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Sample records for clinical proteomic technology

  1. The Clinical Proteomic Technologies for Cancer | About

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  2. The Clinical Proteomic Technologies for Cancer | Partners

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  3. The Clinical Proteomic Technologies for Cancer | Antibody Portal

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  4. The Clinical Proteomic Technologies for Cancer | Antibody Scientific Committee

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  5. The Clinical Proteomic Technologies for Cancer | Characterization Process

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  6. The Clinical Proteomic Technologies for Cancer | Reagent Opportunities

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  7. Urine in clinical proteomics.

    OpenAIRE

    Decramer, Stéphane; Gonzalez de Peredo, Anne; Breuil, Benjamin; Mischak, Harald; Monsarrat, Bernard; Bascands, Jean-Loup; Schanstra, Joost P

    2008-01-01

    Urine has become one of the most attractive biofluids in clinical proteomics as it can be obtained non-invasively in large quantities and is stable compared with other biofluids. The urinary proteome has been studied by almost any proteomics technology, but mass spectrometry-based urinary protein and peptide profiling has emerged as most suitable for clinical application. After a period of descriptive urinary proteomics the field is moving out of the discovery phase into an era of validation ...

  8. Proteomics Technologies and Challenges

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Proteomics is the study of proteins and their interactions in a cell. With the completion of the Human Genome Project, the emphasis is shifting to the protein compliment of the human organism. Because proteome reflects more accurately on the dynamic state of a cell, tissue, or organism, much is expected from proteomics to yield better disease markers for diagnosis and therapy monitoring. The advent of proteomics technologies for global detection and quantitation of proteins creates new opportunities and challenges for those seeking to gain greater understanding of diseases. High-throughput proteomics technologies combining with advanced bioinformatics are extensively used to identify molecular signatures of diseases based on protein pathways and signaling cascades. Mass spectrometry plays a vital role in proteomics and has become an indispensable tool for molecular and cellular biology. While the potential is great, many challenges and issues remain to be solved, such as mining low abundant proteins and integration of proteomics with genomics and metabolomics data. Nevertheless, proteomics is the foundation for constructing and extracting useful knowledge to biomedical research. In this review, a snapshot of contemporary issues in proteomics technologies is discussed.

  9. Developments of mass spectrometry-based technologies for effective drug development linked with clinical proteomes.

    Science.gov (United States)

    Nakayama, Noboru; Bando, Yasuhiko; Fukuda, Tetsuya; Kawamura, Takeshi; Nakamura, Haruhiko; Marko-Varga, György; Nishimura, Toshihide

    2016-02-01

    A strong demand in drug discovery and development today is to overcome "Big Gaps" encountered by differences in species and races, to accelerate effective developments in cost and time, and to meet medical needs. Moreover, drugs of various types have emerged which cover middle-size molecules and polymers rather than conventional small molecules. Upon those challenges, mass spectrometry (MS)-based technologies, which will be described in this paper, will play an increasingly important role, among which the liquid chromatography-tandem mass spectrometry (LC/MS/MS) platform will be powerful as rapid and molecule-based analysis more than ever. nanoPore Optical Interferometry (nPOI) newly introduced can detect even weak interactions in protein-protein and protein-compound, and can be connected directly to LC/MS/MS for identification of binding molecular species, which will be quite useful for affinity ranking and high-throughput interaction screening. Imaging MS provides the molecular information and spatial distribution of targeted molecules within a tissue specimen. MS-based clinical proteomics utilizing clinical specimens and empowered by advanced bioinformatics can attain both key protein-protein interaction (PPI) networks with major protein players responsible for functional mechanisms of a disease subtype. An integration of those MS-based technologies will deliver a seamless platform of drug development from molecules identified in human clinical specimens. PMID:26782309

  10. Letter from the Director - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The NCI’s Clinical Proteomic Technologies for Cancer (CPTC) initiative is focused on developing a better understanding of cancer biology through the proteomic interrogation of genomically characterized tumors from sources such as The Cancer Genome Atlas.

  11. Advances take stage - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Regulatory advances in proteomics will be taking center stage at a Symposia scheduled to occur at the 2011 American Association for Clinical Chemistry (AACC) Annual Meeting. The symposium entitled "Enabling Translational Proteomics with NCI's Clinical Proteomic Technologies for Cancer" is scheduled for July 25, 2011 at AACC's annual Meeting.

  12. Quality Assessment for Clinical Proteomics

    OpenAIRE

    Tabb, David L.

    2012-01-01

    Proteomics has emerged from the labs of technologists to enter widespread application in clinical contexts. This transition, however, has been hindered by overstated early claims of accuracy, concerns about reproducibility, and the challenges of handling batch effects properly. New efforts have produced sets of performance metrics and measurements of variability that establish sound expectations for experiments in clinical proteomics. As researchers begin incorporating these metrics in a qual...

  13. Collaborations in Proteomics Research - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute (NCI), through the Office of Cancer Clinical Proteomics Research (OCCPR), has signed two Memorandums of Understanding (MOUs) in the sharing of proteomics reagents and protocols

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-10

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

  15. Approaching clinical proteomics: current state and future fields of application in fluid proteomics

    OpenAIRE

    Apweiler, Rolf; Aslanidis, Charalampos; Deufel, Thomas; Gerstner, Andreas; Hansen, Jens; Hochstrasser, Dennis; Kellner, Roland; Kubicek, Markus; Lottspeich, Friedrich; Maser, Edmund; Mewes, Hans-Werner; Meyer, Helmut E.; Müllner, Stefan; Mutter, Wolfgang; Neumaier, Michael

    2009-01-01

    The field of clinical proteomics offers opportunities to identify new disease biomarkers in body fluids, cells and tissues. These biomarkers can be used in clinical applications for diagnosis, stratification of patients for specific treatment, or therapy monitoring. New protein array formats and improved spectrometry technologies have brought these analyses to a level with potential for use in clinical diagnostics. The nature of the human body fluid proteome with its large dynamic range of pr...

  16. Proteomic tools in clinical tissues: unlocking the pathology archives

    OpenAIRE

    Faoro, Valentina

    1982-01-01

    Background: Clinical proteomics aims to characterize the protein networks altered by pathologic processes or therapeutic treatment, and to develop biomarker profiling technologies to promptly detect diseases and treat them more effectively. The challenge of translating proteomic profiling to the bedside lies in applying technologies for the analysis of human tissues, which are routinely obtained by biopsy or surgery, without substantially modifying the clinical workflow. Formalin-fixed and...

  17. Ovarian Cancer Proteomic, Phosphoproteomic, and Glycoproteomic Data Released - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have just released a comprehensive dataset of the proteomic analysis of high grade serous ovarian tumor samples,

  18. Statistical data processing in clinical proteomics

    NARCIS (Netherlands)

    S. Smit

    2009-01-01

    The subject of this thesis is the analysis of data in clinical proteomics studies aimed at the discovery of biomarkers. The data sets produced in proteomics studies are huge, characterized by a small number of samples in which many proteins and peptides are measured. The studies described in this th

  19. Biospecimen Solicitation - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    A funding opportunity in support of the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) seeks to prospectively procure tumor samples, collected for proteomics investigation.

  20. Statistical data processing in clinical proteomics

    OpenAIRE

    Smit, S.

    2009-01-01

    The subject of this thesis is the analysis of data in clinical proteomics studies aimed at the discovery of biomarkers. The data sets produced in proteomics studies are huge, characterized by a small number of samples in which many proteins and peptides are measured. The studies described in this thesis compare different patient groups (recovering vs. relapsing patients) or a group of patients with a group of healthy controls. The size of the data and the size of the differences between the g...

  1. Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, Matthew; Gillette, Michael; Carr, Steven A.; Paulovich, Amanda G.; Smith, Richard D.; Rodland, Karin D.; Townsend, Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel

    2013-10-03

    The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verifi cation using targeted mass spectrometry methods.

  2. NCI Launches Proteomics Assay Portal - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    In a paper recently published by the journal Nature Methods, Investigators from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) announced the launch of a proteomics Assay Portal for multiple reaction monitoring-mass

  3. CPTAC Releases Largest-Ever Breast Cancer Proteome Dataset - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have released a dataset of proteins and phophorylated phosphopeptides identified through deep proteomic and phosphoproteomic analysis of breast tumor samples, previously genomically analyzed by The Cancer Genome Atlas (TCGA).

  4. Breast Cancer Proteomic and Phosphoproteomic Data Released - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have released a dataset of proteins and phophorylated phosphopeptides identified through deep proteomic and phosphoproteomic analysis of breast tumor samples, previously genomically analyzed by The Cancer Genome Atlas (TCGA).

  5. Proteomics Data on UCSC Genome Browser - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data.

  6. Progress through Collaboration - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute (NCI), through the Office of Cancer Clinical Proteomics Research (OCCPR), has signed two Memorandums of Understanding (MOUs) in the areas of sharing proteomics reagents and protocols and also in regulatory science.

  7. Director's Update - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) has recently begun the proteomic interrogation of genomically-characterized tumors from The Cancer Genome Atlas.

  8. Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases

    OpenAIRE

    Shiva Kalantari; Ameneh Jafari; Raheleh Moradpoor; Elmira Ghasemi; Ensieh Khalkhal

    2015-01-01

    Urine has been in the center of attention among scientists of clinical proteomics in the past decade, because it is valuable source of proteins and peptides with a relative stable composition and easy to collect in large and repeated quantities with a noninvasive procedure. In this review, we discuss technical aspects of urinary proteomics in detail, including sample preparation, proteomic technologies, and their advantage and disadvantages. Several recent experiments are presented which appl...

  9. Current strategies and findings in clinically relevant post-translational modification-specific proteomics

    OpenAIRE

    Pagel, Oliver; Loroch, Stefan; Sickmann, Albert; Zahedi, René P.

    2015-01-01

    Mass spectrometry-based proteomics has considerably extended our knowledge about the occurrence and dynamics of protein post-translational modifications (PTMs). So far, quantitative proteomics has been mainly used to study PTM regulation in cell culture models, providing new insights into the role of aberrant PTM patterns in human disease. However, continuous technological and methodical developments have paved the way for an increasing number of PTM-specific proteomic studies using clinical ...

  10. ASBMB Journal Club - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    On Wednesday, November 12, 2014 from 2:00 PM to 3:00 PM EST, Daniel Liebler, PhD (Vanderbilt University) and Karin Rodland, PhD (Pacific Northwestern National Laboratory) and Ruedi Aebersold, PhD (Swiss Federal Institute of Technology) will share their research insight as part of the ASBMB Journal Club.  Both Doctors Liebler and Rodland are Principal Investigators in the NCI’s Clinical Proteomic Tumor Analysis Consortium.

  11. Tumor Cold Ischemia - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    In a recently published manuscript in the journal of Molecular and Cellular Proteomics, researchers from the National Cancer Institutes (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigated the effect of cold ischemia on the proteome of fresh frozen tumors.

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

    Energy Technology Data Exchange (ETDEWEB)

    Elzek, Mohamed A.; Rodland, Karin D.

    2015-03-01

    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 applicabil- ity 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. 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.

  13. Proteomics Funding Opportunity - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    To expand the understanding of how cells sense and respond to changes in their physical environment, the NCI is seeking to perform proteomic assays on the panel of cell lines grown on a variety of substrates. These assays will provide insight into changes in protein levels or phosphorylation changes that could reflect the activity of mechano-transduction pathways.

  14. Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases

    Directory of Open Access Journals (Sweden)

    Shiva Kalantari

    2015-01-01

    Full Text Available Urine has been in the center of attention among scientists of clinical proteomics in the past decade, because it is valuable source of proteins and peptides with a relative stable composition and easy to collect in large and repeated quantities with a noninvasive procedure. In this review, we discuss technical aspects of urinary proteomics in detail, including sample preparation, proteomic technologies, and their advantage and disadvantages. Several recent experiments are presented which applied urinary proteome for biomarker discovery in renal diseases including diabetic nephropathy, immunoglobulin A (IgA nephropathy, focal segmental glomerulosclerosis, lupus nephritis, membranous nephropathy, and acute kidney injury. In addition, several available databases in urinary proteomics are also briefly introduced.

  15. Clinical proteomics in cancer research-promises and limitations of current two-dimensional gel electrophoresis.

    Science.gov (United States)

    Iwadate, Yasuo

    2008-01-01

    Cancer can be defined as a deviated protein network system toward dysregulated cellular proliferation. Alteration in the content and functional state of the proteins with many linkages may shift the equilibrium state of the protein signaling network to enhance a survival advantage of the affected cells. Searching for such hub proteins is the main purpose of the cancer proteomics. Although the progression in the vanguard proteomic technologies would largely contribute to cancer diagnosis and treatment in the future, the technology most frequently used for the analysis of clinical tissue samples is the two-dimensional gel electrophoresis (2DE) combined with matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Accumulation of 2DE data has generated many candidate biomarkers with potential clinical value. The identified proteins are restricted to a subset of the predicted human proteome, and ubiquitously exist in all normal cells taking important roles in the basic biological functions. Although these proteins can be used as valuable prognostic markers, the low-abundance proteins which is tissue-specific and useful as diagnostic markers could not easily be found by the standard 2DE technology alone. None of the current proteomic technologies can identify the whole proteome by themselves. Adequate combinations of different approaches not only in proteomics but in immunological methods would be necessary for the tissue specific markers. PMID:18855668

  16. Collaboration - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Despite great strides in proteomics and the growing number of articles citing the discovery of potential biomarkers, the actual rate of introduction of Food and Drug Administration (FDA) approved protein analytes has been relatively unchanged over the past 10 years. One of reasons for the lack of new protein-based biomarkers approved has been a lack of information and understanding by the proteomics research community to the regulatory process used by the FDA.

  17. Transplantation proteomics

    OpenAIRE

    Traum, Avram Z.; Schachter, Asher D.

    2005-01-01

    The field of proteomics is developing at a rapid pace in the post-genome era. Translational proteomics investigations aim to apply a combination of established methods and new technologies to learn about protein expression profiles predictive of clinical events, therapeutic response, and underlying mechanisms. However, in contrast to genetic studies and in parallel with gene expression studies, the dynamic nature of the proteome in conjunction with the challenges of accounting for post-transl...

  18. Shotgun proteomics of bacterial pathogens: advances, challenges and clinical implications.

    Science.gov (United States)

    Semanjski, Maja; Macek, Boris

    2016-02-01

    Mass spectrometry-based proteomics is increasingly used in analysis of bacterial pathogens. Simple experimental set-ups based on high accuracy mass spectrometry and powerful biochemical and bioinformatics tools are capable of reliably quantifying levels of several thousand bacterial proteins in a single experiment, reaching the analytical capacity to completely map whole proteomes. Here the authors present the state-of-the-art in bacterial pathogen proteomics and discuss challenges that the field is facing, especially in analysis of low abundant, modified proteins from organisms that are difficult to culture. Constant improvements in speed and sensitivity of mass spectrometers, as well as in bioinformatic and biochemical workflows will soon allow for comprehensive analysis of regulatory mechanisms of pathogenicity and enable routine application of proteomics in the clinical setting. PMID:26653908

  19. feature - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    "Cancer is a disease of the genome," noted Lynda Chin, M.D., professor of dermatology, Harvard Medical School and Dana-Farber Cancer Institute. "And understanding the impact of genomic changes in the proteome is critically important for converting genomic knowledge into something that a clinician can use on their patients."

  20. Biospecimen Core Resource - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The purpose of this notice is to notify the community that the National Cancer Institute's (NCI’s) Office of Cancer Clinical Proteomics Research (OCCPR) is seeking sources to establish a Biospecimen Core Resource (BCR), capable of receiving, qualifying, processing, and distributing annotated biospecimens.

  1. Computational Omics - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the NVIDIA Foundation are pleased to announce funding opportunities in the fight against cancer. Each organization has launched a request for proposals (RFP) that will collectively fund up to $2 million to help to develop a new generation of data-intensive scientific tools to find new ways to treat cancer.

  2. CPTAC Contributes to Healthdata.gov - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Recently, proteomic data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) funded by National Cancer Institute (NCI) was highlighted to the wider research community at Healthdata.gov. Healthdata.gov aims to make health data more acces

  3. PROTEOMICS: AN EVOLVING TECHNOLOGY IN LABORATORY MEDICINE

    Directory of Open Access Journals (Sweden)

    Dr. D J Venter

    2010-01-01

    Full Text Available The rapid developments in both genomics and proteomics will allow scientists to define the molecular pathways in normal and diseased cells. With these models, researchers will have the ability to predict previously unknown interactions and verify such predictions experimentally. Novel proteins, cellular functions, and pathways will also be unravelled. It is hoped that understanding the connections between cellular pathways and the ability to identify their associated biomarkers will greatly reduce the suffering and loss of life due to diseases.

  4. CPTAC Establishes Formal Relationships with Two Academic Institutions in Taiwan - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) has entered into memorandum of understandings (MOUs) with Chang Gung University and Academia Sinica, in Taipei, Taiwan.

  5. Protein kinase G signaling in cardiac pathophysiology: Impact of proteomics on clinical trials.

    Science.gov (United States)

    Kirk, Jonathan A; Holewinski, Ronald J; Crowgey, Erin L; Van Eyk, Jennifer E

    2016-03-01

    The protective role of cyclic guanosine monophosphate (cGMP)-stimulated protein kinase G (PKG) in the heart makes it an attractive target for therapeutic drug development to treat a variety of cardiac diseases. Phosphodiesterases degrade cGMP, thus phosphodiesterase inhibitors that can increase PKG are of translational interest and the subject of ongoing human trials. PKG signaling is complex, however, and understanding its downstream phosphorylation targets and upstream regulation are necessary steps toward safe and efficacious drug development. Proteomic technologies have paved the way for assays that allow us to peer broadly into signaling minutia, including protein quantity changes and phosphorylation events. However, there are persistent challenges to the proteomic study of PKG, such as the impact of the expression of different PKG isoforms, changes in its localization within the cell, and alterations caused by oxidative stress. PKG signaling is also dependent upon sex and potentially the genetic and epigenetic background of the individual. Thus, the rigorous application of proteomics to the field will be necessary to address how these effectors can alter PKG signaling and interfere with pharmacological interventions. This review will summarize PKG signaling, how it is being targeted clinically, and the proteomic challenges and techniques that are being used to study it. PMID:26670943

  6. Fungal Secretome for Biorefinery: Recent Advances in Proteomic Technology

    OpenAIRE

    Siu Kwan Sze; Adav, Sunil S.

    2013-01-01

    Fungal biotechnology has been well established in food and healthcare sector, and now being explored for lignocellulosic biorefinery due to their great potential to produce a wide array of extracellular enzymes for nutrient recycling. Due to global warming, environmental pollution, green house gases emission and depleting fossil fuel, fungal enzymes for lignocellulosic biomass refinery become a major focus for utilizing renewal bioresources. Proteomic technologies tender better biological und...

  7. CPTAC Scientific Symposium - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    On behalf of the National Cancer Institute and the Office of Cancer Clinical Proteomics Research, you are invited to the First Annual CPTAC Scientific Symposium on Wednesday, November 13, 2013. The purpose of this symposium, which consists of plenary and poster sessions, is for investigators from CPTAC community and beyond to share and discuss novel biological discoveries, analytical methods, and translational approaches using CPTAC data. All scientists who use, or wish to use CPTAC data are welcome to participate at this free event. The symposium will be held at the Natcher Conference Facility on the main campus of the National Institutes of Health in Bethesda, Maryland.

  8. Important options available - from start to finish -for translating proteomics results to clinical chemistry

    DEFF Research Database (Denmark)

    Heegaard, Niels H H; Ostergaard, Ole; Bahl, Justyna M C;

    2015-01-01

    In the realm of clinical chemistry the field of clinical proteomics, i.e., the application of proteomic methods for understanding mechanisms and enabling diagnosis, prediction, measurement of activity, and treatment response in disease, is first and foremost a discovery and research tool that feed......, execution, and interpretation of clinical proteomics studies is thus necessary for translation into clinical practice. We here review and discuss important options associated with clinical proteomics endeavors stretching from the planning phases to the final use in clinical chemistry. This article is...... assay development downstream. Putative new assay candidates generated by proteomics discovery projects compete with well-established assays with known indications, well-described performance, and of known value in specific clinical settings. Careful attention to the many options available in the design...

  9. Clinical Assay Development Support - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The NCI’s Division of Cancer Treatment and Diagnosis and the Cancer Diagnosis Program announce a request for applications for the Clinical Assay Development Program (CADP) for investigators seeking clinical assay development and validation resources.

  10. Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives.

    Science.gov (United States)

    Zhou, Li; Wang, Kui; Li, Qifu; Nice, Edouard C; Zhang, Haiyuan; Huang, Canhua

    2016-04-01

    Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy. PMID:26923776

  11. Proteomics

    DEFF Research Database (Denmark)

    Tølbøll, Trine Højgaard; Danscher, Anne Mette; Andersen, Pia Haubro;

    2012-01-01

    grouped manually to one or more of five major functional groups related to metabolism, cell structure, immunity, apoptosis and angiogenesis. These were chosen to represent basic cell functions and biological processes potentially involved in the pathogenesis of CHD. The LC–MS/MS-based proteomic analysis...... presented here is the largest published survey, so far, of the bovine claw tissue proteome....

  12. Tissue proteomics in pancreatic cancer study: discovery, emerging technologies and challenges

    OpenAIRE

    Pan, Sheng; Brentnall, Teresa A.; Kelly, Kimberly; Chen, Ru

    2013-01-01

    Pancreatic cancer is a highly lethal disease that is difficult to diagnose and treat. The advances of proteomics technology, especially quantitative proteomics, have stimulated a great interest to apply this technology for pancreatic cancer study. A variety of tissue proteomics approaches have been applied to investigate pancreatic cancer and the associated diseases. These studies were carried out with various goals, aiming to better understand the molecular mechanisms underlying pancreatic t...

  13. Proteomics

    DEFF Research Database (Denmark)

    Dam, Svend; Stougaard, Jens

    2014-01-01

    Proteomics is an efficient tool to identify proteins present in specific tissues, cell types, or organelles. The resulting proteome reference maps and/or comparative analyses provide overviews of regulated proteins between wild type and mutants or between different conditions together with a...... comprehensive list of proteins. Post translation modifications (PTMs), such as glycosylation and phosphorylation, are pivotal for protein stability and function. Several strategies for enrichment of PTMs have been developed where targeted proteomic approaches are used to identify these PTMs. The sequenced and...... annotated Lotus japonicus (Lotus) genome has been essential for obtaining high-quality protein identifications from proteomics studies. Furthermore, additional genomics and transcriptomics studies from several Lotus species/ecotypes support putative gene structures and these can be further supported using...

  14. CPTAC-EDRN Joint Session - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute (NCI)’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Early Detection Research Network (EDRN) will host a session during the 9th US-HUPO annual conference entitled “Highlights from NCI Proteomic Research Programs.”

  15. New Molecular Features of Colorectal Cancer Identified - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Investigators from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) who comprehensively analyzed 95 human colorectal tumor samples, have determined how gene alterations identified in previous analyses of the same samples

  16. Computational Omics Pre-Awardees - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) is pleased to announce the pre-awardees of the Computational Omics solicitation. Working with NVIDIA Foundation's Compute the Cure initiative and Leidos Biomedical...

  17. Skyline Reaches Agreement - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The full proteomics analysis of a small tumor sample (similar in mass to a few grains of rice) produces well over 500 megabytes of unprocessed "raw" data when analyzed on a mass spectrometer (MS). Thus, for every proteomics experiment there is a vast amount of raw data that must be analyzed and interrogated in order to extract biological information.

  18. ProteoWizard - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    ProteoWizard highlight - 2007, Dr. Parag Mallick and Darren Kessner had one idea in mind – how could they develop robust proteomics software that is relatively “easy” to use and transferable between labs.

  19. Cardiac extracellular matrix proteomics: Challenges, techniques, and clinical implications.

    Science.gov (United States)

    Chang, Chia Wei; Dalgliesh, Ailsa J; López, Javier E; Griffiths, Leigh G

    2016-01-01

    Extracellular matrix (ECM) has emerged as a dynamic tissue component, providing not only structural support, but also functionally participating in a wide range of signaling events during development, injury, and disease remodeling. Investigation of dynamic changes in cardiac ECM proteome is challenging due to the relative insolubility of ECM proteins, which results from their macromolecular nature, extensive post-translational modification (PTM), and tendency to form protein complexes. Finally, the relative abundance of cellular and mitochondrial proteins in cardiac tissue further complicates cardiac ECM proteomic approaches. Recent developments of various techniques to enrich and analyze ECM proteins are playing a major role in overcoming these challenges. Application of cardiac ECM proteomics in disease tissues can further provide spatial and temporal information relevant to disease diagnosis, prognosis, treatment, and engineering of therapeutic candidates for cardiac repair and regeneration. PMID:26200932

  20. A single lysis solution for the analysis of tissue samples by different proteomic technologies

    DEFF Research Database (Denmark)

    Gromov, P.; Celis, J.E.; Gromova, I.; Rank, Fritz; Timmermans, Vera Jacqueline Marita; Moreira, José

    2008-01-01

    Cancer, being a major healthcare concern worldwide, is one of the main targets for the application of emerging proteomic technologies and these tools promise to revolutionize the way cancer will be diagnosed and treated in the near future. Today, as a result of the unprecedented advances that have...... number of protocols for preparation of tissue lysates has been published, so far no single recipe is able to provide a "one-size fits all" solubilization procedure that can be used to analyse the same lysate using different proteomics technologies. Here we present evidence showing that cell lysis buffer......-based proteomics (reverse-phase lysate arrays or direct antibody arrays), allowing the direct comparison of qualitative and quantitative data yielded by these technologies when applied to the same samples. The usefulness of the CLB1 solution for gel-based proteomics was further established by 2D PAGE analysis of a...

  1. Identifying Predictors of Taxane-Induced Peripheral Neuropathy Using Mass Spectrometry-Based Proteomics Technology.

    Directory of Open Access Journals (Sweden)

    Emily I Chen

    Full Text Available Major advances in early detection and therapy have significantly increased the survival of breast cancer patients. Unfortunately, most cancer therapies are known to carry a substantial risk of adverse long-term treatment-related effects. Little is known about patient susceptibility to severe side effects after chemotherapy. Chemotherapy-induced peripheral neuropathy (CIPN is a common side effect of taxanes. Recent advances in genome-wide genotyping and sequencing technologies have supported the discoveries of a number of pharmacogenetic markers that predict response to chemotherapy. However, effectively implementing these pharmacogenetic markers in the clinic remains a major challenge. On the other hand, recent advances in proteomic technologies incorporating mass spectrometry (MS for biomarker discovery show great promise to provide clinically relevant protein biomarkers. In this study, we evaluated the association between protein content in serum exosomes and severity of CIPN. Women with early stage breast cancer receiving adjuvant taxane chemotherapy were assessed with the FACT-Ntx score and serum was collected before and after the taxane treatment. Based on the change in FACT-Ntx score from baseline to 12 month follow-up, we separated patients into two groups: those who had no change (Group 1, N = 9 and those who had a ≥20% worsening (Group 1, N = 8. MS-based proteomics technology was used to identify proteins present in serum exosomes to determine potential biomarkers. Mann-Whitney-Wilcoxon analysis was applied and maximum FDR was controlled at 20%. From the serum exosomes derived from this cohort, we identified over 700 proteins known to be in different subcellular locations and have different functions. Statistical analysis revealed a 12-protein signature that resulted in a distinct separation between baseline serum samples of both groups (q<0.2 suggesting that the baseline samples can predict subsequent neurotoxicity. These toxicity

  2. Integrating proteomic and functional genomic technologies in discovery-driven translational breast cancer research

    DEFF Research Database (Denmark)

    Celis, Julio E; Gromov, Pavel; Gromova, Irina;

    2003-01-01

    . Here we describe the essence of a long-term initiative undertaken by The Danish Centre for Translational Breast Cancer Research and currently underway for cancer biomarker discovery using fresh tissue biopsies and bio-fluids. The Centre is a virtual hub that brings together scientists working......The application of state-of-the-art proteomics and functional genomics technologies to the study of cancer is rapidly shifting toward the analysis of clinically relevant samples derived from patients, as the ultimate aim of translational research is to bring basic discoveries closer to the bedside...... in various areas of basic cancer research such as cell cycle control, invasion and micro-environmental alterations, apoptosis, cell signaling, and immunology, with clinicians (oncologists, surgeons), pathologists, and epidemiologists, with the aim of understanding the molecular mechanisms underlying breast...

  3. Development and Application of Novel Electron Transfer Dissociation-based Technologies for Proteomics

    OpenAIRE

    Frese, C

    2013-01-01

    Proteins are key actors in all cellular processes and pathways and almost all diseases are linked to perturbations of proteins, their modification state or interaction networks. Mass spectrometry-based proteomics has matured to a high-throughput quantitative technology, aiming to provide sensitive, accurate and complete information on protein abundance, interactions and networks. In the current workflow in MS-based proteomics, proteins are cleaved into peptides by proteolytic digestion follow...

  4. Optimized Clinical Use of RNALater and FFPE Samples for Quantitative Proteomics

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona;

    Introduction and Objectives The availability of patient samples is essential for clinical proteomic research. Biobanks worldwide store mainly samples stabilized in RNAlater as well as formalin-fixed and paraffin embedded (FFPE) biopsies. Biobank material is a potential source for clinical...... proteomics to provide retrospective information concerning biomarkers for diagnosis, prognosis and novel drug discovery. In this study, we assess as the first the influence of sample stabilization using RNAlater (Qiagen) on human derived samples for quantitative proteome analysis and pathway mapping, which...... we compare to FFPE and frozen samples being the control. Methods From the sigmoideum of two healthy participants’ twenty-four biopsies were extracted using endoscopy. The biopsies was stabilized either by being directly frozen, RNAlater, FFPE or incubated for 30 min at room temperature prior to FFPE...

  5. Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling.

    Science.gov (United States)

    Chen, Wendong; Wang, Shuai; Adhikari, Subash; Deng, Zuhui; Wang, Lingjue; Chen, Lan; Ke, Mi; Yang, Pengyuan; Tian, Ruijun

    2016-05-01

    Great efforts have been taken for developing high-sensitive mass spectrometry (MS)-based proteomic technologies, among which sample preparation is one of the major focus. Here, a simple and integrated spintip-based proteomics technology (SISPROT) consisting of strong cation exchange beads and C18 disk in one pipet tip was developed. Both proteomics sample preparation steps, including protein preconcentration, reduction, alkylation, and digestion, and reversed phase (RP)-based desalting and high-pH RP-based peptide fractionation can be achieved in a fully integrated manner for the first time. This easy-to-use technology achieved high sensitivity with negligible sample loss. Proteomic analysis of 2000 HEK 293 cells readily identified 1270 proteins within 1.4 h of MS time, while 7826 proteins were identified when 100000 cells were processed and analyzed within only 22 h of MS time. More importantly, the SISPROT can be easily multiplexed on a standard centrifuge with good reproducibility (Pearson correlation coefficient > 0.98) for both single-shot analysis and deep proteome profiling with five-step high-pH RP fractionation. The SISPROT was exemplified by the triplicate analysis of 100000 stem cells from human exfoliated deciduous teeth (SHED). This led to the identification of 9078 proteins containing 3771 annotated membrane proteins, which was the largest proteome data set for dental stem cells reported to date. We expect that the SISPROT will be well suited for deep proteome profiling for fewer than 100000 cells and applied for translational studies where multiplexed technology with good label-free quantification precision is required. PMID:27062885

  6. New Funding Opportunity: Biospecimen Core Resource - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The purpose of this notice is to notify the community that the National Cancer Institute's (NCI’s) Office of Cancer Clinical Proteomics Research (OCCPR) is seeking sources to establish a Biospecimen Core Resource (BCR), capable of receiving, qualifying, processing, and distributing annotated biospecimens.

  7. Notice of Pre-Application Webinar - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute will hold a public pre-application webinar on Friday, December 11 at 12:00 p.m. (EST) for the Funding Opportunity Announcements (FOAs) RFA-CA-15-021, RFA-CA-15-022, RFA-CA-15-023. These are the RFAs for the reissuance of its Clinical Proteomic Tumor Analysis Consortium (CPTAC).

  8. Current status and prospects of clinical proteomics studies on detection of colorectal cancer: Hopes and fears

    Institute of Scientific and Technical Information of China (English)

    ME de Noo; RAEM Tollenaar; AM Deelder; LH Bouwman

    2006-01-01

    Colorectal adenocarcinoma (CRC) is the third most common type of cancer and the fourth most frequent cause of death due to cancer worldwide. Given the natural history of CRC, early diagnosis appears to be the most appropriate tool to reduce disease-related mortality. A field of recent interest is clinical proteomics, which was reported to lead to high sensitivity and specificities for early detection of several solid tumors. This emerging field uses mass spectrometry-based protein profiles/patterns of easy accessible body fluids to distinguish cancer from non-cancer patients. These discrepancies may be a result of: (1) proteins being abnormally produced or shed and added to the serum proteome, (2) proteins clipped or modified as a consequence of the disease process, or (3) proteins subtracted from the proteome owing to disease-related proteolytic degradation pathways. Therefore, protein pattern diagnostics would provide easy and reliable tools for detection of cancer. This paper focuses on the current status of clinical proteomics research in oncology and in colorectal cancer especially,and will reflect on pitfalls and fears in this relatively new area of clinical medicine, which are reproducibility issues and pre-analytical factors, statistical issues, and identification and nature of discriminating proteins/peptides.

  9. Role of Proteomics in the Development of Personalized Medicine.

    Science.gov (United States)

    Jain, Kewal K

    2016-01-01

    Advances in proteomic technologies have made import contribution to the development of personalized medicine by facilitating detection of protein biomarkers, proteomics-based molecular diagnostics, as well as protein biochips and pharmacoproteomics. Application of nanobiotechnology in proteomics, nanoproteomics, has further enhanced applications in personalized medicine. Proteomics-based molecular diagnostics will have an important role in the diagnosis of certain conditions and understanding the pathomechanism of disease. Proteomics will be a good bridge between diagnostics and therapeutics; the integration of these will be important for advancing personalized medicine. Use of proteomic biomarkers and combination of pharmacoproteomics with pharmacogenomics will enable stratification of clinical trials and improve monitoring of patients for development of personalized therapies. Proteomics is an important component of several interacting technologies used for development of personalized medicine, which is depicted graphically. Finally, cancer is a good example of applications of proteomic technologies for personalized management of cancer. PMID:26827601

  10. A preliminary screening study on the associated proteins in human psoriasis vulgaris by serum proteomics technologies

    Institute of Scientific and Technical Information of China (English)

    Zhankui Liu; Shengshun Tan; Chunshui Yu; Jinghua Fan; Zhuanli Bai; Junjie Li

    2007-01-01

    Objective:To investigate the optimum screening conditions of associated proteins in human psoriasis vulgaris by serum proteomics technique, and to screen the different expression proteins related with psoriasis vulgaris. Methods:Serum samples of peripheral blood were collected from newly diagnosed psoriasis vulgaris patients in the clinic, and 20 matched healthy persons.Serum albumin IgG was removed by filtering with ProteoExtract Albumin/IgG. After comparative proteomics analysis the different protein spots were identified using 2-DE and MS. Results :Electrophoresis figures with high resolution and reproducibility were obtained. Three different expression proteins were found only in the serum from psoriasis vulgaris patients,while nine other different proteins expressing from healthy volunteers. Conclusion:The protein expression was different in the serum between the psoriasis vulgaris patients and healthy volunteers. It was hoped that we could find the biomarkers related to psoriasis vulgaris by using proteomics.

  11. Proteomics in Pancreatic Cancer Research

    Science.gov (United States)

    Geng, Ruihui; Li, Zhaoshen; Li, Shude; Gao, Jun

    2011-01-01

    Pancreatic cancer is a highly aggressive malignancy with a poor prognosis and deeply affects the life of people. Therefore, the earlier diagnosis and better treatments are urgently needed. In recent years, the proteomic technologies are well established and growing rapidly and have been widely applied in clinical applications, especially in pancreatic cancer research. In this paper, we attempt to discuss the development of current proteomic technologies and the application of proteomics to the field of pancreatic cancer research. This will explore the potential perspective in revealing pathogenesis, making the diagnosis earlier and treatment. PMID:22084685

  12. Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects

    Energy Technology Data Exchange (ETDEWEB)

    Karpievitch, Yuliya V.; Polpitiya, Ashoka D.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

    2010-12-01

    Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used, significant challenges remain, and there are many opportunities for statisticians to make important contributions. In the most widely used "bottom-up" approach to proteomics, complex mixtures of proteins are first subjected to enzymatic cleavage, the resulting peptide products are separated based on chemical or physical properties and analyzed using a mass spectrometer. The two fundamental challenges in the analysis of bottom-up MS-based proteomics are: (1) Identifying the proteins that are present in a sample, and (2) Quantifying the abundance levels of the identified proteins. Both of these challenges require knowledge of the biological and technological context that gives rise to observed data, as well as the application of sound statistical principles for estimation and inference. We present an overview of bottom-up proteomics and outline the key statistical issues that arise in protein identification and quantification.

  13. Translating epithelial mesenchymal transition markers into the clinic: Novel insights from proteomics

    Directory of Open Access Journals (Sweden)

    Vergara Daniele

    2016-03-01

    Full Text Available The growing understanding of the molecular mechanisms underlying epithelial-to-mesenchymal transition (EMT may represent a potential source of clinical markers. Despite EMT drivers have not yet emerged as candidate markers in the clinical setting, their association with established clinical markers may improve their specificity and sensitivity. Mass spectrometry-based platforms allow analyzing multiple samples for the expression of EMT candidate markers, and may help to diagnose diseases or monitor treatment efficiently. This review highlights proteomic approaches applied to elucidate the differences between epithelial and mesenchymal tumors and describes how these can be used for target discovery and validation.

  14. CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes

    OpenAIRE

    Avsar, Timucin; Durası, İlknur Melis; Uygunoğlu, Uğur; Tütüncü, Melih; Demirci, Nuri Onat; SAIP, Sabahattin; Sezerman, O. Uğur; Siva, Aksel; Tahir Turanlı, Eda

    2015-01-01

    Multiple sclerosis (MS) is an immune-mediated, neuro-inflammatory, demyelinating and neurodegenerative disease of the central nervous system (CNS) with a heterogeneous clinical presentation and course. There is a remarkable phenotypic heterogeneity in MS, and the molecular mechanisms underlying it remain unknown. We aimed to investigate further the etiopathogenesis related molecular pathways in subclinical types of MS using proteomic and bioinformatics approaches in cerebrospinal fluids of pa...

  15. IMAT PI Meeting - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The Innovative Molecular Analysis Technologies (IMAT) program was established to support the development, technical maturation, and dissemination of novel and potentially transformative next-generation technologies through an approach of balanced but targeted innovation. In support of its mission, the IMAT program utilizes a variety of investigator-initiated research project grant mechanisms while retaining a strong commitment to diversity and to the training of scientists and clinicians in cross-cutting, research-enabling disciplines.

  16. Computational Biology in Clinical Proteomics and Chromatin Genomics

    NARCIS (Netherlands)

    Meuleman, W.

    2012-01-01

    The work in this thesis is concerned with two very distinct biological fields. The first part pertains to the development of techniques to aid in the search for clinical biomarkers for use in the early detection of cancer. The second part aims to elucidate in what way a genome is organised in a cell

  17. Predicting Ovarian Cancer Patients' Clinical Response to Platinum-Based Chemotherapy by Their Tumor Proteomic Signatures.

    Science.gov (United States)

    Yu, Kun-Hsing; Levine, Douglas A; Zhang, Hui; Chan, Daniel W; Zhang, Zhen; Snyder, Michael

    2016-08-01

    Ovarian cancer is the deadliest gynecologic malignancy in the United States with most patients diagnosed in the advanced stage of the disease. Platinum-based antineoplastic therapeutics is indispensable to treating advanced ovarian serous carcinoma. However, patients have heterogeneous responses to platinum drugs, and it is difficult to predict these interindividual differences before administering medication. In this study, we investigated the tumor proteomic profiles and clinical characteristics of 130 ovarian serous carcinoma patients analyzed by the Clinical Proteomic Tumor Analysis Consortium (CPTAC), predicted the platinum drug response using supervised machine learning methods, and evaluated our prediction models through leave-one-out cross-validation. Our data-driven feature selection approach indicated that tumor proteomics profiles contain information for predicting binarized platinum response (P drug responses as well as provided insights into the biological processes influencing the efficacy of platinum-based therapeutics. Our analytical approach is also extensible to predicting response to other antineoplastic agents or treatment modalities for both ovarian and other cancers. PMID:27312948

  18. Clinical proteomics for liver disease: a promising approach for discovery of novel biomarkers

    Directory of Open Access Journals (Sweden)

    Tsubouchi Hirohito

    2010-12-01

    Full Text Available Abstract Hepatocellular carcinoma (HCC is the fifth most common cancer and advanced hepatic fibrosis is a major risk factor for HCC. Hepatic fibrosis including liver cirrhosis and HCC are mainly induced by persistent hepatitis B or C virus infection, with approximately 500 million people infected with hepatitis B or C virus worldwide. Furthermore, the number of patients with non-alcoholic fatty liver disease (NAFLD has recently increased and NAFLD can progress to cirrhosis and HCC. These chronic liver diseases are major causes of morbidity and mortality, and the identification of non-invasive biomarkers is important for early diagnosis. Recent advancements in quantitative and large-scale proteomic methods could be used to optimize the clinical application of biomarkers. Early diagnosis of HCC and assessment of the stage of hepatic fibrosis or NAFLD can also contribute to more effective therapeutic interventions and an improve prognosis. Furthermore, advancements of proteomic techniques contribute not only to the discovery of clinically useful biomarkers, but also in clarifying the molecular mechanisms of disease pathogenesis by using body fluids, such as serum, and tissue samples and cultured cells. In this review, we report recent advances in quantitative proteomics and several findings focused on liver diseases, including HCC, NAFLD, hepatic fibrosis and hepatitis B or C virus infections.

  19. The Cerebrospinal Fluid in Severe Pain Conditions : Clinical, Pharmacological and Proteomic Aspects

    OpenAIRE

    Bäckryd, Emmanuel

    2015-01-01

    The treatment of both cancer pain and non-cancer chronic pain is still suboptimal. The overall aim of this PhD thesis was to conduct translational pain research at the interface between clinical pain medicine and the field of human proteomics, using the practice of intrathecal analgesia at our institution as a starting point. Hence, the cerebrospinal fluid (CSF) is at the centre of the present dissertation, both as a target for infusing analgesics (Papers I and II – clinical and pharmacologic...

  20. Urinary proteomics as a novel tool for biomarker discovery in kidney diseases*

    OpenAIRE

    Wu, Jing; Chen, Yi-ding; Gu, Wei

    2010-01-01

    Urine has become one of the most attractive biofluids in clinical proteomics, for its procurement is easy and noninvasive and it contains sufficient proteins and peptides. Urinary proteomics has thus rapidly developed and has been extensively applied to biomarker discovery in clinical diseases, especially kidney diseases. In this review, we discuss two important aspects of urinary proteomics in detail, namely, sample preparation and proteomic technologies. In addition, data mining in urinary ...

  1. High resolution preparation of monocyte-derived macrophages (MDM protein fractions for clinical proteomics

    Directory of Open Access Journals (Sweden)

    Olivieri Oliviero

    2009-02-01

    Full Text Available Abstract Background Macrophages are involved in a number of key physiological processes and complex responses such as inflammatory, immunological, infectious diseases and iron homeostasis. These cells are specialised for iron storage and recycling from senescent erythrocytes so they play a central role in the fine tuning of iron balancing and distribution. The comprehension of the many physiological responses of macrophages implies the study of the related molecular events. To this regard, proteomic analysis, is one of the most powerful tools for the elucidation of the molecular mechanisms, in terms of changes in protein expression levels. Results Our aim was to optimize a protocol for protein fractionation and high resolution mapping using human macrophages for clinical studies. We exploited a fractionation protocol based on the neutral detergent Triton X-114. The 2D maps of the fractions obtained showed high resolution and a good level of purity. Western immunoblotting and mass spectrometry (MS/MS analysis indicated no fraction cross contamination. On 2D-PAGE mini gels (7 × 8 cm we could count more than five hundred protein spots, substantially increasing the resolution and the number of detectable proteins for the macrophage proteome. The fractions were also evaluated, with preliminary experiments, using Surface Enhanced Laser Desorption Ionization Time of Flight Mass Spectrometry (SELDI-TOF-MS. Conclusion This relatively simple method allows deep investigation into macrophages proteomics producing discrete and accurate protein fractions, especially membrane-associated and integral proteins. The adapted protocol seems highly suitable for further studies of clinical proteomics, especially for the elucidation of the molecular mechanisms controlling iron homeostasis in normal and disease conditions.

  2. Studying Different Clinical Syndromes Of Paediatric Severe Malaria Using Plasma Proteomics

    KAUST Repository

    Ramaprasad, Abhinay

    2012-08-01

    Background- Severe Plasmodium falciparum malaria remains one of the major causes of childhood morbidity and mortality in Africa. Severe malaria manifests itself as three main clinical syndromes-impaired consciousness (cerebral malaria), respiratory distress and severe malarial anaemia. Cerebral malaria and respiratory distress are major contributors to malaria mortality but their pathophysiology remains unclear. Motivation/Objectives- Most children with severe malaria die within the first 24 hours of admission to a hospital because of their pathophysiological conditions. Thus, along with anti-malarial drugs, various adjuvant therapies such as fluid bolus (for hypovolaemia) and anticonvulsants (for seizures) are given to alleviate the sick child’s condition. But these therapies can sometimes have adverse effects. Hence, a clear understanding of severe malaria pathophysiology is essential for making an informed decision regarding adjuvant therapies. Methodology- We used mass spectrometry-based shotgun proteomics to study plasma samples from Gambian children with severe malaria. We compared the proteomic profiles of different severe malaria syndromes and generated hypotheses regarding the underlying disease mechanisms. Results/Conclusions- The main challenges of studying the severe malaria syndromes using proteomics were the high complexity and variability among the samples. We hypothesized that hepatic injury and nitric oxide play roles in the pathophysiology of cerebral malaria and respiratory distress.

  3. A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.

    Science.gov (United States)

    Rudnick, Paul A; Markey, Sanford P; Roth, Jeri; Mirokhin, Yuri; Yan, Xinjian; Tchekhovskoi, Dmitrii V; Edwards, Nathan J; Thangudu, Ratna R; Ketchum, Karen A; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Stein, Stephen E

    2016-03-01

    The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics data sets from the mass spectrometric interrogation of tumor samples previously analyzed by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and proteomic data is enabling proteogenomic study for both reference (i.e., contained in major sequence databases) and nonreference markers of cancer. The CPTAC laboratories have focused on colon, breast, and ovarian tissues in the first round of analyses; spectra from these data sets were produced from 2D liquid chromatography-tandem mass spectrometry analyses and represent deep coverage. To reduce the variability introduced by disparate data analysis platforms (e.g., software packages, versions, parameters, sequence databases, etc.), the CPTAC Common Data Analysis Platform (CDAP) was created. The CDAP produces both peptide-spectrum-match (PSM) reports and gene-level reports. The pipeline processes raw mass spectrometry data according to the following: (1) peak-picking and quantitative data extraction, (2) database searching, (3) gene-based protein parsimony, and (4) false-discovery rate-based filtering. The pipeline also produces localization scores for the phosphopeptide enrichment studies using the PhosphoRS program. Quantitative information for each of the data sets is specific to the sample processing, with PSM and protein reports containing the spectrum-level or gene-level ("rolled-up") precursor peak areas and spectral counts for label-free or reporter ion log-ratios for 4plex iTRAQ. The reports are available in simple tab-delimited formats and, for the PSM-reports, in mzIdentML. The goal of the CDAP is to provide standard, uniform reports for all of the CPTAC data to enable comparisons between different samples and cancer types as well as across the major omics fields. PMID:26860878

  4. MALDI-TOF mass spectrometry proteomic based identification of clinical bacterial isolates

    Directory of Open Access Journals (Sweden)

    Ashutosh Panda

    2014-01-01

    Full Text Available Background & objectives: Pathogenic bacteria often cause life threatening infections especially in immunocompromised individuals. Therefore, rapid and reliable species identification is essential for a successful treatment and disease management. We evaluated a rapid, proteomic based technique for identification of clinical bacterial isolates by protein profiling using matrix-assisted laser desorption-ionization time - of - flight mass spectrometry (MALDI-TOF MS. Methods: Freshly grown bacterial isolates were selected from culture plates. Ethanol/formic acid extraction procedure was carried out, followed by charging of MALDI target plate with the extract and overlaying with α-cyano-4 hydroxy-cinnamic acid matrix solution. Identification was performed using the MALDI BioTyper 1.1, software for microbial identification (Bruker Daltonik GmbH, Bremen, Germany. Results: A comparative analysis of 82 clinical bacterial isolates using MALDI -TOF MS and conventional techniques was carried out. Amongst the clinical isolates, the accuracy at the species level for clinical isolates was 98.78%. One out of 82 isolates was not in accordance with the conventional assays because MALDI-TOF MS established it as Streptococcus pneumoniae and conventional methods as Streptococcus viridans. Interpretation & conclusions: MALDI - TOF MS was found to be an accurate, rapid, cost-effective and robust system for identification of clinical bacterial isolates. This innovative approach holds promise for earlier therapeutic intervention leading to better patient care.

  5. CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes.

    Directory of Open Access Journals (Sweden)

    Timucin Avsar

    Full Text Available Multiple sclerosis (MS is an immune-mediated, neuro-inflammatory, demyelinating and neurodegenerative disease of the central nervous system (CNS with a heterogeneous clinical presentation and course. There is a remarkable phenotypic heterogeneity in MS, and the molecular mechanisms underlying it remain unknown. We aimed to investigate further the etiopathogenesis related molecular pathways in subclinical types of MS using proteomic and bioinformatics approaches in cerebrospinal fluids of patients with clinically isolated syndrome, relapsing remitting MS and progressive MS (n=179. Comparison of disease groups with controls revealed a total of 151 proteins that are differentially expressed in clinically different MS subtypes. KEGG analysis using PANOGA tool revealed the disease related pathways including aldosterone-regulated sodium reabsorption (p=8.02x10-5 which is important in the immune cell migration, renin-angiotensin (p=6.88x10-5 system that induces Th17 dependent immunity, notch signaling (p=1.83x10-10 pathway indicating the activated remyelination and vitamin digestion and absorption pathways (p=1.73x10-5. An emerging theme from our studies is that whilst all MS clinical forms share common biological pathways, there are also clinical subtypes specific and pathophysiology related pathways which may have further therapeutic implications.

  6. The Urine Proteome Profile Is Different in Neuromyelitis Optica Compared to Multiple Sclerosis: A Clinical Proteome Study.

    Directory of Open Access Journals (Sweden)

    Helle H Nielsen

    Full Text Available Inflammatory demyelinating diseases of the CNS comprise a broad spectrum of diseases like neuromyelitis optica (NMO, NMO spectrum disorders (NMO-SD and multiple sclerosis (MS. Despite clear classification criteria, differentiation can be difficult. We hypothesized that the urine proteome may differentiate NMO from MS.The proteins in urine samples from anti-aquaporin 4 (AQP4 seropositive NMO/NMO-SD patients (n = 32, patients with MS (n = 46 and healthy subjects (HS, n = 31 were examined by quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS after trypsin digestion and iTRAQ labelling. Immunoglobulins (Ig in the urine were validated by nephelometry in an independent cohort (n = 9-10 pr. groups.The analysis identified a total of 1112 different proteins of which 333 were shared by all 109 subjects. Cluster analysis revealed differences in the urine proteome of NMO/NMO-SD compared to HS and MS. Principal component analysis also suggested that the NMO/NMO-SD proteome profile was useful for classification. Multivariate regression analysis revealed a 3-protein profile for the NMO/NMO-SD versus HS discrimination, a 6-protein profile for NMO/NMO-SD versus MS discrimination and an 11-protein profile for MS versus HS discrimination. All protein panels yielded highly significant ROC curves (AUC in all cases >0.85, p≤0.0002. Nephelometry confirmed the presence of increased Ig-light chains in the urine of patients with NMO/NMO-SD.The urine proteome profile of patients with NMO/NMO-SD is different from MS and HS. This may reflect differences in the pathogenesis of NMO/NMO-SD versus MS and suggests that urine may be a potential source of biomarkers differentiating NMO/NMO-SD from MS.

  7. Microwave & Magnetic (M2) Proteomics Reveals CNS-Specific Protein Expression Waves that Precede Clinical Symptoms of Experimental Autoimmune Encephalomyelitis

    Science.gov (United States)

    Raphael, Itay; Mahesula, Swetha; Purkar, Anjali; Black, David; Catala, Alexis; Gelfond, Jonathon A. L.; Forsthuber, Thomas G.; Haskins, William E.

    2014-09-01

    Central nervous system-specific proteins (CSPs), transported across the damaged blood-brain-barrier (BBB) to cerebrospinal fluid (CSF) and blood (serum), might be promising diagnostic, prognostic and predictive protein biomarkers of disease in individual multiple sclerosis (MS) patients because they are not expected to be present at appreciable levels in the circulation of healthy subjects. We hypothesized that microwave & magnetic (M2) proteomics of CSPs in brain tissue might be an effective means to prioritize putative CSP biomarkers for future immunoassays in serum. To test this hypothesis, we used M2 proteomics to longitudinally assess CSP expression in brain tissue from mice during experimental autoimmune encephalomyelitis (EAE), a mouse model of MS. Confirmation of central nervous system (CNS)-infiltrating inflammatory cell response and CSP expression in serum was achieved with cytokine ELISPOT and ELISA immunoassays, respectively, for selected CSPs. M2 proteomics (and ELISA) revealed characteristic CSP expression waves, including synapsin-1 and α-II-spectrin, which peaked at day 7 in brain tissue (and serum) and preceded clinical EAE symptoms that began at day 10 and peaked at day 20. Moreover, M2 proteomics supports the concept that relatively few CNS-infiltrating inflammatory cells can have a disproportionally large impact on CSP expression prior to clinical manifestation of EAE.

  8. Technology clinic for wood fuel technologies; Puupolttoaineklinikka - PUUY07

    Energy Technology Data Exchange (ETDEWEB)

    Asplund, D.; Nikku, P. [Jyvaeskylaen Teknologiakeskus Oy, Jyvaeskylae (Finland)

    2001-07-01

    Jyvaeskylae Science Park runs the wood fuel technology clinic, funded by the Technology Development Centre Tekes. The clinic assists the entrepreneurs in starting a project, offers funding and expert services. The services of the woof fuel technology clinic are designed for SM Enterprises, which develop new components or equipment for production or utilisation of wood fuels. In the beginning the services of the clinic were connected to the production of wood fuels. In 2000 the services of the clinic expanded to consist the projects related to small-scale utilisation of wood fuels. These mean development projects related to fireplaces, small and large real estate boilers, district heating and small-scale power plants. Development objectives can include all the components and services related to delivery of a boiler plant. The clinic creates a flexible funding system for the projects of small and medium sized companies, which develop and constructs partial solutions or components. A Company can get expert services needed in the development work. Technology development services include e.g. measuring and reporting services. (orig.)

  9. Current application of proteomics in biomarker discoveryfor inflammatory bowel disease

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    Recently, the field of proteomics has rapidly expanded inits application towards clinical research with objectivesranging from elucidating disease pathogenesis todiscovering clinical biomarkers. As proteins governand/or reflect underlying cellular processes, the studyof proteomics provides an attractive avenue for researchas it allows for the rapid identification of proteinprofiles in a biological sample. Inflammatory boweldisease (IBD) encompasses several heterogeneousand chronic conditions of the gastrointestinal tract.Proteomic technology provides a powerful means ofaddressing major challenges in IBD today, especiallyfor identifying biomarkers to improve its diagnosis andmanagement. This review will examine the current stateof IBD proteomics research and its use in biomarkerresearch. Furthermore, we also discuss the challengesof translating proteomic research into clinically relevanttools. The potential application of this growing field isenormous and is likely to provide significant insightstowards improving our future understanding and managementof IBD.

  10. Biomarker discovery in mass spectrometry-based urinary proteomics.

    Science.gov (United States)

    Thomas, Samuel; Hao, Ling; Ricke, William A; Li, Lingjun

    2016-04-01

    Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS-based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS-based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians. PMID:26703953

  11. Comprehensive and Scalable Highly Automated MS-Based Proteomic Workflow for Clinical Biomarker Discovery in Human Plasma.

    Science.gov (United States)

    Dayon, Loïc; Núñez Galindo, Antonio; Corthésy, John; Cominetti, Ornella; Kussmann, Martin

    2014-07-24

    Over the past decade, mass spectrometric performance has greatly improved in terms of sensitivity, dynamic range, and speed. By contrast, only limited progress has been accomplished with regard to automation, throughput, and robustness of the proteomic sample preparation process upstream of mass spectrometry. The present work delivers an optimized analysis of human plasma samples in both small preclinical and large clinical studies, enabled by the development of a highly automated quantitative proteomic workflow. Several iterative evaluation and validation steps were performed before process "design freeze" and development completion. A robotic liquid handling workflow and platform (including reduction, alkylation, digestion, TMT labeling, pooling, and purification) were shown to provide better quantitative trueness and precision than manual operation at the bench. Depletion of the most abundant human plasma proteins and subsequent buffer exchange were also developed and integrated. Finally, 96 identical pooled human plasma samples were prepared in a 96-well plate format, and each sample was individually subjected to our developed workflow. This test revealed increased throughput and robustness compared with to-date published manual or less automated workflows. Our workflow is ready-to-use for future (pre-) clinical studies. We expect our work to facilitate, accelerate, and improve clinical proteomic discovery in human blood plasma. PMID:25058407

  12. Liquid chromatography mass spectrometry-based proteomics: Biological and technological aspects

    OpenAIRE

    Karpievitch, Yuliya V.; Polpitiya, Ashoka D.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

    2011-01-01

    Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used, significant challenges remain, and there are many opportunities for statisticians to make important contributions. In the most widely used “bottom-up” approach to proteomics, complex mixtures of proteins are first subjected to enzymati...

  13. Microbial Protein-Antigenome Determination (MAD) Technology: A Proteomics-Based Strategy for Rapid Identification of Microbial Targets of Host Humoral Immune Responses

    Science.gov (United States)

    Immunogenic, pathogen-specific proteins have excellent potential for development of novel management modalities. Here, we describe an innovative application of proteomics called Microbial protein-Antigenome Determination (MAD) Technology for rapid identification of native microbial proteins that eli...

  14. Proteomics Core

    Data.gov (United States)

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in...

  15. Uses of internet technology in clinical practice

    International Nuclear Information System (INIS)

    The practice of medicine has extended itself to vast areas and requires active clinicians to systematize and organize their workload through the use of the most up-to-date digital and computer communication technologies. Computerization and worldwide accessibility of information has especially provided great assistance in this regard. The explosive growth of medical information increases the need for the use of these new methods of organizing and accessing data. This article briefly summarizes a few of the vital tools that internet technology has provided clinical practice, with the aid of basic concepts of internet, database systems, hospital systems and data security and reliability. (author)

  16. Urinary proteomic and non-prefractionation quantitative phosphoproteomic analysis during pregnancy and non-pregnancy

    OpenAIRE

    Zheng, Jianhua; Liu, Liguo; Wang, Jin; Jin, Qi

    2013-01-01

    Background Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnant and non-pregnant patients using gel electrophoresis and high-resolution mass spectrometry. Furthermore, we also apply a non-prefractionation quantitative phosphoproteomic appr...

  17. Proteomic signatures of infertile men with clinical varicocele and their validation studies reveal mitochondrial dysfunction leading to infertility

    Science.gov (United States)

    Agarwal, Ashok; Sharma, Rakesh; Samanta, Luna; Durairajanayagam, Damayanthi; Sabanegh, Edmund

    2016-01-01

    To study the major differences in the distribution of spermatozoa proteins in infertile men with varicocele by comparative proteomics and validation of their level of expression. The study-specific estimates for each varicocele outcome were combined to identify the proteins involved in varicocele-associated infertility in men irrespective of stage and laterality of their clinical varicocele. Expression levels of 5 key proteins (PKAR1A, AK7, CCT6B, HSPA2, and ODF2) involved in stress response and sperm function including molecular chaperones were validated by Western blotting. Ninety-nine proteins were differentially expressed in the varicocele group. Over 87% of the DEP involved in major energy metabolism and key sperm functions were underexpressed in the varicocele group. Key protein functions affected in the varicocele group were spermatogenesis, sperm motility, and mitochondrial dysfunction, which were further validated by Western blotting, corroborating the proteomics analysis. Varicocele is essentially a state of energy deprivation, hypoxia, and hyperthermia due to impaired blood supply, which is corroborated by down-regulation of lipid metabolism, mitochondrial electron transport chain, and Krebs cycle enzymes. To corroborate the proteomic analysis, expression of the 5 identified proteins of interest was validated by Western blotting. This study contributes toward establishing a biomarker “fingerprint” to assess sperm quality on the basis of molecular parameters. PMID:26732106

  18. A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

    Directory of Open Access Journals (Sweden)

    Granier Claude

    2008-10-01

    Full Text Available Abstract Background In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user. Results We present Sili2DGel an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.. We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects. Conclusion Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.

  19. The potential clinical impact of the release of two drafts of the human proteome.

    Science.gov (United States)

    Ezkurdia, Iakes; Calvo, Enrique; Del Pozo, Angela; Vázquez, Jesús; Valencia, Alfonso; Tress, Michael L

    2015-01-01

    The authors have carried out an investigation of the two "draft maps of the human proteome" published in 2014 in Nature. The findings include an abundance of poor spectra, low-scoring peptide-spectrum matches and incorrectly identified proteins in both these studies, highlighting clear issues with the application of false discovery rates. This noise means that the claims made by the two papers - the identification of high numbers of protein coding genes, the detection of novel coding regions and the draft tissue maps themselves - should be treated with considerable caution. The authors recommend that clinicians and researchers do not use the unfiltered data from these studies. Despite this these studies will inspire further investigation into tissue-based proteomics. As long as this future work has proper quality controls, it could help produce a consensus map of the human proteome and improve our understanding of the processes that underlie health and disease. PMID:26496066

  20. Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies

    Science.gov (United States)

    Anwar, Nadia; Hunt, Ela

    2009-01-01

    Background This paper summarises the lessons and experiences gained from a case study of the application of semantic web technologies to the integration of data from the bacterial species Francisella tularensis novicida (Fn). Fn data sources are disparate and heterogeneous, as multiple laboratories across the world, using multiple technologies, perform experiments to understand the mechanism of virulence. It is hard to integrate these data sources in a flexible manner that allows new experimental data to be added and compared when required. Results Public domain data sources were combined in RDF. Using this connected graph of database cross references, we extended the annotations of an experimental data set by superimposing onto it the annotation graph. Identifiers used in the experimental data automatically resolved and the data acquired annotations in the rest of the RDF graph. This happened without the expensive manual annotation that would normally be required to produce these links. This graph of resolved identifiers was then used to combine two experimental data sets, a proteomics experiment and a transcriptomic experiment studying the mechanism of virulence through the comparison of wildtype Fn with an avirulent mutant strain. Conclusion We produced a graph of Fn cross references which enabled the combination of two experimental datasets. Through combination of these data we are able to perform queries that compare the results of the two experiments. We found that data are easily combined in RDF and that experimental results are easily compared when the data are integrated. We conclude that semantic data integration offers a convenient, simple and flexible solution to the integration of published and unpublished experimental data. PMID:19796400

  1. New Funding Opportunity: Tissue Purchase Order Acquisitions - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute (NCI) is expanding its basic and translational research programs that rely heavily on sufficient availability of high quality, well annotated biospecimens suitable for use in genomic and proteomic studies. The NCI’s overarching goal with such programs is to improve the ability to diagnose, treat, and prevent cancer.

  2. Ion beam therapy fundamentals, technology, clinical applications

    CERN Document Server

    2012-01-01

    The book provides a detailed, up-to-date account of the basics, the technology, and the clinical use of ion beams for radiation therapy. Theoretical background, technical components, and patient treatment schemes are delineated by the leading experts that helped to develop this field from a research niche to its current highly sophisticated and powerful clinical treatment level used to the benefit of cancer patients worldwide. Rather than being a side-by-side collection of articles, this book consists of related chapters. It is a common achievement by 76 experts from around the world. Their expertise reflects the diversity of the field with radiation therapy, medical and accelerator physics, radiobiology, computer science, engineering, and health economics. The book addresses a similarly broad audience ranging from professionals that need to know more about this novel treatment modality or consider to enter the field of ion beam therapy as a researcher. However, it is also written for the interested public an...

  3. Proteomic analysis of streptomycin resistant and sensitive clinical isolates of Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Venkatesan Krishnamurthy

    2010-11-01

    Full Text Available Abstract Background Streptomycin (SM is a broad spectrum antibiotic and is an important component of any anti-tuberculosis therapy regimen. Several mechanisms have been proposed to explain the emergence of resistance but still our knowledge is inadequate. Proteins form a very complex network and drugs are countered by their modification/efflux or over expression/modification of targets. As proteins manifest most of the biological processes, these are attractive targets for developing drugs, immunodiagnostics or therapeutics. The aim of present study was to analyze and compare the protein profile of whole cell extracts from Mycobacterium tuberculosis clinical isolates susceptible and resistant to SM. Results Two-dimensional gel electrophoresis (2DE and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF mass spectrometry was employed for analyzing the protein profiles. Homology and in silico characterization for identified proteins was assessed using BLAST, InterProScan and KEGG database searches. Computational studies on the possible interactions between SM and identified proteins were carried out by a battery of online servers and softwares, namely, CLUSTALW (KEGG, I-TASSER, VMD, PatchDock and FireDock. On comparing 2DE patterns, nine proteins were found consistently overexpressed in SM resistant isolates and were identified as Rv0350, Rv0440, Rv1240, Rv3075c, Rv2971, Rv3028c, Rv2145c, Rv2031c and Rv0569. In silico docking analysis showed significant interactions of SM with essential (Rv0350, Rv0440 and Rv2971 and non essential (Rv1240, Rv3075c and Rv2031c genes. Conclusions The computational results suggest high protein binding affinity of SM and suggested many possible interactions between identified proteins and the drug. Bioinformatic analysis proves attributive for analysis of diversity of proteins identified by whole proteome analysis. In-depth study of the these proteins will give an insight into probable sites of drug

  4. Application for proteomic techniques in studying osteoarthritis: a review

    Directory of Open Access Journals (Sweden)

    YvesHenrotin

    2011-12-01

    Full Text Available After the genomic era, proteomic corresponds to a wide variety of techniques to study the protein content of cells, tissue or organism and to isolate protein of interest. It offers the choice between gel-based and gel-free methods or shotgun proteomics. Applications of proteomic technology may concern three principal objectives in several biomedical or clinical domains of research as in osteoarthritis: (i to understand the physiopathology and underlying mechanisms leading to a disease or associated to a particular model, (ii, to find disease-specific biomarker and (iii to identify new therapeutic targets. This review aimed at gathering most of the data regarding the proteomic techniques and their applications to arthritis research. It also reported technical limitations and solutions, as for example for sample preparation. Proteomics open wide perspectives in biochemical research but many technical matters still remain to be solved.

  5. Clinical Proteomics: The Potentiality of Urine Analysis for Understanding Diabetic Nephropathy

    Directory of Open Access Journals (Sweden)

    Massimo Paple

    2013-07-01

    Full Text Available The incidence of diabetic nephropathy (DN is constantly rising in parallel with the prevalence of type 2 diabetes and has been predicted to double within the next 15 years. Albuminuria is considered the earliest putative diagnostic sign of diabetic renal damage but it is poorly associated to the complex histopathological picture of glomerular and tubular damage hence, up to now, the accurate diagnosis of the DN requires renal biopsy. The identification of new biomarkers of DN is an urgent need since the proper management of the DN patients requires early and unbiased diagnosis. The Proteomics approach to the study of the human disease allows a large-scale characterisation of the protein content of a biological sample, and its application to urine may be a challenging but powerful strategy to identify new DN biomarkers. In this review we discuss the main results of a decade of proteomic studies focused on the urinary investigation of diabetic nephropathy.

  6. Pan-proteomics, a concept for unifying quantitative proteome measurements when comparing closely-related bacterial strains.

    Science.gov (United States)

    Broadbent, James A; Broszczak, Daniel A; Tennakoon, Imalka U K; Huygens, Flavia

    2016-04-01

    The comparison of proteomes between genetically heterogeneous bacterial strains may offer valuable insights into physiological diversity and function, particularly where such variation aids in the survival and virulence of clinically-relevant strains. However, reports of such comparisons frequently fail to account for underlying genetic variance. As a consequence, the current knowledge regarding bacterial physiological diversity at the protein level may be incomplete or inaccurate. To address this, greater consideration must be given to the impact of genetic heterogeneity on proteome comparisons. This may be possible through the use of pan-proteomics, an analytical concept that permits the ability to qualitatively and quantitatively compare the proteomes of genetically heterogeneous organisms. Limited examples of this emerging technology highlight currently unmet analytical challenges. In this article we define pan-proteomics, where its value lies in microbiology, and discuss the technical considerations critical to its successful execution and potential future application. PMID:26889693

  7. [Challenge to the Development of Molecular Targeted Therapy against a Novel Target Candidate Identified by Antibody Proteomics Technology].

    Science.gov (United States)

    Nagano, Kazuya

    2016-01-01

    Disease proteomics that systemically analyzes and identifies differentially expressed proteins between healthy and diseased samples is a potentially useful approach for obtaining target proteins for drug development. To date, however, very few target proteins have been identified from this field. A key issue that remains to be resolved is how to correctly identify target proteins from a number of potential candidates. To circumvent this problem, we have developed "antibody proteomics technology" in which a single chain Fv phage antibody library is utilized for proteome analysis. Here, we describe the application of this technology by primarily focusing on Eph receptor A10 (EphA10), a novel breast cancer-related protein that is a promising target for antibody drugs. To establish an effective and safe targeted cancer therapy, it is important that the target is specifically expressed in cancer tissues. Therefore, we attempted to analyze the EphA10 expression profiles. Tissue microarray analysis showed that EphA10 was expressed in all subtypes of breast cancer containing triple negative breast cancer cases. On the other hand, EphA10 was only expressed in testis tissue among 36 kinds of normal tissues. Thus, EphA10 could be a highly cancer-specific protein, making it a promising target for female breast cancer patients. Finally, we examined the anti-tumor effect by anti-EphA10 antibody, aiming for the development of a novel EphA10 targeting therapy. Administration of the antibody showed that tumor volumes were significantly inhibited. Our results suggest that targeting EphA10 in breast cancer cases might be a promising new form of therapy. PMID:26831784

  8. Current application of proteomics in biomarker discovery for inflammatory bowel disease.

    Science.gov (United States)

    Chan, Patrick Py; Wasinger, Valerie C; Leong, Rupert W

    2016-02-15

    Recently, the field of proteomics has rapidly expanded in its application towards clinical research with objectives ranging from elucidating disease pathogenesis to discovering clinical biomarkers. As proteins govern and/or reflect underlying cellular processes, the study of proteomics provides an attractive avenue for research as it allows for the rapid identification of protein profiles in a biological sample. Inflammatory bowel disease (IBD) encompasses several heterogeneous and chronic conditions of the gastrointestinal tract. Proteomic technology provides a powerful means of addressing major challenges in IBD today, especially for identifying biomarkers to improve its diagnosis and management. This review will examine the current state of IBD proteomics research and its use in biomarker research. Furthermore, we also discuss the challenges of translating proteomic research into clinically relevant tools. The potential application of this growing field is enormous and is likely to provide significant insights towards improving our future understanding and management of IBD. PMID:26909226

  9. Proteomics Discovery of Disease Biomarkers

    OpenAIRE

    Mamoun Ahram; Petricoin, Emanuel F.

    2008-01-01

    Recent technological developments in proteomics have shown promising initiatives in identifying novel biomarkers of various diseases. Such technologies are capable of investigating multiple samples and generating large amount of data end-points. Examples of two promising proteomics technologies are mass spectrometry, including an instrument based on surface enhanced laser desorption/ionization, and protein microarrays. Proteomics data must, however, undergo analytical processing using bioinfo...

  10. Plasma proteomics to identify biomarkers - Application to cardiovascular diseases

    DEFF Research Database (Denmark)

    Beck, Hans Christian; Overgaard, Martin; Melholt Rasmussen, Lars

    , this technology may therefore identify new biomarkers that previously have not been associated with cardiovascular diseases. In this review, we summarize the key challenges and considerations, including strategies, recent discoveries and clinical applications in cardiovascular proteomics that may lead......There is an unmet need for new cardiovascular biomarkers. Despite this only few biomarkers for the diagnosis or screening of cardiovascular diseases have been implemented in the clinic. Thousands of proteins can be analysed in plasma by mass spectrometry-based proteomics technologies. Therefore...

  11. Plasma proteomics to identify biomarkers – application to cardiovascular diseases

    Directory of Open Access Journals (Sweden)

    Hans Christian Beck

    2015-06-01

    Full Text Available There is an unmet need for new cardiovascular biomarkers. Despite this only few biomarkers for the diagnosis or screening of cardiovascular diseases have been implemented in the clinic. Thousands of proteins can be analysed in plasma by mass spectrometry-based proteomics technologies. Therefore, this technology may therefore identify new biomarkers that previously have not been associated with cardiovascular diseases. In this review, we summarize the key challenges and considerations, including strategies, recent discoveries and clinical applications in cardiovascular proteomics that may lead to the discovery of novel cardiovascular biomarkers.

  12. Application of Proteomics in the Study of Tumor Metastasis

    Institute of Scientific and Technical Information of China (English)

    Zhen Cai; Jen-Fu Chiu; Qing-Yu He

    2004-01-01

    Tumor metastasis is the dominant cause of death in cancer patients. However, the molecular and cellular mechanisms underlying tumor metastasis are still elusive.The identification of protein molecules with their expressions correlated to the metastatic process would help to understand the metastatic mechanisms and thus facilitate the development of strategies for the therapeutic interventions and clinical management of cancer. Proteomics is a systematic research approach aiming to provide the global characterization of protein expression and function under given conditions. Proteomic technology has been widely used in biomarker discovery and pathogenetic studies including tumor metastasis. This article provides a brief review of the application of proteomics in identifying molecular factors in tumor metastasis process. The combination of proteomics with other experimental approaches in biochemistry, cell biology, molecular genetics and chemistry, together with the development of new technologies and improvements in existing method ologies will continue to extend its application in studying cancer metastasis.

  13. Proteomic expression of microfungal ripening starter Geotrichum candidum submitted to cold stress is strain-dependent: studies using 2d-dige technology and samespots software analysis.

    Science.gov (United States)

    Missous, Ghalia; Thammavongs, Bouachanh; Dieuleveux, Virginie; Houssin, Maryline; Henry, Joël; Panoff, Jean-Michel

    2012-01-01

    Geotrichum candidum is a micro-fungus widely used as a ripening starter in cheese making. In anthropogenic environments such as dairy industries, this microorganism is subjected to many environmental and technological stresses including low temperature exposure. Our aim was to study the proteomic response of G. candidum to cold stress using a comparative proteomic approach by two-dimensional Differential In Gel Electrophoresis (2D DIGE). This technique consists on the labeling of proteins by specific fluorescent dyes (CyDyes). The results, obtained with G. candidum cells subjected to cold temperature, show significant proteomic patterns differences compared with the standard conditions. Furthermore, this biochemical response seems strain specific. 2D DIGE technology combined with SameSpots™ software analysis support these results through an important statistical validity. The comparative studies in a single gel, using two different fluorescent CyDyes (Cy3 and Cy5), lead to proteins differentiation. Selected spots were treated and analyzed by mass spectrometry. PMID:22987240

  14. Mass Spectrometry-Based Proteomics for Translational Research: A Technical Overview

    OpenAIRE

    Kadiyala, Vivek; Paulo, Joao A.; Banks, Peter Alan; Steen, Hanno; Conwell, Darwin Lewis

    2012-01-01

    Mass spectrometry-based investigation of clinical samples enables the high-throughput identification of protein biomarkers. We provide an overview of mass spectrometry-based proteomic techniques that are applicable to the investigation of clinical samples. We address sample collection, protein extraction and fractionation, mass spectrometry modalities, and quantitative proteomics. Finally, we examine the limitations and further potential of such technologies. Liquid chromatography fractionati...

  15. Biomarkers in Transplantation-Proteomics and Metabolomics.

    Science.gov (United States)

    Christians, Uwe; Klawitter, Jelena; Klawitter, Jost

    2016-04-01

    Modern multianalyte "omics" technologies allow for the identification of molecular signatures that confer significantly more information than measurement of a single parameter as typically used in current medical diagnostics. Proteomics and metabolomics bioanalytical assays capture a large set of proteins and metabolites in body fluids, cells, or tissues and, complementing genomics, assess the phenome. Proteomics and metabolomics contribute to the development of novel predictive clinical biomarkers in transplantation in 2 ways: they can be used to generate a diagnostic fingerprint or they can be used to discover individual proteins and metabolites of diagnostic potential. Much fewer metabolomics than proteomics biomarker studies in transplant patients have been reported, and, in contrast to proteomics discovery studies, new lead metabolite markers have yet to emerge. Most clinical proteomics studies have been discovery studies. Several of these studies have assessed diagnostic sensitivity and specificity. Nevertheless, none of these newly discovered protein biomarkers have yet been implemented in clinical decision making in transplantation. The currently most advanced markers discovered in proteomics studies in transplant patients are the chemokines CXCL-9 and CXCL-10, which have successfully been validated in larger multicenter trials in kidney transplant patients. These chemokines can be measured using standard immunoassay platforms, which should facilitate clinical implementation. Based on the published evidence, it is reasonable to expect that these chemokine markers can help guiding and individualizing immunosuppressive regimens, may be able to predict acute and chronic T-cell-mediated and antibody-mediated rejection, and may be useful tools for risk stratification of kidney transplant patients. PMID:26418702

  16. Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns.

    Science.gov (United States)

    Jhingan, Gagan Deep; Kumari, Sangeeta; Jamwal, Shilpa V; Kalam, Haroon; Arora, Divya; Jain, Neharika; Kumaar, Lakshmi Krishna; Samal, Areejit; Rao, Kanury V S; Kumar, Dhiraj; Nandicoori, Vinay Kumar

    2016-07-01

    Mycobacterium tuberculosis is an adaptable intracellular pathogen, existing in both dormant as well as active disease-causing states. Here, we report systematic proteomic analyses of four strains, H37Ra, H37Rv, and clinical isolates BND and JAL, to determine the differences in protein expression patterns that contribute to their virulence and drug resistance. Resolution of lysates of the four strains by liquid chromatography, coupled to mass spectrometry analysis, identified a total of 2161 protein groups covering ∼54% of the predicted M. tuberculosis proteome. Label-free quantification analysis of the data revealed 257 differentially expressed protein groups. The differentially expressed protein groups could be classified into seven K-means cluster bins, which broadly delineated strain-specific variations. Analysis of the data for possible mechanisms responsible for drug resistance phenotype of JAL suggested that it could be due to a combination of overexpression of proteins implicated in drug resistance and the other factors. Expression pattern analyses of transcription factors and their downstream targets demonstrated substantial differential modulation in JAL, suggesting a complex regulatory mechanism. Results showed distinct variations in the protein expression patterns of Esx and mce1 operon proteins in JAL and BND strains, respectively. Abrogating higher levels of ESAT6, an important Esx protein known to be critical for virulence, in the JAL strain diminished its virulence, although it had marginal impact on the other strains. Taken together, this study reveals that strain-specific variations in protein expression patterns have a meaningful impact on the biology of the pathogen. PMID:27151218

  17. Quantitative proteomic analysis of ofloxacin resistant and sensitive clinical isolates of Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Xiang-yu HUANG

    2014-10-01

    Full Text Available Objective To identify the proteins related to ofloxacin (OFX resistance of Mycobacterium tuberculosis (MTB. Methods Standard MTB H37Rv strain, clinical isolates of OFX resistant strain (OFXR and sensitive strain (OFXS were obtained from the Chinese Center for Disease Control and Prevention, and they were cultured in Sauton's medium, and then inactivated by 60Co. Whole cellular proteins were extracted from OFXR, OFXS and H37Rv strain of MTB, respectively. The peptides were labeled, separated and identified by isobaric tags of relative and absolute quantitation (iTRAQ combined with Nano LCMS/MS technology. Results One hundred and seventy-five and 134 differential expression proteins were identified in MTB OFXR compared with MTB OFXS and H37Rv, respectively. One hundred and four common differential expression proteins were identified in MTB OFXR compared with both MTB OFXS and H37Rv. The isoelectric point and theoretic relative molecular mass of differential expression proteins were widely distributed. The majority of the common differential expression proteins were involved in intermediary metabolism, respiration, and lipid metabolism. Twelve common differential expression proteins showed significant differences (the ratio>1.2 or <0.55 in MTB OFXR, including Rv0106, Rv0895, Rv2185c, Rv3248c and Rv3841 up-regulation and Rv2524c, Rv2986c, Rv3118 and Rv3597c down-regulation. Conclusion iTRAQ has been used to identify the common differential expression proteins in MTB OFXR compared with both MTB OFXS and H37Rv, which provides a basis for further study of the mechanism of OFX-resistance. DOI: 10.11855/j.issn.0577-7402.2014.09.06

  18. Feasibility study on blood sample investigations from former Wismut employees with respect to possible biomarkers for arsenic or radiation exposure using proteomics and cDNA microarray technologies. Final report

    International Nuclear Information System (INIS)

    The final report on the feasibility of blood sample investigations from former Wismut employees with respect to possible biomarkers for arsenic or radiation exposure using proteomics and cDNA microarray technologies covers the following topics: blood samples; methodologies: 2D gel electrophoresis; protein identification using MALDI-MS; accomplishment and evaluation of the proteomics and cDNA microarray analysis.

  19. Technology Deployment to Improve Clinical Outcomes

    Institute of Scientific and Technical Information of China (English)

    TM Judd; L Jacobs; M Jansen; B Birch

    2016-01-01

    2015年10月21日,《中国医疗设备》杂志社独家承办了“第一届国际临床工程与医疗技术管理大会”(ICEHTMC 2015),大会主席由美国FDA医疗设备顾问委员会主席、美国临床医学工程学会主席Yadin David先生和301医院周丹主任共同担任。来自14个国家的临床医学工程学会的主席、23个国家的60多位医学工程的领军人物、世界卫生组织医疗器械委员会的协调员及国内580多医工专家与会交流,共同搭建世界临床医学工程的学术平台。%Improved child, newborn, and maternal health (CNM) is a top priority in developing countries. Many factors must be addressed simultaneously to improve clinical outcomes for CNM. A public-private project in Haiti that will deploy the World Health Organization (WHO) evidence-based medicine (EBM) and essential interventions utilizing CNM healthcare technologies (HT), is expected to be a model for improving national health systems. The CNM mortality rates in Haiti are the highest in the western hemisphere with rates similar to those found in Afghanistan and several African countries. Several factors perpetuating this crisis are noted, as well as the most cost-effective interventions proven to decrease CNM mortality rates in low-and middle-income countries. To create major change in health system infrastructure, two strategies are presented, requiring appropriate and leading-edge health technologies (HT),e.g., wireless cellular-network-based Telemedicine (TM): (1) Development of a countrywide network of geographical“Community Care Grids” to facilitate implementation of frontline interventions; (2) The construction of a central hospital (called Bethesda Referral and Teaching Hospital-BRTH NGO) that will provide secondary and tertiary care for communities throughout the country, including helping local hospitals and clinics practice EBM care. We believe that these strategies-supported by HT will fast track improvement in

  20. Technology Deployment to Improve Clinical Outcomes

    Institute of Scientific and Technical Information of China (English)

    TM Judd; L Jacobs; M Jansen; B Birch

    2016-01-01

    Improved child, newborn, and maternal health (CNM) is a top priority in developing countries. Many factors must be addressed simultaneously to improve clinical outcomes for CNM. A public-private project in Haiti that will deploy the World Health Organization (WHO) evidence-based medicine (EBM) and essential interventions utilizing CNM healthcare technologies (HT), is expected to be a model for improving national health systems. The CNM mortality rates in Haiti are the highest in the western hemisphere with rates similar to those found in Afghanistan and several African countries. Several factors perpetuating this crisis are noted, as well as the most cost-effective interventions proven to decrease CNM mortality rates in low-and middle-income countries. To create major change in health system infrastructure, two strategies are presented, requiring appropriate and leading-edge health technologies (HT),e.g., wireless cellular-network-based Telemedicine (TM): (1) Development of a countrywide network of geographical“Community Care Grids” to facilitate implementation of frontline interventions; (2) The construction of a central hospital (called Bethesda Referral and Teaching Hospital-BRTH NGO) that will provide secondary and tertiary care for communities throughout the country, including helping local hospitals and clinics practice EBM care. We believe that these strategies-supported by HT will fast track improvement in CNM mortality rates throughout the country and that in a relatively short period of time Haiti’s health care system will be among the leaders in the region. Primary factors contributing to the CNM crisis, all addressed by TM: (1) Limited access: demographics, geography, cost, transportation; (2) Inadequate health care facilities: less than 20 NICU beds for 10 million population; BRTH to provide 80 bed NICU and 40 bed PICU in 225 bed hospital; (3) Health care practitioners: inadequate numbers and training; (4) Low% of skilled attendants now at

  1. [Impact of digital technology on clinical practices: perspectives from surgery].

    Science.gov (United States)

    Zhang, Y; Liu, X J

    2016-04-01

    Digital medical technologies or computer aided medical procedures, refer to imaging, 3D reconstruction, virtual design, 3D printing, navigation guided surgery and robotic assisted surgery techniques. These techniques are integrated into conventional surgical procedures to create new clinical protocols that are known as "digital surgical techniques". Conventional health care is characterized by subjective experiences, while digital medical technologies bring quantifiable information, transferable data, repeatable methods and predictable outcomes into clinical practices. Being integrated into clinical practice, digital techniques facilitate surgical care by improving outcomes and reducing risks. Digital techniques are becoming increasingly popular in trauma surgery, orthopedics, neurosurgery, plastic and reconstructive surgery, imaging and anatomic sciences. Robotic assisted surgery is also evolving and being applied in general surgery, cardiovascular surgery and orthopedic surgery. Rapid development of digital medical technologies is changing healthcare and clinical practices. It is therefore important for all clinicians to purposefully adapt to these technologies and improve their clinical outcomes. PMID:27117211

  2. Clinical Validation of Quantum Dot Barcode Diagnostic Technology.

    Science.gov (United States)

    Kim, Jisung; Biondi, Mia J; Feld, Jordan J; Chan, Warren C W

    2016-04-26

    There has been a major focus on the clinical translation of emerging technologies for diagnosing patients with infectious diseases, cancer, heart disease, and diabetes. However, most developments still remain at the academic stage where researchers use spiked target molecules to demonstrate the utility of a technology and assess the analytical performance. This approach does not account for the biological complexities and variabilities of human patient samples. As a technology matures and potentially becomes clinically viable, one important intermediate step in the translation process is to conduct a full clinical validation of the technology using a large number of patient samples. Here, we present a full detailed clinical validation of Quantum Dot (QD) barcode technology for diagnosing patients infected with Hepatitis B Virus (HBV). We further demonstrate that the detection of multiple regions of the viral genome using multiplexed QD barcodes improved clinical sensitivity from 54.9-66.7% to 80.4-90.5%, and describe how to use QD barcodes for optimal clinical diagnosis of patients. The use of QDs in biology and medicine was first introduced in 1998 but has not reached clinical care. This study describes our long-term systematic development strategy to advance QD technology to a clinically feasible product for diagnosing patients. Our "blueprint" for translating the QD barcode research concept could be adapted for other nanotechnologies, to efficiently advance diagnostic techniques discovered in the academic laboratory to patient care. PMID:27035744

  3. Notice of Changes to RFA-CA-15-022 and Pre-Application Webinar - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute will hold a public pre-application webinar on Wednesday, January 13, 2016 at 12:00 p.m. (EST) for the Funding Opportunity Announcement (FOA) RFA-CA-15-022 entitled “Proteogenomic Translational Research Centers for Clinical Proteomic Tumor Analysis Consortium (U01).” A major change for RFA-CA-15-022 is the new application due date (now May 11, 2016).

  4. Proteomic analysis of hippocampal dentate granule cells in frontotemporal lobar degeneration: Application of laser capture technology.

    Directory of Open Access Journals (Sweden)

    YairM.Gozal

    2011-04-01

    Full Text Available Frontotemporal lobar degeneration (FTLD is the most common cause of dementia with pre-senile onset, accounting for as many as 20% of cases. A common subset of FTLD cases is characterized by the presence of ubiquitinated inclusions in vulnerable neurons (FTLD-U. While the pathophysiological mechanisms underlying neurodegeneration in FTLD-U have not yet been elucidated, the presence of inclusions in this disease indicates enhanced aggregation of one or several proteins. Moreover, these inclusions suggest altered expression, processing, or degradation of proteins during FTLD-U pathogenesis. Thus, one approach to understanding disease mechanisms is to delineate the molecular changes in protein composition in FTLD-U brain. Using a combined approach consisting of laser capture microdissection (LCM and high resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS, we identified 1252 proteins in hippocampal dentate granule cells excised from three post-mortem FTLD-U and three unaffected control cases processed in parallel. Additionally, we employed a labeling-free quantification technique to compare the abundance of the identified proteins between FTLD-U and control cases. Quantification revealed 54 proteins with selective enrichment in FTLD-U, including TAR DNA binding protein 43 (TDP-43, a recently identified component of ubiquitinated inclusions. Moreover, 19 proteins were selectively decreased in FTLD-U. Subsequent immunohistochemical analysis of TDP-43 and three additional protein candidates suggests that our proteomic profiling of FTLD-U dentate granule cells reveals both inclusion-associated proteins and non-aggregated disease-specific proteins. Application of LCM is a valuable tool in the molecular analysis of complex tissues, and its application in the proteomic characterization of neurodegenerative disorders such as FTLD-U may be used to identify proteins altered in disease.

  5. Clinical operations generation next… The age of technology and outsourcing

    Directory of Open Access Journals (Sweden)

    Priya Temkar

    2015-01-01

    Full Text Available Huge cost pressures and the need to drive faster approvals has driven a technology transformation in the clinical trial (CT industry. The CT industry is thus leveraging mobile data, cloud computing, social media, robotic automation, and electronic source to drive efficiencies in a big way. Outsourcing of clinical operations support services to technology companies with a clinical edge is gaining tremendous importance. This paper provides an overview of current technology trends, applicable Food and Drug Administration (FDA guidelines, basic challenges that the pharma industry is facing in trying to implement such changes and its shift towards outsourcing these services to enable it to focus on site operations.

  6. Biomarkers of HIV-1 associated dementia: proteomic investigation of sera

    Directory of Open Access Journals (Sweden)

    Duan Fenghai

    2009-03-01

    Full Text Available Abstract Background New, more sensitive and specific biomarkers are needed to support other means of clinical diagnosis of neurodegenerative disorders. Proteomics technology is widely used in discovering new biomarkers. There are several difficulties with in-depth analysis of human plasma/serum, including that there is no one proteomic platform that can offer complete identification of differences in proteomic profiles. Another set of problems is associated with heterogeneity of human samples in addition intrinsic variability associated with every step of proteomic investigation. Validation is the very last step of proteomic investigation and it is very often difficult to validate potential biomarker with desired sensitivity and specificity. Even though it may be possible to validate a differentially expressed protein, it may not necessarily prove to be a valid diagnostic biomarker. Results In the current study we report results of proteomic analysis of sera from HIV-infected individuals with or without cognitive impairment. Application of SELDI-TOF analysis followed by weak cation exchange chromatography and 1-dimensional electrophoresis led to discovery of gelsolin and prealbumin as differentially expressed proteins which were not detected in this cohort of samples when previously investigated by 2-dimensional electrophoresis with Difference Gel Electrophoresis technology. Conclusion Validation using western-blot analysis led us to conclude that relative change of the levels of these proteins in one patient during a timeframe might be more informative, sensitive and specific than application of average level estimated based on an even larger cohort of patients.

  7. Nanocrystal technology, drug delivery and clinical applications

    OpenAIRE

    Junghanns, Jens-Uwe A H; Müller, Rainer H.

    2008-01-01

    Nanotechnology will affect our lives tremendously over the next decade in very different fields, including medicine and pharmacy. Transfer of materials into the nanodimension changes their physical properties which were used in pharmaceutics to develop a new innovative formulation principle for poorly soluble drugs: the drug nanocrystals. The drug nanocrystals do not belong to the future; the first products are already on the market. The industrially relevant production technologies, pearl mi...

  8. Nanocrystal technology, drug delivery and clinical applications

    OpenAIRE

    Jens-Uwe A H Junghanns Rainer H Müller

    2008-01-01

    Jens-Uwe A H Junghanns, Rainer H MüllerDepartment of Pharmaceutical Technology, Biotechnology and Quality Management, Free University of Berlin, Berlin, GermanyAbstract: Nanotechnology will affect our lives tremendously over the next decade in very different fields, including medicine and pharmacy. Transfer of materials into the nanodimension changes their physical properties which were used in pharmaceutics to develop a new innovative formulation principle for poorly soluble drugs: ...

  9. Funding Opportunities Available for Innovative SBIR Development - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Does your small business need early-stage financing to take its cancer research to the next level? The National Cancer Institute Small Business Innovation Research (NCI SBIR) Development Center has released $5 million for new contract funding opportunities to support cancer research and technology development in key emerging areas of need.

  10. Technology breakthrough and clinic application of gemstone CT

    International Nuclear Information System (INIS)

    Gemstone CT breaks through the conventional CT development model of expending detector's width over the past decade. By gemstone detector and spectral imaging technology, it could provide higher diagnostic accuracy, quicker diagnosis speed and higher definition of imaging, and better meet comprehensive clinical needs than conventional CT. To summarize technical breakthrough and clinical application of Gemstone CT. (authors)

  11. Targeted Proteomics of Human Metapneumovirus in Clinical Samples and Viral Cultures.

    Science.gov (United States)

    Foster, Matthew W; Gerhardt, Geoff; Robitaille, Lynda; Plante, Pier-Luc; Boivin, Guy; Corbeil, Jacques; Moseley, M Arthur

    2015-10-20

    The rapid, sensitive, and specific identification of infectious pathogens from clinical isolates is a critical need in the hospital setting. Mass spectrometry (MS) has been widely adopted for identification of bacterial pathogens, although polymerase chain reaction remains the mainstay for the identification of viral pathogens. Here, we explored the capability of MS for the detection of human metapneumovirus (HMPV), a common cause of respiratory tract infections in children. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) sequencing of a single HMPV reference strain (CAN97-83) was used to develop a multiple reaction monitoring (MRM) assay that employed stable isotope-labeled peptide internal standards for quantitation of HMPV. Using this assay, we confirmed the presence of HMPV in viral cultures from 10 infected patients and further assigned genetic lineage based on the presence/absence of variant peptides belonging to the viral matrix and nucleoproteins. Similar results were achieved for primary clinical samples (nasopharyngeal aspirates) from the same individuals. As validation, virus lineages, and variant coding sequences, were confirmed by next-generation sequencing of viral RNA obtained from the culture samples. Finally, separate dilution series of HMPV A and B lineages were used to further refine and assess the robustness of the assay and to determine limits of detection in nasopharyngeal aspirates. Our results demonstrate the applicability of MRM for identification of HMPV, and assignment of genetic lineage, from both viral cultures and clinical samples. More generally, this approach should prove tractable as an alternative to nucleic-acid based sequencing for the multiplexed identification of respiratory virus infections. PMID:26376123

  12. Effects of fluconazole on the secretome, the wall proteome, and wall integrity of the clinical fungus Candida albicans.

    Science.gov (United States)

    Sorgo, Alice G; Heilmann, Clemens J; Dekker, Henk L; Bekker, Martijn; Brul, Stanley; de Koster, Chris G; de Koning, Leo J; Klis, Frans M

    2011-08-01

    Fluconazole is a commonly used antifungal drug that inhibits Erg11, a protein responsible for 14α-demethylation during ergosterol synthesis. Consequently, ergosterol is depleted from cellular membranes and replaced by toxic 14α-methylated sterols, which causes increased membrane fluidity and drug permeability. Surface-grown and planktonic cultures of Candida albicans responded similarly to fluconazole at 0.5 mg/liter, showing reduced biomass formation, severely reduced ergosterol levels, and almost complete inhibition of hyphal growth. There was no evidence of cell leakage. Mass spectrometric analysis of the secretome showed that its composition was strongly affected and included 17 fluconazole-specific secretory proteins. Relative quantification of (14)N-labeled query walls relative to a reference standard mixture of (15)N-labeled yeast and hyphal walls in combination with immunological analysis revealed considerable fluconazole-induced changes in the wall proteome as well. They were, however, similar for both surface-grown and planktonic cultures. Two major trends emerged: (i) decreased incorporation of hypha-associated wall proteins (Als3, Hwp1, and Plb5), consistent with inhibition of hyphal growth, and (ii) increased incorporation of putative wall repair-related proteins (Crh11, Pga4, Phr1, Phr2, Pir1, and Sap9). As exposure to the wall-perturbing drug Congo red led to a similar response, these observations suggested that fluconazole affects the wall. In keeping with this, the resistance of fluconazole-treated cells to wall-perturbing compounds decreased. We propose that fluconazole affects the integrity of both the cellular membranes and the fungal wall and discuss its potential consequences for antifungal therapy. We also present candidate proteins from the secretome for clinical marker development. PMID:21622905

  13. Genomics and proteomics: Applications in autoimmune diseases

    Directory of Open Access Journals (Sweden)

    Wolfgang Hueber

    2009-08-01

    Full Text Available Wolfgang Hueber1,2,3, William H Robinson1,21VA Palo Alto Health Care System, Palo Alto, CA, USA; 2Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; 3Novartis Institutes of Biomedical Research, Novartis, Basle, SwitzerlandAbstract: Tremendous progress has been made over the past decade in the development and refinement of genomic and proteomic technologies for the identification of novel drug targets and molecular signatures associated with clinically important disease states, disease subsets, or differential responses to therapies. The rapid progress in high-throughput technologies has been preceded and paralleled by the elucidation of cytokine networks, followed by the stepwise clinical development of pathway-specific biological therapies that revolutionized the treatment of autoimmune diseases. Together, these advances provide opportunities for a long-anticipated personalized medicine approach to the treatment of autoimmune disease. The ever-increasing numbers of novel, innovative therapies will need to be harnessed wisely to achieve optimal long-term outcomes in as many patients as possible while complying with the demands of health authorities and health care providers for evidence-based, economically sound prescription of these expensive drugs. Genomic and proteomic profiling of patients with autoimmune diseases holds great promise in two major clinical areas: (1 rapid identification of new targets for the development of innovative therapies and (2 identification of patients who will experience optimal benefit and minimal risk from a specific (targeted therapy. In this review, we attempt to capture important recent developments in the application of genomic and proteomic technologies to translational research by discussing informative examples covering a diversity of autoimmune diseases.Keywords: proteomics, genomics, autoimmune diseases, antigen microarrays, 2-Dih, rheumatoid arthritis

  14. Technology insight: metabonomics in gastroenterology-basic principles and potential clinical applications

    DEFF Research Database (Denmark)

    Bjerrum, Jacob Tveiten; Nielsen, Ole H; Wang, Yulan L;

    2008-01-01

    Metabonomics-the study of metabolic changes in an integrated biologic system-is an emerging field. This discipline joins the other 'omics' (genomics, transcriptomics and proteomics) to give rise to a comprehensive, systems-biology approach to the evaluation of holistic in vivo function. Metabonom...... metabonomics in basic and clinical research, with emphasis on applications in the field of gastroenterology....

  15. Proteomic analysis of tissue samples in translational breast cancer research

    DEFF Research Database (Denmark)

    Gromov, Pavel; Moreira, José; Gromova, Irina

    2014-01-01

    In the last decade, many proteomic technologies have been applied, with varying success, to the study of tissue samples of breast carcinoma for protein expression profiling in order to discover protein biomarkers/signatures suitable for: characterization and subtyping of tumors; early diagnosis, ...... translation of basic discoveries into the daily breast cancer clinical practice. In particular, we address major issues in experimental design by reviewing the strengths and weaknesses of current proteomic strategies in the context of the analysis of human breast tissue specimens....

  16. Innovative Clinical Assessment Technologies : Challenges and Opportunities in Neuroimaging

    OpenAIRE

    Miller, Gregory A.; Elbert, Thomas; Bradley P. Sutton; Heller, Wendy

    2010-01-01

    The authors review the reasons for the contrast between the remarkable advances that hemodynamic and electromagnetic imaging of the human brain appear capable of delivering in clinical practice in psychology and their very limited penetration into practice to date. Both the heritages of the relevant technologies and the historical orientation of clinical psychology away from biological phenomena are factors. Discussion of some technical aspects and prospects of these methods and recommendatio...

  17. Management Information System for Clinics with Cloud Technology

    OpenAIRE

    Nguyen Quang Tan

    2013-01-01

    This paper discusses the problems associated with the development of information management systems clinics. Presentation model of the system, which is based on a platform of technology cloud computing IBM SmartCloud and mobile phones. Giving the composition and structure of the clinics information management system that successfully support for user in managing patient information, medical history of the patients, the images for the diagnosis, prescriptions.

  18. Development of novel drug delivery systems using phage display technology for clinical application of protein drugs.

    Science.gov (United States)

    Nagano, Kazuya; Tsutsumi, Yasuo

    2016-01-01

    Attempts are being made to develop therapeutic proteins for cancer, hepatitis, and autoimmune conditions, but their clinical applications are limited, except in the cases of drugs based on erythropoietin, granulocyte colony-stimulating factor, interferon-alpha, and antibodies, owing to problems with fundamental technologies for protein drug discovery. It is difficult to identify proteins useful as therapeutic seeds or targets. Another problem in using bioactive proteins is pleiotropic actions through receptors, making it hard to elicit desired effects without side effects. Additionally, bioactive proteins have poor therapeutic effects owing to degradation by proteases and rapid excretion from the circulatory system. Therefore, it is essential to establish a series of novel drug delivery systems (DDS) to overcome these problems. Here, we review original technologies in DDS. First, we introduce antibody proteomics technology for effective selection of proteins useful as therapeutic seeds or targets and identification of various kinds of proteins, such as cancer-specific proteins, cancer metastasis-related proteins, and a cisplatin resistance-related protein. Especially Ephrin receptor A10 is expressed in breast tumor tissues but not in normal tissues and is a promising drug target potentially useful for breast cancer treatment. Moreover, we have developed a system for rapidly creating functional mutant proteins to optimize the seeds for therapeutic applications and used this system to generate various kinds of functional cytokine muteins. Among them, R1antTNF is a TNFR1-selective antagonistic mutant of TNF and is the first mutein converted from agonist to antagonist. We also review a novel polymer-conjugation system to improve the in vivo stability of bioactive proteins. Site-specific PEGylated R1antTNF is uniform at the molecular level, and its bioactivity is similar to that of unmodified R1antTNF. In the future, we hope that many innovative protein drugs will be

  19. Innovative Clinical Assessment Technologies: Challenges and Opportunities in Neuroimaging

    Science.gov (United States)

    Miller, Gregory A.; Elbert, Thomas; Sutton, Bradley P.; Heller, Wendy

    2007-01-01

    The authors review the reasons for the contrast between the remarkable advances that hemodynamic and electromagnetic imaging of the human brain appear capable of delivering in clinical practice in psychology and their very limited penetration into practice to date. Both the heritages of the relevant technologies and the historical orientation of…

  20. Proteomics of boar seminal plasma - current studies and possibility of their application in biotechnology of animal reproduction.

    Science.gov (United States)

    Strzeżek, Jerzy; Wysocki, Paweł; Kordan, Władysław; Kuklińska, Magdalena; Mogielnicka, Marzena; Soliwoda, Daniel; Fraser, Leyland

    2005-11-01

    Proteomics is critical to identify the properties and functions of proteins involved in the mechanism regulating the male reproductive tract function. This approach is important in male fertility assessment and clinical diagnosis of the physiological state of individual reproductive organs. Proteomics also provides a tool to understand the interactions of seminal plasma proteins with spermatozoa, which could provide a useful model for studying ligand-cell interaction occurring at the sperm cell surface. This review covers a selection of advances in the realm of functional proteomics of boar seminal plasma proteins and is focused on some fundamental proteomic technologies. Also, this review explores key themes in proteomics and their application in animal reproductive techniques. PMID:16372045

  1. Designing healthcare information technology to catalyse change in clinical care.

    Science.gov (United States)

    Lester, William T; Zai, Adrian H; Grant, Richard W; Chueh, Henry C

    2008-01-01

    The gap between best practice and actual patient care continues to be a pervasive problem in our healthcare system. Efforts to improve on this knowledge-performance gap have included computerised disease management programs designed to improve guideline adherence. However, current computerised reminder and decision support interventions directed at changing physician behaviour have had only a limited and variable effect on clinical outcomes. Further, immediate pay-for-performance financial pressures on institutions have created an environment where disease management systems are often created under duress, appended to existing clinical systems and poorly integrated into the existing workflow, potentially limiting their real-world effectiveness. The authors present a review of disease management as well as a conceptual framework to guide the development of more effective health information technology (HIT) tools for translating clinical information into clinical action. PMID:18534073

  2. Designing healthcare information technology to catalyse change in clinical care

    Directory of Open Access Journals (Sweden)

    William Lester

    2008-05-01

    Full Text Available The gap between best practice and actual patient care continues to be a pervasive problem in our healthcare system. Efforts to improve on this knowledge_performance gap have included computerised disease management programs designed to improve guideline adherence. However, current computerised reminder and decision support interventions directed at changing physician behaviour have had only a limited and variable effect on clinical outcomes. Further, immediate pay-for-performance financial pressures on institutions have created an environmentwhere disease management systems are often created under duress, appended to existing clinical systems and poorly integrated into the existing workflow, potentially limiting their realworld effectiveness. The authors present a review of disease management as well as a conceptual framework to guide the development of more effective health information technology (HIT tools for translating clinical information into clinical action.

  3. New technologies in proteomics: automated excision and digestion of fluorescently stained protein gel spots and identification of proteins by MALDI-QTOF mass spectrometry

    International Nuclear Information System (INIS)

    This presentation is an overview of the techniques and systems we use for large-scale proteomics in plants. This includes a variety of 2D gel electrophoresis methods, and automation of spot-cutting, in-gel digestion, nanoLC-MS/MS tandem mass spectrometry and SEQUEST based protein identification. Examples and applications of several new technologies will also be shown, including the use of a robotic spot cutter in conjunction with high sensitivity fluorescent protein staining and the identification of proteins by redundant peptide identification in a high-throughput fashion using a hybrid MALDI-Qtof mass spectrometer

  4. Proteomics in uveal melanoma.

    LENUS (Irish Health Repository)

    Ramasamy, Pathma

    2014-01-01

    Uveal melanoma is the most common primary intraocular malignancy in adults, with an incidence of 5-7 per million per year. It is associated with the development of metastasis in about 50% of cases, and 40% of patients with uveal melanoma die of metastatic disease despite successful treatment of the primary tumour. The survival rates at 5, 10 and 15 years are 65%, 50% and 45% respectively. Unlike progress made in many other areas of cancer, uveal melanoma is still poorly understood and survival rates have remained similar over the past 25 years. Recently, advances made in molecular genetics have improved our understanding of this disease and stratification of patients into low risk and high risk for developing metastasis. However, only a limited number of studies have been performed using proteomic methods. This review will give an overview of various proteomic technologies currently employed in life sciences research, and discuss proteomic studies of uveal melanoma.

  5. Autoimmune diagnostics: the technology, the strategy and the clinical governance.

    Science.gov (United States)

    Bizzaro, Nicola; Tozzoli, Renato; Villalta, Danilo

    2015-02-01

    In recent years, there has been a profound change in autoimmune diagnostics. From long, tiring and inaccurate manual methods, the art of diagnostics has turned to modern, rapid and automated technology. New antibody tests have been developed, and almost all autoimmune diseases now have some specific diagnostic markers. The current need to make the most of available economic and human resources has led to the production of diagnostic algorithms and guidelines designated for optimal strategic use of the tests and to increase the diagnostic appropriateness. An important role in this scenario was assumed by the laboratory autoimmunologist, whose task is not only to govern the analytical phase, but also to help clinicians in correctly choosing the most suitable test for each clinical situation and provide consultancy support. In this review, we summarize recent advances in technology, describe the diagnostic strategies and highlight the current role of the laboratory autoimmunologist in the clinical governance of autoimmune diagnostics. PMID:25398640

  6. What Is Cancer Proteomics?

    Science.gov (United States)

    ... What is Proteomics? Video Tutorial What is Cancer Proteomics? Print This Page The term "proteome" refers to ... that a cell or organism undergoes. The term "proteomics" is a large-scale comprehensive study of a ...

  7. Clinical utility of RapidArc™ radiotherapy technology

    Science.gov (United States)

    Infusino, Erminia

    2015-01-01

    RapidArc™ is a radiation technique that delivers highly conformal dose distributions through the complete rotation (360°) and speed variation of the linear accelerator gantry. This technique, called volumetric modulated arc therapy (VMAT), compared with conventional radiotherapy techniques, can achieve high-target volume coverage and sparing damage to normal tissues. RapidArc delivers precise dose distribution and conformity similar to or greater than intensity-modulated radiation therapy in a short time, generally a few minutes, to which image-guided radiation therapy is added. RapidArc has become a currently used technology in many centers, which use RapidArc technology to treat a large number of patients. Large and small hospitals use it to treat the most challenging cases, but more and more frequently for the most common cancers. The clinical use of RapidArc and VMAT technology is constantly growing. At present, a limited number of clinical data are published, mostly concerning planning and feasibility studies. Clinical outcome data are increasing for a few tumor sites, even if only a little. The purpose of this work is to discuss the current status of VMAT techniques in clinical use through a review of the published data of planning systems and clinical outcomes in several tumor sites. The study consisted of a systematic review based on analysis of manuscripts retrieved from the PubMed, BioMed Central, and Scopus databases by searching for the keywords “RapidArc”, “Volumetric modulated arc radiotherapy”, and “Intensity-modulated radiotherapy”. PMID:26648755

  8. Clinical utility of RapidArcTM radiotherapy technology

    Directory of Open Access Journals (Sweden)

    Infusino E

    2015-11-01

    Full Text Available Erminia Infusino Department of Radiotherapy, Campus Bio-Medico University Hospital, Rome, Italy Abstract: RapidArcTM is a radiation technique that delivers highly conformal dose distributions through the complete rotation (360° and speed variation of the linear accelerator gantry. This technique, called volumetric modulated arc therapy (VMAT, compared with conventional radiotherapy techniques, can achieve high-target volume coverage and sparing damage to normal tissues. RapidArc delivers precise dose distribution and conformity similar to or greater than intensity-modulated radiation therapy in a short time, generally a few minutes, to which image-guided radiation therapy is added. RapidArc has become a currently used technology in many centers, which use RapidArc technology to treat a large number of patients. Large and small hospitals use it to treat the most challenging cases, but more and more frequently for the most common cancers. The clinical use of RapidArc and VMAT technology is constantly growing. At present, a limited number of clinical data are published, mostly concerning planning and feasibility studies. Clinical outcome data are increasing for a few tumor sites, even if only a little. The purpose of this work is to discuss the current status of VMAT techniques in clinical use through a review of the published data of planning systems and clinical outcomes in several tumor sites. The study consisted of a systematic review based on analysis of manuscripts retrieved from the PubMed, BioMed Central, and Scopus databases by searching for the keywords "RapidArc", "Volumetric modulated arc radiotherapy", and "Intensity-modulated radiotherapy". Keywords: IMRT, VMAT, SBRT, SRS, treatment planning software 

  9. New laser technologies in the clinic of neurosurgery

    Science.gov (United States)

    Stupak, V. V.; Fomichev, N. G.; Tsvetovsky, S. B.; Dmitriev, A. B.; Kobosev, V. V.; Bagaev, S. N.; Mayorov, A. P.; Struts, S. G.

    2005-08-01

    In report summarized more then 10 experience of authors in Novosibirsk Traumatology and orthopedics research institute Neurosurgery clinic on usage of laser technologies in treatment of central nervous system tumors. On the basis of ND-YAG laser application original technologies have been developed and used in surgical treatment of patients with various neurosurgical pathology and protected by 8 Patents of the Russian Federation. 427 patients were operated on with the use of YAG:Nd3+ laser. Out of them 152 patients had extracerebral tumors of various volume and localization, 135 patients - spinal cord tumors, 74 patients - a pathology of cerebrospinal transition (Amold-Chiari syndrome of 1-2 types), and 66 patients - intramedullary tumors of deep localization. Results showed good results of laser technologies usage for central nervous system tumors removal.

  10. Proteomics: an efficient tool to analyze nematode proteins

    Science.gov (United States)

    Proteomic technologies have been successfully used to analyze proteins structure and characterization in plants, animals, microbes and humans. We used proteomics methodologies to separate and characterize soybean cyst nematode (SCN) proteins. Optimizing the quantity of proteins required to separat...

  11. Proteomic-driven biomarker discovery in gestational diabetes mellitus: a review.

    Science.gov (United States)

    Singh, Apoorva; Subramani, Elavarasan; Datta Ray, Chaitali; Rapole, Srikanth; Chaudhury, Koel

    2015-09-01

    Gestational diabetes mellitus (GDM) is defined as any degree of glucose intolerance with onset or first recognition during pregnancy and it affects 18% of pregnant women worldwide. GDM is considered a high-risk state which may lead to type II diabetes which is associated with an increase in a number of interrelated adverse perinatal outcomes. Given the fact that the progress of a successful pregnancy is dependent on the intricate communication between several biological molecules, identification of the proteomic profile perturbations in women with GDM is expected to help in understanding the disease pathogenesis and also discovery of clinical biomarker(s). In recent years, both gel-free and gel-based proteomics have been extensively investigated for improving maternal and child health. Although there are several reports integrating various aspects of proteomics in pregnancy related diseases such as preeclampsia, extensive Pubmed search shows no review so far on the application of proteomics in gestational diabetes. In this review, we focus on various high-throughput proteomic technologies for the identification of unique biosignatures and biomarkers responsible for the early prediction of GDM. Further, different analytical strategies and biological samples involved in proteomic analysis of this pregnancy-related disease are discussed.This article is part of a Special Issue entitled: Proteomics in India. PMID:26216595

  12. The Role of Proteomics in Biomarker Development for Improved Patient Diagnosis and Clinical Decision Making in Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Claire L. Tonry

    2016-07-01

    Full Text Available Prostate Cancer (PCa is the second most commonly diagnosed cancer in men worldwide. Although increased expression of prostate-specific antigen (PSA is an effective indicator for the recurrence of PCa, its intended use as a screening marker for PCa is of considerable controversy. Recent research efforts in the field of PCa biomarkers have focused on the identification of tissue and fluid-based biomarkers that would be better able to stratify those individuals diagnosed with PCa who (i might best receive no treatment (active surveillance of the disease; (ii would benefit from existing treatments; or (iii those who are likely to succumb to disease recurrence and/or have aggressive disease. The growing demand for better prostate cancer biomarkers has coincided with the development of improved discovery and evaluation technologies for multiplexed measurement of proteins in bio-fluids and tissues. This review aims to (i provide an overview of these technologies as well as describe some of the candidate PCa protein biomarkers that have been discovered using them; (ii address some of the general limitations in the clinical evaluation and validation of protein biomarkers; and (iii make recommendations for strategies that could be adopted to improve the successful development of protein biomarkers to deliver improvements in personalized PCa patient decision making.

  13. Multiplexed immunofluorescence delineates proteomic cancer cell states associated with metabolism

    OpenAIRE

    Sood, Anup; Miller, Alexandra M.; Brogi, Edi; Sui, Yunxia; Armenia, Joshua; McDonough, Elizabeth; Santamaria-Pang, Alberto; Carlin, Sean; Stamper, Aleksandra; Campos, Carl; Pang, Zhengyu; Li, Qing; Port, Elisa; Graeber, Thomas G.; Schultz, Nikolaus

    2016-01-01

    The phenotypic diversity of cancer results from genetic and nongenetic factors. Most studies of cancer heterogeneity have focused on DNA alterations, as technologies for proteomic measurements in clinical specimen are currently less advanced. Here, we used a multiplexed immunofluorescence staining platform to measure the expression of 27 proteins at the single-cell level in formalin-fixed and paraffin-embedded samples from treatment-naive stage II/III human breast cancer. Unsupervised cluster...

  14. Novel Serial Positive Enrichment Technology Enables Clinical Multiparameter Cell Sorting

    Science.gov (United States)

    Tschulik, Claudia; Piossek, Christine; Bet, Jeannette; Yamamoto, Tori N.; Schiemann, Matthias; Neuenhahn, Michael; Martin, Klaus; Schlapschy, Martin; Skerra, Arne; Schmidt, Thomas; Edinger, Matthias; Riddell, Stanley R.; Germeroth, Lothar; Busch, Dirk H.

    2012-01-01

    A general obstacle for clinical cell preparations is limited purity, which causes variability in the quality and potency of cell products and might be responsible for negative side effects due to unwanted contaminants. Highly pure populations can be obtained best using positive selection techniques. However, in many cases target cell populations need to be segregated from other cells by combinations of multiple markers, which is still difficult to achieve – especially for clinical cell products. Therefore, we have generated low-affinity antibody-derived Fab-fragments, which stain like parental antibodies when multimerized via Strep-tag and Strep-Tactin, but can subsequently be removed entirely from the target cell population. Such reagents can be generated for virtually any antigen and can be used for sequential positive enrichment steps via paramagnetic beads. First protocols for multiparameter enrichment of two clinically relevant cell populations, CD4high/CD25high/CD45RAhigh ‘regulatory T cells’ and CD8high/CD62Lhigh/CD45RAneg ‘central memory T cells’, have been established to determine quality and efficacy parameters of this novel technology, which should have broad applicability for clinical cell sorting as well as basic research. PMID:22545138

  15. Novel serial positive enrichment technology enables clinical multiparameter cell sorting.

    Directory of Open Access Journals (Sweden)

    Christian Stemberger

    Full Text Available A general obstacle for clinical cell preparations is limited purity, which causes variability in the quality and potency of cell products and might be responsible for negative side effects due to unwanted contaminants. Highly pure populations can be obtained best using positive selection techniques. However, in many cases target cell populations need to be segregated from other cells by combinations of multiple markers, which is still difficult to achieve--especially for clinical cell products. Therefore, we have generated low-affinity antibody-derived Fab-fragments, which stain like parental antibodies when multimerized via Strep-tag and Strep-Tactin, but can subsequently be removed entirely from the target cell population. Such reagents can be generated for virtually any antigen and can be used for sequential positive enrichment steps via paramagnetic beads. First protocols for multiparameter enrichment of two clinically relevant cell populations, CD4(high/CD25(high/CD45RA(high 'regulatory T cells' and CD8(high/CD62L(high/CD45RA(neg 'central memory T cells', have been established to determine quality and efficacy parameters of this novel technology, which should have broad applicability for clinical cell sorting as well as basic research.

  16. Femtosecond laser cataract surgery: technology and clinical practice.

    Science.gov (United States)

    Roberts, Timothy V; Lawless, Michael; Chan, Colin Ck; Jacobs, Mark; Ng, David; Bali, Shveta J; Hodge, Chris; Sutton, Gerard

    2013-03-01

    The recent introduction of femtosecond lasers to cataract surgery has generated much interest among ophthalmologists around the world. Laser cataract surgery integrates high-resolution anterior segment imaging systems with a femtosecond laser, allowing key steps of the procedure, including the primary and side-port corneal incisions, the anterior capsulotomy and fragmentation of the lens nucleus, to be performed with computer-guided laser precision. There is emerging evidence of reduced phacoemulsification time, better wound architecture and a more stable refractive result with femtosecond cataract surgery, as well as reports documenting an initial learning curve. This article will review the current state of technology and discuss our clinical experience. PMID:22788831

  17. Wearable technology as a booster of clinical care

    Science.gov (United States)

    Jonas, Stephan; Hannig, Andreas; Spreckelsen, Cord; Deserno, Thomas M.

    2014-03-01

    Wearable technology defines a new class of smart devices that are accessories or clothing equipped with computational power and sensors, like Google Glass. In this work, we propose a novel concept for supporting everyday clinical pathways with wearable technology. In contrast to most prior work, we are not focusing on the omnipresent screen to display patient information or images, but are trying to maintain existing workflows. To achieve this, our system supports clinical staff as a documenting observer, only intervening adequately if problems are detected. Using the example of medication preparation and administration, a task known to be prone to errors, we demonstrate the full potential of the new devices. Patient and medication identifier are captured with the built-in camera, and the information is send to a transaction server. The server communicates with the hospital information system to obtain patient records and medication information. The system then analyses the new medication for possible side-effects and interactions with already administered drugs. The result is sent to the device while encapsulating all sensitive information respecting data security and privacy. The user only sees a traffic light style encoded feedback to avoid distraction. The server can reduce documentation efforts and reports in real-time on possible problems during medication preparation or administration. In conclusion, we designed a secure system around three basic principles with many applications in everyday clinical work: (i) interaction and distraction is kept as low as possible; (ii) no patient data is displayed; and (iii) device is pure observer, not part of the workflow. By reducing errors and documentation burden, our approach has the capability to boost clinical care.

  18. Proteomics analysis of human oligodendroglioma proteome.

    Science.gov (United States)

    Khaghani-Razi-Abad, Solmaz; Hashemi, Mehrdad; Pooladi, Mehdi; Entezari, Maliheh; Kazemi, Elham

    2015-09-10

    Proteomics analyses enable the identification and quantitation of proteins. From a purely clinical perspective, the application of proteomics based on innovations, may greatly affect the future management of malignant brain tumors. This optimism is based on four main reasons: diagnosis, prognosis, selection of targeted therapy based on molecular profile of the brain tumor and monitoring therapeutic response, or resistance. We extracted the proteins of tumor and normal brain tissues, and then evaluated the protein purity by Bradford test. In this study, we separated the proteins by two-dimensional (2DG) gel electrophoresis methods. Then spots were analyzed, compared using statistical data and specific software and were identified by pH isoelectric, molecular weights and data banks. The protein profiles were determined using 2D gel electrophoresis and MALDI TOF/TOF mass spectrometry approaches. Simple statistical tests were used to establish a putative hierarchy in which the change in protein level was ranked according to a cut-off point with pProteomics is a powerful way to identifying multiple proteins which are altered following a neuropharmacological intervention in a CNS disease. PMID:26002447

  19. 蛋白质组学技术在食品品质检测及鉴伪中的应用%Application of Proteomic Technology in Food Quality Detection and Authenticity Identification

    Institute of Scientific and Technical Information of China (English)

    赵方圆; 吴亚君; 韩建勋; 葛毅强; 陈颖

    2012-01-01

    Proteomics technologys has become the important support of the rapid development of modern biological technology, which have been widely applied in the research of food such as food function, quality evaluation, nutritional analysis, safety detection and authenticity identification. Proteomic techniques provide new thoughts and techniques for food science research and offer a very promising prospect. This paper outlines the concept and techniques of proteomics, analyzes the application of proteomic techniques in the food research, and outlooks the prospect of the development of proteomic techniques in food quality detection and authenticity identification.%蛋白质组学技术的发展已经成为现代生物技术快速发展的重要支撑,被广泛地应用到食品功能研究、品质评价、营养分析、安全检测及真伪鉴别等研究中,为食品科学相关研究提供了新的思路和技术,具有很好的发展前景.本文概述了蛋白质组学的概念及主要研究技术,分析了蛋白质组学技术在食品研究中的应用,展望了蛋白质组学技术在食品品质检测及鉴伪中的发展前景.

  20. Increasing clinical presence of mobile communication technology: avoiding the pitfalls.

    Science.gov (United States)

    Visvanathan, Akila; Gibb, Alan P; Brady, Richard R W

    2011-10-01

    Mobile communication technologies are employed in many diverse areas of healthcare delivery to provide improved quality and efficiency of communication and facilitate increased rapidity of data or information transfer. Mobile phones enable healthcare professionals to possess a portable platform from which to provide many healthcare-related applications and are a popular means to directly communicate with colleagues and patients. As involvement of mobile communication technology in healthcare delivery continues to rapidly expand, there are also important considerations of relevance to patient safety and security as a result. Here, we review the previous evidence of reported clinical risks associated with mobile communication technology, such as electromagnetic interference, confidentiality and data security, distraction/noise, infection control, and cross contamination. In conclusion, although mobile phones provide much putative potential improvement to healthcare delivery, further evaluation and research are required to both inform and protect health professionals and users of such technology in the healthcare environment and provide the evidence base to support the provision of clear and comprehensive guidelines. PMID:21780941

  1. Internet technology for clinical application in a digital radiology department

    International Nuclear Information System (INIS)

    Problem: To provide an overview and to assess the clinical feasibility of internet technology-based systems for hospital-wide image and report distribution as well as for video conferencing. Methods: The paper describes the theoretical concept behind, the various technical approaches and the experience gained from different systems. Results: Image and report distribution: Advantages include the universal availability of images and reports inside and outside hospitals; ease of use; security features; image and report integration; cost savings by reducing support and training efforts and by optimising available hardware. The main critical issues are performance and workflow integration with RIS and PACS. Video conferencing: Main advantages are the standardised, software-based approach and the low investments for hard- and software. Depending on the desired usage the communication performance can be seen as inappropriate. Conclusion: Today, internet technology-based systems appear to satisfy the main clinical needs in radiology. The mentioned drawbacks could be eliminated by means of modified software implementation and focused standardisation efforts. Considering the numerous advantages of these systems a further distribution can be expected for the future. (orig.)

  2. Drug delivery system innovation and Health Technology Assessment: Upgrading from Clinical to Technological Assessment.

    Science.gov (United States)

    Panzitta, Michele; Bruno, Giorgio; Giovagnoli, Stefano; Mendicino, Francesca R; Ricci, Maurizio

    2015-11-30

    Health Technology Assessment (HTA) is a multidisciplinary health political instrument that evaluates the consequences, mainly clinical and economical, of a health care technology; the HTA aim is to produce and spread information on scientific and technological innovation for health political decision making process. Drug delivery systems (DDS), such as nanocarriers, are technologically complex but they have pivotal relevance in therapeutic innovation. The HTA process, as commonly applied to conventional drug evaluation, should upgrade to a full pharmaceutical assessment, considering the DDS complexity. This is useful to study more in depth the clinical outcome and to broaden its critical assessment toward pharmaceutical issues affecting the patient and not measured by the current clinical evidence approach. We draw out the expertise necessary to perform the pharmaceutical assessment and we propose a format to evaluate the DDS technological topics such as formulation and mechanism of action, physicochemical characteristics, manufacturing process. We integrated the above-mentioned three points in the Evidence Based Medicine approach, which is data source for any HTA process. In this regard, the introduction of a Pharmaceutics Expert figure in the HTA could be fundamental to grant a more detailed evaluation of medicine product characteristics and performances and to help optimizing DDS features to overcome R&D drawbacks. Some aspects of product development, such as manufacturing processes, should be part of the HTA as innovative manufacturing processes allow new products to reach more effectively patient bedside. HTA so upgraded may encourage resource allocating payers to invest in innovative technologies and providers to focus on innovative material properties and manufacturing processes, thus contributing to bring more medicines in therapy in a sustainable manner. PMID:26399633

  3. Clinical application and future direction in PET technology

    International Nuclear Information System (INIS)

    This presentation describes that F-18 fluorodeoxyglucose (FDG) is crucial to play the major roles in patients with carcinoma in our institute. Positron emission tomography (PET) center consists of one cyclotron (18/9 Cyclone IBA) and PET scanner (Phillips) associated with GSO crystal. FDG-PET is employed to study approximately 3000 patients with carcinoma. We believe that our institute as cancer center in Fukuoka prefecture acts to give the more information prior to therapeutic management of patients in a clinical setting. First, the presentation describes the incidental finding before therapy, staging before surgery, chemotherapy, and radiotherapy, the therapeutic effect, the elevation of tumor marker, and the clinical application of FDG-PET in the novel therapy. As noted above, the presentation demonstrates, showing the clinical FDG-PET imaging, how to contribute to patients management. Second, the new PET technology has played for rapid advance in molecular imaging. The advantage of new technique in molecular biology and their integration into nuclear medicine provide a critical opportunity to improve the quality of diagnosis and treatment of many diseases. The presentation briefly addresses the history of molecular imaging and the role as monitoring gene therapy with reporter gene. (author)

  4. Centennial Paper: Proteomics in animal science

    Science.gov (United States)

    Proteomics holds significant promise as a method for advancing animal science research. The use of this technology in animal science is still in its infancy. The ability of proteomics to simultaneously identify and quantify potentially thousands of proteins is unparalleled. In this review, we wil...

  5. The promise of proteomics in animal science

    Science.gov (United States)

    Proteomics hold significant promise as a method for advancing animal science research. The use of this technology in animal science is still in its infancy. The ability of proteomics to simultaneously identify and quantify potentially thousands of proteins is unparalleled. In this review, we will...

  6. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  7. Identification of altered plasma proteins by proteomic study in valvular heart diseases and the potential clinical significance.

    Directory of Open Access Journals (Sweden)

    Ge Gao

    Full Text Available BACKGROUND: Little is known about genetic basis and proteomics in valvular heart disease (VHD including rheumatic (RVD and degenerative (DVD valvular disease. The present proteomic study examined the hypothesis that certain proteins may be associated with the pathological changes in the plasma of VHD patients. METHODS AND RESULTS: Differential protein analysis in the plasma identified 18 differentially expressed protein spots and 14 corresponding proteins or polypeptides by two-dimensional electrophoresis and mass spectrometry in 120 subjects. Two up-regulated (complement C4A and carbonic anhydrase 1 and three down-regulated proteins (serotransferrin, alpha-1-antichymotrypsin, and vitronectin were validated by ELISA in enlarging samples. The plasma levels (n = 40 for each of complement C4A in RVD (715.8±35.6 vs. 594.7±28.2 ng/ml, P = 0.009 and carbonic anhydrase 1 (237.70±15.7 vs. 184.7±10.8 U/L, P = 0.007 in DVD patients were significantly higher and that of serotransferrin (2.36±0.20 vs. 2.93±0.16 mg/ml, P = 0.025 and alpha-1-antichymotrypsin (370.0±13.7 vs. 413.0±11.6 µg/ml, P = 0.019 in RVD patients were significantly lower than those in controls. The plasma vitronectin level in both RVD (281.3±11.0 vs. 323.2±10.0 µg/ml, P = 0.006 and DVD (283.6±11.4 vs. 323.2±10.0 µg/ml, P = 0.011 was significantly lower than those in normal controls. CONCLUSIONS: We have for the first time identified alterations of 14 differential proteins or polypeptides in the plasma of patients with various VHD. The elevation of plasma complement C4A in RVD and carbonic anhydrase 1 in DVD and the decrease of serotransferrin and alpha-1-antichymotrypsin in RVD patients may be useful biomarkers for these valvular diseases. The decreased plasma level of vitronectin - a protein related to the formation of valvular structure - in both RVD and DVD patients might indicate the possible genetic deficiency in these patients.

  8. At a glance: Proteomics in China

    Institute of Scientific and Technical Information of China (English)

    HE FuChu

    2011-01-01

    Proteomics is a new science that focuses on the comprehensive analysis of proteins in intact organisms or in molecule machineries,organelles,cells,tissues,or organs.It has become an important area of interests in life sciences and has propelled the rapid development of cutting-edge biotechnology in the 21st century.In response to this,the Human Proteome Organization (HUPO) was launched in 2001.The mission of HUPO is to advocate and promote proteomics worldwide and to initiate the Human Proteome Project (HPP) to decode the human genome and to establish the proteomic basis of human physiology and pathology.Eleven projects including the Human Liver Proteome Project (HLPP) led by China are under way.Governments,multinational companies,particularly pharmaceutical and analytical instrument companies,as well as the genomic company Celera Genomics,have invested heavily,hoping to seize the huge potential of proteomics.=He Fuchu,PhD,is a Member of the Chinese Academy of Sciences,a Member of the Academy of Sciences for the Developing World,and is currently the Director of the State Key Laboratory of Proteomics.He is the President of the Beijing Proteome Research Center and a Professor at the Beijing Institute of Radiation Medicine.He Fuchu is a council member of the Human Proteome Organization (HUPO),co-chair (inaugural chair) of the HUPO Human Liver Proteome Project (HLPP),the vice-president of AOHUPO,and the president of CNHUPO.He received his B.S.degree in genetics from Fudan University,Shanghai,in 1982 and earned his M.S.degree in biochemistry and his PhD in cell biology from the Beijing Institute of Radiation Medicine.His major fields of research are proteomics,genomics,bioinformatics and systems biology,with a special interest in liver physiology and pathology.He is a senior editor of Proteomics and Proteomics-Clinical Application and is an editorial board member of Molecular & Cellular Proteomics and the Journal of Proteome Research and an executive editor of the

  9. The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability

    Directory of Open Access Journals (Sweden)

    Vlaanderen Jelle

    2009-11-01

    Full Text Available Abstract In spite of decades of epidemiological research, the etiology and causal patterns for many common diseases, such as breast and colon cancer or neurodegenerative diseases, are still largely unknown. Such chronic diseases are likely to have an environmental origin. However, "environmental" risks have been often elusive in epidemiological studies. This is a conundrum for current epidemiological research. On the other side, the relative contribution of genes to chronic diseases, as emerging from GWAS, seems to be modest (15-50% increase in disease risk. What is yet to be explored extensively is a model of disease based on long-term effects of low doses of environmental exposures, incorporating both genetic and acquired susceptibility ("clinical vulnerability", and the cumulative effects of different exposures. Such a disease model would be compatible with the weak associations found by GWAS and the still elusive role of many (low-level environmental exposures. We also propose that the introduction of "-omic" high-throughput technologies, such as transcriptomics, proteomics and metabolomics, may provide, in the next years, powerful tools to investigate early effects of environmental exposures and understand the etiology of common diseases better, according to the "clinical vulnerability model". The development of "-omics", in spite of current limitations and lack of sound validation, could greatly contribute to the elucidation of the disease model we propose.

  10. Proteomic classification of breast cancer.

    LENUS (Irish Health Repository)

    Kamel, Dalia

    2012-11-01

    Being a significant health problem that affects patients in various age groups, breast cancer has been extensively studied to date. Recently, molecular breast cancer classification has advanced significantly with the availability of genomic profiling technologies. Proteomic technologies have also advanced from traditional protein assays including enzyme-linked immunosorbent assay, immunoblotting and immunohistochemistry to more comprehensive approaches including mass spectrometry and reverse phase protein lysate arrays (RPPA). The purpose of this manuscript is to review the current protein markers that influence breast cancer prediction and prognosis and to focus on novel advances in proteomic classification of breast cancer.

  11. The human proteome – a scientific opportunity for transforming diagnostics, therapeutics, and healthcare

    Directory of Open Access Journals (Sweden)

    Vidal Marc

    2012-07-01

    Full Text Available Abstract A National Institutes of Health (NIH workshop was convened in Bethesda, MD on September 26–27, 2011, with representative scientific leaders in the field of proteomics and its applications to clinical settings. The main purpose of this workshop was to articulate ways in which the biomedical research community can capitalize on recent technology advances and synergize with ongoing efforts to advance the field of human proteomics. This executive summary and the following full report describe the main discussions and outcomes of the workshop.

  12. Proteomic Serum Biomarkers and Their Potential Application in Cancer Screening Programs

    Directory of Open Access Journals (Sweden)

    André M. Deelder

    2010-10-01

    Full Text Available Early diagnosis of cancer is of pivotal importance to reduce disease-related mortality. There is great need for non-invasive screening methods, yet current screening protocols have limited sensitivity and specificity. The use of serum biomarkers to discriminate cancer patients from healthy persons might be a tool to improve screening programs. Mass spectrometry based proteomics is widely applied as a technology for mapping and identifying peptides and proteins in body fluids. One commonly used approach in proteomics is peptide and protein profiling. Here, we present an overview of profiling methods that have the potential for implementation in a clinical setting and in national screening programs.

  13. Clinical proteomics identifies urinary CD14 as a potential biomarker for diagnosis of stable coronary artery disease.

    Directory of Open Access Journals (Sweden)

    Min-Yi Lee

    Full Text Available Inflammation plays a key role in coronary artery disease (CAD and other manifestations of atherosclerosis. Recently, urinary proteins were found to be useful markers for reflecting inflammation status of different organs. To identify potential biomarker for diagnosis of CAD, we performed one-dimensional SDS-gel electrophoresis followed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS. Among the proteins differentially expressed in urine samples, monocyte antigen CD14 was found to be consistently expressed in higher amounts in the CAD patients as compared to normal controls. Using enzyme-linked immunosorbent assays to analyze the concentrations of CD14 in urine and serum, we confirmed that urinary CD14 levels were significantly higher in patients (n = 73 with multi-vessel and single vessel CAD than in normal control (n = 35 (P < 0.001. Logistic regression analysis further showed that urinary CD14 concentration level is associated with severity or number of diseased vessels and SYNTAX score after adjustment for potential confounders. Concomitantly, the proportion of CD14+ monocytes was significantly increased in CAD patients (59.7 ± 3.6% as compared with healthy controls (14.9 ± 2.1% (P < 0.001, implicating that a high level of urinary CD14 may be potentially involved in mechanism(s leading to CAD pathogenesis. By performing shotgun proteomics, we further revealed that CD14-associated inflammatory response networks may play an essential role in CAD. In conclusion, the current study has demonstrated that release of CD14 in urine coupled with more CD14+ monocytes in CAD patients is significantly correlated with severity of CAD, pointing to the potential application of urinary CD14 as a novel noninvasive biomarker for large-scale diagnostic screening of susceptible CAD patients.

  14. Postgenomics biomarkers for rabies—the next decade of proteomics.

    Science.gov (United States)

    Mehta, Shraddha M; Banerjee, Shefali M; Chowdhary, Abhay S

    2015-02-01

    Rabies is one of the oldest diseases known to mankind. The pathogenic mechanisms by which rabies virus infection leads to development of neurological disease and death are still poorly understood. Analysis of rabies-infected proteomes may help identify novel biomarkers for antemortem diagnosis of the disease and target molecules for therapeutic intervention. This article offers a literature synthesis and critique of the differentially expressed proteins that have been previously reported from various in vitro/in vivo model systems and naturally infected clinical specimens. The emerging data collectively indicate that, in addition to the obvious alterations in proteins involved in synapse and neurotransmission, a majority of cytoskeletal proteins are relevant as well, providing evidence of neuronal degeneration. An interesting observation is that certain molecules, such as KPNA4, could be potential diagnostic markers for rabies. Importantly, proteomic studies with body fluids such as cerebrospinal fluid provide newer insights into antemortem diagnosis. In order to develop a complete integrative biology picture, it is essential to analyze the entire CNS (region-wise) and in particular, the brain. We suggest the use of laboratory animal models over cell culture systems using a combinatorial proteomics approach, as the former is a closer match to the actual host response. While most studies have focused on the terminal stages of the disease in mice, a time-series analysis could provide deeper insights for therapy. Postgenomics technologies such as proteomics warrant more extensive applications in rabies and similar diseases impacting public health around the world. PMID:25611201

  15. Proteome Sci.

    OpenAIRE

    Mann Matthias; Poustka Albert J; Mann Karlheinz

    2010-01-01

    Abstract Background Sea urchin is a major model organism for developmental biology and biomineralization research. However, identification of proteins involved in larval skeleton formation and mineralization processes in the embryo and adult, and the molecular characterization of such proteins, has just gained momentum with the sequencing of the Strongylocentrotus purpuratus genome and the introduction of high-throughput proteomics into the field. Results The present report contains the deter...

  16. Credentialing for advanced technology clinical trials using anthropomorphic phantoms

    International Nuclear Information System (INIS)

    Full text: The Radiological Physics Center (RPC) was established as a resource in radiation dosimetry and physics for cooperative clinical trial groups and radiotherapy facilities that deliver radiation treatments to patients entered onto cooperative group protocols. The RPC's primary responsibility is to assure NCI and the cooperative groups that the participating institutions have adequate quality assurance procedures and no major systematic dosimetry discrepancies, so that radiation treatments that are delivered are clinically comparable to those delivered by other institutions in the cooperative groups. To accomplish this, the RPC monitors the basic machine output and brachytherapy source strengths, the dosimetry data utilized by the institutions, calculational algorithms used for treatment planning, and the institutions' quality control procedures. The methods of monitoring include on-site dosimetry review by an RPC physicist, and several remote audit tools. The remote audit tools include 1) mailed dosimeters (TLD) evaluated on a periodic basis to verify output calibration and questionnaires regarding changes in personnel, equipment, and dosimetry practices; 2) comparison of dosimetry data with RPC 'standard data' to verify the compatibility of dosimetry data; 3) evaluation of reference and actual patient calculations to verify the validity of treatment planning algorithms; 4) review of the institutions' quality assurance procedures and records; and 5) mailable anthropomorphic phantoms to verify tumour dose delivery for special treatment techniques. The RPC has developed an extensive credentialing programme for institutions wishing to participate in clinical trials that use advanced technologies such as stereotactic radiosurgery (SRS) and intensity-modulated radiation therapy (IMRT). This programme requires institutions to submit questionnaires designed to test the participants' knowledge of the specific clinical trial, and to describe the institution

  17. A chemical proteomics approach for the search of pharmacological targets of the antimalarial clinical candidate albitiazolium in Plasmodium falciparum using photocrosslinking and click chemistry.

    Science.gov (United States)

    Penarete-Vargas, Diana Marcela; Boisson, Anaïs; Urbach, Serge; Chantelauze, Hervé; Peyrottes, Suzanne; Fraisse, Laurent; Vial, Henri J

    2014-01-01

    Plasmodium falciparum is responsible for severe malaria which is one of the most prevalent and deadly infectious diseases in the world. The antimalarial therapeutic arsenal is hampered by the onset of resistance to all known pharmacological classes of compounds, so new drugs with novel mechanisms of action are critically needed. Albitiazolium is a clinical antimalarial candidate from a series of choline analogs designed to inhibit plasmodial phospholipid metabolism. Here we developed an original chemical proteomic approach to identify parasite proteins targeted by albitiazolium during their native interaction in living parasites. We designed a bifunctional albitiazolium-derived compound (photoactivable and clickable) to covalently crosslink drug-interacting parasite proteins in situ followed by their isolation via click chemistry reactions. Mass spectrometry analysis of drug-interacting proteins and subsequent clustering on gene ontology terms revealed parasite proteins involved in lipid metabolic activities and, interestingly, also in lipid binding, transport, and vesicular transport functions. In accordance with this, the albitiazolium-derivative was localized in the endoplasmic reticulum and trans-Golgi network of P. falciparum. Importantly, during competitive assays with albitiazolium, the binding of choline/ethanolamine phosphotransferase (the enzyme involved in the last step of phosphatidylcholine synthesis) was substantially displaced, thus confirming the efficiency of this strategy for searching albitiazolium targets. PMID:25470252

  18. A chemical proteomics approach for the search of pharmacological targets of the antimalarial clinical candidate albitiazolium in Plasmodium falciparum using photocrosslinking and click chemistry.

    Directory of Open Access Journals (Sweden)

    Diana Marcela Penarete-Vargas

    Full Text Available Plasmodium falciparum is responsible for severe malaria which is one of the most prevalent and deadly infectious diseases in the world. The antimalarial therapeutic arsenal is hampered by the onset of resistance to all known pharmacological classes of compounds, so new drugs with novel mechanisms of action are critically needed. Albitiazolium is a clinical antimalarial candidate from a series of choline analogs designed to inhibit plasmodial phospholipid metabolism. Here we developed an original chemical proteomic approach to identify parasite proteins targeted by albitiazolium during their native interaction in living parasites. We designed a bifunctional albitiazolium-derived compound (photoactivable and clickable to covalently crosslink drug-interacting parasite proteins in situ followed by their isolation via click chemistry reactions. Mass spectrometry analysis of drug-interacting proteins and subsequent clustering on gene ontology terms revealed parasite proteins involved in lipid metabolic activities and, interestingly, also in lipid binding, transport, and vesicular transport functions. In accordance with this, the albitiazolium-derivative was localized in the endoplasmic reticulum and trans-Golgi network of P. falciparum. Importantly, during competitive assays with albitiazolium, the binding of choline/ethanolamine phosphotransferase (the enzyme involved in the last step of phosphatidylcholine synthesis was substantially displaced, thus confirming the efficiency of this strategy for searching albitiazolium targets.

  19. Viral Reactivation in Astronauts and Technology Transfer to Clinics

    Science.gov (United States)

    Pierson, Duane L.; Renner, Ashley N.; Rooney, Bridgett; Mehta, Satish K.

    2016-01-01

    very valuable in diagnosis of VZV disease without rash. Rapid detection allows early antiviral intervention that can prevent or lessen clinical symptoms and the likelihood of complications. The technology is also utilized at the CDC, NIH, Columbia University, Colorado University, and various other laboratories.

  20. Sakshat Labs: India's Virtual Proteomics Initiative

    OpenAIRE

    Sandipan Ray; Nicole R Koshy; Shyam Diwakar; Bipin Nair; Sanjeeva Srivastava

    2012-01-01

    The first Virtual Proteomics Lab of India has been developed at the IIT Bombay as a part of the “Sakshat” Lab Project, established to develop openly accessible, high-quality educational materials on science and technology.

  1. Analysis of soybean seed proteins using proteomics

    Science.gov (United States)

    This editorial elaborates on investigations consisting of different proteomics technologies and their application to biological sciences. In addition, different classes of soybean seed proteins are discussed. This information will be useful to scientists in obtaining a greater understanding of the...

  2. Establishing research strategies, methodologies and technologies to link genomics and proteomics to seagrass productivity, community metabolism and ecosystem carbon fluxes

    Directory of Open Access Journals (Sweden)

    Silvia eMazzuca

    2013-03-01

    Full Text Available A complete understanding of the mechanistic basis of marine ecosystem functioning is only possible through integrative and interdisciplinary research. This enables the prediction of change and possibly the mitigation of the consequences of anthropogenic impacts. One major aim of the COST Action ES0609 Seagrasses productivity. From genes to ecosystem management, is the calibration and synthesis of various methods and the development of innovative techniques and protocols for studying seagrass ecosystems.During ten days, twenty researchers representing a range of disciplines (molecular biology, physiology, botany, ecology, oceanography, underwater acoustics gathered at the marine station of STARESO (Corsica to study together the nearby Posidonia oceanica meadow. The Station de Recherches Sous-marine et Océanographiques (STARESO is located in an oligotrophic area classified as "pristine site" where environmental disturbances caused by anthropogenic pressure are exceptionally low. The healthy P. oceanica meadow, that grows in front of the lab, colonizes the sea bottom from the surface to 37 m depth. During the study, genomic and proteomic approaches were integrated with ecophysiological and physical approaches with the aim of understanding changes in seagrass productivity and metabolism at different depths and along daily cycles. In this paper we report details on the approaches utilized and we forecast the potential of the data that will come from this synergistic approach not only for P. oceanica but for seagrasses in general.

  3. Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome

    DEFF Research Database (Denmark)

    Grassl, Niklas; Kulak, Nils Alexander; Pichler, Garwin;

    2016-01-01

    , disruptions in saliva secretion and changes in the oral microbiome contribute to conditions such as tooth decay and respiratory tract infections. Here we set out to quantitatively map the saliva proteome in great depth with a rapid and in-depth mass spectrometry-based proteomics workflow. METHODS: We used...... next-generation sequencing data from the Human Microbiome Project as well as a comparison to MALDI-TOF mass spectrometry on microbial cultures revealed strong agreement. The oral microbiome differs between individuals and changes drastically upon eating and tooth brushing. CONCLUSION: Rapid shotgun and...... robust technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid and is therefore a valuable complement to genomic studies. This opens new frontiers for the study of host-pathogen interactions and clinical saliva diagnostics....

  4. Myelin Abnormalities in Schizophrenia: Insights from Proteomic Investigations of Post-Mortem Schizophrenia and Pre-Clinical Animal Models

    OpenAIRE

    Farrelly, Lorna

    2014-01-01

    Accumulating evidence from epidemiologic and clinical findings report that both exposure to prenatal inflammation and prenatal iron deficiency significantly increase the risk of developing Schizophrenia in the offspring. Abnormalities in myelin are the most robust neuropathological findings in post-mortem human Schizophrenia, however the exact mechanisms at the protein and pathway levels owing to the myelin deficits are largely unknown. Animal models offer a fruitful approach to study the ...

  5. Mass spectrometry-based proteomics in cell biology

    OpenAIRE

    Walther, T. C.; Mann, M

    2010-01-01

    The global analysis of protein composition, modifications, and dynamics are important goals in cell biology. Mass spectrometry (MS)–based proteomics has matured into an attractive technology for this purpose. Particularly, high resolution MS methods have been extremely successful for quantitative analysis of cellular and organellar proteomes. Rapid advances in all areas of the proteomic workflow, including sample preparation, MS, and computational analysis, should make the technology more eas...

  6. Platelet proteomics in cardiovascular diseases

    Directory of Open Access Journals (Sweden)

    Paula Vélez

    2015-06-01

    Full Text Available In recent years, platelet proteomics has been applied successfully to the study of cardiovascular diseases (CVDs. It is very well known that platelets play a pivotal role in the pathophysiological mechanisms underlying many CVDs, especially acute coronary syndromes (ACSs, since they are implied in thrombus formation after atheroma plaque rupture. This is the reason why molecules involved in platelet activation and aggregation are primary targets for treatment of ACSs. Many efforts are aimed at finding drugs that inhibit platelet activation; however it is difficult to separate the therapeutic benefits from harmful effects because pathological and physiological functions of platelets are due to the same mechanisms. Given that platelets lack a nucleus, proteomics is regarded as an ideal method to approach their biochemistry. Current platelet proteomic studies are focusing on the identification of platelet molecular and functional changes in normal and pathological states, enriching the comprehension of platelet biological function, and screening for new biomarkers and antiplatelet agents. In the present article, we introduce the reader to platelet biology and function, and revise recent advances in platelet proteomics applied to the study of CVDs, including a special emphasis on sample preparation requirements for proteome analysis of platelet clinical samples.

  7. Proteomic insights into floral biology.

    Science.gov (United States)

    Li, Xiaobai; Jackson, Aaron; Xie, Ming; Wu, Dianxing; Tsai, Wen-Chieh; Zhang, Sheng

    2016-08-01

    The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics - a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:26945514

  8. Digital Technology in the 21st Century: Considerations for Clinical Supervision in Rehabilitation Education

    Science.gov (United States)

    Byrne, Andrew M.; Hartley, Michael T.

    2010-01-01

    Technological innovations are increasingly affecting the delivery of clinical supervision. Yet there is limited information on how supervisors can use digital technology to broaden settings in which students record client interviews, enhance evaluation of students' clinical performance, and increase accessibility for students with disabilities.…

  9. The Modified Technology Acceptance Model for Private Clinical Physicians: A Case Study in Malaysia, Penang

    OpenAIRE

    Annie Ng Cheng San; Choy Johnn Yee

    2013-01-01

    Malaysia’s private clinic is wealth creator. To enhance its sustainable future, healthcare Information Technology (IT) change is inevitable. However, its’ IT acceptance is limited. The past literatures showed physicians have different technology acceptance decision as compare to common users. Hence, understanding the physicians’ technology acceptance is critical for technology management success. This study aims to gauge the factors influence technology acceptance decision among the physician...

  10. Clinical engineering and risk management in healthcare technological process using architecture framework.

    Science.gov (United States)

    Signori, Marcos R; Garcia, Renato

    2010-01-01

    This paper presents a model that aids the Clinical Engineering to deal with Risk Management in the Healthcare Technological Process. The healthcare technological setting is complex and supported by three basics entities: infrastructure (IS), healthcare technology (HT), and human resource (HR). Was used an Enterprise Architecture - MODAF (Ministry of Defence Architecture Framework) - to model this process for risk management. Thus, was created a new model to contribute to the risk management in the HT process, through the Clinical Engineering viewpoint. This architecture model can support and improve the decision making process of the Clinical Engineering to the Risk Management in the Healthcare Technological process. PMID:21096536

  11. Technology-based strategies for promoting clinical reasoning skills in nursing education.

    Science.gov (United States)

    Shellenbarger, Teresa; Robb, Meigan

    2015-01-01

    Faculty face the demand of preparing nursing students for the constantly changing health care environment. Effective use of online, classroom, and clinical conferencing opportunities helps to enhance nursing students' clinical reasoning capabilities needed for practice. The growth of technology creates an avenue for faculty to develop engaging learning opportunities. This article presents technology-based strategies such as electronic concept mapping, electronic case histories, and digital storytelling that can be used to facilitate clinical reasoning skills. PMID:25402714

  12. Recent technological advances in computed tomography and the clinical impact therein.

    Science.gov (United States)

    Runge, Val M; Marquez, Herman; Andreisek, Gustav; Valavanis, Anton; Alkadhi, Hatem

    2015-02-01

    Current technological advances in CT, specifically those with a major impact on clinical imaging, are discussed. The intent was to provide for both medical physicists and practicing radiologists a summary of the clinical impact of each advance, offering guidance in terms of utility and day-to-day clinical implementation, with specific attention to radiation dose reduction. PMID:25521851

  13. Using Technology Within the Treatment of Eating Disorders: A Clinical Practice Review

    OpenAIRE

    Shingleton, Rebecca M.; Richards, Lauren K.; Thompson-Brenner, Heather

    2013-01-01

    The focus of this clinical practice review is to provide clinicians a framework for incorporating technology into the treatment of eating disorders (EDs). We detailed studies that were published within the past 11 years (2002–2012) and that included at least 10 participants. Our primary aims were to describe how technology has been used to enhance the delivery of ED treatment as well as report the effectiveness of these technology-based interventions. We also provided clinical applications an...

  14. Metrological sharp shooting for plasma proteins and peptides: The need for reference materials for accurate measurements in clinical proteomics and in vitro diagnostics to generate reliable results.

    Science.gov (United States)

    Vitzthum, Frank; Siest, Gérard; Bunk, David M; Preckel, Tobias; Wenz, Christian; Hoerth, Patric; Schulz-Knappe, Peter; Tammen, Harald; Adamkiewicz, Juergen; Merlini, Giampaolo; Anderson, N Leigh

    2007-09-01

    Reliable study results are necessary for the assessment of discoveries, including those from proteomics. Reliable study results are also crucial to increase the likelihood of making a successful choice of biomarker candidates for verification and subsequent validation studies, a current bottleneck for the transition to in vitro diagnostic (IVD). In this respect, a major need for improvement in proteomics appears to be accuracy of measurements, including both trueness and precision of measurement. Standardization and total quality management systems (TQMS) help to provide accurate measurements and reliable results. Reference materials are an essential part of standardization and TQMS in IVD and are crucial to provide metrological correct measurements and for the overall quality assurance process. In this article we give an overview on how reference materials are defined, prepared and what role they play in standardization and TQMS to support the generation of reliable results. We discuss how proteomics can support the establishment of reference materials and biomarker tests for IVD applications, how current reference materials used in IVD may be beneficially applied in proteomics, and we provide considerations on the establishment of reference materials specific for proteomics. For clarity, we solely focus on reference materials related to serum and plasma. PMID:21136754

  15. Affinity Proteomics in the mountains: Alpbach 2015.

    Science.gov (United States)

    Taussig, Michael J

    2016-09-25

    The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting. PMID:27118167

  16. Connecting Clinical Practices with Microbiological and Biochemical Technologies

    OpenAIRE

    Martínez Espinosa, Rosa María

    2016-01-01

    The word technology refers to the knowledge of techniques, skills, methods or processes used to produce goods, services or to reach specific objectives (research, business, etc.). The concept technology can also be used to make reference to devices, computers and factories.

  17. The proteomics in prostate cancer biomarker discovery

    Directory of Open Access Journals (Sweden)

    V. E. Shevchenko

    2015-06-01

    Full Text Available Prostate cancer (PC represents the second most frequent type of tumor in men worldwide. Proteomics represents a promising approach for the discovery of new biomarkers able to improve the management of PC patients. Markers more specific and sensitive than prostate-specific antigen are needed for PC diagnosis, prognosis and response to treatment. Moreover, proteomics could represent an important tool to identify new molecular targets for PC tailored therapy. Now several possible PC biomarkers sources, each with advantages and limitations, are under investigation, including tissues, urine, serum, plasma and prostatic fluids. Innovative high-throughput proteomic platforms are now identifying and quantifying new specific and sensitive biomarkers for PC detection, stratification and treatment. Nevertheless, many putative biomarkers are still far from being applied in clinical practice.This review aims to discuss the recent advances in PC proteomics, emphasizing biomarker discovery and their application to clinical utility for diagnosis and patient stratification.

  18. Proteomic maps of breast cancer subtypes.

    Science.gov (United States)

    Tyanova, Stefka; Albrechtsen, Reidar; Kronqvist, Pauliina; Cox, Juergen; Mann, Matthias; Geiger, Tamar

    2016-01-01

    Systems-wide profiling of breast cancer has almost always entailed RNA and DNA analysis by microarray and sequencing techniques. Marked developments in proteomic technologies now enable very deep profiling of clinical samples, with high identification and quantification accuracy. We analysed 40 oestrogen receptor positive (luminal), Her2 positive and triple negative breast tumours and reached a quantitative depth of >10,000 proteins. These proteomic profiles identified functional differences between breast cancer subtypes, related to energy metabolism, cell growth, mRNA translation and cell-cell communication. Furthermore, we derived a signature of 19 proteins, which differ between the breast cancer subtypes, through support vector machine (SVM)-based classification and feature selection. Remarkably, only three proteins of the signature were associated with gene copy number variations and eleven were also reflected on the mRNA level. These breast cancer features revealed by our work provide novel insights that may ultimately translate to development of subtype-specific therapeutics. PMID:26725330

  19. Analysis of mass spectrometry data in proteomics

    DEFF Research Database (Denmark)

    Matthiesen, Rune; Jensen, Ole N

    2008-01-01

    The systematic study of proteins and protein networks, that is, proteomics, calls for qualitative and quantitative analysis of proteins and peptides. Mass spectrometry (MS) is a key analytical technology in current proteomics and modern mass spectrometers generate large amounts of high-quality data...... that in turn allow protein identification, annotation of secondary modifications, and determination of the absolute or relative abundance of individual proteins. Advances in mass spectrometry-driven proteomics rely on robust bioinformatics tools that enable large-scale data analysis. This chapter...

  20. Proteomics and the dynamic plasma membrane

    DEFF Research Database (Denmark)

    Sprenger, Richard R; Jensen, Ole Nørregaard

    2010-01-01

    plasma membrane is of particular interest, by not only serving as a barrier between the "cell interior" and the external environment, but moreover by organizing and clustering essential components to enable dynamic responses to internal and external stimuli. Defining and characterizing the dynamic plasma...... the challenges in functional proteomic studies of the plasma membrane. We review the recent progress in MS-based plasma membrane proteomics by presenting key examples from eukaryotic systems, including mammals, yeast and plants. We highlight the importance of enrichment and quantification technologies...... required for detailed functional and comparative analysis of the dynamic plasma membrane proteome....

  1. Hospital technology management: the Tao of clinical engineering.

    Science.gov (United States)

    Gordon, G J

    1990-01-01

    Planning a profession's future is a formidable task that must be based on both what the members want to become and what is natural to the marketplace. The hospital industry, however, will not wait for clinical engineering to establish its profession. Competition will arise and push aside the unprepared. Clinical engineering's leadership has not created a clear vision of their profession's role in improving healthcare, nor have they helped others to internalize a sincere professional purpose and to share the responsibility for change. This paper examines the profession and articulates action that only clinical engineers can take to increase their value in the hospital industry. PMID:10104536

  2. Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level

    OpenAIRE

    Keller, Martin; Hettich, Robert

    2009-01-01

    Summary: The increase in sequencing capacity led to a new wave of metagenomic projects, enabling and setting the prerequisite for the application of environmental proteomics technologies. This review describes the current status of environmental proteomics. It describes sample preparation as well as the two major technologies applied within this field: two-dimensional electrophoresis-based environmental proteomics and liquid chromatography-mass spectrometry-based environmental proteomics. It ...

  3. [Technophobia: a clinical disorder associated with digital technologies].

    Science.gov (United States)

    Luque, Leticia E; Avila, Rodolfo

    2008-01-01

    The technophobia is among the various negative impacts of technology on human life. The disease changes according to the cultural context. Therefore, the objective was to describe the disorder in the argentine adult population (22-50 years), using a scale developed locally; 12.9% of the sample meets the criteria of technophobia; 27.2% had high levels of anxiety before the technology but other indicators of technophobia. In general, the perception of the social impact of technology in Argentina is negative. Results obtained confirm the presence of disorder in the argentine population and the assumption of specific phobia. PMID:19142241

  4. Novel Serial Positive Enrichment Technology Enables Clinical Multiparameter Cell Sorting

    OpenAIRE

    Christian Stemberger; Stefan Dreher; Claudia Tschulik; Christine Piossek; Jeannette Bet; Yamamoto, Tori N.; Matthias Schiemann; Michael Neuenhahn; Klaus Martin; Martin Schlapschy; Arne Skerra; Thomas Schmidt; Matthias Edinger; Riddell, Stanley R.; Lothar Germeroth

    2012-01-01

    A general obstacle for clinical cell preparations is limited purity, which causes variability in the quality and potency of cell products and might be responsible for negative side effects due to unwanted contaminants. Highly pure populations can be obtained best using positive selection techniques. However, in many cases target cell populations need to be segregated from other cells by combinations of multiple markers, which is still difficult to achieve--especially for clinical cell product...

  5. Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer

    Directory of Open Access Journals (Sweden)

    Nelson Laura D

    2012-06-01

    Full Text Available Abstract Background Tri- and tetra-nucleotide repeats in mammalian genomes can induce formation of alternative non-B DNA structures such as triplexes and guanine (G-quadruplexes. These structures can induce mutagenesis, chromosomal translocations and genomic instability. We wanted to determine if proteins that bind triplex DNA structures are quantitatively or qualitatively different between colorectal tumor and adjacent normal tissue and if this binding activity correlates with patient clinical characteristics. Methods Extracts from 63 human colorectal tumor and adjacent normal tissues were examined by gel shifts (EMSA for triplex DNA-binding proteins, which were correlated with clinicopathological tumor characteristics using the Mann-Whitney U, Spearman’s rho, Kaplan-Meier and Mantel-Cox log-rank tests. Biotinylated triplex DNA and streptavidin agarose affinity binding were used to purify triplex-binding proteins in RKO cells. Western blotting and reverse-phase protein array were used to measure protein expression in tissue extracts. Results Increased triplex DNA-binding activity in tumor extracts correlated significantly with lymphatic disease, metastasis, and reduced overall survival. We identified three multifunctional splicing factors with biotinylated triplex DNA affinity: U2AF65 in cytoplasmic extracts, and PSF and p54nrb in nuclear extracts. Super-shift EMSA with anti-U2AF65 antibodies produced a shifted band of the major EMSA H3 complex, identifying U2AF65 as the protein present in the major EMSA band. U2AF65 expression correlated significantly with EMSA H3 values in all extracts and was higher in extracts from Stage III/IV vs. Stage I/II colon tumors (p = 0.024. EMSA H3 values and U2AF65 expression also correlated significantly with GSK3 beta, beta-catenin, and NF- B p65 expression, whereas p54nrb and PSF expression correlated with c-Myc, cyclin D1, and CDK4. EMSA values and expression of all three splicing factors correlated

  6. Imaging retinal ganglion cells: enabling experimental technology for clinical application.

    Science.gov (United States)

    Smith, Corey A; Chauhan, Balwantray C

    2015-01-01

    Recent advances in clinical ophthalmic imaging have enhanced patient care. However, the ability to differentiate retinal neurons, such as retinal ganglion cells (RGCs), would advance many areas within ophthalmology, including the screening and monitoring of glaucoma and other optic neuropathies. Imaging at the single cell level would take diagnostics to the next level. Experimental methods have provided techniques and insight into imaging RGCs, however no method has yet to be translated to clinical application. This review provides an overview of the importance of non-invasive imaging of RGCs and the clinically relevant capabilities. In addition, we report on experimental data from wild-type mice that received an in vivo intravitreal injection of a neuronal tracer that labelled RGCs, which in turn were monitored for up to 100 days post-injection with confocal scanning laser ophthalmoscopy. We were able to demonstrate efficient and consistent RGC labelling with this delivery method and discuss the issue of cell specificity. This type of experimental work is important in progressing towards clinically applicable methods for monitoring loss of RGCs in glaucoma and other optic neuropathies. We discuss the challenges to translating these findings to clinical application and how this method of tracking RGCs in vivo could provide valuable structural and functional information to clinicians. PMID:25448921

  7. Mining the granule proteome

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Goetze, Jens P; Johnsen, Anders H

    2015-01-01

    Proteomics of secretory granules is an emerging strategy for identifying secreted proteins, including potentially novel candidate biomarkers and peptide hormones. In addition, proteomics can provide information about the abundance, localization and structure (post-translational modification) of...... granule proteins and peptides. Analytical strategies within this research line include so-called 'subtractive proteomics', 'peptidomics' and granule purification by the use of multiple gradient centrifugations. Here we review the literature, and describe the challenges and opportunities in proteomics of...

  8. Inconvenient truth: cancer biomarker development by using proteomics.

    Science.gov (United States)

    Kondo, Tadashi

    2014-05-01

    A biomarker is a crucial tool for measuring the progress of disease and the effects of treatment for better clinical outcomes in cancer patients. Diagnostic, predictive, and prognostic biomarkers are required in various clinical settings. The proteome, a functional translation of the genome, is considered a rich source of biomarkers; therefore, sizable time and funding have been spent in proteomics to develop biomarkers. Although significant progress has been made in technologies toward comprehensive protein expression profiling, and many biomarker candidates published, none of the reported biomarkers have proven to be beneficial for cancer patients. The present deceleration in biomarker research can be attributed to technical limitations. Additional efforts are required to further technical progress; however, there are many examples demonstrating that problems in biomarker research are not so much with the technology but in the study design. In the study of biomarkers for early diagnosis, candidates are screened and validated by comparing cases and controls of similar sample size, and the low prevalence of disease is often ignored. Although it is reasonable to take advantage of multiple rather than single biomarkers when studying diverse disease mechanisms, the annotation of individual components of reported multiple biomarkers does not often explain the variety of molecular events underlying the clinical observations. In tissue biomarker studies, the heterogeneity of disease tissues and pathological observations are often not considered, and tissues are homogenized as a whole for protein extraction. In addition to the challenge of technical limitations, the fundamental aspects of biomarker development in a disease study need to be addressed. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge. PMID:23896458

  9. EHDViz: clinical dashboard development using open-source technologies

    Science.gov (United States)

    Badgeley, Marcus A; Shameer, Khader; Glicksberg, Benjamin S; Tomlinson, Max S; Levin, Matthew A; McCormick, Patrick J; Kasarskis, Andrew; Reich, David L; Dudley, Joel T

    2016-01-01

    Objective To design, develop and prototype clinical dashboards to integrate high-frequency health and wellness data streams using interactive and real-time data visualisation and analytics modalities. Materials and methods We developed a clinical dashboard development framework called electronic healthcare data visualization (EHDViz) toolkit for generating web-based, real-time clinical dashboards for visualising heterogeneous biomedical, healthcare and wellness data. The EHDViz is an extensible toolkit that uses R packages for data management, normalisation and producing high-quality visualisations over the web using R/Shiny web server architecture. We have developed use cases to illustrate utility of EHDViz in different scenarios of clinical and wellness setting as a visualisation aid for improving healthcare delivery. Results Using EHDViz, we prototyped clinical dashboards to demonstrate the contextual versatility of EHDViz toolkit. An outpatient cohort was used to visualise population health management tasks (n=14 221), and an inpatient cohort was used to visualise real-time acuity risk in a clinical unit (n=445), and a quantified-self example using wellness data from a fitness activity monitor worn by a single individual was also discussed (n-of-1). The back-end system retrieves relevant data from data source, populates the main panel of the application and integrates user-defined data features in real-time and renders output using modern web browsers. The visualisation elements can be customised using health features, disease names, procedure names or medical codes to populate the visualisations. The source code of EHDViz and various prototypes developed using EHDViz are available in the public domain at http://ehdviz.dudleylab.org. Conclusions Collaborative data visualisations, wellness trend predictions, risk estimation, proactive acuity status monitoring and knowledge of complex disease indicators are essential components of implementing data

  10. Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers

    LENUS (Irish Health Repository)

    Dakna, Mohammed

    2010-12-10

    Abstract Background The purpose of this manuscript is to provide, based on an extensive analysis of a proteomic data set, suggestions for proper statistical analysis for the discovery of sets of clinically relevant biomarkers. As tractable example we define the measurable proteomic differences between apparently healthy adult males and females. We choose urine as body-fluid of interest and CE-MS, a thoroughly validated platform technology, allowing for routine analysis of a large number of samples. The second urine of the morning was collected from apparently healthy male and female volunteers (aged 21-40) in the course of the routine medical check-up before recruitment at the Hannover Medical School. Results We found that the Wilcoxon-test is best suited for the definition of potential biomarkers. Adjustment for multiple testing is necessary. Sample size estimation can be performed based on a small number of observations via resampling from pilot data. Machine learning algorithms appear ideally suited to generate classifiers. Assessment of any results in an independent test-set is essential. Conclusions Valid proteomic biomarkers for diagnosis and prognosis only can be defined by applying proper statistical data mining procedures. In particular, a justification of the sample size should be part of the study design.

  11. Health Technology Assessment of pathogen reduction technologies applied to plasma for clinical use

    Science.gov (United States)

    Cicchetti, Americo; Berrino, Alexandra; Casini, Marina; Codella, Paola; Facco, Giuseppina; Fiore, Alessandra; Marano, Giuseppe; Marchetti, Marco; Midolo, Emanuela; Minacori, Roberta; Refolo, Pietro; Romano, Federica; Ruggeri, Matteo; Sacchini, Dario; Spagnolo, Antonio G.; Urbina, Irene; Vaglio, Stefania; Grazzini, Giuliano; Liumbruno, Giancarlo M.

    2016-01-01

    Although existing clinical evidence shows that the transfusion of blood components is becoming increasingly safe, the risk of transmission of known and unknown pathogens, new pathogens or re-emerging pathogens still persists. Pathogen reduction technologies may offer a new approach to increase blood safety. The study is the output of collaboration between the Italian National Blood Centre and the Post-Graduate School of Health Economics and Management, Catholic University of the Sacred Heart, Rome, Italy. A large, multidisciplinary team was created and divided into six groups, each of which addressed one or more HTA domains. Plasma treated with amotosalen + UV light, riboflavin + UV light, methylene blue or a solvent/detergent process was compared to fresh-frozen plasma with regards to current use, technical features, effectiveness, safety, economic and organisational impact, and ethical, social and legal implications. The available evidence is not sufficient to state which of the techniques compared is superior in terms of efficacy, safety and cost-effectiveness. Evidence on efficacy is only available for the solvent/detergent method, which proved to be non-inferior to untreated fresh-frozen plasma in the treatment of a wide range of congenital and acquired bleeding disorders. With regards to safety, the solvent/detergent technique apparently has the most favourable risk-benefit profile. Further research is needed to provide a comprehensive overview of the cost-effectiveness profile of the different pathogen-reduction techniques. The wide heterogeneity of results and the lack of comparative evidence are reasons why more comparative studies need to be performed. PMID:27403740

  12. Health Technology Assessment of pathogen reduction technologies applied to plasma for clinical use.

    Science.gov (United States)

    Cicchetti, Americo; Berrino, Alexandra; Casini, Marina; Codella, Paola; Facco, Giuseppina; Fiore, Alessandra; Marano, Giuseppe; Marchetti, Marco; Midolo, Emanuela; Minacori, Roberta; Refolo, Pietro; Romano, Federica; Ruggeri, Matteo; Sacchini, Dario; Spagnolo, Antonio G; Urbina, Irene; Vaglio, Stefania; Grazzini, Giuliano; Liumbruno, Giancarlo M

    2016-07-01

    Although existing clinical evidence shows that the transfusion of blood components is becoming increasingly safe, the risk of transmission of known and unknown pathogens, new pathogens or re-emerging pathogens still persists. Pathogen reduction technologies may offer a new approach to increase blood safety. The study is the output of collaboration between the Italian National Blood Centre and the Post-Graduate School of Health Economics and Management, Catholic University of the Sacred Heart, Rome, Italy. A large, multidisciplinary team was created and divided into six groups, each of which addressed one or more HTA domains.Plasma treated with amotosalen + UV light, riboflavin + UV light, methylene blue or a solvent/detergent process was compared to fresh-frozen plasma with regards to current use, technical features, effectiveness, safety, economic and organisational impact, and ethical, social and legal implications. The available evidence is not sufficient to state which of the techniques compared is superior in terms of efficacy, safety and cost-effectiveness. Evidence on efficacy is only available for the solvent/detergent method, which proved to be non-inferior to untreated fresh-frozen plasma in the treatment of a wide range of congenital and acquired bleeding disorders. With regards to safety, the solvent/detergent technique apparently has the most favourable risk-benefit profile. Further research is needed to provide a comprehensive overview of the cost-effectiveness profile of the different pathogen-reduction techniques. The wide heterogeneity of results and the lack of comparative evidence are reasons why more comparative studies need to be performed. PMID:27403740

  13. GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data

    OpenAIRE

    Rigbolt, K. T. G.; Vanselow, J. T.; Blagoev, B.

    2011-01-01

    Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)1. The program requires no special bioinf...

  14. Healthcare Technology Management (HTM) of mechanical ventilators by clinical engineers

    OpenAIRE

    Yoshioka, Jun; Nakane, Masaki; Kawamae, Kaneyuki

    2014-01-01

    Mechanical ventilator failures expose patients to unacceptable risks, and maintaining mechanical ventilator safety is an important issue. We examined the usefulness of maintaining mechanical ventilators by clinical engineers (CEs) using a specialized calibrator. These evaluations and the ability to make in-house repairs proved useful for obviating the need to rent ventilators which, in turn, might prove faulty themselves. The CEs' involvement in maintaining mechanical ventilators is desirable...

  15. Recent advances in atherosclerosis-based proteomics: new biomarkers and a future perspective.

    Science.gov (United States)

    Alvarez-Llamas, Gloria; de la Cuesta, Fernando; Barderas, Maria Eugenia G; Darde, Veronica; Padial, Luis R; Vivanco, Fernando

    2008-10-01

    Vascular proteomics is providing two main types of data: proteins that actively participate in vascular pathophysiological processes and novel protein candidates that can potentially serve as useful clinical biomarkers. Although both types of proteins can be identified by similar proteomic strategies and methods, it is important to clearly distinguish biomarkers from mediators of disease. A particular protein, or group of proteins, may participate in a pathogenic process but not serve as an effective biomarker. Alternatively, a useful biomarker may not mediate pathogenic pathways associated with disease (i.e., C-reactive protein). To date, there are no clear successful examples in which discovery proteomics has led to a novel useful clinical biomarker in cardiovascular diseases. Nevertheless, new sources of biomarkers are being explored (i.e., secretomes, circulating cells, exosomes and microparticles), an increasing number of novel proteins involved in atherogenesis are constantly described, and new technologies and analytical strategies (i.e., quantitative proteomics) are being developed to access low abundant proteins. Therefore, this presages a new era of discovery and a further step in the practical application to diagnosis, prognosis and early action by medical treatment of cardiovascular diseases. PMID:18937558

  16. MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes

    DEFF Research Database (Denmark)

    Zhang, Yanling; Zhang, Yong; Adachi, Jun;

    2007-01-01

    Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several...... body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and......://www.mapuproteome.com using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic...

  17. Clinical application of MR PROPELLER technology in artifacts reduction

    International Nuclear Information System (INIS)

    Objective: The aim of this study was to assess the clinical value of PROPELLER (periodically rotated overlapping parallel lines enhanced reconstruction, PROPELLER). Methods: Four sequences of conventionality and PROPELLER axial T2-weighted imaging (T2WI) and/or diffusion weighted imaging (DWI) were performed in ten normal volunteers with head ceaseless motion and 64 clinical subjects. Motion artifacts were observed in 56 patients in unconsciousness and magnetic-sensitive artifacts in other 8 patients with metallic implants. PROPELLER images and the conventionality images were compared. Results: Sixty-four clinical subjects included the cerebral infarction (n=41), brain metastasis (n=3) and other's disorders (n=20). PROPELLER T2WI had clearer and motion-artifact-free images in both volunteers and patients in unconsciousness. In dental treatment cases, magnetic-susceptibility artifacts were greatly reduced to an accepted level. Comparing with conventional sequences, PROPELLER T2WI/DWI sequences showed promising feature in reduction of artifacts and distinctly defined pathological profile. Conclusion: MR PROPELLER technique offers a means of reducing motion and metallic artifacts, and improving image quality. Intracranial pathology is equally or better demonstrated with PROPELLER. (authors)

  18. Neural Stem Cells (NSCs) and Proteomics.

    Science.gov (United States)

    Shoemaker, Lorelei D; Kornblum, Harley I

    2016-02-01

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

  19. Neural Stem Cells (NSCs) and Proteomics*

    Science.gov (United States)

    Shoemaker, Lorelei D.; Kornblum, Harley I.

    2016-01-01

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

  20. Proteomics and Mass Spectrometry for Cancer Biomarker Discovery

    Directory of Open Access Journals (Sweden)

    Ming Lu

    2007-01-01

    Full Text Available Proteomics is a rapidly advancing field not only in the field of biology but also in translational cancer research. In recent years, mass spectrometry and associated technologies have been explored to identify proteins or a set of proteins specific to a given disease, for the purpose of disease detection and diagnosis. Such biomarkers are being investigated in samples including cells, tissues, serum/plasma, and other types of body fluids. When sufficiently refined, proteomic technologies may pave the way for early detection of cancer or individualized therapy for cancer. Mass spectrometry approaches coupled with bioinformatic tools are being developed for biomarker discovery and validation. Understanding basic concepts and application of such technology by investigators in the field may accelerate the clinical application of protein biomarkers in disease management.Abbreviations: 2DE: two-dimensional gel electrophoresis; ABPP: activity-based protein profiling; CEA: carcinoembryonic antigen; CI: confidence interval; ESI: electrospray ionization; FP: fluorophosphonate; HPLC: high performance liquid chromatography; ICAT: isotope coded affi nitytags; IEF: isoelectric focusing; iTRAQ: isobaric tags for relative and absolute quantification; LCMS: combined liquid chromatography-mass spectrometry; LCMSMS: liquid chromatography tandem mass spectrometry; LOD: limit of detection; m/z: mass to charge ratio; MALDI: matrix-assisted laser desorption ionization; MS: mass spectrometry; MUDPIT: multidimensional protein identification technology; NAF: nipple aspirate fluid; PMF: peptide mass fingerprinting; PSA: prostate specifi c antigen; PTMs: post-translational modifications; RPMA: reverse phase protein microarray; SELDI: surface enhanced laser desorption ionization; TOF: time-of-flight.

  1. Adoption of health information technologies by physicians for clinical practice

    DEFF Research Database (Denmark)

    Villalba-Mora, Elena; Casas, Isabel; Lupiañez-Villanueva, Francisco;

    2015-01-01

    OBJECTIVES: We investigated the level of adoption of Health Information Technologies (HIT) services, and the factors that influence this, amongst specialised and primary care physicians; in Andalusia, Spain. METHODS: We analysed the physicians' responses to an online survey. First, we performed...... a statistical descriptive analysis of the data; thereafter, a principal component analysis; and finally an order logit model to explain the effect of the use in the adoption and to analyse which are the existing barriers. RESULTS: The principal component analysis revealed three main uses of Health Information...... Technologies: Electronic Health Records (EHR), ePrescription and patient management and telemedicine services. Results from an ordered logit model showed that the frequency of use of HIT is associated with the physicians' perceived usefulness. Lack of financing appeared as a common barrier to the adoption...

  2. Information Technology in Clinical Research in Rheumatology Domain

    Czech Academy of Sciences Publication Activity Database

    Hanzlíček, Petr; Zvárová, Jana; Dostál, C.

    Amsterdam : IOS Press, 2006 - (Hasman, A.; Haux, R.; van der Lei, J.; De Clercq, E.; France, F.), s. 187-192 ISBN 1-58603-647-5. - (Studies in Health Technology and Informatics. 124). [MIE 2006. International Conference of the European Federation for Medical Informatics /20./. Maastricht (NL), 27.08.2006-30.08.2006] Institutional research plan: CEZ:AV0Z10300504 Keywords : medical informatics * rheumatology * electronic health record Subject RIV: IN - Informatics, Computer Science

  3. Technologies for Clinical Diagnosis Using Expired Human Breath Analysis

    OpenAIRE

    Thalakkotur Lazar Mathew; Prabhahari Pownraj; Sukhananazerin Abdulla; Biji Pullithadathil

    2015-01-01

    This review elucidates the technologies in the field of exhaled breath analysis. Exhaled breath gas analysis offers an inexpensive, noninvasive and rapid method for detecting a large number of compounds under various conditions for health and disease states. There are various techniques to analyze some exhaled breath gases, including spectrometry, gas chromatography and spectroscopy. This review places emphasis on some of the critical biomarkers present in exhaled human breath, and its relate...

  4. Health-care technology assessment: a clinical perspective.

    Science.gov (United States)

    Chantler, Cyril

    2004-01-01

    Health technology assessment needs to relate to contemporary questions which concern public health-care systems: how to keep people healthy, how to focus on the needs of those with chronic disabilities and integrate care between the hospital and the community, how to encourage and audit effective teamwork, and how to establish a consensus about what is effective and affordable. Clinicians have an ethical responsibility to practice efficiently and economically, for profligacy in the care of one patient may mean that another is treated inadequately. For similar reasons, clinicians need to play a full role in the management of services. Advice from health technology assessment is vital and needs to be accurate, relevant, timely, clear, and accessible. As well as being concerned about what works, we need also to eliminate from practice what does not. Regular audit and appraisal of practice against the evidence base should be useful in this respect. Alternative approaches to management, such as the provision of care as opposed to aggressive treatments, need to be evaluated, and health technology assessment needs to consider how services are delivered, not just specific treatments. PMID:15176183

  5. Mass Spectrometry Instrumentation in Proteomics

    DEFF Research Database (Denmark)

    Sprenger, Richard Remko; Roepstorff, Peter

    2012-01-01

    Mass spectrometry has evolved into a crucial technology for the field of proteomics, enabling the comprehensive study of proteins in biological systems. Innovative developments have yielded flexible and versatile mass spectrometric tools, including quadrupole time-of-flight, linear ion trap......, Orbitrap and ion mobility instruments. Together they offer various and complementary capabilities in terms of ionization, sensitivity, speed, resolution, mass accuracy, dynamic range and methods of fragmentation. Mass spectrometers can acquire qualitative and quantitative information on a large scale...

  6. Advancing Porous Silicon Biosensor Technology for Use in Clinical Diagnostics

    Science.gov (United States)

    Bonanno, Lisa Marie

    Inexpensive and robust analytical techniques for detecting molecular recognition events are in great demand in healthcare, food safety, and environmental monitoring. Despite vast research in this area, challanges remain to develop practical biomolecular platforms that, meet the rigorous demands of real-world applications. This includes maintaining low-cost devices that are sensitive and specific in complex test specimens, are stable after storage, have short assay time, and possess minimal complexity of instrumentation for readout. Nanostructured porous silicon (PSi) material has been identified as an ideal candidate towards achieving these goals and the past decade has seen diverse proof-of-principle studies developing optical-based sensing techniques. In Part 1 of this thesis, the impact of surface chemistry and PSi morphology on detection sensitivity of target molecules is investigated. Initial proof-of-concept that PSi devices facilitate detection of protein in whole blood is demonstrated. This work highlights the importance of material stability and blocking chemistry for sensor use in real world biological samples. In addition, the intrinisic filtering capability of the 3-D PSi morphology is shown as an advantage in complex solutions, such as whole blood. Ultimately, this initial work identified a need to improve detection sensitivity of the PSI biosensor technique to facilitate clinical diagnostic use over relevant target concentration ranges. The second part of this thesis, builds upon sensitivity challenges that are highlighted in the first part of the thesis and development of a surface-bound competitive inhibition immunoassay facilitated improved detection sensitivity of small molecular weight targets (opiates) over a relevant clinical concentration range. In addition, optimization of assay protocol addressed issues of maintaining stability of sensors after storage. Performance of the developed assay (specificity and sensitivity) was then validated in a

  7. Human saliva proteome: an overview

    Science.gov (United States)

    Griffin, Timothy J.

    2014-06-01

    Human saliva contains a rich mixture of biomolecules. Proteins are a major component of this mixture. Given their role as the molecular effectors within biological systems, ranging from catalysis to transport to structure, proteins have great potential as biomarkers of health and disease. The ability to collect these salivary biomarkers easily using non-invasive means makes saliva proteins even more attractive for diagnostic applications. Thousands of proteins are now to be known to be present in human saliva - discovered using proteomic technologies. Emerging technologies are now making it possible to go beyond large-scale cataloging of salivary proteins. These include approaches to catalog protein contributions from the community of microorganisms residing in the oral cavity (metaproteomics) that may reflect the health state of the human host. New mass spectrometry-based proteomics methods are also emerging, shifting the emphasis from large-scale discovery experiments to hypothesis-driven assays for profiling proteins of interest within saliva, enabling validation of their association with specific health conditions. This paper provides a brief overview of efforts to catalog the proteome of human saliva. Recent developments making possible characterization of the metaproteome of human saliva will be discussed, and technologies driving new mass spectrometry-based assays for targeted analysis of proteins within complex samples, such as saliva.

  8. Unraveling the pathogenesis of type 1 diabetes with proteomics: present and future directions

    DEFF Research Database (Denmark)

    Sparre, Thomas; Larsen, Martin Røssel; Heding, Peter E; Karlsen, Allan E; Jensen, Ole N; Pociot, Flemming Michael

    2005-01-01

    . Proteomics may be useful in describing the protein expression profile and thus the diabetic phenotype. Relatively few studies using proteomics technologies to investigate the T1D pathogenesis have been published to date despite the defined target organ, the beta-cell. Proteomics has been applied in studies...

  9. Proteomics of human mitochondria

    DEFF Research Database (Denmark)

    Palmfeldt, Johan; Bross, Peter

    2016-01-01

    Proteomics have passed through a tremendous development in the recent years by the development of ever more sensitive, fast and precise mass spectrometry methods. The dramatically increased research in the biology of mitochondria and their prominent involvement in all kinds of diseases and ageing...... sensitivity of mass spectrometry technology aids in lowering this hurdle and new approaches like generation of induced pluripotent cells from somatic cells allow to produce patient-specific cellular disease models with great potential. We describe which human sample types are accessible, review the status of...... the catalog of human mitochondrial proteins and discuss proteins with dual localization in mitochondria and other cellular compartments. We describe the status and developments of pertinent mass spectrometric strategies, and the use of databases and bioinformatics. Using selected illustrative examples...

  10. Plasma Proteome Profiling to Assess Human Health and Disease.

    Science.gov (United States)

    Geyer, Philipp E; Kulak, Nils A; Pichler, Garwin; Holdt, Lesca M; Teupser, Daniel; Mann, Matthias

    2016-03-23

    Proteins in the circulatory system mirror an individual's physiology. In daily clinical practice, protein levels are generally determined using single-protein immunoassays. High-throughput, quantitative analysis using mass-spectrometry-based proteomics of blood, plasma, and serum would be advantageous but is challenging because of the high dynamic range of protein abundances. Here, we introduce a rapid and robust "plasma proteome profiling" pipeline. This single-run shotgun proteomic workflow does not require protein depletion and enables quantitative analysis of hundreds of plasma proteomes from 1 μl single finger pricks with 20 min gradients. The apolipoprotein family, inflammatory markers such as C-reactive protein, gender-related proteins, and >40 FDA-approved biomarkers are reproducibly quantified (CV proteome obtained by simple peptide pre-fractionation. Plasma proteome profiling delivers an informative portrait of a person's health state, and we envision its large-scale use in biomedicine. PMID:27135364

  11. Integration of proteomics into systems biology of cancer

    OpenAIRE

    Hanash, S; Schliekelman, M.; Q. Zhang; Taguchi, A

    2012-01-01

    Deciphering the complexity and heterogeneity of cancer benefits from integration of proteomic level data into systems biology efforts. The opportunities available as a result of advances in proteomic technologies, the successes to date and the challenges involved in integrating diverse datasets are addressed in this review.

  12. Virtual Labs in proteomics: new E-learning tools.

    Science.gov (United States)

    Ray, Sandipan; Koshy, Nicole Rachel; Reddy, Panga Jaipal; Srivastava, Sanjeeva

    2012-05-17

    Web-based educational resources have gained enormous popularity recently and are increasingly becoming a part of modern educational systems. Virtual Labs are E-learning platforms where learners can gain the experience of practical experimentation without any direct physical involvement on real bench work. They use computerized simulations, models, videos, animations and other instructional technologies to create interactive content. Proteomics being one of the most rapidly growing fields of the biological sciences is now an important part of college and university curriculums. Consequently, many E-learning programs have started incorporating the theoretical and practical aspects of different proteomic techniques as an element of their course work in the form of Video Lectures and Virtual Labs. To this end, recently we have developed a Virtual Proteomics Lab at the Indian Institute of Technology Bombay, which demonstrates different proteomics techniques, including basic and advanced gel and MS-based protein separation and identification techniques, bioinformatics tools and molecular docking methods, and their applications in different biological samples. This Tutorial will discuss the prominent Virtual Labs featuring proteomics content, including the Virtual Proteomics Lab of IIT-Bombay, and E-resources available for proteomics study that are striving to make proteomic techniques and concepts available and accessible to the student and research community. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 14). Details can be found at: http://www.proteomicstutorials.org/. PMID:22484059

  13. Proteomics and Its Application in Biomarker Discovery and Drug Development

    Institute of Scientific and Technical Information of China (English)

    He Qing-Yu; Chiu Jen-Fu

    2004-01-01

    Proteomics is a research field aiming to characterize molecular and cellular dynamics in protein expression and function on a global level. The introduction of proteomics has been greatly broadening our view and accelerating our path in various medical researches. The most significant advantage of proteomics is its ability to examine a whole proteome or sub-proteome in a single experiment so that the protein alterations corresponding to a pathological or biochemical condition at a given time can be considered in an integrated way. Proteomic technology has been extensively used to tackle a wide variety of medical subjects including biomarker discovery and drug development. By complement with other new technique advance in genomics and bioinformatics,proteomics has a great potential to make considerable contribution to biomarker identification and revolutionize drug development process. A brief overview of the proteomic technologies will be provided and the application of proteomics in biomarker discovery and drug development will be discussed using our current research projects as examples.

  14. The Modified Technology Acceptance Model for Private Clinical Physicians: A Case Study in Malaysia, Penang

    Directory of Open Access Journals (Sweden)

    Annie Ng Cheng San

    2013-02-01

    Full Text Available Malaysia’s private clinic is wealth creator. To enhance its sustainable future, healthcare Information Technology (IT change is inevitable. However, its’ IT acceptance is limited. The past literatures showed physicians have different technology acceptance decision as compare to common users. Hence, understanding the physicians’ technology acceptance is critical for technology management success. This study aims to gauge the factors influence technology acceptance decision among the physicians in Malaysia, Penang private clinics. Due to different trait of physicians, a modified Technology Acceptance Model has been proposed with seven independent variables: physician’s attitude, perceived usefulness, perceived ease of use, IT vendor support, cost factor, training and education and social influence. Questionnaire was distributed to 350 registered private clinics under Penang Medical Practitioner Society. Total 189 questionnaires were returned and useable. Result of multiple regression analysis showed all the independent variables have a significant relationship with the physician’s behavioral intention of IT usage. The proposed model fitness is confirmed with coefficient of determination (R² of 90.8%. The proposed model provides a platform to enhance understanding and direction to conceptualize the clinical physician’s technology acceptance.

  15. Considerations in the development of circulating tumor cell technology for clinical use

    Directory of Open Access Journals (Sweden)

    Parkinson David R

    2012-07-01

    Full Text Available Abstract This manuscript summarizes current thinking on the value and promise of evolving circulating tumor cell (CTC technologies for cancer patient diagnosis, prognosis, and response to therapy, as well as accelerating oncologic drug development. Moving forward requires the application of the classic steps in biomarker development–analytical and clinical validation and clinical qualification for specific contexts of use. To that end, this review describes methods for interactive comparisons of proprietary new technologies, clinical trial designs, a clinical validation qualification strategy, and an approach for effectively carrying out this work through a public-private partnership that includes test developers, drug developers, clinical trialists, the US Food & Drug Administration (FDA and the US National Cancer Institute (NCI.

  16. PROTEOMICS in aquaculture

    DEFF Research Database (Denmark)

    Rodrigues, Pedro M.; Silva, Tomé S.; Dias, Jorge;

    2012-01-01

    proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological...... questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined...... nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue. This article is part of a Special Issue entitled: Farm animal proteomics....

  17. Proteomic Approaches for Biomarker Panels in Cancer.

    Science.gov (United States)

    Tanase, Cristiana; Albulescu, Radu; Neagu, Monica

    2016-01-01

    Proteomic technologies remain the main backbone of biomarkers discovery in cancer. The continuous development of proteomic technologies also enlarges the bioinformatics domain, thus founding the main pillars of cancer therapy. The main source for diagnostic/prognostic/therapy monitoring biomarker panels are molecules that have a dual role, being both indicators of disease development and therapy targets. Proteomic technologies, such as mass-spectrometry approaches and protein array technologies, represent the main technologies that can depict these biomarkers. Herein, we will illustrate some of the most recent strategies for biomarker discovery in cancer, including the development of immune-markers and the use of cancer stem cells as target therapy. The challenges of proteomic biomarker discovery need new forms of cross-disciplinary conglomerates that will result in increased and tailored access to treatments for patients; diagnostic companies would benefit from the enhanced co-development of companion diagnostics and pharmaceutical companies. In the technology optimization in biomarkers, immune assays are the leaders of discovery machinery. PMID:26565430

  18. Application of proteome technology in screening biomarkers associated with gastric cancer%蛋白质组技术在胃癌相关标志物筛查中的应用

    Institute of Scientific and Technical Information of China (English)

    Chibo Liu; Yong Liang; Haibao Wang; Chunqin Pan

    2008-01-01

    Objective:To initially explore the application of proteome technologies in study of serum,to establish two-dimensional gel electrophoresis (2-DE) profiles of human gastric cancer serum and paired normal serum,and to screen and identify differentially expressed proteins in poorly-differentiated gastric cancer serum and paired normal serum,in which try to find out significant biomarker candidates for gastric cancer.Methods:2-DE was adopted to separate the total proteins of poorly-differentiated gastric cancer serum and paired normal serum.After staining and analyzing by ImageMaster 2D Elite software,the differentially expressed proteins were identified by matrix-assisted laser desorption/ionization-time of flight- mass spectrometry (MALDI-TOF-MS).Results:2-DE serum profiles with high resolution were obtained.Five protein spots were found as differentially-expressed proteins and identified as Serpin B6 (Placental thrombin inhibitor) Cytoplasmic antiproteinase (CAP)(Protease inhibitor6) (P1-6),Septin-1 (LARP) (Serologically defined breast cancer antigen NY-BR-24),Kallikrein-6 precursor (Protease M) (Neurosin) (Zyme) (SP59),Hemoglobin beta chain,Hemoglobin beta chain and Beta-defensin 108 precursor (Beta-defensin 8) (DEFB-8).Conclusion:The differential proteins were demonstrated to present in poorly-differentiated gastric cancer serum and paired normal serum.The molecular biomarkers associated with poorly differentiated gastric cancer could be possibly identified by the high throughput screening proteome technology.

  19. STEM CELLS AND PROTEOMICS

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yong-ming; GUO Tian-nan; HUANG Shi-ang

    2006-01-01

    The distinctive features of proteomics are large-scale and high throughput. The key techniques of proteomics are two-dimensional gel electrophoresis, mass spectrometry and bioinformatics. Stem cell can differentiate into all kinds of cells, tissues and organs. There are many proteins and cytokines involved in the process of differentiation. Applying proteomics techniques to the research of the complex process of stem cell differentiation is of great importance to study the mechanism and applications of stem cell differentiation.

  20. Proteomic Analysis of Mrr1p- and Tac1p-Associated Differential Protein Expression in Azole-Resistant Clinical Isolates of Candida albicans

    OpenAIRE

    Hoehamer, Christopher F.; Cummings, Edwin D.; Hilliard, George M.; Morschhäuser, Joachim; Rogers, P. David

    2009-01-01

    Azole resistance in Candida albicans is frequently caused by the overexpression of multi-drug efflux pump genes MDR1, CDR1, and CDR2 due to gain-of-function mutations in the zinc cluster transcription factors Mrr1p and Tac1p. In this study, we performed a comparative proteomic analysis to identify proteins whose expression level is influenced by these transcription factors. Both 2-DE and PMF were used to examine the expression profiles of six pairs of matched C. albicans isolates carrying gai...

  1. Treatment of Clinical Solid Waste Using a Steam Autoclave as a Possible Alternative Technology to Incineration

    OpenAIRE

    Mohd Omar Ab Kadir; Nik Norulaini Nik Ab Rahman; Md. Sohrab Hossain; Md. Zaidul Islam Sarker; Venugopal Balakrishnan

    2012-01-01

    A steam autoclave was used to sterilize bacteria in clinical solid waste in order to determine an alternative to incineration technology in clinical solid waste management. The influence of contact time (0, 5, 15, 30 and 60 min) and temperature (111 °C, 121 °C and 131 °C) at automated saturated steam pressure was investigated. Results showed that with increasing contact time and temperature, the number of surviving bacteria decreased. The optimum experimental conditions as measured by degree ...

  2. Incorporating INTERACT II Clinical Decision Support Tools into Nursing Home Health Information Technology

    OpenAIRE

    Handler, Steven M.; Sharkey, Siobhan S.; Hudak, Sandra; Ouslander, Joseph G.

    2011-01-01

    A substantial reduction in hospitalization rates has been associated with the implementation of the Interventions to Reduce Acute Care Transfers (INTERACT) quality improvement intervention using the accompanying paper-based clinical practice tools (INTERACT II). There is significant potential to further increase the impact of INTERACT by integrating INTERACT II tools into nursing home (NH) health information technology (HIT) via standalone or integrated clinical decision support (CDS) systems...

  3. A comparison of methods for classifying clinical samples based on proteomics data: a case study for statistical and machine learning approaches.

    Directory of Open Access Journals (Sweden)

    Dayle L Sampson

    Full Text Available The discovery of protein variation is an important strategy in disease diagnosis within the biological sciences. The current benchmark for elucidating information from multiple biological variables is the so called "omics" disciplines of the biological sciences. Such variability is uncovered by implementation of multivariable data mining techniques which come under two primary categories, machine learning strategies and statistical based approaches. Typically proteomic studies can produce hundreds or thousands of variables, p, per observation, n, depending on the analytical platform or method employed to generate the data. Many classification methods are limited by an n≪p constraint, and as such, require pre-treatment to reduce the dimensionality prior to classification. Recently machine learning techniques have gained popularity in the field for their ability to successfully classify unknown samples. One limitation of such methods is the lack of a functional model allowing meaningful interpretation of results in terms of the features used for classification. This is a problem that might be solved using a statistical model-based approach where not only is the importance of the individual protein explicit, they are combined into a readily interpretable classification rule without relying on a black box approach. Here we incorporate statistical dimension reduction techniques Partial Least Squares (PLS and Principal Components Analysis (PCA followed by both statistical and machine learning classification methods, and compared them to a popular machine learning technique, Support Vector Machines (SVM. Both PLS and SVM demonstrate strong utility for proteomic classification problems.

  4. Proteomic-coupled-network analysis of T877A-androgen receptor interactomes can predict clinical prostate cancer outcomes between White (non-Hispanic and African-American groups.

    Directory of Open Access Journals (Sweden)

    Naif Zaman

    Full Text Available The androgen receptor (AR remains an important contributor to the neoplastic evolution of prostate cancer (CaP. CaP progression is linked to several somatic AR mutational changes that endow upon the AR dramatic gain-of-function properties. One of the most common somatic mutations identified is Thr877-to-Ala (T877A, located in the ligand-binding domain, that results in a receptor capable of promiscuous binding and activation by a variety of steroid hormones and ligands including estrogens, progestins, glucocorticoids, and several anti-androgens. In an attempt to further define somatic mutated AR gain-of-function properties, as a consequence of its promiscuous ligand binding, we undertook a proteomic/network analysis approach to characterize the protein interactome of the mutant T877A-AR in LNCaP cells under eight different ligand-specific treatments (dihydrotestosterone, mibolerone, R1881, testosterone, estradiol, progesterone, dexamethasone, and cyproterone acetate. In extending the analysis of our multi-ligand complexes of the mutant T877A-AR we observed significant enrichment of specific complexes between normal and primary prostatic tumors, which were furthermore correlated with known clinical outcomes. Further analysis of certain mutant T877A-AR complexes showed specific population preferences distinguishing primary prostatic disease between white (non-Hispanic vs. African-American males. Moreover, these cancer-related AR-protein complexes demonstrated predictive survival outcomes specific to CaP, and not for breast, lung, lymphoma or medulloblastoma cancers. Our study, by coupling data generated by our proteomics to network analysis of clinical samples, has helped to define real and novel biological pathways in complicated gain-of-function AR complex systems.

  5. Proteomics of Rice Seed Germination

    Directory of Open Access Journals (Sweden)

    Dongli eHe

    2013-07-01

    Full Text Available Seed is a condensed form of plant. Under suitable environmental conditions, it can resume the metabolic activity from physiological quiescent status, and mobilize the reserves, biosynthesize new proteins, regenerate organelles and cell membrane, eventually protrude the radicle and enter into seedling establishment. So far, how these activities are regulated in a coordinated and sequential manner is largely unknown. With the availability of more and more genome sequence information and the development of mass spectrometry (MS technology, proteomics has been widely applied in analyzing the mechanisms of different biological processes, and proved to be very powerful. Regulation of rice seed germination is critical for rice cultivation. In recent years, a lot of proteomic studies have been conducted in exploring the gene expression regulation, reserves mobilization and metabolisms reactivation, which brings us new insights on the mechanisms of metabolism regulation during this process. Nevertheless, it also invokes a lot of questions. In this mini-review, we summarized the progress in the proteomic studies of rice seed germination. The current challenges and future perspectives were also discussed, which might be helpful for the following studies.

  6. Proteomic Investigations into Hemodialysis Therapy

    Directory of Open Access Journals (Sweden)

    Mario Bonomini

    2015-12-01

    Full Text Available The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane’s performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane’s bio(incompatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research.

  7. Pre-clinical research in small animals using radiotherapy technology. A bidirectional translational approach

    International Nuclear Information System (INIS)

    For translational cancer research, pre-clinical in-vivo studies using small animals have become indispensable in bridging the gap between in-vitro cell experiments and clinical implementation. When setting up such small animal experiments, various biological, technical and methodical aspects have to be considered. In this work we present a comprehensive topical review based on relevant publications on irradiation techniques used for pre-clinical cancer research in mice and rats. Clinical radiotherapy treatment devices for the application of external beam radiotherapy and brachytherapy as well as dedicated research irradiation devices are feasible for small animal irradiation depending on the animal model and the experimental goals. In this work, appropriate solutions for the technological transfer of human radiation oncology to small animal radiation research are summarised. Additionally, important information concerning the experimental design is provided such that reliable and clinically relevant results can be attained.

  8. Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

    Science.gov (United States)

    Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W; Moritz, Robert L

    2015-02-01

    Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. PMID:25418363

  9. Using technology within the treatment of eating disorders: a clinical practice review.

    Science.gov (United States)

    Shingleton, Rebecca M; Richards, Lauren K; Thompson-Brenner, Heather

    2013-12-01

    The focus of this clinical practice review is to provide clinicians a framework for incorporating technology into the treatment of eating disorders (EDs). We detailed studies that were published within the past 11 years (2002-2012) and that included at least 10 participants. Our primary aims were to describe how technology has been used to enhance the delivery of ED treatment as well as report the effectiveness of these technology-based interventions. We also provided clinical applications and considerations for clinicians who wish to use technology within their own practice. We found that a range of technologies (e.g., televideo, e-mail, CD-ROM, Internet, text message) have been used as a means to either deliver or enhance treatment at various levels of care (e.g., therapy, guided self-help, treatment adjunct). The majority of the studies were based on cognitive-behavioral principles and included samples diagnosed with bulimia nervosa (BN), binge eating disorder (BED), or subclinical levels of BN or BED. Most researchers reported positive results, with a few caveats such as technology-based interventions may not be optimal for individuals with more severe pathology, and some individuals described wanting more personal interaction. The overarching finding was that technology may be successfully integrated within ED treatment and may offer new ways to extend ED interventions to individuals who may not otherwise have access to specialty ED care. PMID:23527906

  10. Shotgun MS proteomic analysis of bronchoalveolar lavage fluid in normal subjects.

    Science.gov (United States)

    Nguyen, Elizabeth V; Gharib, Sina A; Schnapp, Lynn M; Goodlett, David R

    2014-10-01

    We provide a review of proteomic techniques used to characterize the bronchoalveolar lavage fluid (BALF) proteome of normal healthy subjects. Bronchoalveolar lavage (BAL) is the most common technique for sampling the components of the alveolar space. The proteomic techniques used to study normal BALF include protein separation by 2DE, whereby proteins were identified by comparison to a reference gel as well as high pressure liquid chromatography (HPLC)-MS/MS, also known as shotgun proteomics. We summarize recent progress using shotgun MS technologies to define the normal BALF proteome. Surprisingly, we find that despite advances in shotgun proteomic technologies over the course of the last 10 years, which have resulted in greater numbers of proteins being identified, the functional landscape of normal BALF proteome was similarly described by all methods examined. PMID:24616423

  11. Mandibular fibular graft reconstruction with CAD/CAM technology: A clinical report and literature review.

    Science.gov (United States)

    Mehra, Mamta; Somohano, Tanya; Choi, Mijin

    2016-01-01

    This clinical report describes the treatment of a partially dentate patient who presented with dental implants placed in a reconstructed fibula graft in the mandible. A complete mouth rehabilitation with a maxillary complete denture and a mandibular implant-supported fixed complete denture was fabricated with computer-aided design and computer-aided machining technology. PMID:26372630

  12. SPS’ Digest: the Swiss Proteomics Society selection of proteomics articles

    OpenAIRE

    Hoogland, C.; Lion, N.; Palagi, P.M.; Sanchez, J. C.; Tissot, J. D.

    2005-01-01

    Despite the consolidation of the specialized proteomics literature around a few established journals, such as Proteomics, Molecular and Cellular Proteomics, and the Journal of Proteome Research, a lot of information is still spread in many different publications from different fields, such as analytical sciences, MS, bioinformatics, etc. The purpose of SPS’ Digest is to gather a selection of proteomics articles, to categorize them, and to make the list available on a periodic basis through a ...

  13. Shotgun Proteomic Analysis of Arabidopsis thaliana Leaves

    Science.gov (United States)

    Two shotgun tandem mass spectrometry proteomics approaches, Multidimensional Protein Identification Technology (MudPIT) and 1D-Gel-LC-MS/MS, were used to identify Arabidopsis thaliana leaf proteins. These methods utilize different protein/peptide separation strategies. Detergents not compatible wit...

  14. Human maternal plasma proteomic changes with parturition

    Directory of Open Access Journals (Sweden)

    Robert J. Phillips

    2014-12-01

    Significance: Proteomic technology is constantly advancing, and the latest techniques enable gel-free analysis of minimally preprocessed, complex biological samples, enabling simultaneous identification and quantification of many hundreds of proteins. The technique of TMT labelling and Orbitrap mass spectrometry is applicable to the analysis of serial maternal plasma samples in order to identify potential markers of the onset of labour.

  15. Proteomics in evolutionary ecology.

    Science.gov (United States)

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  16. IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomic biomarker discovery

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Tujin; Zhou, Jianying; Gritsenko, Marina A.; Hossain, Mahmud; Camp, David G.; Smith, Richard D.; Qian, Weijun

    2012-02-01

    Interest in the application of advanced proteomics technologies to human blood plasma- or serum-based clinical samples for the purpose of discovering disease biomarkers continues to grow; however, the enormous dynamic range of protein concentrations in these types of samples (often >10 orders of magnitude) represents a significant analytical challenge, particularly for detecting low-abundance candidate biomarkers. In response, immunoaffinity separation methods for depleting multiple high- and moderate-abundance proteins have become key tools for enriching low-abundance proteins and enhancing detection of these proteins in plasma proteomics. Herein, we describe IgY14 and tandem IgY14-Supermix separation methods for removing 14 high-abundance and up to 60 moderate-abundance proteins, respectively, from human blood plasma and highlight their utility when combined with liquid chromatography-tandem mass spectrometry for interrogating the human plasma proteome.

  17. Comparative proteomic study of colorectal carcinoma with different clinical stages%不同临床分期大肠癌组织的蛋白质组学比较研究

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Objective: Colorectal carcinoma clinical stage associated proteins would be found by comparing differential expressed proteins from colorectal carcinoma tissues with different clinical stages. Methods: Total protein from colorectal carcinoma tissues were extracted; differential proteome profiles were established and analyzed by means of immobilized pH gradient-based two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). Results: Well-resolved, reproducible 2-DE profiles of human colorectal carcinoma tissues were obtained. Average protein spots were 970±41,980±32,1010±43,1240±34 in stage Ⅰ, stage Ⅱ,stage Ⅲ, stage Ⅳ respectively; Compared to stage Ⅰ, differential expressed protein spots was 52.00 ± 12 in stage Ⅱ, 42.00± 11 in stage Ⅲ, 72.00 ± 15 in stage Ⅳ; Part of differential expressing proteins were analyzed by mass spectrometry and bioinformation, 19 of them were well characterized. Three proteins were overexpressed in stage Ⅰ, stage Ⅲ, stage Ⅳ, and one protein were overexpressed in stage Ⅳ exclusively. Conclusion: Differential expressed proteins exist in clinical stage of colorectal carcinoma, which would be biomarkers for diagnosis and prediction of prognosis.

  18. Comprehensive proteomic analysis of human pancreatic juice

    DEFF Research Database (Denmark)

    Grønborg, Mads; Bunkenborg, Jakob; Kristiansen, Troels Zakarias;

    2004-01-01

    chromatography tandem mass spectrometry (LC-MS/MS). A total of 170 unique proteins were identified including known pancreatic cancer tumor markers (e.g., CEA, MUC1) and proteins overexpressed in pancreatic cancers (e.g., hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein (HIP/PAP) and lipocalin 2......Proteomic technologies provide an excellent means for analysis of body fluids for cataloging protein constituents and identifying biomarkers for early detection of cancers. The biomarkers currently available for pancreatic cancer, such as CA19-9, lack adequate sensitivity and specificity...... in this study could be directly assessed for their potential as biomarkers for pancreatic cancer by quantitative proteomics methods or immunoassays....

  19. Unraveling pancreatic islet biology by quantitative proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jianying; Dann, Geoffrey P.; Liew, Chong W.; Smith, Richard D.; Kulkarni, Rohit N.; Qian, Weijun

    2011-08-01

    The pancreatic islets of Langerhans play a critical role in maintaining blood glucose homeostasis by secreting insulin and several other important peptide hormones. Impaired insulin secretion due to islet dysfunction is linked to the pathogenesis underlying both Type 1 and Type 2 diabetes. Over the past 5 years, emerging proteomic technologies have been applied to dissect the signaling pathways that regulate islet functions and gain an understanding of the mechanisms of islet dysfunction relevant to diabetes. Herein, we briefly review some of the recent quantitative proteomic studies involving pancreatic islets geared towards gaining a better understanding of islet biology relevant to metabolic diseases.

  20. Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level

    Energy Technology Data Exchange (ETDEWEB)

    Hettich, Robert {Bob} L [ORNL

    2009-01-01

    The increase in sequencing capacity led to a new wave of metagenomic projects, enabling and setting the prerequisite for the application of environmental proteomics technologies. This review describes the current status of environmental proteomics. It describes sample preparation as well as the two major technologies applied within this field: two-dimensional electrophoresis-based environmental proteomics and liquid chromatography-mass spectrometry-based environmental proteomics. It also highlights current publications and describes major scientific findings. The review closes with a discussion of critical improvements in the area of integrating experimental mass spectrometry technologies with bioinformatics as well as improved sample handling.

  1. Knowledge Translation: Moving Proteomics Science to Innovation in Society.

    Science.gov (United States)

    Holmes, Christina; McDonald, Fiona; Jones, Mavis; Graham, Janice

    2016-06-01

    Proteomics is one of the pivotal next-generation biotechnologies in the current "postgenomics" era. Little is known about the ways in which innovative proteomics science is navigating the complex socio-political space between laboratory and society. It cannot be assumed that the trajectory between proteomics laboratory and society is linear and unidirectional. Concerned about public accountability and hopes for knowledge-based innovations, funding agencies and citizens increasingly expect that emerging science and technologies, such as proteomics, are effectively translated and disseminated as innovation in society. Here, we describe translation strategies promoted in the knowledge translation (KT) and science communication literatures and examine the use of these strategies within the field of proteomics. Drawing on data generated from qualitative interviews with proteomics scientists and ethnographic observation of international proteomics conferences over a 5-year period, we found that proteomics science incorporates a variety of KT strategies to reach knowledge users outside the field. To attain the full benefit of KT, however, proteomics scientists must challenge their own normative assumptions and approaches to innovation dissemination-beyond the current paradigm relying primarily on publication for one's scientific peers within one's field-and embrace the value of broader (interdisciplinary) KT strategies in promoting the uptake of their research. Notably, the Human Proteome Organization (HUPO) is paying increasing attention to a broader range of KT strategies, including targeted dissemination, integrated KT, and public outreach. We suggest that increasing the variety of KT strategies employed by proteomics scientists is timely and would serve well the omics system sciences community. PMID:27223900

  2. Mass spectrometry in food proteomics: a tutorial.

    Science.gov (United States)

    Cunsolo, Vincenzo; Muccilli, Vera; Saletti, Rosaria; Foti, Salvatore

    2014-09-01

    In the last decades, the continuous and rapid evolution of proteomic approaches has provided an efficient platform for the characterization of food-derived proteins. Particularly, the impressive increasing in performance and versatility of the MS instrumentation has contributed to the development of new analytical strategies for proteins, evidencing how MS arguably represents an indispensable tool in food proteomics. Investigation of protein composition in foodstuffs is helpful for understanding the relationship between the protein content and the nutritional and technological properties of foods, the production of methods for food traceability, the assessment of food quality and safety, including the detection of allergens and microbial contaminants in foods, or even the characterization of genetically modified products. Given the high variety of the food-derived proteins and considering their differences in chemical and physical properties, a single proteomic strategy for all purposes does not exist. Rather, proteomic approaches need to be adapted to each analytical problem, and development of new strategies is necessary in order to obtain always the best results. In this tutorial, the most relevant aspects of MS-based methodologies in food proteomics will be examined, and their advantages and drawbacks will be discussed. PMID:25230173

  3. Human Pituitary Adenoma Proteomics: New Progresses and Perspectives.

    Science.gov (United States)

    Zhan, Xianquan; Wang, Xiaowei; Cheng, Tingting

    2016-01-01

    Pituitary adenoma (PA) is a common intracranial neoplasm that impacts on human health through interfering hypothalamus-pituitary-target organ axis systems. The development of proteomics gives great promises in the clarification of molecular mechanisms of a PA and discovery of effective biomarkers for prediction, prevention, early-stage diagnosis, and treatment for a PA. A great progress in the field of PA proteomics has been made in the past 10 years, including (i) the use of laser-capture microdissection, (ii) proteomics analyses of functional PAs (such as prolactinoma), invasive and non-invasive non-functional pituitary adenomas (NFPAs), protein post-translational modifications such as phosphorylation and tyrosine nitration, NFPA heterogeneity, and hormone isoforms, (iii) the use of protein antibody array, (iv) serum proteomics and peptidomics, (v) the integration of proteomics and other omics data, and (vi) the proposal of multi-parameter systematic strategy for a PA. This review will summarize these progresses of proteomics in PAs, point out the existing drawbacks, propose the future research directions, and address the clinical relevance of PA proteomics data, in order to achieve our long-term goal that is use of proteomics to clarify molecular mechanisms, construct molecular networks, and discover effective biomarkers. PMID:27303365

  4. Human pituitary adenoma proteomics: new progresses and perspectives

    Directory of Open Access Journals (Sweden)

    Xianquan eZhan

    2016-05-01

    Full Text Available Pituitary adenoma (PA is a commonly intracranial neoplasm that impacts on human health through interfering hypothalamus-pituitary-target organ axis systems. The development of proteomics gives great promises in clarification of molecular mechanisms of a pituitary adenoma and discovery of effective biomarkers for prediction, prevention, early-stage diagnosis and treatment of a PA. A great progress in the field of PA proteomics has been made in the past ten years, including (i the use of laser capture microdissection, (ii proteomics analyses of functional PAs (FPAs, such as prolactinoma, invasive and noninvasive nonfunctional PAs (NFPAs, protein post-translational modifications (PTMs including phosphorylation and tyrosine nitration, NFPA heterogeneity, and hormone isoforms, (iii the use of protein antibody array, (iv serum proteomics and peptidomics, (v integration of proteomics and other omics data, and (vi proposal of multi-parameter systematic strategy for a PA. This review will summarize those progresses of proteomics in PAs, point out the existing drawbacks, propose the future research directions, and address the clinical relevance of PA proteomics data, in order to achieve our long-term goal that is use of proteomics to clarify molecular mechanisms, construct molecular networks, and discover effective biomarkers.

  5. Can eye-tracking technology improve situational awareness in paramedic clinical education?

    Directory of Open Access Journals (Sweden)

    Williams B

    2013-11-01

    Full Text Available Brett Williams,1 Andrew Quested,1 Simon Cooper21Department of Community Emergency Health and Paramedic Practice, 2School of Nursing and Midwifery, Berwick, Monash University, Frankston, VIC, AustraliaAbstract: Human factors play a significant part in clinical error. Situational awareness (SA means being aware of one's surroundings, comprehending the present situation, and being able to predict outcomes. It is a key human skill that, when properly applied, is associated with reducing medical error: eye-tracking technology can be used to provide an objective and qualitative measure of the initial perception component of SA. Feedback from eye-tracking technology can be used to improve the understanding and teaching of SA in clinical contexts, and consequently, has potential for reducing clinician error and the concomitant adverse events.Keywords: eye-tracking, paramedic, situational awareness, medical error, pre hospital

  6. A systematic approach to modeling, capturing, and disseminating proteomics experimental data.

    Science.gov (United States)

    Taylor, Chris F; Paton, Norman W; Garwood, Kevin L; Kirby, Paul D; Stead, David A; Yin, Zhikang; Deutsch, Eric W; Selway, Laura; Walker, Janet; Riba-Garcia, Isabel; Mohammed, Shabaz; Deery, Michael J; Howard, Julie A; Dunkley, Tom; Aebersold, Ruedi; Kell, Douglas B; Lilley, Kathryn S; Roepstorff, Peter; Yates, John R; Brass, Andy; Brown, Alistair J P; Cash, Phil; Gaskell, Simon J; Hubbard, Simon J; Oliver, Stephen G

    2003-03-01

    Both the generation and the analysis of proteome data are becoming increasingly widespread, and the field of proteomics is moving incrementally toward high-throughput approaches. Techniques are also increasing in complexity as the relevant technologies evolve. A standard representation of both the methods used and the data generated in proteomics experiments, analogous to that of the MIAME (minimum information about a microarray experiment) guidelines for transcriptomics, and the associated MAGE (microarray gene expression) object model and XML (extensible markup language) implementation, has yet to emerge. This hinders the handling, exchange, and dissemination of proteomics data. Here, we present a UML (unified modeling language) approach to proteomics experimental data, describe XML and SQL (structured query language) implementations of that model, and discuss capture, storage, and dissemination strategies. These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository. PMID:12610571

  7. New applications of Antrad Medical's thawing technology : Applications within the clinical and laboratory segment

    OpenAIRE

    Truvé, Malin; Kilegran, Johanna

    2016-01-01

    Antrad Medical has developed an ultra-fast blood plasma thawing device named UFT100. The method is based on thawing with an oscillating electrical field and unlike water baths it is a dry method. Fast and homogeneous thawing is achieved. This project investigates new possible applications where this thawing technology could be used within the clinical and laboratory segment. The aim was to identify existing thawing and heating methods for a substance that can be improved and potentially repla...

  8. High intensity focused ultrasound treatment of small renal masses: Clinical effectiveness and technological advances

    OpenAIRE

    Nabi, G; Goodman, C; Melzer, A.

    2010-01-01

    The review summarises the technological advances in the application of high-intensity focused ultrasound for small renal masses presumed to be cancer including the systematic review of its clinical application. Current progress in the area of magnetic resonance image guided ultrasound ablation is also appraised. Specifically, organ tracking and real time monitoring of temperature changes during the treatment are discussed. Finally, areas of future research interest are outlined.

  9. Integration Of Microarray Technology Into Prenatal Diagnosis: Counseling Issues Generated During The NICHD Clinical Trial

    OpenAIRE

    Wapner, Ronald J.; Driscoll, Deborah A.; Simpson, Joe Leigh

    2012-01-01

    Cytogenetic microarray analysis (CMA) in prenatal testing detects chromosome abnormalities and new genetic syndromes that would be missed by conventional cytogenetics and has the potential to significantly enhance prenatal genetic evaluation. A large NICHD-sponsored multi-centered trial to assess the role of CMA as a primary prenatal diagnostic tool has been completed, and results will soon be available. Integration of this technology into clinical care will require thoughtful changes in pati...

  10. [Proteomics in infectious diseases].

    Science.gov (United States)

    Quero, Sara; Párraga-Niño, Noemí; García-Núñez, Marian; Sabrià, Miquel

    2016-04-01

    Infectious diseases have a high incidence in the population, causing a major impact on global health. In vitro culture of microorganisms is the first technique applied for infection diagnosis which is laborious and time consuming. In recent decades, efforts have been focused on the applicability of «Omics» sciences, highlighting the progress provided by proteomic techniques in the field of infectious diseases. This review describes the management, processing and analysis of biological samples for proteomic research. PMID:25583331

  11. The Redox Proteome*

    OpenAIRE

    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,...

  12. Proteomics study revealed altered proteome of Dichogaster curgensis upon exposure to fly ash.

    Science.gov (United States)

    Markad, Vijaykumar L; Adav, Sunil S; Ghole, Vikram S; Sze, Siu Kwan; Kodam, Kisan M

    2016-10-01

    Fly ash is toxic and its escalating use as a soil amendment and disposal by dumping into environment is receiving alarming attention due to its impact on environment. Proteomics technology is being used for environmental studies since proteins respond rapidly when an organism is exposed to a toxicant, and hence soil engineers such as earthworms are used as model organisms to assess the toxic effects of soil toxicants. This study adopted proteomics technology and profiled proteome of earthworm Dichogaster curgensis that was exposed to fly ash, with main aim to elucidate fly ash effects on cellular and metabolic pathways. The functional classification of identified proteins revealed carbohydrate metabolism (14.36%), genetic information processing (15.02%), folding, sorting and degradation (10.83%), replication and repair (3.95%); environmental information processing (2.19%), signal transduction (9.61%), transport and catabolism (17.27%), energy metabolism (6.69%), etc. in the proteome. Proteomics data and functional assays revealed that the exposure of earthworm to fly ash induced protein synthesis, up-regulation of gluconeogenesis, disturbed energy metabolism, oxidative and cellular stress, and mis-folding of proteins. The regulation of ubiquitination, proteasome and modified alkaline comet assay in earthworm coelomocytes suggested DNA-protein cross link affecting chromatin remodeling and protein folding. PMID:27371791

  13. Contribution of proteomics to the management of vascular disorders

    Directory of Open Access Journals (Sweden)

    Fernando de la Cuesta

    2015-06-01

    Full Text Available Vascular disorders, and in particular atherothrombosis, are currently a leading cause of morbidity and mortality in Western societies. Proteomics research into these disorders has helped improving our knowledge of the underlying mechanisms involved in the development of atherothrombosis, as well as providing novel biomarkers to diagnose and for the prognosis of this disease. However, the application of these advances into clinical use has not followed this trend. In this review we explore the potential of Proteomics and Metabolomics for the management of vascular disorders, paying special attention to atherothrombosis and aiming to guide the reader from the experimental design of proteomic analysis through the initial discovery phase to the clinical implementation of biomarkers or therapeutic targets (Fig. 1, providing state-of-the-art proteomic studies to exemplify the concepts addressed.

  14. Web Resources for Mass Spectrometry-based Proteomics

    Institute of Scientific and Technical Information of China (English)

    Tao Chen; Jie Zhao; Jie Ma; Yunping Zhu

    2015-01-01

    With the development of high-resolution and high-throughput mass spectrometry (MS) technology, a large quantum of proteomic data is continually being generated. Collecting and shar-ing these data are a challenge that requires immense and sustained human effort. In this report, we provide a classification of important web resources for MS-based proteomics and present rating of these web resources, based on whether raw data are stored, whether data submission is supported, and whether data analysis pipelines are provided. These web resources are important for biologists involved in proteomics research.

  15. Exploring the use of mobile technologies for the acquisition of clinical skills.

    Science.gov (United States)

    Clay, Collette A

    2011-08-01

    Mobile learning has the potential to supplement information communication technology (ICT), online learning and the traditional teaching and learning methods to educate practitioners in the clinical practice area. Following the development of several Post Graduate modules of learning for the theory and clinical skills required to undertake the Newborn Infant Physical Examination (NIPE), a small research study was undertaken to combine mobile learning and NIPE. The research study explored the hypothesis that mobile devices could be used in pedagogically effective ways to support and enhance the learning and acquisition of clinical skills in the clinical arena. Participants in the study each received a handheld mobile device (iPod) that had been loaded with several Reusable Learning Objects (RLO) outlining each aspect of the physical examination to be performed. At the end of the module (12 weeks in duration), each participant completed an evaluation questionnaire. Participants confirmed that mobile learning afforded flexibility in time and place of learning and captured their interest in the learning material. This study reports that the use of mobile technology for skill acquisition is creative and innovative, placing learning firmly in the hands of the learner. PMID:21112132

  16. Telerehabilitation Clinical and Vocational Applications for Assistive Technology: Research, Opportunities, and Challenges

    Directory of Open Access Journals (Sweden)

    Mark R. Schmeler

    2009-09-01

    Full Text Available Rehabilitation service providers in rural or underserved areas are often challenged in meeting the needs of their complex patients due to limited resources in their geographical area. Recruitment and retention of the rural clinical workforce are beset by the ongoing problems associated with limited continuing education opportunities, professional isolation, and the challenges inherent in coordinating rural community healthcare. People with disabilities who live in rural communities also face challenges accessing healthcare. Traveling long distances to a specialty clinic for necessary expertise may be troublesome due to inadequate or unavailable transportation, disability specific limitations, and financial limitations. Distance and lack of access are just two threats to quality of care that now being addressed by the use of videoconferencing, information exchange, and other telecommunication technologies that facilitate telerehabilitation. This white paper illustrates and summarizes clinical and vocational applications of telerehabilitation. We provide definitions related to the fields of telemedicine, telehealth, and telerehabilitation, and consider the impetus for telerehabilitation. We review the telerehabilitation literature for assistive technology applications; pressure ulcer prevention; virtual reality applications; speech-language pathology applications; seating and wheeled mobility applications; vocational rehabilitation applications; and cost effectiveness. We then discuss external telerehabilitation influencers, such as the positions of professional organizations. Finally, we summarize clinical and policy issues in a limited context appropriate to the scope of this paper. Keywords: Telerehabilitation, Telehealth, Telemedicine, Telepractice

  17. Telerehabilitation clinical and vocational applications for assistive technology: research, opportunities, and challenges.

    Science.gov (United States)

    Schmeler, Mark R; Schein, Richard M; McCue, Michael; Betz, Kendra

    2009-01-01

    Rehabilitation service providers in rural or underserved areas are often challenged in meeting the needs of their complex patients due to limited resources in their geographical area. Recruitment and retention of the rural clinical workforce are beset by the ongoing problems associated with limited continuing education opportunities, professional isolation, and the challenges inherent in coordinating rural community healthcare. People with disabilities who live in rural communities also face challenges accessing healthcare. Traveling long distances to a specialty clinic for necessary expertise may be troublesome due to inadequate or unavailable transportation, disability specific limitations, and financial limitations. Distance and lack of access are just two threats to quality of care that now being addressed by the use of videoconferencing, information exchange, and other telecommunication technologies that facilitate telerehabilitation. This white paper illustrates and summarizes clinical and vocational applications of telerehabilitation. We provide definitions related to the fields of telemedicine, telehealth, and telerehabilitation, and consider the impetus for telerehabilitation. We review the telerehabilitation literature for assistive technology applications; pressure ulcer prevention; virtual reality applications; speech-language pathology applications; seating and wheeled mobility applications; vocational rehabilitation applications; and cost-effectiveness. We then discuss external telerehabilitation influencers, such as the positions of professional organizations. Finally, we summarize clinical and policy issues in a limited context appropriate to the scope of this paper. PMID:25945163

  18. Understanding information synthesis in oral surgery for the design of systems for clinical information technology.

    Science.gov (United States)

    Suebnukarn, Siriwan; Chanakarn, Piyawadee; Phisutphatthana, Sirada; Pongpatarat, Kanchala; Wongwaithongdee, Udom; Oupadissakoon, Chanekrid

    2015-12-01

    An understanding of the processes of clinical decision-making is essential for the development of health information technology. In this study we have analysed the acquisition of information during decision-making in oral surgery, and analysed cognitive tasks using a "think-aloud" protocol. We studied the techniques of processing information that were used by novices and experts as they completed 4 oral surgical cases modelled from data obtained from electronic hospital records. We studied 2 phases of an oral surgeon's preoperative practice including the "diagnosis and planning of treatment" and "preparing for a procedure". A framework analysis approach was used to analyse the qualitative data, and a descriptive statistical analysis was made of the quantitative data. The results showed that novice surgeons used hypotheticodeductive reasoning, whereas experts recognised patterns to diagnose and manage patients. Novices provided less detail when they prepared for a procedure. Concepts regarding "signs", "importance", "decisions", and "process" occurred most often during acquisition of information by both novices and experts. Based on these results, we formulated recommendations for the design of clinical information technology that would help to improve the acquisition of clinical information required by oral surgeons at all levels of expertise in their clinical decision-making. PMID:26292558

  19. Single-Cell Sequencing Technology in Oncology: Applications for Clinical Therapies and Research

    Directory of Open Access Journals (Sweden)

    Baixin Ye

    2016-01-01

    Full Text Available Cellular heterogeneity is a fundamental characteristic of many cancers. A lack of cellular homogeneity contributes to difficulty in designing targeted oncological therapies. Therefore, the development of novel methods to determine and characterize oncologic cellular heterogeneity is a critical next step in the development of novel cancer therapies. Single-cell sequencing (SCS technology has been recently employed for analyzing the genetic polymorphisms of individual cells at the genome-wide level. SCS requires (1 precise isolation of the single cell of interest; (2 isolation and amplification of genetic material; and (3 descriptive analysis of genomic, transcriptomic, and epigenomic data. In addition to targeted analysis of single cells isolated from tumor biopsies, SCS technology may be applied to circulating tumor cells, which may aid in predicting tumor progression and metastasis. In this paper, we provide an overview of SCS technology and review the current literature on the potential application of SCS to clinical oncology and research.

  20. Web Resources for Mass Spectrometry-based Proteomics

    OpenAIRE

    Tao CHEN; Zhao, Jie; Ma, Jie; Zhu, Yunping

    2015-01-01

    With the development of high-resolution and high-throughput mass spectrometry (MS) technology, a large quantum of proteomic data is continually being generated. Collecting and sharing these data are a challenge that requires immense and sustained human effort. In this report, we provide a classification of important web resources for MS-based proteomics and present rating of these web resources, based on whether raw data are stored, whether data submission is supported, and whether data analy...

  1. A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

    Directory of Open Access Journals (Sweden)

    Vitor M Faca

    2008-06-01

    Full Text Available BACKGROUND: The complexity and heterogeneity of the human plasma proteome have presented significant challenges in the identification of protein changes associated with tumor development. Refined genetically engineered mouse (GEM models of human cancer have been shown to faithfully recapitulate the molecular, biological, and clinical features of human disease. Here, we sought to exploit the merits of a well-characterized GEM model of pancreatic cancer to determine whether proteomics technologies allow identification of protein changes associated with tumor development and whether such changes are relevant to human pancreatic cancer. METHODS AND FINDINGS: Plasma was sampled from mice at early and advanced stages of tumor development and from matched controls. Using a proteomic approach based on extensive protein fractionation, we confidently identified 1,442 proteins that were distributed across seven orders of magnitude of abundance in plasma. Analysis of proteins chosen on the basis of increased levels in plasma from tumor-bearing mice and corroborating protein or RNA expression in tissue documented concordance in the blood from 30 newly diagnosed patients with pancreatic cancer relative to 30 control specimens. A panel of five proteins selected on the basis of their increased level at an early stage of tumor development in the mouse was tested in a blinded study in 26 humans from the CARET (Carotene and Retinol Efficacy Trial cohort. The panel discriminated pancreatic cancer cases from matched controls in blood specimens obtained between 7 and 13 mo prior to the development of symptoms and clinical diagnosis of pancreatic cancer. CONCLUSIONS: Our findings indicate that GEM models of cancer, in combination with in-depth proteomic analysis, provide a useful strategy to identify candidate markers applicable to human cancer with potential utility for early detection.

  2. Severe childhood malaria syndromes defined by plasma proteome profiles.

    Directory of Open Access Journals (Sweden)

    Florence Burté

    Full Text Available BACKGROUND: Cerebral malaria (CM and severe malarial anemia (SMA are the most serious life-threatening clinical syndromes of Plasmodium falciparum infection in childhood. Therefore it is important to understand the pathology underlying the development of CM and SMA, as opposed to uncomplicated malaria (UM. Different host responses to infection are likely to be reflected in plasma proteome-patterns that associate with clinical status and therefore provide indicators of the pathogenesis of these syndromes. METHODS AND FINDINGS: Plasma and comprehensive clinical data for discovery and validation cohorts were obtained as part of a prospective case-control study of severe childhood malaria at the main tertiary hospital of the city of Ibadan, an urban and densely populated holoendemic malaria area in Nigeria. A total of 946 children participated in this study. Plasma was subjected to high-throughput proteomic profiling. Statistical pattern-recognition methods were used to find proteome-patterns that defined disease groups. Plasma proteome-patterns accurately distinguished children with CM and with SMA from those with UM, and from healthy or severely ill malaria-negative children. CONCLUSIONS: We report that an accurate definition of the major childhood malaria syndromes can be achieved using plasma proteome-patterns. Our proteomic data can be exploited to understand the pathogenesis of the different childhood severe malaria syndromes.

  3. Proteomics approaches to fibrotic disorders

    OpenAIRE

    Gucek Marjan

    2012-01-01

    Abstract This review provides an introduction to mass spectrometry based proteomics and discusses several proteomics approaches that are relevant in understanding the pathophysiology of fibrotic disorders and the approaches that are frequently used in biomarker discovery.

  4. Locating assistive technology research in a clinical setting: an occupational perspective.

    Science.gov (United States)

    Fowler-Davis, Sally; Evans, Laura; Cudd, Peter

    2015-01-01

    Peer research was used to identify the experience and perceptions of assistive technology and telecare adoption in a UK healthcare context. A narrative account of participation and learning is intended to provoke further dialogue. There have been a range of policy and implementation initiatives that are within the direct experience of organisational actors over the last 15 years and this engagement allows for specific reflection on the service achievements and some of the barriers to implementation of technology changes in rehabilitation practice and service design. Insights are presented that suggest a reification of research priorities and a need to align technology, through patient and public engagement, to provider priorities. In addition, an improvement in adoption would be based on sustained capacity building within the Occupational Therapy workforce and a re-focus on specific knowledge sharing and learning about technology. Given the shared desire to promote the sustained adoption of appropriate technology for assistance and rehabilitation it is suggested the voice of practitioners is strengthened through research and knowledge exchange in the clinical setting. PMID:26294543

  5. The prevalence of medical/clinical technology over psychosocial care actions in outpatient mental health services

    Directory of Open Access Journals (Sweden)

    Regina Celia Fiorati

    2013-10-01

    Full Text Available The scope of this study was to evaluate how aspects of mental health policy in Brazil have been conceived and implemented in outpatient services, such as the Regional Outpatient Mental Health Clinic and the Psychosocial Care Center II, both in Ribeirão Preto, São Paulo. Semi-direct interviews and focus groups were conducted with 22 health professionals. The theoretical method and data analysis were supported by the dialectical hermeneutic framework of Jürgen Habermas. The following aspects were detected: considerable technological advancement in health actions and centrality of clinical-medical technology in relation to other nonmedical therapeutic actions; the prioritization of treatment options emphasizing pathology and drug therapy, and a process of mounting precariousness in labor relations. With respect to psychosocial rehabilitation, analysis revealed that instrumental and technically-oriented treatment is imposed upon the practical and dialogical rationale proposed by Brazilian Psychiatric Reform. As an alternative, participatory evaluative research is required in order to unify clinical and psychosocial rehabilitation actions in therapeutic projects, while establishing mechanisms to promote the improvement of care based on the psychosocial care model.

  6. The prevalence of medical/clinical technology over psychosocial care actions in outpatient mental health services.

    Science.gov (United States)

    Fiorati, Regina Celia; Saeki, Toyoko

    2013-10-01

    The scope of this study was to evaluate how aspects of mental health policy in Brazil have been conceived and implemented in outpatient services, such as the Regional Outpatient Mental Health Clinic and the Psychosocial Care Center II, both in Ribeirão Preto, São Paulo. Semi-direct interviews and focus groups were conducted with 22 health professionals. The theoretical method and data analysis were supported by the dialectical hermeneutic framework of Jürgen Habermas. The following aspects were detected: considerable technological advancement in health actions and centrality of clinical-medical technology in relation to other nonmedical therapeutic actions; the prioritization of treatment options emphasizing pathology and drug therapy, and a process of mounting precariousness in labor relations. With respect to psychosocial rehabilitation, analysis revealed that instrumental and technically-oriented treatment is imposed upon the practical and dialogical rationale proposed by Brazilian Psychiatric Reform. As an alternative, participatory evaluative research is required in order to unify clinical and psychosocial rehabilitation actions in therapeutic projects, while establishing mechanisms to promote the improvement of care based on the psychosocial care model. PMID:24061022

  7. Proteomics - new analytical approaches

    International Nuclear Information System (INIS)

    Full text: Recent developments in the sequencing of the human genome have indicated that the number of coding gene sequences may be as few as 30,000. It is clear, however, that the complexity of the human species is dependent on the much greater diversity of the corresponding protein complement. Estimates of the diversity (discrete protein species) of the human proteome range from 200,000 to 300,000 at the lower end to 2,000,000 to 3,000,000 at the high end. In addition, proteomics (the study of the protein complement to the genome) has been subdivided into two main approaches. Global proteomics refers to a high throughput examination of the full protein set present in a cell under a given environmental condition. Focused proteomics refers to a more detailed study of a restricted set of proteins that are related to a specified biochemical pathway or subcellular structure. While many of the advances in proteomics will be based on the sequencing of the human genome, de novo characterization of protein microheterogeneity (glycosylation, phosphorylation and sulfation as well as the incorporation of lipid components) will be required in disease studies. To characterize these modifications it is necessary to digest the protein mixture with an enzyme to produce the corresponding mixture of peptides. In a process analogous to sequencing of the genome, shot-gun sequencing of the proteome is based on the characterization of the key fragments produced by such a digest. Thus, a glycopeptide and hence a specific glycosylation motif will be identified by a unique mass and then a diagnostic MS/MS spectrum. Mass spectrometry will be the preferred detector in these applications because of the unparalleled information content provided by one or more dimensions of mass measurement. In addition, highly efficient separation processes are an absolute requirement for advanced proteomic studies. For example, a combination of the orthogonal approaches, HPLC and HPCE, can be very powerful

  8. Global and targeted proteomics in Arabidopsis thaliana: A study of secondary metabolism and phytohormone signaling

    OpenAIRE

    Slade Jr, William O

    2013-01-01

    Proteomics is defined as a tool to explore how proteins control and regulate important molecular and physiological processes. Further, peptide-centric approaches, or bottom-up methods, provide more comprehensive coverage of a proteome compared to whole-protein approaches. This body of work assesses the technical feasibility of several bottom-up proteomics technologies applied to Arabidopsis thaliana, including gel-based methods, those that require peptide derivitization, and those that do n...

  9. Proteomics in biomarker research : Insights into the effects of aging and environment on biological systems

    OpenAIRE

    Amelina, Hanna

    2011-01-01

    Proteomics is the global analysis of proteins that covers a broad range of technologies aimed at determining the identity and quantity of proteins expressed in the cell, their three-dimensional structure and interaction partners. In contrast to genome, proteome reflects more accurately on the dynamic state of the cell, tissue, or an organism. Therefore much is expected from proteomics to yield better disease markers for early diagnosis and therapy monitoring, as well as biomarkers that would ...

  10. A survey of computational tools for downstream analysis of proteomic and other omic datasets

    OpenAIRE

    Karimpour-Fard, Anis; Epperson, L. Elaine; HUNTER, LAWRENCE E.

    2015-01-01

    Proteomics is an expanding area of research into biological systems with significance for biomedical and therapeutic applications ranging from understanding the molecular basis of diseases to testing new treatments, studying the toxicity of drugs, or biotechnological improvements in agriculture. Progress in proteomic technologies and growing interest has resulted in rapid accumulation of proteomic data, and consequently, a great number of tools have become available. In this paper, we review ...

  11. Mass Spectrometry-based Proteomics and Peptidomics for Systems Biology and Biomarker Discovery

    OpenAIRE

    Cunningham, Robert; Ma, Di; Li, Lingjun

    2012-01-01

    The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large datasets of proteins or peptides involved in various biological and disease progression processes producing testable hypothesis for complex biological questions. This review provides an introduction and insight to relevant topics in proteomics and peptidomics including biological material sel...

  12. Large-scale quantitative proteomics of cassava: achievements, current limitations and strategic advances

    OpenAIRE

    Vanderschuren, Hervé

    2016-01-01

    Vanderschuren Hervé1,2* 1) Plant Genetics Lab, Gembloux Agro-Bio Tech, University of Liège, Belgium, 2) Plant Biotechnology Lab, Swiss Federal Institute of Technology (ETH), Switzerland * Proteomics studies have gained increasing importance in crop research over the last decade. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins have been particularly instrumental to characterize pro...

  13. Translational plant proteomics: A perspective

    NARCIS (Netherlands)

    Agrawal, G.K.; Pedreschi, R.; Barkla, B.J.; Bindschedler, L.V.; Cramer, R.; Sarkar, A.; Renaut, J.; Job, D.; Rakwal, R.

    2012-01-01

    Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic v

  14. Comparative and Quantitative Global Proteomics Approaches: An Overview

    Directory of Open Access Journals (Sweden)

    Barbara Deracinois

    2013-10-01

    Full Text Available Proteomics became a key tool for the study of biological systems. The comparison between two different physiological states allows unravelling the cellular and molecular mechanisms involved in a biological process. Proteomics can confirm the presence of proteins suggested by their mRNA content and provides a direct measure of the quantity present in a cell. Global and targeted proteomics strategies can be applied. Targeted proteomics strategies limit the number of features that will be monitored and then optimise the methods to obtain the highest sensitivity and throughput for a huge amount of samples. The advantage of global proteomics strategies is that no hypothesis is required, other than a measurable difference in one or more protein species between the samples. Global proteomics methods attempt to separate quantify and identify all the proteins from a given sample. This review highlights only the different techniques of separation and quantification of proteins and peptides, in view of a comparative and quantitative global proteomics analysis. The in-gel and off-gel quantification of proteins will be discussed as well as the corresponding mass spectrometry technology. The overview is focused on the widespread techniques while keeping in mind that each approach is modular and often recovers the other.

  15. Mass-spectrometry-based draft of the human proteome.

    Science.gov (United States)

    Wilhelm, Mathias; Schlegl, Judith; Hahne, Hannes; Moghaddas Gholami, Amin; Lieberenz, Marcus; Savitski, Mikhail M; Ziegler, Emanuel; Butzmann, Lars; Gessulat, Siegfried; Marx, Harald; Mathieson, Toby; Lemeer, Simone; Schnatbaum, Karsten; Reimer, Ulf; Wenschuh, Holger; Mollenhauer, Martin; Slotta-Huspenina, Julia; Boese, Joos-Hendrik; Bantscheff, Marcus; Gerstmair, Anja; Faerber, Franz; Kuster, Bernhard

    2014-05-29

    Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all of which carry biological information that is not accessible by genomics or transcriptomics. Here we present a mass-spectrometry-based draft of the human proteome and a public, high-performance, in-memory database for real-time analysis of terabytes of big data, called ProteomicsDB. The information assembled from human tissues, cell lines and body fluids enabled estimation of the size of the protein-coding genome, and identified organ-specific proteins and a large number of translated lincRNAs (long intergenic non-coding RNAs). Analysis of messenger RNA and protein-expression profiles of human tissues revealed conserved control of protein abundance, and integration of drug-sensitivity data enabled the identification of proteins predicting resistance or sensitivity. The proteome profiles also hold considerable promise for analysing the composition and stoichiometry of protein complexes. ProteomicsDB thus enables navigation of proteomes, provides biological insight and fosters the development of proteomic technology. PMID:24870543

  16. Implementation of proteomics for cancer research: past, present, and future.

    Science.gov (United States)

    Karimi, Parisa; Shahrokni, Armin; Ranjbar, Mohammad R Nezami

    2014-01-01

    Cancer is the leading cause of the death, accounts for about 13% of all annual deaths worldwide. Many different fields of science are collaborating together studying cancer to improve our knowledge of this lethal disease, and find better solutions for diagnosis and treatment. Proteomics is one of the most recent and rapidly growing areas in molecular biology that helps understanding cancer from an omics data analysis point of view. The human proteome project was officially initiated in 2008. Proteomics enables the scientists to interrogate a variety of biospecimens for their protein contents and measure the concentrations of these proteins. Current necessary equipment and technologies for cancer proteomics are mass spectrometry, protein microarrays, nanotechnology and bioinformatics. In this paper, we provide a brief review on proteomics and its application in cancer research. After a brief introduction including its definition, we summarize the history of major previous work conducted by researchers, followed by an overview on the role of proteomics in cancer studies. We also provide a list of different utilities in cancer proteomics and investigate their advantages and shortcomings from theoretical and practical angles. Finally, we explore some of the main challenges and conclude the paper with future directions in this field. PMID:24761843

  17. Optical coherence tomography-current technology and applications in clinical and biomedical research

    DEFF Research Database (Denmark)

    Marschall, Sebastian; Sander, Birgit; Mogensen, Mette;

    2011-01-01

    as birefringence, motion, or the distributions of certain substances can be detected with high spatial resolution. Its main field of application is biomedical imaging and diagnostics. In ophthalmology, OCT is accepted as a clinical standard for diagnosing and monitoring the treatment of a number of...... retinal diseases, and OCT is becoming an important instrument for clinical cardiology. New applications are emerging in various medical fields, such as early-stage cancer detection, surgical guidance, and the early diagnosis of musculoskeletal diseases. OCT has also proven its value as a tool for...... developmental biology. The number of companies involved in manufacturing OCT systems has increased substantially during the last few years (especially due to its success in opthalmology), and this technology can be expected to continue to spread into various fields of application....

  18. Ubiquitous Diabetes Management System via Interactive Communication Based on Information Technologies: Clinical Effects and Perspectives

    Science.gov (United States)

    Cho, Jae-Hyoung; Kim, Hun-Sung; Han, Jae-Hoon; Lee, Jin-Hee; Oh, Jeong-Ah; Choi, Yoon-Hee

    2010-01-01

    New diabetes management systems based on interactive communication have been introduced recently, accompanying rapid advances in information technology; these systems are referred to as "ubiquitous diabetes management systems." In such ubiquitous systems, patients and medical teams can communicate via Internet or telecommunications, with patients uploading their glucose data and personal information, and medical teams sending optimal feedback. Clinical evidence from both long-term and short-term trials has been reported by some researchers. Such systems appear to be effective not only in reducing the levels of HbA1c but also in stabilizing glucose control. However, most notably, evidence for the cost-effectiveness of such a system should be demonstrated before it can be propagated out to the general population in actual clinical practice. To establish a cost-effective model, various types of clinical decision supporting software designed to reduce the labor time of physicians must first be developed. A number of sensors and devices for monitoring patients' data are expected to be available in the near future; thus, methods for automatic interconnections between devices and web charts were also developed. Further investigations to demonstrate the clinical outcomes of such a system should be conducted, hopefully leading to a new paradigm of diabetes management. PMID:21076573

  19. Participation of nurses in the execution of clinical research protocol about technological innovation

    Directory of Open Access Journals (Sweden)

    Luciane Patrícia Andreani Cabral

    2015-10-01

    Full Text Available AbstractOBJECTIVETo report the nurse's experience of inclusion in interdisciplinary clinical study about technological innovation, involving people with spinal cord injury.METHODDescriptive experience report. The empirical support was based on notes about perspectives and practice of clinical research, with a multi-professional nursing, physical education, physiotherapy and engineering staff.RESULTThe qualification includes the elaboration of the document for the Ethics Committee, familiarization among the members of staff and with the studied topic, and also an immersion into English. The nurse's knowledge gave support to the uptake of participants and time adequacy for data collection, preparation and assistance of the participants during the intervention and after collection. Nursing theories and processes have contributed to reveal risky diagnoses and the plan of care. It was the nurse's role to monitor the risk of overlapping methodological strictness to the human aspect. The skills for the clinical research must be the object of learning, including students in multidisciplinary researches.CONCLUSIONTo qualify the nurse for clinical research and to potentialize its caregiver essence, some changes are needed in the educational system, professional behavior, attitude and educational assistance.

  20. ProfileDB: a resource for proteomics and cross-omics biomarker discovery.

    Science.gov (United States)

    Bauer, Chris; Glintschert, Alexander; Schuchhardt, Johannes

    2014-05-01

    The increasing size and complexity of high-throughput datasets pose a growing challenge for researchers. Often very different (cross-omics) techniques with individual data analysis pipelines are employed making a unified biomarker discovery strategy and a direct comparison of different experiments difficult and time consuming. Here we present the comprehensive web-based application ProfileDB. The application is designed to integrate data from different high-throughput 'omics' data types (Transcriptomics, Proteomics, Metabolomics) with clinical parameters and prior knowledge on pathways and ontologies. Beyond data storage, ProfileDB provides a set of dedicated tools for study inspection and data visualization. The user can gain insights into a complex experiment with just a few mouse clicks. We will demonstrate the application by presenting typical use cases for the identification of proteomics biomarkers. All presented analyses can be reproduced using the public ProfileDB web server. The ProfileDB application is available by standard browser (Firefox 18+, Internet Explorer Version 9+) technology via http://profileDB.-microdiscovery.de/ (login and pass-word: profileDB). The installation contains several public datasets including different cross-'omics' experiments. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge. PMID:24270047

  1. Sympathetic Resonance Technology: scientific foundation and summary of biologic and clinical studies.

    Science.gov (United States)

    Rubik, Beverly

    2002-12-01

    Sympathetic Resonance Technology (SRT; Clarus Products, International, L.L.C., San Rafael, CA) is a novel technology used in consumer health care products to protect humans from the potentially harmful effects of stress. A summary of the previously unpublished studies on SRT, both basic and clinical, is presented. These studies collectively show that SRT mitigates the stress response for a variety of stressors such as chemical and electromagnetic stress in various biologic systems and multiple levels of organization, ranging from the molecular to the behavioral. A rudimentary model of how SRT may work at the level of the biofield, the endogenous electromagnetic field of the organism, is proposed. By interacting with key component frequencies in the biofield, SRT may stabilize the organism homeodynamically, thereby protecting it from the effects of stressful stimuli. PMID:12614535

  2. Inherited retinal disorders in South Africa and the clinical impact of evolving technologies.

    Science.gov (United States)

    Roberts, L; Goliath, R; Rebello, G; Bardien, S; September, A V; Bartmann, L; Loubser, F; Greenberg, L J; Ramesar, R S

    2016-01-01

    Retinal degenerative disorders (RDDs) encompass a group of inherited diseases characterised by vision loss. The genetic and clinical complexity poses a challenge in unravelling the molecular genetic aetiology of this group of disorders. Furthermore, the population diversity in South Africa (SA) presents researchers with a particularly complicated task. Rapid advances in the development of cutting-edge technological platforms over the past two decades, however, have assisted in overcoming some of the challenges. The RDD research team has utilised these escalating technologies, which has facilitated a corresponding increase in molecular diagnoses. A biorepository has been established and comprises ~3 200 patient DNA samples archived with many forms of RDD (including retinitis pigmentosa, macular dystrophies, Stargardt disease, Leber congenital amaurosis, Usher syndrome and Bardet Biedl syndrome). A comprehensive review is presented of the SA journey spanning 25 years, into elucidating the molecular genetic basis of various forms of RDD in SA. PMID:27245521

  3. Clinical Application of Three-Dimensional Printing Technology in Craniofacial Plastic Surgery

    OpenAIRE

    Choi, Jong Woo; Kim, Namkug

    2015-01-01

    Three-dimensional (3D) printing has been particularly widely adopted in medical fields. Application of the 3D printing technique has even been extended to bio-cell printing for 3D tissue/organ development, the creation of scaffolds for tissue engineering, and actual clinical application for various medical parts. Of various medical fields, craniofacial plastic surgery is one of areas that pioneered the use of the 3D printing concept. Rapid prototype technology was introduced in the 1990s to m...

  4. Cancer Proteomics: The State of the Art

    Directory of Open Access Journals (Sweden)

    Paul C. Herrmann

    2001-01-01

    Full Text Available Now that the human genome has been determined, the field of proteomics is ramping up to tackle the vast protein networks that both control and are controlled by the information encoded by the genome. The study of proteomics should yield an unparalleled understanding of cancer as well as an invaluable new target for therapeutic intervention and markers for early detection. This rapidly expanding field attempts to track the protein interactions responsible for all cellular processes. By careful analysis of these systems, a detailed understanding of the molecular causes and consequences of cancer should emerge. A brief overview of some of the cutting edge technologies employed by this rapidly expanding field is given, along with specific examples of how these technologies are employed. Soon cellular protein networks will be understood at a level that will permit a totally new paradigm of diagnosis and will allow therapy tailored to individual patients and situations.

  5. Mining the active proteome of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Renier A. L. Van Der Hoorn

    2011-11-01

    Full Text Available Assigning functions to the >30.000 proteins encoded by the Arabidopsis genome is a challenging task of the Arabidopsis Functional Genomics Network. Although genome-wide technologies like proteomics and transcriptomics have generated a wealth of information that significantly accelerated gene annotation, protein activities are poorly predicted by transcript or protein levels as protein activities are post-translationally regulated. To directly display protein activities in Arabidopsis proteomes, we developed and applied Activity-based Protein Profiling (ABPP. ABPP is based on the use of small molecule probes that react with the catalytic residues of distinct protein classes in an activity-dependent manner. Labeled proteins are separated and detected from proteins gels and purified and identified by mass spectrometry. Using probes of six different chemotypes we have displayed of activities of 76 Arabidopsis proteins. These proteins represent over ten different protein classes that contain over 250 Arabidopsis proteins, including cysteine- serine- and metallo-proteases, lipases, acyltransferases, and the proteasome. We have developed methods for identification of in vivo labeled proteins using click-chemistry and for in vivo imaging with fluorescent probes. In vivo labeling has revealed novel protein activities and unexpected subcellular activities of the proteasome. Labeling of extracts displayed several differential activities e.g. of the proteasome during immune response and methylesterases during infection. These studies illustrate the power of ABPP to display the functional proteome and testify to a successful interdisciplinary collaboration involving chemical biology, organic chemistry and proteomics.

  6. Putting a Number on Pain: Technology Has an Increased Role in Measuring Subjective Symptoms in Clinical Trials.

    Science.gov (United States)

    Mertz, Leslie

    2016-01-01

    Will new technologies substantially change the way subjective complaints are measured in clinical trials, and, if so, by how much? Depending on the expert consulted, the answer ranges from a little to a lot. PMID:26978849

  7. High-Throughput Proteomics

    Science.gov (United States)

    Zhang, Zhaorui; Wu, Si; Stenoien, David L.; Paša-Tolić, Ljiljana

    2014-06-01

    Mass spectrometry (MS)-based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.

  8. Establishing Substantial Equivalence: Proteomics

    Science.gov (United States)

    Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

    Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

  9. Proteomics and insect immunity

    Directory of Open Access Journals (Sweden)

    L Shi

    2006-01-01

    Full Text Available Insect innate immunity is both a model for vertebrate immunity as well as a key system that impactsmedically important pathogens that are transmitted by insects. Recent developments in proteomics andprotein identification techniques combined with the completion of genome sequences for Anophelesgambiae and Drosophila melanogaster provided the tools for examining insect immunity at a new level ofmolecular detail. Application of proteomics to insect immunity resulted in predictions of new roles inimmunity for proteins already known in other contexts (e.g. ferritin, transferrin, Chi-lectins and helped totarget specific members of multi-gene families that respond to different pathogens (e.g. serine proteases,thioester proteins. In addition, proteomics studies verify that post-translational modifications play a keyrole in insect immunity since many of the identified proteins are modified in some way. These studiescomplement recent work on insect transcriptomes and provide new directions for further investigation ofinnate immunity.

  10. SU-E-P-10: Imaging in the Cardiac Catheterization Lab - Technologies and Clinical Applications

    Energy Technology Data Exchange (ETDEWEB)

    Fetterly, K [Mayo Clinic, Rochester, MN (United States)

    2014-06-01

    Purpose: Diagnosis and treatment of cardiovascular disease in the cardiac catheterization laboratory is often aided by a multitude of imaging technologies. The purpose of this work is to highlight the contributions to patient care offered by the various imaging systems used during cardiovascular interventional procedures. Methods: Imaging technologies used in the cardiac catheterization lab were characterized by their fundamental technology and by the clinical applications for which they are used. Whether the modality is external to the patient, intravascular, or intracavity was specified. Specific clinical procedures for which multiple modalities are routinely used will be highlighted. Results: X-ray imaging modalities include fluoroscopy/angiography and angiography CT. Ultrasound imaging is performed with external, trans-esophageal echocardiography (TEE), and intravascular (IVUS) transducers. Intravascular infrared optical coherence tomography (IVOCT) is used to assess vessel endothelium. Relatively large (>0.5 mm) anatomical structures are imaged with x-ray and ultrasound. IVUS and IVOCT provide high resolution images of vessel walls. Cardiac CT and MRI images are used to plan complex cardiovascular interventions. Advanced applications are used to spatially and temporally merge images from different technologies. Diagnosis and treatment of coronary artery disease frequently utilizes angiography and intra-vascular imaging, and treatment of complex structural heart conditions routinely includes use of multiple imaging modalities. Conclusion: There are several imaging modalities which are routinely used in the cardiac catheterization laboratory to diagnose and treat both coronary artery and structural heart disease. Multiple modalities are frequently used to enhance the quality and safety of procedures. The cardiac catheterization laboratory includes many opportunities for medical physicists to contribute substantially toward advancing patient care.

  11. SU-E-P-10: Imaging in the Cardiac Catheterization Lab - Technologies and Clinical Applications

    International Nuclear Information System (INIS)

    Purpose: Diagnosis and treatment of cardiovascular disease in the cardiac catheterization laboratory is often aided by a multitude of imaging technologies. The purpose of this work is to highlight the contributions to patient care offered by the various imaging systems used during cardiovascular interventional procedures. Methods: Imaging technologies used in the cardiac catheterization lab were characterized by their fundamental technology and by the clinical applications for which they are used. Whether the modality is external to the patient, intravascular, or intracavity was specified. Specific clinical procedures for which multiple modalities are routinely used will be highlighted. Results: X-ray imaging modalities include fluoroscopy/angiography and angiography CT. Ultrasound imaging is performed with external, trans-esophageal echocardiography (TEE), and intravascular (IVUS) transducers. Intravascular infrared optical coherence tomography (IVOCT) is used to assess vessel endothelium. Relatively large (>0.5 mm) anatomical structures are imaged with x-ray and ultrasound. IVUS and IVOCT provide high resolution images of vessel walls. Cardiac CT and MRI images are used to plan complex cardiovascular interventions. Advanced applications are used to spatially and temporally merge images from different technologies. Diagnosis and treatment of coronary artery disease frequently utilizes angiography and intra-vascular imaging, and treatment of complex structural heart conditions routinely includes use of multiple imaging modalities. Conclusion: There are several imaging modalities which are routinely used in the cardiac catheterization laboratory to diagnose and treat both coronary artery and structural heart disease. Multiple modalities are frequently used to enhance the quality and safety of procedures. The cardiac catheterization laboratory includes many opportunities for medical physicists to contribute substantially toward advancing patient care

  12. Integrating Genomics with Proteomics - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Approximately 60 percent of patients diagnosed with cancer present as early stage disease (Stage I and II). Despite the favorable prognosis associated with treatment intervention of such early stage disease (typically surgical excision), there are a small, but significant, fraction of these cancers that appear to be hardwired for aggressive metastatic behavior and ultimately lethal outcome.

  13. Global MS-Based Proteomics Drug Profiling.

    Science.gov (United States)

    Carvalho, Ana Sofia; Matthiesen, Rune

    2016-01-01

    DNA-based technologies such as RNAi, chemical-genetic profiling, or gene expression profiling by DNA microarrays combined with other biochemical methods are established strategies for surveying drug mechanisms. Such approaches can provide mechanistic information on how drugs act and affect cellular pathways. By studying how cancer cells compensate for the drug treatment, novel targets used in a combined treatment can be designed. Furthermore, toxicity effects on cells not targeted can be obtained on a molecular level. For example, drug companies are particularly interested in studying the molecular side effects of drugs in the liver. In addition, experiments with the purpose of elucidating liver toxicity can be studied using samples obtained from animal models exposed to different concentrations of a drug over time. More recently considerable advances in mass spectrometry (MS) technologies and bioinformatics tools allows informative global drug profiling experiments to be performed at a cost comparable to other large-scale technologies such as DNA-based technologies. Moreover, MS-based proteomics provides an additional layer of information on the dynamic regulation of proteins translation and particularly protein degradation. MS-based proteomics approaches combined with other biochemical methods delivers information on regulatory networks, signaling cascades, and metabolic pathways upon drug treatment. Furthermore, MS-based proteomics can provide additional information on single amino acid polymorphisms, protein isoform distribution, posttranslational modifications, and subcellular localization. In this chapter, we will share our experience using MS based proteomics as a pharmacoproteomics strategy to characterize drug mechanisms of action in single drug therapy or in multidrug combination. Finally, the emergence of integrated proteogenomics analysis, such as "The Cancer Genome Atlas" program, opened interesting perspectives to extend this approach to drug target

  14. Computing the functional proteome

    DEFF Research Database (Denmark)

    O'Brien, Edward J.; Palsson, Bernhard

    2015-01-01

    -Models). Recent expansions in network content to encompass proteome synthesis have resulted in models of metabolism and protein expression (ME-Models). ME-Models advance the predictions possible with constraint-based models from network flux states to the spatially resolved molecular composition of a cell....... Specifically, ME-Models enable the prediction of transcriptome and proteome allocation and limitations, and basal expression states and regulatory needs. Continued expansion in reconstruction content and constraints will result in an increasingly refined representation of cellular composition and behavior....

  15. The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Weckwerth, Wolfram; Baginsky, Sacha; Van Wijk, Klass; Heazlewood, Joshua; Millar, Harvey

    2009-12-01

    In the past 10 years, we have witnessed remarkable advances in the field of plant molecular biology. The rapid development of proteomic technologies and the speed with which these techniques have been applied to the field have altered our perception of how we can analyze proteins in complex systems. At nearly the same time, the availability of the complete genome for the model plant Arabidopsis thaliana was released; this effort provides an unsurpassed resource for the identification of proteins when researchers use MS to analyze plant samples. Recognizing the growth in this area, the Multinational Arabidopsis Steering Committee (MASC) established a subcommittee for A. thaliana proteomics in 2006 with the objective of consolidating databases, technique standards, and experimentally validated candidate genes and functions. Since the establishment of the Multinational Arabidopsis Steering Subcommittee for Proteomics (MASCP), many new approaches and resources have become available. Recently, the subcommittee established a webpage to consolidate this information (www.masc-proteomics.org). It includes links to plant proteomic databases, general information about proteomic techniques, meeting information, a summary of proteomic standards, and other relevant resources. Altogether, this website provides a useful resource for the Arabidopsis proteomics community. In the future, the website will host discussions and investigate the cross-linking of databases. The subcommittee members have extensive experience in arabidopsis proteomics and collectively have produced some of the most extensive proteomics data sets for this model plant (Table S1 in the Supporting Information has a list of resources). The largest collection of proteomics data from a single study in A. thaliana was assembled into an accessible database (AtProteome; http://fgcz-atproteome.unizh.ch/index.php) and was recently published by the Baginsky lab.1 The database provides links to major Arabidopsis online

  16. A Biologist's Field Guide to Multiplexed Quantitative Proteomics.

    Science.gov (United States)

    Bakalarski, Corey E; Kirkpatrick, Donald S

    2016-05-01

    High-throughput genomic and proteomic studies have generated near-comprehensive catalogs of biological constituents within many model systems. Nevertheless, static catalogs are often insufficient to fully describe the dynamic processes that drive biology. Quantitative proteomic techniques address this need by providing insight into closely related biological states such as the stages of a therapeutic response or cellular differentiation. The maturation of quantitative proteomics in recent years has brought about a variety of technologies, each with their own strengths and weaknesses. It can be difficult for those unfamiliar with this evolving landscape to match the experiment at hand with the best tool for the job. Here, we outline quantitative methods for proteomic mass spectrometry and discuss their benefits and weaknesses from the perspective of the biologist aiming to generate meaningful data and address mechanistic questions. PMID:26873251

  17. Mass Spectrometry-Based Label-Free Quantitative Proteomics

    Directory of Open Access Journals (Sweden)

    Wenhong Zhu

    2010-01-01

    Full Text Available In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptide peak areas or peak heights. The second is based on the spectral counting of identified proteins. In this paper, we will discuss the technologies of these label-free quantitative methods, statistics, available computational software, and their applications in complex proteomics studies.

  18. Cancer Multidisciplinary Team Meetings: Evidence, Challenges, and the Role of Clinical Decision Support Technology

    International Nuclear Information System (INIS)

    Multidisciplinary team (MDT) model in cancer care was introduced and endorsed to ensure that care delivery is consistent with the best available evidence. Over the last few years, regular MDT meetings have become a standard practice in oncology and gained the status of the key decision-making forum for patient management. Despite the fact that cancer MDT meetings are well accepted by clinicians, concerns are raised over the paucity of good-quality evidence on their overall impact. There are also concerns over lack of the appropriate support for this important but overburdened decision-making platform. The growing acceptance by clinical community of the health information technology in recent years has created new opportunities and possibilities of using advanced clinical decision support (CDS) systems to realise full potential of cancer MDT meetings. In this paper, we present targeted summary of the available evidence on the impact of cancer MDT meetings, discuss the reported challenges, and explore the role that a CDS technology could play in addressing some of these challenges

  19. From Usability Testing to Clinical Simulations: Bringing Context into the Design and Evaluation of Usable and Safe Health Information Technologies

    DEFF Research Database (Denmark)

    Kushniruk, Andre; Nøhr, Christian; Jensen, Sanne;

    2013-01-01

    Objectives: The objective of this paper is to explore human factors approaches to understanding the use of health information technology (HIT) by extending usability engineering approaches to include analysis of the impact of clinical context through use of clinical simulations. Methods: Methods...

  20. Highlights of recent articles on data mining in genomics & proteomics

    Science.gov (United States)

    This editorial elaborates on investigations consisting of different “OMICS” technologies and their application to biological sciences. In addition, advantages and recent development of the proteomic, genomic and data mining technologies are discussed. This information will be useful to scientists ...

  1. Proteomic characterization of the interstitial fluid perfusing the breast tumor microenvironment

    DEFF Research Database (Denmark)

    Celis, Julio E; Gromov, Pavel; Cabezón, Teresa;

    2004-01-01

    Clinical cancer proteomics aims at the identification of markers for early detection and predictive purposes, as well as to provide novel targets for drug discovery and therapeutic intervention. Proteomics-based analysis of traditional sources of biomarkers, such as serum, plasma, or tissue lyzat...

  2. Utilization of information and communication technology (ICT) among sexually transmitted disease clinics attendees with coexisting drinking problems

    OpenAIRE

    Hu, Xingdi; Dodd, Virginia J.; Oliverio, James C; Cook, Robert L

    2014-01-01

    Background Alcohol misuse remains a major risk factor for contracting sexually transmitted diseases (STDs) not typically addressed in STD clinic settings. Information and communication technology (ICT) can offer new avenues to deliver evidence-based screening and treatment for problematic drinking, however, few data exists regarding the utilization of ICT among STD clinic attendees with coexisting drinking problems. The objectives of this study are to identify STD clinics attendees with hazar...

  3. A Chemical Proteomics Approach for the Search of Pharmacological Targets of the Antimalarial Clinical Candidate Albitiazolium in Plasmodium falciparum Using Photocrosslinking and Click Chemistry

    OpenAIRE

    Diana Marcela Penarete-Vargas; Anaïs Boisson; Serge Urbach; Hervé Chantelauze; Suzanne Peyrottes; Laurent Fraisse; Vial, Henri J

    2014-01-01

    Plasmodium falciparum is responsible for severe malaria which is one of the most prevalent and deadly infectious diseases in the world. The antimalarial therapeutic arsenal is hampered by the onset of resistance to all known pharmacological classes of compounds, so new drugs with novel mechanisms of action are critically needed. Albitiazolium is a clinical antimalarial candidate from a series of choline analogs designed to inhibit plasmodial phospholipid metabolism. Here we developed an origi...

  4. Mass spectrometry based proteomic studies on viruses and hosts - A review

    International Nuclear Information System (INIS)

    Graphical abstract: a) In the background, scanning electron micrograph of RSV infected cells reveals viral filaments budding from the surface of virus infected cells. b) Inserted at the top, MS spectrum represents the characterization of the digested RSV virus particles. c) Inserted at the bottom, RSV infected cells were imaged using immunofluorescence microscopy: red represents virus filaments; green is HSP90; yellow staining represents co-localization of both antigens within the virus filaments. Highlights: → The current proteomic researches on viruses and hosts are described. → TAP, IP, SILAC, ICAT, and iTRAQ facilitate sample enrichment and quantification. → Clinically important viruses are discussed on their interactions with hosts. → Functional validation is essential to confirm the roles of the identified proteins. - Abstract: In terms of proteomic research in the 21st century, the realm of virology is still regarded as an enormous challenge mainly brought by three aspects, namely, studying on the complex proteome of the virus with unexpected variations, developing more accurate analytical techniques as well as understanding viral pathogenesis and virus-host interaction dynamics. Progresses in these areas will be helpful to vaccine design and antiviral drugs discovery. Mass spectrometry based proteomics have shown exceptional display of capabilities, not only precisely identifying viral and cellular proteins that are functionally, structurally, and dynamically changed upon virus infection, but also enabling us to detect important pathway proteins. In addition, many isolation and purification techniques and quantitative strategies in conjunction with MS can significantly improve the sensitivity of mass spectrometry for detecting low-abundant proteins, replenishing the stock of virus proteome and enlarging the protein-protein interaction maps. Nevertheless, only a small proportion of the infectious viruses in both of animal and plant have been studied

  5. Mass spectrometry based proteomic studies on viruses and hosts - A review

    Energy Technology Data Exchange (ETDEWEB)

    Zheng Jie [Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore); Sugrue, Richard J. [Division of Molecular and Cell Biology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore); Tang Kai, E-mail: ktang@pmail.ntu.edu.sg [Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)

    2011-09-30

    Graphical abstract: a) In the background, scanning electron micrograph of RSV infected cells reveals viral filaments budding from the surface of virus infected cells. b) Inserted at the top, MS spectrum represents the characterization of the digested RSV virus particles. c) Inserted at the bottom, RSV infected cells were imaged using immunofluorescence microscopy: red represents virus filaments; green is HSP90; yellow staining represents co-localization of both antigens within the virus filaments. Highlights: {yields} The current proteomic researches on viruses and hosts are described. {yields} TAP, IP, SILAC, ICAT, and iTRAQ facilitate sample enrichment and quantification. {yields} Clinically important viruses are discussed on their interactions with hosts. {yields} Functional validation is essential to confirm the roles of the identified proteins. - Abstract: In terms of proteomic research in the 21st century, the realm of virology is still regarded as an enormous challenge mainly brought by three aspects, namely, studying on the complex proteome of the virus with unexpected variations, developing more accurate analytical techniques as well as understanding viral pathogenesis and virus-host interaction dynamics. Progresses in these areas will be helpful to vaccine design and antiviral drugs discovery. Mass spectrometry based proteomics have shown exceptional display of capabilities, not only precisely identifying viral and cellular proteins that are functionally, structurally, and dynamically changed upon virus infection, but also enabling us to detect important pathway proteins. In addition, many isolation and purification techniques and quantitative strategies in conjunction with MS can significantly improve the sensitivity of mass spectrometry for detecting low-abundant proteins, replenishing the stock of virus proteome and enlarging the protein-protein interaction maps. Nevertheless, only a small proportion of the infectious viruses in both of animal and

  6. Moving forward in colorectal cancer research, what proteomics has to tell

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Colorectal cancer is the third most common cancer and is highly fatal. During the last several years, research has been primarily based on the study of expression profiles using microarray technology. But now, investigators are putting into practice proteomic analyses of cancer tissues and cells to identify new diagnostic or therapeutic biomarkers for this cancer. Because the proteome reflects the state of a cell, tissue or organism more accurately, much is expected from proteomics to yield better tumor markers for disease diagnosis and therapy monitoring. This review summarizes the most relevant applications of proteomics the biomarker discovery for colorectal cancer.

  7. TOPICAL REVIEW: Stem cell technology using bioceramics: hard tissue regeneration towards clinical application

    Science.gov (United States)

    Ohnishi, Hiroe; Oda, Yasuaki; Ohgushi, Hajime

    2010-02-01

    Mesenchymal stem cells (MSCs) are adult stem cells which show differentiation capabilities toward various cell lineages. We have already used MSCs for treatments of osteoarthritis, bone necrosis and bone tumor. For this purpose, culture expanded MSCs were combined with various ceramics and then implanted. Because of rejection response to allogeneic MSC implantation, we have utilized patients' own MSCs for the treatment. Bone marrow is a good cell source of MSCs, although the MSCs also exist in adipose tissue. When comparing osteogenic differentiation of these MSCs, bone marrow MSCs show more extensive bone forming capability than adipose MSCs. Thus, the bone marrow MSCs are useful for bone tissue regeneration. However, the MSCs show limited proliferation and differentiation capabilities that hindered clinical applications in some cases. Recent advances reveal that transduction of plural transcription factors into human adult cells results in generation of new type of stem cells called induced pluripotent stem cells (iPS cells). A drawback of the iPS cells for clinical applications is tumor formation after their in vivo implantation; therefore it is difficult to use iPS cells for the treatment. To circumvent the problem, we transduced a single factor of either SOX2 or NANOG into the MSCs and found high proliferation as well as osteogenic differentiation capabilities of the MSCs. The stem cells could be combined with bioceramics for clinical applications. Here, we summarize our recent technologies using adult stem cells in viewpoints of bone tissue regeneration.

  8. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

    Science.gov (United States)

    Sheynkman, Gloria M.; Shortreed, Michael R.; Cesnik, Anthony J.; Smith, Lloyd M.

    2016-06-01

    Mass spectrometry–based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications.

  9. The Path to Enlightenment: Making Sense of Genomic and Proteomic Information

    Institute of Scientific and Technical Information of China (English)

    Martin H. Maurer

    2004-01-01

    Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.

  10. Current Trends in Computational Inference from Mass Spectrometry-based Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Webb-Robertson, Bobbie-Jo M.; Cannon, William R.

    2007-07-20

    Mass spectrometry offers a high-throughput approach to quantifying the proteome associated with a biological sample and hence has become the primary approach of proteomic analyses. Computation is tightly coupled to this advanced technological platform as a required component of not only peptide and protein identification, but quantification and functional inference, such as protein modifications and interactions. Proteomics faces several key computational challenges such as identification of proteins and peptides from tandem mass spectra as well as their quantitation. In addition, the application of proteomics to systems biology requires understanding the functional proteome including how the dynamics of the cell change in response to protein modifications and complex interactions between biomolecules. This review presents an overview of recently developed methods and their impact on these core computational challenges currently facing proteomics.

  11. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.

    Science.gov (United States)

    Sheynkman, Gloria M; Shortreed, Michael R; Cesnik, Anthony J; Smith, Lloyd M

    2016-06-12

    Mass spectrometry-based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications. PMID:27049631

  12. Cutting edge proteomics

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; Espadas, Guadalupe; Molina, Henrik

    2013-01-01

    Tryptic digestion is an important component of most proteomics experiments, and trypsin is available from many sources with a cost that varies by more than 1000-fold. This high-mass-accuracy LC-MS study benchmarks six commercially available trypsins with respect to autolytic species and sequence...

  13. Teaching Expression Proteomics: From the Wet-Lab to the Laptop

    Science.gov (United States)

    Teixeira, Miguel C.; Santos, Pedro M.; Rodrigues, Catarina; Sa-Correia, Isabel

    2009-01-01

    Expression proteomics has become, in recent years, a key genome-wide expression approach in fundamental and applied life sciences. This postgenomic technology aims the quantitative analysis of all the proteins or protein forms (the so-called proteome) of a given organism in a given environmental and genetic context. It is a challenge to provide…

  14. MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics

    DEFF Research Database (Denmark)

    Mortensen, Peter; Gouw, Joost W; Olsen, Jesper V;

    2010-01-01

    Mass spectrometry-based proteomics critically depends on algorithms for data interpretation. A current bottleneck in the rapid advance of proteomics technology is the closed nature and slow development cycle of vendor-supplied software solutions. We have created an open source software environmen...

  15. Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community

    DEFF Research Database (Denmark)

    Olsen, Jesper V; Mann, Matthias

    2011-01-01

    Mass spectrometry-based proteomics has emerged as a technology of choice for global analysis of cell signaling networks. However, reporting and sharing of MS data are often haphazard, limiting the usefulness of proteomics to the signaling community. We argue that raw data should always be provided...... there are few mechanisms for community-wide sharing of these data....

  16. A scheme for the audit of scientific and technological standards in clinical nuclear medicine

    International Nuclear Information System (INIS)

    Aim: Audit is the process whereby the quality of a service is monitored and optimised. It forms an essential component of the quality assurance process, whether by self-assessment or by external peer review. In the UK the British Nuclear Medicine Society (BNMS) has undertaken external organisational audit of departments providing clinical nuclear medicine services. This work aimed to develop a more thorough and service specific process for the audit of scientific and technological standards in nuclear medicine. Materials and Methods: The audit process has been implemented using written audit documents to facilitate the audit procedure. A questionnaire forms part of the formal documentation for audit of the scientific and technical standards of a clinical service. Scientific and technical standards were derived from a number of sources including legal requirements, regulatory obligations, notes for guidance, peer reviewed publications and accepted good clinical practice (GCP). Results: The audit process graded the standards of an individual department according to legal or safety requirements (Grade A), good practice (Grade B) and desirable aspects of service delivery (Grade C). The standards have been allocated into eight main categories. These are: Instrumentation; Software and data protection; Electrical Safety; Mechanical Safety; Workstation Safety; The Control of Substances Hazardous to Health (COSHH); Radiation Protection; Scientific and Technical staffing levels. During the audit visit a detailed inspection of clinical and laboratory areas and department written documentation is also necessary to validate the data obtained. Conclusion: The printed scheme now provides a means for external audit or self-assessment. There should be evidence of a well-organised and safe environment for both patients and staff. Health and Safety legislation requires written local rules and these records should be available to demonstrate the standard of service provision. Other

  17. The quest of the human proteome and the missing proteins: digging deeper.

    Science.gov (United States)

    Reddy, Panga Jaipal; Ray, Sandipan; Srivastava, Sanjeeva

    2015-05-01

    Given the diverse range of transcriptional and post-transcriptional mechanisms of gene regulation, the estimates of the human proteome is likely subject to scientific surprises as the field of proteomics has gained momentum worldwide. In this regard, the establishment of the "Human Proteome Draft" using high-resolution mass spectrometry (MS), tissue microarrays, and immunohistochemistry by three independent research groups (laboratories of Pandey, Kuster, and Uhlen) accelerated the pace of proteomics research. The Chromosome Centric Human Proteome Project (C-HPP) has taken initiative towards the completion of the Human Proteome Project (HPP) so as to understand the proteomics correlates of common complex human diseases and biological diversity, not to mention person-to-person and population differences in response to drugs, nutrition, vaccines, and other health interventions and host-environment interactions. Although high-resolution MS-based and antibody microarray approaches have shown enormous promises, we are still unable to map the whole human proteome due to the presence of numerous "missing proteins." In December 2014, at the Indian Institute of Technology Bombay, Mumbai the 6(th) Annual Meeting of the Proteomics Society, India (PSI) and the International Proteomics Conference was held. As part of this interdisciplinary summit, a panel discussion session on "The Quest of the Human Proteome and Missing Proteins" was organized. Eminent scientists in the field of proteomics and systems biology, including Akhilesh Pandey, Gilbert S. Omenn, Mark S. Baker, and Robert L. Mortiz, shed light on different aspects of the human proteome drafts and missing proteins. Importantly, the possible reasons for the "missing proteins" in shotgun MS workflow were identified and debated by experts as low tissue expression, lack of enzymatic digestion site, or protein lost during extraction, among other contributing factors. To capture the missing proteins, the experts' collective

  18. Building a medical multimedia database system to integrate clinical information: an application of high-performance computing and communications technology.

    Science.gov (United States)

    Lowe, H J; Buchanan, B G; Cooper, G F; Vries, J K

    1995-01-01

    The rapid growth of diagnostic-imaging technologies over the past two decades has dramatically increased the amount of nontextual data generated in clinical medicine. The architecture of traditional, text-oriented, clinical information systems has made the integration of digitized clinical images with the patient record problematic. Systems for the classification, retrieval, and integration of clinical images are in their infancy. Recent advances in high-performance computing, imaging, and networking technology now make it technologically and economically feasible to develop an integrated, multimedia, electronic patient record. As part of The National Library of Medicine's Biomedical Applications of High-Performance Computing and Communications program, we plan to develop Image Engine, a prototype microcomputer-based system for the storage, retrieval, integration, and sharing of a wide range of clinically important digital images. Images stored in the Image Engine database will be indexed and organized using the Unified Medical Language System Metathesaurus and will be dynamically linked to data in a text-based, clinical information system. We will evaluate Image Engine by initially implementing it in three clinical domains (oncology, gastroenterology, and clinical pathology) at the University of Pittsburgh Medical Center. PMID:7703940

  19. Proteomics: a biotechnology tool for crop improvement.

    Science.gov (United States)

    Eldakak, Moustafa; Milad, Sanaa I M; Nawar, Ali I; Rohila, Jai S

    2013-01-01

    A sharp decline in the availability of arable land and sufficient supply of irrigation water along with a continuous steep increase in food demands have exerted a pressure on farmers to produce more with fewer resources. A viable solution to release this pressure is to speed up the plant breeding process by employing biotechnology in breeding programs. The majority of biotechnological applications rely on information generated from various -omic technologies. The latest outstanding improvements in proteomic platforms and many other but related advances in plant biotechnology techniques offer various new ways to encourage the usage of these technologies by plant scientists for crop improvement programs. A combinatorial approach of accelerated gene discovery through genomics, proteomics, and other associated -omic branches of biotechnology, as an applied approach, is proving to be an effective way to speed up the crop improvement programs worldwide. In the near future, swift improvements in -omic databases are becoming critical and demand immediate attention for the effective utilization of these techniques to produce next-generation crops for the progressive farmers. Here, we have reviewed the recent advances in proteomics, as tools of biotechnology, which are offering great promise and leading the path toward crop improvement for sustainable agriculture. PMID:23450788

  20. Proteomics in the Study of Bacterial Keratitis

    Directory of Open Access Journals (Sweden)

    Rachida Bouhenni

    2015-12-01

    Full Text Available Bacterial keratitis is a serious ocular infection that can cause severe visual loss if treatment is not initiated at an early stage. It is most commonly caused by Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, or Serratia species. Depending on the invading organism, bacterial keratitis can progress rapidly, leading to corneal destruction and potential blindness. Common risk factors for bacterial keratitis include contact lens wear, ocular trauma, ocular surface disease, ocular surgery, lid deformity, chronic use of topical steroids, contaminated ocular medications or solutions, and systemic immunosuppression. The pathogenesis of bacterial keratitis, which depends on the bacterium-host interaction and the virulence of the invading bacterium, is complicated and not completely understood. This review highlights some of the proteomic technologies that have been used to identify virulence factors and the host response to infections of bacterial keratitis in order to understand the disease process and develop improved methods of diagnosis and treatment. Although work in this field is not abundant, proteomic technologies have provided valuable information toward our current knowledge of bacterial keratitis. More studies using global proteomic approaches are warranted because it is an important tool to identify novel targets for intervention and prevention of corneal damage caused by these virulent microorganisms.

  1. Proteomics: A Biotechnology Tool for Crop Improvement

    Directory of Open Access Journals (Sweden)

    Moustafa eEldakak

    2013-02-01

    Full Text Available A sharp decline in the availability of arable land and sufficient supply of irrigation water along with a continuous steep increase in food demands have exerted a pressure on farmers to produce more with fewer resources. A viable solution to release this pressure is to speed up the plant breeding process by employing biotechnology in breeding programs. The majority of biotechnological applications rely on information generated from various -omic technologies. The latest outstanding improvements in proteomic platforms and many other but related advances in plant biotechnology techniques offer various new ways to encourage the usage of these technologies by plant scientists for crop improvement programs. A combinatorial approach of accelerated gene discovery through genomics, proteomics, and other associated -omic branches of biotechnology, as an applied approach, is proving to be an effective way to speed up the crop improvement programs worldwide. In the near future, swift improvements in -omic databases are becoming critical and demand immediate attention for the effective utilization of these techniques to produce next-generation crops for the progressive farmers. Here, we have reviewed the recent advances in proteomics, as tools of biotechnology, which are offering great promise and leading the path towards crop improvement for sustainable agriculture.

  2. Significance of Urinary Proteome Pattern in Renal Allograft Recipients

    Science.gov (United States)

    Suhail, Sufi M.

    2014-01-01

    Urinary proteomics is developing as a platform of urinary biomarkers of immense potential in recent years. The definition of urinary proteome in the context of renal allograft and characterization of different proteome patterns in various graft dysfunctions have led to the development of a distinct science of this noninvasive tool. Substantial numbers of studies have shown that different renal allograft disease states, both acute and chronic, could portray unique urinary proteome pattern enabling early diagnosis of graft dysfunction and proper manipulation of immunosuppressive strategy that could impact graft prognosis. The methodology of the urinary proteome is nonetheless not more complex than that of other sophisticated assays of conventional urinary protein analysis. Moreover, the need for a centralized database is also felt by the researchers as more and more studies have been presenting their results from different corners and as systems of organizing these newly emerging data being developed at international and national levels. In this context concept of urinary proteomics in renal allograft recipients would be of significant importance in clinical transplantation. PMID:24757556

  3. Significance of Urinary Proteome Pattern in Renal Allograft Recipients

    Directory of Open Access Journals (Sweden)

    Sufi M. Suhail

    2014-01-01

    Full Text Available Urinary proteomics is developing as a platform of urinary biomarkers of immense potential in recent years. The definition of urinary proteome in the context of renal allograft and characterization of different proteome patterns in various graft dysfunctions have led to the development of a distinct science of this noninvasive tool. Substantial numbers of studies have shown that different renal allograft disease states, both acute and chronic, could portray unique urinary proteome pattern enabling early diagnosis of graft dysfunction and proper manipulation of immunosuppressive strategy that could impact graft prognosis. The methodology of the urinary proteome is nonetheless not more complex than that of other sophisticated assays of conventional urinary protein analysis. Moreover, the need for a centralized database is also felt by the researchers as more and more studies have been presenting their results from different corners and as systems of organizing these newly emerging data being developed at international and national levels. In this context concept of urinary proteomics in renal allograft recipients would be of significant importance in clinical transplantation.

  4. Discovery based and targeted Mass Spectrometry in farm animal proteomics

    DEFF Research Database (Denmark)

    Bendixen, Emøke

    2013-01-01

    Technological advances in mass spectrometry have greatly improved accuracy and speed of analyses of proteins and biochemical pathways. These proteome technologies have transformed research and diagnostic methods in the biomedical fields, and in food and farm animal sciences proteomics can be used...... experiments from tissues and body fluids from pig, cow and horse, and currently provides the primary public resource for designing SRM methods for farm animal applications...... approach for investigating farm animal biology. SRM is particularly important for validation biomarker candidates This talk will introduce the use of different mass spectrometry approaches through examples related to food quality and animal welfare, including studies of gut health in pigs, host pathogen...

  5. Using semantic web technologies for cohort identification from electronic health records for clinical research.

    Science.gov (United States)

    Pathak, Jyotishman; Kiefer, Richard C; Chute, Christopher G

    2012-01-01

    The ability to conduct genome-wide association studies (GWAS) has enabled new exploration of how genetic variations contribute to health and disease etiology. One of the key requirements to perform GWAS is the identification of subject cohorts with accurate classification of disease phenotypes. In this work, we study how emerging Semantic Web technologies can be applied in conjunction with clinical data stored in electronic health records (EHRs) to accurately identify subjects with specific diseases for inclusion in cohort studies. In particular, we demonstrate the role of using Resource Description Framework (RDF) for representing EHR data and enabling federated querying and inferencing via standardized Web protocols for identifying subjects with Diabetes Mellitus. Our study highlights the potential of using Web-scale data federation approaches to execute complex queries. PMID:22779040

  6. Optical coherence tomography—current technology and applications in clinical and biomedical research

    DEFF Research Database (Denmark)

    Marschall, Sebastian; Sander, Birgit; Mogensen, Mette;

    2011-01-01

    Optical coherence tomography (OCT) is a noninvasive imaging technique that provides real-time two- and three-dimensional images of scattering samples with micrometer resolution. By mapping the local reflectivity, OCT visualizes the morphology of the sample. In addition, functional properties such...... as birefringence, motion, or the distributions of certain substances can be detected with high spatial resolution. Its main field of application is biomedical imaging and diagnostics. In ophthalmology, OCT is accepted as a clinical standard for diagnosing and monitoring the treatment of a number of...... developmental biology. The number of companies involved in manufacturing OCT systems has increased substantially during the last few years (especially due to its success in opthalmology), and this technology can be expected to continue to spread into various fields of application....

  7. Approaches for targeted proteomics and its potential applications in neuroscience

    Indian Academy of Sciences (India)

    Sumit Sethi; Dipti Chourasia; Ishwar S Parhar

    2015-09-01

    An extensive guide on practicable and significant quantitative proteomic approaches in neuroscience research is important not only because of the existing overwhelming limitations but also for gaining valuable understanding into brain function and deciphering proteomics from the workbench to the bedside. Early methodologies to understand the functioning of biological systems are now improving with high-throughput technologies, which allow analysis of various samples concurrently, or of thousand of analytes in a particular sample. Quantitative proteomic approaches include both gel-based and non-gel-based methods that can be further divided into different labelling approaches. This review will emphasize the role of existing technologies, their advantages and disadvantages, as well as their applications in neuroscience. This review will also discuss advanced approaches for targeted proteomics using isotope-coded affinity tag (ICAT) coupled with laser capture microdissection (LCM) followed by liquid chromatography tandem mass spectrometric (LC-MS/MS) analysis. This technology can further be extended to single cell proteomics in other areas of biological sciences and can be combined with other ‘omics’ approaches to reveal the mechanism of a cellular alterations. This approach may lead to further investigation in basic biology, disease analysis and surveillance, as well as drug discovery. Although numerous challenges still exist, we are confident that this approach will increase the understanding of pathological mechanisms involved in neuroendocrinology, neuropsychiatric and neurodegenerative disorders by delivering protein biomarker signatures for brain dysfunction.

  8. Clinical applications of custom-made vaginal cylinders constructed using three-dimensional printing technology

    Science.gov (United States)

    Cunha, Adam; Mellis, Katherine; Siauw, Timmy; Diederich, Chris; Pouliot, Jean; Hsu, I-Chow

    2016-01-01

    Purpose Three-dimensional (3D) printing technology allows physicians to rapidly create customized devices for patients. We report our initial clinical experience using this technology to create custom applicators for vaginal brachytherapy. Material and methods Three brachytherapy patients with unique clinical needs were identified as likely to benefit from a customized vaginal applicator. Patient 1 underwent intracavitary vaginal cuff brachytherapy after hysterectomy and chemotherapy for stage IA papillary serous endometrial cancer using a custom printed 2.75 cm diameter segmented vaginal cylinder with a central channel. Patient 2 underwent interstitial brachytherapy for a vaginal cuff recurrence of endometrial cancer after prior hysterectomy, whole pelvis radiotherapy, and brachytherapy boost. We printed a 2 cm diameter vaginal cylinder with one central and six peripheral catheter channels to fit a narrow vaginal canal. Patient 3 underwent interstitial brachytherapy boost for stage IIIA vulvar cancer with vaginal extension. For more secure applicator fit within a wide vaginal canal, we printed a 3.5 cm diameter solid cylinder with one central tandem channel and ten peripheral catheter channels. The applicators were printed in a biocompatible, sterilizable thermoplastic. Results Patient 1 received 31.5 Gy to the surface in three fractions over two weeks. Patient 2 received 36 Gy to the CTV in six fractions over two implants one week apart, with interstitial hyperthermia once per implant. Patient 3 received 18 Gy in three fractions over one implant after 45 Gy external beam radiotherapy. Brachytherapy was tolerated well with no grade 3 or higher toxicity and no local recurrences. Conclusions We established a workflow to rapidly manufacture and implement customized vaginal applicators that can be sterilized and are made of biocompatible material, resulting in high-quality brachytherapy for patients whose anatomy is not ideally suited for standard, commercially

  9. Two-dimensional gel electrophoresis in platelet proteomics research.

    Science.gov (United States)

    García, Angel

    2007-01-01

    Proteomics technology allows a comprehensive and efficient analysis of the proteome and has become an indispensable tool in biomedical research. Since the late 80s, advances on mass spectrometry (MS) instrumentation and techniques have revolutionized the way proteins can be analyzed. Such analysis would only be possible with a proper sample preparation and separation ahead of the MS step. Different gel and nongel-based methods are available for protein separation. This chapter will focus on the use of two-dimensional gel electrophoresis (2-DE) in proteomics and its application to platelet research. 2-DE separates proteins according to their isoelectric point (pI) and size (molecular weight) and allows the detection of thousands of proteins at a time. Platelets are enucleated cells that play a critical function in the control of bleeding and wound healing. As platelets do not have a nucleus, proteomics offers a powerful alternative approach to provide data on protein expression in these cells, helping to address their biology. This chapter presents a protocol for an efficient sample preparation, protein separation by 2-DE, and protein digestion ahead of the MS analysis. The experimental approach, already successfully applied to the study of the platelet proteome, includes recommendations for an efficient platelet preparation for proteomics studies. PMID:18287684

  10. Mass spectrometry-based proteomics: existing capabilities and future directions

    Energy Technology Data Exchange (ETDEWEB)

    Angel, Thomas E.; Aryal, Uma K.; Hengel, Shawna M.; Baker, Erin Shammel; Kelly, Ryan T.; Robinson, Errol W.; Smith, Richard D.

    2012-05-21

    Mass spectrometry-based proteomics provides a means for identification, characterization, and quantification of biomolecules that are integral components of the processes essential for life. Characterization of proteins present in a biological system at the proteome and sub-proteomes (e.g., the phosphoproteome, proteoglycome, or degradome/peptidome) levels provides a foundation for understanding fundamental aspects as well as potentially a range of translational applications. Emerging technologies such as ion mobility separations coupled with mass spectrometry and microchip-based - proteome measurements combined with continued enhancement of MS instrumentation and separation techniques, such as reversed phase liquid chromatography and potentially capillary electrophoresis, show great promise for both broad undirected as well as targeted measurements and will be critical for e.g., the proteome-wide characterization of post translational modifications and identification, or the verification, and validation of potential biomarkers of disease. MS-based proteomics is also increasingly demonstrating great potential for contributing to our understanding of the dynamics, reactions, and roles proteins and peptides play advancing our understanding of biology on a system wide level for a wide range of applications, from investigations of microbial communities, bioremediation, and human health and disease states alike.

  11. Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer

    Science.gov (United States)

    Kim, Yunee; Jeon, Jouhyun; Mejia, Salvador; Yao, Cindy Q; Ignatchenko, Vladimir; Nyalwidhe, Julius O; Gramolini, Anthony O; Lance, Raymond S; Troyer, Dean A; Drake, Richard R; Boutros, Paul C; Semmes, O. John; Kislinger, Thomas

    2016-01-01

    Biomarkers are rapidly gaining importance in personalized medicine. Although numerous molecular signatures have been developed over the past decade, there is a lack of overlap and many biomarkers fail to validate in independent patient cohorts and hence are not useful for clinical application. For these reasons, identification of novel and robust biomarkers remains a formidable challenge. We combine targeted proteomics with computational biology to discover robust proteomic signatures for prostate cancer. Quantitative proteomics conducted in expressed prostatic secretions from men with extraprostatic and organ-confined prostate cancers identified 133 differentially expressed proteins. Using synthetic peptides, we evaluate them by targeted proteomics in a 74-patient cohort of expressed prostatic secretions in urine. We quantify a panel of 34 candidates in an independent 207-patient cohort. We apply machine-learning approaches to develop clinical predictive models for prostate cancer diagnosis and prognosis. Our results demonstrate that computationally guided proteomics can discover highly accurate non-invasive biomarkers. PMID:27350604

  12. Integrating Interactive Web-Based Technology to Assess Adherence and Clinical Outcomes in Pediatric Sickle Cell Disease

    Directory of Open Access Journals (Sweden)

    Lori E. Crosby

    2012-01-01

    Full Text Available Research indicates that the quality of the adherence assessment is one of the best predictors for improving clinical outcomes. Newer technologies represent an opportunity for developing high quality standardized assessments to assess clinical outcomes such as patient experience of care but have not been tested systematically in pediatric sickle cell disease (SCD. The goal of the current study was to pilot an interactive web-based tool, the Take-Charge Program, to assess adherence to clinic visits and hydroxyurea (HU, barriers to adherence, solutions to overcome these barriers, and clinical outcomes in 43 patients with SCD age 6–21 years. Results indicate that the web-based tool was successfully integrated into the clinical setting while maintaining high patient satisfaction (>90%. The tool provided data consistent with the medical record, staff report, and/or clinical lab data. Participants reported that forgetting and transportation were major barriers for adherence to both clinic attendance and HU. A greater number of self-reported barriers (P<.01 and older age (P<.05 were associated with poorer clinic attendance and HU adherence. In summary, the tool represents an innovative approach to integrate newer technology to assess adherence and clinical outcomes for pediatric patients with SCD.

  13. Basic Technology and Clinical Applications of the Updated Model of Laser Speckle Flowgraphy to Ocular Diseases

    Directory of Open Access Journals (Sweden)

    Tetsuya Sugiyama

    2014-08-01

    Full Text Available Laser speckle flowgraphy (LSFG allows for quantitative estimation of blood flow in the optic nerve head (ONH, choroid and retina, utilizing the laser speckle phenomenon. The basic technology and clinical applications of LSFG-NAVI, the updated model of LSFG, are summarized in this review. For developing a commercial version of LSFG, the special area sensor was replaced by the ordinary charge-coupled device camera. In LSFG-NAVI, the mean blur rate (MBR has been introduced as a new parameter. Compared to the original LSFG model, LSFG-NAVI demonstrates a better spatial resolution of the blood flow map of human ocular fundus. The observation area is 24 times larger than the original system. The analysis software can separately calculate MBRs in the blood vessels and tissues (capillaries of an entire ONH and the measurements have good reproducibility. The absolute values of MBR in the ONH have been shown to linearly correlate with the capillary blood flow. The Analysis of MBR pulse waveform provides parameters including skew, blowout score, blowout time, rising and falling rates, flow acceleration index, acceleration time index, and resistivity index for comparing different eyes. Recently, there have been an increasing number of reports on the clinical applications of LSFG-NAVI to ocular diseases, including glaucoma, retinal and choroidal diseases.

  14. Impact of men's dairy intake on assisted reproductive technology outcomes among couples attending a fertility clinic.

    Science.gov (United States)

    Xia, Wei; Chiu, Yu-Han; Afeiche, Myriam C; Williams, Paige L; Ford, Jennifer B; Tanrikut, Cigdem; Souter, Irene; Hauser, Russ; Chavarro, Jorge E

    2016-03-01

    Intake of full-fat dairy has been linked to lower semen quality but whether this leads to decreased fertility is unknown. To address this question, we prospectively evaluated the association of men's dairy intake with treatment outcomes of subfertile couples undergoing assisted reproductive technology (ART). We followed 142 men from couples undergoing infertility treatment with ART at an academic fertility centre between 2007 and 2014. Couples completed dietary assessments prior to treatment, and the female partners underwent a total of 248 ART cycles. Multivariable generalized linear mixed models were used to examine the association of dairy intake with fertilization, implantation, clinical pregnancy and live birth rates adjusting for age, body mass index, smoking status, total exercise time, dietary patterns, alcohol, caffeine, total energy intake, and female dairy intake. Intake of dairy foods, regardless of their fat content, was not associated with fertilization, implantation, clinical pregnancy or live birth rates. The adjusted live birth rates (95% confidence interval) for couples in increasing quartiles of men's dairy intake were 0.42 (0.25, 0.60), 0.25 (0.13, 0.42), 0.26 (0.15, 0.41), and 0.44 (0.27, 0.63) (p linear trend = 0.73). Results remained similar after adjustment for female partner intake of dairy foods. Overall, men's dairy intake was not associated with treatment outcomes of couples undergoing ART. PMID:26825777

  15. BioinformatiqTM - integrating data types for proteomic discovery

    International Nuclear Information System (INIS)

    Proteomics (Wilkins et al. 1997) involves the large-scale analysis of expressed proteins. At each stage of the discovery process the researcher accumulates large volumes of data. These include: clinical or biological data about the sample being studied; details of sample purification and separation; images of 2D gels and associated information; MALDI mass spectra; MS/MS and PSD spectra; as well as meta-data relating to the projects undertaken and experiments performed. All this must be combined with existing databases of protein and EST sequences, post-translational modifications, and protein glycosylation, then processed with sophisticated bioinformatics tools in order to extract meaningful answers to questions of biological, clinical, and agricultural significance. BioinformatlQTM is a web-based application for the storage, management, and automated bioinformatic analysis of proteomic information. This poster will demonstrate the integration of these disparate data sources in proteomics

  16. Workshop on body composition in basic and clinical research and the emerging technologies

    Energy Technology Data Exchange (ETDEWEB)

    Wielopolski, L.

    2000-12-14

    A special one-day workshop was held to review the status, the need for, and the future role of BNL in the Body Composition Analysis Program (BCAP). Two speakers succinctly outlined the status and future new developments using gamma nuclear resonance technology as it applies to BCAP. Seven speakers from three institutions outlined the continued need for BCAP and presented new clinical applications of BCAP in theirs respective fields of expertise. Extensive increase in the use of surrogate instrumentation, e.g., DXA and BIA, in BCAP was recognized as a significant contributing factor to the growth in BCAP. The growing role of MRI in BCAP was also emphasized. In light of these developments BCAP at BNL, with its specialized In Vivo Neutron Activation (IVNA) facilities, was recognized as a unique user oriented resource that may serve the community hospitals in the area. Three regional large institutions expressed their desire to use these facilities. In addition, IVNA provides direct measure of the human compartments in vivo, thus providing a gold standard for the surrogate methodologies that are in use or to be developed. It was strongly felt that there is a need for a calibration center with a national stature for the different methodologies for in vivo measurements, a role that befits very well a national laboratory. This offers an exquisite justification for DOE to support this orphan technology and to develop BCAP at BNL to, 1, provide a user oriented regional resource, 2, provide a national reference laboratory, and 3, develop new advanced technologies for BCAP.

  17. The plant mitochondrial proteome

    DEFF Research Database (Denmark)

    Millar, A.H.; Heazlewood, J.L.; Kristensen, B.K.;

    2005-01-01

    The plant mitochondrial proteome might contain as many as 2000-3000 different gene products, each of which might undergo post-translational modification. Recent studies using analytical methods, such as one-, two- and three-dimensional gel electrophoresis and one- and two-dimensional liquid...... context to be defined for them. There are indications that some of these proteins add novel activities to mitochondrial protein complexes in plants....

  18. Proteomics of the Lysosome

    OpenAIRE

    Lübke, Torben; Lobel, Peter; Sleat, David

    2008-01-01

    Defects in lysosomal function have been associated with numerous monogenic human diseases typically classified as lysosomal storage diseases. However, there is increasing evidence that lysosomal proteins are also involved in more widespread human diseases including cancer and Alzheimer disease. Thus, there is a continuing interest in understanding the cellular functions of the lysosome and an emerging approach to this is the identification of its constituent proteins by proteomic analyses. To...

  19. An Investigation About Attitude of Clinical Physicians in the Implementation of Telemedicine Technology in TUMS Hospitals 2003-2004

    Directory of Open Access Journals (Sweden)

    H Dargahi

    2005-05-01

    Full Text Available Background: This research have presented focuses upon the cultural side of managerial coordination and control as manifested in Telemedicine Technology. Specifically, the research seeks to analyze and determines the attitude of clinical physicians about the role of specific dimensions of organizational culture and organizational structure may have upon effective managerial coordination and control in Telemedicine Technology in TUMS hospitals. Materials and methods: We assessed the attitude of 82 clinical physicians in five randomly selected TUMS teaching hospitals in a mixed method of pooling Quantitative and Qualitative data using unstructured interview technique. Results: For successful telemedicine utilization, most of clinical physicians believed that we need organic organizations that have involved leadership, open and free communication of mistakes and success, desire to experiment with new ideas, support for continuing education, support for new things, clear rules to follow and acknowledge performance goals. Conclusion: The data indicate that organizational is most important to utilize successfur telemedicine technology.

  20. Application of pressurized solvents for ultra fast trypsin hydrolysis in proteomics: Proteomics on the fly

    OpenAIRE

    López-Ferrer, Daniel; Petritis, Konstantinos; Hixson, Kim K.; Heibeck, Tyler H.; Moore, Ronald J.; Belov, Mikhail E.; Camp, David G; Smith, Richard D.

    2008-01-01

    A new method for rapid proteolytic digestion of proteins under high pressure that uses pressure cycling technology in the range of 5 to 35 kpsi was demonstrated for proteomic analysis. Successful in-solution digestions of single proteins and complex protein mixtures were achieved in 60 s and then analyzed by reversed phase liquid chromatography-electrospray ionization ion trap-mass spectrometry. Method performance in terms of the number of Shewanella oneidensis peptides and proteins identifie...

  1. An Investigation About Attitude of Clinical Physicians in the Implementation of Telemedicine Technology in TUMS Hospitals 2003-2004

    OpenAIRE

    H Dargahi

    2005-01-01

    Background: This research have presented focuses upon the cultural side of managerial coordination and control as manifested in Telemedicine Technology. Specifically, the research seeks to analyze and determines the attitude of clinical physicians about the role of specific dimensions of organizational culture and organizational structure may have upon effective managerial coordination and control in Telemedicine Technology in TUMS hospitals. Materials and methods: We assessed the attitude of...

  2. Proteomic evaluation of sheep serum proteins

    Directory of Open Access Journals (Sweden)

    Chiaradia Elisabetta

    2012-05-01

    Full Text Available Abstract Background The applications of proteomic strategies to ovine medicine remain limited. The definition of serum proteome may be a good tool to identify useful protein biomarkers for recognising sub-clinical conditions and overt disease in sheep. Findings from bovine species are often directly translated for use in ovine medicine. In order to characterize normal protein patterns and improve knowledge of molecular species-specific characteristics, we generated a two-dimensional reference map of sheep serum. The possible application of this approach was tested by analysing serum protein patterns in ewes with mild broncho-pulmonary disease, which is very common in sheep and in the peripartum period which is a stressful time, with a high incidence of infectious and parasitic diseases. Results This study generated the first reference 2-DE maps of sheep serum. Overall, 250 protein spots were analyzed, and 138 identified. Compared with healthy sheep, serum protein profiles of animals with rhino-tracheo-bronchitis showed a significant decrease in protein spots identified as transthyretin, apolipoprotein A1 and a significant increase in spots identified as haptoglobin, endopin 1b and alpha1B glycoprotein. In the peripartum period, haptoglobin, alpha-1-acid glycoprotein, apolipoprotein A1 levels rose, while transthyretin content dropped. Conclusions This study describes applications of proteomics in putative biomarker discovery for early diagnosis as well as for monitoring the physiological and metabolic situations critical for ovine welfare.

  3. Optimized method for identification of the proteomes secreted by cardiac cells

    Czech Academy of Sciences Publication Activity Database

    Šťastná, Miroslava; Van Eyk, J.E.

    2013-01-01

    Roč. 1005, č. 1005 (2013), s. 225-235. ISSN 1940-6029 Institutional support : RVO:68081715 Keywords : cardiac cells * secreted proteins * proteomic technology Subject RIV: CB - Analytical Chemistry, Separation

  4. The Proteomics Stock Market Project: A Cross-Disciplinary Collaboration in Biochemistry and Business Education

    Science.gov (United States)

    Keller, Heath; Cox, James R.

    2004-01-01

    A collaborative effort between business and chemistry resulted in a class project called the Proteomics Stock Market Project. The project includes biochemical and marketing concepts, technology, writing assignments and group work.

  5. From genomes to vaccines via the proteome

    Directory of Open Access Journals (Sweden)

    R Alan Wilson

    2004-08-01

    Full Text Available An effective vaccine against schistosomiasis mansoni would be a valuable control tool and the high levels of protection elicited in rodents and primates by radiation-attenuated cercariae provide proof of principle. A major obstacle to vaccine development is the difficulty of identifying the antigens that mediate protection, not least because of the size of the genome at 280Mb DNA encoding 14,000 to 20,000 genes. The technologies collectively called proteomics, including 2D electrophoresis, liquid chromatography and mass spectrometry, now permit any protein to be identified provided there is extensive DNA data, and preferably a genome sequence. Applied to soluble (cytosolic proteins from schistosomes, proteomics reveals the great similarity in composition between life cycle stages, with several WHO vaccine candidates amongst the most abundant constituents. The proteomic approach has been successfully applied to identify the secretions used by cercaria to penetrate host skin, the gut secretions of adult worms and the proteins exposed on the tegument surface. Soluble proteins can also be separated by 2D electrophoresis before western blotting to identify the full range of antigenic targets present in a parasite preparation. The next step is to discover which target proteins represent the weak points in the worm's defences.

  6. Extending mass spectrometry's reach in proteome analysis

    International Nuclear Information System (INIS)

    Full text: Mass spectrometry is an essential component of proteome analysis. The accuracy, speed and sensitivity of mass spectrometric analysis is further aided by an ability to analyse proteins and peptides directly from two-dimensional sample arrays. This is accomplished either by gel excision and recovery of proteins or their proteolysis products, or after blotting of gel-separated proteins onto membranes. The protein components are most often analysed in each case by matrix-assisted laser desorption ionisation (MALDI) mass spectrometry. Beyond automated protein identification, proteomics ultimately demands that protein function and activity be characterised. We have developed new mass spectrometry methodologies that enable protein-protein associations to be analysed by MALDI mass spectrometry. Methods to preserve protein-protein associations on 2D sample surfaces and to affect their ionisation and detection have been developed. This presentation will describe the features of protocol that are required for the successful analysis of protein-protein complexes. Data will be shown to illustrate the application of the technology to the study of important biological and immunological processes. The methods form the basis of powerful new mass spectrometric based assays for screening and affinity studies. Details of our investigations and their implications for high-throughput proteomics applications will be discussed in conjunction with directions of our future research

  7. Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles

    Science.gov (United States)

    Kieselbach, Thomas; Zijnge, Vincent; Granström, Elisabeth; Oscarsson, Jan

    2015-01-01

    Aggregatibacter actinomycetemcomitans is an oral and systemic pathogen associated with aggressive forms of periodontitis and with endocarditis. Outer membrane vesicles (OMVs) released by this species have been demonstrated to deliver effector proteins such as cytolethal distending toxin (CDT) and leukotoxin (LtxA) into human host cells and to act as triggers of innate immunity upon carriage of NOD1- and NOD2-active pathogen-associated molecular patterns (PAMPs). To improve our understanding of the pathogenicity-associated functions that A. actinomycetemcomitans exports via OMVs, we studied the proteome of density gradient-purified OMVs from a rough-colony type clinical isolate, strain 173 (serotype e) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). This analysis yielded the identification of 151 proteins, which were found in at least three out of four independent experiments. Data are available via ProteomeXchange with identifier PXD002509. Through this study, we not only confirmed the vesicle-associated release of LtxA, and the presence of proteins, which are known to act as immunoreactive antigens in the human host, but we also identified numerous additional putative virulence-related proteins in the A. actinomycetemcomitans OMV proteome. The known and putative functions of these proteins include immune evasion, drug targeting, and iron/nutrient acquisition. In summary, our findings are consistent with an OMV-associated proteome that exhibits several offensive and defensive functions, and they provide a comprehensive basis to further disclose roles of A. actinomycetemcomitans OMVs in periodontal and systemic disease. PMID:26381655

  8. Detecting differential protein expression in large-scale population proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Ryu, Soyoung; Qian, Weijun; Camp, David G.; Smith, Richard D.; Tompkins, Ronald G.; Davis, Ronald W.; Xiao, Wenzhong

    2014-06-17

    Mass spectrometry-based high-throughput quantitative proteomics shows great potential in clinical biomarker studies, identifying and quantifying thousands of proteins in biological samples. However, methods are needed to appropriately handle issues/challenges unique to mass spectrometry data in order to detect as many biomarker proteins as possible. One issue is that different mass spectrometry experiments generate quite different total numbers of quantified peptides, which can result in more missing peptide abundances in an experiment with a smaller total number of quantified peptides. Another issue is that the quantification of peptides is sometimes absent, especially for less abundant peptides and such missing values contain the information about the peptide abundance. Here, we propose a Significance Analysis for Large-scale Proteomics Studies (SALPS) that handles missing peptide intensity values caused by the two mechanisms mentioned above. Our model has a robust performance in both simulated data and proteomics data from a large clinical study. Because varying patients’ sample qualities and deviating instrument performances are not avoidable for clinical studies performed over the course of several years, we believe that our approach will be useful to analyze large-scale clinical proteomics data.

  9. The Transcriptomics to Proteomics of Hair Cell Regeneration: Looking for a Hair Cell in a Haystack

    Directory of Open Access Journals (Sweden)

    Michael E. Smith

    2013-07-01

    Full Text Available Mature mammals exhibit very limited capacity for regeneration of auditory hair cells, while all non-mammalian vertebrates examined can regenerate them. In an effort to find therapeutic targets for deafness and balance disorders, scientists have examined gene expression patterns in auditory tissues under different developmental and experimental conditions. Microarray technology has allowed the large-scale study of gene expression profiles (transcriptomics at whole-genome levels, but since mRNA expression does not necessarily correlate with protein expression, other methods, such as microRNA analysis and proteomics, are needed to better understand the process of hair cell regeneration. These technologies and some of the results of them are discussed in this review. Although there is a considerable amount of variability found between studies owing to different species, tissues and treatments, there is some concordance between cellular pathways important for hair cell regeneration. Since gene expression and proteomics data is now commonly submitted to centralized online databases, meta-analyses of these data may provide a better picture of pathways that are common to the process of hair cell regeneration and lead to potential therapeutics. Indeed, some of the proteins found to be regulated in the inner ear of animal models (e.g., IGF-1 have now gone through human clinical trials.

  10. Proteomics of Trypanosoma evansi infection in rodents.

    Directory of Open Access Journals (Sweden)

    Nainita Roy

    Full Text Available BACKGROUND: Trypanosoma evansi infections, commonly called 'surra', cause significant economic losses to livestock industry. While this infection is mainly restricted to large animals such as camels, donkeys and equines, recent reports indicate their ability to infect humans. There are no World Animal Health Organization (WAHO prescribed diagnostic tests or vaccines available against this disease and the available drugs show significant toxicity. There is an urgent need to develop improved methods of diagnosis and control measures for this disease. Unlike its related human parasites T. brucei and T. cruzi whose genomes have been fully sequenced T. evansi genome sequence remains unavailable and very little efforts are being made to develop improved methods of prevention, diagnosis and treatment. With a view to identify potential diagnostic markers and drug targets we have studied the clinical proteome of T. evansi infection using mass spectrometry (MS. METHODOLOGY/PRINCIPAL FINDINGS: Using shot-gun proteomic approach involving nano-lc Quadrupole Time Of Flight (QTOF mass spectrometry we have identified over 160 proteins expressed by T. evansi in mice infected with camel isolate. Homology driven searches for protein identification from MS/MS data led to most of the matches arising from related Trypanosoma species. Proteins identified belonged to various functional categories including metabolic enzymes; DNA metabolism; transcription; translation as well as cell-cell communication and signal transduction. TCA cycle enzymes were strikingly missing, possibly suggesting their low abundances. The clinical proteome revealed the presence of known and potential drug targets such as oligopeptidases, kinases, cysteine proteases and more. CONCLUSIONS/SIGNIFICANCE: Previous proteomic studies on Trypanosomal infections, including human parasites T. brucei and T. cruzi, have been carried out from lab grown cultures. For T. evansi infection this is indeed the

  11. Proteomics research in India: an update.

    Science.gov (United States)

    Reddy, Panga Jaipal; Atak, Apurva; Ghantasala, Saicharan; Kumar, Saurabh; Gupta, Shabarni; Prasad, T S Keshava; Zingde, Surekha M; Srivastava, Sanjeeva

    2015-09-01

    After a successful completion of the Human Genome Project, deciphering the mystery surrounding the human proteome posed a major challenge. Despite not being largely involved in the Human Genome Project, the Indian scientific community contributed towards proteomic research along with the global community. Currently, more than 76 research/academic institutes and nearly 145 research labs are involved in core proteomic research across India. The Indian researchers have been major contributors in drafting the "human proteome map" along with international efforts. In addition to this, virtual proteomics labs, proteomics courses and remote triggered proteomics labs have helped to overcome the limitations of proteomics education posed due to expensive lab infrastructure. The establishment of Proteomics Society, India (PSI) has created a platform for the Indian proteomic researchers to share ideas, research collaborations and conduct annual conferences and workshops. Indian proteomic research is really moving forward with the global proteomics community in a quest to solve the mysteries of proteomics. A draft map of the human proteome enhances the enthusiasm among intellectuals to promote proteomic research in India to the world.This article is part of a Special Issue entitled: Proteomics in India. PMID:25868663

  12. Utility of proteomics techniques for assessing protein expression

    Science.gov (United States)

    In recent years, proteomic technologies have been frequently used as an effective analytical tool for examining modifications of protein profiles for accessing the bio-safety of genetically modified crops (GMO). Understanding of natural variation of soybean seed proteins is critical for determining...

  13. Proteomics approach for study of glycation during the malting process

    Czech Academy of Sciences Publication Activity Database

    Smětalová, Dagmar; Laštovičková, Markéta; Mazanec, Karel; Bobálová, Janette

    Vienna : Vienna University of Technology, 2010. s. 61. [Central and Eastern European Proteomics Conference meets Metabolomics Austria /4./. 29.08.2010-03.09.2010, Vienna] R&D Projects: GA MŠk 1M0570 Institutional research plan: CEZ:AV0Z40310501 Keywords : barley * glycation * MALDI-TOF Subject RIV: CB - Analytical Chemistry, Separation

  14. The Utility, Limitations, and Promise of Proteomics in Animal Science

    Science.gov (United States)

    Proteomics experiments have the ability to simultaneously identify and quantify potentially thousands of proteins in one experiment. The use of this technology in animal science is still in its infancy, yet it holds significant promise as a method for advancing animal science research. Examples of...

  15. The time is right: proteome biology of stem cells.

    NARCIS (Netherlands)

    Whetton, A.D.; Williamson, A.J.K.; Krijgsveld, J.; Lee, B.H.; Lemischka, I.; Oh, S.; Pera, M.; Mummery, C.L.; Heck, A.J.R.

    2008-01-01

    In stem cell biology, there is a growing need for advanced technologies that may help to unravel the molecular mechanisms of self-renewal and differentiation. Proteomics, the comprehensive analysis of proteins, is such an emerging technique. To facilitate interactions between specialists in proteomi

  16. Proteome and Antigens of Mycobacterium avium subspecies Paratuberculosis

    Science.gov (United States)

    This chapter will review what is known about the proteome of this significant veterinary pathogen by discussing the use of various whole cell preparations and fractionated components thereof. With improvements in technology, many new modifications to the traditional ELISA assay have been introduced...

  17. Recent developments and clinical studies utilizing engineered zinc finger nuclease technology.

    Science.gov (United States)

    Jo, Young-Il; Kim, Hyongbum; Ramakrishna, Suresh

    2015-10-01

    Efficient methods for creating targeted genetic modifications have long been sought for the investigation of gene function and the development of therapeutic modalities for various diseases, including genetic disorders. Although such modifications are possible using homologous recombination, the efficiency is extremely low. Zinc finger nucleases (ZFNs) are custom-designed artificial nucleases that make double-strand breaks at specific sequences, enabling efficient targeted genetic modifications such as corrections, additions, gene knockouts and structural variations. ZFNs are composed of two domains: (i) a DNA-binding domain comprised of zinc finger modules and (ii) the FokI nuclease domain that cleaves the DNA strand. Over 17 years after ZFNs were initially developed, a number of improvements have been made. Here, we will review the developments and future perspectives of ZFN technology. For example, ZFN activity and specificity have been significantly enhanced by modifying the DNA-binding domain and FokI cleavage domain. Advances in culture methods, such as the application of a cold shock and the use of small molecules that affect ZFN stability, have also increased ZFN activity. Furthermore, ZFN-induced mutant cells can be enriched using episomal surrogate reporters. Additionally, we discuss several ongoing clinical studies that are based on ZFN-mediated genome editing in humans. These breakthroughs have substantially facilitated the use of ZFNs in research, medicine and biotechnology. PMID:26089249

  18. Implementation of the concept of home hospitalisation for heart patients by means of telehomecare technology: integration of clinical tasks

    Directory of Open Access Journals (Sweden)

    Birthe Dinesen

    2007-05-01

    Full Text Available Purpose: To explore how the implementation of the concept ‘Home hospitalisation of heart patients’ by means of telehomecare technology influences the integration of clinical tasks across healthcare sectors. Theory: Inter-organisational theory. Methods: The case study approach was applied. Triangulations of data collection techniques were used: documentary materials, participant observation, qualitative and focus group interviews. Results: The clinical decision-making and task solving became multidisciplinary and integrated with the implementation of telehomecare and, therefore, complex in terms of the prescription and adjustment of patient medicine. Workflows between healthcare professionals across sectors changed from sequential to collective client flows. Pre-existing procedures for patient care, treatment, and responsibility were challenged. In addition, the number of tasks for the district nurses increased. Integration in the clinical task-solving area increases fragmentation in the knowledge technologies in a network perspective. Conclusions: Implementing the concept of ‘Home hospitalisation of heart patients’ by means of telehomecare technology will result in a more integrated clinical task-solving process that involves healthcare professionals from various sectors. Overall, the integration of clinical tasks between hospital and district nursing will result in a direct benefit for the heart patients.

  19. The minotaur proteome

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; García, Guadalupe Espadas; Paz, Marcia Ivonne Peña;

    2010-01-01

    Cell culture is a fundamental tool in proteomics where mammalian cells are cultured in vitro using a growth medium often supplemented with 5-15% FBS. Contamination by bovine proteins is difficult to avoid because of adherence to the plastic vessel and the cultured cells. We have generated peptides...... from bovine serum using four sample preparation methods and analyzed the peptides by high mass accuracy LC-MS/MS. Distinguishing between bovine and human peptides is difficult because of a considerable overlap of identical tryptic peptide sequences. Pitfalls in interpretation, different database search...

  20. Antibodies - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    NCI announces the release of monoclonal antipeptide antibodies from rabbit for distribution on the antibody portal. There are 60 recently added monoclonal antibodies, with 56 generated from mouse and 4 generated from rabbit.

  1. Proteomics in biomarker discovery and drug development

    OpenAIRE

    He, Q.; Chiu, J

    2003-01-01

    Proteomics is a research field aiming to characterize molecular and cellular dynamics in protein expression and function on a global level. The introduction of proteomics has been greatly broadening our view and accelerating our path in various medical researches. The most significant advantage of proteomics is its ability to examine a whole proteome or sub-proteome in a single experiment so that the protein alterations corresponding to a pathological or biochemical condition at a given time ...

  2. The HUPO Human Proteome Project (HPP, a Global Health Research Collaboration

    Directory of Open Access Journals (Sweden)

    Gilbert S. Omenn

    2012-09-01

    Full Text Available The global Human Proteome Project (HPP was announced by the Human Proteome Organization (HUPO at the 2010 World Congress of Proteomics in Sydney, Australia, and launched at the 2011 World Congress of Proteomics in Geneva, Switzerland, with analogies to the highly successful Human Genome Project. Extensive progress was reported at the September 2012 World Congress in Boston, USA. The HPP is designed to map the entire human proteome using available and emerging technologies. The HPP aims to create a molecular and biological foundation for improving health globally through better understanding of disease processes, more accurate diagnoses, and targets for more effective therapies and preventive interventions against many diseases. There are opportunities for individual investigators everywhere to access advanced datasets and to join HPP research teams.

  3. A proteomics perspective: from animal welfare to food safety.

    Science.gov (United States)

    Bassols, Anna; Turk, Romana; Roncada, Paola

    2014-03-01

    A fundamental issue of farm animal welfare is to keep animals clinically healthy, without disease or stress, particularly in intensive breeding, in order to produce safe and quality food. This issue is highly relevant for the food industry worldwide as they are directly linked to public health and welfare. The aim of this review is to explore how proteomics can assess and improve the knowledge useful for the strategic management of products of animal origin. Useful indications are provided about the latest proteomics tools for the development of novel biotechnologies serving the public health. The multivariate proteomics approach provides the bases for the discovery of biomarkers useful to investigate adaptation syndromes and oxidative stress. These two responses represent the milestones for the study of animal welfare. Moreover their implementation in the characterization and standardization of raw materials, process development, and quality and safety control of the final product of animal origin represents the current frontier in official surveillance and tests development. PMID:24555902

  4. Definition of Valid Proteomic Biomarkers: A Bayesian Solution

    Science.gov (United States)

    Harris, Keith; Girolami, Mark; Mischak, Harald

    Clinical proteomics is suffering from high hopes generated by reports on apparent biomarkers, most of which could not be later substantiated via validation. This has brought into focus the need for improved methods of finding a panel of clearly defined biomarkers. To examine this problem, urinary proteome data was collected from healthy adult males and females, and analysed to find biomarkers that differentiated between genders. We believe that models that incorporate sparsity in terms of variables are desirable for biomarker selection, as proteomics data typically contains a huge number of variables (peptides) and few samples making the selection process potentially unstable. This suggests the application of a two-level hierarchical Bayesian probit regression model for variable selection which assumes a prior that favours sparseness. The classification performance of this method is shown to improve that of the Probabilistic K-Nearest Neighbour model.

  5. Improving clinical communication of students with English as a second language (ESL) using online technology: a small scale evaluation study.

    Science.gov (United States)

    Rogan, Fran; San Miguel, Caroline

    2013-09-01

    Increasingly, students with English as a second language (ESL) are enrolled in nursing degrees in English speaking countries (Wang et al., 2008). However, they may be at risk of clinical practice failure due to communication difficulties associated with unfamiliar linguistic and cultural factors (Guhde, 2003). This paper describes and evaluates an innovation to assist ESL nursing students at an Australian university develop their clinical communication skills and practice readiness by providing online learning resources, using podcast and vodcast technology, that blend with classroom activities and facilitate flexible and independent learning. The innovation builds on an intensive clinical language workshop program called 'Clinically Speaking' which has evolved through a cyclical process of ongoing research to produce resources in response to students' learning needs. Whilst uptake of the resources was modest, students of ESL as well as English speaking backgrounds (ESB) found the resources improved their clinical preparation and confidence by increasing their understanding of expectations, clinical language and communication skills. The innovation, developed with a modest budget, shows potential in developing ESL and ESB students' readiness for clinical communication, enabling them to engage in clinical practice to develop competency standards required of nursing graduates and registration authorities. PMID:23337389

  6. Quantitative iTRAQ-Based Proteomic Identification of Candidate Biomarkers for Diabetic Nephropathy in Plasma of Type 1 Diabetic Patients

    DEFF Research Database (Denmark)

    Overgaard, Anne Julie; Thingholm, Tine Engberg; Larsen, Martin R;

    2010-01-01

    INTRODUCTION: As part of a clinical proteomics programme focused on diabetes and its complications, it was our goal to investigate the proteome of plasma in order to find improved candidate biomarkers to predict diabetic nephropathy. METHODS: Proteins derived from plasma from a cross-sectional co...

  7. Application of proteomics to translational research

    International Nuclear Information System (INIS)

    Deriving public benefit from basic biomedical research requires a dedicated and highly coordinated effort between basic scientists, physicians, bioinformaticians, clinical trial coordinators, MD and PhD trainees and fellows, and a host of other skilled participants. The Istituto Superiore di Sanita/George Mason University US-Italy Oncoproteomics program, established in 2005, is a successful example of a synergistic creative collaboration between basic scientists and clinical investigators conducting translational research. This program focuses on the application of the new field of proteomics to three urgent and fundamental clinical needs in cancer medicine: 1.) Biomarkers for early diagnosis of cancer, when it is still treatable, 2.) Individualizing patient therapy for molecular targeted inhibitors that block signal pathways driving cancer pathogenesis and 3.) Cancer Progenitor Cells (CSCs): When do the lethal progenitors of cancer first emerge, and how can we treat these CSCs with molecular targeted inhibitors

  8. Multi-dimensional liquid chromatography in proteomics-A review

    International Nuclear Information System (INIS)

    Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. This still-emerging combination of technologies aims to describe and characterize all expressed proteins in a biological system. Because of upper limits on mass detection of mass spectrometers, proteins are usually digested into peptides and the peptides are then separated, identified and quantified from this complex enzymatic digest. The problem in digesting proteins first and then analyzing the peptide cleavage fragments by mass spectrometry is that huge numbers of peptides are generated that overwhelm direct mass spectral analyses. The objective in the liquid chromatography approach to proteomics is to fractionate peptide mixtures to enable and maximize identification and quantification of the component peptides by mass spectrometry. This review will focus on existing multidimensional liquid chromatographic (MDLC) platforms developed for proteomics and their application in combination with other techniques such as stable isotope labeling. We also provide some perspectives on likely future developments.

  9. Sherlock Holmes and the proteome--a detective story.

    Science.gov (United States)

    Righetti, Pier Giorgio; Boschetti, Egisto

    2007-02-01

    The performance of a hexapeptide ligand library in capturing the 'hidden proteome' is illustrated and evaluated. This library, insolubilized on an organic polymer and available under the trade name 'Equalizer Bead Technology', acts by capturing all components of a given proteome, by concentrating rare and very rare proteins, and simultaneously diluting the abundant ones. This results in a proteome of 'normalized' relative abundances, amenable to analysis by MS and any other analytical tool. Examples are given of analysis of human urine and serum, as well as cell and tissue lysates, such as Escherichia coli and Saccharomyces cerevisiae extracts. Another important application is impurity tracking and polishing of recombinant DNA products, especially biopharmaceuticals meant for human consumption. PMID:17241233

  10. Orange proteomic fingerprinting: From fruit to commercial juices.

    Science.gov (United States)

    Lerma-García, María Jesús; D'Amato, Alfonsina; Simó-Alfonso, Ernesto F; Righetti, Pier Giorgio; Fasoli, Elisa

    2016-04-01

    Combinatorial peptide ligand library technology, coupled to mass spectrometry, has been applied to extensively map the proteome of orange pulp and peel and, via this fingerprinting, to detect its presence in commercial orange juices and drinks. The native and denaturing extraction protocols have captured 1109 orange proteins, as identified by LC-MS/MS. This proteomic map has been searched in an orange concentrate, from a Spanish juice manufacturer, as well as in commercial orange juices and soft drinks. The presence of numerous orange proteins in commercial juices has demonstrated the genuineness of these products, prepared by using orange fruits as original ingredients. However, the low number of identified proteins in sparkling beverages has suggested that they were prepared with scarce amounts of fruit extract, thus imparting lower quality to the final products. These findings not only increase the knowledge of the orange proteome but also present a reliable analytical method to assess quality and genuineness of commercial products. PMID:26593549

  11. Identification and characterization of N-glycosylated proteins using proteomics

    DEFF Research Database (Denmark)

    Selby, David S; Larsen, Martin R; Calvano, Cosima Damiana; Jensen, Ole Nørregaard

    2008-01-01

    complex task and is currently achieved by mass spectrometry-based methods that enable identification of glycoproteins and localization, classification, and analysis of individual glycan structures on proteins. In this chapter we briefly introduce a range of analytical technologies for recovery and...... analysis of glycoproteins and glycopeptides. Combinations of affinity-enrichment techniques, chemical and biochemical protocols, and advanced mass spectrometry facilitate detailed glycoprotein analysis in proteomics, from fundamental biological studies to biomarker discovery in biomedicine.......Glycoproteins constitute a large fraction of the proteome. The fundamental role of protein glycosylation in cellular development, growth, and differentiation, tissue development, and in host-pathogen interactions is by now widely accepted. Proteome-wide characterization of glycoproteins is a...

  12. Standard guidelines for the chromosome-centric human proteome project.

    Science.gov (United States)

    Paik, Young-Ki; Omenn, Gilbert S; Uhlen, Mathias; Hanash, Samir; Marko-Varga, György; Aebersold, Ruedi; Bairoch, Amos; Yamamoto, Tadashi; Legrain, Pierre; Lee, Hyoung-Joo; Na, Keun; Jeong, Seul-Ki; He, Fuchu; Binz, Pierre-Alain; Nishimura, Toshihide; Keown, Paul; Baker, Mark S; Yoo, Jong Shin; Garin, Jerome; Archakov, Alexander; Bergeron, John; Salekdeh, Ghasem Hosseini; Hancock, William S

    2012-04-01

    The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-HPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of individual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, introduce topics associated with experimental approaches, data production, quality control, treatment, and transparency of data, governance of the consortium, and collaborative benefits. A companion approach for the Biology and Disease-Driven HPP (B/D-HPP) component of the Human Proteome Project is currently being organized, building upon the Human Proteome Organization's organ-based and biofluid-based initiatives (www.hupo.org/research). The common application of these guidelines in the participating laboratories is expected to facilitate the goal of a comprehensive analysis of the human proteome. PMID:22443261

  13. Ultra-Fast Sample Preparation for High-Throughput Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Ferrer, Daniel; Hixson, Kim K.; Belov, Mikhail E.; Smith, Richard D.

    2011-06-21

    Sample preparation oftentimes can be the Achilles Heel of any analytical process and in the field of proteomics, preparing samples for mass spectrometric analysis is no exception. Current goals, concerning proteomic sample preparation on a large scale, include efforts toward improving reproducibility, reducing the time of processing and ultimately the automation of the entire workflow. This chapter reviews an array of recent approaches applied to bottom-up proteomics sample preparation to reduce the processing time down from hours to minutes. The current state-of-the-art in the field uses different energy inputs like microwave, ultrasound or pressure to perform the four basic steps in sample preparation: protein extraction, denaturation, reduction and alkylation, and digestion. No single energy input for enhancement of proteome sample preparation has become the universal gold standard. Instead, a combination of different energy inputs tend to produce the best results. This chapter further describes the future trends in the field such as the hyphenation of sample preparation with downstream detection and analysis systems. Finally, a detailed protocol describing the combined use of both pressure cycling technology and ultrasonic energy inputs to hasten proteomic sample preparation is presented.

  14. Proteomics: Analysis of Spectral Data

    Directory of Open Access Journals (Sweden)

    Harry B Burke

    2005-01-01

    Full Text Available Abstract: The goal of disease-related proteogenomic research is a complete description of the unfolding of the disease process from its origin to its cure. With a properly selected patient cohort and correctly collected, processed, analyzed data, large scale proteomic spectra may be able to provide much of the information necessary for achieving this goal. Protein spectra, which are one way of representing protein expression, can be extremely useful clinically since they can be generated from blood rather than from diseased tissue. At the same time, the analysis of circulating proteins in blood presents unique challenges because of their heterogeneity, blood contains a large number of different abundance proteins generated by tissues throughout the body. Another challenge is that protein spectra are massively parallel information. One can choose to perform top-down analysis, where the entire spectra is examined and candidate peaks are selected for further assessment. Or one can choose a bottom-up analysis, where, via hypothesis testing, individual proteins are identified in the spectra and related to the disease process. Each approach has advantages and disadvantages that must be understood if protein spectral data are to be properly analyzed. With either approach, several levels of information must be integrated into a predictive model. This model will allow us to detect disease and it will allow us to discover therapeutic interventions that reduce the risk of disease in at-risk individuals and effectively treat newly diagnosed disease.

  15. Proteomic Biomarkers of Atherosclerosis

    Directory of Open Access Journals (Sweden)

    Natacha Diaz-Prieto

    2008-01-01

    Full Text Available Biomarkers provide a powerful approach to understanding the spectrum of cardiovascular diseases. They have application in screening, diagnostic, prognostication, prediction of recurrences and monitoring of therapy. The “omics” tool are becoming very useful in the development of new biomarkers in cardiovascular diseases. Among them, proteomics is especially fitted to look for new proteins in health and disease and is playing a significant role in the development of new diagnostic tools in cardiovascular diagnosis and prognosis. This review provides an overview of progress in applying proteomics to atherosclerosis. First, we describe novel proteins identified analysing atherosclerotic plaques directly. Careful analysis of proteins within the atherosclerotic vascular tissue can provide a repertoire of proteins involved in vascular remodelling and atherogenesis. Second, we discuss recent data concerning proteins secreted by atherosclerotic plaques. The definition of the atheroma plaque secretome resides in that proteins secreted by arteries can be very good candidates of novel biomarkers. Finally we describe proteins that have been differentially expressed (versus controls by individual cells which constitute atheroma plaques (endothelial cells, vascular smooth muscle cells, macrophages and foam cells as well as by circulating cells (monocytes, platelets or novel biomarkers present in plasma.

  16. Proteomic Biomarkers of Atherosclerosis.

    Science.gov (United States)

    Vivanco, F; Padial, L R; Darde, V M; de la Cuesta, F; Alvarez-Llamas, G; Diaz-Prieto, Natacha; Barderas, M G

    2008-01-01

    SUMMARY: Biomarkers provide a powerful approach to understanding the spectrum of cardiovascular diseases. They have application in screening, diagnostic, prognostication, prediction of recurrences and monitoring of therapy. The "omics" tool are becoming very useful in the development of new biomarkers in cardiovascular diseases. Among them, proteomics is especially fitted to look for new proteins in health and disease and is playing a significant role in the development of new diagnostic tools in cardiovascular diagnosis and prognosis. This review provides an overview of progress in applying proteomics to atherosclerosis. First, we describe novel proteins identified analysing atherosclerotic plaques directly. Careful analysis of proteins within the atherosclerotic vascular tissue can provide a repertoire of proteins involved in vascular remodelling and atherogenesis. Second, we discuss recent data concerning proteins secreted by atherosclerotic plaques. The definition of the atheroma plaque secretome resides in that proteins secreted by arteries can be very good candidates of novel biomarkers. Finally we describe proteins that have been differentially expressed (versus controls) by individual cells which constitute atheroma plaques (endothelial cells, vascular smooth muscle cells, macrophages and foam cells) as well as by circulating cells (monocytes, platelets) or novel biomarkers present in plasma. PMID:19578499

  17. Telemedicine and M-Health in Hypertension Management: Technologies, Applications and Clinical Evidence.

    Science.gov (United States)

    Omboni, Stefano; Caserini, Marina; Coronetti, Claudio

    2016-09-01

    Electronic processes and communication technologies are more and more often employed to provide healthcare services to caregivers and their patients. Such solutions are currently referred as e-health, the most popular and widely distributed being those based on telemedicine and mobile health (m-health). A specific application of telemedicine for hypertension management is blood pressure telemonitoring (BPT), which allows remote data transmission of BP and additional information on patients' health status from their living site or from a community setting to the doctor's office or the hospital. Several randomized studies have documented a significant BP reduction with regular BPT compared to usual care, particularly in high risk hypertensive patients. Additional benefits are observed when BPT is offered under the supervision of a team of healthcare professionals, including a community pharmacist. BPT may also be provided in the context of m-health solutions, which commonly include wireless diagnostic and clinical decision support tools. M-health has the potential to promote patient's self-management, as a complement to the doctor's intervention, and encourage greater participation in medical decision making. Current statistics show that half of smartphone owners gather health information through their phone and 19 % use a health app. In case of hypertensive patients the most popular apps are those with tracking function, including BPT. Thus, e-health, and in particular BPT and m-health, are progressively gaining a key role in the management of hypertensive patients, having the potential to improve the quality of the delivered care and to more effectively prevent cardiovascular consequences of high BP. PMID:27072129

  18. Non invasive radiofrequency diagnostics of cancer. The Bioscanner — Trimprob technology and clinical applications

    International Nuclear Information System (INIS)

    A new paper by Pokorny, Vedruccio, Cifra, Kucera, titled Cancer physics: Diagnostics based on damped cellular elasto-electrical vibrations in microtubules, recently available on Eur. Biophys. J., discloses the mechanism of active grown cancer tissues interaction with a Non- Linear Resonance Interaction (NLRI) Bioscanner Trimprob diagnostic device that is certified and ready to be used to investigate suspected cases of disease and cancer. This technology spreads early capabilities of cancer detection by means of low level radiofrequency oscillations in UHF band. The system is based on an unique and extremely innovative non- linear radiofrequency oscillator working on 462-465 MHz plus the harmonics. The diseased tissues suspected of cancer, are irradiated by means of a handy probe near field emission, while a spectrum analyzer placed in the far field detects by means of a small antenna, the oscillator interaction within the tissues. The Bioscanner is characterized by a high dynamic range, in the order of 30 or more decibel, and is useful for detection of small cancer agglomerates, if used by a well trained operator. At the resonance, the free running oscillator locks-in on the specific interaction frequency, in a sharp frequency window centered on 462 MHz; the resulting effect is evidenced by a deep decrease of the 462 MHz spectral line propagation in the far field around the oscillator probe. The NLRI provides a selective characterization, like a sort of a electronic biopsy response of biologic tissues in support of modern imaging diagnostics. Further to existing literature describing methods for cancer detections by means of electromagnetic fields this paper shows this innovative in vivo medical diagnostic equipment and some clinical applications.

  19. Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome

    Directory of Open Access Journals (Sweden)

    Tue Bjerg Bennike

    2015-12-01

    In addition, we analyzed the proteome of human plasma, and compared the proteomes to the obtained porcine synovial fluid proteome. The proteome of the two body fluids were found highly similar, underlining the detected plasma derived nature of many synovial fluid components. The healthy porcine synovial fluid proteomics data, human rheumatoid arthritis synovial fluid proteomics data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935.

  20. Analysis of Peanut Leaf Proteome

    DEFF Research Database (Denmark)

    Ramesh, R.; Suravajhala, Prashanth; Pechan, T.

    2010-01-01

    approach to define function of their associated genes. Proteome analysis linked to genome sequence information is critical for functional genomics. However, the available protein expression data is extremely inadequate. Proteome analysis of peanut leaf was conducted using two-dimensional gel....... Furthermore, the leaf proteome map will lead to development of protein markers for cultivar identification at seedling stage of the plant. Overall, this study will contribute to improve our understanding of plant genetics and metabolism, and overall assist in the selection and breeding programs geared toward...

  1. The Clinical Impact of Recent Advances in LC-MS for Cancer Biomarker Discovery and Verification

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hui; Shi, Tujin; Qian, Weijun; Liu, Tao; Kagan, Jacob; Srivastava, Sudhir; Smith, Richard D.; Rodland, Karin D.; Camp, David G.

    2016-01-01

    Mass spectrometry-based proteomics has become an indispensable tool in biomedical research with broad applications ranging from fundamental biology, systems biology, and biomarker discovery. Recent advances in LC-MS have made it become a major technology in clinical applications, especially in cancer biomarker discovery and verification. To overcome the challenges associated with the analysis of clinical samples, such as extremely wide dynamic range of protein concentrations in biofluids and the need to perform high throughput and accurate quantification, significant efforts have been devoted to improve the overall performance of LC-MS bases clinical proteomics. In this review, we summarize the recent advances in LC-MS in the aspect of cancer biomarker discovery and quantification, and discuss its potentials, limitations, and future perspectives.

  2. Understanding the dynamics of information technology implementation: a study of clinical information systems.

    Science.gov (United States)

    Paré, G; Elam, J J

    1995-01-01

    Health care institutions are considering a variety of emerging information technologies (ITs) in the hope of increasing efficiency, reducing costs, re-engineering work processes, and improving quality of care. The recent, rapid advances made in the use of innovative ITs in the health care field can present a plethora of problems to the administrative staff. Perhaps the most pressing of these concerns is the ability of today's hospitals to effectively create and utilize computer-based information systems. IT implementation has long been of great interest for information systems researchers. This branch of information system study seeks to identify those factors that are integral to optimizing the usage of IT. For example, researchers have advised practitioners that managerial support, high quality system design, commitment to advancing with the field, and extensive project planning are all key elements of successful system. In sum, previous research has produced a set of managerial proscriptions which, taken as a whole, constitute the "ideal" way to implement an IT system. Yet despite these normative principles and proscriptions, many health care institutions continue to find their attempts to make use of IT fraught with difficulty. Therefore, the objective of this study is to broaden and edify our understanding of IT implementation. More specifically, we seek to dispel the myth of the "ideal" system setup by exploring some of the alternative systems in use. We wish to investigate how and why the components of these alternative systems interact to produce utilization success (or failure). The study investigates the establishment and subsequent use of three clinical information systems (CIS) in a large tertiary care teaching hospital. The first case study is that of the hospital-wide implementation of a computer system that allows physicians to sign their medical records electronically. The second case examines the use of an electronic patient chart used to support

  3. Analyzing shotgun proteomic data with PatternLab for proteomics

    OpenAIRE

    Carvalho, Paulo C; Yates, John R.; Barbosa, Valmir C

    2010-01-01

    PatternLab for proteomics is a one-stop-shop computational environment for analyzing shotgun proteomic data. Its modules provide means to pinpoint proteins / peptides that are differentially expressed, those that are unique to a state, and can also cluster the ones that share similar expression profiles in time-course experiments as well as help in interpreting results according to Gene Ontology. PatternLab is user-friendly, simple, and provides a graphical user interface.

  4. Next-generation long-term transplant clinics: improving resource utilization and the quality of care through health information technology.

    Science.gov (United States)

    Rioth, M J; Warner, J; Savani, B N; Jagasia, M

    2016-01-01

    By the year 2020, potentially one-half a million hematopoietic cell transplant (HCT) recipients will need long-term follow-up care to address not only chronic GvHD but also multiple other late consequences of transplant. Despite this increase in patients, there will not be a concomitant increase in the HCT workforce. Thus, the future of long-term patient management will require a new 'next-generation' clinical model that utilizes technological solutions to make the care of the HCT patient efficient, safe and cost-effective. Guideline-based decision support will be embedded in clinical workflows. Documentation requirements will be reduced as automated data collection from electronic medical records (EMRs) will populate registries and provide feedback for a rapid learning health system. Interoperable EMRs will disseminate treatment protocols to multiple care providers in a distributed long-term clinic model, such that providers outside of the transplant center can provide services closer to the patient. Patients will increase their participatory role through patient portals and mobile devices. At Vanderbilt, we have responded to some of these future challenges by embedding guideline-based decision support, structuring clinical documentation and being early adopters of communication technology. This manuscript describes the current state of some of these innovations, and a vision for the future of the long-term transplant clinic. PMID:26367235

  5. Next generation long term transplant clinics: Improving resource utilization and the quality of care through health information technology

    Science.gov (United States)

    Rioth, Matthew J; Warner, Jeremy; Savani, Bipin N; Jagasia, Madan

    2016-01-01

    By the year 2020, potentially one half million hematopoietic cell transplant (HCT) recipients will need long-term follow up care to address not only chronic GvHD but also multiple other late consequences of transplant. Despite this increase in patients, there will not be a concomitant increase in the HCT workforce. Thus the future of long-term patient management will require a new “next-generation” clinical model that utilizes technological solutions to make the care of the HCT patient efficient, safe, and cost-effective. Guideline-based decision support will be embedded in clinical workflows. Documentation requirements will be reduced as automated data collection from electronic medical records (EMRs) will populate registries and provide feedback for a rapid learning health system. Interoperable EMRs will disseminate treatment protocols to multiple care providers in a distributed long-term clinic model, such that providers outside of the transplant center can provide services closer to the patient. Patients will increase their participatory role through patient portals and mobile devices. At Vanderbilt, we have responded so some of these future challenges by embedding guideline-based decision support, structuring clinical documentation, and being early adopters of communication technology. This manuscript describes the current state of some of these innovations, and a vision for the future of the long-term transplant clinic. PMID:26367235

  6. Urinary proteomics to support diagnosis of stroke.

    Directory of Open Access Journals (Sweden)

    Jesse Dawson

    Full Text Available Accurate diagnosis in suspected ischaemic stroke can be difficult. We explored the urinary proteome in patients with stroke (n = 69, compared to controls (n = 33, and developed a biomarker model for the diagnosis of stroke. We performed capillary electrophoresis online coupled to micro-time-of-flight mass spectrometry. Potentially disease-specific peptides were identified and a classifier based on these was generated using support vector machine-based software. Candidate biomarkers were sequenced by liquid chromatography-tandem mass spectrometry. We developed two biomarker-based classifiers, employing 14 biomarkers (nominal p-value <0.004 or 35 biomarkers (nominal p-value <0.01. When tested on a blinded test set of 47 independent samples, the classification factor was significantly different between groups; for the 35 biomarker model, median value of the classifier was 0.49 (-0.30 to 1.25 in cases compared to -1.04 (IQR -1.86 to -0.09 in controls, p<0.001. The 35 biomarker classifier gave sensitivity of 56%, specificity was 93% and the AUC on ROC analysis was 0.86. This study supports the potential for urinary proteomic biomarker models to assist with the diagnosis of acute stroke in those with mild symptoms. We now plan to refine further and explore the clinical utility of such a test in large prospective clinical trials.

  7. The human proteomics initiative (HPI).

    Science.gov (United States)

    O'Donovan, C; Apweiler, R; Bairoch, A

    2001-05-01

    The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focussed on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. PMID:11301130

  8. [Progress in Proteomic Study of the Penicillin Producer---Penicillium Chrysogenum].

    Science.gov (United States)

    Wang, Shun; Wang, Peihong; Zhang, Nan; Gao, Ruichang

    2015-12-01

    Penicillin is a kind of β-lactam drug which has been applied in the clinical treatment firstly in the world, and it has still been widely used at present. The synthesis and regulation mechanism of Penicillium chrysogenum, which is used to produce penicillin, has been studied quite maturely, but its proteomics research started relatively late and fewer reports were published. This paper reviews the synthesis and application of penicillin, transformation of Penicillium chrysogenum, and the research progress of its proteomics. On this basis, the study highlights the advantages of proteomics in the research of protein expression. PMID:27079113

  9. Spectral library searching in proteomics.

    Science.gov (United States)

    Griss, Johannes

    2016-03-01

    Spectral library searching has become a mature method to identify tandem mass spectra in proteomics data analysis. This review provides a comprehensive overview of available spectral library search engines and highlights their distinct features. Additionally, resources providing spectral libraries are summarized and tools presented that extend experimental spectral libraries by simulating spectra. Finally, spectrum clustering algorithms are discussed that utilize the same spectrum-to-spectrum matching algorithms as spectral library search engines and allow novel methods to analyse proteomics data. PMID:26616598

  10. Perfluorooctanoic Acid for Shotgun Proteomics

    OpenAIRE

    Kadiyala, Chandra Sekhar Rao; Tomechko, Sara E.; Miyagi, Masaru

    2010-01-01

    Here, we describe the novel use of a volatile surfactant, perfluorooctanoic acid (PFOA), for shotgun proteomics. PFOA was found to solubilize membrane proteins as effectively as sodium dodecyl sulfate (SDS). PFOA concentrations up to 0.5% (w/v) did not significantly inhibit trypsin activity. The unique features of PFOA allowed us to develop a single-tube shotgun proteomics method that used all volatile chemicals that could easily be removed by evaporation prior to mass spectrometry analysis. ...

  11. The Chordate Proteome History Database

    OpenAIRE

    Anthony Levasseur; Julien Paganini; Jacques Dainat; Thompson, Julie D; Olivier Poch; Pierre Pontarotti; Philippe Gouret

    2012-01-01

    The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each i...

  12. Plant biology through quantitative proteomics

    OpenAIRE

    Bygdell, Joakim

    2013-01-01

    Over the last decade the field of mass spectrometry based proteomics has advanced from qualitative, analyses leading to publications revolving around lists of identified proteins and peptides, to addressing more biologically relevant issues requiring measurement of the abundance of identified proteins and hence quantitive mass spectrometry. The work described in this thesis addresses problems with quantitive proteomics in plant sciences, particularly complications caused by the complexity...

  13. Application of proteomics in non-small-cell lung cancer.

    Science.gov (United States)

    Cho, William C S

    2016-01-01

    Non-small-cell lung cancer (NSCLC) is a heterogeneous disease with diverse pathological features. Clinical proteomics allows the discovery of molecular markers and new therapeutic targets for this most prevalent type of lung cancer. Some of them may be used to detect early lung cancer, while others may serve as predictive markers of resistance to different therapies. Therapeutic targets and prognostic markers in NSCLC have also been discovered. These proteomics biomarkers may help to pair the individual NSCLC patient with the best treatment option. Despite the fact that implementation of these biomarkers in the clinic appears to be scarce, the recently launched Precision Medicine Initiative may encourage their translation into clinical practice. PMID:26577456

  14. The Succinated Proteome

    Energy Technology Data Exchange (ETDEWEB)

    Merkley, Eric D.; Metz, Thomas O.; Smith, Richard D.; Baynes, John; Frizell, Norma

    2014-03-30

    Succination is a chemical modification of cysteine in protein by the Krebs cycle intermediate, fumarate, yielding S-(2-succino)cysteine (2SC). Intracellular fumarate concentration and succination of proteins are increased by hyperpolarization of the inner mitochondrial membrane, in concert with mitochondrial, endoplasmic reticulum (ER) and oxidative stress in adipocytes grown in high glucose medium and in adipose tissue in obesity and diabetes. Increased succination of proteins is also detected in the kidney of a fumarase conditional knock-out mouse which develops renal tumors. Keap1, the gatekeeper of the antioxidant response, was identified as a major succinated protein in renal cancer cells, suggesting that succination may play a role in activation of the antioxidant response. A wide range of proteins is subject to succination, including enzymes, adipokines, cytoskeletal proteins and ER chaperones with functional cysteine residues. There is also significant overlap between succinated and glutathionylated proteins, and with proteins containing cysteine residues that are readily oxidized to the sulfenic (cysteic) acid. Succination of adipocyte proteins is inhibited by uncouplers, which discharge the mitochondrial membrane potential (Δψm) and by ER stress inhibitors. 2SC serves as a biomarker of mitochondrial stress or dysfunction in chronic diseases, such as obesity, diabetes and cancer, and recent studies suggest that succination is a mechanistic link between mitochondrial dysfunction, oxidative and ER stress, and cellular progression toward apoptosis. In this article, we review the history of the succinated proteome and the challenges associated with measuring this non-enzymatic post-translational modification of proteins by proteomics approaches.

  15. Plumbagin elicits differential proteomic responses mainly involving cell cycle, apoptosis, autophagy, and epithelial-to-mesenchymal transition pathways in human prostate cancer PC-3 and DU145 cells

    Directory of Open Access Journals (Sweden)

    Qui JX

    2015-01-01

    Full Text Available Jia-Xuan Qiu,1,2 Zhi-Wei Zhou, 3,4 Zhi-Xu He,4 Ruan Jin Zhao,5 Xueji Zhang,6 Lun Yang,7 Shu-Feng Zhou,3,4 Zong-Fu Mao11School of Public Health, Wuhan University, Wuhan, Hubei, People’s Republic of China; 2Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People’s Republic of China; 3Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA; 4Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center and Sino-US Joint Laboratory for Medical Sciences, Guiyang Medical University, Guiyang, Guizhou, People’s Republic of China; 5Center for Traditional Chinese Medicine, Sarasota, FL, USA; 6Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing, People’s Republic of China; 7Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education, Shanghai Jiao Tong University, Shanghai, People’s Republic of ChinaAbstract: Plumbagin (PLB has exhibited a potent anticancer effect in preclinical studies, but the molecular interactome remains elusive. This study aimed to compare the quantitative proteomic responses to PLB treatment in human prostate cancer PC-3 and DU145 cells using the approach of stable-isotope labeling by amino acids in cell culture (SILAC. The data were finally validated using Western blot assay. First, the bioinformatic analysis predicted that PLB could interact with 78 proteins that were involved in cell proliferation and apoptosis, immunity, and signal transduction. Our quantitative proteomic study using SILAC revealed that there were at least 1,225 and 267 proteins interacting with PLB and there were 341 and 107 signaling pathways and cellular functions potentially regulated by PLB in PC-3 and DU145 cells, respectively. These proteins and pathways played a

  16. Assessing the Use of Mobile Health Technology by Patients: An Observational Study in Primary Care Clinics

    OpenAIRE

    Ramirez, Veronica; Johnson, Emily; Gonzalez, Cesar; Ramirez, Vanessa; Rubino, Barbara; Rossetti, Gina

    2016-01-01

    Background There is significant potential for mobile health technology to improve health outcomes for patients with chronic diseases. However, there is a need for further development of mobile health technology that would help to improve the health of lower-income communities. Objective The study objective was to assess mobile phone and app usage among a culturally diverse patient population, and to determine whether patients would be interested in using mobile health technology to help manag...

  17. Properties and Clinical Application of Three Types of Dental Glass-Ceramics and Ceramics for CAD-CAM Technologies

    OpenAIRE

    Christian Ritzberger; Elke Apel; Wolfram Höland; Arnd Peschke; Volker M. Rheinberger

    2010-01-01

    The main properties (mechanical, thermal and chemical) and clinical application for dental restoration are demonstrated for three types of glass-ceramics and sintered polycrystalline ceramic produced by Ivoclar Vivadent AG. Two types of glass-ceramics are derived from the leucite-type and the lithium disilicate-type. The third type of dental materials represents a ZrO2 ceramic. CAD/CAM technology is a procedure to manufacture dental ceramic restoration. Leucite-type glass-ceramics demonstrate...

  18. Techniques for identifying the applicability of new information management technologies in the clinical setting: an example focusing on handheld computers.

    OpenAIRE

    Sittig, D. F.; Jimison, H. B.; Hazlehurst, B. L.; Churchill, B. E.; Lyman, J. A.; Mailhot, M. F.; Quick, E. A.; Simpson, D A

    2000-01-01

    This article describes techniques and strategies used to judge the potential applicability of new information management technologies in the clinical setting and to develop specific design recommendations for new features and services. We focus on a project carried out to identify the potential uses of handheld computers (i.e., the Palm Pilot or a small WinCE-based device) in the ambulatory practice setting. We found that the potential for a robust handheld computing device to positively affe...

  19. Differential Proteome Analysis of the Preeclamptic Placenta Using Optimized Protein Extraction

    Directory of Open Access Journals (Sweden)

    Magnus Centlow

    2010-01-01

    Full Text Available The human placenta is a difficult tissue to work with using proteomic technology since it contains large amounts of lipids and glycogen. Both lipids and glycogen are known to interfere with the first step in the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE, the isoelectric focusing. In order to gain the best possible protein separation on 2D-PAGE, an optimized sample preparation protocol for placental proteins was developed. Two different buffers, urea/CHAPS and Hepes, were used for solubilization in combination with six different precipitation methods. The removal of glycogen from the samples by centrifugation was crucial for the final proteome maps. Solubilization with urea/CHAPS in combination with dichloromethane/methanol or acidified acetone proved to be the best precipitation procedures. When applied to clinical placenta samples apolipoprotein A1 was found to be accumulated in the preeclamptic placenta, where it may either have a nutritional effect or act as a modifier of signal transduction.

  20. Substrate-Mediated Laser Ablation under Ambient Conditions for Spatially-Resolved Tissue Proteomics

    Science.gov (United States)

    Fatou, Benoit; Wisztorski, Maxence; Focsa, Cristian; Salzet, Michel; Ziskind, Michael; Fournier, Isabelle

    2015-12-01

    Numerous applications of ambient Mass Spectrometry (MS) have been demonstrated over the past decade. They promoted the emergence of various micro-sampling techniques such as Laser Ablation/Droplet Capture (LADC). LADC consists in the ablation of analytes from a surface and their subsequent capture in a solvent droplet which can then be analyzed by MS. LADC is thus generally performed in the UV or IR range, using a wavelength at which analytes or the matrix absorb. In this work, we explore the potential of visible range LADC (532 nm) as a micro-sampling technology for large-scale proteomics analyses. We demonstrate that biomolecule analyses using 532 nm LADC are possible, despite the low absorbance of biomolecules at this wavelength. This is due to the preponderance of an indirect substrate-mediated ablation mechanism at low laser energy which contrasts with the conventional direct ablation driven by sample absorption. Using our custom LADC system and taking advantage of this substrate-mediated ablation mechanism, we were able to perform large-scale proteomic analyses of micro-sampled tissue sections and demonstrated the possible identification of proteins with relevant biological functions. Consequently, the 532 nm LADC technique offers a new tool for biological and clinical applications.

  1. Structural proteomics by NMR spectroscopy.

    Science.gov (United States)

    Shin, Joon; Lee, Woonghee; Lee, Weontae

    2008-08-01

    Structural proteomics is one of the powerful research areas in the postgenomic era, elucidating structure-function relationships of uncharacterized gene products based on the 3D protein structure. It proposes biochemical and cellular functions of unannotated proteins and thereby identifies potential drug design and protein engineering targets. Recently, a number of pioneering groups in structural proteomics research have achieved proof of structural proteomic theory by predicting the 3D structures of hypothetical proteins that successfully identified the biological functions of those proteins. The pioneering groups made use of a number of techniques, including NMR spectroscopy, which has been applied successfully to structural proteomics studies over the past 10 years. In addition, advances in hardware design, data acquisition methods, sample preparation and automation of data analysis have been developed and successfully applied to high-throughput structure determination techniques. These efforts ensure that NMR spectroscopy will become an important methodology for performing structural proteomics research on a genomic scale. NMR-based structural proteomics together with x-ray crystallography will provide a comprehensive structural database to predict the basic biological functions of hypothetical proteins identified by the genome projects. PMID:18761469

  2. Research of proteomics and its application in tumour treatment by heavy ion

    International Nuclear Information System (INIS)

    With the accomplishment of the human genome project, proteomics becomes a new subject on the buildup of the whole proteins and their dynamic changes in cell emerge. Cancer is a kind of complex disease involved in multi-genes and proteins. Heavy ion therapy is an arising and potential radiation treatment nowadays. This paper reviews on the main methods and technology in proteomics--two-dimensional gel electrophoresis (2-DE), biological mass spectrometry, protein biochips, bioinformatics and its application on identification of cancer biomarkers, evaluation of curative effect on tumour and the mechanisms of tumour formation. This paper also presents some prospects on the application of proteomics in heavy ion therapy. (authors)

  3. Designing biomedical proteomics experiments: state-of-the-art and future perspectives.

    Science.gov (United States)

    Maes, Evelyne; Kelchtermans, Pieter; Bittremieux, Wout; De Grave, Kurt; Degroeve, Sven; Hooyberghs, Jef; Mertens, Inge; Baggerman, Geert; Ramon, Jan; Laukens, Kris; Martens, Lennart; Valkenborg, Dirk

    2016-05-01

    With the current expanded technical capabilities to perform mass spectrometry-based biomedical proteomics experiments, an improved focus on the design of experiments is crucial. As it is clear that ignoring the importance of a good design leads to an unprecedented rate of false discoveries which would poison our results, more and more tools are developed to help researchers designing proteomic experiments. In this review, we apply statistical thinking to go through the entire proteomics workflow for biomarker discovery and validation and relate the considerations that should be made at the level of hypothesis building, technology selection, experimental design and the optimization of the experimental parameters. PMID:27031651

  4. Multiplexed immunofluorescence delineates proteomic cancer cell states associated with metabolism

    Science.gov (United States)

    Sood, Anup; Miller, Alexandra M.; Brogi, Edi; Sui, Yunxia; Armenia, Joshua; McDonough, Elizabeth; Santamaria-Pang, Alberto; Carlin, Sean; Stamper, Aleksandra; Campos, Carl; Pang, Zhengyu; Li, Qing; Port, Elisa; Graeber, Thomas G.; Schultz, Nikolaus; Ginty, Fiona; Larson, Steven M.; Mellinghoff, Ingo K.

    2016-01-01

    The phenotypic diversity of cancer results from genetic and nongenetic factors. Most studies of cancer heterogeneity have focused on DNA alterations, as technologies for proteomic measurements in clinical specimen are currently less advanced. Here, we used a multiplexed immunofluorescence staining platform to measure the expression of 27 proteins at the single-cell level in formalin-fixed and paraffin-embedded samples from treatment-naive stage II/III human breast cancer. Unsupervised clustering of protein expression data from 638,577 tumor cells in 26 breast cancers identified 8 clusters of protein coexpression. In about one-third of breast cancers, over 95% of all neoplastic cells expressed a single protein coexpression cluster. The remaining tumors harbored tumor cells representing multiple protein coexpression clusters, either in a regional distribution or intermingled throughout the tumor. Tumor uptake of the radiotracer 18F-fluorodeoxyglucose was associated with protein expression clusters characterized by hormone receptor loss, PTEN alteration, and HER2 gene amplification. Our study demonstrates an approach to generate cellular heterogeneity metrics in routinely collected solid tumor specimens and integrate them with in vivo cancer phenotypes. PMID:27182557

  5. Analysis of Proteomic Differential Expression of Lysosomes in Mammary Gland between Healthy Dairy Cow and Dairy Cow with Clinical Mastiffs%健康奶牛与临床型乳腺炎奶牛乳腺 溶酶体蛋白组差异表达分析

    Institute of Scientific and Technical Information of China (English)

    邢耀潭; 赵兴绪

    2011-01-01

    In order to understand the etiopathogenesis of mastitis for milch cow, the galactophore samples were collected from eight healthy milch cow and milch cow with mastitis. Separating lysosomes from galactophore, and the lysosomes protein was extracted to conduct study on proteomics. The results showed that there were six differential proteins were found out from tissue lysosomes proteins in mammary gland of healthy dairy cows and dairy cows suffered from clinical mastitis through sub-cellular comparative proteomic technique, and the six kinds of proteins were identified, which were related to energy metabolism, lipid metabolism, anti-infection and anti-inflammation. The study of the function of the proteins has great help for the further elucidation of the pathogenesis of cow mastitis.%为了解奶牛乳房炎的发病机理,采集8头健康奶牛乳腺和临床型乳房炎奶牛乳腺,从乳腺分离溶酶体,提取溶酶体蛋白进行蛋白组学研究.结果从健康奶牛和乳房炎奶牛溶酶体蛋白中找到6个差异蛋白,质谱鉴定出6种蛋白,这些蛋白涉及能量代谢、脂肪代谢、抗感染、抗炎功能.

  6. A study on the perception of students in the radiologic technology study on the clinical practices

    International Nuclear Information System (INIS)

    The clinical practices provide the students with a good opportunity to study the practical experiences in their field through the clinical training education in hospital. Now, in this study, comparing the perceptions of the clinic teachers with those of students at the clinical site. The study was conducted to the students attending universities located in Seoul and who finished the clinical practices in 2013. The questionnaires were distributed to the student and collected from them. The study were conducted to 275 questionnaires with frequency analysis, crosstabs, chi-square test and McNemar test. The major motivation was of the select radiography course was high employment rate(44.0%) and the satisfaction of radiography course was general(53.1%). 51.3% of the study answered 8 weeks current duration of clinical practices is proper. The 3-year course students answered that the period of clinical practices would be proper if it is performed in the winter vacation in their second year in college(47.3%). The 4-year course students answered that the first semester in their third years is proper for clinical practices(27.7%). The students answered that they felt the lack in their knowledge on the professional field(32.4%) during the clinical practices and some of the practical training is different from the education performed at school(68.4%). Most of answered that they were satisfied with the clinical practices and among them they recognized the importance of the clinical practices (3.94 ± 0.89). After the clinical practices, their desire for getting job as a radiography has changed from 84.1% to 82.9%. The reason why they want the job related to the radiation is because the job is stable (changed from 49.0% to 46.0% after the clinical practice) while the reason why they do not want be a radigrapher because that job is not proper for them (changed from 37.0% to 40.7% after the clinical practice) The effort should be made to enhance the position of radiation

  7. Review of Information and Communication Technology Devices for Monitoring Functional and Cognitive Decline in Alzheimer's Disease Clinical Trials

    Directory of Open Access Journals (Sweden)

    Jagan A. Pillai

    2015-01-01

    Full Text Available Detecting and monitoring early cognitive impairment in Alzheimer's disease (AD is a significant need in the field of AD therapeutics. Successful AD clinical trial designs have to overcome challenges related to the subtle nature of early cognitive changes. Continuous unobtrusive assessments using Information and Communication Technology (ICT devices to capture markers of intra-individual change over time to assess cognitive and functional disability therefore offers significant benefits. We review the literature and provide an overview on randomized clinical trials in AD that use intelligent systems to monitor functional decline, as well as strengths, weaknesses, and future directions for the use of ICTs in a new generation of AD clinical trials.

  8. Stressor-induced proteome alterations in zebrafish: A meta-analysis of response patterns

    International Nuclear Information System (INIS)

    Highlights: • We compared reported proteome changes induced by various stressors in zebrafish. • Several proteins groups frequently responding to diverse stressors were identified. • These included energy metabolism enzymes, heat shock and cytoskeletal proteins. • Insufficient proteome coverage impedes identification of more specific responses. • Further research needs for proteomics in ecotoxicology are discussed. - Abstract: Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action

  9. Stressor-induced proteome alterations in zebrafish: A meta-analysis of response patterns

    Energy Technology Data Exchange (ETDEWEB)

    Groh, Ksenia J., E-mail: ksenia.groh@eawag.ch [Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf (Switzerland); ETH Zürich, Swiss Federal Institute of Technology, Department of Chemistry and Applied Biosciences, 8093 Zürich (Switzerland); Suter, Marc J.-F. [Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf (Switzerland); ETH Zürich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, 8092 Zürich (Switzerland)

    2015-02-15

    Highlights: • We compared reported proteome changes induced by various stressors in zebrafish. • Several proteins groups frequently responding to diverse stressors were identified. • These included energy metabolism enzymes, heat shock and cytoskeletal proteins. • Insufficient proteome coverage impedes identification of more specific responses. • Further research needs for proteomics in ecotoxicology are discussed. - Abstract: Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action

  10. CKD273, a New Proteomics Classifier Assessing CKD and Its Prognosis

    OpenAIRE

    Argilés, Àngel; Siwy, Justyna; Duranton, Flore; Gayrard, Nathalie; Dakna, Mohammed; Lundin, Ulrika; Osaba, Lourdes; Delles, Christian; Mourad, Georges; Weinberger, Klaus M.; Mischak, Harald

    2013-01-01

    National Kidney Foundation CKD staging has allowed uniformity in studies on CKD. However, early diagnosis and predicting progression to end stage renal disease are yet to be improved. Seventy six patients with different levels of CKD, including outpatients and dialysed patients were studied for transcriptome, metabolome and proteome description. High resolution urinary proteome analysis was blindly performed in the 53 non-anuric out of the 76 CKD patients. In addition to routine clinical para...

  11. Not low hanging but still sweet: Metabolic proteomes in cardiovascular disease.

    Science.gov (United States)

    Monte, Emma; Lopez, Rachel; Vondriska, Thomas M

    2016-01-01

    The application of proteomics in biology and medicine has reached a moment of truth. The demand of biologists for transformative insights into how cells work, plus the mandate of basic science research to ultimately impact clinical medicine, crystallize as a test on the rigor and reproducibility of any 'omics measurement. Studies like that by Boylston et al. indicate that proteomics can pass that test. PMID:26611885

  12. Mass Spectrometry-Based Proteomics in Molecular Diagnostics: Discovery of Cancer Biomarkers Using Tissue Culture

    OpenAIRE

    Debasish Paul; Avinash Kumar; Akshada Gajbhiye; Santra, Manas K.; Rapole Srikanth

    2013-01-01

    Accurate diagnosis and proper monitoring of cancer patients remain a key obstacle for successful cancer treatment and prevention. Therein comes the need for biomarker discovery, which is crucial to the current oncological and other clinical practices having the potential to impact the diagnosis and prognosis. In fact, most of the biomarkers have been discovered utilizing the proteomics-based approaches. Although high-throughput mass spectrometry-based proteomic approaches like SILAC, 2D-DIGE,...

  13. Microbial proteomics: a mass spectrometry primer for biologists

    Directory of Open Access Journals (Sweden)

    Graham Ciaren

    2007-08-01

    Full Text Available Abstract It is now more than 10 years since the publication of the first microbial genome sequence and science is now moving towards a post genomic era with transcriptomics and proteomics offering insights into cellular processes and function. The ability to assess the entire protein network of a cell at a given spatial or temporal point will have a profound effect upon microbial science as the function of proteins is inextricably linked to phenotype. Whilst such a situation is still beyond current technologies rapid advances in mass spectrometry, bioinformatics and protein separation technologies have produced a step change in our current proteomic capabilities. Subsequently a small, but steadily growing, number of groups are taking advantage of this cutting edge technology to discover more about the physiology and metabolism of microorganisms. From this research it will be possible to move towards a systems biology understanding of a microorganism. Where upon researchers can build a comprehensive cellular map for each microorganism that links an accurately annotated genome sequence to gene expression data, at a transcriptomic and proteomic level. In order for microbiologists to embrace the potential that proteomics offers, an understanding of a variety of analytical tools is required. The aim of this review is to provide a basic overview of mass spectrometry (MS and its application to protein identification. In addition we will describe how the protein complexity of microbial samples can be reduced by gel-based and gel-free methodologies prior to analysis by MS. Finally in order to illustrate the power of microbial proteomics a case study of its current application within the Bacilliaceae is given together with a description of the emerging discipline of metaproteomics.

  14. Potential of robots as next-generation technology for clinical assessment of neurological disorders and upper-limb therapy

    Directory of Open Access Journals (Sweden)

    Stephen H. Scott, PhD

    2011-05-01

    Full Text Available Robotic technologies have profoundly affected the identification of fundamental properties of brain function. This success is attributable to robots being able to control the position of or forces applied to limbs, and their inherent ability to easily, objectively, and reliably quantify sensorimotor behavior. Our general hypothesis is that these same attributes make robotic technologies ideal for clinically assessing sensory, motor, and cognitive impairments in stroke and other neurologi-cal disorders. Further, they provide opportunities for novel therapeutic strategies. The present opinionated review describes how robotic technologies combined with virtual/augmented reality systems can support a broad range of behavioral tasks to objectively quantify brain function. This information could potentially be used to provide more accurate diagnostic and prognostic information than is available from current clinical assessment techniques. The review also highlights the potential benefits of robots to provide upper-limb therapy. Although the capital cost of these technologies is substantial, it pales in comparison with the potential cost reductions to the overall healthcare system that improved assessment and therapeutic interventions offer.

  15. Implementation of newly adopted technology in acute care settings: a qualitative analysis of clinical staff

    Science.gov (United States)

    Langhan, Melissa L.; Riera, Antonio; Kurtz, Jordan C.; Schaeffer, Paula; Asnes, Andrea G.

    2015-01-01

    Objective Technologies are not always successfully implemented into practise. We elicited experiences of acute care providers with the introduction of technology and identified barriers and facilitators in the implementation process. Methods A qualitative study using one-on-one interviews among a purposeful sample of 19 physicians and nurses within ten emergency departments and intensive care units was performed. Grounded theory, iterative data analysis and the constant comparative method were used to inductively generate ideas and build theories. Results Five major categories emerged: decision-making factors, the impact on practise, technology's perceived value, facilitators and barriers to implementation. Barriers included negative experiences, age, infrequent use, and access difficulties. A positive outlook, sufficient training, support staff, and user friendliness were facilitators. Conclusions This study describes strategies implicated in the successful implementation of newly adopted technology in acute care settings. Improved implementation methods and evaluation of implementation processes are necessary for successful adoption of new technology. PMID:25367721

  16. Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes.

    OpenAIRE

    Karlsson, Christofer; Malmström, Lars; Aebersold, Ruedi; Malmström, Johan

    2012-01-01

    Selected reaction monitoring mass spectrometry (SRM-MS) is a targeted proteomics technology used to identify and quantify proteins with high sensitivity, specificity and high reproducibility. Execution of SRM-MS relies on protein-specific SRM assays, a set of experimental parameters that requires considerable effort to develop. Here we present a proteome-wide SRM assay repository for the gram-positive human pathogen group A Streptococcus. Using a multi-layered approach we generated SRM assays...

  17. Application of Proteomics to the Study of Hepatocellular Carcinoma and Some Related Diseases

    Institute of Scientific and Technical Information of China (English)

    Yueguo Li; Xin Geng; Weiming Zhang

    2005-01-01

    Hepatocellular carcinoma is a malignant tumor causing one of the highest death rates in the world. Viral hepatitis, hepatic fibrosis and hepatocirrhosis etc. Are some of the most important causes of hepatocellular carcinoma. With the advent of the post-genomic age, studying carcinoma and some related diseases using the developing technology of proteomics has become a major focus of researchers. This article is a review of the application of proteomics to study hepatocellular carcinoma and some related diseases.

  18. Methods for Pseudopodia Purification and Proteomic Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yingchun; Ding, Shi-Jian; Wang, Wei; Yang, Feng; Jacobs, Jon M.; Camp, David G.; Smith, Richard D.; Klemke, Richard L.

    2007-08-21

    Directional cell migration (chemotaxis) plays a central role in a wide spectrum of physiological and pathological processes, including embryo development, wounding healing, immunity, and cancer metastasis (1, 2). The process of chemotaxis is characterized by the sustained migration of cells in the direction of an increasing concentration of chemoattractant and/or ECM protein. Upon sensing the chemoattractant cells response with localized amplification of signals on the side facing the gradient (3-7). The spatial signal propagation facilitates reorganization of the actin-myosin cytoskeleton leading to extension of a dominant pseudopodium (PD) only in the direction of chemoattractant (7-10). While it is clear that localized signaling is critical for pseudopodium formation and chemotaxis, the molecular mechanisms that mediate this response remain poorly defined. To investigate mechanisms of pseudopodia formation, we recently described a novel approach to separate the PD and cell body (CB) compartments for large scale proteomic and phosphoproteomic analyses using chambers equipped with microporous filters (Fig. 1) (3, 7, 11). This in vitro system recapitulates physiological events associates with pseudopodial protrusion through small openings in the ECM and the vessel wall during immune cell intravasation and cancer cell metastasis (12, 13). The model system has been used to reveal important signaling pathways and novel proteins that mediate cell migration. This model, combined with the state-of-the-art proteomics and phosphoproteomics technology, will provide an effective approach to systematically analyze the proteins that differentially localized or phosphorylated in the front and the back of polarized migrating cells. In the following sections, we will describe in detail the protocols used to purify the PD and CB compartments for large-scale proteomic and phosphoproteomic analyses using mass spectrometry.

  19. Nuclear technology and chronic diseases: an exploratory study evolving the clinical physician perception

    International Nuclear Information System (INIS)

    This research is an exploratory cross-sectional study about the relationship of chronic disease and the use of nuclear technology. There is a concern over the increase of the prevalence of chronic disease in developing countries and it should hence be carefully evaluated in the context of societies, organizations and individuals. The technological advances experienced in the last decades especially in the nuclear technology area have created expectations to deal more efficiently with the challenge of chronic diseases. However little has been explored in this area under the point-of-view of medical doctors as agents who make this system of relations between disease and technology. The necessity for public and private planning to deal with this set of problems can benefit through an initial evaluation about the forthcoming theme, but should incorporate the agenda of health and technology planning for the following years. Using mixed methodology, made up of qualitative and quantitative approach, this research sought to reveal and configure important dimensions around the theme of this study. The field research was made up of interviews analyzed using techniques of fundamental theory and also of questionnaires sent by web analyzed statistically using exploratory factor analysis. These ventures allowed dimensions to be revealed that make up the perception of chronic disease and the use of nuclear technology. These dimensions presented in a form of a theoretical construct that were then discussed under the point of view of social theory and technological innovation. (author)

  20. Merging technology and clinical research for optimized post-surgical rehabilitation of lung cancer patients

    Science.gov (United States)

    Brintnall, Ruth Ann; Cooper, Julie

    2016-01-01

    Background The 21st century has ushered in an age of wireless communication and technological breakthroughs providing researchers with opportunities and challenges as they incorporate this technology into their research. This paper presents the challenges our team encountered introducing new technologies and how they were overcome for an intervention for post-thoracotomy non-small cell lung cancer (NSCLC) patients. Methods Our intervention incorporated the Nintendo Wii Fit Plus virtual-reality walking and balance exercise into a home-based rehabilitation program. The intervention is novel and innovative in that the intervention provides light-intensity exercise post-thoracotomy for NSCLC patients immediately after return to home from the hospital. The intervention overcomes the barriers of conventional exercise programs that require travel, conventional exercise equipment, and begin months after surgery. Results When translating new technology to research, researchers need to consider a number of factors that need to be addressed. Institutional Review Boards may need further explanation as to why the technology is safe, potential participants may need to have unfounded concerns explained before enrolling, and the research team needs a plan for introducing the technology to participants with a vast range of skill sets and environments in which they will be using technology. In our study, we addressed each of these factors using varying approaches as we translated how the Wii would be used in a home-based exercise intervention by a highly vulnerable, post-thoracotomy NSCLC population. Conclusions While technology brings with it multiple barriers for successful implementation, our team showed that with proper planning and teamwork, researchers can navigate these issues bringing the full benefit of technology to even the most vulnerable of patient populations. PMID:26889481

  1. Cell death proteomics database: consolidating proteomics data on cell death.

    Science.gov (United States)

    Arntzen, Magnus Ø; Bull, Vibeke H; Thiede, Bernd

    2013-05-01

    Programmed cell death is a ubiquitous process of utmost importance for the development and maintenance of multicellular organisms. More than 10 different types of programmed cell death forms have been discovered. Several proteomics analyses have been performed to gain insight in proteins involved in the different forms of programmed cell death. To consolidate these studies, we have developed the cell death proteomics (CDP) database, which comprehends data from apoptosis, autophagy, cytotoxic granule-mediated cell death, excitotoxicity, mitotic catastrophe, paraptosis, pyroptosis, and Wallerian degeneration. The CDP database is available as a web-based database to compare protein identifications and quantitative information across different experimental setups. The proteomics data of 73 publications were integrated and unified with protein annotations from UniProt-KB and gene ontology (GO). Currently, more than 6,500 records of more than 3,700 proteins are included in the CDP. Comparing apoptosis and autophagy using overrepresentation analysis of GO terms, the majority of enriched processes were found in both, but also some clear differences were perceived. Furthermore, the analysis revealed differences and similarities of the proteome between autophagosomal and overall autophagy. The CDP database represents a useful tool to consolidate data from proteome analyses of programmed cell death and is available at http://celldeathproteomics.uio.no. PMID:23537399

  2. Improving the Clinical Evidence of Bone Graft Substitute Technology in Lumbar Spine Surgery

    OpenAIRE

    Hsu, Wellington K.; Nickoli, M. S.; Wang, J.C.; Lieberman, J. R.; An, H S; Yoon, S. T.; Youssef, J. A.; Brodke, D.S.; McCullough, C. M.

    2012-01-01

    Bone graft substitutes have been used routinely for spine fusion for decades, yet clinical evidence establishing comparative data remains sparse. With recent scrutiny paid to the outcomes, complications, and costs associated with osteobiologics, a need to improve available data guiding efficacious use exists. We review the currently available clinical literature, studying the outcomes of various biologics in posterolateral lumbar spine fusion, and establish the need for a multicenter, indepen...

  3. Quantitative Phospho-proteomics to Investigate the Polo-like Kinase 1-Dependent Phospho-proteome*

    OpenAIRE

    Grosstessner-Hain, Karin; Hegemann, Björn; Novatchkova, Maria; Rameseder, Jonathan; Joughin, Brian A.; Hudecz, Otto; Roitinger, Elisabeth; Pichler, Peter; Kraut, Norbert; Yaffe, Michael B.; Peters, Jan-Michael; Mechtler, Karl

    2011-01-01

    Polo-like kinase 1 (PLK1) is a key regulator of mitotic progression and cell division, and small molecule inhibitors of PLK1 are undergoing clinical trials to evaluate their utility in cancer therapy. Despite this importance, current knowledge about the identity of PLK1 substrates is limited. Here we present the results of a proteome-wide analysis of PLK1-regulated phosphorylation sites in mitotic human cells. We compared phosphorylation sites in HeLa cells that were or were not treated with ...

  4. A medical study on wireless inertial measurement technology as a tool for identifying patients at risk of death or imminent clinical deterioration

    OpenAIRE

    Walsh, Michael; Gaffney, Mark; Barton, John,; O'flynn, Brendan; Ó Mathúna, S. Cian; Hickey, Anne; Kellett, John

    2011-01-01

    This paper provides a system description and preliminary results for an ongoing clinical study currently being carried out at the Mid-Western Regional Hospital, Nenagh, Ireland. The goal of the trial is to determine if wireless inertial measurement technology can be employed to identify elderly patients at risk of death or imminent clinical deterioration. The system measures cumulative movement and provides a score that will help provide a robust early warning to clinical staff of clinical de...

  5. Sustainable and responsible preventive medicine : Conceptualising ethical dilemmas arising from clinical implementation of advancing medical technology

    OpenAIRE

    Getz, Linn

    2006-01-01

    Background and setting Health care has become one of the most expansive activities in contemporary societies, and technology is one of its most influential factors. The modern medical-technological enterprise is however facing unprecedented practical, ethical and epistemic challenges. This thesis arises from a well-founded concern that medicine in general, and individually targeted preventive medicine in particular, may be about to become technified and dehumanised to an extent where its inte...

  6. Proteomics analysis of cancer exosomes using a novel modified aptamer-based array (SOMAscan™) platform.

    Science.gov (United States)

    Webber, Jason; Stone, Timothy C; Katilius, Evaldas; Smith, Breanna C; Gordon, Bridget; Mason, Malcolm D; Tabi, Zsuzsanna; Brewis, Ian A; Clayton, Aled

    2014-04-01

    We have used a novel affinity-based proteomics technology to examine the protein signature of small secreted extracellular vesicles called exosomes. The technology uses a new class of protein binding reagents called SOMAmers® (slow off-rate modified aptamers) and allows the simultaneous precise measurement of over 1000 proteins. Exosomes were highly purified from the Du145 prostate cancer cell line, by pooling selected fractions from a continuous sucrose gradient (within the density range of 1.1 to 1.2 g/ml), and examined under standard conditions or with additional detergent treatment by the SOMAscan™ array (version 3.0). Lysates of Du145 cells were also prepared, and the profiles were compared. Housekeeping proteins such as cyclophilin-A, LDH, and Hsp70 were present in exosomes, and we identified almost 100 proteins that were enriched in exosomes relative to cells. These included proteins of known association with cancer exosomes such as MFG-E8, integrins, and MET, and also those less widely reported as exosomally associated, such as ROR1 and ITIH4. Several proteins with no previously known exosomal association were confirmed as exosomally expressed in experiments using individual SOMAmer® reagents or antibodies in micro-plate assays. Western blotting confirmed the SOMAscan™-identified enrichment of exosomal NOTCH-3, L1CAM, RAC1, and ADAM9. In conclusion, we describe here over 300 proteins of hitherto unknown association with prostate cancer exosomes and suggest that the SOMAmer®-based assay technology is an effective proteomics platform for exosome-associated biomarker discovery in diverse clinical settings. PMID:24505114

  7. Microfluidic integration for automated targeted proteomic assays.

    Science.gov (United States)

    Hughes, Alex J; Lin, Robert K C; Peehl, Donna M; Herr, Amy E

    2012-04-17

    A dearth of protein isoform-based clinical diagnostics currently hinders advances in personalized medicine. A well-organized protein biomarker validation process that includes facile measurement of protein isoforms would accelerate development of effective protein-based diagnostics. Toward scalable protein isoform analysis, we introduce a microfluidic "single-channel, multistage" immunoblotting strategy. The multistep assay performs all immunoblotting steps: separation, immobilization of resolved proteins, antibody probing of immobilized proteins, and all interim wash steps. Programmable, low-dispersion electrophoretic transport obviates the need for pumps and valves. A three-dimensional bulk photoreactive hydrogel eliminates manual blotting. In addition to simplified operation and interfacing, directed electrophoretic transport through our 3D nanoporous reactive hydrogel yields superior performance over the state-of-the-art in enhanced capture efficiency (on par with membrane electroblotting) and sparing consumption of reagents (ca. 1 ng antibody), as supported by empirical and by scaling analyses. We apply our fully integrated microfluidic assay to protein measurements of endogenous prostate specific antigen isoforms in (i) minimally processed human prostate cancer cell lysate (1.1 pg limit of detection) and (ii) crude sera from metastatic prostate cancer patients. The single-instrument functionality establishes a scalable microfluidic framework for high-throughput targeted proteomics, as is relevant to personalized medicine through robust protein biomarker verification, systematic characterization of new antibody probes for functional proteomics, and, more broadly, to characterization of human biospecimen repositories. PMID:22474344

  8. Isotope dilution strategies for absolute quantitative proteomics

    International Nuclear Information System (INIS)

    The development of mass spectrometry (MS)-based methodologies for high-throughput protein identification has generated a concomitant need for protein quantification. Numerous MS-based relative quantification methodologies have been dedicated to the extensive comparison of multiple proteomes. On the other hand, absolute quantification methodologies, which allow the determination of protein concentrations in biological samples, are generally restricted to defined sets of proteins. Depending on the selected analytical procedure, absolute quantification approaches can provide accurate and precise estimations. These analytical performances are crucial for specific applications such as the evaluation of clinical bio-marker candidates. According to bioanalytical guidelines, accurate analytical processes require internal standards and quality controls. Regarding MS-based analysis of small molecules, isotope dilution has been recognized as the reference method for internal standardization. However, protein quantification methodologies which rely on the isotope dilution principle have been implemented in the proteomic field only recently. In these approaches, the sample is spiked with defined amounts of isotope-labeled analogue(s) of specific proteolytic peptide(s) (AQUA and QconCAT strategies) or protein(s) (PSAQ strategy). In this review, we present a critical overview of these isotope dilution methodologies. (authors)

  9. The proteome of human brain microdialysate

    Directory of Open Access Journals (Sweden)

    Feldmann Robert E

    2003-12-01

    Full Text Available Abstract Background Cerebral microdialysis has been established as a monitoring tool in neurocritically ill patients suffering from severe stroke. The technique allows to sample small molecules in the brain tissue for subsequent biochemical analysis. In this study, we investigated the proteomic profile of human cerebral microdialysate and if the identified proteins might be useful predictors for disease characteristics in stroke for tissue at risk in the contralateral hemisphere. We analysed cerebral protein expression in microdialysate from three stroke patients sampled from the hemisphere contralateral to the lesion. Using a proteomic approach based on two-dimensional gel electrophoresis and subsequent mass spectrometry, we created a protein map for the global protein expression pattern of human microdialyste. Results We found an average of 158 ± 24 (N = 18 protein spots in the human cerebral microdialysate and could identify 95 spots, representing 27 individual proteins. Most of these have been detected in human cerebrospinal fluid before, but 10 additional proteins mainly of cerebral intracellular origin were identified exclusively in the microdialysate. Conclusions The 10 proteins found exclusively in human cerebral microdialysate, but not in cerebrospinal fluid, indicate the possibility to monitor the progression of the disease towards deterioration. The correlation of protein composition in the human cerebral microdialysate with the patients' clinical condition and results of cerebral imaging may be a useful approach to future applications for neurological stroke diagnosis, prognosis, and treatment.

  10. Proteomics Study of Cotton Fiber Cells

    Institute of Scientific and Technical Information of China (English)

    LIU Jin-yuan

    2008-01-01

    @@ A comparative proteomic analysis was applied to explore the mechanism of fiber cell development in cotton.Initially,an efficient protein preparation method was established for proteomic analysis of developing cotton fibers by two-dimensional gel electrophoresis,and a microwave enhanced ink staining technique also was created for fast and sensitive protein quantification in proteomic studies.

  11. Proteomic Biomarkers for Spontaneous Preterm Birth

    DEFF Research Database (Denmark)

    Kacerovsky, Marian; Lenco, Juraj; Musilova, Ivana;

    2014-01-01

    This review aimed to identify, synthesize, and analyze the findings of studies on proteomic biomarkers for spontaneous preterm birth (PTB). Three electronic databases (Medline, Embase, and Scopus) were searched for studies in any language reporting the use of proteomic biomarkers for PTB published...... literature, there are no specific proteomic biomarkers capable of accurately predicting PTB....

  12. Development and standardization of multiplexed antibody microarrays for use in quantitative proteomics

    Directory of Open Access Journals (Sweden)

    Sorette M

    2004-12-01

    Full Text Available Abstract Background Quantitative proteomics is an emerging field that encompasses multiplexed measurement of many known proteins in groups of experimental samples in order to identify differences between groups. Antibody arrays are a novel technology that is increasingly being used for quantitative proteomics studies due to highly multiplexed content, scalability, matrix flexibility and economy of sample consumption. Key applications of antibody arrays in quantitative proteomics studies are identification of novel diagnostic assays, biomarker discovery in trials of new drugs, and validation of qualitative proteomics discoveries. These applications require performance benchmarking, standardization and specification. Results Six dual-antibody, sandwich immunoassay arrays that measure 170 serum or plasma proteins were developed and experimental procedures refined in more than thirty quantitative proteomics studies. This report provides detailed information and specification for manufacture, qualification, assay automation, performance, assay validation and data processing for antibody arrays in large scale quantitative proteomics studies. Conclusion The present report describes development of first generation standards for antibody arrays in quantitative proteomics. Specifically, it describes the requirements of a comprehensive validation program to identify and minimize antibody cross reaction under highly multiplexed conditions; provides the rationale for the application of standardized statistical approaches to manage the data output of highly replicated assays; defines design requirements for controls to normalize sample replicate measurements; emphasizes the importance of stringent quality control testing of reagents and antibody microarrays; recommends the use of real-time monitors to evaluate sensitivity, dynamic range and platform precision; and presents survey procedures to reveal the significance of biomarker findings.

  13. Comparative bioinformatics analyses and profiling of lysosome-related organelle proteomes

    Science.gov (United States)

    Hu, Zhang-Zhi; Valencia, Julio C.; Huang, Hongzhan; Chi, An; Shabanowitz, Jeffrey; Hearing, Vincent J.; Appella, Ettore; Wu, Cathy

    2007-01-01

    Complete and accurate profiling of cellular organelle proteomes, while challenging, is important for the understanding of detailed cellular processes at the organelle level. Mass spectrometry technologies coupled with bioinformatics analysis provide an effective approach for protein identification and functional interpretation of organelle proteomes. In this study, we have compiled human organelle reference datasets from large-scale proteomic studies and protein databases for seven lysosome-related organelles (LROs), as well as the endoplasmic reticulum and mitochondria, for comparative organelle proteome analysis. Heterogeneous sources of human organelle proteins and rodent homologs are mapped to human UniProtKB protein entries based on ID and/or peptide mappings, followed by functional annotation and categorization using the iProXpress proteomic expression analysis system. Cataloging organelle proteomes allows close examination of both shared and unique proteins among various LROs and reveals their functional relevance. The proteomic comparisons show that LROs are a closely related family of organelles. The shared proteins indicate the dynamic and hybrid nature of LROs, while the unique transmembrane proteins may represent additional candidate marker proteins for LROs. This comparative analysis, therefore, provides a basis for hypothesis formulation and experimental validation of organelle proteins and their functional roles.

  14. Proteomic approaches to bacterial differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Norbeck, Angela D.; Callister, Stephen J.; Monroe, Matthew E.; Jaitly, Navdeep; Elias, Dwayne A.; Lipton, Mary S.; Smith, Richard D.

    2006-12-01

    While genomic approaches have been applied for the detection and identification of individual bacteria within microbial communities, analogous proteomics approaches have been effectively precluded due to their inherent complexity. An in silico assessment of peptides that could potentially be present in the proteomes of artificial simple and complex communities was performed to evaluate the effect of proteome complexity on species detection. A mass spectrometry-based proteomics approach was employed to experimentally detect and validate the predicted tryptic peptides initially identified as distinctive within the simple community. An assessment of peptide distinctiveness and the potential for mapping to a particular bacterium within a community was made throughout each step of the study. A second in silico assessment of peptide distinctiveness for a complex community of 25 microorganisms was conducted to investigate the levels of instrumental performance that would be required to experimentally detect these peptides, as well as how performance varied with complexity (e.g., the number of different microorganisms). The experimental data for a simple community showed that it is feasible to predict, observe, and to quantify distinctive peptides from one organism in the presence of at least a 100-fold greater abundance of another, thus yielding putative markers for identifying a bacterium of interest. This work represents a first step towards quantitative proteomic characterization of complex microbial communities and the possible development of community wide markers of perturbations to such communities.

  15. Proteome of Hydra Nematocyst*

    Science.gov (United States)

    Balasubramanian, Prakash G.; Beckmann, Anna; Warnken, Uwe; Schnölzer, Martina; Schüler, Andreas; Bornberg-Bauer, Erich; Holstein, Thomas W.; Özbek, Suat

    2012-01-01

    Stinging cells or nematocytes of jellyfish and other cnidarians represent one of the most poisonous and sophisticated cellular inventions in animal evolution. This ancient cell type is unique in containing a giant secretory vesicle derived from the Golgi apparatus. The organelle structure within the vesicle comprises an elastically stretched capsule (nematocyst) to which a long tubule is attached. During exocytosis, the barbed part of the tubule is accelerated with >5 million g in <700 ns, enabling a harpoon-like discharge (Nüchter, T., Benoit, M., Engel, U., Ozbek, S., and Holstein, T. W. (2006) Curr. Biol. 16, R316–R318). Hitherto, the molecular components responsible for the organelle's biomechanical properties were largely unknown. Here, we describe the proteome of nematocysts from the freshwater polyp Hydra magnipapillata. Our analysis revealed an unexpectedly complex secretome of 410 proteins with venomous and lytic but also adhesive or fibrous properties. In particular, the insoluble fraction of the nematocyst represents a functional extracellular matrix structure of collagenous and elastic nature. This finding suggests an evolutionary scenario in which exocytic vesicles harboring a venomous secretome assembled a sophisticated predatory structure from extracellular matrix motif proteins. PMID:22291027

  16. Structural Proteomics of Herpesviruses.

    Science.gov (United States)

    Leroy, Baptiste; Gillet, Laurent; Vanderplasschen, Alain; Wattiez, Ruddy

    2016-01-01

    Herpesviruses are highly prevalent viruses associated with numerous pathologies both in animal and human populations. Until now, most of the strategies used to prevent or to cure these infections have been unsuccessful because these viruses have developed numerous immune evasion mechanisms. Therefore, a better understanding of their complex lifecycle is needed. In particular, while the genome of numerous herpesviruses has been sequenced, the exact composition of virions remains unknown for most of them. Mass spectrometry has recently emerged as a central method and has permitted fundamental discoveries in virology. Here, we review mass spectrometry-based approaches that have recently allowed a better understanding of the composition of the herpesvirus virion. In particular, we describe strategies commonly used for proper sample preparation and fractionation to allow protein localization inside the particle but also to avoid contamination by nonstructural proteins. A collection of other important data regarding post-translational modifications or the relative abundance of structural proteins is also described. This review also discusses the poorly studied importance of host proteins in herpesvirus structural proteins and the necessity to develop a quantitative workflow to better understand the dynamics of the structural proteome. In the future, we hope that this collaborative effort will assist in the development of new strategies to fight these infections. PMID:26907323

  17. Using Mobile Technologies to Access Evidence-Based Resources: A Rural Health Clinic Experience.

    Science.gov (United States)

    Carter-Templeton, Heather D; Wu, Lin

    2015-09-01

    This study describes the feasibility and usability of a mobile device and selected electronic evidence-based information programs used to support clinical decision making in a rural health clinic. The study focused on nurses' perceptions on when they needed more information, where they sought information, what made them feel comfortable about the information they found, and rules and guidelines they used to determine if the information should be used in patient care. ATLAS.ti, the qualitative analysis software, was used to assist with qualitative data analysis and management. PMID:26333613

  18. Facile preparation of salivary extracellular vesicles for cancer proteomics

    Science.gov (United States)

    Sun, Yan; Xia, Zhijun; Shang, Zhi; Sun, Kaibo; Niu, Xiaomin; Qian, Liqiang; Fan, Liu-Yin; Cao, Cheng-Xi; Xiao, Hua

    2016-04-01

    Extracellular vesicles (EVs) are membrane surrounded structures released by cells, which have been increasingly recognized as mediators of intercellular communication. Recent reports indicate that EVs participate in important biological processes and could serve as potential source for cancer biomarkers. As an attractive EVs source with merit of non-invasiveness, human saliva is a unique medium for clinical diagnostics. Thus, we proposed a facile approach to prepare salivary extracellular vesicles (SEVs). Affinity chromatography column combined with filter system (ACCF) was developed to efficiently remove the high abundant proteins and viscous interferences of saliva. Protein profiling in the SEVs obtained by this strategy was compared with conventional centrifugation method, which demonstrated that about 70% more SEVs proteins could be revealed. To explore its utility for cancer proteomics, we analyzed the proteome of SEVs in lung cancer patients and normal controls. Shotgun proteomic analysis illustrated that 113 and 95 proteins have been identified in cancer group and control group, respectively. Among those 63 proteins that have been consistently discovered only in cancer group, 12 proteins are lung cancer related. Our results demonstrated that SEVs prepared through the developed strategy are valuable samples for proteomics and could serve as a promising liquid biopsy for cancer.

  19. Proteomics and mass spectrometry in the diagnosis of renal amyloidosis.

    Science.gov (United States)

    Picken, Maria M

    2015-12-01

    The amyloidoses are a 'group' of disorders, all of which are associated with deposits that display similar staining and ultrastructural features and are toxic to tissues. Many proteins-currently 31 protein types and many more variants-have been shown to undergo such transformations. Among the various currently known amyloidoses, there are marked differences with regard to their pathogenesis and incidence, while the associated clinical picture is frequently overlapping. However, the therapies that are currently available are amyloid-type specific. The diagnosis of amyloidosis thus involves two steps: (i) a generic diagnosis, followed by (ii) an amyloid type-specific diagnosis or 'amyloid typing'. Immunofluorescence in frozen sections or immunohistochemistry (IHC) in paraffin sections has traditionally been used in the typing of amyloid. However, IHC of amyloid differs significantly from IHC in other areas of surgical pathology; both caution and experience are necessary for its interpretation. The rationale for the application of proteomic methods to amyloid typing lies in the relative abundance of amyloid proteins in tissue where, frequently, it is the 'dominant' protein. Proteomic techniques include the following steps: sample preparation, protein extraction and digestion into peptide fragments, followed by their subsequent separation and measurement by mass spectrometry (MS) and protein identification by informatics. The advantages as well as the limitations of both methods-immunohistochemistry and MS-based proteomics-are discussed. The current recommendations for the application of proteomics in renal amyloidosis are summarized. PMID:26613021

  20. New technologies in the gastrointestinal clinic and research: Impedance and high-resolution manometry

    Institute of Scientific and Technical Information of China (English)

    John E Pandolfino; Peter J Kahrilas

    2009-01-01

    The last five years have been an exciting time in the study of esophageal motor disorders due to the recent advances in esophageal function testing. New technologies have emerged, such as intraluminal impedance,while conventional techniques, such as manometry,have enjoyed many improvements due to advances in transducer technology, computerization and graphic data presentation. While these techniques provide more detailed information regarding esophageal function,our understanding of whether they can improve our ability to diagnose and treat patients more effectively is evolving. These techniques are also excellent research tools and they have added substantially to our understanding of esophageal motor function in dysphagia. This review describes the potential benefits that these new technologies may have over conventional techniques for the evaluation of dysphagia.

  1. Proteomic Response to Acupuncture Treatment in Spontaneously Hypertensive Rats

    OpenAIRE

    Xinsheng Lai; Jiayou Wang; Nabar, Neel R.; Sanqiang Pan; Chunzhi Tang; Yong Huang; Mufeng Hao; Zhonghua Yang; Chunmei Ma; Jin Zhang; Helen Chew; Zhenquan He; Junjun Yang; Baogui Su; Jian Zhang

    2012-01-01

    Previous animal and clinical studies have shown that acupuncture is an effective alternative treatment in the management of hypertension, but the mechanism is unclear. This study investigated the proteomic response in the nervous system to treatment at the Taichong (LR3) acupoint in spontaneously hypertensive rats (SHRs). Unanesthetized rats were subject to 5-min daily acupuncture treatment for 7 days. Blood pressure was monitored over 7 days. After euthanasia on the 7(th) day, rat medullas w...

  2. Mass spectrometry-based proteomic analyses of contact lens deposition

    OpenAIRE

    Green-Church, Kari B.; Nichols, Jason J.

    2008-01-01

    Purpose The purpose of this report is to describe the contact lens deposition proteome associated with two silicone hydrogel contact lenses and care solutions using a mass spectrometric-based approach. Methods This was a randomized, controlled, examiner-masked crossover clinical trial that included 48 participants. Lenses and no-rub care solutions evaluated included galyfilcon A (Acuvue Advance, Vistakon Inc., Jacksonville, FL), lotrafilcon B (O2 Optix, CIBA Vision Inc., Duluth, GA), AQuify (...

  3. Clinical Training at Remote Sites Using Mobile Technology: An India-USA Partnership

    Science.gov (United States)

    Vyas, R.; Albright, S.; Walker, D.; Zachariah, A.; Lee, M. Y.

    2010-01-01

    Christian Medical College (CMC), India, and Tufts University School of Medicine, USA, have developed an "institutional hub and spokes" model (campus-based e-learning supporting m-learning in the field) to facilitate clinical education and training at remote secondary hospital sites across India. Iterative research, design, development, and testing…

  4. Scenario drafting for early technology assessment of next generation sequencing in clinical oncology

    NARCIS (Netherlands)

    Joosten, S.E.P.; Retel, V.P.; Coupé, V.M.H.; Heuvel, van den M.M.; Harten, van W.H.

    2016-01-01

    Background Next Generation Sequencing (NGS) is expected to lift molecular diagnostics in clinical oncology to the next level. It enables simultaneous identification of mutations in a patient tumor, after which targeted therapy may be assigned. This approach could improve patient survival and/or assi

  5. Information Technology and the Clinical Curriculum: Some Predictions and Their Implications for the Class of 2003.

    Science.gov (United States)

    Faughnan, John G.; Elson, Robert

    1998-01-01

    Drawing on academic studies and on personal clinical and industry experiences, argues that ubiquitous, simple network computing and "power tools" for managing medical knowledge are coming to medicine in the near future. Implications are drawn for how medical school curricula cover issues such as patient confidentiality, systems thinking and error…

  6. Management of stress and stress-related diseases:Emerging computer-based technologies and the rationale for clinical laboratory assessment

    Directory of Open Access Journals (Sweden)

    Ezekiel Uba Nwose

    2009-11-01

    Full Text Available Background: Over the years, the issue of stress management in mental health has been discussed without reference to the clinical laboratory perspectives. Translational research and the vast array of emerging diagnostic technologies in alternative medical practice are now bridging the gap. While it would be scientific arrogance for the clinical practitioner and scientist to ignore the trend, the new technologies seeking clinical acceptability necessarily require expatiation of the scientific aspects of their products. Aims: This commentary builds on a comparative critical review to further our hypothesis that oxidative stress is the biochemical basis of the emerging computer-based diagnostic technologies. Materials & Method: The available information on Computer Meridian Diagnostics, Neuropattern and Virtual Scanning technologies were critically reviewed. The differences and similarities were articulated. Results: The technologies seem different, but have similarities that have not been articulated before. The seemingly different theories are traceable to Russian scientists and are based upon stress-induced adrenal secretions and the associated effect on glucose metabolism. The therapeutic effects of antioxidant nutrition, exercise or relaxation that are inherent in the technologies are highlighted. Conclusion: This commentary furthers explanation of the alterations in antioxidant activities as a result of biofeedback, oxidative stress and/or physiological effects as the biochemical basis of the technologies. The place for antioxidant indices and whole blood viscosity are also highlighted. This provides a rationale for the evaluation of available clinical diagnostic tests both to validate the technologies and as clinical laboratory correlates in stress management.

  7. Historical review of clinical vaccine studies at Oswaldo Cruz Institute and Oswaldo Cruz Foundation - technological development issues

    Directory of Open Access Journals (Sweden)

    Reinaldo de Menezes Martins

    2015-02-01

    Full Text Available This paper presents, from the perspective of technological development and production, the results of an investigation examining 61 clinical studies with vaccines conducted in Brazil between 1938-2013, with the participation of the Oswaldo Cruz Institute (IOC and the Oswaldo Cruz Foundation (Fiocruz. These studies have been identified and reviewed according to criteria, such as the kind of vaccine (viral, bacterial, parasitic, their rationale, design and methodological strategies. The results indicate that IOC and Fiocruz have accumulated along this time significant knowledge and experience for the performance of studies in all clinical phases and are prepared for the development of new vaccines products and processes. We recommend national policy strategies to overcome existing regulatory and financing constraints.

  8. Effect of male body mass index on clinical outcomes following assisted reproductive technology: a meta-analysis.

    Science.gov (United States)

    Le, W; Su, S-H; Shi, L-H; Zhang, J-F; Wu, D-L

    2016-05-01

    Overweight and obese males might exhibit a great risk of infertility. However, according to the current studies, the association between elevated male body mass index (BMI) and the clinical adverse results after assisted reproductive technology (ART) remains controversial. Hence, we conducted a meta-analysis to evaluate the effects of raised male BMI on clinical outcomes following ART. PubMed, EMBASE and three Chinese databases were used to identify relevant studies. The primary outcome was clinical pregnancy rate. Secondary outcomes included live birth rate and sperm parameters. A total of 5262 male participants from 10 cohort studies were subjected to meta-analysis. Results indicated that overweight or obese had no significant impact on clinical pregnancy rate [in vitro fertilisation (IVF): odds ratio (OR), 0.73; 95% confidence interval (CI), 0.39-1.39; intracytoplasmic sperm injection (ICSI): OR, 1.03; 95% CI, 0.92-1.15], live birth rate (IVF: OR, 0.91; 95% CI, 0.78-1.06; ICSI: OR, 1.00; 95% CI, 0.50-1.99) and sperm concentration (SMD, -0.28; 95% CI, -0.65 to 0.08) compared with normal weight following IVF/ICSI treatments. Exclusion of any single study and almost all the sensitivity analyses showed that our results were reliable. At present, the role of male BMI in the process of ART is only partly understood and should be further investigated. PMID:26276351

  9. Application of digital technology in the prosthodontic management of a patient with myasthenia gravis: A clinical report.

    Science.gov (United States)

    AlHelal, Abdulaziz; Jekki, Rami; Richardson, Paul M; Kattadiyil, Mathew T

    2016-05-01

    Application of digital technology in the treatment of a patient with myasthenia gravis and an excessively resorbed mandibular residual alveolar ridge is presented. The patient requested replacement of worn maxillary and mandibular prostheses. Treatment involved fabricating a new maxillary complete denture that was similar in appearance to the one being replaced and rebasing the existing and clinically acceptable mandibular fixed framework. The interim phase of treatment involved fabricating a mandibular milled prosthesis similar in morphology to the existing fixed complete denture with computer-aided design and computer-aided manufacturing technology. This facilitated conversion of an interim prosthesis by using an orientation device and eliminated the need for the patient to adapt to an interim removable complete denture. PMID:26775246

  10. Visualizing the Future: Technology Competency Development in Clinical Medicine, and Implications for Medical Education

    Science.gov (United States)

    Srinivasan, Malathi; Keenan, Craig R.; Yager, Joel

    2006-01-01

    Objective: In this article, the authors ask three questions. First, what will physicians need to know in order to be effective in the future? Second, what role will technology play in achieving that high level of effectiveness? Third, what specific skill sets will physicians need to master in order to become effective? Method: Through three case…

  11. Use of proteomics in the study of microbial diseases of small ruminants.

    Science.gov (United States)

    Katsafadou, A I; Tsangaris, G Th; Billinis, C; Fthenakis, G C

    2015-12-14

    Objective of the paper is to review potential applications of proteomics methodologies in the study of microbial diseases of small ruminants. Proteomics has been employed for the elucidation of pathogenesis of various diseases, i.e., in the study of determinants of microbial agents and the study of host-pathogen interactions, as well as in improved disease diagnosis by the identification of biomarkers. Extensive uses of proteomics in sheep and goat diseases have been applied primarily in mastitis, in reproductive infections, in paratuberculosis, in respiratory infections and in scrapie. Mining deeper into the various proteomes and application of new methodological strategies in clinical studies will provide information about disease processes. Improvement of diagnostic techniques, development of vaccines against diseases and establishment of tools for optimum animal production are key-areas for targeted research. PMID:26233680

  12. Advances of Proteomic Sciences in Dentistry

    Science.gov (United States)

    Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

    2016-01-01

    Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed. PMID:27187379

  13. Respiratory Mucosal Proteome Quantification in Human Influenza Infections.

    OpenAIRE

    Marion, Tony; Elbahesh, Husni; Paul G Thomas; DeVincenzo, John P.; Webby, Richard; Schughart, Klaus

    2016-01-01

    Respiratory influenza virus infections represent a serious threat to human health. Underlying medical conditions and genetic make-up predispose some influenza patients to more severe forms of disease. To date, only a few studies have been performed in patients to correlate a selected group of cytokines and chemokines with influenza infection. Therefore, we evaluated the potential of a novel multiplex micro-proteomics technology, SOMAscan, to quantify proteins in the respiratory mucosa of infl...

  14. Respiratory Mucosal Proteome Quantification in Human Influenza Infections

    OpenAIRE

    Marion, Tony; Elbahesh, Husni; Paul G Thomas; DeVincenzo, John P.; Webby, Richard; Schughart, Klaus

    2016-01-01

    Respiratory influenza virus infections represent a serious threat to human health. Underlying medical conditions and genetic make-up predispose some influenza patients to more severe forms of disease. To date, only a few studies have been performed in patients to correlate a selected group of cytokines and chemokines with influenza infection. Therefore, we evaluated the potential of a novel multiplex micro-proteomics technology, SOMAscan, to quantify proteins in the respiratory mucosa of infl...

  15. Selected reaction monitoring for quantitative proteomics: a tutorial

    OpenAIRE

    Lange, Vinzenz; Picotti, Paola; Domon, Bruno; Aebersold, Ruedi

    2008-01-01

    Systems biology relies on data sets in which the same group of proteins is consistently identified and precisely quantified across multiple samples, a requirement that is only partially achieved by current proteomics approaches. Selected reaction monitoring (SRM)—also called multiple reaction monitoring—is emerging as a technology that ideally complements the discovery capabilities of shotgun strategies by its unique potential for reliable quantification of analytes of low abundance in comple...

  16. Characterisation of Caenorhabditis elegans sperm transcriptome and proteome

    OpenAIRE

    Ma, Xuan; Zhu, Yingjie; Li, Chunfang; Xue, Peng; Zhao, Yanmei; Chen, Shilin; Yang, Fuquan; Miao, Long

    2014-01-01

    Background Although sperm is transcriptionally and translationally quiescent, complex populations of RNAs, including mRNAs and non-coding RNAs, exist in sperm. Previous microarray analysis of germ cell mutants identified hundreds of sperm genes in Caenorhabditis elegans. To take a more comprehensive view on C. elegans sperm genes, here, we isolate highly pure sperm cells and employ high-throughput technologies to obtain sperm transcriptome and proteome. Results First, sperm transcriptome cons...

  17. MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data

    Directory of Open Access Journals (Sweden)

    Rader Robert

    2007-06-01

    Full Text Available Abstract Background The advancements of proteomics technologies have led to a rapid increase in the number, size and rate at which datasets are generated. Managing and extracting valuable information from such datasets requires the use of data management platforms and computational approaches. Results We have developed the MAss SPECTRometry Analysis System (MASPECTRAS, a platform for management and analysis of proteomics LC-MS/MS data. MASPECTRAS is based on the Proteome Experimental Data Repository (PEDRo relational database schema and follows the guidelines of the Proteomics Standards Initiative (PSI. Analysis modules include: 1 import and parsing of the results from the search engines SEQUEST, Mascot, Spectrum Mill, X! Tandem, and OMSSA; 2 peptide validation, 3 clustering of proteins based on Markov Clustering and multiple alignments; and 4 quantification using the Automated Statistical Analysis of Protein Abundance Ratios algorithm (ASAPRatio. The system provides customizable data retrieval and visualization tools, as well as export to PRoteomics IDEntifications public repository (PRIDE. MASPECTRAS is freely available at http://genome.tugraz.at/maspectras Conclusion Given the unique features and the flexibility due to the use of standard software technology, our platform represents significant advance and could be of great interest to the proteomics community.

  18. Proteomics of Skeletal Muscle: Focus on Insulin Resistance and Exercise Biology

    Directory of Open Access Journals (Sweden)

    Atul S. Deshmukh

    2016-02-01

    Full Text Available Skeletal muscle is the largest tissue in the human body and plays an important role in locomotion and whole body metabolism. It accounts for ~80% of insulin stimulated glucose disposal. Skeletal muscle insulin resistance, a primary feature of Type 2 diabetes, is caused by a decreased ability of muscle to respond to circulating insulin. Physical exercise improves insulin sensitivity and whole body metabolism and remains one of the most promising interventions for the prevention of Type 2 diabetes. Insulin resistance and exercise adaptations in skeletal muscle might be a cause, or consequence, of altered protein expressions profiles and/or their posttranslational modifications (PTMs. Mass spectrometry (MS-based proteomics offer enormous promise for investigating the molecular mechanisms underlying skeletal muscle insulin resistance and exercise-induced adaptation; however, skeletal muscle proteomics are challenging. This review describes the technical limitations of skeletal muscle proteomics as well as emerging developments in proteomics workflow with respect to samples preparation, liquid chromatography (LC, MS and computational analysis. These technologies have not yet been fully exploited in the field of skeletal muscle proteomics. Future studies that involve state-of-the-art proteomics technology will broaden our understanding of exercise-induced adaptations as well as molecular pathogenesis of insulin resistance. This could lead to the identification of new therapeutic targets.

  19. Review of technology development and clinical trials of transcranial laser therapy for acute ischemic stroke treatment

    Science.gov (United States)

    Catanzaro, Brian E.; Streeter, Jackson; de Taboada, Luis

    2010-02-01

    Stroke is the one of the leading causes of mortality in the United States, claiming 600,000 lives each year. Evidence suggests that near infrared (NIR) illumination has a beneficial effect on a variety of cells when these cells are exposed to adverse conditions. Among these conditions is the hypoxic state produced by acute ischemic stroke (AIS). To demonstrate the impact NIR Transcranial Laser Therapy (TLT) has on AIS in humans, a series of double blind, placebo controlled clinical trials were designed using the NeuroThera(R) System (NTS). The NTS was designed and developed to treat subjects non-invasively using 808 nm NIR illumination. TLT, as it applies to stroke therapy, and the NTS will be described. The results of the two clinical trials: NeuroThera(R) Safety and Efficacy Trial 1 (NEST-1) and NeuroThera(R) Safety and Efficacy Trial 2 (NEST-2) will be reviewed and discussed.

  20. Modern dental imaging: a review of the current technology and clinical applications in dental practice

    International Nuclear Information System (INIS)

    A review of modern imaging techniques commonly used in dental practice and their clinical applications is presented. The current dental examinations consist of intraoral imaging with digital indirect and direct receptors, while extraoral imaging is divided into traditional tomographic/panoramic imaging and the more recently introduced cone beam computed tomography. Applications, limitations and current trends of these dental ''in-office'' radiographic techniques are discussed. (orig.)

  1. Modern dental imaging: a review of the current technology and clinical applications in dental practice

    Energy Technology Data Exchange (ETDEWEB)

    Vandenberghe, Bart; Jacobs, Reinhilde [Katholieke Universiteit Leuven, Oral Imaging Centre, Faculty of Medicine, School of Dentistry, Oral Pathology and Maxillofacial Surgery, Leuven (Belgium); Bosmans, Hilde [Katholieke Universiteit Leuven, Radiology Section, Department of Medical Diagnostic Sciences, Leuven (Belgium)

    2010-11-15

    A review of modern imaging techniques commonly used in dental practice and their clinical applications is presented. The current dental examinations consist of intraoral imaging with digital indirect and direct receptors, while extraoral imaging is divided into traditional tomographic/panoramic imaging and the more recently introduced cone beam computed tomography. Applications, limitations and current trends of these dental ''in-office'' radiographic techniques are discussed. (orig.)

  2. Database independent proteomics analysis of the ostrich and human proteome.

    NARCIS (Netherlands)

    Altelaar, A.F.; Navarro, D.; Boekhorst, J.; Breukelen, B. van; Snel, B.; Mohammed, S.; Heck, A.J.R. van

    2012-01-01

    Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search s

  3. Biodegradable device applied in flatfoot surgery: Comparative studies between clinical and technological aspects of removed screws

    International Nuclear Information System (INIS)

    Poly-L-lactide (PLLA) is one of the most used polymers for biomedical application; its use in sutures and other implants has been widely investigated. Although the knowledge of PLLA biodegradation and biocompatibility features is deep, PLLA screws used to correct the flat foot deformity have deserved attention since they are not degraded in most of cases after a long period of years (3–7) from the implantation. In this article, a clinical and radiological evaluation (NMR, histological and clinical outcomes) on patients was correlated with physico-chemical characterization (by SEM, DSC, GPC and XRD analysis at different temperatures) on both native and patient-recovered screws together with the theoretical degradation processes of PLLA-based implants. The data demonstrated the need for crossing the biodegradation and bioabsorption of the polymer with the characteristics of both the device (geometry, structure and fabrication process) and the implantation site. Highlights: ► Resorbable PLLA screws were proposed for arthroereisis in pediatric flatfoot. ► Satisfactory clinical results were obtained almost in the totality of patients. ► The bioabsorption period is slightly longer than what is expected. ► Patient-recovered screws were analyzed to evaluate the biodegradation stage. ► Degradability/structural integrity during implantation should be ameliorated

  4. Biodegradable device applied in flatfoot surgery: Comparative studies between clinical and technological aspects of removed screws

    Energy Technology Data Exchange (ETDEWEB)

    Ruozi, Barbara, E-mail: barbara.ruozi@unimore.it [Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, MO (Italy); Belletti, Daniela, E-mail: daniela.belletti@unimore.it [Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, MO (Italy); Manfredini, Giuseppe, E-mail: giuseppe626@virgilio.it [Orthopaedic and Traumatologic Clinic, University Hospital of Modena and Reggio Emilia, Modena Italy, Director Prof. F. Catani, Via del Pozzo 71, Policlinico, 41100 Modena, MO (Italy); Tonelli, Massimo, E-mail: massimo.tonelli@unimore.it [CIGS, University of Modena and Reggio Emilia, Via Campi 213/A, 41100 Modena, MO (Italy); Sena, Paola, E-mail: paola.sena@unimore.it [Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via del Pozzo 71, Policlinico, 41100 Modena, MO (Italy); Vandelli, Maria Angela, E-mail: mariaangela.vandelli@unimore.it [Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, MO (Italy); Forni, Flavio, E-mail: flavio.forni@unimore.it [Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, MO (Italy); Tosi, Giovanni, E-mail: giovanni.tosi@unimore.it [Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, MO (Italy)

    2013-04-01

    Poly-L-lactide (PLLA) is one of the most used polymers for biomedical application; its use in sutures and other implants has been widely investigated. Although the knowledge of PLLA biodegradation and biocompatibility features is deep, PLLA screws used to correct the flat foot deformity have deserved attention since they are not degraded in most of cases after a long period of years (3–7) from the implantation. In this article, a clinical and radiological evaluation (NMR, histological and clinical outcomes) on patients was correlated with physico-chemical characterization (by SEM, DSC, GPC and XRD analysis at different temperatures) on both native and patient-recovered screws together with the theoretical degradation processes of PLLA-based implants. The data demonstrated the need for crossing the biodegradation and bioabsorption of the polymer with the characteristics of both the device (geometry, structure and fabrication process) and the implantation site. Highlights: ► Resorbable PLLA screws were proposed for arthroereisis in pediatric flatfoot. ► Satisfactory clinical results were obtained almost in the totality of patients. ► The bioabsorption period is slightly longer than what is expected. ► Patient-recovered screws were analyzed to evaluate the biodegradation stage. ► Degradability/structural integrity during implantation should be ameliorated.

  5. Proteomics of renal disorders: Urinary proteome analysis by two-dimensional gel electrophoresis and MALDI-TOF mass spectrometry

    OpenAIRE

    Kumar, Yadunanda; Venkata Uppuluri, Nageshwar Rao; Babu, Kishore; Phadke, Kishore; Kumar, Prasanna; Ballal, Sudarshan; Tatu, Utpal

    2002-01-01

    The proteomes of urinary samples from patients with different renal conditions were analysed by two dimensional electrophoresis and MALDI-TOF technology. Samples from three different renal conditions, namely kidney failure, nephrotic syndrome and microalbuminuria, were included in the analysis. Apart from the presence of albumin, the profiles of protein spots found in these urine samples were quite distinct. While kidney failure patients showed predominantly low molecular weight proteins, the...

  6. Evaluation of magnocellular pathway abnormalities in schizophrenia: a frequency doubling technology study and clinical implications

    Directory of Open Access Journals (Sweden)

    Fabiana Benites Vaz de Lima

    2013-04-01

    Full Text Available BACKGROUND: Visual processing deficits have been reported for patients with schizophrenia. Previous studies demonstrated differences in early-stage processing of schizophrenics, although the nature, extent, and localization of the disturbance are unknown. The magnocellular and parvocellular visual pathways are associated with transient and sustained channels, but their respective contributions to schizophrenia-related visual deficits remains controversial. PURPOSE: The aim of this study was to evaluate magnocellular dysfunction in schizophrenia using frequency doubling technology. METHODS: Thirty-one patients with schizophrenia and 34 healthy volunteers were examined. Frequency doubling technology testing was performed in one session, consisting of a 15-minute screening strategy followed by the C-20 program for frequency doubling technology. RESULTS: Schizophrenic patients showed lower global mean sensitivity (30,97 ± 2,25 dB compared with controls (32,17 ± 3,08 dB, p<0.009. Although there was no difference in the delta sensitivity of hemispheres, there was a difference in sensitivity analysis of the fibers crossing the optic chiasm, with lower mean sensitivity in the patient group (28,80 dB versus controls (30,66 dB. The difference was higher in fibers that do not cross the optic chiasm, with lower mean sensitivity in patients (27,61 dB versus controls (30,26 dB, p<0.005. CONCLUSIONS: Our results suggest that there are differences between global sensitivity and fiber sensitivity measured by frequency doubling technology. The different sensitivity of fibers that do not cross the optic chiasm is consistent with most current etiological hypotheses for schizophrenia. The decreased sensitivity responses in the optic radiations may significantly contribute to research assessing early-stage visual processing deficits for patients with schizophrenia.

  7. Impact of Barcode Medication Administration Technology on How Nurses Spend Their Time On Clinical Care

    OpenAIRE

    Poon, Eric G; Keohane, Carol; Featherstone, Erica; Hays, Brandon; Dervan, Andrew; Woolf, Seth; Hayes, Judy; Bane, Anne; Newmark, Lisa; Gandhi, Tejal K.

    2006-01-01

    In a time-motion study conducted in a hospital that recently implemented barcode medication administration (BCMA) technology, we found that the BCMA system did not increase the amount of time nurses spend on medication administration activities, and did not compromise the amount of time nurses spent on direct care of patients. Our results should allay concerns regarding the impact of BCMA on nursing workflow.

  8. Clinical application of high-throughput genomic technologies for treatment selection in breast cancer

    OpenAIRE

    Hansen, Aaron R.; Bedard, Philippe L.

    2013-01-01

    Large-scale collaborative initiatives using next-generation DNA sequencing and other high-throughput technologies have begun to characterize the genomic landscape of breast cancer. These landmark studies have identified infrequent driver mutations that are potential targets for therapeutic intervention with approved or investigational drug treatments, among other important discoveries. Recently, many institutions have launched molecular screening programs that apply high-throughput genomic te...

  9. Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples

    Science.gov (United States)

    Mougeot, Jean-Luc C.; Stevens, Craig B.; Cotton, Sean L.; Morton, Darla S.; Krishnan, Keerthana; Brennan, Michael T.; Lockhart, Peter B.; Paster, Bruce J.; Bahrani Mougeot, Farah K.

    2016-01-01

    Background Over 700 bacterial species reside in human oral cavity, many of which are associated with local or distant site infections. Extensive characterization of the oral microbiome depends on the technologies used to determine the presence and proportions of specific bacterial species in various oral sites. Objective The objective of this study was to compare the microbial composition of dental plaque at baseline using Human Oral Microbe Identification Microarray (HOMIM) and Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technologies, which are based on 16S rRNA. Methods Dental plaque samples were collected from 96 patients at baseline prior to a dental procedure involving manipulation of gingival tissues. The samples were surveyed for 293 and 597 oral bacterial species via HOMIM and HOMINGS, respectively, based on 16S rRNA gene sequences. We determined the concordance between the two technologies for common species. Genus level analysis was performed using HOMINGS-specific genus identification capabilities. Results HOMINGS detected twice the number of species in the same dental plaque samples compared to HOMIM. For the species detected by both HOMIM and HOMINGS, there was no difference in relative proportions of overall bacterial composition at the species, genus or phylum levels. Additionally, there was no difference in relative proportion for total species per patient between the two technologies. Conclusion HOMINGS significantly expanded oral bacterial species identification compared to HOMIM. The genus and species probes, combined in HOMINGS, provided a more comprehensive representation of oral bacterial community, critical for future characterization of oral microbes in distant site infections. PMID:27065347

  10. Designing a Computer-Assisted Clinic to Cope with the Evolution of Pacemaker Technology

    OpenAIRE

    Pfeil, Catherine N.; Keltz, Paul D.; Gertz, Edward W.; Okawachi, Melanie H.

    1983-01-01

    A computer-assisted program for follow-up monitoring of implanted cardiac pacemakers has been in operation at the San Francisco Veterans Administration Medical Center since 1977. It was originally created at a time when the technology of pacemakers was stable and only a few parameters could be measured or telemetered. Two recent developments have necessitated a major reassessment of this project as a well as redesign of the entire computer infrastructure: the advent of multi-programmable and ...

  11. Clinical Decision Support System to Enhance Quality Control of Spirometry Using Information and Communication Technologies

    OpenAIRE

    Burgos Rincón, Felip; Melia, Umberto Sergio Pio; Vallverdú Ferrer, Montserrat; Velickovski, Filip; Lluch-Ariet, Magí; Caminal Magrans, Pere; Roca-Torrent, Josep

    2014-01-01

    Background: We recently demonstrated that quality of spirometry in primary care could markedly improve with remote offline support from specialized professionals. It is hypothesized that implementation of automatic online assessment of quality of spirometry using information and communication technologies may significantly enhance the potential for extensive deployment of a high quality spirometry program in integrated care settings. Objective: The objective of the study was to elaborate a...

  12. Novel Cadmium Zinc Telluride Devices for Myocardial Perfusion Imaging-Technological Aspects and Clinical Applications.

    Science.gov (United States)

    Ben-Haim, Simona; Kennedy, John; Keidar, Zohar

    2016-07-01

    Myocardial perfusion imaging plays an important role in the assessment of patients with known or suspected coronary artery disease and is well established for diagnosis and for prognostic evaluation in these patients. The dedicated cardiac SPECT cameras with solid-state cadmium zinc telluride (CZT) detectors were first introduced a decade ago. A large body of evidence is building up, showing the superiority of the new technology compared with conventional gamma cameras. Not only the CZT detectors, but also new collimator geometries, the ability to perform focused imaging optimized for the heart and advances in data processing algorithms all contribute to the significantly improved sensitivity up to 8-10 times, as well as improved energy resolution and improved reconstructed spatial resolution compared with conventional technology. In this article, we provide an overview of the physical characteristics of the CZT cameras, as well as a review of the literature published so far, including validation studies in comparison with conventional myocardial perfusion imaging and with invasive coronary angiography, significant reduction in radiation dose, and new imaging protocols enabled by the new technology. PMID:27237438

  13. Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: mapping of neurotransmitter receptors and ion channels

    DEFF Research Database (Denmark)

    Olsen, Jesper V; Nielsen, Peter Aa; Andersen, Jens R;

    2007-01-01

    Analysis of the brain proteome and studying brain diseases through clinical biopsies and animal disease models require methods of quantitative proteomics that are sensitive and allow identification and quantification of low abundant membrane proteins from minute amount of tissue. Taking advantage...

  14. Proteomic profiling of exosomes: Current perspectives

    DEFF Research Database (Denmark)

    Simpson, Richard J; Jensen, Søren S; Lim, Justin W E

    2008-01-01

    Exosomes are 40-100 nm membrane vesicles of endocytic origin secreted by most cell types in vitro. Recent studies have shown that exosomes are also found in vivo in body fluids such as blood, urine, amniotic fluid, malignant ascites, bronchoalveolar lavage fluid, synovial fluid, and breast milk....... While the biological function of exosomes is still unclear, they can mediate communication between cells, facilitating processes such as antigen presentation and in trans signaling to neighboring cells. Exosome-like vesicles identified in Drosophila (referred to as argosomes) may be potential vehicles...... for the spread of morphogens in epithelia. The advent of current MS-based proteomic technologies has contributed significantly to our understanding of the molecular composition of exosomes. In addition to a common set of membrane and cytosolic proteins, it is becoming increasingly apparent that exosomes harbor...

  15. Tissue proteomics of the human mammary gland

    DEFF Research Database (Denmark)

    Moreira, José Manuel Alfonso; Cabezón, Teresa; Gromova, Irina;

    2010-01-01

    phenotypes of the different cell subpopulations present in normal human mammary tissue, partly due to the formidable heterogeneity of mammary tissue, but also due to limitations of the current proteomic technologies. Work in our laboratories has attempted to address in a systematic fashion some of these...... biomarker discovery program. We review and present new data on the putative cell-progenitor marker cytokeratin 15 (CK15), and describe a novel marker, dihydropyriminidase-related protein 3 (DRP3) that in combination with CK15 and other well known proteins were used to define molecular phenotypes of normal...... human breast epithelial cells and their progenitors in resting acini, lactating alveoli, and large collecting ducts of the nipple. Preliminary results are also presented concerning DRP3 positive usual ductal hyperplasias (UDHs) and on single cell layer columnar cells (CCCs). At least two bona fide...

  16. The prevalence of medical/clinical technology over psychosocial care actions in outpatient mental health services

    OpenAIRE

    Regina Celia Fiorati; Toyoko Saeki

    2013-01-01

    The scope of this study was to evaluate how aspects of mental health policy in Brazil have been conceived and implemented in outpatient services, such as the Regional Outpatient Mental Health Clinic and the Psychosocial Care Center II, both in Ribeirão Preto, São Paulo. Semi-direct interviews and focus groups were conducted with 22 health professionals. The theoretical method and data analysis were supported by the dialectical hermeneutic framework of Jürgen Habermas. The following aspects we...

  17. Proteomics of foodborne bacterial pathogens

    Science.gov (United States)

    This chapter focuses on recent research on foodborne bacterial pathogens that use mass spectrometry-based proteomic techniques as well as protein microarrays. Mass spectrometry ionization techniques (e.g. electrospray ionization and matrix-assisted laser desorption/ionization), analyzers (e.g. ion ...

  18. The potato tuber mitochondrial proteome

    DEFF Research Database (Denmark)

    Møller, Ian Max; Salvato, Fernanda; Havelund, Jesper;

    ) and in silico-predicted mitochondrial proteins (2000-3000). Thus, before starting to look for oxidized peptides, we wanted to expand the current compendium of plant mitochondrial proteins while obtaining what could be termed the "baseline proteome" from our model organelle, the potato tuber...

  19. Quantitative proteomics of Chlorobaculum tepidum

    DEFF Research Database (Denmark)

    Falkenby, Lasse Gaarde; Szymanska, Monika; Holkenbrink, Carina;

    2011-01-01

    Chlorobaculum (Cba.) tepidum is a green sulfur bacterium that oxidizes sulfide, elemental sulfur, and thiosulfate for photosynthetic growth. To gain insight into the sulfur metabolism, the proteome of Cba. tepidum cells sampled under different growth conditions has been quantified using a rapid gel...

  20. Proteomic interrogation of human chromatin.

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    Mariana P Torrente

    Full Text Available Chromatin proteins provide a scaffold for DNA packaging and a basis for epigenetic regulation and genomic maintenance. Despite understanding its functional roles, mapping the chromatin proteome (i.e. the "Chromatome" is still a continuing process. Here, we assess the biological specificity and proteomic extent of three distinct chromatin preparations by identifying proteins in selected chromatin-enriched fractions using mass spectrometry-based proteomics. These experiments allowed us to produce a chromatin catalog, including several proteins ranging from highly abundant histone proteins to less abundant members of different chromatin machinery complexes. Using a Normalized Spectral Abundance Factor approach, we quantified relative abundances of the proteins across the chromatin enriched fractions giving a glimpse into their chromosomal abundance. The large-scale data sets also allowed for the discovery of a variety of novel post-translational modifications on the identified chromatin proteins. With these comparisons, we find one of the probed methods to be qualitatively superior in specificity for chromatin proteins, but inferior in proteomic extent, evidencing a compromise that must be made between biological specificity and broadness of characterization. Additionally, we attempt to identify proteins in eu- and heterochromatin, verifying the enrichments by characterizing the post-translational modifications detected on histone proteins from these chromatin regions. In summary, our results provide insights into the value of different methods to extract chromatin-associated proteins and provide starting points to study the factors that may be involved in directing gene expression and other chromatin-related processes.