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- Apweiler, Rolf, et al.
(författare)
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Approaching clinical proteomics : current state and future fields of application in cellular proteomics
- 2009
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Ingår i: Cytometry. Part A : the journal of the International Society for Analytical Cytology. - : Wiley. - 1552-4922. ; 75A:10, s. 816-832
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Forskningsöversikt (refereegranskat)abstract
- Recent developments in proteomics technology offer new opportunities for clinical applications in hospital or specialized laboratories including the identification of novel biomarkers, monitoring of disease, detecting adverse effects of drugs, and environmental hazards. Advanced spectrometry technologies and the development of new protein array formats have brought these analyses to a standard, which now has the potential to be used in clinical diagnostics. Besides standardization of methodologies and distribution of proteomic data into public databases, the nature of the human body fluid proteome with its high dynamic range in protein concentrations, its quantitation problems, and its extreme complexity present enormous challenges. Molecular cell biology (cytomics) with its link to proteomics is a new fast moving scientific field, which addresses functional cell analysis and bioinformatic approaches to search for novel cellular proteomic biomarkers or their release products into body fluids that provide better insight into the enormous biocomplexity of disease processes and are suitable for patient stratification, therapeutic monitoring, and prediction of prognosis. Experience from studies of in vitro diagnostics and especially in clinical chemistry showed that the majority of errors occurs in the preanalytical phase and the setup of the diagnostic strategy. This is also true for clinical proteomics where similar preanalytical variables such as inter- and intra-assay variability due to biological variations or proteolytical activities in the sample will most likely also influence the results of proteomics studies. However, before complex proteomic analysis can be introduced at a broader level into the clinic, standardization of the preanalytical phase including patient preparation, sample collection, sample preparation, sample storage, measurement, and data analysis is another issue which has to be improved. In this report, we discuss the recent advances and applications that fulfill the criteria for clinical proteomics with the focus on cellular proteomics (cytoproteomics) as related to preanalytical and analytical standardization and to quality control measures required for effective implementation of these technologies and analytes into routine laboratory testing to generate novel actionable health information. It will then be crucial to design and carry out clinical studies that can eventually identify novel clinical diagnostic strategies based on these techniques and validate their impact on clinical decision making.
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| 2. |
- Apweiler, Rolf, et al.
(författare)
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Approaching clinical proteomics : current state and future fields of application in fluid proteomics
- 2009
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Ingår i: Clinical Chemistry and Laboratory Medicine. - 1434-6621 .- 1437-4331. ; 47:6, s. 724-744
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Forskningsöversikt (refereegranskat)abstract
- 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 protein concentrations presents problems with quantitation. The extreme complexity of the proteome in body fluids presents enormous challenges and requires the establishment of standard operating procedures for handling of specimens, increasing sensitivity for detection and bioinformatical tools for distribution of proteomic data into the public domain. From studies of in vitro diagnostics, especially in clinical chemistry, it is evident that most errors occur in the preanalytical phase and during implementation of the diagnostic strategy. This is also true for clinical proteomics, and especially for fluid proteomics because of the multiple pretreatment processes. These processes include depletion of high-abundance proteins from plasma or enrichment processes for urine where biological variation or differences in proteolytic activities in the sample along with preanalytical variables such as inter- and intra-assay variability will likely influence the results of proteomics studies. However, before proteomic analysis can be introduced at a broader level into the clinical setting, standardization of the preanalytical phase including patient preparation, sample collection, sample preparation, sample storage, measurement and data analysis needs to be improved. In this review, we discuss the recent technological advances and applications that fulfil the criteria for clinical proteomics, with the focus on fluid proteomics. These advances relate to preanalytical factors, analytical standardization and quality-control measures required for effective implementation into routine laboratory testing in order to generate clinically useful information. With new disease biomarker candidates, it will be crucial to design and perform clinical studies that can identify novel diagnostic strategies based on these techniques, and to validate their impact on clinical decision-making.
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| 6. |
- Demuth, Andreas, et al.
(författare)
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Pathogenomics: An updated European Research Agenda
- 2008
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Ingår i: Infection, Genetics and Evolution. - : Elsevier BV. - 1567-7257 .- 1567-1348. ; 8:3, s. 386-393
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Tidskriftsartikel (refereegranskat)abstract
- The emerging genomic technologies and bioinformatics provide novel opportunities for studying life-threatening human pathogens and to develop new applications for the improvement of human and animal health and the prevention, treatment, and diagnosis of infections. Based on the ecology and population biology of pathogens and related organisms and their connection to epidemiology, more accurate typing technologies and approaches will lead to better means of disease control. The analysis of the genome plasticity and gene pools of pathogenic bacteria including antigenic diversity and antigenic variation results in more effective vaccines and vaccine implementation programs. The study of newly identified and uncultivated microorganisms enables the identification of new threats. The scrutiny of the metabolism of the pathogen in the host allows the identification of new targets for anti-infectives and therapeutic approaches. The development of modulators of host responses and mediators of host damage will be facilitated by the research on interactions of microbes and hosts, including mechanisms of host damage, acute and chronic relationships as well as commensalisms. The study of multiple pathogenic and non-pathogenic microbes interacting in the host will improve the management of multiple infections and will allow probiotic and prebiotic interventions. Needless to iterate, the application of the results of improved prevention and treatment of infections into clinical tests will have a positive impact on the management of human and animal disease. The Pathogenomics Research Agenda draws on discussions with experts of the Network of Excellence "EuroPathoGenomics" at the management board meeting of the project held during 18-21 April 2007, in the Villa Vigoni, Menaggio, Italy. Based on a proposed European Research Agenda in the field of pathogenomics by the ERA-NET PathoGenoMics the meeting's participants updated the established list of topics as the research agenda for the future.
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| 7. |
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Human-Centered Visualization Environments : GI-Dagstuhl Research Seminar, Dagstuhl Castle, Germany, March 5-8, 2006, Revised Lectures
- 2007
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Samlingsverk (redaktörskap) (refereegranskat)abstract
- This tutorial book presents an augmented selection of the material presented at the GI-Dagstuhl Research Seminar on Human-Centered Visualization Environments, HCVE 2006, held in Dagstuhl Castle, Germany in March 2006. The 8 tutorial lectures presented are the thoroughly cross-reviewed and revised versions of the summaries and findings, presented and discussed at the seminar. After an introduction to human-centered visualization environments the fundamental principles and methods in that area are shown such as human-centered aspects, interacting with visualizations, visual representations, as well as challenges and unsolved problems. The book is concluded with lectures on domain-specific visualization describing geographic visualization, algorithm animation, and biomedical information visualization.
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| 8. |
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| 9. |
- Kjellman, Arne, et al.
(författare)
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Open Peer Commentaries
- 2008
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Ingår i: Constructivist Foundations. - : ALEXANDER RIEGLER. - 1782-348X. ; 3:2, s. 65-108
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Open peer commentary on the target article "Who Conceives of Society?" by Ernst von Glasersfeld. First paragraph: Ernst von Glasersfeld sets out to explain how familiar patterns (signs) arise in private experience - and how they are extracted or " recognized" as such. These patterns are recursive, which imposes significance (familiarity) on them, and are, in the course of time, collected into a " bulk of experience." I think a convinced constructivist can - if hesitantly - accept his rendering, even though it is one that lacks the stringency one expects from a supposedly natural scientist ( 46). However, the crucial point is that this paper does not address the convinced constructivist but rather the opposite camps, and I doubt he succeeds in convincing them.
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| 10. |
- Larsson, Andreas, et al.
(författare)
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Orientation of individual C60 molecules adsorbed on Cu(111) : Low-temperature scanning tunneling microscopy and density functional calculations
- 2008
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 77:11
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Tidskriftsartikel (refereegranskat)abstract
- Density functional theory (DFT) and low-temperature scanning tunneling microscopy (STM) have been combined to examine the bonding of individual C60 molecules on Cu(111). Energy-resolved differential-conductance maps have been measured for individual C60 molecules adsorbed on a Cu(111) surface by means of low-temperature STM, which are compared to and complemented by theoretically computed spectral images. It has been found that C60 chemisorbs with a six-membered ring parallel to the surface at two different Cu(111) binding sites that constitute two exclusive hexagonal sublattices. On each sublattice, C60 is bonded in one particular rotational conformer, i.e., C60 molecules bind to the Cu(111) surface in two different azimuthal orientations differing by 60°depending on which sublattice the binding site belongs to. The binding conformation of C60 and its orientation with regard to the copper surface can be deduced by this joint experimental-theoretical approach. Six possible pairs of C60 configurations on three different Cu surface binding sites have been identified that fulfil the requirements of the two sublattices and are consistent with all experimental and theoretical data. Theory proposes that two of these configuration pairs are most likely. We have found that DFT does not get the binding energy between rotational conformers in the correct order. We also report two different C60 monolayers on Cu(111): one with alternating orientations of neighboring molecules at low temperature and the other with (4×4) structure after annealing above room temperature.
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| 11. |
- Walz, Anke, et al.
(författare)
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Identification of glycoprotein receptors within the human salivary proteome for the lectin-like BabA and SabA adhesins of Helicobacter pylori by fluorescence-based 2-D bacterial overlay
- 2009
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 9:6, s. 1582-1592
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Tidskriftsartikel (refereegranskat)abstract
- Because gastric infection by Helicobacter pylori takes place via the oral route, possible interactions of this bacterium with human salivary proteins could occur. By using modified 1- and 2-D bacterial overlay, binding of H. pylori adhesins BabA and SabA to the whole range of salivary proteins was explored. Bound salivary receptor molecules were identified by MALDI-MS and by comparison to previously established proteome maps of whole and glandular salivas. By use of adhesin-deficient mutants, binding of H. pylori to MUC7 and gp-340 could be linked to the SabA and BabA adhesins, respectively, whereas binding to MUC5B was associated with both adhesins. Binding of H. pylori to the proline-rich glycoprotein was newly detected and assigned to BabA adhesin whereas the SabA adhesin was found to mediate binding to newly detected receptor molecules, including carbonic anhydrase VI, secretory component, heavy chain of secretory IgA1, parotid secretory protein and zinc-alpha(2)-glycoprotein. Some of these salivary glycoproteins are known to act as scavenger molecules or are involved in innate immunity whereas others might come to modify the pathogenetic properties of this organism. In general, this 2-D bacterial overlay technique represents a useful supplement in adhesion studies of bacteria with complex protein mixtures.
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