32,037 results on '"PROTEOMICS"'
Search Results
2. A Synopsis of Proteins and Their Purification.
- Author
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Walls D, Cooney G, and Loughran ST
- Subjects
- Chromatography, Affinity, Computational Biology, Proteomics, Molecular Biology
- Abstract
The goal of protein purification is to separate a specific protein from all other biomolecules. Classical chromatographic procedures have been designed to exploit particular distinguishing features of individual target proteins, such as size, shape, physicochemical properties, and binding affinity. Advances in molecular biology and bioinformatics have positively contributed at every level to the challenge of purifying individual proteins and more recently have led to the development of high-throughput proteomic platforms. In this chapter, a synopsis of advancements in the field of protein chromatography is presented, with reference to the principal tools and resources that are available to assist with protein purification strategies., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
- Published
- 2023
- Full Text
- View/download PDF
3. How AlphaFold can realize AI's full potential in structural biology.
- Subjects
- Artificial Intelligence trends, Molecular Biology trends, Protein Folding, Proteins chemistry, Software
- Published
- 2022
- Full Text
- View/download PDF
4. Integrative illustration of a JCVI-syn3A minimal cell.
- Author
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Goodsell DS
- Subjects
- Cryoelectron Microscopy, Models, Molecular, Proteomics, Genomics, Molecular Biology
- Abstract
Data from genomics, proteomics, structural biology and cryo-electron microscopy are integrated into a structural illustration of a cross section through an entire JCVI-syn3.0 minimal cell. The illustration is designed with several goals: to inspire excitement in science, to depict the underlying scientific results accurately, and to be feasible in traditional media. Design choices to achieve these goals include reduction of visual complexity with simplified representations, use of orthographic projection to retain scale relationships, and an approach to color that highlights functional compartments of the cell. Given that this simple cell provides an attractive laboratory for exploring the central processes needed for life, several functional narratives are included in the illustration, including division of the cell and the first depiction of an entire cellular proteome. The illustration lays the foundation for 3D molecular modeling of this cell., (© 2022 the author(s), published by De Gruyter, Berlin/Boston.)
- Published
- 2022
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- View/download PDF
5. A protocol to visualize cytosolic aggresome-like bodies using confocal microscopy.
- Author
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Kim S, Hwang Y, and Kang HC
- Subjects
- Fluorescent Antibody Technique, HeLa Cells, Histone Deacetylase 6 immunology, Histone Deacetylase 6 metabolism, Humans, Immunohistochemistry methods, Inclusion Bodies metabolism, NEDD8 Protein immunology, NEDD8 Protein metabolism, Ubiquitin metabolism, Cytosol, Microscopy, Confocal methods, Molecular Biology methods
- Abstract
Ubiquitin stress-induced NEDDylation leads to the formation of aggresome-like bodies (ALBs) in the perinuclear region of cells. Therefore, imaging analysis is essential for characterizing the biological phenotypes of ALBs. Here, we describe a protocol to monitor ALBs induced by ubiquitin stress using immunocytochemistry and to quantify cells containing ALBs. This optimized protocol details the use of readily available materials and reagents and can be applied to explore diverse molecules involved in stress-induced ALBs. For complete details on the use and execution of this protocol, please refer to Kim et al. (2021)., Competing Interests: The authors declare no competing interests., (© 2021 The Authors.)
- Published
- 2021
- Full Text
- View/download PDF
6. Artificial intelligence in structural biology is here to stay.
- Subjects
- Protein Folding, Protein Structure, Tertiary, Software, Artificial Intelligence, Molecular Biology trends
- Published
- 2021
- Full Text
- View/download PDF
7. What Did We Learn from the Molecular Biology of Adrenal Cortical Neoplasia? From Histopathology to Translational Genomics.
- Author
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Juhlin CC, Bertherat J, Giordano TJ, Hammer GD, Sasano H, and Mete O
- Subjects
- Adrenal Cortex Neoplasms diagnosis, Humans, Prognosis, Proteomics, Translational Research, Biomedical, Adrenal Cortex Neoplasms genetics, Adrenal Cortex Neoplasms pathology, Genomics, Molecular Biology
- Abstract
Approximately one-tenth of the general population exhibit adrenal cortical nodules, and the incidence has increased. Afflicted patients display a multifaceted symptomatology-sometimes with rather spectacular features. Given the general infrequency as well as the specific clinical, histological, and molecular considerations characterizing these lesions, adrenal cortical tumors should be investigated by endocrine pathologists in high-volume tertiary centers. Even so, to distinguish specific forms of benign adrenal cortical lesions as well as to pinpoint malignant cases with the highest risk of poor outcome is often challenging using conventional histology alone, and molecular genetics and translational biomarkers are therefore gaining increased attention as a possible discriminator in this context. In general, our understanding of adrenal cortical tumorigenesis has increased tremendously the last decade, not least due to the development of next-generation sequencing techniques. Comprehensive analyses have helped establish the link between benign aldosterone-producing adrenal cortical proliferations and ion channel mutations, as well as mutations in the protein kinase A (PKA) signaling pathway coupled to cortisol-producing adrenal cortical lesions. Moreover, molecular classifications of adrenal cortical tumors have facilitated the distinction of benign from malignant forms, as well as the prognostication of the individual patients with verified adrenal cortical carcinoma, enabling high-resolution diagnostics that is not entirely possible by histology alone. Therefore, combinations of histology, immunohistochemistry, and next-generation multi-omic analyses are all needed in an integrated fashion to properly distinguish malignancy in some cases. Despite significant progress made in the field, current clinical and pathological challenges include the preoperative distinction of non-metastatic low-grade adrenal cortical carcinoma confined to the adrenal gland, adoption of individualized therapeutic algorithms aligned with molecular and histopathologic risk stratification tools, and histological confirmation of functional adrenal cortical disease in the context of multifocal adrenal cortical proliferations. We herein review the histological, genetic, and epigenetic landscapes of benign and malignant adrenal cortical neoplasia from a modern surgical endocrine pathology perspective and highlight key mechanisms of value for diagnostic and prognostic purposes.
- Published
- 2021
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8. Transcript specific mRNP capture from Drosophila egg-chambers for proteomic analysis.
- Author
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Wippich F and Ephrussi A
- Subjects
- Animals, Drosophila genetics, Gene Expression Regulation genetics, Protein Binding genetics, Ribonucleoproteins genetics, Molecular Biology methods, Proteomics, Ribonucleoproteins isolation & purification
- Abstract
mRNA binding proteins (RBPs) play a major role in post-transcriptional control of gene expression. To understand the complex regulatory processes regulating a specific mRNA during its life-time, a comprehensive view of the bound RBPs is essential. Here, we describe a method for transcript-specific isolation of endogenous ribonucleoprotein complexes (RNPs) from Drosophila egg-chambers. The method, which is based on in-solution hybridization of short biotinylated antisense DNA oligonucleotide probes to multiple segments of a transcript of interest allows unbiased identification of associated proteins by quantitative proteomics., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
9. Omics and the molecular exercise physiology.
- Author
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Gomes C, Almeida JA, Franco OL, and Petriz B
- Subjects
- Humans, Lipidomics, Metabolomics, Proteomics, Exercise physiology, Molecular Biology
- Abstract
Exercise is a well-known non-pharmacologic agent used to prevent and treat a wide range of pathologic conditions such as metabolic and cardiovascular disease. In this sense, the classic field of exercise physiology has determined the main theoretical and practical bases of physiologic adaptations in response to exercise. However, the last decades were marked by significant advances in analytical laboratory techniques, where the field of biochemistry, genetics and molecular biology promoted exercise science to enter a new era. Regardless of its application, whether in the field of disease prevention or performance, the association of molecular biology with exercise physiology has been fundamental for unveiling knowledge of the molecular mechanisms related to the adaptation to exercise. This chapter will address the natural evolution of exercise physiology toward genetics and molecular biology, emphasizing the collection of integrated analytical approaches that composes the OMICS and their contribution to the field of molecular exercise physiology., (© 2020 Elsevier Inc. All rights reserved.)
- Published
- 2020
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10. Systems structural biology measurements by in vivo cross-linking with mass spectrometry.
- Author
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Chavez JD, Mohr JP, Mathay M, Zhong X, Keller A, and Bruce JE
- Subjects
- Animals, Cells, Cultured, Escherichia coli, Humans, Lysine analysis, Lysine chemistry, Mice, Peptides analysis, Peptides chemistry, Proteins analysis, Proteomics, Systems Biology, Mass Spectrometry methods, Molecular Biology methods, Protein Interaction Mapping methods, Proteins chemistry
- Abstract
This protocol describes a workflow for utilizing large-scale cross-linking with mass spectrometry (XL-MS) to make systems-level structural biology measurements in complex biological samples, including cells, isolated organelles, and tissue samples. XL-MS is a structural biology technique that provides information on the molecular structure of proteins and protein complexes using chemical probes that report the proximity of probe-reactive amino acids within proteins, typically lysine residues. Information gained through XL-MS studies is often complementary to more traditional methods, such as X-ray crystallography, nuclear magnetic resonance, and cryo-electron microscopy. The use of MS-cleavable cross-linkers, including protein interaction reporter (PIR) technologies, enables XL-MS studies on protein structures and interactions in extremely complex biological samples, including intact living cells. PIR cross-linkers are designed to contain chemical bonds at specific locations within the cross-linker molecule that can be selectively cleaved by collision-induced dissociation or UV light. When broken, these bonds release the intact peptides that were cross-linked, as well as a reporter ion. Conservation of mass dictates that the sum of the two released peptide masses and the reporter mass equals the measured precursor mass. This relationship is used to identify cross-linked peptide pairs. Release of the individual peptides permits accurate measurement of their masses and independent amino acid sequence determination by tandem MS, allowing the use of standard proteomics search engines such as Comet for peptide sequence assignment, greatly simplifying data analysis of cross-linked peptide pairs. Search results are processed with XLinkProphet for validation and can be uploaded into XlinkDB for interaction network and structural analysis.
- Published
- 2019
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11. A unique large-scale undergraduate research experience in molecular systems biology for non-mathematics majors.
- Author
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Kappler U, Rowland SL, and Pedwell RK
- Subjects
- Australia, Curriculum, Genomics, Humans, Metabolomics, Proteomics, Universities, Biomedical Research, Computational Biology education, Educational Measurement, Mathematics education, Molecular Biology education, Systems Biology education
- Abstract
Systems biology is frequently taught with an emphasis on mathematical modeling approaches. This focus effectively excludes most biology, biochemistry, and molecular biology students, who are not mathematics majors. The mathematical focus can also present a misleading picture of systems biology, which is a multi-disciplinary pursuit requiring collaboration between biochemists, bioinformaticians, and mathematicians. This article describes an authentic large-scale undergraduate research experience (ALURE) in systems biology that incorporates proteomics, bacterial genomics, and bioinformatics in the one exercise. This project is designed to engage students who have a basic grounding in protein chemistry and metabolism and no mathematical modeling skills. The pedagogy around the research experience is designed to help students attack complex datasets and use their emergent metabolic knowledge to make meaning from large amounts of raw data. On completing the ALURE, participants reported a significant increase in their confidence around analyzing large datasets, while the majority of the cohort reported good or great gains in a variety of skills including "analysing data for patterns" and "conducting database or internet searches." An environmental scan shows that this ALURE is the only undergraduate-level system-biology research project offered on a large-scale in Australia; this speaks to the perceived difficulty of implementing such an opportunity for students. We argue however, that based on the student feedback, allowing undergraduate students to complete a systems-biology project is both feasible and desirable, even if the students are not maths and computing majors. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):235-248, 2017., (© 2016 The International Union of Biochemistry and Molecular Biology.)
- Published
- 2017
- Full Text
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12. Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture.
- Author
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Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, and Hentze MW
- Subjects
- HeLa Cells, Humans, Multiprotein Complexes genetics, Proteomics, RNA genetics, RNA-Binding Proteins genetics, Ribonucleoproteins genetics, Molecular Biology methods, Multiprotein Complexes isolation & purification, RNA-Binding Proteins isolation & purification, Ribonucleoproteins isolation & purification
- Abstract
RNA associates with RNA-binding proteins (RBPs) from synthesis to decay, forming dynamic ribonucleoproteins (RNPs). In spite of the preeminent role of RBPs regulating RNA fate, the scope of cellular RBPs has remained largely unknown. We have recently developed a novel and comprehensive method to identify the repertoire of active RBPs of cultured cells, called RNA interactome capture. Using in vivo UV cross-linking on cultured cells, proteins are covalently bound to RNA if the contact between the two is direct ("zero distance"). Protein-RNA complexes are purified by poly(A) tail-dependent oligo(dT) capture and analyzed by quantitative mass spectrometry. Because UV irradiation is applied to living cells and purification is performed using highly stringent washes, RNA interactome capture identifies physiologic and direct protein-RNA interactions. Applied to HeLa cells, this protocol revealed the near-complete repertoire of RBPs, including hundreds of novel RNA binders. Apart from its RBP discovery capacity, quantitative and comparative RNA interactome capture can also be used to study the responses of the RBP repertoire to different physiological cues and processes, including metabolic stress, differentiation, development, or the response to drugs.
- Published
- 2016
- Full Text
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13. Computational prediction of protein-protein interactions.
- Author
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Ehrenberger T, Cantley LC, and Yaffe MB
- Subjects
- Algorithms, Amino Acid Motifs, Binding Sites, Computational Biology, Databases, Protein, Phosphorylation, Protein Binding, Proteins metabolism, Proteomics, Software, Molecular Biology methods, Phosphotransferases chemistry, Protein Interaction Maps, Proteins chemistry
- Abstract
The prediction of protein-protein interactions and kinase-specific phosphorylation sites on individual proteins is critical for correctly placing proteins within signaling pathways and networks. The importance of this type of annotation continues to increase with the continued explosion of genomic and proteomic data, particularly with emerging data categorizing posttranslational modifications on a large scale. A variety of computational tools are available for this purpose. In this chapter, we review the general methodologies for these types of computational predictions and present a detailed user-focused tutorial of one such method and computational tool, Scansite, which is freely available to the entire scientific community over the Internet.
- Published
- 2015
- Full Text
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14. Special issues from High 1: KSBMB Winter Workshop.
- Author
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Kim SY
- Subjects
- Drug Discovery, Korea, Molecular Probes metabolism, Molecular Targeted Therapy, Proteomics, Seasons, Societies, Scientific, Stem Cell Research, Translational Research, Biomedical, Biochemistry, Congresses as Topic, Molecular Biology
- Published
- 2014
15. Automated cell-free protein production methods for structural studies.
- Author
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Beebe ET, Makino S, Markley JL, and Fox BG
- Subjects
- Automation methods, Humans, Protein Conformation, Proteomics, Recombinant Proteins chemistry, Recombinant Proteins genetics, Triticum genetics, Cell-Free System, Molecular Biology methods, Protein Biosynthesis
- Abstract
In contrast to cell-based protein expression, cell-free production is highly consistent, scalable, and amenable to automation. Robots can handle many samples and perform repetitive procedures that are otherwise prone to human error. Here is described commercially available robotics for a wheat germ cell-free system with emphasis on practical applications for structural and functional studies. In addition, described is a cell-free method for preparing protein complexes.
- Published
- 2014
- Full Text
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16. Characterization of extracellular HSV-1 virions by proteomics.
- Author
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Lippé R
- Subjects
- Herpesvirus 1, Human metabolism, Humans, Mass Spectrometry, Proteomics, Herpesvirus 1, Human genetics, Molecular Biology methods, Viral Proteins biosynthesis, Virion genetics
- Abstract
The analysis of herpes simplex virus type 1 mature extracellular virions by proteomics requires highly enriched samples to limit false positives and favor the detection of true components. The protocol described below involves the removal of highly contaminating serum proteins and purification of the virions by a series of differential and density centrifugation steps. In addition, L-particles, which are viral particles devoid of genome and capsid but present in the extracellular milieu, are depleted on Ficoll 400 gradients. As previously reported, the resulting viral particles are free of most contaminants and suitable for mass spectrometry.
- Published
- 2014
- Full Text
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17. Detection of protein-protein interactions using tandem affinity purification.
- Author
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Goodfellow I and Bailey D
- Subjects
- Carrier Proteins chemistry, Endopeptidases chemistry, Protein Binding, Proteins chemistry, Proteins genetics, Proteomics, Chromatography, Affinity methods, Molecular Biology methods, Protein Interaction Maps, Proteins isolation & purification
- Abstract
Tandem affinity purification (TAP) is an invaluable technique for identifying interaction partners for an affinity tagged bait protein. The approach relies on the fusion of dual tags to the bait before separate rounds of affinity purification and precipitation. Frequently two specific elution steps are also performed to increase the specificity of the overall technique. In the method detailed here, the two tags used are protein G and a short streptavidin binding peptide; however, many variations can be employed. In our example the tags are separated by a cleavable tobacco etch virus protease target sequence, allowing for specific elution after the first round of affinity purification. Proteins isolated after the final elution step in this process are concentrated before being identified by mass spectrometry. The use of dual affinity tags and specific elution in this technique dramatically increases both the specificity and stringency of the pull-downs, ensuring a low level of background nonspecific interactions.
- Published
- 2014
- Full Text
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18. Integrative chemical proteomics and cell biology methods to study endocytosis and vesicular trafficking in Arabidopsis.
- Author
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Takáč T, Pechan T, Samajová O, and Samaj J
- Subjects
- Androstadienes administration & dosage, Arabidopsis drug effects, Arabidopsis Proteins biosynthesis, Brefeldin A administration & dosage, Vesicular Transport Proteins biosynthesis, Wortmannin, Endocytosis drug effects, Molecular Biology methods, Proteomics, Transport Vesicles drug effects
- Abstract
We present a comprehensive approach combining proteomics and cell biology to study vesicular trafficking in plants. Within this approach, we exploit chemical compounds inhibiting particular vesicular trafficking events in plant cells. Treatment of plants with these relatively specific inhibitors results in intracellular accumulation of proteins being transported by vesicles as well as in a change in abundance of regulatory proteins. Such pharmacological inhibition allows for identification of key proteins, and for further detailed functional investigation using cell biological, molecular biological, and biochemical methods used for validation of proteomic results.
- Published
- 2014
- Full Text
- View/download PDF
19. Global identification of caspase substrates using PROTOMAP (protein topography and migration analysis platform).
- Author
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Dix MM, Simon GM, and Cravatt BF
- Subjects
- Apoptosis genetics, Caspases isolation & purification, Caspases metabolism, Electrophoresis, Polyacrylamide Gel, Humans, Substrate Specificity, Tandem Mass Spectrometry, Caspases chemistry, Molecular Biology methods, Proteomics
- Abstract
Delineation of the natural substrate scope of proteases is important for understanding the functions of proteolytic pathways in physiology and disease. Herein we describe the protocol for PROTOMAP, a technique that combines SDS-PAGE with tandem mass spectrometry to globally identify shifts in protein migration indicative of proteolytic processing. When applied to cells undergoing apoptosis, this unbiased global method provides a snapshot of the topography and magnitude of proteolytic events associated with programmed cell death.
- Published
- 2014
- Full Text
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20. Diagnosis and treatment of small renal masses: the role for molecular biology.
- Author
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Kurban G, Gedye C, Morales C, Yousef GM, Almatar A, and Jewett MA
- Subjects
- Animals, Biomarkers, Biopsy, Chromosome Aberrations, Diagnostic Imaging, Humans, Prognosis, Proteomics, RNA, Messenger biosynthesis, RNA, Messenger genetics, Kidney Neoplasms diagnosis, Kidney Neoplasms therapy, Molecular Biology
- Abstract
Renal cell carcinoma (RCC), the most common type of kidney cancer, is increasing in incidence and is the most lethal genitourinary cancer. Due to the increasing use of abdominal imaging, incidentally detected, asymptomatic small renal masses (SRMs), most of which are RCC, have become the most common presentation of kidney cancer. Most RCC SRMs initially grow slowly or not at all, but others progress to advanced and metastatic cancer. Several diagnostic and prognostic genomic, transcriptomic and proteomic studies have been completed in RCC, however signatures for SRM progression have not been identified. In the absence of useful factors to distinguish those tumors requiring treatment for progression from those that can be managed by active surveillance alone, most SRMs are treated as RCC with surgery. Currently, the only prognostic factor at diagnosis is tumor size. Tumor growth rate also appears to identify potential progressive tumours. Identifying signatures for progression and the utilization of needle biopsies will be important for SRM patients and will guide therapy.
- Published
- 2013
21. Abstracts of the 22nd IUBMB & 37th FEBS Congress. Seville, Spain. September 4-9, 2012.
- Subjects
- Biochemistry, Molecular Biology, Proteomics
- Published
- 2012
- Full Text
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22. Convenience experimentation.
- Author
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Krohs U
- Subjects
- Data Collection, Genomics, Proteomics, Automation, Computational Biology, Models, Biological, Molecular Biology, Research Design, Systems Biology
- Abstract
Systems biology aims at explaining life processes by means of detailed models of molecular networks, mainly on the whole-cell scale. The whole cell perspective distinguishes the new field of systems biology from earlier approaches within molecular cell biology. The shift was made possible by the high throughput methods that were developed for gathering 'omic' (genomic, proteomic, etc.) data. These new techniques are made commercially available as semi-automatic analytic equipment, ready-made analytic kits and probe arrays. There is a whole industry of supplies for what may be called convenience experimentation. My paper inquires some epistemic consequences of strong reliance on convenience experimentation in systems biology. In times when experimentation was automated to a lesser degree, modeling and in part even experimentation could be understood fairly well as either being driven by hypotheses, and thus proceed by the testing of hypothesis, or as being performed in an exploratory mode, intended to sharpen concepts or initially vague phenomena. In systems biology, the situation is dramatically different. Data collection became so easy (though not cheap) that experimentation is, to a high degree, driven by convenience equipment, and model building is driven by the vast amount of data that is produced by convenience experimentation. This results in a shift in the mode of science. The paper shows that convenience driven science is not primarily hypothesis-testing, nor is it in an exploratory mode. It rather proceeds in a gathering mode. This shift demands another shift in the mode of evaluation, which now becomes an exploratory endeavor, in response to the superabundance of gathered data., (Copyright © 2011 Elsevier Ltd. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
23. Advanced molecular biologic techniques in toxicologic disease.
- Author
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Ward J, Szabo G, McManus D, and Boyer E
- Subjects
- Gene Expression Profiling, Genomics, Humans, Metabolomics, MicroRNAs physiology, Proteomics, Systems Biology, Drug-Related Side Effects and Adverse Reactions, Molecular Biology methods
- Abstract
The advancement of molecular biologic techniques and their capabilities to answer questions pertaining to mechanisms of pathophysiologic events have greatly expanded over the past few years. In particular, these opportunities have provided researchers and clinicians alike the framework from with which to answer clinical questions not amenable for elucidation using previous, more antiquated methods. Utilizing extremely small molecules, namely microRNA, DNA, protein, and nanoparticles, we discuss the background and utility of these approaches to the progressive, practicing physician. Finally, we consider the application of these tools employed as future bedside point of care tests, aiding in the ultimate goal of unsurpassed patient care.
- Published
- 2011
- Full Text
- View/download PDF
24. Recent advances in microfluidic technologies for biochemistry and molecular biologys.
- Author
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Cho S, Kang DK, Choo J, de Mello AJ, and Chang SI
- Subjects
- Humans, Proteomics, Biochemistry trends, Microfluidic Analytical Techniques methods, Microfluidic Analytical Techniques trends, Molecular Biology trends
- Abstract
Advances in the fields of proteomics and genomics have necessitated the development of high-throughput screening methods (HTS) for the systematic transformation of large amounts of biological chemical data into an organized database of knowledge. Microfluidic systems are ideally suited for high-throughput biochemical experimentation since they offer high analytical throughput, consume minute quantities of expensive biological reagents, exhibit superior sensitivity and functionality compared to traditional micro-array techniques and can be integrated within complex experimental work flows. A range of basic biochemical and molecular biological operations have been transferred to chip-based microfluidic formats over the last decade, including gene sequencing, emulsion PCR, immunoassays, electrophoresis, cell-based assays, expression cloning and macromolecule blotting. In this review, we highlight some of the recent advances in the application of microfluidics to biochemistry and molecular biology.
- Published
- 2011
- Full Text
- View/download PDF
25. Identification and quantification of mucin expression.
- Author
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Thomsson KA and Hansson GC
- Subjects
- Alcian Blue analysis, Animals, Antibodies immunology, Antibodies metabolism, Cystic Fibrosis physiopathology, Cystic Fibrosis Transmembrane Conductance Regulator metabolism, Electrophoresis, Polyacrylamide Gel, Gene Expression, Glycosylation, Humans, Immunoblotting, Mice, Mucins genetics, Mucins immunology, Mucins isolation & purification, Mucociliary Clearance, Mucus chemistry, Proteomics, Solubility, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Trypsin metabolism, Cystic Fibrosis metabolism, Molecular Biology methods, Mucins metabolism, Mucus metabolism
- Abstract
The major phenotype of CF is the accumulation of mucus, a phenomenon whose relation to the dysfunctional CFTR is still not fully understood. This means that studies of mucus and its main component, the mucins, are important. Due to the large size and high glycosylation level, such questions need special considerations and methodology. We describe methods for the general quantification of heavily glycosylated proteins as the mucins using dot/slot blot. We also describe the separation of the mucins by gel electrophoresis and the identification with specific antibodies on Western blot and by proteomics.
- Published
- 2011
- Full Text
- View/download PDF
26. Genetics for the pediatric anesthesiologist: a primer on congenital malformations, pharmacogenetics, and proteomics.
- Author
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Galinkin JL, Demmer L, and Yaster M
- Subjects
- Anesthesia adverse effects, Anesthetics administration & dosage, Anesthetics adverse effects, Congenital Abnormalities genetics, Congenital Abnormalities metabolism, Genetic Predisposition to Disease, Humans, Patient Selection, Precision Medicine, Risk Assessment, Risk Factors, Systems Biology, Anesthesia methods, Anesthetics pharmacokinetics, Congenital Abnormalities surgery, Molecular Biology, Pharmacogenetics, Proteomics
- Abstract
Molecular genetics is the study, at the molecular level, of how genetic information is stored, inherited, and expressed and of how it influences the structure and function of cells in health and in disease. Although molecular approaches have been used for decades in the laboratory and are at the core of modern medical education, they are only now beginning to influence clinical practice. A variety of sophisticated techniques permit rapid and affordable DNA sequencing, gene expression profiling, gene cloning, gene manipulation, gene transfer, recombinant protein production, and other technologies of enormous biomedical importance. Success in genomics has spawned additional ambitious endeavors, including proteomics, pharmacogenomics, and bioinformatics. These techniques are providing new diagnostic, prognostic, and therapeutic opportunities in all areas of medicine, including anesthesiology. With the use of molecular criteria and the diminishing cost of analytic technologies, anesthetic practice will become more individualized, and greater emphasis will be placed on the patient's genetic makeup. Both surgical and nonsurgical decisions will increasingly accommodate molecular data crucial to perioperative anesthetic management. In this article we have summarized three lectures on congenital malformations, pharmacogenetics, and proteomics presented at the 22nd Annual Meeting of the Society for Pediatric Anesthesia.
- Published
- 2010
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27. Leading applications and technologies in bioinformatics. Proceedings of the European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Martina Franca, Italy. September 18-20, 2008.
- Subjects
- Animals, Genomics, Humans, Proteomics, Computational Biology, Molecular Biology
- Published
- 2009
28. Identification of tumor-associated antigens as diagnostic and predictive biomarkers in cancer.
- Author
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Zhang JY, Looi KS, and Tan EM
- Subjects
- Cell Line, Tumor, Gene Library, Humans, Prognosis, Proteomics, Antigens, Neoplasm analysis, Biomarkers, Tumor analysis, Molecular Biology methods, Neoplasms diagnosis
- Abstract
Many studies demonstrated that cancer sera contain antibodies which react with autologous cellular antigens generally known as tumor-associated antigens (TAAs). In our laboratories, the approach used in the identification of TAAs has involved initially examining the sera of cancer patients using extracts of tissue culture cells as source of antigens in Western blotting and by indirect immunofluorescence on whole cells. With these two techniques, we identify sera which have high-titer fluorescent staining or strong signals to cell extracts on Western blotting and subsequently use these sera as probes in immunoscreening cDNA expression libraries, and also in proteomic approaches to isolate and identify targeted antigens which might potentially be involved in malignant transformation. In this manner, several novel TAAs including HCC1, p62, p90, and others have been identified. In extension of these studies, we evaluate the sensitivity and specificity of different antigen-antibody systems as markers in cancer in order to develop "tumor-associated antigen array" systems for cancer diagnosis, cancer prediction, and for following the response of patients to treatment.
- Published
- 2009
- Full Text
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29. Inflammation and genomics in the critical care unit.
- Author
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Winkelman C
- Subjects
- Arachidonic Acid genetics, Blood Coagulation genetics, Chromosome Mapping, Complement System Proteins genetics, Critical Illness therapy, Cytokines genetics, Defensins genetics, Gene Expression Profiling, Genetic Variation genetics, Histamine genetics, Humans, Inflammation diagnosis, Inflammation therapy, Nurse's Role, Nursing Assessment, Proteomics, Risk Assessment, Specialties, Nursing methods, Toll-Like Receptors genetics, Critical Care methods, Genomics methods, Inflammation genetics, Molecular Biology methods
- Abstract
Inflammation is a physiologic response to irritants, injury, and infection. Inflammatory dysregulation is believed to contribute to mortality and morbidity in illnesses common to critical care units, such as burns, trauma, sepsis, and cardiovascular disease. This article reviews the approaches used to investigate the molecular basis of inflammatory function. Genomic findings are providing insight into clinical diagnosis and treatment of inflammatory derangements in critically ill patients.
- Published
- 2008
- Full Text
- View/download PDF
30. [Life sciences: a new area of action for the physician].
- Author
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Confalonieri M
- Subjects
- Female, Gene Expression Profiling, Humans, Male, Protein Biosynthesis, Proteomics, Randomized Controlled Trials as Topic, Biological Science Disciplines trends, Biotechnology, Computational Biology trends, Computing Methodologies, Genetic Research, Genomics, Medicine trends, Molecular Biology
- Abstract
The development of the medical knowledge has became a multidisciplinary process that can be called life sciences. The new biotechnologies are changing the insight of pathology and medical therapy itself. So, the rule of the physician is changing together with the overwhelming centrality of the patient into the health system. Also, the evidence based medicine is no more considered a crucial task for the physician who cares the single ill person, albeit its importance is still high for health organizations. A genomic and post-genomic approach could indeed help to create an actual personalised medicine. Nevertheless, "omics" probably need the development of new bioinformatic tools capable to manage a huge amount of data by means of Grid computing. The development of the life sciences involves new formative and professional needs for the physician. The translational knowledge can be favoured by the closeness of clinical centres and basic science areas as suggested by several examples spreading all over the world. These experiences could open new exciting horizons for the medical science.
- Published
- 2008
31. Adapting to changes in molecular biosciences and technologies.
- Author
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Ford P, Seymour G, Beeley JA, Curro F, Depaola D, Ferguson D, Finkelstein M, Gaengler P, Neo J, Niessen L, Oktay I, Park BK, Wolowski A, and Claffey N
- Subjects
- Biocompatible Materials, Biomedical Technology, Dental Research, Forecasting, Genomics, Humans, Nanotechnology, Proteomics, Biotechnology education, Education, Dental trends, Molecular Biology education
- Abstract
Dental education, like any other educational programme in a research-intensive university environment, must be research led or at least research informed. In this context, as the research and knowledge base of dentistry lies in the biological and physical sciences, dental education must be led by advances in research in both these areas. There is no doubt that biotechnology and nanotechnology have, over the past 25 years, led research in both these areas. It is therefore logical to assume that this has also impacted on dental education. The aim of this paper is twofold; on one hand to examine the effects of biotechnology and nanotechnology and their implications for dental education and on the other to make recommendations for future developments in dental education led by research in biotechnology and nanotechnology. It is now generally accepted that dental education should be socially and culturally relevant and directed to the community it serves. In other words, there can be no universal approach and each dental school or indeed curriculum must apply the outcomes in their own social, cultural and community settings.
- Published
- 2008
- Full Text
- View/download PDF
32. Abstracts of the 12th World Congress on Advances in Oncology and the 10 International Symposium on Molecular Medicine, 11-13 October 2007, Hersonissos, Crete, Greece.
- Subjects
- Animals, Humans, Disease Susceptibility, Molecular Biology, Neoplasms genetics, Neoplasms metabolism, Neoplasms therapy, Proteomics
- Published
- 2007
33. Personalized medicine and development of targeted therapies: The upcoming challenge for diagnostic molecular pathology. A review.
- Author
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Dietel M and Sers C
- Subjects
- Genomics, Humans, Proteomics, Drug Design, Molecular Biology, Molecular Diagnostic Techniques methods, Pathology methods, Personal Health Services
- Abstract
Due to continuous technical developments and new insights into the high complexity of many diseases, molecular pathology is a rapidly growing field gaining center stage in the clinical management of tumors as well as in the pharmaceutical development of new anti-cancer drugs. The application of novel compounds in clinical trials has revealed promising results; however, the current diagnostic procedures available for determining which patients will primarily benefit from rational tumor therapy are insufficient. To read a patient's tissue as "deeply" as possible, in the future, gaining information on the morphology and on genetic, proteomic, and epigenetic alterations will be the upcoming task of surgical pathologists experienced in molecular diagnostics to provide the clinicians with information relevant for an individualized medicine. Among the different high-throughput technologies, DNA microarrays are now the first array approach close to enter routine diagnostics. Technically advanced and well-established microarray platforms can nowadays be evaluated by distinct bioinformatic tools capable of identifying both novel genes associated with disease development and clusters of genes predicting clinical outcome of an individual tumor. The automatic, highly parallel analysis of proteins and complex proteins lysates for early detection of cancers such as breast, prostate and ovary as proteomic patterns in the serum also appears at the horizon. In addition, an improved analysis of tumor samples via antibody or reverse-phase protein arrays is likely to provide the pathologist in the future with information about activated oncogenic signaling pathways and other cell functions, such as drug response or the potential to metastasize. While expression microarrays and proteomic analysis rely on relatively unstable material incompatible with paraffin-embedded tissue samples, an investigation of DNA methylation using specialized high-throughput platforms has revealed the potential of being used in future diagnostics. Each of these approaches on its own might not suffice to extract all information required for an efficient individualized diagnostics. Therefore, a "multiplex approach" combining the different biological levels DNA, RNA, and protein, may be necessary to functionally classify malignant tumors. This appears to become a major challenge for diagnostic pathologists.
- Published
- 2006
- Full Text
- View/download PDF
34. [Methodology in molecular nephrology].
- Author
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Yoh K and Koyama A
- Subjects
- Animals, Animals, Genetically Modified, Computational Biology, Genetic Therapy, Humans, In Situ Hybridization, Kidney Diseases therapy, Mice, Molecular Diagnostic Techniques, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Proteomics, Kidney Diseases genetics, Molecular Biology methods, Nephrology methods
- Published
- 2006
35. [Some achievements of the Russian Program "molecular and cell biology" in 2003].
- Author
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Georggiev GP
- Subjects
- Gene Expression Regulation, Genetic Engineering, Protein Biosynthesis, Proteomics, Russia, Cell Biology, Molecular Biology
- Published
- 2005
36. How much is enough to accept hormesis as the default? or 'At what point, if ever, could/should hormesis be employed as the principal dose-response default assumption in risk assessment?'.
- Author
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Jayjock MA
- Subjects
- Animals, No-Observed-Adverse-Effect Level, Dose-Response Relationship, Drug, Molecular Biology trends, Proteomics, Risk Assessment methods, Toxicology trends
- Abstract
Hormesis as the principal human dose-response default assumption must reasonably await the development of the science of toxicology and molecular biology before this dramatic change can occur. The inherent quality of typical toxicological data is simply too limited to allow for an understanding of what really occurs in human tissues at the relatively low doses generally extant in the environment. Thus, forwarding or asserting the quantitative use of hormesis (or any model of low dose-response) without this reasonable knowledge is simply an argument without data. It is this writer's opinion that any widespread and default acceptance of hormesis will need to look forward to and draw upon the inevitable development and use of tools from the realm of molecular biology and a resulting and distinct change in the entire toxicological testing paradigm.
- Published
- 2005
- Full Text
- View/download PDF
37. Passing the torch.
- Subjects
- Exobiology, History, 20th Century, History, 21st Century, Molecular Biology history, Proteomics, Models, Biological, Molecular Biology trends
- Published
- 2004
- Full Text
- View/download PDF
38. National Center for Biotechnology Information.
- Author
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Dooley EE
- Subjects
- Computational Biology, Genomics, Humans, Proteomics, United States, Algorithms, Biotechnology statistics & numerical data, Databases, Nucleic Acid, Information Services, Molecular Biology trends, National Library of Medicine (U.S.)
- Published
- 2004
- Full Text
- View/download PDF
39. The molecular medicine revolution and psychiatry: bridging the gap between basic neuroscience research and clinical psychiatry.
- Author
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Gould TD and Manji HK
- Subjects
- Diagnostic Imaging methods, Diagnostic Imaging trends, Disease Models, Animal, Gene Expression genetics, Gene Expression physiology, Gene Expression Profiling methods, Humans, Mental Disorders genetics, Mental Disorders physiopathology, Phenotype, Proteomics, Molecular Biology trends, Neurosciences trends, Psychiatry trends
- Abstract
Recent years have witnessed a considerable increase in both fundamental knowledge and available experimental techniques in the basic neurosciences. Unfortunately, clinical translation of these findings vis-à-vis a direct benefit to patients who suffer from psychiatric diseases has not been as rapid. It is likely that this will change in the near future. We discuss some of the knowledge and expanding techniques of basic neuroscience, focusing on those that may be most promising regarding the future impact of the current molecular medicine revolution in psychiatry. Some of the more exciting findings (basic mechanisms, techniques, and clinical methodologies) that are expected to have a major impact on both our understanding of the biological underpinnings of psychiatric diseases and the development of novel and/or improved therapies include genetics, epigenetics, transcriptomics/proteomics, neuroimaging, animal models, and improved psychiatric endophenotypes.
- Published
- 2004
- Full Text
- View/download PDF
40. Biomarkers of cancer risk and therapeutic benefit: new technologies, new opportunities, and some challenges.
- Author
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MacGregor JT
- Subjects
- Animals, Biomarkers, Tumor, Biotechnology trends, Forecasting, Genetic Predisposition to Disease, Genetic Variation, Genomics, Humans, Molecular Biology trends, Polymorphism, Genetic, Proteomics, Biotechnology methods, Molecular Biology methods, Neoplasms drug therapy, Neoplasms genetics
- Abstract
The biotechnology revolution offers unprecedented opportunities for identification of mechanistically-based biomarkers that report and predict cancer and other pathologies. The combination of genomic technologies with a knowledge of gene sequence and sequence conservation has made available markers that facilitate the correlation of genetic variation with biological outcomes, and "-omic" technologies allow efficient biochemical characterization of functional pathways--providing new markers of the susceptibility of individuals to cancer development, and of tumor susceptibility to specific therapies. New therapeutic agents targeted to individuals with specific genetic or biochemical characteristics already exist. The powerful -omic technologies allow efficient monitoring of gene transcripts, proteins, and intermediary metabolites, making it possible to monitor a large number of key cellular pathways simultaneously. This has enabled the identification of key biomarkers and signaling molecules associated with cell growth, cell death, and cellular metabolism. These new markers are facilitating monitoring of functional disturbance, molecular and cellular damage, and damage-response. Improved imaging technologies have made it feasible to image some of these molecular events noninvasively. To meet the challenge of evaluating and developing consensus criteria for the application of these new technologies and biomarkers, consortium approaches are being increasingly undertaken to share resources and to build a common understanding among the research, industry, and regulatory communities. These developments promise more efficient pharmaceutical product development, safer and more efficacious drugs, and provide clinical practitioners with new and better biomarkers for cancer screening, patient monitoring, and choice of therapy.
- Published
- 2004
- Full Text
- View/download PDF
41. The revolution of the biology of the genome.
- Author
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Hennig W
- Subjects
- Animals, Computational Biology, Evolution, Molecular, Gene Duplication, Genomics, Humans, Polyploidy, Proteomics, RNA Interference physiology, RNA, Small Interfering genetics, RNA, Small Interfering physiology, Recombination, Genetic genetics, Repetitive Sequences, Nucleic Acid genetics, Genome, Molecular Biology
- Abstract
Sequence data of entire eukaryotic genomes and their detailed comparison have provided new evidence on genome evolution. The major mechanisms involved in the increase of genome sizes are polyploidization and gene duplication. Subsequent gene silencing or mutations, preferentially in regulatory sequences of genes, modify the genome and permit the development of genes with new properties. Mechanisms such as lateral gene transfer, exon shuffling or the creation of new genes by transposition contribute to the evolution of a genome, but remain of relatively restricted relevance. Mechanisms to decrease genome sizes and, in particular, to remove specific DNA sequences, such as blocks of satellite DNAs, appear to involve the action of RNA interference (RNAi). RNAi mechanisms have been proven to be involved in chromatin packaging related with gene inactivation as well as in DNA excision during the macronucleus development in ciliates.
- Published
- 2004
- Full Text
- View/download PDF
42. ZIP codes for delivering SH2 domains.
- Author
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Songyang Z and Cantley LC
- Subjects
- History, 20th Century, History, 21st Century, Polyomavirus immunology, Protein-Tyrosine Kinases chemistry, Proteomics, src Homology Domains genetics, Carrier Proteins metabolism, Molecular Biology history, Polyomavirus metabolism, Protein-Tyrosine Kinases metabolism, src Homology Domains physiology
- Published
- 2004
- Full Text
- View/download PDF
43. Molecular therapeutics: are we making progress?
- Author
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McLeod HL and Watson MA
- Subjects
- Animals, Genome, Human, Genomics, Humans, Proteomics, Genetic Therapy, Molecular Biology
- Published
- 2003
44. HUPO 2nd and IUBMB XIX World Congress, October 8-11, 2003, Montreal, Canada. Abstracts.
- Subjects
- Biochemistry, Molecular Biology, Proteomics
- Published
- 2003
45. An ecdysone and tetracycline dual regulatory expression system for studies on Rac1 small GTPase-mediated signaling.
- Author
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Lai JF, Juang SH, Hung YM, Cheng HY, Cheng TL, Mostov KE, and Jou TS
- Subjects
- Animals, Flow Cytometry, Gene Expression Regulation drug effects, Genes, Reporter, Green Fluorescent Proteins, Humans, Indicators and Reagents metabolism, Kidney cytology, Luminescent Proteins genetics, Proteomics, Signal Transduction genetics, rac1 GTP-Binding Protein metabolism, Ecdysone pharmacology, Molecular Biology methods, Tetracyclines pharmacology, rac1 GTP-Binding Protein genetics
- Abstract
Regulated expression systems are invaluable for studying gene function, offer advantages of dosage-dependent and temporally defined gene expression, and limit possible clonal variation when toxic or pleiotropic genes are overexpressed. Previously, establishment of inducible expression systems, such as tetracycline- and ecdysone-inducible systems, required assessment of the inducible characteristics of individual clones by tedious luciferase assays. Taking advantage of a green fluorescent protein (GFP) reporter controlled by tetracycline- or ecdysone-responsive element and fluorescence-activated cell sorting, we propose a simple and efficient strategy to select highly inducible cell lines according to their fluorescence profiles after transiently transfecting the candidate cell pools with a surrogate GFP reporter. We have demonstrated that tetracycline- and ecdysone-inducible systems could be set up in Madin-Darby canine kidney and HEK-293 cells by employing this selection scheme. Importantly, this dual regulatory expression system is applied in studying the complex interplay between two Ras-related small GTPases, Cdc42 and Rac1, on detachment-induced apoptosis. Furthermore, establishment of two tightly regulated expression systems in one target cell line could be of great advantage for dissecting small GTPase Rac1-transduced signaling pathways by using global gene expression approaches such as proteomic assays.
- Published
- 2003
- Full Text
- View/download PDF
46. Exploiting genetic knowledge: the double helix 50 years on. Conference report from the United Kingdom.
- Author
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Skene L
- Subjects
- Commerce, Community-Institutional Relations, Drug Industry, Health Policy, Pharmacogenetics, Proteomics, Technology, Pharmaceutical, United Kingdom, Molecular Biology
- Published
- 2003
47. Cambridge Healthtech Institute's 5th Annual 'Molecular Display: The Chemistry Set for Proteins and Small Molecules' Conference.
- Author
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Coley AM and Casey JL
- Subjects
- Drug Design, Genetic Therapy, Humans, Pharmacology, Proteomics, Molecular Biology trends, Peptide Library
- Abstract
This meeting covered recent advances in the molecular display of peptides, proteins and nucleotides, including selection and mutational technologies. The scientific organisers assembled an impressive array of 'molecular display' heavyweights. It promised to be a stimulating meeting and the events of the following 2 days did not disappoint. The majority of the presentations were concerned with the development of novel display technologies and processes. Antibodies currently represent > 30% of the biopharmaceutical market, but are likely to be superseded by more efficient display frameworks which avoid their inherent drawbacks. In order to generate such novel therapeutics and diagnostics, high affinity reagents must be selected and/or generated from hitherto unexplored nucleic acid sequences and displayed on suitable frameworks. This meeting was concerned with the identification, generation and validation of novel sequences and framework molecules. The keynote addresses were followed by four themed sessions entitled New technologies and target selection, The discovery of small molecules using phage display, Applications in proteomics, and Novel therapeutics and diagnostics. There was a panel discussion after each session.
- Published
- 2003
- Full Text
- View/download PDF
48. Proteomics and systems biology approaches to signal transduction in sepsis.
- Author
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Nguyen A and Yaffe MB
- Subjects
- Humans, Sepsis therapy, Molecular Biology, Proteomics, Sepsis genetics, Sepsis physiopathology, Signal Transduction genetics, Signal Transduction physiology
- Abstract
Sepsis and resulting multiple system organ failure are the leading causes of mortality in intensive care units. Although it is generally appreciated that rampant, deregulated inflammatory pathways play a major role in sepsis, a comprehensive understanding based on the integrated response of multiple signal transduction pathways has remained elusive. Here we review the main signal transduction pathways involved in the progression from inflammation to sepsis and discuss emerging genomic, proteomic, and systems biology approaches to decipher how these signaling pathways converge to cause the septic state. We propose that an integrative approach involving functional proteomics will provide a quantitative and mechanistic description that unifies inflammatory signaling networks in sepsis and will identify critical regulatory nodes for therapeutic manipulation. These types of systems biology-based approaches may lead to more effective therapies than those currently available.
- Published
- 2003
- Full Text
- View/download PDF
49. Genetics, genomics and molecular medicine.
- Author
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Shagam JY
- Subjects
- Genetic Engineering, Genetic Predisposition to Disease, Human Genome Project, Humans, Proteomics, Genetics, Medical, Genomics, Molecular Biology, Technology, Radiologic
- Abstract
Genomics and the Human Genome Project are creating important changes in medical care and radiologic practice. Readers of this article will: Recall that deoxyribonucleic acid (DNA) is the information-containing molecule. Understand the relationship between DNA and protein synthesis. Learn that changes in DNA-encoded proteins produce pathogenesis. Distinguish between genomics and proteomics. Describe the Human Genome Project. Define and give examples of molecular medicine and its imaging applications. Discuss how genomics, genetic engineering and the Human Genome Project may influence radiologic practice.
- Published
- 2003
50. The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes.
- Author
-
Riley, Amanda, Grant, Michael, Snell, Aidan, Cromwell, Elizabeth, Vichas, Athea, Moorthi, Sitapriya, Rominger, Callie, Modukuri, Shrikar, Urisman, Anatoly, Castel, Pau, Wan, Lixin, and Berger, Alice
- Subjects
Cancer ,Molecular biology ,Proteomics - Abstract
RIT1 is a rare and understudied oncogene in lung cancer. Despite structural similarity to other RAS GTPase proteins such as KRAS, oncogenic RIT1 activity does not appear to be tightly regulated by nucleotide exchange or hydrolysis. Instead, there is a growing understanding that the protein abundance of RIT1 is important for its regulation and function. We previously identified the deubiquitinase USP9X as a RIT1 dependency in RIT1-mutant cells. Here, we demonstrate that both wild-type and mutant forms of RIT1 are substrates of USP9X. Depletion of USP9X leads to decreased RIT1 protein stability and abundance and resensitizes cells to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in vitro and in vivo. Our work expands upon the current understanding of RIT1 protein regulation and presents USP9X as a key regulator of RIT1-driven oncogenic phenotypes.
- Published
- 2024
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