Relevant bibliographies by topics / Proteins Analysis

Academic literature on the topic 'Proteins Analysis'

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Published: 4 June 2021
Last updated: 31 July 2024

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Journal articles on the topic "Proteins Analysis"

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Meraj, Syeda Shaizadi, and Tanusree Chaudhuri. "Structurally Significant Analysis of Tuberculosis Proteins." International Journal of Scientific Research 3, no. 6 (June 1, 2012): 39–41. http://dx.doi.org/10.15373/22778179/june2014/16.

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Scopes, R. K., and John A. Smith. "Analysis of Proteins." Current Protocols in Molecular Biology 76, no. 1 (October 2006): 10.0.1–10.0.22. http://dx.doi.org/10.1002/0471142727.mb1000s76.

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Gupal, Anatoliy M., Ivan I. Andreychuk, Alexandra A. Vagis, and Ludmila A. Zakrevskaya. "Statistical Analysis of Proteins." Journal of Automation and Information Sciences 36, no. 12 (2004): 25–29. http://dx.doi.org/10.1615/jautomatinfscien.v36.i12.20.

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Trimpin, Sarah, and Bill Brizzard. "Analysis of insoluble proteins." BioTechniques 46, no. 5 (April 2009): 321–26. http://dx.doi.org/10.2144/000113135.

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Trimpin, Sarah, and Bill Brizzard. "Analysis of insoluble proteins." BioTechniques 46, no. 6 (May 2009): 409–19. http://dx.doi.org/10.2144/000113168.

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MADDY, A. H. "Analysis of Membrane Proteins." Biochemical Society Transactions 15, no. 3 (June 1, 1987): 571. http://dx.doi.org/10.1042/bst0150571.

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Chatterjee, Devjani, and Jacob V. Maizel. "Sequence analysis of proteins." Gene Analysis Techniques 4, no. 2 (March 1987): 27–40. http://dx.doi.org/10.1016/0735-0651(87)90015-x.

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Kelly, Robert H. "Electrophoretic analysis of proteins." Clinical Immunology Newsletter 13, no. 8 (August 1993): 93. http://dx.doi.org/10.1016/0197-1859(93)90015-c.

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Tanaka, I. "Structure analysis of ribosomal proteins." Seibutsu Butsuri 40, supplement (2000): S104. http://dx.doi.org/10.2142/biophys.40.s104_3.

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Swanson, Jessica MJ. "Multiscale kinetic analysis of proteins." Current Opinion in Structural Biology 72 (February 2022): 169–75. http://dx.doi.org/10.1016/j.sbi.2021.11.005.

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Dissertations / Theses on the topic "Proteins Analysis"

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Nguyen, Giang Huong. "A functional analysis of the human LPA₁G protein coupled receptor." Thesis, Available online, Georgia Institute of Technology, 2004:, 2004. http://etd.gatech.edu/theses/available/etd-06072004-131304/unrestricted/nguyen%5Fgiang%5Fh%5F200405%5Fms.pdf.

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Collins, Malcolm Robert. "Characterisation of the human α2(I) procollagen promoter-binding proteins." Doctoral thesis, University of Cape Town, 1993. http://hdl.handle.net/11427/27139.

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In an attempt to elucidate the transcriptional mechanisms that regulate the expression of the human α2(I) procollagen gene, cis-acting DNA-elements within the proximal promoter were identified and their corresponding trans-acting factors characterised. The fibroblast cell lines used in this study had previously been transformed with either simian virus 40 (SVWI-38) or by γ-radiation (CT-1). The SVWI-38 fibroblasts do not produce any α2(I) collagen chains, whereas the CT-1 cell line produces normal type I collagen. Previous studies suggested that trans-acting factor(s) may be responsible for the inactivation of the α2(I) procollagen gene in SVWI-38 fibroblasts (Parker et. al. (1989) J. Biol. Chem 264, 7147-7152; Parker et. al. (1992) Nucleic Acids Res. 20, 5825-5830). In this study, the SVWI-38 proximal promoter (-350 to +54) was sequenced and shown to be normal, thereby ruling out any possibility that mutations within this region was responsible for inactivation of the gene.
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Hennessy, Fritha. "Characterisation of the J domain aminoacid residues important for the interaction of DNAJ-like proteins with HSP70 chaperones." Thesis, Rhodes University, 2004. http://hdl.handle.net/10962/d1003996.

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The 70 kDa heat shock proteins (Hsp70s) are vital for normal protein folding, as they stabilise the unfolded state of nascent polypeptides, allowing these sufficient time to attain a correct tertiary structure. Hsp70s are aided by the DnaJ-like family of proteins, which interact with Hsp70s in order to enhance the chaperone activity of these proteins. DnaJ-like proteins contain a J domain, a seventy amino acid domain consisting of four α-helices, which is defined by the presence of an invariant tripeptide of histidine, proline and aspartic acid (HPD motif). This motif is key to the interaction between DnaJ-like proteins and Hsp70s. This thesis has focused on determining the presence of other conserved residues in the J domain and their role in mediating the interaction of DnaJ-like proteins with partner Hsp70s. DnaJ-like proteins from Agrobacterium tumefaciens RUOR were isolated and used as a model system. A. tumefaciens DnaJ (Agt DnaJ) was able to replace the lack of E. coli DnaJ in an E. coli null mutant strain, however, additional A. tumefaciens DnaJ-like proteins Agt DjC1/DjlA, Agt DjC2 and Agt DjC5 were unable to complement for the lack of E. coli DnaJ. Replacement of the Agt DnaJ J domain with J domains from these proteins resulted in non-functional chimeric proteins, despite some sequence conservation. The kinetics of the basal specific ATPase activity of Agt DnaK, and its ability to have this activity stimulated by Agt DnaJ and Agt DnaJ-H33Q were also investigated. Stimulation of the ATPase activity by Agt DnaJ ranged between 1.5 to 2 fold, but Agt DnaJ-H33Q was unable to stimulate the basal ATPase activity. Conserved amino acids in the J domain were identified in silico, and these residues were substituted in the J domain of Agt DnaJ. The ability of these derivative proteins to replace E. coli DnaJ was investigated. Alterations in the HPD motif gave rise to proteins unable to complement for lack of E. coli DnaJ, consistent with literature. Agt DnaJ-R26A was unable to replace E. coli DnaJ suggesting that Arg26 could be key to the interaction with partner Hsp70s. Agt DnaJ-D59A was unable to replace E. coli DnaJ; substitutions in Asp59 have not previously been shown to impact on the function of DnaJ. Substituting Arg63 in Agt DnaJ abrogated the levels of complementation. Substitution of several structural residues was also found to disrupt the in vivo function of Agt DnaJ suggesting that the maintenance of the structural integrity of the J domain was important for function. This study has identified a number of residues critical to the structure and function of the J domain of Agt DnaJ, and potentially of general importance as molecular determinants for DnaJ-Hsp70 interaction.
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Nilsson, Johan. "Membrane protein topology : prediction, experimental mapping and genome-wide analysis /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-963-3/.

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Tavner, Fiona Jane. "A molecular analysis of two related c-Myb-binding proteins : p160 and p67 /." Title page, table of contents and summary only, 1998. http://web4.library.adelaide.edu.au/theses/09PH/09pht234.pdf.

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Mi, Jia. "Proteomic Analysis of Peroxisomal Proteins." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7943.

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Pereira, Morais Marta. "Biophysical analysis of glycated proteins." Thesis, University of Bath, 2011. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.547628.

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Leuchowius, Karl-Johan. "High Content Analysis of Proteins and Protein Interactions by Proximity Ligation." Doctoral thesis, Uppsala universitet, Molekylära verktyg, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-119530.

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Fundamental to all biological processes is the interplay between biomolecules such as proteins and nucleic acids. Studies of interactions should therefore be more informative than mere detection of expressed proteins. Preferably, such studies should be performed in material that is as biologically and clinically relevant as possible, i.e. in primary cells and tissues. In addition, to be able to take into account the heterogeneity of such samples, the analyses should be performed in situ to retain information on the sub-cellular localization where the interactions occur, enabling determination of the activity status of individual cells and allowing discrimination between e.g. tumor cells and surrounding stroma. This requires assays with an utmost level of sensitivity and selectivity. Taking these issues into consideration, the in situ proximity-ligation assay (in situ PLA) was developed, providing localized detection of proteins, protein-protein interactions and post-translational modifications in fixed cells and tissues. The high sensitivity and selectivity afforded by the assay's requirement for dual target recognition in combination with powerful signal amplification enables visualization of single protein molecules in intact single cells and tissue sections. To further increase the usefulness and application of in situ PLA, the assay was adapted to high content analysis techniques such as flow cytometry and high content screening. The use of in situ PLA in flow cytometry offers the possibility for high-throughput analysis of cells in solution with the unique characteristics offered by the assay. For high content screening, it was demonstrated that in situ PLA can enable cell-based drug screening of compounds affecting post-translational modifications and protein-protein interactions in primary cells, offering superior abilities over current assays. The methods presented in this thesis provide powerful new tools to study proteins in genetically unmodified cells and tissues, and should offer exciting new possibilities for molecular biology, diagnostics and drug discovery. 
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Chivian, Dylan Casey. "Application of information from homologous proteins for the prediction of protein structure /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9264.

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Xu, Qifang. "Statistical Analysis of Biological Interactions from Homologous Proteins." Diss., Temple University Libraries, 2008. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/25686.

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Computer and Information Science
Ph.D.
Information fusion aims to develop intelligent approaches of integrating information from complementary sources, such that a more comprehensive basis is obtained for data analysis and knowledge discovery. Our Protein Biological Unit (ProtBuD) database is the first database that integrated the biological unit information from the Protein Data Bank (PDB), Protein Quaternary Server (PQS) and Protein Interfaces, Surfaces and Assemblies (PISA) server, and compared the three biological units side-by-side. The statistical analyses show that the inconsistency within these databases and between them is significant. In order to improve the inconsistency, we studied interfaces across different PDB entries in a protein family using an assumption that interfaces shared by different crystal forms are likely to be biologically relevant. A novel computational method is proposed to achieve this goal. First, redundant data were removed by clustering similar crystal structures, and a representative entry was used for each cluster. Then a modified k-d tree algorithm was applied to facilitate the computation of identifying interfaces from crystals. The interface similarity functions were derived from Gaussian distributions fit to the data. Hierarchical clustering was used to cluster interfaces to define the likely biological interfaces by the number of crystal forms in a cluster. Benchmark data sets were used to determine whether the existence or lack of existence of interfaces across multiple crystal forms can be used to predict whether a protein is an oligomer or not. The probability that a common interface is biological is given. An interface shared in two different crystal forms by divergent proteins is very likely to be biologically important. The interface data not only provide new interaction templates for computational modeling, but also provide more accurate data for training sets and testing sets in data-mining research to predict protein-protein interactions. In summary, we developed a framework which is based on databases where different biological unit information is integrated and new interface data are stored. In order for users from the biology community to use the data, a stand-alone software program, a web site with a user-friendly graphical interface, and a web service are provided.
Temple University--Theses
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Books on the topic "Proteins Analysis"

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Hogue, Angeletti Ruth, ed. Proteins: Analysis and design. San Diego: Academic Press, 1998.

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Ron, Elber, ed. Recent developments in theoretical studies of proteins. Singapore: World Scientific, 1996.

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Kyte, Jack. Structure in protein chemistry. New York: Garland Pub., 2006.

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Kyte, Jack. Structure in protein chemistry. New York: Garland Pub., 1995.

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Ronald, Wetzel, ed. Protein misassembly. San Diego: Academic Press, 1997.

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M, Holtzhauer, and Behlke J, eds. Methoden in der Proteinanalytik. Berlin: Springer, 1996.

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M, Hatano, ed. Protein structural analysis, folding, and design. Tokyo: Japan Scientific Societies Press, 1990.

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1927-, Jollès Pierre, and Jörnvall Hans, eds. Proteomics in functional genomics: Protein structure analysis. Basel: Birkhäuser Verlag, 2000.

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Permi͡akov, E. A. Luminescent spectroscopy of proteins. Boca Raton: CRC Press, 1993.

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T, Fung Eric, ed. Protein arrays: Methods and protocols. Totowa, N.J: Humana Press, 2004.

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Book chapters on the topic "Proteins Analysis"

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Hunkapiller, Michael W. "PTH Amino Acid Analysis." In Proteins, 363–81. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4613-1787-6_37.

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Aurand, Leonard W., A. Edwin Woods, and Marion R. Wells. "Proteins." In Food Composition and Analysis, 232–82. Dordrecht: Springer Netherlands, 1987. http://dx.doi.org/10.1007/978-94-015-7398-6_6.

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Cohen, Steven A., Thomas L. Tarvin, and Brian A. Bidlingmeyer. "Amino Acid Analysis Using Pre-Column Derivatization with Phenylisothiocyanate: Matrix Effects and Tryptophan Analysis." In Proteins, 207–13. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4613-1787-6_22.

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Froelich, Norman, Lynn C. Williams, John T. Casagrande, and Minnie McMillan. "Computer Analysis of Protein Sequencing Data." In Proteins, 455–60. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4613-1787-6_45.

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Clore, G. Marius, and Angela M. Gronenborn. "Analysis of backbone dynamics of interleukin-1β." In Proteins, 53–56. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-010-9063-6_6.

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Marshak, Daniel R. "Structural Analysis of Proteins of the Nervous System." In Proteins, 283–98. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4613-1787-6_29.

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Petrides, Petro E., Peter Bohlen, and Frederick S. Esch. "Microisolation and Sequence Analysis of Human Epidermal Growth Factor." In Proteins, 29–36. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4613-1787-6_3.

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Rosenberg, Ian M. "Membrane Proteins." In Protein Analysis and Purification, 153–76. Boston, MA: Birkhäuser Boston, 1996. http://dx.doi.org/10.1007/978-1-4612-2056-5_6.

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Prendergast, F. G., Z. Bajzer, P. H. Axelsen, and C. Haydock. "Analysis and interpretation of tryptophan fluorescence intensity decays in proteins." In Proteins, 208–19. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-010-9063-6_30.

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Fraser, Blair A. "Fast Atom Bombardment Mass Spectrometry: Application to Peptide Structural Analysis." In Proteins, 241–49. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4613-1787-6_26.

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Conference papers on the topic "Proteins Analysis"

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Shahbazi, Zahra, Horea T. Ilies¸, and Kazem Kazerounian. "Protein Molecules as Natural Nano Bio Devices: Mobility Analysis." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13021.

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Proteins are nature’s nano-robots in the form of functional molecular components of living cells. The function of these natural nano-robots often requires conformational transitions between two or more native conformations that are made possible by the intrinsic mobility of the proteins. Understanding these transitions is essential to the understanding of how proteins function, as well as to the ability to design and manipulate protein-based nano-mechanical systems [1]. Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process.
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Schoenrock, Andrew, Daniel Burnside, Houman Moteshareie, Alex Wong, Ashkan Golshani, Frank Dehne, and James R. Green. "Engineering inhibitory proteins with InSiPS: the in-silico protein synthesizer." In SC15: The International Conference for High Performance Computing, Networking, Storage and Analysis. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2807591.2807630.

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Nepal, Chirag, and Kyungsook Han. "Analysis of HCV Envelope Proteins Interacting with Human Proteins." In 2007 Frontiers in the Convergence of Bioscience and Information Technologies. IEEE, 2007. http://dx.doi.org/10.1109/fbit.2007.47.

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Samarawickrama, O., R. Jayatillake, and D. Amaratunga. "Identifying Proteins Associated with Disease Severity." In SLIIT INTERNATIONAL CONFERENCE ON ADVANCEMENTS IN SCIENCES AND HUMANITIES [SICASH]. Faculty of Humanities and Sciences, SLIIT, 2022. http://dx.doi.org/10.54389/eegc3170.

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Proteomic studies or studies of protein expression levels are growing swiftly with the steady improvement in technology and knowledge on understanding various anomalies affecting humans. Since differentially expressed proteins have an influence on overall cell functionality, this improves discrimination between healthy and diseased states. Identifying prime proteins offers prospective insights for developing optimized and targeted treatment methods. This research involves analyzing data from an early-stage study whose main purpose was to identify differentially expressed proteins. The presence of 3 progressively serious states of disease (healthy to mild to severe) escalates the importance of this study because there is not much research literature that considers ordinal outcomes in studies of this nature. The analysis can be segregated into 2 stages, univariate and multiprotein analysis. Approach of the univariate analysis was to implement continuation ratio model considering one protein at a time to pick those that exhibits potential ordinality. Penalized continuation ratio model using lasso regularization incorporated with bootstrapping proteins was performed as the next stage to identify protein combinationsthat perform well together. Compound results of the univariate and multi-protein analysis identified 20 most dominant proteins that have the capability to discriminate between the disease states in an ordinal manner satisfactorily. Keywords: Proteomic studies; Ordinal nature; Trend tests; Lasso regularization; Bootstrapping
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Tomita, Noriko, Kazuyo Abe, and Makoto Ohta. "Quantitative Analysis of Subunit Mismatch Arrangement in Staphylococcal Gamma-Hemolysin Heteroheptameric Transmembrane Pore." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-63645.

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Pore-forming cytolytic proteins distributed in a wide variety of eukaryotic and prokaryotic organisms have been intensively studied in terms of pathophysiological functions and molecular architecture of transmembrane pores. These proteins are also being developed for various analytical applications such as detector of proteins and DNA by engineering the structure of the pore. Staphylococcal gamma-hemolysin (Hlg), a pore-forming protein, which consists of two separate proteins, LukF and Hlg2, has potential to be a useful tool as a multifunctional biosensor. However, the fine structure of the Hlg pore has not been clarified. Our previous studies revealed that LukF and Hlg2 assemble alternately on the membrane in a molar ratio of 3:4 and 4:3 and form cylindrical heteroheptameric transmembrane pores. In the present study, we conducted quantitative analysis of the subunit arrangement of the pore by using two-dimensional (2-D) image analysis based on high-resolution transmission electron microscopy (TEM) images. Results of this study suggest a new aspect of the characteristic structure in two-component pore-forming protein and can contribute to the engineering of the Hlg pore.
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Shchyogolev, S. Yu, G. L. Burygin, and M. G. Pyatibratov. "Prokaryotic cell surface biopolymers: bioinformatic analysis." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.221.

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Using the example of a number of representatives of bacteria and archaea, the structure of their cell surface biopolymers is considered, taking into account post-translational modifications of proteins and contemporary views on the features of protein folding.
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"PROTEINS POCKETS ANALYSIS AND DESCRIPTION." In International Conference on Bioinformatics. SciTePress - Science and and Technology Publications, 2010. http://dx.doi.org/10.5220/0002725302110216.

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Kazerounian, Kazem, Khalid Latif, Kimberly Rodriguez, and Carlos Alvarado. "ProtoFold: Part I — Nanokinematics for Analysis of Protein Molecules." In ASME 2004 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/detc2004-57243.

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Proteins are evolution’s mechanisms of choice. Study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. ProtoFold is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In this paper, we present the methods utilized in the kinematics notion and kinematics analysis of protein molecules. The kinematics portion of ProtoFold incorporates the Zero-Position Analysis Method and draws upon other recent advances in robot manipulation theories. We claim that the methodology presented is a computationally superior and more stable alternative to traditional molecular dynamics simulation techniques.
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Dovichi, Norman J., Shade Wu, and Da Yung Chen. "High Sensitivity Fluorescence Detection of Biological Molecules." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1990. http://dx.doi.org/10.1364/laca.1990.tha1.

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Fluorescein is a good fluorescent label for high sensitivity analysis. The molecule has high molar absorptivity, 5 × 104 L mol-1 cm-1 at 488 nm and near unit fluorescence quantum yield in the pH range of 8 to 10. Unfortunately, the molecule is not photostable undergoing irreversible photobleaching after absorbance of about 8,000 photons. Fluorescein may be used to label amino groups in amino acids, peptides, and proteins through the isothiocyanate derivative. Under basic conditions, the thiocarbamoyl derivative is formed, with relatively good stability. The reaction between amino acids and fluorescein isothiocyanate is first order in bod the concentration of amino acid and derivative, with an activation energy of about 16 kcal/mol. Under acidic conditions, the cyclic thiohydantoin derivative is formed, cleaving the terminal amino acid from proteins and peptides. This thiohydantoin derivative possesses greater photostability than the thiocarbamoyl derivative, decomposing after absorbance of about 12,000 photons. The thiocarbamoyl-thiohydantoin derivative series is the basis of an Edmon degradation scheme for protein sequencing. In addition to amino acid labeling, fluorescein may be used to label thiols through the bromobimane derivatives; a high sensitivity DNA analysis is based on this compound. Last, succinylfluorescein labeled chain terminating dideoxynucleotides are used in DNA sequencing, these molecules have similar spectral properties as fluorescein.
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Sodnomov, T. C., and I. A. Kutyrev. "STUDY ON POTENTIAL IMMUNOREGULATORY PROTEINS IN THE EXCRETORY-SECRETORY PRODUCTS OF CESTODES." In THEORY AND PRACTICE OF PARASITIC DISEASE CONTROL. VNIIP – FSC VIEV, 2024. http://dx.doi.org/10.31016/978-5-6050437-8-2.2024.25.388-393.

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This article studied excretory-secretory products of parasitic flatworms aimed at searching for potential immunoregulatory proteins. Immunoregulatory proteins are poorly studied at the moment. Recent years have showed increased interest in identifying immunoregulatory molecules produced by parasitic worms. Potential immunoregulatory proteins will make a significant contribution to the development of medicine and biotechnology and will make it possible to effectively treat allergic and other autoimmune diseases. The study used methods of bioinformatics, proteomics, and transcriptomics. Potential immunoregulatory proteins were identified in the Ligula interrupta secretome proteins and listed. Each protein was analyzed for possible immunoregulatory functions in the parasite-host system. Based on identification data of SEP proteins using parasite transcriptomes, annotation of secretome proteins (SEP) was made in the NCBI and Swissprot international databases. A table was compiled with identified potential immunoregulatory proteins. A functional analysis of each protein was performed. Protein functions were determined based on analysis of scientific articles, patents and publications. By comparing different proteins, it is possible to identify those that are similar in domain structure, phylogeny, and description. The discovered potential immunoregulatory proteins will make a significant contribution to the development of medicine and biotechnology and will make it possible to effectively treat allergic and other autoimmune diseases.
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Reports on the topic "Proteins Analysis"

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Matthews, Lisa, Guanming Wu, Robin Haw, Timothy Brunson, Nasim Sanati, Solomon Shorser, Deidre Beavers, Patrick Conley, Lincoln Stein, and Peter D'Eustachio. Illuminating Dark Proteins using Reactome Pathways. Reactome, October 2022. http://dx.doi.org/10.3180/poster/20221027matthews.

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Diseases are often the consequence of proteins or protein complexes that are non-functional or that function improperly. An active area of research has focused on the identification of molecules that can interact with defective proteins and restore their function. While 22% percent of human proteins are estimated to be druggable, less than fifteen percent are targeted by FDA-approved drugs, and the vast majority of untargeted proteins are understudied or so-called "dark" proteins. Elucidation of the function of these dark proteins, particularly those in commonly drug-targeted protein families, may offer therapeutic opportunities for many diseases. Reactome is the most comprehensive, open-access pathway knowledgebase covering 2585 pathways and including 14246 reactions, 11088 proteins, 13984 complexes, and 1093 drugs. Placing dark proteins in the context of Reactome pathways provides a framework of reference for these proteins facilitating the generation of hypotheses for experimental biologists to develop targeted experiments, unravel the potential functions of these proteins, and then design drugs to manipulate them. To this end, we have trained a random forest with 106 protein/gene pairwise features collected from multiple resources to predict functional interactions between dark proteins and proteins annotated in Reactome and then developed three scores to measure the interactions between dark proteins and Reactome pathways based on enrichment analysis and fuzzy logic simulations. Literature evidence via manual checking and systematic NLP-based analysis support predicted interacting pathways for dark proteins. To visualize dark proteins in the context of Reactome pathways, we have also developed a new website, idg.reactome.org, by extending the Reactome web application with new features illustrating these proteins together with tissue-specific protein and gene expression levels and drug interactions.
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Barakat, Dr Shima, Dr Samuel Short, Dr Bernhard Strauss, and Dr Pantea Lotfian. https://www.food.gov.uk/research/research-projects/alternative-proteins-for-human-consumption. Food Standards Agency, June 2022. http://dx.doi.org/10.46756/sci.fsa.wdu243.

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The UK is seeing growing interest in alternative protein sources to traditional animal-based proteins such as beef, lamb, pork, poultry, fish, eggs, and dairy. There is already an extensive market in alternative protein materials, however, technological advances combined with the pressure for more sustainable sources of protein has led to an acceleration of innovation and product development and the introduction of a large amount of new alternative protein ingredients and products to the market. These have the potential to dramatically impact on the UK food system. This report is a combination of desk research, based on thorough review of the academic and non-academic literature and of the alternative proteins start-up scene, and presents an analysis of the emerging market for alternative proteins, the potential implications and the potential policy responses that the FSA might need to consider. Four main categories of alternative proteins are presented and reviewed in this report: Plant-based meat substitutes Novel protein sources Proteins and biomass biosynthesised by microorganisms Cultured meat
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Morrison, Mark, and Joshuah Miron. Molecular-Based Analysis of Cellulose Binding Proteins Involved with Adherence to Cellulose by Ruminococcus albus. United States Department of Agriculture, November 2000. http://dx.doi.org/10.32747/2000.7695844.bard.

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At the beginning of this project, it was clear that R. albus adhered tightly to cellulose and its efficient degradation of this polysaccharide was dependent on micromolar concentrations of phenylacetic acid (PAA) and phenylpropionic acid (PPA). The objectives for our research were: i) to identify how many different kinds of cellulose binding proteins are produced by Ruminococcus albus; ii) to isolate and clone the genes encoding some of these proteins from the same bacterium; iii) to determine where these various proteins were located and; iv) quantify the relative importance of these proteins in affecting the rate and extent to which the bacterium becomes attached to cellulose. BARD support has facilitated a number of breakthroughs relevant to our fundamental understanding of the adhesion process. First, R. albus possesses multiple mechanisms for adhesion to cellulose. The P.I.'s laboratory has discovered a novel cellulose-binding protein (CbpC) that belongs to the Pil-protein family, and in particular, the type 4 fimbrial proteins. We have also obtained genetic and biochemical evidence demonstrating that, in addition to CbpC-mediated adhesion, R. albus also produces a cellulosome-like complex for adhesion. These breakthroughs resulted from the isolation (in Israel and the US) of spontaneously arising mutants of R. albus strains SY3 and 8, which were completely or partially defective in adhesion to cellulose, respectively. While the SY3 mutant strain was incapable of growth with cellulose as the sole carbon source, the strain 8 mutants showed varying abilities to degrade and grow with cellulose. Biochemical and gene cloning experiments have been used in Israel and the US, respectively, to identify what are believed to be key components of a cellulosome. This combination of cellulose adhesion mechanisms has not been identified previously in any bacterium. Second, differential display, reverse transcription polymerase chain reaction (DD RT-PCR) has been developed for use with R. albus. A major limitation to cellulose research has been the intractability of cellulolytic bacteria to genetic manipulation by techniques such as transposon mutagenesis and gene displacement. The P.I.'s successfully developed DD RT- PCR, which expanded the scope of our research beyond the original objectives of the project, and a subset of the transcripts conditionally expressed in response to PAA and PPA have been identified and characterized. Third, proteins immunochemically related to the CbpC protein of R. albus 8 are present in other R. albus strains and F. intestinalis, Western immunoblots have been used to examine additional strains of R. albus, as well as other cellulolytic bacteria of ruminant origin, for production of proteins immunochemically related to the CbpC protein. The results of these experiments showed that R. albus strains SY3, 7 and B199 all possess a protein of ~25 kDa which cross-reacts with polyclonal anti-CbpC antiserum. Several strains of Butyrivibrio fibrisolvens, Ruminococcus flavefaciens strains C- 94 and FD-1, and Fibrobacter succinogenes S85 produced no proteins that cross-react with the same antiserum. Surprisingly though, F. intestinalis strain DR7 does possess a protein(s) of relatively large molecular mass (~200 kDa) that was strongly cross-reactive with the anti- CbpC antiserum. Scientifically, our studies have helped expand the scope of our fundamental understanding of adhesion mechanisms in cellulose-degrading bacteria, and validated the use of RNA-based techniques to examine physiological responses in bacteria that are nor amenable to genetic manipulations. Because efficient fiber hydrolysis by many anaerobic bacteria requires both tight adhesion to substrate and a stable cellulosome, we believe our findings are also the first step in providing the resources needed to achieve our long-term goal of increasing fiber digestibility in animals.
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Sherman, L. A. Analysis of the PS II proteins MSP and CP43. Office of Scientific and Technical Information (OSTI), July 1995. http://dx.doi.org/10.2172/100110.

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5

Wetzel, Carolyn M. Functional analysis of chloroplast early light inducible proteins (ELIPs). Office of Scientific and Technical Information (OSTI), February 2005. http://dx.doi.org/10.2172/836992.

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Tsvetkov, Tvetan, and Denica Daskalova. Analysis of Seminal Plasma Proteins Related to Sperm Hyperactivation. "Prof. Marin Drinov" Publishing House of Bulgarian Academy of Sciences, January 2021. http://dx.doi.org/10.7546/crabs.2021.01.09.

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7

Barkan, Alice, and Zach Adam. The Role of Proteases in Regulating Gene Expression and Assembly Processes in the Chloroplast. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7695852.bard.

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Chloroplasts house many biochemical processes that are essential for plant viability. Foremost, among these is photosynthesis, which requires the protein-rich thylakoid membrane system. The activation of chloroplast genes encoding thylakoid membrane proteins and the targeting and assembly of these proteins together with their nuclear-encoded partners are essential for the elaboration of the thylakoid membrane. Several nuclear-encoded proteins that regulate chloroplast gene expression and that mediate the targeting of proteins to the thylakoid membrane have been identified in recent years, and many more remain to be discovered. The abundance of such proteins is critical and is likely to be determined to a significant extent by their stability, which in turn, is influenced by chloroplast protease activities. The primary goal of this project was to link specific proteases to specific substrates, and in particular, to specific regulatory and assembly proteins. We proposed a two-pronged approach, involving genetic analysis of the consequences of the mutational loss of chloroplast proteases, and biochemical analysis of the degradation pathways of specific proteins that have been shown to control chloroplast gene expression. Our initial bioinformatic analysis of chloroplast proteases allowed us to identify the set of pro teases that is targeted to the chloroplast. We used that information to recover three Arabidopsis mutants with T - DNA insertions in specific chloroplast protease genes. We carried out the first analysis of the stability of a regulator of chloroplast gene expression (CRS2), and found that the protein is much less stable than are typical components of the photosynthetic apparatus. Genetic reagents and analytical methods were developed that have set the stage for a rapid advancement of our understanding of chloroplast proteolysis. The results obtained may be useful for manipulating the expression of transgenes in the chloroplast and for engineering plants whose photosynthetic activity is optimized under harsh environmental conditions.
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Zhu, Mucheng, Zhenhua Lu, Hao Guo, Xiaoting Gu, Defang Wei, and Zhengyi Zhang. Diagnostic Value of Combination of Biomarkers for Malignant Pleural Mesothelioma：Systematic Review and Meta-Analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, October 2022. http://dx.doi.org/10.37766/inplasy2022.10.0043.

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Review question / Objective: Tumor biomarkers have become increasingly attractive due to their non-invasive properties and relatively inexpensive nature for early diagnosis of Malignant pleural mesothelioma (MPM) .Many scholars have published studies on DNA and protein as biomarkers for early diagnosis of MPM, which might be a new breakthrough. A new meta-analysis is necessary to compare the accuracy of combination of three kinds of DNA and three kinds of proteins. Condition being studied: XAs the previous studies have a certain controversy about DNA as a biomarker of MPM, we conducted a systematic search using EMBASE, PubMed and Cochrane Library to identify relevant studies from the inception to October 2021. we used QUADAS-2 for Quality Assessment to Diagnostic Accuracy Studies to evaluate the quality of eligible studies. We used Stata 15.0 and Review Manager 5.4 software to perform the meta-analysis to compare the accuracy of combination of three kinds of DNA and three kinds of proteins.
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Jensen, Kirk B. Functional Analysis of Nova Proteins: Gene Regulation and Breast Tumor Immunity. Fort Belvoir, VA: Defense Technical Information Center, July 1998. http://dx.doi.org/10.21236/ada358057.

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Hellinga, Homme W. Instrumentation for the Interfacial Analysis for Biosensor Microsystems Containing Genetically Engineered Proteins. Fort Belvoir, VA: Defense Technical Information Center, October 2002. http://dx.doi.org/10.21236/ada408298.

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