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Experimental Protocols for Generation and Evaluation of Articular Cartilage
Published in Kyriacos A. Athanasiou, Eric M. Darling, Grayson D. DuRaine, Jerry C. Hu, A. Hari Reddi, Articular Cartilage, 2017
Kyriacos A. Athanasiou, Eric M. Darling, Grayson D. DuRaine, Jerry C. Hu, A. Hari Reddi
The pathway analysis paradigm includes several steps: applying a stimulus, determining a measurable output, detecting changes in the signaling of target pathway components (usually changes in phosphorylation), and then altering that signaling via inhibition or activation (commonly by pharmacological means) to determine changes in the previously determined output. Through systematic probing, it can be determined if pathway components are sufficient or necessary for a specific stimulus to result in a specific output.
From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology
Published in Shaker A. Mousa, Raj Bawa, Gerald F. Audette, The Road from Nanomedicine to Precision Medicine, 2020
Maria Eugenia Gallo Cantafio, Katia Grillone, Daniele Caracciolo, Francesca Scionti, Mariamena Arbitrio, Vito Barbieri, Licia Pensabene, Pietro Hiram Guzzi, Maria Teresa Di Martino
Proteomics is the study of the entire set of proteins in any given cell, including the set of all protein isoforms and modifications, the interactions between them, the structural description of proteins, and their higher-order complexes [65, 66]. Therefore, proteomics is the next step to study biological systems because proteins are responsible for most cellular processes; their analysis would more accurately reflect cellular status to determine the mechanism that underlies disease initiation, progression, and dissemination [67, 68]. To analyze the complex protein mixtures with higher sensitivity, the main technology presently in use is mass spectrometry (MS) [69], combined with liquid chromatography or matrix-assisted laser desorption ionization (MALDI-TOF/TOF) [68, 70, 71]. However, new methods were recently developed for quantitative proteomic such as isotope-coded affinity tag (ICAT) labeling, stable isotope labeling with amino acids in cell culture (SILAC), and isobaric tag for relative and absolute quantitation (iTRAQ) [72–74]. X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are two major high-throughput techniques that provide 3D structure of proteins [75]. These technologies are adopted in cancer research to generate data on (i) differential protein expression levels, (ii) protein–gene expression correlation, (iii) differential protein expression comparisons between different cancer phenotypes and subtypes, and (iv) the associations of protein expression with survival prognosis in cancer patients. Proteomic data are collected in several databases including PRIDE (proteomics identification database) and Global Proteome Machine [76]. Other databases such as KEGG, IPA (Ingenuity Pathway Analysis), Pathway Knowledge Base Reactome, or BioCarta include comprehensive data regarding metabolism, signaling, and protein interactions [77–79]. Global proteomic profile is increasingly being carried out in both cancer cell lines and patient-derived samples to provide information that are useful for cancer type classification [80–83] and drug sensitivity/resistance prediction [84, 85].
Advancements of next generation sequencing in the field of Rheumatoid Arthritis
Published in Egyptian Journal of Basic and Applied Sciences, 2023
Ankita Pati, Dattatreya Kar, Jyoti Ranjan Parida, Ananya Kuanar
NGS technologies have scope for evaluating and analysing the non-coding single stranded RNAs or miRNAs involved in 20 to 22 nucleotides, which are responsible for dysregulations in the cellular process for causing several diseases [4]. The condition for bone homeostasis related to the NGS technologies can be derived through the next generation sequencing process to locate the genetic changes in RA [77]. High-throughput profiling of the genome sequences related to NGS technology can specifically identify the functional annotation reported in the miRNAs from RA patient. Moreover, NGS technology can provide the opportunity for deriving the miRNAs-mRNA interactions to investigate the different conditions for RA patient including osteoblasts. Gene expression related to the regulation of the pathway analysis can be derived through the integration of sequencing process and bioinformatics. However, RA-related adverse conditions such as bone erosion in RA and loss of bone in peri-articular area can be developed through the application of NGS technology through wide genome sequencing process.
Evaluation of the carcinogenicity of carbon tetrachloride
Published in Journal of Toxicology and Environmental Health, Part B, 2023
Samuel M. Cohen, Christopher Bevan, Bhaskar Gollapudi, James E. Klaunig
In recent years, more sophisticated and extensive gene expression platforms have been developed. Several large databases are now available that enable sharing of RNA sequences (RNA-Seq), pathway analysis, and general gene expression results from experimental studies. These include DrugMatrix which contains results from thousands of experiments where rats or primary rat hepatocytes were treated with over 600 therapeutic, industrial, or environmental chemicals (TG-Gates, a public rat DNA microarray database of studies). In addition, with new advances major efforts are underway to utilize next-generation RNA-Seq as well as conventional DNA microarrays to identify differentially expressed protein-coding genes (DEGs) in treated versus control liver. These approaches have been involved in predicting potential rodent and human carcinogens using short term in vivo and in vitro results as well as examining ways to distinguish genotoxic versus nongenotoxic MOA of a chemical (Furihata and Suzuki 2023). A review of the databases where CCl4 was employed has not revealed major new differences in gene expression findings from those described above. These all support the overall MOA of cytotoxicity with consequent regenerative proliferation for CCl4-induced hepatocellular carcinogenesis. More detailed analyses of the extensive databases that are available are beyond the scope of this review.
Pulsed electric field promotes the growth metabolism of aerobic denitrifying bacteria Pseudomonas putida W207-14 by improving cell membrane permeability
Published in Environmental Technology, 2023
Fan Wang, Liang Li, Xuejie Li, Xiaomin Hu, Bo Zhang
In this study, the stimulation mechanism of PEF on aerobic denitrifying bacteria Pseudomonas putida W207-14 was explored from the macro and micro levels, respectively. PEF can significantly promote the growth metabolism of strain W207-14, which is mainly attributed to the improvement of membrane permeability induced by PEF. Flow cytometry analysis confirmed that most of the cells with membrane damage still had high physiological activity, which obviously provided evidence for the formation of reversible electroporation on the cell membrane. Transcriptomic analysis indicated that PEF activated the highly significant differential expression of membrane porin and cytochrome oxidoreductase related genes on the cell membrane, which promoted the transport of nutrients through the cell membrane and electron transfer during aerobic respiration. The metabolic mechanism of aerobic denitrifying bacteria Pseudomonas putida W207-14 treated with PEF needs to be further explored by the metabolic pathway analysis of transcriptomic.