questions about the toxicity and biocompatibility of CNT in humans and domestic animals are becoming matters of serious concern. This study used proteomic methods to profile gene expression in chicken macrophages and heterophils in response to CNT exposure. Two-dimensional gel electrophoresis identified 12 proteins in macrophages and 15 in heterophils, with differential expression patterns in response to CNT co-incubation (0, 1, 10, and 100 µg/mL of CNT for 6 h) (p < 0.05). Gene ontology analysis showed that most of the differentially expressed proteins are associated with protein interactions, cellular metabolic processes, and cell mobility, suggesting activation of innate immune functions. Western blot analysis with heat shock protein 70, high mobility group protein, and peptidylprolyl isomerase A confirmed the alterations of the profiled proteins. The functional annotations were further confirmed by effective cell migration, promoted interleukin-1β secretion, and more cell death in both macrophages and heterophils exposed to CNT (p < 0.05). In conclusion, results of this study suggest that CNT exposure affects protein expression, leading to activation of macrophages and heterophils, resulting in altered cytoskeleton remodeling, cell migration, and cytokine production, and thereby mediates tissue immune responses.

  20. Cytoskeleton and nuclear lamina affection in recessive osteogenesis imperfecta: A functional proteomics perspective.

    PubMed

    Gagliardi, Assunta; Besio, Roberta; Carnemolla, Chiara; Landi, Claudia; Armini, Alessandro; Aglan, Mona; Otaify, Ghada; Temtamy, Samia A; Forlino, Antonella; Bini, Luca; Bianchi, Laura

    2017-09-07

    Osteogenesis imperfecta (OI) is a collagen-related disorder associated to dominant, recessive or X-linked transmission, mainly caused by mutations in type I collagen genes or in genes involved in type I collagen metabolism. Among the recessive forms, OI types VII, VIII, and IX are due to mutations in CRTAP, P3H1, and PPIB genes, respectively. They code for the three components of the endoplasmic reticulum complex that catalyzes 3-hydroxylation of type I collagen α1Pro986. Under-hydroxylation of this residue leads to collagen structural abnormalities and results in moderate to lethal OI phenotype, despite the exact molecular mechanisms are still not completely clear. To shed light on these recessive forms, primary fibroblasts from OI patients with mutations in CRTAP (n=3), P3H1 (n=3), PPIB (n=1) genes and from controls (n=4) were investigated by a functional proteomic approach. Cytoskeleton and nucleoskeleton asset, protein fate, and metabolism were delineated as mainly affected. While western blot experiments confirmed altered expression of lamin A/C and cofilin-1, immunofluorescence analysis using antibody against lamin A/C and phalloidin showed an aberrant organization of nucleus and cytoskeleton. This is the first report describing an altered organization of intracellular structural proteins in recessive OI and pointing them as possible novel target for OI treatment. OI is a prototype for skeletal dysplasias. It is a highly heterogeneous collagen-related disorder with dominant, recessive and X-linked transmission. There is no definitive cure for this disease, thus a better understanding of the molecular basis of its pathophysiology is expected to contribute in identifying potential targets to develop new treatments. Based on this concept, we performed a functional proteomic study to delineate affected molecular pathways in primary fibroblasts from recessive OI patients, carrying mutations in CRTAP (OI type VII), P3H1 (OI type VIII), and PPIB (OI type IX) genes

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

    SciTech Connect

    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, 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.

  2. A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses.

    PubMed

    Sobhy, Haitham

    2017-04-01

    Proteins harbor domains or short linear motifs, which facilitate their functions and interactions. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. In this study, we present Shetti-Motif, which is an interactive tool to (i) map UniProt and PROSITE flat files, (ii) search for multiple pre-defined consensus patterns or experimentally validated functional motifs in large datasets protein sequences (proteome-wide), (iii) search for motifs containing repeated residues (low-complexity regions, e.g., Leu-, SR-, PEST-rich motifs, etc.). As proof of principle, using this comparative proteomics pipeline, eleven proteomes encoded by member of Poxviridae family were searched against about 100 experimentally validated functional motifs. The closely related viruses and viruses infect the same host cells (e.g. vaccinia and variola viruses) show similar motif-containing proteins profile. The motifs encoded by these viruses are correlated, which explains why poxviruses are able to interact with wide range of host cells. In conclusion, this in silico analysis is useful to establish a dataset(s) or potential proteins for further investigation or compare between species.

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

    USDA-ARS?s Scientific Manuscript database

    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. A unified perspective on robot control - The energy Lyapunov function approach

    NASA Technical Reports Server (NTRS)

    Wen, John T.

    1990-01-01

    A unified framework for the stability analysis of robot tracking control is presented. By using an energy-motivated Lyapunov function candidate, the closed-loop stability is shown for a large family of control laws sharing a common structure of proportional and derivative feedback and a model-based feedforward. The feedforward can be zero, partial or complete linearized dynamics, partial or complete nonlinear dynamics, or linearized or nonlinear dynamics with parameter adaptation. As result, the dichotomous approaches to the robot control problem based on the open-loop linearization and nonlinear Lyapunov analysis are both included in this treatment. Furthermore, quantitative estimates of the trade-offs between different schemes in terms of the tracking performance, steady state error, domain of convergence, realtime computation load and required a prior model information are derived.

  5. Workspace and pivot point for robot-assisted endoscope guidance in functional endonasal sinus surgery (FESS).

    PubMed

    Eichhorn, Klaus Wolfgang; Westphal, Ralf; Last, Carsten; Rilk, Markus; Bootz, Friedrich; Wahl, Friedrich M; Jakob, Mark

    2015-03-01

    For the further development of robot-assisted endoscope guidance in functional endoscopic sinus surgery (FESS), ground data about the workspaces and endoscope movements in conventional FESS are needed. Applying a self-developed marker-based tracking system, we collected the pose data (position and orientation) of the endoscope and all other instruments used in five real sinus surgeries. The automated segmentation of the endoscope poses shows the shape of a hourglass, with a pivot region or pivot point at the 'waistline' of the hourglass, close to the nasal entrance in the nasal dome. We were able to identify a pivot point at the waistline of the segmented endoscope poses. The size of the pivot point corresponds with the diameter of the 4 mm endoscope. Because of the reduction to four degrees of freedom for endoscope motions (three rotations and one translation), easier and safer robot-assisted endoscope guidance becomes feasible. Copyright © 2014 John Wiley & Sons, Ltd.

  6. 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.

  7. 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

  8. Functional and proteomic alterations of plasma high density lipoproteins in type 1 diabetes mellitus.

    PubMed

    Manjunatha, Shankarappa; Distelmaier, Klaus; Dasari, Surendra; Carter, Rickey E; Kudva, Yogish C; Nair, K Sreekumaran

    2016-09-01

    Higher HDL-cholesterol (HDL-C) is linked to lower cardiovascular risk but individuals with type 1 diabetes mellitus (T1DM) with normal or high HDL-C have higher cardiovascular events compared to age matched non-diabetic controls (ND). We determined whether altered HDL functions despite having normal HDL-C concentration may explain increased cardiovascular risk in T1DM individuals. We also determined whether irreversible posttranslational modifications (PTMs) of HDL bound proteins occur in T1DM individuals with altered HDL functions. T1DM with poor glycemic control (T1D-PC, HbA1c≥8.5%, n=15) and T1DM with good glycemic control (T1D-GC, HbA1c≤6.6%, n=15) were compared with equal numbers of NDs, ND-PC and ND-GC respectively, matched for age, sex and body mass index (BMI). We measured cholesterol efflux capacity (CEC) of HDL in the serum using J774 macrophages, antioxidant function of HDL as the ability to reverse the oxidative damage of LDL and PON1 activity using commercially available kit. For proteomic analysis, HDL was isolated by density gradient ultracentrifugation and was analyzed by mass spectrometry and shotgun proteomics method. Plasma HDL-C concentrations in both T1DM groups were similar to their ND. However, CEC (%) of T1D-PC (16.9±0.8) and T1D-GC (17.1±1) were lower than their respective ND (17.9±1, p=0.01 and 18.2±1.4, p=0.02). HDL antioxidative function also was lower (p<0.05). The abundance of oxidative PTMs of apolipoproteins involved in CEC and antioxidative functions of HDL were higher in T1D-PC (ApoA4, p=0.041) and T1D-GC (ApoA4, p=0.025 and ApoE, p=0.041) in comparison with ND. Both T1D-PC and T1D-GC groups had higher abundance of amadori modification of ApoD (p=0.002 and p=0.041 respectively) and deamidation modification of ApoA4 was higher in T1D-PC (p=0.025). Compromised functions of HDL particles in T1DM individuals, irrespective of glycemic control, could be explained by higher abundance of irreversible PTMs of HDL proteins. These

  9. Functional classification of cellular proteome profiles support the identification of drug resistance signatures in melanoma cells.

    PubMed

    Paulitschke, Verena; Haudek-Prinz, Verena; Griss, Johannes; Berger, Walter; Mohr, Thomas; Pehamberger, Hubert; Kunstfeld, Rainer; Gerner, Christopher

    2013-07-05

    Drug resistance is a major obstacle in melanoma treatment. Recognition of specific resistance patterns, the understanding of the patho-physiology of drug resistance, and identification of remaining options for individual melanoma treatment would greatly improve therapeutic success. We performed mass spectrometry-based proteome profiling of A375 melanoma cells and HeLa cells characterized as sensitive to cisplatin in comparison to cisplatin resistant M24met and TMFI melanoma cells. Cells were fractionated into cytoplasm, nuclei and secretome and the proteome profiles classified according to Gene Ontology. The cisplatin resistant cells displayed increased expression of lysosomal as well as Ca²⁺ ion binding and cell adherence proteins. These findings were confirmed using Lysotracker Red staining and cell adhesion assays with a panel of extracellular matrix proteins. To discriminate specific survival proteins, we selected constitutively expressed proteins of resistant M24met cells which were found expressed upon challenging the sensitive A375 cells. Using the CPL/MUW proteome database, the selected lysosomal, cell adherence and survival proteins apparently specifying resistant cells were narrowed down to 47 proteins representing a potential resistance signature. These were tested against our proteomics database comprising more than 200 different cell types/cell states for its predictive power. We provide evidence that this signature enables the automated assignment of resistance features as readout from proteome profiles of any human cell type. Proteome profiling and bioinformatic processing may thus support the understanding of drug resistance mechanism, eventually guiding patient tailored therapy.

  10. Proteomics and functional analyses of Arabidopsis nitrilases involved in the defense response to microbial pathogens.

    PubMed

    Choi, Du Seok; Lim, Chae Woo; Hwang, Byung Kook

    2016-08-01

    Proteomics and functional analyses of the Arabidopsis - Pseudomonas syringae pv. tomato interactions reveal that Arabidopsis nitrilases are required for plant defense and R gene-mediated resistant responses to microbial pathogens. A high-throughput in planta proteome screen has identified Arabidopsis nitrilase 2 (AtNIT2), which was de novo-induced by Pseudomonas syringae pv. tomato (Pst) infection. The AtNIT2, AtNIT3, and AtNIT4 genes, but not AtNIT1, were distinctly induced in Arabidopsis leaves by Pst infection. Notably, avirulent Pst DC3000 (avrRpt2) infection led to significant induction of AtNIT2 and AtNIT4 in leaves. Pst DC3000 and Pst DC3000 (avrRpt2) significantly grew well in leaves of nitrilase transgenic (nit2i-2) and mutant (nit1-1 and nit3-1) lines compared to the wild-type leaves. In contrast, NIT2 overexpression in nit2 mutants led to significantly high growth of the two Pst strains in leaves. The nitrilase transgenic and mutant lines exhibited enhanced susceptibility to Hyaloperonospora arabidopsidis infection. The nit2 mutation enhanced Pst DC3000 (avrRpt2) growth in salicylic acid (SA)-deficient NahG transgenic and sid2 and npr1 mutant lines. Infection with Pst DC3000 or Pst DC3000 (avrRpt2) induced lower levels of indole-3-acetic acid (IAA) in nit2i and nit2i NahG plants than in wild-type plants, but did not alter the IAA level in NahG transgenic plants. This suggests that Arabidopsis nitrilase 2 is involved in IAA signaling of defense and R gene-mediated resistance responses to Pst infection. Quantification of SA in these transgenic and mutant plants demonstrates that Arabidopsis nitrilase 2 is not required for SA-mediated defense response to the virulent Pst DC3000 but regulates SA-mediated resistance to the avirulent Pst DC3000 (avrRpt2). These results collectively suggest that Arabidopsis nitrilase genes are involved in plant defense and R gene-mediated resistant responses to microbial pathogens.

  11. Quantitative proteomics and bioinformatic analysis provide new insight into protein function during avian eggshell biomineralization.

    PubMed

    Marie, Pauline; Labas, Valérie; Brionne, Aurélien; Harichaux, Grégoire; Hennequet-Antier, Christelle; Nys, Yves; Gautron, Joël

    2015-01-15

    are associated with distinct populations of matrix proteins that are secreted into the acellular uterine fluid as modulators of the process. The recent development of high-throughput methods has led to the identification of many proteins in the shell, but little is known concerning their role in shell formation. In order to determine precisely the importance of particular proteins relative to eggshell mineralization, this project used qualitative and quantitative proteomics of the uterine fluid constituents, coupled with bioinformatic analysis, to predict the functional role of proteins secreted at each of the three main stages of shell calcification. Besides its relevance to food production and to hen reproduction, eggshell calcification is furthermore a relevant model for studying calcium carbonate biomineralization on a two-dimensional membrane support. Better understanding of this process will provide insight into the fabrication of ceramics at ambient pressure and temperature. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. First insight into the proteome landscape of the porcine short posterior ciliary arteries: Key signalling pathways maintaining physiologic functions

    PubMed Central

    Manicam, Caroline; Perumal, Natarajan; Pfeiffer, Norbert; Grus, Franz H.; Gericke, Adrian

    2016-01-01

    Short posterior ciliary arteries (sPCA) provide the major blood supply to the optic nerve head. Emerging evidence has linked structural and functional anomalies of sPCA to the pathogenesis of several ocular disorders that cause varying degrees of visual loss, particularly anterior ischaemic optic neuropathy and glaucoma. Although the functional relevance of this vascular bed is well-recognized, the proteome of sPCA remains uncharacterized. Since the porcine ocular system closely resembles that of the human’s and is increasingly employed in translational ophthalmic research, this study characterized the proteome of porcine sPCA employing the mass spectrometry-based proteomics strategy. A total of 1742 proteins and 10527 peptides were identified in the porcine sPCA. The major biological processes involved in the maintenance of physiological functions of the sPCA included redox and metabolic processes, and cytoskeleton organization. These proteins were further clustered into diverse signalling pathways that regulate vasoactivity of sPCA, namely the tight junction, α- and β-adrenoceptor, 14-3-3, nitric oxide synthase and endothelin-1 -mediated signalling pathways. This study provides the first insight into the complex mechanisms dictating the vast protein repertoire in normal vascular physiology of the porcine sPCA. It is envisioned that our findings will serve as important benchmarks for future studies of sPCA. PMID:27922054

  13. Impact of obesity on early erectile function recovery after robotic radical prostatectomy.

    PubMed

    Uffort, Ekong E; Jensen, James C

    2011-01-01

    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. 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. 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). 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.

  14. Proteomic analysis of physiological function response to hot summer in liver from lactating dairy cows.

    PubMed

    Wang, Qiangjun; Zhao, Xiaowei; Zhang, Zijun; Zhao, Huiling; Huang, Dongwei; Cheng, Guanglong; Yang, Yongxin

    2017-04-01

    Lactation performance of dairy cattle is susceptible to heat stress. The liver is one of the most crucial organs affected by high temperature in dairy cows. However, the physiological adaption by the liver to hot summer conditions has not been well elucidated in lactating dairy cows. In the present study, proteomic analysis of the liver in dairy cows in spring and hot summer was performed using a label-free method. In total, 127 differentially expressed proteins were identified; most of the upregulated proteins were involved in protein metabolic processes and responses to stimuli, whereas most of the downregulated proteins were related to oxidation-reduction. Pathway analysis indicated that 3 upregulated heat stress proteins (HSP90α, HSP90β, and endoplasmin) were enriched in the NOD-like receptor signaling pathway, whereas several downregulated NADH dehydrogenase proteins were involved in the oxidative phosphorylation pathway. The protein-protein interaction network indicated that several upregulated HSPs (HSP90α, HSP90β, and GRP78) were involved in more interactions than other proteins and were thus considered as central hub nodes. Our findings provide novel insights into the physiological adaption of liver function in lactating dairy cows to natural high temperature. Copyright © 2017. Published by Elsevier Ltd.

  15. Functional Proteomic And Structural Insights Into Molecular Recognition in the Nitrilase Family Enzymes

    SciTech Connect

    Barglow, K.T.; Saikatendu, K.; Bracey, M.H.; Huey, R.; Morris, G.M.; Olson, A.J.; Stevens, R.C.; Cravatt, B.F.

    2009-05-11

    Nitrilases are a large and diverse family of nonpeptidic C-N hydrolases. The mammalian genome encodes eight nitrilase enzymes, several of which remain poorly characterized. Prominent among these are nitrilase-1 (Nit1) and nitrilase-2 (Nit2), which, despite having been shown to exert effects on cell growth and possibly serving as tumor suppressor genes, are without known substrates or selective inhibitors. In previous studies, we identified several nitrilases, including Nit1 and Nit2, as targets for dipeptide-chloroacetamide activity-based proteomics probes. Here, we have used these probes, in combination with high-resolution crystallography and molecular modeling, to systematically map the active site of Nit2 and identify residues involved in molecular recognition. We report the 1.4 {angstrom} crystal structure of mouse Nit2 and use this structure to identify residues that discriminate probe labeling between the Nit1 and Nit2 enzymes. Interestingly, some of these residues are conserved across all vertebrate Nit2 enzymes and, conversely, not found in any vertebrate Nit1 enzymes, suggesting that they are key discriminators of molecular recognition between these otherwise highly homologous enzymes. Our findings thus point to a limited set of active site residues that establish distinct patterns of molecular recognition among nitrilases and provide chemical probes to selectively perturb the function of these enzymes in biological systems.

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

    DOE PAGES

    Allen, Michael S.; Hurst, Gregory B.; Lu, Tse-Yuan S.; ...

    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

  17. Functional proteomics-aided selection of protease inhibitors for herbivore insect control

    PubMed Central

    Rasoolizadeh, Asieh; Munger, Aurélie; Goulet, Marie-Claire; Sainsbury, Frank; Cloutier, Conrad; Michaud, Dominique

    2016-01-01

    Studies have reported the potential of protease inhibitors to engineer insect resistance in transgenic plants but the general usefulness of this approach in crop protection still remains to be established. Insects have evolved strategies to cope with dietary protease inhibitors, such as the use of proteases recalcitrant to inhibition, that often make the selection of effective inhibitors very challenging. Here, we used a functional proteomics approach for the ‘capture’ of Cys protease targets in crude protein extracts as a tool to identify promising cystatins for plant improvement. Two cystatins found to differ in their efficiency to capture Cys proteases of the coleopteran pest Leptinotarsa decemlineata also differed in their usefulness to produce transgenic potato lines resistant to this insect. Plants expressing the most potent cystatin at high level had a strong repressing effect on larval growth and leaf intake, while plants expressing the weakest cystatin showed no effect on both two parameters compared to untransformed parental line used for genetic transformation. Our data underline the relevance of considering the whole range of possible protease targets when selecting an inhibitor for plant pest control. They also confirm the feasibility of developing cystatin-expressing transgenics resistant to a major pest of potato. PMID:27958307

  18. 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.

  19. Functional Differentiation of Bundle Sheath and Mesophyll Maize Chloroplasts Determined by Comparative ProteomicsW⃞

    PubMed Central

    Majeran, Wojciech; Cai, Yang; Sun, Qi; van Wijk, Klaas J.

    2005-01-01

    Chloroplasts of maize (Zea mays) leaves differentiate into specific bundle sheath (BS) and mesophyll (M) types to accommodate C4 photosynthesis. Consequences for other plastid functions are not well understood but are addressed here through a quantitative comparative proteome analysis of purified M and BS chloroplast stroma. Three independent techniques were used, including cleavable stable isotope coded affinity tags. Enzymes involved in lipid biosynthesis, nitrogen import, and tetrapyrrole and isoprenoid biosynthesis are preferentially located in the M chloroplasts. By contrast, enzymes involved in starch synthesis and sulfur import preferentially accumulate in BS chloroplasts. The different soluble antioxidative systems, in particular peroxiredoxins, accumulate at higher levels in M chloroplasts. We also observed differential accumulation of proteins involved in expression of plastid-encoded proteins (e.g., EF-Tu, EF-G, and mRNA binding proteins) and thylakoid formation (VIPP1), whereas others were equally distributed. Enzymes related to the C4 shuttle, the carboxylation and regeneration phase of the Calvin cycle, and several regulators (e.g., CP12) distributed as expected. However, enzymes involved in triose phosphate reduction and triose phosphate isomerase are primarily located in the M chloroplasts, indicating that the M-localized triose phosphate shuttle should be viewed as part of the BS-localized Calvin cycle, rather than a parallel pathway. PMID:16243905

  20. 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.

  1. Identification of brain substrates of transglutaminase by functional proteomics supports its role in neurodegenerative diseases.

    PubMed

    André, William; Nondier, Isabelle; Valensi, Maud; Guillonneau, François; Federici, Christian; Hoffner, Guylaine; Djian, Philippe

    2017-05-01

    Transglutaminases are calcium-dependent enzymes that catalyze the formation of ε-(γ-glutamyl)lysine isopeptide bonds between specific glutamine and lysine residues. Some transglutaminase isoforms are present in the brain and are thought to participate in the protein aggregation characteristic of neurological diseases such as Huntington, Alzheimer's and Parkinson's disease. We have developed a functional proteomics strategy in which biotinylated amine-donor and amine-acceptor probes were used to identify the transglutaminase substrates present in brain. Bioinformatics analyses revealed that most of the 166 brain substrates identified interacted with huntingtin, the amyloid precursor protein or α-synuclein and that neurological disease was the most significant canonical pathway associated with the substrates. The physiological relevance of the substrates identified by mass spectrometry was confirmed by the fact that three of them (actin, β-tubulin and a neurofilament subunit) were polymerized in neuronal cells when cytosolic calcium concentration was raised. We also showed by in-situ immunolabeling that some of the substrates were part of the protein aggregates found in neurological diseases. These results strongly support the idea that the crosslinking activity of brain transglutaminase participates in the formation of the protein aggregates found in diseases of the central nervous system.

  2. 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.

  3. 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.

  4. 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.

  5. SUMOylation Pathway in Trypanosoma cruzi: Functional Characterization and Proteomic Analysis of Target Proteins*

    PubMed Central

    Bayona, Julio C.; Nakayasu, Ernesto S.; Laverrière, Marc; Aguilar, Clemente; Sobreira, Tiago J. P.; Choi, Hyungwon; Nesvizhskii, Alexey I.; Almeida, Igor C.; Cazzulo, Juan J.; Alvarez, Vanina E.

    2011-01-01

    SUMOylation is a relevant protein post-translational modification in eukaryotes. The C terminus of proteolytically activated small ubiquitin-like modifier (SUMO) is covalently linked to a lysine residue of the target protein by an isopeptide bond, through a mechanism that includes an E1-activating enzyme, an E2-conjugating enzyme, and transfer to the target, sometimes with the assistance of a ligase. The modification is reversed by a protease, also responsible for SUMO maturation. A number of proteins have been identified as SUMO targets, participating in the regulation of cell cycle progression, transcription, translation, ubiquitination, and DNA repair. In this study, we report that orthologous genes corresponding to the SUMOylation pathway are present in the etiological agent of Chagas disease, Trypanosoma cruzi. Furthermore, the SUMOylation system is functionally active in this protozoan parasite, having the requirements for SUMO maturation and conjugation. Immunofluorescence analysis showed that T. cruzi SUMO (TcSUMO) is predominantly found in the nucleus. To identify SUMOylation targets and get an insight into their physiological roles we generated transfectant T. cruzi epimastigote lines expressing a double-tagged T. cruzi SUMO, and SUMOylated proteins were enriched by tandem affinity chromatography. By two-dimensional liquid chromatography-mass spectrometry a total of 236 proteins with diverse biological functions were identified as potential T. cruzi SUMO targets. Of these, metacaspase-3 was biochemically validated as a bona fide SUMOylation substrate. Proteomic studies in other organisms have reported that orthologs of putative T. cruzi SUMOylated proteins are similarly modified, indicating conserved functions for protein SUMOylation in this early divergent eukaryote. PMID:21832256

  6. Alterations in high-density lipoprotein proteome and function associated with persistent organic pollutants.

    PubMed

    Ljunggren, Stefan A; Helmfrid, Ingela; Norinder, Ulf; Fredriksson, Mats; Wingren, Gun; Karlsson, Helen; Lindahl, Mats

    2017-01-01

    There is a growing body of evidence that persistent organic pollutants (POPs) may increase the risk for cardiovascular disease (CVD), but the mechanisms remain unclear. High-density lipoprotein (HDL) acts protective against CVD by different processes, and we have earlier found that HDL from subjects with CVD contains higher levels of POPs than healthy controls. In the present study, we have expanded analyses on the same individuals living in a contaminated community and investigated the relationship between the HDL POP levels and protein composition/function. HDL from 17 subjects was isolated by ultracentrifugation. HDL protein composition, using nanoliquid chromatography tandem mass spectrometry, and antioxidant activity were analyzed. The associations of 16 POPs, including polychlorinated biphenyls (PCBs) and organochlorine pesticides, with HDL proteins/functions were investigated by partial least square and multiple linear regression analysis. Proteomic analyses identified 118 HDL proteins, of which ten were significantly (p<0.05) and positively associated with the combined level of POPs or with highly chlorinated PCB congeners. Among these, cholesteryl ester transfer protein and phospholipid transfer protein, as well as the inflammatory marker serum amyloid A, were found. The serum paraoxonase/arylesterase 1 activity was inversely associated with POPs. Pathway analysis demonstrated that up-regulated proteins were associated with biological processes involving lipoprotein metabolism, while down-regulated proteins were associated with processes such as negative regulation of proteinases, acute phase response, platelet degranulation, and complement activation. These results indicate an association between POP levels, especially highly chlorinated PCBs, and HDL protein alterations that may result in a less functional particle. Further studies are needed to determine causality and the importance of other environmental factors. Nevertheless, this study provides a

  7. 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.

  8. 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

  9. Design of a robotic device for assessment and rehabilitation of hand sensory function.

    PubMed

    Lambercy, Olivier; Robles, Alejandro Juárez; Kim, Yeongmi; Gassert, Roger

    2011-01-01

    This paper presents the design and implementation of the Robotic Sensory Trainer, a robotic interface for assessment and therapy of hand sensory function. The device can provide three types of well controlled stimuli: (i) angular displacement at the metacarpophalangeal (MCP) joint using a remote-center-of-motion double-parallelogram structure, (ii) vibration stimuli at the fingertip, proximal phalange and palm, and (iii) pressure at the fingertip, while recording position, interaction force and feedback from the user over a touch screen. These stimuli offer a novel platform to investigate sensory perception in healthy subjects and patients with sensory impairments, with the potential to assess deficits and actively train detection of specific sensory cues in a standardized manner. A preliminary study with eight healthy subjects demonstrates the feasibility of using the Robotic Sensory Trainer to assess the sensory perception threshold in MCP angular position. An average just noticeable difference (JND) in the MCP joint angle of 2.46° (14.47%) was found, which is in agreement with previous perception studies. © 2011 IEEE

  10. Which activities threaten independent living of elderly when becoming problematic: inspiration for meaningful service robot functionality.

    PubMed

    Bedaf, Sandra; Gelderblom, Gert Jan; Syrdal, Dag Sverre; Lehmann, Hagen; Michel, Hervé; Hewson, David; Amirabdollahian, Farshid; Dautenhahn, Kerstin; de Witte, Luc

    2014-11-01

    In light of the increasing elderly population and the growing demand for home care, the potential of robot support is given increasing attention. In this paper, an inventory of activities was made that threaten independent living of elderly when becoming problematic. Results will guide the further development of an existing service robot, the Care-O-bot®. A systematic literature search of PubMed was performed, focused on the risk factors for institutionalization. Additionally, focus group sessions were conducted in the Netherlands, United Kingdom and France. In these focus group sessions, problematic activities threatening the independence of elderly people were discussed. Three separate target groups were included in the focus group sessions: (1) elderly persons (n = 41), (2) formal caregivers (n = 40) and (3) informal caregivers (n = 32). Activities within the International Classification of Functioning domains mobility, self-care, and interpersonal interaction and relationships were found to be the most problematic. A distinct set of daily activities was identified that may threaten independent living, but no single activity could be selected as the main activity causing a loss of independence as it is often a combination of problematic activities that is person-specific. Supporting the problematic activities need not involve a robotic solution.

  11. Yeast Proteome Analysis

    NASA Astrophysics Data System (ADS)

    Matros, Andrea; Mock, Hans-Peter

    Yeast organisms, and specifically Saccharomyces cerevisiae, have become model systems for many aspects in fundamental and applied research. Consistently, many papers have been published applying proteome techniques to study these organisms. The review will give an overview on the proteome research performed on yeast systems so far; however, due to the large number of publications, only selected reports can be cited neglecting many more interesting ones in the interest of space. The review will focus on research involving mass spectrom-etry as a basic proteome technique, although many more approaches are relevant for the functional characterization of proteins in the cell, e.g. the yeast two-hybrid system. We will provide an overview on yeasts as models in the context of pro-teome analysis, and explain the basic techniques currently applied in proteome approaches. The main part of the review will deal with a survey on the current status of proteomic studies in yeasts. In a first part of this chapter, we will deal with the currently available proteome maps of yeasts, and in the following part we will discuss studies dealing with fundamental aspects, but also mention proteome studies related to applied microbiology. Finally, we will envisage future perspectives of the proteome technology for studying yeasts, and draw major conclusion on the current status reached in this field of functional genomics.

  12. A Systematic Bioinformatics Approach to Identify High Quality Mass Spectrometry Data and Functionally Annotate Proteins and Proteomes.

    PubMed

    Islam, Mohammad Tawhidul; Mohamedali, Abidali; Ahn, Seong Beom; Nawar, Ishmam; Baker, Mark S; Ranganathan, Shoba

    2017-01-01

    In the past decade, proteomics and mass spectrometry have taken tremendous strides forward, particularly in the life sciences, spurred on by rapid advances in technology resulting in generation and conglomeration of vast amounts of data. Though this has led to tremendous advancements in biology, the interpretation of the data poses serious challenges for many practitioners due to the immense size and complexity of the data. Furthermore, the lack of annotation means that a potential gold mine of relevant biological information may be hiding within this data. We present here a simple and intuitive workflow for the research community to investigate and mine this data, not only to extract relevant data but also to segregate usable, quality data to develop hypotheses for investigation and validation. We apply an MS evidence workflow for verifying peptides of proteins from one's own data as well as publicly available databases. We then integrate a suite of freely available bioinformatics analysis and annotation software tools to identify homologues and map putative functional signatures, gene ontology and biochemical pathways. We also provide an example of the functional annotation of missing proteins in human chromosome 7 data from the NeXtProt database, where no evidence is available at the proteomic, antibody, or structural levels. We give examples of protocols, tools and detailed flowcharts that can be extended or tailored to interpret and annotate the proteome of any novel organism.

  13. “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.

  14. 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

  15. 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

  16. Corticospinal excitability as a predictor of functional gains at the affected upper limb following robotic training in chronic stroke survivors.

    PubMed

    Milot, Marie-Hélène; Spencer, Steven J; Chan, Vicky; Allington, James P; Klein, Julius; Chou, Cathy; Pearson-Fuhrhop, Kristin; Bobrow, James E; Reinkensmeyer, David J; Cramer, Steven C

    2014-01-01

    Robotic training can help improve function of a paretic limb following a stroke, but individuals respond differently to the training. A predictor of functional gains might improve the ability to select those individuals more likely to benefit from robot-based therapy. Studies evaluating predictors of functional improvement after a robotic training are scarce. One study has found that white matter tract integrity predicts functional gains following a robotic training of the hand and wrist. Objective. To determine the predictive ability of behavioral and brain measures in order to improve selection of individuals for robotic training. Twenty subjects with chronic stroke participated in an 8-week course of robotic exoskeletal training for the arm. Before training, a clinical evaluation, functional magnetic resonance imaging (fMRI), diffusion tensor imaging, and transcranial magnetic stimulation (TMS) were each measured as predictors. Final functional gain was defined as change in the Box and Block Test (BBT). Measures significant in bivariate analysis were fed into a multivariate linear regression model. Training was associated with an average gain of 6 ± 5 blocks on the BBT (P < .0001). Bivariate analysis revealed that lower baseline motor-evoked potential (MEP) amplitude on TMS, and lower laterality M1 index on fMRI each significantly correlated with greater BBT change. In the multivariate linear regression analysis, baseline MEP magnitude was the only measure that remained significant. Subjects with lower baseline MEP magnitude benefited the most from robotic training of the affected arm. These subjects might have reserve remaining for the training to boost corticospinal excitability, translating into functional gains. © The Author(s) 2014.

  17. 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

  18. 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.

  19. Towards a Semen Proteome of the Dengue Vector Mosquito: Protein Identification and Potential Functions

    PubMed Central

    Sirot, Laura K.; Ribeiro, José M. C.; Kimura, Mari; Deewatthanawong, Prasit; Wolfner, Mariana F.; Harrington, Laura C.

    2011-01-01

    Background No commercially licensed vaccine or treatment is available for dengue fever, a potentially lethal infection that impacts millions of lives annually. New tools that target mosquito control may reduce vector populations and break the cycle of dengue transmission. Male mosquito seminal fluid proteins (Sfps) are one such target since these proteins, in aggregate, modulate the reproduction and feeding patterns of the dengue vector, Aedes aegypti. As an initial step in identifying new targets for dengue vector control, we sought to identify the suite of proteins that comprise the Ae. aegypti ejaculate and determine which are transferred to females during mating. Methodology and Principal Findings Using a stable-isotope labeling method coupled with proteomics to distinguish male- and female-derived proteins, we identified Sfps and sperm proteins transferred from males to females. Sfps were distinguished from sperm proteins by comparing the transferred proteins to sperm-enriched samples derived from testes and seminal vesicles. We identified 93 male-derived Sfps and 52 predicted sperm proteins that are transferred to females during mating. The Sfp protein classes we detected suggest roles in protein activation/inactivation, sperm utilization, and ecdysteroidogenesis. We also discovered that several predicted membrane-bound and intracellular proteins are transferred to females in the seminal fluids, supporting the hypothesis that Ae. aegypti Sfps are released from the accessory gland cells through apocrine secretion, as occurs in mammals. Many of the Ae. aegypti predicted sperm proteins were homologous to Drosophila melanogaster sperm proteins, suggesting conservation of their sperm-related function across Diptera. Conclusion and Significance This is the first study to directly identify Sfps transferred from male Ae. aegypti to females. Our data lay the groundwork for future functional analyses to identify individual seminal proteins that may trigger female post

  20. 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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26140532

  2. Proteomic Assessment of Poultry Spermatozoa

    USDA-ARS?s Scientific Manuscript database

    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...

  3. Structural and functional proteomics of intracytoplasmic membrane assembly in Rhodobacter sphaeroides.

    PubMed

    Woronowicz, Kamil; Harrold, John W; Kay, Joseph M; Niederman, Robert A

    2013-01-01

    The results of a detailed structural and functional proteomic analysis of intracytoplasmic membrane (ICM) assembly in the model purple phototrophic bacterium Rhodobacter sphaeroides are reviewed in this report. Proteomics approaches have focused upon identification of membrane proteins temporally expressed during ICM development and spatially localized within the internal cell membranes, together with their structural and functional correlates. For the examination of temporal protein expression, procedures were established for the induction of ICM formation at low oxygen tension and for ICM remodeling in cells adapting to low intensity illumination, which permitted isolation by rate-zone sedimentation of ICM growth initiation sites (CM invaginations) in an upper-pigmented band (UPB), together with more mature ICM vesicles (chromatophores) as the main band. Nondenaturing clear native gel electrophoresis of the chromatophore fraction gave rise to four pigmented bands: the top and bottom bands contained the reaction center-light-harvesting 1 (RC-LH1) core complex and the LH2 peripheral antenna, respectively, while two bands of intermediate migration exhibited distinct associations of LH2 and core complexes. Proteomic analysis of the gel bands revealed developmental changes including increasing levels of LH2 polypeptides relative to those of core complexes as ICM development proceeded, as well as a large array of other associated proteins including high spectral counts for the F1FO-ATP synthase subunits, and the cytochrome bc1 complex. High counts were also observed for RSP6124, a protein of unknown function, that were correlated with increasing LH2 levels. RC-LH1-containing clear native electrophoresis gel bands from the UPB were enriched in cytoplasmic membrane (CM) markers, including electron transfer and transport proteins, as well as general membrane assembly factors (viz., preprotein translocases YidC, YajC and SecY, bacterial type 1 signal peptidase and twin arg

  4. Shared and Unique Proteins in Human, Mouse and Rat Saliva Proteomes: Footprints of Functional Adaptation

    PubMed Central

    Karn, Robert C.; Chung, Amanda G.; Laukaitis, Christina M.

    2013-01-01

    The overall goal of our study was to compare the proteins found in the saliva proteomes of three mammals: human, mouse and rat. Our first objective was to compare two human proteomes with very different analysis depths. The 89 shared proteins in this comparison apparently represent a core of highly-expressed human salivary proteins. Of the proteins unique to each proteome, one-half to 2/3 lack signal peptides and probably are contaminants instead of less highly-represented salivary proteins. We recently published the first rodent saliva proteomes with saliva collected from the genome mouse (C57BL/6) and the genome rat (BN/SsNHsd/Mcwi). Our second objective was to compare the proteins in the human proteome with those we identified in the genome mouse and rat to determine those common to all three mammals, as well as the specialized rodent subset. We also identified proteins unique to each of the three mammals, because differences in the secreted protein constitutions can provide clues to differences in the evolutionary adaptation of the secretions in the three different mammals. PMID:24926433

  5. Corticospinal excitability as a predictor of functional gains at the affected upper limb following robotic training in chronic stroke survivors

    PubMed Central

    Milot, Marie-Hélène; Spencer, Steven J.; Chan, Vicky; Allington, James P.; Klein, Julius; Chou, Cathy; Pearson-Fuhrhop, Kristin; Bobrow, James E.; Reinkensmeyer, David J.; Cramer, Steven C.

    2014-01-01

    Background Robotic training can help improve function of a paretic limb following a stroke, but individuals respond differently to the training. A predictor of functional gains might improve the ability to select those individuals more likely to benefit from robot based therapy. Studies evaluating predictors of functional improvement after a robotic training are scarce. One study has found that white matter tract integrity predicts functional gains following a robotic training of the hand and wrist. Objective Determine the predictive ability of behavioral and brain measures to improve selection of individuals for robotic training. Methods Twenty subjects with chronic stroke participated in an 8-week course of robotic exoskeletal training for the arm. Before training, a clinical evaluation, fMRI, diffusion tensor imaging, and transcranial magnetic stimulation (TMS) were each measured as predictors. Final functional gain was defined as change in the Box and Block Test (BBT). Measures significant in bivariate analysis were fed into a multivariate linear regression model. Results Training was associated with an average gain of 6±5 blocks on the BBT (p<0.0001). Bivariate analysis revealed that lower baseline motor evoked potential (MEP) amplitude on TMS, and lower laterality M1 index on fMRI each significantly correlated with greater BBT change. In the multivariate linear regression analysis, baseline MEP magnitude was the only measure that remained significant. Conclusion Subjects with lower baseline MEP magnitude benefited the most from robotic training of the affected arm. These subjects might have reserve remaining for the training to boost corticospinal excitability, translating into functional gains. PMID:24642382

  6. Impact of robotic surgery on sexual and urinary functions after fully robotic nerve-sparing total mesorectal excision for rectal cancer.

    PubMed

    Luca, Fabrizio; Valvo, Manuela; Ghezzi, Tiago Leal; Zuccaro, Massimiliano; Cenciarelli, Sabina; Trovato, Cristina; Sonzogni, Angelica; Biffi, Roberto

    2013-04-01

    Urinary and sexual dysfunctions are recognized complications of rectal cancer surgery. Their incidence after robotic surgery is as yet unknown. The aim of this study was to prospectively evaluate the impact of robotic surgery for rectal cancer on sexual and urinary functions in male and female patients. From April 2008 to December 2010, 74 patients undergoing fully robotic resection for rectal cancer were prospectively included in the study. Urinary and sexual dysfunctions affecting quality of life were assessed with specific self-administered questionnaires in all patients undergoing robotic total mesorectal excision (RTME). Results were calculated with validated scoring systems and statistically analyzed. The analyses of the questionnaires completed by the 74 patients who underwent RTME showed that sexual function and general sexual satisfaction decreased significantly 1 month after intervention: 19.1 ± 8.7 versus 11.9 ± 10.2 (P < 0.05) for erectile function and 6.9 ± 2.4 versus 5.3 ± 2.5 (P < 0.05) for general satisfaction in men; 2.6 ± 3.3 versus 0.8 ± 1.4 (P < 0.05) and 2.4 ± 2.5 versus 0.7 ± 1.6 (P < 0.05) for arousal and general satisfaction, respectively, in women. Subsequently, both parameters increased progressively, and 1 year after surgery, the values were comparable to those measured before surgery. Concerning urinary function, the grade of incontinence measured 1 year after the intervention was unchanged for both sexes. RTME allows for preservation of urinary and sexual functions. This is probably due to the superior movements of the wristed instruments that facilitate fine dissection, coupled with a stable and magnified view that helps in recognizing the inferior hypogastric plexus.

  7. Anatomic and technical considerations for optimizing recovery of sexual function during robotic-assisted radical prostatectomy.

    PubMed

    Carter, Stacey; Le, Jesse D; Hu, Jim C

    2013-01-01

    Although cure of prostate cancer is the primary goal of radical prostatectomy, preserving erectile function is also tantamount, given the indolent clinical course of most prostate cancers, particularly low-risk disease. In order to optimize postprostatectomy erectile function during a robotic-assisted radical prostatectomy, there must be a detailed understanding of pelvic anatomy to recognize the optimal nerve-sparing plane and technical finesse to minimize stretch injury to the neurovascular bundle. The magnified, well illuminated robotic-operative field coupled with less blood loss has paralleled greater understanding of the periprostatic 'fascial' planes, leading to differentiation of intrafascial versus interfascial nerve-sparing approaches. However, refinement of tissue handling during nerve-sparing to minimize lateral displacement of the neurovascular bundle and attenuate neurapraxia enables earlier and better recovery of erectile function. The critical maneuvers to preserving erectile function are atraumatic dissection of the prostate away from the optimal nerve-sparing plane to maximally preserve nerve fibers while minimizing neurapraxia. Therefore, attaining these principles involves a conceptual paradigm shift from 'radical' prostatectomy to neurosurgery of the prostate.

  8. Evaluation of renal function under controlled hypotension in zero ischemia robotic assisted partial nephrectomy.

    PubMed

    Forastiere, Ester; Claroni, Claudia; Sofra, Maria; Torregiani, Giulia; Covotta, Marco; Marchione, Maria Grazia; Giannarelli, Diana; Papalia, Rocco

    2013-01-01

    In partial nephrectomy with hilar clamping every minute of ischemia can impair renal function, thus great importance is having the controlled hypotension as a part of zero ischemia technique. The aim of the study is to evaluate the effects of hypotensive anesthesia on renal function, in patients undergoing robotic assisted partial nephrectomy (RAPN) , during surgery and at 3 months follow up. This is a prospective study of 100 patients, ASA 1-2, who underwent zero ischemia RAPN under controlled hypotension (CH) from December 2011 through to May 2013. Serum creatinine, BUN, estimated glomerular filtration rates (eGFR), fractional excretion of sodium (FSE) and technetium Tc 99m mercaptoacetyltriglycine (99mTC-MAG-3), renal scintigraphy with effective renal plasma flow (ERPF) were evaluated. Mean duration of CH was 50 ± 4 minutes. Acute renal failure wasn't observed in any of the patients. A significant variation of eGFR during the procedure and 24 hours after surgery was observed. No significant variation of BUN and FSE was detected. Comparing preoperative ERPF of the operated kidney with ERPF 3 months after surgery, it decreased by 2%. In patients with normal preoperative renal function CH didn't show any detrimental impact on renal function during and after robotic assisted partial nephrectomy.

  9. 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

  10. The effects of cardiopulmonary bypass on pulmonary function during robotic cardiac surgery.

    PubMed

    Wang, G; Xiao, S; Gao, C

    2015-04-01

    We aimed to investigate the effects of cardiopulmonary bypass (CPB) on pulmonary function under the conditions of one-lung ventilation (OLV) and carbon dioxide pneumothorax in robotic cardiac surgery. Ninety-eight patients underwent robotic cardiac surgery using the da Vinci Surgical System, including 58 on-pump surgeries and 40 off-pump surgeries. Respiratory parameters and arterial blood gases were assessed at the following time points: 25 min after the induction of anesthesia under two-lung ventilation (T1), 25 min after OLV (T2), 25 min after the termination of CPB under OLV in the on-pump group or 25 min after the main surgery intervention in the off-pump group (T3) and 20 min before the end of surgery (T4). Dynamic lung compliance (Cdyn), alveolar-arterial PO2 difference (PA-aDO2), oxygenation index (OI) and artery-alveolar O2 pressure ratio (a/A) were calculated. No significant differences in pulmonary function parameters between T2 and T3 were observed in the off-pump group. However, in the on-pump group, compared with those at T2, PETCO2, Ppeak, PaCO2 and PA-aDO2 at T3 were higher, whereas SpO2, Cdyn, PaO2, OI and a/A were lower (p<0.05). Comparisons between the two groups at T3 indicated that SpO2, Cdyn, PaO2, OI and a/A were higher, while Ppeak, PaCO2 and PA-aDO2 were lower in the off-pump group (p<0.01). In robotic cardiac surgery under the conditions of OLV and carbon dioxide pneumothorax, CPB worsened pulmonary function and tolerance to OLV and carbon dioxide pneumothorax. © The Author(s) 2014.

  11. Multifactorial Comparative Proteomic Study of Cytochrome P450 2E1 Function in Chronic Alcohol Administration

    PubMed Central

    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. PMID:24658151

  12. Functional proteomic approach to discover geographic variations of king cobra venoms from Southeast Asia and China.

    PubMed

    Chang, Hui-Ching; Tsai, Tein-Shun; Tsai, Inn-Ho

    2013-08-26

    This study deciphers the geographic variations of king cobra (Ophiophagus hannah) venom using functional proteomics. Pooled samples of king cobra venom (abbreviated as Ohv) were obtained from Indonesia, Malaysia, Thailand, and two provinces of China, namely Guangxi and Hainan. Using two animal models to test and compare the lethal effects, we found that the Chinese Ohvs were more fatal to mice, while the Southeast Asian Ohvs were more fatal to lizards (Eutropis multifasciata). Various phospholipases A2 (PLA2s), three-finger toxins (3FTxs) and Kunitz-type inhibitors were purified from these Ohvs and compared. Besides the two Chinese Ohv PLA2s with known sequences, eight novel PLA2s were identified from the five Ohv samples and their antiplatelet activities were compared. While two 3FTxs (namely oh-55 and oh-27) were common in all the Ohvs, different sets of 3FTx markers were present in the Chinese and Southeast Asian Ohvs. All the Ohvs contain the Kunitz inhibitor, OH-TCI, while only the Chinese Ohvs contain the inhibitor variant, Oh11-1. Relative to the Chinese Ohvs which contained more phospholipases, the Southeast Asian Ohvs had higher metalloproteinase, acetylcholine esterase, and alkaline phosphatase activities. Remarkable variations in five king cobra geographic samples reveal fast evolution and dynamic translational regulation of the venom which probably adapted to different prey ecology as testified by the lethal tests on mice and lizards. Our results predict possible variations of the king cobra envenoming to human and the importance of using local antivenin for snakebite treatment. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Proteomic Profiles Reveal the Function of Different Vegetative Tissues of Moringa oleifera.

    PubMed

    Wang, Lei; Zou, Qiong; Wang, Jinxing; Zhang, Junjie; Liu, Zeping; Chen, Xiaoyang

    2016-12-01

    Moringa oleifera is a rich source of bioactive compounds and is widely used in traditional medicine and food for its nutritional value; however, the protein and peptide components of different tissues are rarely discussed. Here, we describe the first investigation of M. oleifera proteomes using mass spectrometry and bioinformatics methods. We aimed to elucidate the protein profiles of M. oleifera leaves, stem, bark, and root. Totally 202 proteins were identified from four vegetative organs. We identified 101 proteins from leaves, 51 from stem, 94 from bark and 67 from root, finding that only five proteins existed in both four vegetative parts. The calculated pI of most of the proteins is distributed in 5-10 and the molecular weight distributed below 100 kDa. Functional classification analysis revealed that proteins which are involved in catalytic activities are the most abundant both in leaves, stem, bark and root. Identification of several heat shock proteins in four vegetative tissues might be adaptive for resistance to high temperature environmental stresses of tropical or subtropical areas. Some enzymes involved in antioxidant processes were also identified in M. oleifera leaves, stem, bark and root. Among the four tissues studies here, leaves protein content and molecular diversity were the highest. The identification of the flocculating protein MO2.1 and MO2.2 in the bark and root provides clue to clarify the antimicrobial molecular mechanisms of root and bark. This study provides information on the protein compositions of M. oleifera vegetative tissues that will be beneficial for potential drug and food supplement development and plant physiology research.

  14. Mass spectrometry-based targeted proteomics as a tool to elucidate the expression and function of intestinal drug transporters.

    PubMed

    Oswald, Stefan; Gröer, Christian; Drozdzik, Marek; Siegmund, Werner

    2013-10-01

    Intestinal transporter proteins affect the oral bioavailability of many drugs in a significant manner. In order to estimate or predict their impact on oral drug absorption, data on their intestinal expression levels are needed. So far, predominantly mRNA expression data are available which are not necessarily correlated with the respective protein content. All available protein data were assessed by immunoblotting techniques such as Western blotting which both possess a number of limitations for reliable protein quantification. In contrast to this, mass spectrometry-based targeted proteomics may represent a promising alternative method to provide comprehensive protein expression data. In this review, we will summarize so far available intestinal mRNA and protein expression data for relevant human multidrug transporters. Moreover, recently observed mass spectrometry-based targeted proteomic data will be presented and discussed with respect to potential functional consequences. Associated to this, we will provide a short tutorial how to set up these methods and emphasize critical aspects in method development. Finally, potential limitations and pitfalls of this emerging technique will be discussed. From our perspective, LC-MS/MS-based targeted proteomics represents a valuable new method to comprehensively analyse the intestinal expression of transporter proteins. The resulting expression data are expected to improve our understanding about the intestinal processing of drugs.

  15. Analysis of transcriptomic and proteomic profiles demonstrates improved Madin-Darby canine kidney cell function in a renal microfluidic biochip.

    PubMed

    Snouber, Leila Choucha; Letourneur, Franck; Chafey, Philippe; Broussard, Cedric; Monge, Matthieu; Legallais, Cécile; Leclerc, Eric

    2012-01-01

    We have evaluated the influence of the microfluidic environment on renal cell functionality. For that purpose, we performed a time lapse transcriptomic and proteomic analysis in which we compared gene and protein expressions of Madin-Darby canine kidney cells after 24 h and 96 h of culture in both microfluidic biochips and plates. The transcriptomic and proteomic integration revealed that the ion transporters involved in calcium, phosphate, and sodium homoeostasis and several genes involved in H(+) transporters and pH regulation were up-regulated in microfluidic biochips. Concerning drug metabolism, we found Phase I (CYP P450), Phase II enzymes (GST), various multidrug resistance genes (MRP), and Phase III transporters (SLC) were also up-regulated in the biochips. Furthermore, the study shows that those inductions were correlated with the induction of the Ahr and Nrf-2 dependent pathways, which results in a global cytoprotective response induced by the microenvironment. However, there was no apoptosis situation or cell death in the biochips. Microfluidic biochips may thus provide an important insight into exploring xenobiotic injury and transport modifications in this type of bioartificial microfluidic kidney. Finally, the investigation demonstrated that combining the transcriptomic and proteomic analyses obtained from a cell "on chip" culture would provide a pertinent new tool in the mechanistic interpretation of cellular mechanisms for predicting kidney cell toxicity and renal clearance in vitro. Copyright © 2011 American Institute of Chemical Engineers (AIChE).

  16. 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

  17. Gestational Exposure to Bisphenol A Affects the Function and Proteome Profile of F1 Spermatozoa in Adult Mice

    PubMed Central

    Rahman, Md Saidur; Kwon, Woo-Sung; Karmakar, Polash Chandra; Yoon, Sung-Jae; Ryu, Buom-Yong; Pang, Myung-Geol

    2016-01-01

    Background: Maternal exposure to the endocrine disruptor bisphenol A (BPA) has been linked to offspring reproductive abnormalities. However, exactly how BPA affects offspring fertility remains poorly understood. Objectives: The aim of the present study was to evaluate the effects of gestational BPA exposure on sperm function, fertility, and proteome profile of F1 spermatozoa in adult mice. Methods: Pregnant CD-1 mice (F0) were gavaged with BPA at three different doses (50 μg/kg bw/day, 5 mg/kg bw/day, and 50 mg/kg bw/day) on embryonic days 7 to 14. We investigated the function, fertility, and related processes of F1 spermatozoa at postnatal day 120. We also evaluated protein profiles of F1 spermatozoa to monitor their functional affiliation to disease. Results: BPA inhibited sperm count, motility parameters, and intracellular ATP levels in a dose-dependent manner. These effects appeared to be caused by reduced numbers of stage VIII seminiferous epithelial cells in testis and decreased protein kinase A (PKA) activity and tyrosine phosphorylation in spermatozoa. We also found that BPA compromised average litter size. Proteins differentially expressed in spermatozoa from BPA treatment groups are known to play a critical role in ATP generation, oxidative stress response, fertility, and in the pathogenesis of several diseases. Conclusions: Our study provides mechanistic support for the hypothesis that gestational exposure to BPA alters sperm function and fertility via down-regulation of tyrosine phosphorylation through a PKA-dependent mechanism. In addition, we anticipate that the BPA-induced changes in the sperm proteome might be partly responsible for the observed effects in spermatozoa. Citation: Rahman MS, Kwon WS, Karmakar PC, Yoon SJ, Ryu BY, Pang MG. 2017. Gestational exposure to bisphenol-A affects the function and proteome profile of F1 spermatozoa in adult mice. Environ Health Perspect 125:238–245; http://dx.doi.org/10.1289/EHP378 PMID:27384531

  18. Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.

    PubMed

    Ayyar, Vivaswath S; Almon, Richard R; DuBois, Debra C; Sukumaran, Siddharth; Qu, Jun; Jusko, William J

    2017-03-14

    Corticosteroids (CS) are anti-inflammatory agents that cause extensive pharmacogenomic and proteomic changes in multiple tissues. An understanding of the proteome-wide effects of CS in liver and its relationships to altered hepatic and systemic physiology remains incomplete. Here, we report the application of a functional pharmacoproteomic approach to gain integrated insight into the complex nature of CS responses in liver in vivo. An in-depth functional analysis was performed using rich pharmacodynamic (temporal-based) proteomic data measured over 66h in rat liver following a single dose of methylprednisolone (MPL). Data mining identified 451 differentially regulated proteins. These proteins were analyzed on the basis of temporal regulation, cellular localization, and literature-mined functional information. Of the 451 proteins, 378 were clustered into six functional groups based on major clinically-relevant effects of CS in liver. MPL-responsive proteins were highly localized in the mitochondria (20%) and cytosol (24%). Interestingly, several proteins were related to hepatic stress and signaling processes, which appear to be involved in secondary signaling cascades and in protecting the liver from CS-induced oxidative damage. Consistent with known adverse metabolic effects of CS, several rate-controlling enzymes involved in amino acid metabolism, gluconeogenesis, and fatty-acid metabolism were altered by MPL. In addition, proteins involved in the metabolism of endogenous compounds, xenobiotics, and therapeutic drugs including cytochrome P450 and Phase-II enzymes were differentially regulated. Proteins related to the inflammatory acute-phase response were up-regulated in response to MPL. Functionally-similar proteins showed large diversity in their temporal profiles, indicating complex mechanisms of regulation by CS.

  19. Robots and manipulators

    NASA Technical Reports Server (NTRS)

    Heer, E.

    1981-01-01

    Robots are defined and described for various applications. The key feature of robots is programmability, which allows teleoperation, repair work in hazardous situations, and unsupervised operation in industrial functions. Two types of robots now exist: special purpose, with equipment for a specific task; and general purpose, which include nonservo-controlled robots, servo-controlled robots, and sensory control robots. Sensory robots are the most sophisticated, and are equipped with both internal control sensors and external sensors such as TV cameras, pressure detectors, laser range finders, etc. Sensory feedback to a central computer enables the robots to make appropriate modifications to the control program to adapt to new situations. Pattern recognition and scans for size are features of the TV sensors, and programs to develop a universal effector (hand) are outlined. Finally, robot programming in terms of manual, walkthrough, and textual methods are described, and the potential uses of robots for space and undersea construction and repair are discussed.

  20. Comparative proteomic analyses of the nuclear envelope and pore complex suggests a wide range of heretofore unexpected functions.

    PubMed

    Batrakou, Dzmitry G; Kerr, Alastair R W; Schirmer, Eric C

    2009-02-15

    Since the discovery of several inherited diseases linked to the nuclear envelope the number of functions ascribed to this subcellular organelle has skyrocketed. However the molecular pathways underlying these functions are not clear in most cases, perhaps because of missing components. Several recent proteomic analyses of the nuclear envelope and nuclear pore complex proteomes have yielded not only enough missing components to potentially elucidate these pathways, but suggest an exponentially greater number of functions at the nuclear periphery than ever imagined. Many of these functions appear to derive from recapitulation of pathways utilized at the plasma membrane and from other membrane systems. Additionally, many proteins identified in the comparative nuclear envelope studies have sequence characteristics suggesting that they might also contribute to nuclear pore complex functions. In particular, the striking enrichment for proteins in the nuclear envelope fractions that carry phenylalanine-glycine (FG) repeats may be significant for the mechanism of nuclear transport. In retrospect, these findings are only surprising in context of the notion held for many years that the nuclear envelope was only a barrier protecting the genome. In fact, it is arguably the most complex membrane organelle in the cell.

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

    DOE PAGES

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

    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

  2. Characterization of a Highly Conserved Histone Related Protein, Ydl156w, and Its Functional Associations Using Quantitative Proteomic Analyses*

    PubMed Central

    Gilmore, Joshua M.; Sardiu, Mihaela E.; Venkatesh, Swaminathan; Stutzman, Brent; Peak, Allison; Seidel, Chris W.; Workman, Jerry L.; Florens, Laurence; Washburn, Michael P.

    2012-01-01

    A significant challenge in biology is to functionally annotate novel and uncharacterized proteins. Several approaches are available for deducing the function of proteins in silico based upon sequence homology and physical or genetic interaction, yet this approach is limited to proteins with well-characterized domains, paralogs and/or orthologs in other species, as well as on the availability of suitable large-scale data sets. Here, we present a quantitative proteomics approach extending the protein network of core histones H2A, H2B, H3, and H4 in Saccharomyces cerevisiae, among which a novel associated protein, the previously uncharacterized Ydl156w, was identified. In order to predict the role of Ydl156w, we designed and applied integrative bioinformatics, quantitative proteomics and biochemistry approaches aiming to infer its function. Reciprocal analysis of Ydl156w protein interactions demonstrated a strong association with all four histones and also to proteins strongly associated with histones including Rim1, Rfa2 and 3, Yku70, and Yku80. Through a subsequent combination of the focused quantitative proteomics experiments with available large-scale genetic interaction data and Gene Ontology functional associations, we provided sufficient evidence to associate Ydl156w with multiple processes including chromatin remodeling, transcription and DNA repair/replication. To gain deeper insights into the role of Ydl156w in histone biology we investigated the effect of the genetic deletion of ydl156w on H4 associated proteins, which lead to a dramatic decrease in the association of H4 with RNA polymerase III proteins. The implication of a role for Ydl156w in RNA Polymerase III mediated transcription was consequently verified by RNA-Seq experiments. Finally, using these approaches we generated a refined network of Ydl156w-associated proteins. PMID:22199229

  3. Robotic Intracorporeal Orthotopic Neobladder: Urodynamic Outcomes, Urinary Function, and Health-related Quality of Life.

    PubMed

    Satkunasivam, Raj; Santomauro, Michael; Chopra, Sameer; Plotner, Elisabeth; Cai, Jie; Miranda, Gus; Salibian, Salpi; Aron, Monish; Ginsberg, David; Daneshmand, Siamak; Desai, Mihir; Gill, Inderbir S

    2016-02-01

    Intracorporeal orthotopic neobladder (iONB) creation following robotic radical cystectomy is an emerging procedure and robust functional data are required. To evaluate urodynamic features of iONB and bladder cancer-specific and general health-related quality-of-life (HRQOL) outcomes. We retrospectively assessed 28 men who underwent iONB creation (January 2012 to October 2013) and compared results to a previously characterized cohort of 79 of open ONB procedures. iONB pressure-volume properties were characterized using multichannel urodynamics (UDS). The Bladder Cancer Index (BCI) questionnaire, modified with mucus- and pad-related questions, and the Short Form Health Survey (SF-36) were used to evaluate urinary function and HRQOL. ONB cohorts were compared for functional outcomes and BCI score. Multivariable linear regression was used to assess predictors of BCI score. The median follow-up was 9.4 mo for the iONB and 62.1 mo for the open ONB group (p<0.0001); ≥2-yr follow-up had been completed for one (4%) patient in the iONB group compared to 75 (95%) patients in the open ONB group (p<0.0001). In UDS tests, the iONB group had minimal postvoid residual volume, normal compliance, and a mean capacity of 514 cm(3) (range 339-1001). BCI mean scores for urinary function (p=0.58) and urinary bother (p=0.31) were comparable between the groups. The surgical approach was not associated with the BCI score on multivariable analysis. Rates of 24-h pad use were comparable between iONB and open ONB groups (pad-free 17% vs. 19%; ≤2 pads 84% vs. 79%), as reflected by total pad usage (p=0.1); pad size and daytime wetness were worse in the iONB group. The clean intermittent catheterization rate was 10.7% in the iONB and 6.3% in the open ONB group. Limitations include the retrospective comparison, small number of patients and short follow-up for the iONB group. iONB had adequate UDS characteristics and comparable bladder cancer-specific HRQOL scores to open ONB. However, pad size

  4. Extracellular Matrix Proteome and Phosphoproteome of Potato Reveals Functionally Distinct and Diverse Canonical and Non-Canonical Proteoforms

    PubMed Central

    Elagamey, Eman; Narula, Kanika; Sinha, Arunima; Aggarwal, Pooja Rani; Ghosh, Sudip; Chakraborty, Niranjan; Chakraborty, Subhra

    2016-01-01

    The extracellular matrix (ECM) has a molecular machinery composed of diverse proteins and proteoforms that combine properties of tensile strength with extensibility exhibiting growth-regulatory functions and self- and non-self-recognition. The identification of ECM proteoforms is the prerequisite towards a comprehensive understanding of biological functions accomplished by the outermost layer of the cell. Regulatory mechanisms of protein functions rely on post-translational modifications, phosphorylation in particular, affecting enzymatic activity, interaction, localization and stability. To investigate the ECM proteoforms, we have isolated the cell wall proteome and phosphoproteome of a tuberous crop, potato (Solanum tuberosum). LC-MS/MS analysis led to the identification of 38 proteins and 35 phosphoproteins of known and unknown functions. The findings may provide a better understanding of biochemical machinery and the integrated protein and phosphoprotein network of ECM for future functional studies of different developmental pathways and guidance cues in mechanosensing and integrity signaling. PMID:28248230

  5. 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

    USDA-ARS?s Scientific Manuscript database

    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...

  6. Shotgun proteomics in neuroscience.

    PubMed

    Liao, Lujian; McClatchy, Daniel B; Yates, John R

    2009-07-16

    Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and posttranslational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun-proteomics-based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and posttranslational modification analysis and discusses several strategies to improve the coverage of the proteome.

  7. Lyapunov function-based control laws for revolute robot arms - Tracking control, robustness, and adaptive control

    NASA Technical Reports Server (NTRS)

    Wen, John T.; Kreutz-Delgado, Kenneth; Bayard, David S.

    1992-01-01

    A new class of joint level control laws for all-revolute robot arms is introduced. The analysis is similar to a recently proposed energy-like Liapunov function approach, except that the closed-loop potential function is shaped in accordance with the underlying joint space topology. This approach gives way to a much simpler analysis and leads to a new class of control designs which guarantee both global asymptotic stability and local exponential stability. When Coulomb and viscous friction and parameter uncertainty are present as model perturbations, a sliding mode-like modification of the control law results in a robustness-enhancing outer loop. Adaptive control is formulated within the same framework. A linear-in-the-parameters formulation is adopted and globally asymptotically stable adaptive control laws are derived by simply replacing unknown model parameters by their estimates (i.e., certainty equivalence adaptation).

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

    PubMed Central

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

    2015-01-01

    [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

  9. Robotic assessment of the influence of age on upper-limb sensorimotor function.

    PubMed

    Llinares, Ana; Badesa, Francisco Javier; Morales, Ricardo; Garcia-Aracil, Nicolas; Sabater, J M; Fernandez, Eduardo

    2013-01-01

    This paper examines the influence of age on several attributes of sensorimotor performance while performing a reaching task. Our hypothesis, based on previous studies, is that aged persons will show differences in one or more of the attributes of sensorimotor performance. Fifty-one subjects (aged 20-80 years) with no known neuromotor disorders of the upper limbs participated in the study. Subjects were asked to grasp the end-effector of a pneumatic robotic device with two degrees of freedom in order to reach peripheral targets (1.0 cm radius), "quickly and accurately", from a centrally located target (1.0 cm radius). Subjects began each trial by holding the hand within the central target for 2000 milliseconds. Afterwards, a peripheral target was illuminated. Then participants were given 3000 milliseconds to complete the movement. When a target was reached, the participant had to return to the central target in order to start a new trial. A total of 64 trials were completed and each peripheral target was illuminated in a random block design. SUBJECTS WERE DIVIDED INTO THREE GROUPS ACCORDING TO AGE: group 1 (age 20-40 years), group 2 (age 41-60 years), and group 3 (age 61-80 years). The Kruskal-Wallis test showed significant differences (P < 0.05) between groups, except for the variables postural speed in the dominant arm, and postural speed and initial deviation in the non-dominant arm (P > 0.05). These results suggest that age introduces significant differences in upper-limb motor function. Our findings show that there are objective differences in sensorimotor function due to age, and that these differences are greater for the dominant arm. Therefore for the assessment of upper-limb function, we should take into account the influence of age. Moreover, these results suggest that robotic systems can provide a new and effective approach in the assessment of sensorimotor function.

  10. Robotic assessment of the influence of age on upper-limb sensorimotor function

    PubMed Central

    LLinares, Ana; Badesa, Francisco Javier; Morales, Ricardo; Garcia-Aracil, Nicolas; Sabater, JM; Fernandez, Eduardo

    2013-01-01

    Purpose This paper examines the influence of age on several attributes of sensorimotor performance while performing a reaching task. Our hypothesis, based on previous studies, is that aged persons will show differences in one or more of the attributes of sensorimotor performance. Patients and methods Fifty-one subjects (aged 20–80 years) with no known neuromotor disorders of the upper limbs participated in the study. Subjects were asked to grasp the end-effector of a pneumatic robotic device with two degrees of freedom in order to reach peripheral targets (1.0 cm radius), “quickly and accurately”, from a centrally located target (1.0 cm radius). Subjects began each trial by holding the hand within the central target for 2000 milliseconds. Afterwards, a peripheral target was illuminated. Then participants were given 3000 milliseconds to complete the movement. When a target was reached, the participant had to return to the central target in order to start a new trial. A total of 64 trials were completed and each peripheral target was illuminated in a random block design. Results Subjects were divided into three groups according to age: group 1 (age 20–40 years), group 2 (age 41–60 years), and group 3 (age 61–80 years). The Kruskal–Wallis test showed significant differences (P < 0.05) between groups, except for the variables postural speed in the dominant arm, and postural speed and initial deviation in the non-dominant arm (P > 0.05). These results suggest that age introduces significant differences in upper-limb motor function. Conclusion Our findings show that there are objective differences in sensorimotor function due to age, and that these differences are greater for the dominant arm. Therefore for the assessment of upper-limb function, we should take into account the influence of age. Moreover, these results suggest that robotic systems can provide a new and effective approach in the assessment of sensorimotor function. PMID:23885170

  11. Anatomic and technical considerations for optimizing recovery of urinary function during robotic-assisted radical prostatectomy.

    PubMed

    Vora, Anup A; Dajani, Daoud; Lynch, John H; Kowalczyk, Keith J

    2013-01-01

    The advent of robotic-assisted radical prostatectomy purported fewer complications including postprostatectomy incontinence (PPI). PPI is associated with worse quality of life. We evaluate recently reported robot-assisted radical prostatectomy surgical techniques aimed at limiting PPI, describe their anatomic basis and summarize their outcomes. RARP techniques to reduce PPI include bladder neck preservation, bladder neck reconstruction, urethral length preservation, periurethral suspension stitch, posterior reconstruction, combined anterior and posterior reconstruction, preservation of the endopelvic fascia, complete anterior preservation, selective suturing of dorsal venous complex and nerve sparing approach. Outcomes of reconstructive techniques seem to be conflicting, whereas outcomes of techniques aiming to preserve the native urinary continence system seem to hasten urinary function recovery. However, few of these techniques have been shown to affect long-term urinary continence. Surgical techniques preserving the natural urinary continence mechanism appear to improve short-term urinary continence, whereas techniques reconstructing pelvic anatomy have mixed results. The search for the ideal technique to minimize PPI remains hampered by the lack of prospective multi-institutional studies and the long-term follow up. Although reconstructive techniques are safe with few drawbacks, meticulous surgical technique and preservation of the natural continence mechanism should remain the mainstay of PPI prevention.

  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. 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

    2012-11-02

    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.

  15. 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

  16. 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.

  17. 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…

  18. 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…

  19. Robotic intelligence kernel

    DOEpatents

    Bruemmer, David J [Idaho Falls, ID

    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.

  20. Development of an evaluation function for eye-hand coordination robotic therapy.

    PubMed

    Pernalete, N; Tang, F; Chang, S M; Cheng, F Y; Vetter, P; Stegemann, M; Grantner, J

    2011-01-01

    This paper is the continuation of a work presented at ICORR 07, in which we discussed the possibility of improving eye-hand coordination in children diagnosed with this problem, using a robotic mapping from a haptic user interface to a virtual environment. Our goal is to develop, implement and refine a system that will assess and improve the eye-hand coordination and grip strength in children diagnosed with poor graphomotor skills. A detailed analysis of patters (e.g., labyrinths, letters and angles) was conducted in order to select three very distinguishable levels of difficulty that could be included in the system, and which would yield the greatest benefit in terms of assessment of coordination and strength issues as well as in training. Support algorithms (position, force, velocity, inertia and viscosity) were also developed and incorporated into the tasks in order to introduce general computer assistance to the mapping of the user's movements to the computer screen without overriding the user's commands to the robotic device. In order to evaluate performance (given by %accuracy and time) of the executed tasks, a sophisticated evaluation function was designed based on image analysis and edge detection algorithms. This paper presents the development of the haptic tasks, the various assistance algorithms, the description of the evaluation function and the results of a study implemented at the Motor Development Clinic at Cal Poly Pomona. The results (Accuracy and Time) of this function are currently being used as inputs to an Intelligent Decision Support System (described in), which in turn, suggests the next task to be executed by the subject based on his/her performance. © 2011 IEEE

  1. The natural history of voiding function after robot-assisted laparoscopic radical prostatectomy.

    PubMed

    Wang, Lushun; Chung, Stephanie Fook-Chong Man; Yip, Sidney Kam Hung; Lau, Weber Kam On; Cheng, Christopher Wai Sam; Sim, Hong Gee

    2011-01-01

    We report the natural history of voiding function in men with clinically localized prostate cancer after robot-assisted laparoscopic radical prostatectomy (RLRP), describing the trend of functional recovery, which is currently not well described using the robot-assisted laparoscopic approach. We determined the impact on voiding function by prospectively evaluating 100 consecutive men who underwent RLRP between May 2005 and December 2006 and compared their reported International Prostate Symptom Score (IPSS) and Quality of Life (QOL) scores at 3, 6, and 12 months with preoperative scores after surgery. Patients with preoperative IPSS of 0-7 and 8-35 were defined as having mild lower urinary tract symptoms (LUTS) and moderate to severe LUTS, respectively. Continence was achieved in 82%, 87%, and 91% of men at 3, 6, and 12 months after RLRP, respectively. There were statistically and clinically significant improvements in both IPSS and QOL preoperative scores at all studied time points for patients with moderate to severe preexisting LUTS. The mean IPSS scores for these patients preoperatively and at 3, 6, and 12 months after surgery were 14.1, 5.2, 3.0, and 2.9, respectively and the corresponding mean QOL scores were 3.4, 2.1, 1.6, and 1.6, respectively. Patients with mild preexisting LUTS showed no statistically significant improvement in IPSS at 3 and 6 months after surgery but significant improvement was found at 1 year (P = 0.04). Good continence recovery is expected in most patients undergoing RLRP. Patients with moderate to severe preexisting LUTS can expect early and clinically significant symptom and QOL improvements after RLRP. Patients with mild preexisting LUTS show significant symptom improvement at 1 year. Copyright © 2011 Elsevier Inc. All rights reserved.

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

    PubMed

    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; Nono, Justin Komguep

    2016-10-01

    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.

  3. 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

  4. 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.

  5. 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.

  6. Effect of a robotic rehabilitation device on upper limb function in a sub-acute cervical spinal cord injury population.

    PubMed

    Zariffa, José; Kapadia, Naaz; Kramer, John L K; Taylor, Philippa; Alizadeh-Meghrazi, Milad; Zivanovic, Vera; Willms, Rhonda; Townson, Andrea; Curt, Armin; Popovic, Milos R; Steeves, John D

    2011-01-01

    Robotic rehabilitation devices have been suggested as a tool to increase the amount of rehabilitation delivered after a neurological injury. Clinical robotic rehabilitation studies of the upper extremity have generally focused on stroke survivors. We present the results of a multi-center pilot study where an upper-limb robotic rehabilitation device (Armeo Spring®, Hocoma AG) was incorporated into the rehabilitation program of 12 subjects with sub-acute cervical spinal cord injury (motor level C4-C6, AIS A-D). Outcomes were measured using two tests of upper extremity function: ARAT and GRASSP. The change in scores for the arm receiving the Armeo training were not statistically significant when compared to the arm not receiving the Armeo training at discharge from therapy and over follow up assessments (8.7 +/- 2.9 compared to 7.4 +/- 2.5 for ARAT at discharge, p = 0.98, and 13.0 +/- 3.2 compared to 13.3 +/- 3.3 for GRASSP at discharge, p = 0.69). Nevertheless, subjects with some minimal (partial) hand function at baseline had a significantly larger increase in GRASSP scores than subjects with no minimal hand function preserved at baseline (19.3 +/- 2.4 compared to 6.6 +/- 4.7, p = 0.02). This suggests that the initial functional capabilities of patients can influence the benefits measured after robotic rehabilitation training and heterogeneous subject populations should be avoided in early phase studies. © 2011 IEEE

  7. The neuroscience of vision-based grasping: a functional review for computational modeling and bio-inspired robotics.

    PubMed

    Chinellato, Eris; Del Pobil, Angel P

    2009-06-01

    The topic of vision-based grasping is being widely studied in humans and in other primates using various techniques and with different goals. The fundamental related findings are reviewed in this paper, with the aim of providing researchers from different fields, including intelligent robotics and neural computation, a comprehensive but accessible view on the subject. A detailed description of the principal sensorimotor processes and the brain areas involved is provided following a functional perspective, in order to make this survey especially useful for computational modeling and bio-inspired robotic applications.

  8. Effect of minimizing tension during robotic-assisted laparoscopic radical prostatectomy on urinary function recovery.

    PubMed

    Kowalczyk, Keith J; Huang, Andy C; Hevelone, Nathanael D; Lipsitz, Stuart R; Yu, Hua-yin; Lynch, John H; Hu, Jim C

    2013-06-01

    Although most prostatectomy studies emphasize optimal nerve-sparing dissection planes, subtle technical variation also affects functional outcomes. The impact of minimizing assistant/surgeon tension on urinary function has not been quantified. We assess urinary function after attenuating neurovascular bundle (NVB) and rhabdosphincter tension during robotic-assisted radical prostatectomy (RARP). Retrospective study of prospectively collected data for 268 (RARP-T) versus 342 (RARP-0T) men with versus without tension on the NVB and rhabdosphincter during RARP. Outcomes compared include Expanded Prostate Cancer Index (EPIC) urinary function, estimated blood loss (EBL), operative time, and positive surgical margins (PSM). In unadjusted analysis, men undergoing RARP-T versus RARP-0T were older, had higher biopsy and pathologic Gleason grade, and higher preoperative prostate specific antigen (all p ≤ 0.023). Baseline urinary function was similar. Postoperatively, RARP-0T versus RARP-T was associated with higher 5-month urinary function scores (69.7 versus 64, p = 0.049). In adjusted analyses, RARP-0T versus RARP-T was associated with improved 5-month urinary function [Parameter Estimate (PE) 7.37, Standard Error (SE) 2.67, p = 0.006], while bilateral versus non-/unilateral nerve-sparing was associated with improved 12-month urinary function and continence (both p ≤ 0.035). RARP-0T versus RARP-T was associated with shorter operative times (PE 6.66, SE 1.90, p = 0.001) and higher EBL (PE 20.88, SE 6.49, p = 0.001). There were no significant differences in PSM. While the use of tension aids in dissection of anatomic planes, avoidance of NVB counter-traction and minimizing tension on the rhabdosphincter during apical dissection attenuates neuropraxia and leads to earlier urinary function recovery. Bilateral versus non-/unilateral nerve-sparing also improves urinary function recovery.

  9. Feedback Error Learning Controller for Functional Electrical Stimulation Assistance in a Hybrid Robotic System for Reaching Rehabilitation.

    PubMed

    Resquín, Francisco; Gonzalez-Vargas, Jose; Ibáñez, Jaime; Brunetti, Fernando; Pons, José Luis

    2016-06-13

    Hybrid robotic systems represent a novel research field, where functional electrical stimulation (FES) is combined with a robotic device for rehabilitation of motor impairment. Under this approach, the design of robust FES controllers still remains an open challenge. In this work, we aimed at developing a learning FES controller to assist in the performance of reaching movements in a simple hybrid robotic system setting. We implemented a Feedback Error Learning (FEL) control strategy consisting of a feedback PID controller and a feedforward controller based on a neural network. A passive exoskeleton complemented the FES controller by compensating the effects of gravity. We carried out experiments with healthy subjects to validate the performance of the system. Results show that the FEL control strategy is able to adjust the FES intensity to track the desired trajectory accurately without the need of a previous mathematical model.

  10. Feedback Error Learning Controller for Functional Electrical Stimulation Assistance in a Hybrid Robotic System for Reaching Rehabilitation

    PubMed Central

    Resquín, Francisco; Gonzalez-Vargas, Jose; Ibáñez, Jaime; Brunetti, Fernando; Pons, José Luis

    2016-01-01

    Hybrid robotic systems represent a novel research field, where functional electrical stimulation (FES) is combined with a robotic device for rehabilitation of motor impairment. Under this approach, the design of robust FES controllers still remains an open challenge. In this work, we aimed at developing a learning FES controller to assist in the performance of reaching movements in a simple hybrid robotic system setting. We implemented a Feedback Error Learning (FEL) control strategy consisting of a feedback PID controller and a feedforward controller based on a neural network. A passive exoskeleton complemented the FES controller by compensating the effects of gravity. We carried out experiments with healthy subjects to validate the performance of the system. Results show that the FEL control strategy is able to adjust the FES intensity to track the desired trajectory accurately without the need of a previous mathematical model. PMID:27990245

  11. 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.

  12. Urinary Bother as a Predictor of Postsurgical Changes in Urinary Function After Robotic Radical Prostatectomy.

    PubMed

    Murphy, Gregory; Haddock, Peter; Doak, Hoyt; Jackson, Max; Dorin, Ryan; Meraney, Anoop; Kesler, Stuart; Staff, Ilene; Wagner, Joseph R

    2015-10-01

    To characterize changes in indices of urinary function in prostatectomy patients with presurgical voiding symptoms. A retrospective analysis of our prostate cancer database identified robot-assisted radical prostatectomy patients between April 2007 and December 2011 who completed pre- and postsurgical (24 months) Expanded Prostate Cancer Index Composite-26 surveys. Gleason score, margins, D'Amico risk, prostate-specific antigen, radiotherapy, and nerve-sparing status were tabulated. Survey questions addressed urinary irritation/obstruction, incontinence, and overall bother. Responses were averaged to calculate a urinary sum (US) score. Patients were stratified according to the severity of their baseline urinary bother (UB), and changes in urinary indices determined at 24 months. A total of 737 patients were included. Postsurgical improvement in urinary obstruction, bother, and sum score was related to baseline UB (P <.001). Men with severe baseline bother had the greatest improvement in US (+9.3), whereas those with asymptomatic baseline UB experienced a decline in US (-2.8). All patients experienced a decline in urinary incontinence of 6.3-8.3 that was independent of baseline bother (P = .507). Patients with severe UB experienced positive outcomes, whereas those at asymptomatic baseline experienced negative US outcomes. Negative urinary incontinence outcomes were unrelated to baseline UB. Age, radiotherapy, and nerve-sparing status were not associated with improved UB (P = .029). However, baseline UB was significantly associated with improvement in postsurgical UB (P = .001). Baseline UB is a predictor of postsurgical improvement in urinary function. These data are helpful when counseling a subset of robot-assisted laparoscopic radical prostatectomy patients with severe preoperative urinary symptoms. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Quantitative Analysis of the Human Milk Whey Proteome Reveals Developing Milk and Mammary-Gland Functions across the First Year of Lactation

    PubMed Central

    Zhang, Qiang; Cundiff, Judy K.; Maria, Sarah D.; McMahon, Robert J.; Woo, Jessica G.; Davidson, Barbara S.; Morrow, Ardythe L.

    2013-01-01

    In-depth understanding of the changing functions of human milk (HM) proteins and the corresponding physiological adaptions of the lactating mammary gland has been inhibited by incomplete knowledge of the HM proteome. We analyzed the HM whey proteome (n = 10 women with samples at 1 week and 1, 3, 6, 9 and 12 months) using a quantitative proteomic approach. One thousand three hundred and thirty three proteins were identified with 615 being quantified. Principal component analysis revealed a transition in the HM whey proteome-throughout the first year of lactation. Abundance changes in IgG, sIgA and sIgM display distinct features during the first year. Complement components and other acute-phase proteins are generally at higher levels in early lactation. Proteomic analysis further suggests that the sources of milk fatty acids (FA) shift from more direct blood influx to more de novo mammary synthesis over lactation. The abundances of the majority of glycoproteins decline over lactation, which is consistent with increased enzyme expression in glycoprotein degradation and decreased enzyme expression in glycoprotein synthesis. Cellular detoxification machinery may be transformed as well, thereby accommodating increased metabolic activities in late lactation. The multiple developing functions of HM proteins and the corresponding mammary adaption become more apparent from this study. PMID:28250401

  14. Quantitative Analysis of the Human Milk Whey Proteome Reveals Developing Milk and Mammary-Gland Functions across the First Year of Lactation.

    PubMed

    Zhang, Qiang; Cundiff, Judy K; Maria, Sarah D; McMahon, Robert J; Woo, Jessica G; Davidson, Barbara S; Morrow, Ardythe L

    2013-09-03

    In-depth understanding of the changing functions of human milk (HM) proteins and the corresponding physiological adaptions of the lactating mammary gland has been inhibited by incomplete knowledge of the HM proteome. We analyzed the HM whey proteome (n = 10 women with samples at 1 week and 1, 3, 6, 9 and 12 months) using a quantitative proteomic approach. One thousand three hundred and thirty three proteins were identified with 615 being quantified. Principal component analysis revealed a transition in the HM whey proteome-throughout the first year of lactation. Abundance changes in IgG, sIgA and sIgM display distinct features during the first year. Complement components and other acute-phase proteins are generally at higher levels in early lactation. Proteomic analysis further suggests that the sources of milk fatty acids (FA) shift from more direct blood influx to more de novo mammary synthesis over lactation. The abundances of the majority of glycoproteins decline over lactation, which is consistent with increased enzyme expression in glycoprotein degradation and decreased enzyme expression in glycoprotein synthesis. Cellular detoxification machinery may be transformed as well, thereby accommodating increased metabolic activities in late lactation. The multiple developing functions of HM proteins and the corresponding mammary adaption become more apparent from this study.

  15. Specialisation of the venom gland proteome in predatory cone snails reveals functional diversification of the conotoxin biosynthetic pathway.

    PubMed

    Safavi-Hemami, Helena; Siero, William A; Gorasia, Dhana G; Young, Neil D; Macmillan, David; Williamson, Nicholas A; Purcell, Anthony W

    2011-09-02

    Conotoxins, venom peptides from marine cone snails, diversify rapidly as speciation occurs. It has been suggested that each species can synthesize between 1000 and 1900 different toxins with little to no interspecies overlap. Conotoxins exhibit an unprecedented degree of post-translational modifications, the most common one being the formation of disulfide bonds. Despite the great diversity of structurally complex peptides, little is known about the glandular proteins responsible for their biosynthesis and maturation. Here, proteomic interrogations on the Conus venom gland led to the identification of novel glandular proteins of potential importance for toxin synthesis and secretion. A total of 161 and 157 proteins and protein isoforms were identified in the venom glands of Conus novaehollandiae and Conus victoriae, respectively. Interspecies differences in the venom gland proteomes were apparent. A large proportion of the proteins identified function in protein/peptide translation, folding, and protection events. Most intriguingly, however, we demonstrate the presence of a multitude of isoforms of protein disulfide isomerase (PDI), the enzyme catalyzing the formation and isomerization of the native disulfide bond. Investigating whether different PDI isoforms interact with distinct toxin families will greatly advance our knowledge on the generation of cone snail toxins and disulfide-rich peptides in general.

  16. Characterization of the HIV-1 RNA associated proteome identifies Matrin 3 as a nuclear cofactor of Rev function

    PubMed Central

    2011-01-01

    Background Central to the fully competent replication cycle of the human immunodeficiency virus type 1 (HIV-1) is the nuclear export of unspliced and partially spliced RNAs mediated by the Rev posttranscriptional activator and the Rev response element (RRE). Results Here, we introduce a novel method to explore the proteome associated with the nuclear HIV-1 RNAs. At the core of the method is the generation of cell lines harboring an integrated provirus carrying RNA binding sites for the MS2 bacteriophage protein. Flag-tagged MS2 is then used for affinity purification of the viral RNA. By this approach we found that the viral RNA is associated with the host nuclear matrix component MATR3 (Matrin 3) and that its modulation affected Rev activity. Knockdown of MATR3 suppressed Rev/RRE function in the export of unspliced HIV-1 RNAs. However, MATR3 was able to associate with Rev only through the presence of RRE-containing viral RNA. Conclusions In this work, we exploited a novel proteomic method to identify MATR3 as a cellular cofactor of Rev activity. MATR3 binds viral RNA and is required for the Rev/RRE mediated nuclear export of unspliced HIV-1 RNAs. PMID:21771346

  17. Plant cell wall proteomics: mass spectrometry data, a trove for research on protein structure/function relationships.

    PubMed

    Albenne, Cécile; Canut, Hervé; Boudart, Georges; Zhang, Yu; San Clemente, Hélène; Pont-Lezica, Rafael; Jamet, Elisabeth

    2009-09-01

    Proteomics allows the large-scale study of protein expression either in whole organisms or in purified organelles. In particular, mass spectrometry (MS) analysis of gel-separated proteins produces data not only for protein identification, but for protein structure, location, and processing as well. An in-depth analysis was performed on MS data from etiolated hypocotyl cell wall proteomics of Arabidopsis thaliana. These analyses show that highly homologous members of multigene families can be differentiated. Two lectins presenting 93% amino acid identity were identified using peptide mass fingerprinting. Although the identification of structural proteins such as extensins or hydroxyproline/proline-rich proteins (H/PRPs) is arduous, different types of MS spectra were exploited to identify and characterize an H/PRP. Maturation events in a couple of cell wall proteins (CWPs) were analyzed using site mapping. N-glycosylation of CWPs as well as the hydroxylation or oxidation of amino acids were also explored, adding information to improve our understanding of CWP structure/function relationships. A bioinformatic tool was developed to locate by means of MS the N-terminus of mature secreted proteins and N-glycosylation.

  18. Functional impacts of exoskeleton-based rehabilitation in chronic stroke: multi-joint versus single-joint robotic training

    PubMed Central

    2013-01-01

    Stroke is a major cause of disability in the world. The activities of upper limb segments are often compromised following a stroke, impairing most daily tasks. Robotic training is now considered amongst the rehabilitation methods applied to promote functional recovery. However, the implementation of robotic devices remains a major challenge for the bioengineering and clinical community. Latest exoskeletons with multiple degrees of freedom (DOF) may become particularly attractive, because of their low apparent inertia, the multiple actuators generating large torques, and the fact that patients can move the arm in the normal wide workspace. A recent study published in JNER by Milot and colleagues underlines that training with a 6-DOF exoskeleton impacts positively on motor function in patients being in stable phase of recovery after a stroke. Also, multi-joint robotic training was not found to be superior to single-joint robotic training. Although it is often considered that rehabilitation should start from simple movements to complex functional movements as the recovery evolves, this study challenges this widespread notion whose scientific basis has remained uncertain. PMID:24354518

  19. Functional impacts of exoskeleton-based rehabilitation in chronic stroke: multi-joint versus single-joint robotic training.

    PubMed

    Grimaldi, Giuliana; Manto, Mario

    2013-12-19

    Stroke is a major cause of disability in the world. The activities of upper limb segments are often compromised following a stroke, impairing most daily tasks. Robotic training is now considered amongst the rehabilitation methods applied to promote functional recovery. However, the implementation of robotic devices remains a major challenge for the bioengineering and clinical community. Latest exoskeletons with multiple degrees of freedom (DOF) may become particularly attractive, because of their low apparent inertia, the multiple actuators generating large torques, and the fact that patients can move the arm in the normal wide workspace. A recent study published in JNER by Milot and colleagues underlines that training with a 6-DOF exoskeleton impacts positively on motor function in patients being in stable phase of recovery after a stroke. Also, multi-joint robotic training was not found to be superior to single-joint robotic training. Although it is often considered that rehabilitation should start from simple movements to complex functional movements as the recovery evolves, this study challenges this widespread notion whose scientific basis has remained uncertain.

  20. Proteomic and functional analyses of the venom of Porthidium lansbergii lansbergii (Lansberg's hognose viper) from the Atlantic Department of Colombia.

    PubMed

    Jiménez-Charris, Eliécer; Montealegre-Sanchez, Leonel; Solano-Redondo, Luis; Mora-Obando, Diana; Camacho, Erika; Castro-Herrera, Fernando; Fierro-Pérez, Leonardo; Lomonte, Bruno

    2015-01-30

    The venom of the Lansberg's hognose pitviper, Porthidium lansbergii lansbergii, a species found in the northern region of Colombia, is poorly known. Aiming to increase knowledge on Porthidium species venoms, its proteomic analysis and functional evaluation of in vitro and in vivo activities relevant to its toxicity were undertaken. Out of 51 protein components resolved by a combination of RP-HPLC and SDS-PAGE, 47 were assigned to 12 known protein families. In similarity with two previously characterized venoms from species within this genus, Porthidium nasutum and Porthidium ophryomegas, that of P. lansbergii lansbergii was dominated by metalloproteinases, although in lower proportion. A common feature of the three Porthidium venoms appears to be a high content of disintegrins. Proteins not previously observed in Porthidium venoms belong to the vascular endothelium growth factor, phosphodiesterase, and phospholipase B families. P. lansbergii lansbergii venom showed relatively weak lethal activity to mice, and induced a moderate local myotoxicity, but considerable hemorrhage. Its isolated VEGF component showed potent edema-inducing activity in the mouse footpad assay. Significant thrombocytopenia, but no other major hematological changes, were observed in envenomed mice. In vitro, this venom lacked coagulant effect on human plasma, and induced a potent inhibition of platelet aggregation which was reproduced by its purified disintegrin components. Phospholipase A2 and proteolytic activities were also demonstrated. Overall, the compositional and functional data herein described for the venom of P. lansbergii lansbergii may contribute to a better understanding of envenomings by this pitviper species, for which specific clinical information is lacking. Porthidium lansbergii lansbergii is estimated to be responsible for nearly 20% of snakebite envenoming cases at the Atlantic Department of Colombia, but the identity and functional properties of its venom components are

  1. Seed proteomics.

    PubMed

    Miernyk, Ján A; Hajduch, Martin

    2011-04-01

    Seeds comprise a protective covering, a small embryonic plant, and a nutrient-storage organ. Seeds are protein-rich, and have been the subject of many mass spectrometry-based analyses. Seed storage proteins (SSP), which are transient depots for reduced nitrogen, have been studied for decades by cell biologists, and many of the complicated aspects of their processing, assembly, and compartmentation are now well understood. Unfortunately, the abundance and complexity of the SSP requires that they be avoided or removed prior to gel-based analysis of non-SSP. While much of the extant data from MS-based proteomic analysis of seeds is descriptive, it has nevertheless provided a preliminary metabolic picture explaining much of their biology. Contemporary studies are moving more toward analysis of protein interactions and posttranslational modifications, and functions of metabolic networks. Many aspects of the biology of seeds make then an attractive platform for heterologous protein expression. Herein we present a broad review of the results from the proteomic studies of seeds, and speculate on a potential future research directions. Copyright © 2010 Elsevier B.V. All rights reserved.

  2. Erectile Function Outcomes after Robot-Assisted Radical Prostatectomy: Is It Superior to Open Retropubic or Laparoscopic Approach?

    PubMed

    Isgoren, Abidin Egemen; Saitz, Theodore R; Serefoglu, Ege Can

    2014-01-01

    Erectile dysfunction (ED) is one of the most commonly affected domains of health-related quality of life after prostate cancer therapy. Functional outcomes after radical prostatectomy (RP) have continued to improve through refinement of surgical techniques and development of several procedural modifications. In this context, it has been hypothesized that robotic technologies should simplify the preservation of the neurovascular bundle, thus possibly providing improved functional outcomes. To compare the prevalence of post-RP ED and identify whether recently developed robotic technologies are able to improve erectile function (EF) recovery after RP. Literature Review. To evaluate whether post-therapy ED rates after robotic surgery have shown improvement when compared with the other forms of nerve-sparing RP. Previously published series have shown EF recovery rates after robot-assisted RP (RARP) ranging between 40% and 90% of patients at 12 months, postoperatively. Some claim that the RARP procedure can also significantly shorten recovery time in return of EF when compared with open RP. On the other hand, some authors have reported that patients undergoing minimally invasive RP have experienced even more ED on comparison. Although it has been widely promoted by the industry and hospitals, at the moment there are not enough evidence-based data to answer the question, "Does RARP surgery provide better EF outcomes?." Because of the current market trends and patient preferences, the perfect randomized study will probably never be performed, and thus the question of which procedure's results are superior will most likely remain unanswered. Isgoren AE, Saitz TR, and Serefoglu EC. Erectile function outcomes after robot-assisted radical prostatectomy: Is it superior to open retropubic or laparoscopic approach? Sex Med Rev 2014;2:10-23. Copyright © 2014 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

  3. 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

  4. 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

  5. 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

  6. Robotic treadmill training improves cardiovascular function in spinal cord injury patients.

    PubMed

    Turiel, Maurizio; Sitia, Simona; Cicala, Silvana; Magagnin, Valentina; Bo, Ivano; Porta, Alberto; Caiani, Enrico; Ricci, Cristian; Licari, Vittorio; De Gennaro Colonna, Vito; Tomasoni, Livio

    2011-06-16

    Body weight supported treadmill training (BWSTT) assisted with a robotic driven gait orthosis (DGO) is an emerging tool in rehabilitating patients with lost sensorimotor function. Few information about the effects of BWSTT on cardiovascular system are available. The purpose of this study was to determine the effects of BWSTT on: 1) left ventricular (LV) systo-diastolic function; 2) coronary flow reserve (CFR); 3) endothelial function in patients with lost sensorimotor function due to neurologic lesions. Fourteen adults (males 10, age 50.6±17.1years) with motor incomplete spinal cord injuries (SCI) due to trauma or spondylotic diseases underwent standard echocardiographic examination, non invasive assessment of CFR by dipyridamole stress echo and determination of plasma asymmetric dimethylarginine (ADMA) levels at baseline and after 6weeks of BWSTT. At post training evaluation we observed lower LV end-diastolic (P=0.0164) and end-systolic volumes (P=0.0029) with increased ejection fraction (EF) (P=0.0266). We also observed a LV interventricular septum (IVS) (P=0.00469) increase. At the same time, we detected an improvement of LV diastolic function as witnessed by the reduction of isovolumic relaxation time (IVRT) (P=0.0404) and deceleration time (DT) (P=0.0405) with an increased E/A ratio (P=0.0040). Improved CFR (P=0.020) and reduced plasma ADMA levels (P=0.0005) have been observed too, in association with a reduction of the inflammatory status (C-reactive protein (CRP) (P=0.0022) and erythrocyte sedimentation rate (ESR) (P=0.0005)). For the first time, this study demonstrated that 6weeks of BWSTT improved not only the sensorimotor function but also systo-diastolic LV function, CFR and endothelial dysfunction associated with a reduction of the inflammatory status in patients with incomplete SCI. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  7. Proteomic Assessment of Polar Bacteria Phylogeny and Functional Shifts During POM Degradation at 0°C

    NASA Astrophysics Data System (ADS)

    Mikan, M.; Nunn, B. L.; Timmins-Schiffman, E.; Harvey, H. R.

    2016-02-01

    Polar marine bacterial community and metabolic response was tracked over a ten-day shipboard incubation experiment at 0°C, measured by high-mass accuracy tandem mass spectrometry. Planktonic bacteria were collected from Bering Strait surface waters and bottom water of the Chukchi Sea to target bacterial communities with unique metabolic capacities for particulate organic matter (POM) decomposition. From each location, resident POM was concentrated and amended as a treatment to one incubation, with the second as a control. Metagenomics was completed on both incubations and metaproteomics expression was tracked as a function of time. The Bering Strait surface water proteomic signature was dominated by microbial classes Alphaproteobacteria (31%), Gammaproteobacteria (30%) and Flavobacteriia (22%) . TonB-dependent transporter (TBDT) receptors accounted for 20% of the proteins that exhibited an increased abundance before incubation, a quarter of which were attributed to siderophore transport, an important iron chelator. Flavobacteriia and Gammaproteobacteria (48% and 39%, respectively) regulated expression of the TBDT receptors. ATP-binding cassette (ABC) transporter protein expression was controlled by the bacterial family Rhodobacteraceae and included functional groups specific to the transport of polyamines, peptides and branched-chain amino acids. By day 10, 63 proteins in the POM amended incubation increased abundance relative to the control experiment. Bacterial class Flavobacteriia dominated this signature (64%) with TBDT activity, iron-sulfur binding, glutamine biosynthesis, and calcium ion binding. 88 proteins were uniquely identified in the control experiment at day 10, and the population responsible for this set of expressed proteins differed from that of the POM addition experiment. This study demonstrates the potential to use proteomics to link the structures and functions of natural marine bacterial communities.

  8. 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

  9. Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity.

    PubMed

    Kanapin, Alexander A; Mulder, Nicola; Kuznetsov, Vladimir A

    2010-02-10

    We consider the problem of biological complexity via a projection of protein-coding genes of complex organisms onto the functional space of the proteome. The latter can be defined as a set of all functions committed by proteins of an organism. Alternative splicing (AS) allows an organism to generate diverse mature RNA transcripts from a single mRNA strand and thus it could be one of the key mechanisms of increasing of functional complexity of the organism's proteome and a driving force of biological evolution. Thus, the projection of transcription units (TU) and alternative splice-variant (SV) forms onto proteome functional space could generate new types of relational networks (e.g. SV-protein function networks, SFN) and lead to discoveries of novel evolutionarily conservative functional modules. Such types of networks might provide new reliable characteristics of organism complexity and a better understanding of the evolutionary integration and plasticity of interconnection of genome-transcriptome-proteome functions. We use the InterPro and UniProt databases to attribute descriptive features (keywords) to protein sequences. UniProt database includes a controlled and curated vocabulary of specific descriptors or keywords. The keywords have been assigned to a protein sequence via conserved domains or via similarity with annotated sequences. Then we consider the unique combinations of keywords as the protein functional labels (FL), which characterize the biological functions of the given protein and construct the contingency tables and graphs providing the projections of transcription units (TU) and alternative splice-variants (SV) onto all FL of the proteome of a given organism. We constructed SFNs for organisms with different evolutionary history and levels of complexity, and performed detailed statistical parameterization of the networks. The application of the algorithm to organisms with different evolutionary history and level of biological complexity (nematode

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

    PubMed Central

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

    2016-01-01

    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 occur 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. PMID:26458787

  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. 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

  13. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. 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

  15. Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome.

    PubMed

    Severing, Edouard I; van Dijk, Aalt D J; Stiekema, Willem J; van Ham, Roeland C H J

    2009-04-09

    Alternative splicing (AS) is a widespread phenomenon in higher eukaryotes but the extent to which it leads to functional protein isoforms and to proteome expansion at large is still a matter of debate. In contrast to animal species, for which AS has been studied extensively at the protein and functional level, protein-centered studies of AS in plant species are scarce. Here we investigate the functional impact of AS in dicot and monocot plant species using a comparative approach. Detailed comparison of AS events in alternative spliced orthologs from the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice) revealed that the vast majority of AS events in both species do not result from functional conservation. Transcript isoforms that are putative targets for the nonsense-mediated decay (NMD) pathway are as likely to contain conserved AS events as isoforms that are translated into proteins. Similar results were obtained when the same comparison was performed between the two more closely related monocot species rice and Zea mays (maize).Genome-wide computational analysis of functional protein domains encoded in alternatively and constitutively spliced genes revealed that only the RNA recognition motif (RRM) is overrepresented in alternatively spliced genes in all species analyzed. In contrast, three domain types were overrepresented in constitutively spliced genes. AS events were found to be less frequent within than outside predicted protein domains and no domain type was found to be enriched with AS introns. Analysis of AS events that result in the removal of complete protein domains revealed that only a small number of domain types is spliced-out in all species analyzed. Finally, in a substantial fraction of cases where a domain is completely removed, this domain appeared to be a unit of a tandem repeat. The results from the ortholog comparisons suggest that the ability of a gene to produce more than one functional protein through AS does not persist

  16. Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism.

    PubMed

    Casanovas, Albert; Sprenger, Richard R; Tarasov, Kirill; Ruckerbauer, David E; Hannibal-Bach, Hans Kristian; Zanghellini, Jürgen; Jensen, Ole N; Ejsing, Christer S

    2015-03-19

    Elucidating how and to what extent lipid metabolism is remodeled under changing conditions is essential for understanding cellular physiology. Here, we analyzed proteome and lipidome dynamics to investigate how regulation of lipid metabolism at the global scale supports remodeling of cellular architecture and processes during physiological adaptations in yeast. Our results reveal that activation of cardiolipin synthesis and remodeling supports mitochondrial biogenesis in the transition from fermentative to respiratory metabolism, that down-regulation of de novo sterol synthesis machinery prompts differential turnover of lipid droplet-associated triacylglycerols and sterol esters during respiratory growth, that sphingolipid metabolism is regulated in a previously unrecognized growth stage-specific manner, and that endogenous synthesis of unsaturated fatty acids constitutes an in vivo upstream activator of peroxisomal biogenesis, via the heterodimeric Oaf1/Pip2 transcription factor. Our work demonstrates the pivotal role of lipid metabolism in adaptive processes and provides a resource to investigate its regulation at the cellular level.

  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. 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

  19. A Snapshot of the Plant Glycated Proteome: STRUCTURAL, FUNCTIONAL, AND MECHANISTIC ASPECTS.

    PubMed

    Bilova, Tatiana; Lukasheva, Elena; Brauch, Dominic; Greifenhagen, Uta; Paudel, Gagan; Tarakhovskaya, Elena; Frolova, Nadezhda; Mittasch, Juliane; Balcke, Gerd Ulrich; Tissier, Alain; Osmolovskaya, Natalia; Vogt, Thomas; Wessjohann, Ludger A; Birkemeyer, Claudia; Milkowski, Carsten; Frolov, Andrej

    2016-04-01

    Glycation is the reaction of carbonyl compounds (reducing sugars and α-dicarbonyls) with amino acids, lipids, and proteins, yielding early and advanced glycation end products (AGEs). The AGEs can be formed via degradation of early glycation intermediates (glycoxidation) and by interaction with the products of monosaccharide autoxidation (autoxidative glycosylation). Although formation of these potentially deleterious compounds is well characterized in animal systems and thermally treated foods, only a little information about advanced glycation in plants is available. Thus, the knowledge of the plant AGE patterns and the underlying pathways of their formation are completely missing. To fill this gap, we describe the AGE-modified proteome ofBrassica napusand characterize individual sites of advanced glycation by the methods of liquid chromatography-based bottom-up proteomics. The modification patterns were complex but reproducible: 789 AGE-modified peptides in 772 proteins were detected in two independent experiments. In contrast, only 168 polypeptides contained early glycated lysines, which did not resemble the sites of advanced glycation. Similar observations were made withArabidopsis thaliana The absence of the early glycated precursors of the AGE-modified protein residues indicated autoxidative glycosylation, but not glycoxidation, as the major pathway of AGE formation. To prove this assumption and to identify the potential modifying agents, we estimated the reactivity and glycative potential of plant-derived sugars using a model peptide approach and liquid chromatography-mass spectrometry-based techniques. Evaluation of these data sets together with the assessed tissue carbohydrate contents revealed dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, ribulose, erythrose, and sucrose as potential precursors of plant AGEs. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Haemodynamics and cardiac function during robotic-assisted laparoscopic prostatectomy in steep Trendelenburg position.

    PubMed

    Haas, Sebastian; Haese, Alexander; Goetz, Alwin E; Kubitz, Jens C

    2011-12-01

    Robotic-assisted laparoscopic prostatectomy (RALP) is usually performed in steep Trendelenburg position, which can be associated with cardiac impairment due to positioning and capnoperitoneum. This study investigated haemodynamic consequences and cardiac function in this type of surgery and evaluated the hypothesis that steep Trendelenburg position and capnoperitoneum results in haemodynamic and ventricular impairment. 10 patients (ASA I-III) scheduled for RALP in steep Trendelenburg position with capnoperitoneum were prospectively studied. Heart rate (HR), mean arterial pressure (MAP) and central venous pressure (CVP) were recorded. Stroke volume variation (SVV) and cardiac output (CO) were measured using pulse-contour analysis. Further, cardiac function was assessed using trans-oesophageal echocardiography before positioning (T1) and 10 min (T2) and 60 min (T3) after implementation of steep Trendelenburg position and capnoperitoneum. HR did not change statistically. MAP (T1, 69.7 ± 1.55; T2, 82.9 ± 3.05; T3, 79.4 ± 2.18 mmHg), CVP (T1, 7.7 ± 1.3; T2, 17.3 ± 2.01; T3, 16.9 ± 1.66 mmHg) and CO (T1, 4.0 ± 0.15; T2, 4.9 ± 0.26; T3, 4.9 ± 0.36 l/min) increased significantly at T2 and T3. Echocardiography showed no deterioration of left or right ventricular function. In one patient with pre-existing mitral valve insufficiency (I°) an aggravation of the insufficiency (III°) was observed. No other valve dysfunctions were observed. The steep Trendelenburg position may improve haemodynamic function and does not deteriorate left or right ventricular function during RALP. However, mitral valve insufficiency may be aggravated by positioning and capnoperitoneum. Copyright © 2011 John Wiley & Sons, Ltd.

  1. Improved Functional Outcomes with Robotic Compared with Manual Total Hip Arthroplasty.

    PubMed

    Bukowski, Brandon R; Anderson, Paul; Khlopas, Anton; Chughtai, Morad; Mont, Michael A; Illgen, Richard L

    2016-10-26

    Functional outcome following total hip arthroplasty (THA) is affected by accurate component positioning and restoration of hip biomechanics. Robotic-assisted THA (rTHA) has been shown to improve accuracy of component positioning, but its impact on functional outcomes has not been demonstrated. The purpose of this study was to compare: 1) operative time; 2) estimated blood loss; 3) postoperative complications; and 4) patient-reported outcome measures (PROMs) between patients who either underwent rTHA or manual THA (mTHA). In this retrospective cohort study, a single-center database was used to identify all patients who underwent primary THA since introduction of rTHA at a large academic medical center. Surgical factors including operative time and estimated blood loss as well as postoperative complications were recorded. Validated PROMs following rTHA (n = 100) were compared with consecutive mTHA cases (n = 100) performed by the same fellowship-trained surgeon at a minimum one-year follow-up (24 ± 6 months). PROMs included the Short-Form 12 Health Survey (SF-12), UCLA activity score (UCLA), Western Ontario and McMaster (WOMAC) Osteoarthritis Index, and modified Harris Hip Score (mHHS). A categorical analysis was performed to determine differences in proportions of patients with mHHS scores of 90 to 100, 80 to 89, 70 to 79, and < 70 points between the two groups. Chi-square and two-tailed t-tests were used to compare categorical and continuous data between cohorts. Mean operative time was nine minutes longer for the rTHA group compared with the mTHA group (131 ± 23 min vs. 122 ± 29 min, respectively, p = 0.012). Estimated intraoperative blood loss was significantly reduced for the rTHA group when compared to the mTHA group (374 ± 133 mL vs. 423 ± 186 mL, p = 0.035), and there was no difference in overall complication rates between the two groups (p = 0.101). Robotic-assisted THA demonstrated significantly higher mean postoperative mHHS (92.1 ± 10.5 vs. 86.1

  2. Functional MRI of Rehabilitation in Chronic Stroke Patients Using Novel MR-Compatible Hand Robots.

    PubMed

    Mintzopoulos, Dionyssios; Khanicheh, Azadeh; Konstas, Angelos A; Astrakas, Loukas G; Singhal, Aneesh B; Moskowitz, Michael A; Rosen, Bruce R; Tzika, A Aria

    2008-09-27

    We monitored brain activation after chronic stroke by combining functional magnetic resonance imaging (fMRI) with a novel MR-compatible, hand-induced, robotic device (MR_CHIROD). We evaluated 60 fMRI datasets on a 3 T MR system from five right-handed patients with left-sided stroke >/=6 months prior and mild to moderate hemiparesis. Patients trained the paretic right hand at approximately 75% of maximum strength with an exercise ball for 1 hour/day, 3 days/week for 4 weeks. Multi-level fMRI data were acquired before, during training, upon completion of training, and after a non-training period using parallel imaging employing GeneRalized Autocalibrating Partially Parallel Acquisitions (GRAPPA) while the participant used the MR_CHIROD. Training increased the number of activated sensorimotor cortical voxels, indicating functional cortical plasticity in chronic stroke patients. The effect persisted four weeks after training completion, indicating the potential of rehabilitation in inducing cortical plasticity in chronic stroke patients.

  3. Electromechanical and robot-assisted arm training for improving arm function and activities of daily living after stroke.

    PubMed

    Mehrholz, Jan; Platz, Thomas; Kugler, Joachim; Pohl, Marcus

    2008-10-08

    Electromechanical and robot-assisted arm training devices are used in rehabilitation and might help to improve arm function after stroke. To assess the effectiveness of electromechanical and robot-assisted arm training for improving activities of daily living and arm function and motor strength of patients after stroke, and the acceptability and safety of the therapy. We searched the Cochrane Stroke Group Trials Register (last searched October 2007), the Cochrane Central Register of Controlled Trials (The Cochrane Library, Issue 3, 2007), MEDLINE (1950 to October 2007), EMBASE (1980 to October 2007), CINAHL (1982 to October 2007), AMED (1985 to October 2007), SPORTDiscus (1949 to October 2007), PEDro (searched October 2007), COMPENDEX (1972 to October 2007) and INSPEC (1969 to October 2007). We also handsearched relevant conference proceedings, searched trials and research registers, checked reference lists, and contacted trialists, experts and researchers in our field, and manufacturers of commercial devices. Randomised controlled trials comparing electromechanical and robot-assisted arm training for recovery of arm function with other rehabilitation interventions or no treatment for patients after stroke. Two review authors independently selected trials for inclusion, assessed trial quality and extracted data. We contacted trialists for additional information. We analysed the results as standardised mean differences (SMDs) for continuous variables and relative risk differences (RD) for dichotomous variables. We included 11 trials (328 participants) in this review. Electromechanical and robot-assisted arm training did not improve activities of daily living (SMD = 0.29; 95% confidence interval (CI) -0.47 to 1.06; P = 0.45; I(2 )= 85%). Arm motor function and arm motor strength improved (SMD = 0.68, 95% CI 0.24 to 1.11; P = 0.002; I(2 )= 56% and SMD = 01.03, 95% CI 0.29 to 1.78; P = 0.007; I(2 )= 79% respectively). Electromechanical and robot-assisted arm training

  4. Robotic Intracorporeal Padua Ileal Bladder: Surgical Technique, Perioperative, Oncologic and Functional Outcomes.

    PubMed

    Simone, Giuseppe; Papalia, Rocco; Misuraca, Leonardo; Tuderti, Gabriele; Minisola, Francesco; Ferriero, Mariaconsiglia; Vallati, Giulio; Guaglianone, Salvatore; Gallucci, Michele

    2016-10-22

    Robot-assisted radical cystectomy (RARC) with intracorporeal neobladder reconstruction is a challenging procedure. The need for surgical skills and the long operative times have led to concern about its reproducibility. To illustrate our technique for RARC and totally intracorporeal orthotopic Padua ileal bladder. From August 2012 to February 2014, 45 patients underwent this technique at a single tertiary referral centre. RARC, extended pelvic lymph node dissection, and intracorporeal partly stapled neobladder. Surgical steps are demonstrated in the accompanying video. Demographics, clinical, and pathological data were collected. Perioperative, 2-yr oncologic and 2-yr functional outcomes were reported. Intraoperative transfusion or conversion to open surgery was not necessary in any case and intracorporeal neobladder was successfully performed in all 45 patients. Median operative time was 305min (interquartile range [IQR]: 282-345). Median estimated blood loss was 210ml (IQR: 50-250). Median hospital stay was 9 d (IQR: 7-12). The overall incidence of perioperative, 30-d and 180-d complications were 44.4%, 57.8%, and 77.8%, respectively, while severe complications occurred in17.8%, 17.8%, and 35.5%, respectively. Two-yr daytime and night-time continence rates were 73.3% and 55.5%, respectively. Two-yr disease free survival, cancer specific survival, and overall survival rates were 72.5%, 82.3%, and 82.4%, respectively. The small sample size and high caseload of the centre might affect the reproducibility of these results. Our experience supports the feasibility of totally intracorporeal neobladder following RARC. Operative times and perioperative complication rates are likely to be reduced with increasing experience. We report the outcomes of our first 45 consecutive patients who underwent robot-assisted radical cystectomy with intracorporeal neobladders. Perioperative, oncologic, and functional outcomes support this technique as a feasible and safe surgical option

  5. 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

  6. Technical refinement and learning curve for attenuating neurapraxia during robotic-assisted radical prostatectomy to improve sexual function.

    PubMed

    Alemozaffar, Mehrdad; Duclos, Antoine; Hevelone, Nathanael D; Lipsitz, Stuart R; Borza, Tudor; Yu, Hua-Yin; Kowalczyk, Keith J; Hu, Jim C

    2012-06-01

    While radical prostatectomy surgeon learning curves have characterized less blood loss, shorter operative times, and fewer positive margins, there is a dearth of studies characterizing learning curves for improving sexual function. Additionally, while learning curve studies often define volume thresholds for improvement, few of these studies demonstrate specific technical modifications that allow reproducibility of improved outcomes. Demonstrate and quantify the learning curve for improving sexual function outcomes based on technical refinements that reduce neurovascular bundle displacement during nerve-sparing robot-assisted radical prostatectomy (RARP). We performed a retrospective study of 400 consecutive RARPs, categorized into groups of 50, performed after elimination of continuous surgeon/assistant neurovascular bundle countertraction. Our approach to RARP has been described previously. A single-console robotic system was used for all cases. Expanded Prostate Cancer Index Composite sexual function was measured within 1 yr of RARP. Linear regression was performed to determine factors influencing the recovery of sexual function. Greater surgeon experience was associated with better 5-mo sexual function (p = 0.007) and a trend for better 12-mo sexual function (p = 0.061), with improvement plateauing after 250-300 cases. Additionally, younger patient age (both p<0.02) and better preoperative sexual function (<0.001) were associated with better 5- and 12-mo sexual function. Moreover, trainee robotic console time during nerve sparing was associated with worse 12-mo sexual function (p=0.021), while unilateral nerve sparing/non-nerve sparing was associated with worse 5-mo sexual function (p = 0.009). Limitations include the retrospective single-surgeon design. With greater surgeon experience, attenuating lateral displacement of the neurovascular bundle and resultant neurapraxia improve postoperative sexual function. However, to maximize outcomes, appropriate patient

  7. Emergence of Functional Hierarchy in a Multiple Timescale Neural Network Model: A Humanoid Robot Experiment

    PubMed Central

    Yamashita, Yuichi; Tani, Jun

    2008-01-01

    It is generally thought that skilled behavior in human beings results from a functional hierarchy of the motor control system, within which reusable motor primitives are flexibly integrated into various sensori-motor sequence patterns. The underlying neural mechanisms governing the way in which continuous sensori-motor flows are segmented into primitives and the way in which series of primitives are integrated into various behavior sequences have, however, not yet been clarified. In earlier studies, this functional hierarchy has been realized through the use of explicit hierarchical structure, with local modules representing motor primitives in the lower level and a higher module representing sequences of primitives switched via additional mechanisms such as gate-selecting. When sequences contain similarities and overlap, however, a conflict arises in such earlier models between generalization and segmentation, induced by this separated modular structure. To address this issue, we propose a different type of neural network model. The current model neither makes use of separate local modules to represent primitives nor introduces explicit hierarchical structure. Rather than forcing architectural hierarchy onto the system, functional hierarchy emerges through a form of self-organization that is based on two distinct types of neurons, each with different time properties (“multiple timescales”). Through the introduction of multiple timescales, continuous sequences of behavior are segmented into reusable primitives, and the primitives, in turn, are flexibly integrated into novel sequences. In experiments, the proposed network model, coordinating the physical body of a humanoid robot through high-dimensional sensori-motor control, also successfully situated itself within a physical environment. Our results suggest that it is not only the spatial connections between neurons but also the timescales of neural activity that act as important mechanisms leading to

  8. Emergence of functional hierarchy in a multiple timescale neural network model: a humanoid robot experiment.

    PubMed

    Yamashita, Yuichi; Tani, Jun

    2008-11-01

    It is generally thought that skilled behavior in human beings results from a functional hierarchy of the motor control system, within which reusable motor primitives are flexibly integrated into various sensori-motor sequence patterns. The underlying neural mechanisms governing the way in which continuous sensori-motor flows are segmented into primitives and the way in which series of primitives are integrated into various behavior sequences have, however, not yet been clarified. In earlier studies, this functional hierarchy has been realized through the use of explicit hierarchical structure, with local modules representing motor primitives in the lower level and a higher module representing sequences of primitives switched via additional mechanisms such as gate-selecting. When sequences contain similarities and overlap, however, a conflict arises in such earlier models between generalization and segmentation, induced by this separated modular structure. To address this issue, we propose a different type of neural network model. The current model neither makes use of separate local modules to represent primitives nor introduces explicit hierarchical structure. Rather than forcing architectural hierarchy onto the system, functional hierarchy emerges through a form of self-organization that is based on two distinct types of neurons, each with different time properties ("multiple timescales"). Through the introduction of multiple timescales, continuous sequences of behavior are segmented into reusable primitives, and the primitives, in turn, are flexibly integrated into novel sequences. In experiments, the proposed network model, coordinating the physical body of a humanoid robot through high-dimensional sensori-motor control, also successfully situated itself within a physical environment. Our results suggest that it is not only the spatial connections between neurons but also the timescales of neural activity that act as important mechanisms leading to functional

  9. 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. ...

  10. 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.

  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. Differences in postoperative outcomes, function, and cosmesis: open versus robotic thyroidectomy.

    PubMed

    Lee, Jandee; Nah, Kuk Young; Kim, Ra Mi; Ahn, Yeun Hee; Soh, Euy-Young; Chung, Woong Youn

    2010-12-01

    Robotic thyroidectomy using a gasless transaxillary approach, first described in 2008, has become popular. This study compared outcomes, including postoperative distress and patient satisfaction, for patients undergoing robotic thyroidectomy with those for patients treated by conventional open thyroidectomy. Of 84 prospectively enrolled patients, 41 underwent robotic thyroidectomy (the robot group), and 43 received conventional open thyroidectomy (the open group). All the patients were followed up for at least 3 months after surgery. Videolaryngostroboscopic examinations were performed preoperatively and after 1 week and after 3 months postoperatively. Postoperative pain and discomfort were evaluated using a symptom scale. Subjective voice and swallowing changes were assessed by questionnaires; and satisfaction with cosmetic outcome was measured by verbal response at 3 months. The two groups were similar in age, gender, type of operation, and final pathologic diagnosis. Although the mean operating time was significantly longer with the robotic technique than with open surgery, there were no between-group differences in postoperative pain or duration of hospital stay. No patient in either group experienced any major postoperative complication. Postoperative discomfort in the neck and swallowing disturbances were significantly more frequent in the open group than in the robot group, both at 1 week and at 3 months after surgery. However, there was no significant between-group difference in subjective voice parameters. At 3 months, the mean cosmetic satisfaction score was significantly higher in the robotic than in the open group. Although postoperative pain levels and complications were comparable in the two groups, conventional open thyroidectomy requires a shorter operative time. The robotic technique, however, offers several distinct advantages including very good to excellent cosmetic results, reduced postoperative neck discomfort, and fewer adverse swallowing

  14. 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.

  15. Proteomic and functional analyses reveal MAPK1 regulates milk protein synthesis.

    PubMed

    Lu, Li-Min; Li, Qing-Zhang; Huang, Jian-Guo; Gao, Xue-Jun

    2012-12-27

    L-Lysine (L-Lys) is an essential amino acid that plays fundamental roles in protein synthesis. Many nuclear phosphorylated proteins such as Stat5 and mTOR regulate milk protein synthesis. However, the details of milk protein synthesis control at the transcript and translational levels are not well known. In this current study, a two-dimensional gel electrophoresis (2-DE)/MS-based proteomic technology was used to identify phosphoproteins responsible for milk protein synthesis in dairy cow mammary epithelial cells (DCMECs). The effect of L-Lys on DCMECs was analyzed by CASY technology and reversed phase high performance liquid chromatography (RP-HPLC). The results showed that cell proliferation ability and β-casein expression were enhanced in DCMECs treated with L-Lys. By phosphoproteomics analysis, six proteins, including MAPK1, were identified up-expressed in DCMECs treated with 1.2 mM L-Lys for 24 h, and were verified by quantitative real-time PCR (qRT-PCR) and western blot. Overexpression and siRNA inhibition of MAPK1 experiments showed that MAPK1 upregulated milk protein synthesis through Stat5 and mTOR pathway. These findings that MAPK1 involves in regulation of milk synthesis shed new insights for understanding the mechanisms of milk protein synthesis.

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

    PubMed

    Wu, Chun-Yi; Wang, Don-Hong; Wang, Xiaobing; Dixon, Seth M; Meng, Liping; Ahadi, Sara; Enter, Daniel H; Chen, Chao-Yu; Kato, Jason; Leon, Leonardo J; Ramirez, Laura M; Maeda, Yoshiko; Reis, Carolina F; Ribeiro, Brianna; Weems, Brittany; Kung, Hsing-Jien; Lam, Kit S

    2016-06-13

    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 10(13) 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.

  17. 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

  18. Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions

    PubMed Central

    Brocard, Lysiane; Immel, Françoise; Coulon, Denis; Esnay, Nicolas; Tuphile, Karine; Pascal, Stéphanie; Claverol, Stéphane; Fouillen, Laëtitia; Bessoule, Jean-Jacques; Bréhélin, Claire

    2017-01-01

    Lipid droplets (LDs) are cell compartments specialized for oil storage. Although their role and biogenesis are relatively well documented in seeds, little is known about their composition, structure and function in senescing leaves where they also accumulate. Here, we used a label free quantitative mass spectrometry approach to define the LD proteome of aging Arabidopsis leaves. We found that its composition is highly different from that of seed/cotyledon and identified 28 proteins including 9 enzymes of the secondary metabolism pathways involved in plant defense response. With the exception of the TRIGALACTOSYLDIACYLGLYCEROL2 protein, we did not identify enzymes implicated in lipid metabolism, suggesting that growth of leaf LDs does not occur by local lipid synthesis but rather through contact sites with the endoplasmic reticulum (ER) or other membranes. The two most abundant proteins of the leaf LDs are the CALEOSIN3 and the SMALL RUBBER PARTICLE1 (AtSRP1); both proteins have structural functions and participate in plant response to stress. CALEOSIN3 and AtSRP1 are part of larger protein families, yet no other members were enriched in the LD proteome suggesting a specific role of both proteins in aging leaves. We thus examined the function of AtSRP1 at this developmental stage and found that AtSRP1 modulates the expression of CALEOSIN3 in aging leaves. Furthermore, AtSRP1 overexpression induces the accumulation of triacylglycerol with an unusual composition compared to wild-type. We demonstrate that, although AtSRP1 expression is naturally increased in wild type senescing leaves, its overexpression in senescent transgenic lines induces an over-accumulation of LDs organized in clusters at restricted sites of the ER. Conversely, atsrp1 knock-down mutants displayed fewer but larger LDs. Together our results reveal that the abundancy of AtSRP1 regulates the neo-formation of LDs during senescence. Using electron tomography, we further provide evidence that LDs in

  19. 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.

  20. 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

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

    PubMed

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

    2014-08-01

    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. From April 2011 to December 2012, NIRF imaging-enhanced RPN with selective clamping was used in 42 cases. Functional outcomes of successful cases were compared with a cohort of patients, matched by tumor size, preoperative estimated glomerular filtration rate (eGFR), functional kidney status, age, sex, body mass index, and American Society of Anesthesiologists score, who underwent RPN without selective clamping and NIRF imaging. 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/1.73 m(2); P = .04), absolute reduction of eGFR (-2.5 vs -14.0 mL/min/1.73 m(2); P <.01), and percent change in eGFR (-1.9% vs -16.8%; P <.01). Similar trends were noted at 3 month follow-up, but these differences became nonsignificant (P[eGFR] = .07; P[absolute reduction of eGFR] = .10; and P[percent change in eGFR] = .07). In the selective clamping group, a total of 4 perioperative complications occurred in 3 patients, all of which were Clavien grade I-III. Use of NIRF imaging was associated with improved short-term renal functional outcomes when compared with 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Nerve sparing can preserve orgasmic function in most men after robotic-assisted laparoscopic radical prostatectomy.

    PubMed

    Tewari, Ashutosh; Grover, Sonal; Sooriakumaran, Prasanna; Srivastava, Abhishek; Rao, Sandhya; Gupta, Amit; Gray, Robert; Leung, Robert; Paduch, Darius A

    2012-02-01

    •  To investigate orgasmic outcomes in patients undergoing robotic-assisted laparoscopic radical prostatectomy (RALP) and the effects of age and nerve sparing on these outcomes. •  Between January 2005 and June 2007, 708 patients underwent RALP at our institution. •  We analysed postoperative potency and orgasmic outcomes in the 408 men, of the 708, who were potent, able to achieve orgasm preoperatively and available for follow-up. •  Of men aged ≤60 years, 88.4% (198/224) were able to achieve orgasm postoperatively in comparison to 82.6% (152/184) of older men (P < 0.001). •  Of patients who received bilateral nerve sparing (BNS) during surgery, 273/301 (90.7%) were able to achieve orgasm postoperatively compared with 46/56 (82.1%) patients who received unilateral nerve sparing and 31/51 (60.8%) men who received non-nerve-sparing surgery (P < 0.001). •  In men ≤60 years who also underwent BNS, decreased sensation of orgasm was present in 3.2% of men, and postoperative orgasmic rates were significantly better than men ≤60 years who underwent unilateral or no nerve sparing (92.9% vs 83.3% vs 65.4%, respectively; P < 0.001). •  Potency rates were also significantly higher in men ≤60 years and in those who underwent BNS. •  Age and nerve sparing influence recovery of orgasm and erectile function after RALP. •  Men ≤60 years old and those who undergo BNS are most likely to maintain normal sexual function. © 2011 THE AUTHORS. BJU INTERNATIONAL © 2011 BJU INTERNATIONAL.

  3. Association of Urine Dipstick Proteinuria and Postoperative Renal Function Following Robotic Partial Nephrectomy.

    PubMed

    Krane, Louis S; Heavner, Matthew G; Peyton, Charles; Rague, James T; Hemal, Ashok K

    2016-05-01

    In patients with normal estimated renal function before robot-assisted partial nephrectomy (RPN), there is still a risk for de Novo chronic kidney disease (CKD). We assessed the role of dipstick spot proteinuria in risk stratifying patients for CKD progression. From our prospectively maintained, institutional review board-approved database of patients undergoing RPN, we queried those with estimated glomerular filtration rate (eGFR) >60 and bilateral functional units. We assessed proteinuria through dipstick (trace or above) on voided urine in preoperative urologic appointment <3 weeks before RPN. Proteinuric patients were compared with the remainder of the cohort with parametric comparisons for continuous and chi-squared analysis for categoric variables. Multivariate logistic regression analyses were performed assessing the risk of de Novo CKD stage III development, estimated by the CKD-EPI equation. We found 269 patients with eGFR >60 preoperatively, of whom 57 (21%) had proteinuria preoperatively. In univariate analysis, these patients were more likely to be diabetic (p = 0.023) and to be on an angiotensin converting enzyme inhibitor or angiotensin receptor blocker (p = 0.001) but had similar age (p = 0.13), body mass index (p = 0.09), and tumor size (p = 0.56) with similar rates of hypertension (p = 0.07). At a median 16 months, controlling for confounding variables, preoperative proteinuria on urinary dipstick was associated with a 2.3× (95% confidence interval 1.03-4.95) increased risk of de Novo CKD stage III progression. Patients with proteinuria preoperatively, despite a normal eGFR, likely have intrinsic medicorenal disease. These patients should be counseled preoperatively that they have a higher risk of CKD progression following RPN.

  4. Robotic resistance/assistance training improves locomotor function in individuals poststroke: a randomized controlled study.

    PubMed

    Wu, Ming; Landry, Jill M; Kim, Janis; Schmit, Brian D; Yen, Sheng-Che; Macdonald, Jillian

    2014-05-01

    To determine whether providing a controlled resistance versus assistance to the paretic leg at the ankle during treadmill training will improve walking function in individuals poststroke. Repeated assessment of the same patients with parallel design and randomized controlled study between 2 groups. Research units of rehabilitation hospitals. Patients (N=30) with chronic stroke. Subjects were stratified based on self-selected walking speed and were randomly assigned to the resistance or assistance training group. For the resistance group, a controlled resistance load was applied to the paretic leg at the ankle to resist leg swing during treadmill walking. For the assistance group, a load that assists swing was applied. Primary outcome measures were walking speed and 6-minute walking distance. Secondary measures included clinical assessments of balance, muscle tone, and quality of life. Outcome measures were evaluated before and after 6 weeks of training and at 8 weeks' follow-up, and compared within group and between the 2 groups. After 6 weeks of robotic training, walking speed significantly increased for both groups, with no significant differences in walking speed gains observed between the 2 groups. In addition, 6-minute walking distance and balance significantly improved for the assistance group but not for the resistance group. Applying a controlled resistance or an assistance load to the paretic leg during treadmill training may induce improvements in walking speed in individuals poststroke. Resistance training was not superior to assistance training in improving locomotor function in individuals poststroke. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  5. [Minimally invasive radical prostatectomy: Contribution of robotic support, functional and oncological outcomes].

    PubMed

    Hoepffner, Jean-Luc; Gaston, Richard; Mugnier, Camille; Rey, Denis; Lopez, Laurent; Roche, Jean-Baptiste; Riviere, Julien; Piechaud, Pierre-Thierry

    2016-05-01

    Radical prostatectomy (RP) remains a standard for localized prostate cancer treatment. The objective of this study is to present this operating technique of the robot-assisted radical prostatectomy (PR-RA) and to evaluate oncological and functional results as well as on the surgical safety. A first series of 1679 patients consecutively operated in our institution with this technique from 2005 to 2010 and with a 5-year follow-up evaluated in 2014. The oncology monitoring is ensured with a PSA test every six months during the first three years and once a year the years after if the level remains undetectable. The oncologic outcomes show 17.4% for pT2 stages and 36.9% for pT3 stages positive margins. The level of biological recurrence is 21.27% with an average delay of 88 months as the time needed for the recurrence to occur. At 12 months, urinary continence (0-1pad/day) returned at 94% of all patients and potency with successful penetration for all men is 61.1% and 88.8% for men with sexual activity before surgery. The technique PRRA seems to be a reliable technique whose functional results studied from meta-analysis seem to be superior in terms of rapidity of recovery of the continence and erection in comparison with classical surgical or laparoscopic approach. Copyright © 2016 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.

  6. Laparoscopic and robotic partial nephrectomy without renal ischaemia for tumours larger than 4 cm: perioperative and functional outcomes.

    PubMed

    Papalia, Rocco; Simone, Giuseppe; Ferriero, Mariaconsiglia; Guaglianone, Salvatore; Costantini, Manuela; Giannarelli, Diana; Maini, Carlo Ludovico; Forastiere, Ester; Gallucci, Michele

    2012-10-01

    To evaluate the technical feasibility, safety and functional outcomes of zero ischaemia laparoscopic and robotic partial nephrectomy with controlled hypotension for renal tumours larger than 4 cm. We evaluated 121 consecutive patients with American Society of Anaesthesiologists (ASA) scores 1-2 who underwent laparoscopic (n = 70) or robotic (n = 51) partial nephrectomy with controlled hypotension with either tumour size ≤4 cm (group 1, n = 78) or tumour size >4 cm (group 2, n = 43) performed by a single surgeon from December 2010 to December 2011. Operative data, complications, serum creatinine, estimated glomerular filtration rates and effective renal plasma flow calculated from 99mTc-mercaptoacetyltriglycine renal scintigraphy were compared. Differences between groups were evaluated by the Chi-square test and the Student's t test. A significant difference in mean intraoperative blood loss and postoperative complications was found between the two groups: 168 ml (range: 10-600 ml in group 1) and 205 ml (range: 90-700 ml in group 2); p = 0.005, and 6.4 % versus 18.6 %; p = 0.004, respectively. The mean percentage decrease of ERPF of the operated kidney was 1.8 % in group 1 and 4.1 % in group 2. Laparoscopic and robotic partial nephrectomy with controlled hypotension for tumours >4 cm in ASA 1-2 patients was feasible with significant higher intraoperative blood loss and postoperative complications compared to smaller renal masses. The benefits of avoiding hilar clamping to preserve kidney function seem excellent.

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

    PubMed

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

    2013-04-05

    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).

  8. The Redox Proteome*

    PubMed Central

    Go, Young-Mi; Jones, Dean P.

    2013-01-01

    The redox proteome consists of reversible and irreversible covalent modifications that link redox metabolism to biologic structure and function. These modifications, especially of Cys, function at the molecular level in protein folding and maturation, catalytic activity, signaling, and macromolecular interactions and at the macroscopic level in control of secretion and cell shape. Interaction of the redox proteome with redox-active chemicals is central to macromolecular structure, regulation, and signaling during the life cycle and has a central role in the tolerance and adaptability to diet and environmental challenges. PMID:23861437

  9. 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.

  10. 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

  11. Glyoxalase 1-knockdown in human aortic endothelial cells – effect on the proteome and endothelial function estimates

    PubMed Central

    Stratmann, Bernd; Engelbrecht, Britta; Espelage, Britta C.; Klusmeier, Nadine; Tiemann, Janina; Gawlowski, Thomas; Mattern, Yvonne; Eisenacher, Martin; Meyer, Helmut E.; Rabbani, Naila; Thornalley, Paul J.; Tschoepe, Diethelm; Poschmann, Gereon; Stühler, Kai

    2016-01-01

    Methylglyoxal (MG), an arginine-directed glycating agent, is implicated in diabetic late complications. MG is detoxified by glyoxalase 1 (GLO1) of the cytosolic glyoxalase system. The aim was to investigate the effects of MG accumulation by GLO1-knockdown under hyperglycaemic conditions in human aortic endothelial cells (HAECs) hypothesizing that the accumulation of MG accounts for the deleterious effects on vascular function. SiRNA-mediated knockdown of GLO1 was performed and MG concentrations were determined. The impact of MG on the cell proteome and targets of MG glycation was analysed, and confirmed by Western blotting. Markers of endothelial function and apoptosis were assessed. Collagen content was assayed in cell culture supernatant. GLO1-knockdown increased MG concentration in cells and culture medium. This was associated with a differential abundance of cytoskeleton stabilisation proteins, intermediate filaments and proteins involved in posttranslational modification of collagen. An increase in fibrillar collagens 1 and 5 was detected. The extracellular concentration of endothelin-1 was increased following GLO1-knockdown, whereas the phosphorylation and amount of eNOS was not influenced by GLO1-knockdown. The expression of ICAM-1, VCAM-1 and of MCP-1 was elevated and apoptosis was increased. MG accumulation by GLO1-knockdown provoked collagen expression, endothelial inflammation and dysfunction and apoptosis which might contribute to vascular damage. PMID:27898103

  12. Optimal strategy for penile rehabilitation after robot-assisted radical prostatectomy based on preoperative erectile function.

    PubMed

    Basal, Seref; Wambi, Chris; Acikel, Cengizhan; Gupta, Mantu; Badani, Ketan

    2013-04-01

    WHAT'S KNOWN ON THE SUBJECT? AND WHAT DOES THE STUDY ADD?: Removing of prostate for the treatment of localized prostate cancer is associated with a variable loss of erectile function due to injury of the nerves of erection during operation. Some researchers have reported that after nerve-sparing radical prostatectomy (RP), the natural recovery time of erectile function is at least 2 years. Factors such as thermal damage, ischaemic injury, mechanically induced nerve stretching and the local inflammatory effects of surgical trauma may also impair the cavernous nerves during RP. The concept of penile rehabilitation was first studied by Montorsi et al. in 1997. They showed that the use of any drug or device at or after RP could maximize the recovery of erectile function. Penile rehabilitation programmes (PRPs) with vasoactive agents, such as oral phosphodiesterase-5 inhibitors (PDE5Is), intraurethral and intracavernosal vasoactive agents, and vacuum erection devices (VEDs) can protect erectile tissue integrity and prevent corporal smooth muscle atrophy and diminish collagen formation. The present findings are consistent with previous reports that PRPs have a significant beneficial effect on early erectile function recovery and that preoperative erectile function is one of the important predictors of erectile function after RP. Patients can be referred for penile rehabilitation if they have any degree of erectile function (mild, moderate or normal) before operation. We also showed that the combination of PDE5Is and VEDs for PRPs offers the shortest erectile function recovery period. To define the optimal penile rehabilitation programme (PRP) based on preoperative Sexual Health Inventory for Men (SHIM) scores after robot-assisted radical prostatectomy (RARP). The medical records of 203 patients who underwent bilateral nerve-sparing RARP between 2007 and 2011 were reviewed for the present retrospective study. According to patients' preoperative erection status, group 1

  13. The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study.

    PubMed

    Romero, Roberto; Erez, Offer; Maymon, Eli; Chaemsaithong, Piya; Xu, Zhonghui; Pacora, Percy; Chaiworapongsa, Tinnakorn; Done, Bogdan; Hassan, Sonia S; Tarca, Adi L

    2017-07-01

    Pregnancy is accompanied by dramatic physiological changes in maternal plasma proteins. Characterization of the maternal plasma proteome in normal pregnancy is an essential step for understanding changes to predict pregnancy outcome. The objective of this study was to describe maternal plasma proteins that change in abundance with advancing gestational age and determine biological processes that are perturbed in normal pregnancy. A longitudinal study included 43 normal pregnancies that had a term delivery of an infant who was appropriate for gestational age without maternal or neonatal complications. For each pregnancy, 3 to 6 maternal plasma samples (median, 5) were profiled to measure the abundance of 1125 proteins using multiplex assays. Linear mixed-effects models with polynomial splines were used to model protein abundance as a function of gestational age, and the significance of the association was inferred via likelihood ratio tests. Proteins considered to be significantly changed were defined as having the following: (1) >1.5-fold change between 8 and 40 weeks of gestation; and (2) a false discovery rate-adjusted value of P < .1. Gene ontology enrichment analysis was used to identify biological processes overrepresented among the proteins that changed with advancing gestation. The following results were found: (1) Ten percent (112 of 1125) of the profiled proteins changed in abundance as a function of gestational age; (2) of the 1125 proteins analyzed, glypican-3, sialic acid-binding immunoglobulin-type lectin-6, placental growth factor, C-C motif-28, carbonic anhydrase 6, prolactin, interleukin-1 receptor 4, dual-specificity mitogen-activated protein kinase 4, and pregnancy-associated plasma protein-A had more than a 5-fold change in abundance across gestation (these 9 proteins are known to be involved in a wide range of both physiological and pathological processes, such as growth regulation, embryogenesis, angiogenesis immunoregulation, inflammation

  14. Subcellular proteomics in neuroscience.

    PubMed

    Li, Ka Wan; Smit, August B

    2008-05-01

    The brain is the most complex and dynamically organized organ of the human body, with a high degree of computation capability enabling the execution of a wide spectrum of physiological processes and behaviors. In the past decades a large number of genomics studies have been undertaken to investigate brain function and brain disorders, but despite these efforts many of the underlying molecular mechanisms still remain largely unknown. The implementation of mass spectrometry based quantitative proteomics in recent years enabled to tap into condition-specific protein trafficking and protein interaction that are the key to organelle proteome (dys)function. The technology for neuroproteomics is still evolving; currently there are no standardized protocols. In this review we describe the most commonly used methods to prepare brain subcellular fractions suitable for proteomics analysis, and highlight the various approaches for quantitative neuroproteomics.

  15. Predicting clinically significant changes in motor and functional outcomes after robot-assisted stroke rehabilitation.

    PubMed

    Hsieh, Yu-wei; Lin, Keh-chung; Wu, Ching-yi; Lien, Hen-yu; Chen, Jean-lon; Chen, Chih-chi; Chang, Wei-han

    2014-02-01

    To investigate the predictors of minimal clinically important changes on outcome measures after robot-assisted therapy (RT). Observational cohort study. Outpatient rehabilitation clinics. A cohort of outpatients with stroke (N=55). Patients with stroke received RT for 90 to 105min/d, 5d/wk, for 4 weeks. Outcome measures, including the Fugl-Meyer Assessment (FMA) and Motor Activity Log (MAL), were measured before and after the intervention. Potential predictors include age, sex, side of lesion, time since stroke onset, finger extension, Box and Block Test (BBT) score, and FMA distal score. Statistical analysis showed that the BBT score (odds ratio[OR]=1.06; P=.04) was a significant predictor of clinically important changes in the FMA. Being a woman (OR=3.9; P=.05) and BBT score (OR=1.07; P=.02) were the 2 significant predictors of clinically significant changes in the MAL amount of use subscale. The BBT score was the significant predictor of an increased probability of achieving clinically important changes in the MAL quality of movement subscale (OR=1.07; P=.02). The R(2) values for the 3 logistic regression models were low (.114-.272). The results revealed that patients with stroke who had greater manual dexterity measured by the BBT appear to have a higher probability of achieving clinically significant motor and functional outcomes after RT. Further studies are needed to evaluate other potential predictors to improve the models and validate the findings. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  16. Functional and Integrative Analysis of the Proteomic Profile of Radish Root under Pb Exposure

    PubMed Central

    Wang, Yan; Xu, Liang; Tang, Mingjia; Jiang, Haiyan; Chen, Wei; Zhang, Wei; Wang, Ronghua; Liu, Liwang

    2016-01-01

    Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO3)2 at 500 mg L−1(Pb500) and 1000 mg L−1(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification). A total of 3898 protein species were successfully detected and 2141 were quantified. Among them, a subset of 721 protein species were differentially accumulated upon at least one Pb treatment, and 135 ones showed significantly abundance changes under both two Pb-stressed conditions. Many critical protein species related to protein translation, processing, and degradation, reactive oxygen species (ROS) scavenging, photosynthesis, and respiration and carbon metabolism were successfully identified. Gene Ontology (GO) and pathway enrichment analysis of the 135 differential abundance protein species (DAPS) revealed that the overrepresented GO terms included “cell wall,” “apoplast,” “response to metal ion,” “vacuole,” and “peroxidase activity,” and the critical enriched pathways were involved in “citric acid (TCA) cycle and respiratory electron transport,” “pyruvate metabolism,” “phenylalanine metabolism,” “phenylpropanoid biosynthesis,” and “carbon metabolism.” Furthermore, the integrative analysis of transcriptomic, miRNA, degradome, metabolomics and proteomic data provided a strengthened understanding of radish response to Pb stress at multiple levels. Under Pb stress, many key enzymes (i.e., ATP citrate lyase, Isocitrate dehydrogenase, fumarate hydratase and malate dehydrogenase) involved in the glycolysis and TCA cycle were severely affected, which ultimately cause alteration of some

  17. The application of Markov decision process with penalty function in restaurant delivery robot

    NASA Astrophysics Data System (ADS)

    Wang, Yong; Hu, Zhen; Wang, Ying

    2017-05-01

    As the restaurant delivery robot is often in a dynamic and complex environment, including the chairs inadvertently moved to the channel and customers coming and going. The traditional Markov decision process path planning algorithm is not save, the robot is very close to the table and chairs. To solve this problem, this paper proposes the Markov Decision Process with a penalty term called MDPPT path planning algorithm according to the traditional Markov decision process (MDP). For MDP, if the restaurant delivery robot bumps into an obstacle, the reward it receives is part of the current status reward. For the MDPPT, the reward it receives not only the part of the current status but also a negative constant term. Simulation results show that the MDPPT algorithm can plan a more secure path.

  18. An integrated gait rehabilitation training based on Functional Electrical Stimulation cycling and overground robotic exoskeleton in complete spinal cord injury patients: Preliminary results.

    PubMed

    Mazzoleni, S; Battini, E; Rustici, A; Stampacchia, G

    2017-07-01

    The aim of this study is to investigate the effects of an integrated gait rehabilitation training based on Functional Electrical Stimulation (FES)-cycling and overground robotic exoskeleton in a group of seven complete spinal cord injury patients on spasticity and patient-robot interaction. They underwent a robot-assisted rehabilitation training based on two phases: n=20 sessions of FES-cycling followed by n= 20 sessions of robot-assisted gait training based on an overground robotic exoskeleton. The following clinical outcome measures were used: Modified Ashworth Scale (MAS), Numerical Rating Scale (NRS) on spasticity, Penn Spasm Frequency Scale (PSFS), Spinal Cord Independence Measure Scale (SCIM), NRS on pain and International Spinal Cord Injury Pain Data Set (ISCI). Clinical outcome measures were assessed before (T0) after (T1) the FES-cycling training and after (T2) the powered overground gait training. The ability to walk when using exoskeleton was assessed by means of 10 Meter Walk Test (10MWT), 6 Minute Walk Test (6MWT), Timed Up and Go test (TUG), standing time, walking time and number of steps. Statistically significant changes were found on the MAS score, NRS-spasticity, 6MWT, TUG, standing time and number of steps. The preliminary results of this study show that an integrated gait rehabilitation training based on FES-cycling and overground robotic exoskeleton in complete SCI patients can provide a significant reduction of spasticity and improvements in terms of patient-robot interaction.

  19. 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. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  20. Proteomic Characterization of the Whole Secretome of Legionella pneumophila and Functional Analysis of Outer Membrane Vesicles▿ †

    PubMed Central

    Galka, Frank; Wai, Sun Nyunt; Kusch, Harald; Engelmann, Susanne; Hecker, Michael; Schmeck, Bernd; Hippenstiel, Stefan; Uhlin, Bernt Eric; Steinert, Michael

    2008-01-01

    Secretion of effector molecules is one of the major mechanisms by which the intracellular human pathogen Legionella pneumophila interacts with host cells during infection. Specific secretion machineries which are responsible for the subfraction of secreted proteins (soluble supernatant proteins [SSPs]) and the production of bacterial outer membrane vesicles (OMVs) both contribute to the protein composition of the extracellular milieu of this lung pathogen. Here we present comprehensive proteome reference maps for both SSPs and OMVs. Protein identification and assignment analyses revealed a total of 181 supernatant proteins, 107 of which were specific to the SSP fraction and 33 of which were specific to OMVs. A functional classification showed that a large proportion of the identified OMV proteins are involved in the pathogenesis of Legionnaires' disease. Zymography and enzyme assays demonstrated that the SSP and OMV fractions possess proteolytic and lipolytic enzyme activities which may contribute to the destruction of the alveolar lining during infection. Furthermore, it was shown that OMVs do not kill host cells but specifically modulate their cytokine response. Binding of immunofluorescently stained OMVs to alveolar epithelial cells, as visualized by confocal laser scanning microscopy, suggested that there is delivery of a large and complex group of proteins and lipids in the infected tissue in association with OMVs. On the basis of these new findings, we discuss the relevance of protein sorting and compartmentalization of virulence factors, as well as environmental aspects of the vesicle-mediated secretion. PMID:18250176

  1. Army Medical Robotics Research

    DTIC Science & Technology

    2007-01-01

    Army Medical Robotics Research Gary Gilbert, Ph.D., U.S. Army TATRC, Ph: (301) 619-4043, Fax: (301) 619-2518 gilbert@tatrc.org, www.tatrc.org...politically sensitive low intensity combat in urban terrain. Research progress has been made in the areas of robotics ; artificial intelligence...institutions have demonstrated intelligent robots that execute functions ranging from performing mechanical repairs to playing soccer. The military has

  2. An efficient proteomics based strategy for the functional characterization of a novel halophilic enzyme from Halobacterium salinarum.

    PubMed

    Choi, Jiyeon; Joo, Won-A; Park, Soo-Jin; Lee, So-Hee; Kim, Chan-Wha

    2005-03-01

    The extremely halophilic archaeon, Halobacterium salinarum grows in environments containing over 25% NaCl. The enzymes of this organism have thus been adapted to be active and stable in hypersaline conditions, which makes them strong candidates as robust industrial enzymes. In this study, the proteomics approach was applied to screen novel halophilic enzymes. We focused initially on proteins that are differentially expressed under different salt concentrations in culture media. After two-dimensional gel electrophoresis over a pH 3.5-4.5 range, 29 differentially expressed protein spots were identified by tandem mass spectrometry and six of these had no similarity to preexisting genes of known function. To predict the function of them, we used various bioinformatic methods. Among other proteins, we selected Vng0487h, which showed a high similarity to acetyltransferases. As a step toward assaying the enzymatic activity of this protein, we cloned the Vng0487h gene of H. salinarum and expressed and purified the recombinant protein with a glutathione-S-transferase (GST) tag in Escherichia coli. Using a GST-pulldown assay, a protein fragment derived from E. coli could interact with recombinant Vng0487h, and was identified to be the ribosomal protein L3. This protein showed high sequence homology with ribosomal protein L7/12 from E. coli and ribosomal protein L13p from H. salinarum. This suggests that Vng0487h acetylates a subunit of ribosomal protein, possibly L13p, in H. salinarum. During the present study, an efficient procedure was established to screen novel halophilic enzymes, and to predict and assess their functions.

  3. 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.

  4. Functional annotation of proteomic sequences based on consensus of sequence and structural analysis.

    PubMed

    Kitson, David H; Badretdinov, Azat; Zhu, Zhan-yang; Velikanov, Mikhail; Edwards, David J; Olszewski, Krzysztof; Szalma, Sándor; Yan, Lisa

    2002-03-01

    To maximise the assignment of function of the proteins encoded by a genome and to aid the search for novel drug targets, there is an emerging need for sensitive methods of predicting protein function on a genome-wide basis. GeneAtlas is an automated, high-throughput pipeline for the prediction of protein structure and function using sequence similarity detection, homology modelling and fold recognition methods. GeneAtlas is described in detail here. To test GeneAtlas, a 'virtual' genome was used, a subset of PDB structures from the SCOP database, in which the functional relationships are known. GeneAtlas detects additional relationships by building 3D models in comparison with the sequence searching method PSI-BLAST. Functionally related proteins with sequence identity below the twilight zone can be recognised correctly.

  5. Integrating cell biology and proteomic approaches in plants.

    PubMed

    Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

    2017-04-22

    representative studies combining proteomic and cell biology methods for various purposes. Integrating cell biology approaches with proteomic ones allow validation and better interpretation of proteomic data. Moreover, cell biology methods remarkably extend the knowledge provided by proteomic studies and might be fundamental for the functional complementation of proteomic data. This review article summarizes current literature linking proteomics with cell biology. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. 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.

  7. Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

    PubMed Central

    Dewhurst, Henry; Sundararaman, Niveda

    2016-01-01

    Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

  8. Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

    PubMed

    Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

    2016-11-01

    Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

  9. Application of robots in space.

    NASA Technical Reports Server (NTRS)

    Johnsen, E. G.

    1971-01-01

    Robots are defined as electromechanical systems (with local computers) receiving inputs from sensors, and in turn, controlling motors and effectors to do tasks requiring some measure of intelligence and permitting the whole system to interact with the real world. Robot systems for space applications are categorized into three general groups consisting of roving exploration robots, spacecraft robots, and planet development robots. The functions of systems in each category are defined in terms of intended applications, and requirements for operating and decision making are outlined. Further developments which must be achieved in robot technology are summarized.

  10. Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement

    NASA Astrophysics Data System (ADS)

    Cohen-Gihon, Inbar; Sharan, Roded; Nussinov, Ruth

    2011-06-01

    During evolution, organisms have gained functional complexity mainly by modifying and improving existing functioning systems rather than creating new ones ab initio. Here we explore the interplay between two processes which during evolution have had major roles in the acquisition of new functions: gene duplication and protein domain rearrangements. We consider four possible evolutionary scenarios: gene families that have undergone none of these event types; only gene duplication; only domain rearrangement, or both events. We characterize each of the four evolutionary scenarios by functional attributes. Our analysis of ten fungal genomes indicates that at least for the fungi clade, species significantly appear to gain complexity by gene duplication accompanied by the expansion of existing domain architectures via rearrangements. We show that paralogs gaining new domain architectures via duplication tend to adopt new functions compared to paralogs that preserve their domain architectures. We conclude that evolution of protein families through gene duplication and domain rearrangement is correlated with their functional properties. We suggest that in general, new functions are acquired via the integration of gene duplication and domain rearrangements rather than each process acting independently.

  11. Apolipoprotein AI could be a significant determinant of epithelial integrity in rainbow trout gill cell cultures: a study in functional proteomics.

    PubMed

    Smith, Richard W; Wood, Chris M; Cash, Phil; Diao, Linda; Pärt, Peter

    2005-05-20

    The freshwater fish gill forms a barrier against an external hypotonic environment. By culturing rainbow trout gill cells on permeable supports, as intact epithelia, this study investigates barrier property mechanisms. Under symmetrical conditions the apical and basolateral epithelial surfaces contact cell culture media. Replacing apical media with water, to generate asymmetrical conditions (i.e. the situation encountered by the freshwater gill), rapidly increases transepithelial resistance (TER). Proteomic analysis revealed that this is associated with enhanced expression of pre-apolipoprotein AI (pre-apoAI). To test the physiological relevance, gill cells were treated with a dose of 50 microg ml(-1) human apolipoprotein (apoAI). This was found to elevate TER in those epithelia which displayed a lower TER prior to apoAI treatment. These results demonstrate the action of apoAI and provide evidence that the rainbow trout gill may be a site of apoAI synthesis. TER does not differentiate between the trans-cellular (via the cell membrane) and para-cellular (via intercellular tight junctions) pathways. However, despite the apoAI-induced changes in TER, para-cellular permeability (measured by polyethylene glycol efflux) remained unaltered suggesting apoAI specifically reduces trans-cellular permeability. This investigation combines proteomics with functional measurements to show how a proteome change may be associated with freshwater gill function.

  12. 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. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  13. Proteomic identification and functional validation of activins and bone morphogenetic protein 11 as candidate novel muscle mass regulators.

    PubMed

    Souza, Tatyana A; Chen, Xuan; Guo, Yongjing; Sava, Parid; Zhang, Jimin; Hill, Jennifer J; Yaworsky, Paul J; Qiu, Yongchang

    2008-12-01

    Myostatin is a secreted TGF-beta family member that controls skeletal muscle growth. Humans, cattle, and dogs carrying natural loss-of-function mutations in the myostatin gene and myostatin knockout mice exhibit significant increases in skeletal muscle mass. Treatment of adult mice with antimyostatin antibodies also resulted in significant muscle mass increases. However, myostatin-knockout mice that were treated with a soluble form of the activin type II receptor (ActRII) B increased their muscle mass by an additional 15-25%, indicating that there is at least one additional ligand, in addition to myostatin, that functions to limit muscle growth. Here, both soluble ActRII and -IIB fragment-crystallizable proteins were used to affinity purify their native ligands from human and mouse sera. Using mass spectrometry-based proteomics and in vitro binding assays we have identified and confirmed that a number of TGF-beta family members, including myostatin, activins-A, -B, and -AB, bone morphogenetic proteins (BMPs) -9, -10, and -11, bind to both ActRIIs. Many of these factors, such as BMPs-11, -9, and -10 were discovered in systemic circulation for the first time, indicating that these ligands may also act in an endocrine fashion. Using a promoter-specific gene reporter assay, we demonstrated that soluble ActRIIB fragment-crystallizable proteins can inhibit the canonical signaling induced by these ligands. In addition, like myostatin, these factors were able to block the differentiation of myoblast cells into myotubes. However, in addition to myostatin, only BMP-11, and activins-A, -B, and -AB could be blocked from inhibiting the myoblast-to-myotube differentiation with both soluble ActRIIs, thus implicating them as potential novel regulators of muscle growth.

  14. 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.

  15. EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes

    PubMed Central

    Kumar, Narendra; Skolnick, Jeffrey

    2012-01-01

    Summary: High-quality enzyme function annotation is essential for understanding the biochemistry, metabolism and disease processes of organisms. Previously, we developed a multi-component high-precision enzyme function predictor, EFICAz2 (enzyme function inference by a combined approach). Here, we present an updated improved version, EFICAz2.5, that is trained on a significantly larger data set of enzyme sequences and PROSITE patterns. We also present the results of the application of EFICAz2.5 to the enzyme reannotation of 396 genomes cataloged in the ENSEMBL database. Availability: The EFICAz2.5 server and database is freely available with a use-friendly interface at http://cssb.biology.gatech.edu/EFICAz2.5. Contact: skolnick@gatech.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22923291

  16. EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes.

    PubMed

    Kumar, Narendra; Skolnick, Jeffrey

    2012-10-15

    High-quality enzyme function annotation is essential for understanding the biochemistry, metabolism and disease processes of organisms. Previously, we developed a multi-component high-precision enzyme function predictor, EFICAz(2) (enzyme function inference by a combined approach). Here, we present an updated improved version, EFICAz(2.5), that is trained on a significantly larger data set of enzyme sequences and PROSITE patterns. We also present the results of the application of EFICAz(2.5) to the enzyme reannotation of 396 genomes cataloged in the ENSEMBL database. The EFICAz(2.5) server and database is freely available with a use-friendly interface at http://cssb.biology.gatech.edu/EFICAz2.5.

  17. 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.

  18. In vivo protein trapping produces a functional expression codex of the vertebrate proteome.

    PubMed

    Clark, Karl J; Balciunas, Darius; Pogoda, Hans-Martin; Ding, Yonghe; Westcot, Stephanie E; Bedell, Victoria M; Greenwood, Tammy M; Urban, Mark D; Skuster, Kimberly J; Petzold, Andrew M; Ni, Jun; Nielsen, Aubrey L; Patowary, Ashok; Scaria, Vinod; Sivasubbu, Sridhar; Xu, Xiaolei; Hammerschmidt, Matthias; Ekker, Stephen C

    2011-06-01

    We describe a conditional in vivo protein-trap mutagenesis system that reveals spatiotemporal protein expression dynamics and can be used to assess gene function in the vertebrate Danio rerio. Integration of pGBT-RP2.1 (RP2), a gene-breaking transposon containing a protein trap, efficiently disrupts gene expression with >97% knockdown of normal transcript amounts and simultaneously reports protein expression for each locus. The mutant alleles are revertible in somatic tissues via Cre recombinase or splice-site-blocking morpholinos and are thus to our knowledge the first systematic conditional mutant alleles outside the mouse model. We report a collection of 350 zebrafish lines that include diverse molecular loci. RP2 integrations reveal the complexity of genomic architecture and gene function in a living organism and can provide information on protein subcellular localization. The RP2 mutagenesis system is a step toward a unified 'codex' of protein expression and direct functional annotation of the vertebrate genome.

  19. in vivo protein trapping produces a functional expression codex of the vertebrate proteome

    PubMed Central

    Clark, Karl J.; Balciunas, Darius; Pogoda, Hans-Martin; Ding, Yonghe; Westcot, Stephanie E.; Bedell, Victoria M.; Greenwood, Tammy M.; Urban, Mark D.; Skuster, Kimberly J.; Petzold, Andrew M.; Ni, Jun; Nielsen, Aubrey; Patowary, Ashok; Scaria, Vinod; Sivasubbu, Sridhar; Xu, Xiaolei; Hammerschmidt, Matthias; Ekker, Stephen C.

    2012-01-01

    We describe a conditional in vivo protein trap mutagenesis system that reveals spatio-temporal protein expression dynamics and assesses gene function in the vertebrate Danio rerio. Integration of pGBT-RP2 (RP2), a gene-breaking transposon containing a protein trap, efficiently disrupts gene expression with >97% knockdown of normal transcript levels while simultaneously reporting protein expression of each locus. The mutant alleles are revertible in somatic tissues via Cre recombinase or splice-site blocking morpholinos, thus representing the first systematic conditional mutant alleles outside the mouse model. We report a collection of 350 zebrafish lines including a diverse array of molecular loci. RP2 integrations reveal the complexity of genomic architecture and gene function in a living organism and can provide information on protein subcellular localization. The RP2 mutagenesis system is a step towards a unified codex of protein expression and direct functional annotation of the vertebrate genome. PMID:21552255

  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. 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.

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

    PubMed

    Harper, J Wade; Bennett, Eric J

    2016-09-15

    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.

  3. 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

  4. 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…

  5. Robotics, assistive technology, and occupational therapy management to improve upper limb function in pediatric neuromuscular diseases.

    PubMed

    Rahman, Tariq; Basante, Joseph; Alexander, Michael

    2012-08-01

    This article presents an overview of occupational therapy assessments and treatment options for individuals with neuromuscular disabilities, with a particular focus on children with neuromuscular disorders. The discussion includes descriptions of standard treatments, commercial adaptive equipment, and homemade adaptive solutions. The state of the art in therapeutic and assistive robots and orthoses for the upper and lower extremity is also provided. Copyright © 2012. Published by Elsevier Inc.

  6. The Proteome of BLOC-1 Genetic Defects Identifies the Arp2/3 Actin Polymerization Complex to Function Downstream of the Schizophrenia Susceptibility Factor Dysbindin at the Synapse

    PubMed Central

    Hartwig, Cortnie; Freeman, Amanda H.; Das, Ravi; Zlatic, Stephanie A.; Vistein, Rachel; Burch, Amelia; Carrot, Guillemette; Lewis, Arielle F.; Nelms, Sheldon; Dickman, Dion K.; Puthenveedu, Manojkumar A.; Cox, Daniel N.

    2016-01-01

    Proteome modifications downstream of monogenic or polygenic disorders have the potential to uncover novel molecular mechanisms participating in pathogenesis and/or extragenic modification of phenotypic expression. We tested this idea by determining the proteome sensitive to genetic defects in a locus encoding dysbindin, a protein required for synapse biology and implicated in schizophrenia risk. We applied quantitative mass spectrometry to identify proteins expressed in neuronal cells the abundance of which was altered after downregulation of the schizophrenia susceptibility factor dysbindin (Bloc1s8) or two other dysbindin-interacting polypeptides, which assemble into the octameric biogenesis of lysosome-related organelles complex 1 (BLOC-1). We found 491 proteins sensitive to dysbindin and BLOC-1 loss of function. Gene ontology of these 491 proteins singled out the actin cytoskeleton and the actin polymerization factor, the Arp2/3 complex, as top statistical molecular pathways contained within the BLOC-1-sensitive proteome. Subunits of the Arp2/3 complex were downregulated by BLOC-1 loss of function, thus affecting actin dynamics in early endosomes of BLOC-1-deficient cells. Furthermore, we demonstrated that Arp2/3, dysbindin, and subunits of the BLOC-1 complex biochemically and genetically interact, modulating Drosophila melanogaster synapse morphology and homeostatic synaptic plasticity. Our results indicate that ontologically prioritized proteomics identifies novel pathways that modify synaptic phenotypes associated with neurodevelopmental disorder gene defects. SIGNIFICANCE STATEMENT The mechanisms associated with schizophrenia are mostly unknown despite the increasing number of genetic loci identified that increase disease risk. We present an experimental strategy that impartially and comprehensively interrogates the proteome of neurons to identify effects of genetic mutations in a schizophrenia risk factor, dysbindin. We find that the expression of the

  7. The Proteome of BLOC-1 Genetic Defects Identifies the Arp2/3 Actin Polymerization Complex to Function Downstream of the Schizophrenia Susceptibility Factor Dysbindin at the Synapse.

    PubMed

    Gokhale, Avanti; Hartwig, Cortnie; Freeman, Amanda H; Das, Ravi; Zlatic, Stephanie A; Vistein, Rachel; Burch, Amelia; Carrot, Guillemette; Lewis, Arielle F; Nelms, Sheldon; Dickman, Dion K; Puthenveedu, Manojkumar A; Cox, Daniel N; Faundez, Victor

    2016-12-07

    Proteome modifications downstream of monogenic or polygenic disorders have the potential to uncover novel molecular mechanisms participating in pathogenesis and/or extragenic modification of phenotypic expression. We tested this idea by determining the proteome sensitive to genetic defects in a locus encoding dysbindin, a protein required for synapse biology and implicated in schizophrenia risk. We applied quantitative mass spectrometry to identify proteins expressed in neuronal cells the abundance of which was altered after downregulation of the schizophrenia susceptibility factor dysbindin (Bloc1s8) or two other dysbindin-interacting polypeptides, which assemble into the octameric biogenesis of lysosome-related organelles complex 1 (BLOC-1). We found 491 proteins sensitive to dysbindin and BLOC-1 loss of function. Gene ontology of these 491 proteins singled out the actin cytoskeleton and the actin polymerization factor, the Arp2/3 complex, as top statistical molecular pathways contained within the BLOC-1-sensitive proteome. Subunits of the Arp2/3 complex were downregulated by BLOC-1 loss of function, thus affecting actin dynamics in early endosomes of BLOC-1-deficient cells. Furthermore, we demonstrated that Arp2/3, dysbindin, and subunits of the BLOC-1 complex biochemically and genetically interact, modulating Drosophila melanogaster synapse morphology and homeostatic synaptic plasticity. Our results indicate that ontologically prioritized proteomics identifies novel pathways that modify synaptic phenotypes associated with neurodevelopmental disorder gene defects. The mechanisms associated with schizophrenia are mostly unknown despite the increasing number of genetic loci identified that increase disease risk. We present an experimental strategy that impartially and comprehensively interrogates the proteome of neurons to identify effects of genetic mutations in a schizophrenia risk factor, dysbindin. We find that the expression of the actin polymerization

  8. 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.

  9. A fully automated multi-functional ultrahigh pressure liquid chromatography system for advanced proteome analyses

    PubMed Central

    Lee, Jung Hwa; Hyung, Seok-Won; Mun, Dong-Gi; Jung, Hee-Jung; Kim, Hokeun; Lee, Hangyeore; Kim, Su-Jin; Park, Kyong Soo; Moore, Ronald J.; Smith, Richard D.; Lee, Sang-Won

    2012-01-01

    A multi-functional liquid chromatography system that performs 1-dimensional, 2-dimensional (strong cation exchange/reverse phase liquid chromatography, or SCX/RPLC) separations and online phosphopeptide enrichment using a single binary nano-flow pump has been developed. With a simple operation of a function selection valve equipped with a SCX column and a TiO2 (titanium dioxide) column, a fully automated selection of three different experiment modes was achieved. Because the current system uses essentially the same solvent flow paths, the same trap column, and the same separation column for reverse-phase separation of 1D, 2D, and online phosphopeptides enrichment experiments, the elution time information obtained from these experiments is in excellent agreement, which facilitates correlating peptide information from different experiments. The final reverse-phase separation of the three experiments is completely decoupled from all of function selection processes; thereby salts or acids from SCX or TiO2 column do not affect the efficiency of the reverse-phase separation. PMID:22709424

  10. Robot-assisted upper and lower limb rehabilitation after stroke: walking and arm/hand function.

    PubMed

    Hesse, Stefan; Mehrholz, Jan; Werner, Cordula

    2008-05-01

    Robots help to intensify motor rehabilitation of the upper and lower limbs after stroke. This article presents controlled studies relating to this topic, and an overview. A search was carried out for relevant randomized controlled trials, published between 1980 and 2007, on Medline (PubMed), Embase, and CINHAL. Two studies showed benefit for an electromechanical gait trainer, with significantly more patients resuming walking as compared to conventional physiotherapy. Two studies showed no evidence of benefit for an exoskeleton-based system. A pooled analysis was not conducted due to the small numbers of studies and high heterogeneity. In arm/hand rehabilitation a number of unilateral or bilateral end-effector based systems proved effective in patients with stroke, and a simple one-dimensional system and a passive exoskeleton system proved effective in patients with chronic symptoms. Robot-assisted motor rehabilitation after stroke appears promising. More trials, including comparative studies, are mandatory. The robot cannot be considered a substitute for the patient-therapist relationship.

  11. 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

  12. Functional and proteomic analysis of submandibular saliva in rats exposed to chronic stress by immobilization or constant light.

    PubMed

    Alterman, A; Mathison, R; Coronel, C E; Stroppa, M M; Finkelberg, A B; Gallará, R V

    2012-06-01

    In this study, we have evaluated the effects of stress on functional and proteomic changes in submandibular saliva of rats. Male adult rats were divided in three groups: IMO (2 h/day of immobilization for 7 days), LL (constant light during 20 days), C (unstressed controls submitted to 14 h light-10h dark cycle). Body weight, food intake and the dry weight of submandibular gland were recorded. Saliva samples, collected under anaesthesia following i.p. administration of isoproterenol and pilocarpine (5 mg/kg), were assayed for total proteins (TP), amylase activity and SDS-PAGE electrophoresis. Body weight, food intake and the dry weight of submandibular gland of IMO rats were lower than those of C and LL groups. The salivary volumes secreted in IMO and LL rats, were significantly higher than in controls. The TP output (μg protein/μg saliva/mg of dry tissue) and amylase activity output (AU/μg of saliva/mg of dry tissue) in IMO were significantly higher than in C and LL animals. The electrophoretic pattern of saliva proteins of LL rats, revealed the absence of a protein band of approximately 25 kDa. This band was composed by the common salivary protein-1 and a prolactin-induced protein as identified by peptide mass fingerprinting. Differences in body weight and food intake between IMO and LL might be attributed to the sort and intensity of stressors stimuli. The changes in the volume of secreted saliva could be a compensatory mechanism in response to stressors. The increase of total protein in IMO rats and the absence of 25 kDa proteins in LL, would suggest that the submandibular glands respond to the sympathetic nervous system stimuli induced by the stress with an increase of activity of the sympathetic nerves in IMO and a reduction in LL rats. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. The SAV1322 gene from Staphylococcus aureus: genomic and proteomic approaches to identification and characterization of gene function.

    PubMed

    Kim, Jung Wook; Kim, Hyun-Kyung; Kang, Gi Su; Kim, Il-Hwan; Kim, Hwa Su; Lee, Yeong Seon; Yoo, Jae Il

    2016-09-06

    Bacterial two-component regulatory systems (TCRS) are associated with the expression of virulence factors and antibiotic susceptibility. In Staphylococcus aureus, 16 TCRS types have been identified. The histidine kinase/response regulator SAV1321/SAV1322 in the S. aureus shares considerable homology with the TCRS DesKR in Bacillus subtilis. However, a function for the SAV1322 locus has not yet been assigned. Deletion of the SAV1322 locus in S. aureus results in reduced growth when cultured under low (25 °C) and high (46 °C) temperature conditions. The sav1322 deletion mutant is more tolerant to oxidative stress in vitro and is less pathogenic in a murine infection model when compared with wild-type parent strain Mu50. Furthermore, the sav1322 mutant exhibits lower MICs for gentimicin, tetracyclines and glycopeptides, increased autolysis, and a thinner cell wall when compared with the wild-type strain. Microarray and proteomic analyses show that the expression of cell-wall-associated genes glmS and murZ are lower, and the expression of heat shock and stress-related genes (hrcA, ctsR, dnaK, dnaJ, grpE, clpB, and clpC) are higher in the sav1322 mutant when compared with the wild-type strain. In addition, the sav1322 mutant displays altered expression of proteins involved in carbohydrate/energy metabolism, cell wall metabolism, and stress or heat shock response, as well as other metabolic processes including lipid metabolism, amino acid biosynthesis, purine or pyrimidine metabolism, transcription, and protein biosynthesis. The S. aureus SAV1322 locus plays a pronounced role in temperature adaptation, antibiotic resistance, and virulence by regulating a wide range of genes and proteins involved in metabolism and stress tolerance.

  14. Proteomic analysis of mitochondria in respiratory epithelial cells infected with human respiratory syncytial virus and functional implications for virus and cell biology.

    PubMed

    Munday, Diane C; Howell, Gareth; Barr, John N; Hiscox, Julian A

    2015-03-01

    The aim of this study was to quantitatively characterise the mitochondrial proteome of airway epithelial cells infected with human respiratory syncytial virus (HRSV), a major cause of paediatric illness. Quantitative proteomics, underpinned by stable isotope labelling with amino acids in cell culture, coupled to LC-MS/MS, was applied to mitochondrial fractions prepared from HRSV-infected and mock-infected cells 12 and 24 h post-infection. Datasets were analysed using ingenuity pathway analysis, and the results were validated and characterised using bioimaging, targeted inhibition and gene depletion. The data quantitatively indicated that antiviral signalling proteins converged on mitochondria during HRSV infection. The mitochondrial receptor protein Tom70 was found to act in an antiviral manner, while its chaperone, Hsp90, was confirmed to be a positive viral factor. Proteins associated with different organelles were also co-enriched in the mitochondrial fractions from HRSV-infected cells, suggesting that alterations in organelle dynamics and membrane associations occur during virus infection. Protein and pathway-specific alterations occur to the mitochondrial proteome in a spatial and temporal manner during HRSV infection, suggesting that this organelle may have altered functions. These could be targeted as part of potential therapeutic strategies to disrupt virus biology. © 2014 Royal Pharmaceutical Society.

  15. From Proteomic Analysis to Potential Therapeutic Targets: Functional Profile of Two Lung Cancer Cell Lines, A549 and SW900, Widely Studied in Pre-Clinical Research

    PubMed Central

    Soto-Cerrato, Vanessa; Vitorino, Rui; Fardilha, Margarida; Pérez-Tomás, Ricardo

    2016-01-01

    Lung cancer is a serious health problem and the leading cause of cancer death worldwide. The standard use of cell lines as in vitro pre-clinical models to study the molecular mechanisms that drive tumorigenesis and access drug sensitivity/effectiveness is of undisputable importance. Label-free mass spectrometry and bioinformatics were employed to study the proteomic profiles of two representative lung cancer cell lines and to unravel the specific biological processes. Adenocarcinoma A549 cells were enriched in proteins related to cellular respiration, ubiquitination, apoptosis and response to drug/hypoxia/oxidative stress. In turn, squamous carcinoma SW900 cells were enriched in proteins related to translation, apoptosis, response to inorganic/organic substances and cytoskeleton organization. Several proteins with differential expression were related to cancer transformation, tumor resistance, proliferation, migration, invasion and metastasis. Combined analysis of proteome and interactome data highlighted key proteins and suggested that adenocarcinoma might be more prone to PI3K/Akt/mTOR and topoisomerase IIα inhibitors, and squamous carcinoma to Ck2 inhibitors. Moreover, ILF3 overexpression in adenocarcinoma, and PCNA and NEDD8 in squamous carcinoma shows them as promising candidates for therapeutic purposes. This study highlights the functional proteomic differences of two main subtypes of lung cancer models and hints several targeted therapies that might assist in this type of cancer. PMID:27814385

  16. In-Depth Proteome Analysis of Arabidopsis Leaf Peroxisomes Combined with in Vivo Subcellular Targeting Verification Indicates Novel Metabolic and Regulatory Functions of Peroxisomes1[W][OA

    PubMed Central

    Reumann, Sigrun; Quan, Sheng; Aung, Kyaw; Yang, Pingfang; Manandhar-Shrestha, Kalpana; Holbrook, Danielle; Linka, Nicole; Switzenberg, Robert; Wilkerson, Curtis G.; Weber, Andreas P.M.; Olsen, Laura J.; Hu, Jianping

    2009-01-01

    Peroxisomes are metabolically diverse organelles with essential roles in plant development. The major protein constituents of plant peroxisomes are well characterized, whereas only a few low-abundance and regulatory proteins have been reported to date. We performed an in-depth proteome analysis of Arabidopsis (Arabidopsis thaliana) leaf peroxisomes using one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry. We detected 65 established plant peroxisomal proteins, 30 proteins whose association with Arabidopsis peroxisomes had been previously demonstrated only by proteomic data, and 55 putative novel proteins of peroxisomes. We subsequently tested the subcellular targeting of yellow fluorescent protein fusions for selected proteins and confirmed the peroxisomal localization for 12 proteins containing predicted peroxisome targeting signals type 1 or 2 (PTS1/2), three proteins carrying PTS-related peptides, and four proteins that lack conventional targeting signals. We thereby established the tripeptides SLM> and SKV> (where > indicates the stop codon) as new PTS1s and the nonapeptide RVx5HF as a putative new PTS2. The 19 peroxisomal proteins conclusively identified from this study potentially carry out novel metabolic and regulatory functions of peroxisomes. Thus, this study represents an important step toward defining the complete plant peroxisomal proteome. PMID:19329564

  17. A crossover pilot study evaluating the functional outcomes of two different types of robotic movement training in chronic stroke survivors using the arm exoskeleton BONES.

    PubMed

    Milot, Marie-Hélène; Spencer, Steven J; Chan, Vicky; Allington, James P; Klein, Julius; Chou, Cathy; Bobrow, James E; Cramer, Steven C; Reinkensmeyer, David J

    2013-12-19

    To date, the limited degrees of freedom (DOF) of most robotic training devices hinders them from providing functional training following stroke. We developed a 6-DOF exoskeleton ("BONES") that allows movement of the upper limb to assist in rehabilitation. The objectives of this pilot study were to evaluate the impact of training with BONES on function of the affected upper limb, and to assess whether multijoint functional robotic training would translate into greater gains in arm function than single joint robotic training also conducted with BONES. Twenty subjects with mild to moderate chronic stroke participated in this crossover study. Each subject experienced multijoint functional training and single joint training three sessions per week, for four weeks, with the order of presentation randomized. The primary outcome measure was the change in Box and Block Test (BBT). The secondary outcome measures were the changes in Fugl-Meyer Arm Motor Scale (FMA), Wolf Motor Function Test (WMFT), Motor Activity Log (MAL), and quantitative measures of strength and speed of reaching. These measures were assessed at baseline, after each training period, and at a 3-month follow-up evaluation session. Training with the robotic exoskeleton resulted in significant improvements in the BBT, FMA, WMFT, MAL, shoulder and elbow strength, and reaching speed (p < 0.05); these improvements were sustained at the 3 month follow-up. When comparing the effect of type of training on the gains obtained, no significant difference was noted between multijoint functional and single joint robotic training programs. However, for the BBT, WMFT and MAL, inequality of carryover effects were noted; subsequent analysis on the change in score between the baseline and first period of training again revealed no difference in the gains obtained between the types of training. Training with the 6 DOF arm exoskeleton improved motor function after chronic stroke, challenging the idea that robotic therapy is only

  18. A crossover pilot study evaluating the functional outcomes of two different types of robotic movement training in chronic stroke survivors using the arm exoskeleton BONES

    PubMed Central

    2013-01-01

    Background To date, the limited degrees of freedom (DOF) of most robotic training devices hinders them from providing functional training following stroke. We developed a 6-DOF exoskeleton (“BONES”) that allows movement of the upper limb to assist in rehabilitation. The objectives of this pilot study were to evaluate the impact of training with BONES on function of the affected upper limb, and to assess whether multijoint functional robotic training would translate into greater gains in arm function than single joint robotic training also conducted with BONES. Methods Twenty subjects with mild to moderate chronic stroke participated in this crossover study. Each subject experienced multijoint functional training and single joint training three sessions per week, for four weeks, with the order of presentation randomized. The primary outcome measure was the change in Box and Block Test (BBT). The secondary outcome measures were the changes in Fugl-Meyer Arm Motor Scale (FMA), Wolf Motor Function Test (WMFT), Motor Activity Log (MAL), and quantitative measures of strength and speed of reaching. These measures were assessed at baseline, after each training period, and at a 3-month follow-up evaluation session. Results Training with the robotic exoskeleton resulted in significant improvements in the BBT, FMA, WMFT, MAL, shoulder and elbow strength, and reaching speed (p < 0.05); these improvements were sustained at the 3 month follow-up. When comparing the effect of type of training on the gains obtained, no significant difference was noted between multijoint functional and single joint robotic training programs. However, for the BBT, WMFT and MAL, inequality of carryover effects were noted; subsequent analysis on the change in score between the baseline and first period of training again revealed no difference in the gains obtained between the types of training. Conclusions Training with the 6 DOF arm exoskeleton improved motor function after chronic stroke

  19. The proteome of lysosomes.

    PubMed

    Schröder, Bernd A; Wrocklage, Christian; Hasilik, Andrej; Saftig, Paul

    2010-11-01

    Lysosomes are organelles of eukaryotic cells that are critically involved in the degradation of macromolecules mainly delivered by endocytosis and autophagocytosis. Degradation is achieved by more than 60 hydrolases sequestered by a single phospholipid bilayer. The lysosomal membrane facilitates interaction and fusion with other compartments and harbours transport proteins catalysing the export of catabolites, thereby allowing their recycling. Lysosomal proteins have been addressed in various proteomic studies that are compared in this review regarding the source of material, the organelle/protein purification scheme, the proteomic methodology applied and the proteins identified. Distinguishing true constituents of an organelle from co-purifying contaminants is a central issue in subcellular proteomics, with additional implications for lysosomes as being the site of degradation of many cellular and extracellular proteins. Although many of the lysosomal hydrolases were identified by classical biochemical approaches, the knowledge about the protein composition of the lysosomal membrane has remained fragmentary for a long time. Using proteomics many novel lysosomal candidate proteins have been discovered and it can be expected that their functional characterisation will help to understand functions of lysosomes at a molecular level that have been characterised only phenomenologically so far and to generally deepen our understanding of this indispensable organelle.

  20. Diversity and function of maize pollen coat proteins: from biochemistry to proteomics

    PubMed Central

    Gong, Fangping; Wu, Xiaolin

    2015-01-01

    Maize (Zea mays L.) is globally cultivated as one of the most important grain crops. As a wind-pollinated species, maize produces a large quantity of pollen grains that heavier and larger compared to Arabidopsis. Maize is an important model plant in pollen biology of monocots. The pollen coat, the outermost layer of pollen, plays a vital role in pollen–stigma interactions and successful fertilization. Pollen coat proteins (PCPs), which confer species specificity, are required for pollen adhesion, recognition, hydration, and germination on the stigma. Thus, PCPs have attracted intensive research efforts in plant science for decades. However, only a few PCPs in maize have been characterized to date, whereas the functions of most maize PCPs remain unclear. In this review, we summarize the current knowledge of maize PCPs with regard to protein constituents, synthesis and transport, and functions by comparison with the model plant Arabidopsis thaliana and Brassica plants. An understanding of the comprehensive knowledge of maize PCPs will help to illuminate the mechanism by which PCPs are involved in pollen–stigma interactions in maize and other crop plants. PMID:25870606

  1. The neuro-robotics paradigm: NEURARM, NEUROExos, HANDEXOS.

    PubMed

    Lenzi, Tommaso; De Rossi, Stefano; Vitiello, Nicola; Chiri, Azzurra; Roccella, Stefano; Giovacchini, Francesco; Vecchi, Fabrizio; Carrozza, Maria Chiara

    2009-01-01

    This work describes the neuro-robotics paradigm: the fusion of neuroscience and robotics. The fusion of neuroscience and robotics, called neuro-robotics, is fundamental to develop robotic systems to be used in functional support, personal assistance and neuro-rehabilitation. While usually the robotic device is considered as a "tool" for neuroscientific studies, a breakthrough is obtained if the two scientific competences and methodologies converge to develop innovative platforms to go beyond robotics by including novel models to design better robots. This paper describes three robotic platforms developed at the ARTS lab of Scuola Superiore Sant'Anna, implementing neuro-robotic design paradigm.

  2. Intensity fading MALDI-TOF mass spectrometry and functional proteomics assignments to identify protease inhibitors in marine invertebrates.

    PubMed

    Covaleda, Giovanni; Trejo, Sebastian A; Salas-Sarduy, Emir; Del Rivero, Maday Alonso; Chavez, Maria Angeles; Aviles, Francesc X

    2017-08-08

    Proteases and their inhibitors have become molecules of increasing fundamental and applicative value. Here we report an integrated strategy to identify and analyze such inhibitors from Caribbean marine invertebrates extracts by a fast and sensitive functional proteomics-like approach. The strategy works in three steps: i) multiplexed enzymatic inhibition kinetic assays, ii) Intensity Fading MALDI-TOF MS to establish a link between inhibitory molecules and the related MALDI signal(s) detected in the extract(s), and iii) ISD-CID-T(3) MS fragmentation on the parent MALDI signals selected in the previous step, enabling the partial or total top-down sequencing of the molecules. The present study has allowed validation of the whole approach, identification of a substantial number of novel protein protease inhibitors, as well as full or partial sequencing of reference molecular species and of many unknown ones, respectively. Such inhibitors correspond to six protease subfamilies (metallocarboxypeptidases-A and -B, pepsin, papain, trypsin and subtilisin), are small (1-10KDa) disulfide-rich proteins, and have been found at diverse frequencies among the invertebrates (13 to 41%). The overall procedure could be tailored to other enzyme-inhibitor and protein interacting systems, analyzing samples at medium-throughput level and leading to the functional and structural characterization of proteinaceous ligands from complex biological extracts. Invertebrate animals, and marine ones among, display a remarkable diversity of species and contained biomolecules. Many of their proteins-peptides have high biological, biotechnological and biomedical potential interest but, because of the lack of sequenced genomes behind, their structural and functional characterization constitutes a great challenge. Here, looking at the small, disulfide-rich, proteinaceous inhibitors of proteases found in them, it is shown that such problem can be significatively facilitated by integrative multiplexed

  3. 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…

  4. Applying a soft-robotic glove as assistive device and training tool with games to support hand function after stroke: Preliminary results on feasibility and potential clinical impact.

    PubMed

    Prange-Lasonder, Gerdienke B; Radder, Bob; Kottink, Anke I R; Melendez-Calderon, Alejandro; Buurke, Jaap H; Rietman, Johan S

    2017-07-01

    Recent technological developments regarding wearable soft-robotic devices extend beyond the current application of rehabilitation robotics and enable unobtrusive support of the arms and hands during daily activities. In this light, the HandinMind (HiM) system was developed, comprising a soft-robotic, grip supporting glove with an added computer gaming environment. The present study aims to gain first insight into the feasibility of clinical application of the HiM system and its potential impact. In order to do so, both the direct influence of the HiM system on hand function as assistive device and its therapeutic potential, of either assistive or therapeutic use, were explored. A pilot randomized clinical trial was combined with a cross-sectional measurement (comparing performance with and without glove) at baseline in 5 chronic stroke patients, to investigate both the direct assistive and potential therapeutic effects of the HiM system. Extended use of the soft-robotic glove as assistive device at home or with dedicated gaming exercises in a clinical setting was applicable and feasible. A positive assistive effect of the soft-robotic glove was proposed for pinch strength and functional task performance 'lifting full cans' in most of the five participants. A potential therapeutic impact was suggested with predominantly improved hand strength in both participants with assistive use, and faster functional task performance in both participants with therapeutic application.

  5. The effect of steep Trendelenburg positioning on intraocular pressure and visual function during