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Is the Human Embryo an Organism?
Published in Nicholas Colgrove, Bruce P. Blackshaw, Daniel Rodger, Agency, Pregnancy and Persons, 2023
Distinguishing between cyclic changes, cell-type-specific maturational changes and changes that signal the initiation of a new cell type requires observation over time, yet these three classes of alterations can be reliably segregated from each other, based on objective evidence. Using the previously noted criteria, an international consortium is currently collecting single-cell transcriptomic, epigenomic and imaging data both to determine how many human cell types exist and to distinguish between changes in cell type and cyclic changes in cell state (Regev et al. 2017).
Understanding the Proteomics of Medicinal Plants under Environmental Pollution
Published in Azamal Husen, Environmental Pollution and Medicinal Plants, 2022
Pooja Singh, V.K. Mishra, Rohit Kashyap, Rahul Rawat
The novel ‘omics’ technologies enable researchers to identify the genetics underlying medicinal plant responses to adaptation mechanisms providing impetus to investigate the complex interplay between medicinal plants, their metabolism, secondary metabolite production, and the effect of polluting environment. The genome can be defined as the complete set of genes inside a cell. Genomics is, therefore, the study of the genetic make-up of organisms. Transcriptomics is the complete set of transcripts in a cell, and their abundance, for a specific developmental stage or physiological condition (Wang et al. 2009). Proteins play an important role in biological processes by providing structural support as well as physiological functions (Figure 12.1). The complete set of proteins in a cell refers to as proteome (Park 2004). Metabolomics is the latest technique, is defined as the quantitative complement of low-molecular-weight metabolites present in a cell under a given set of physiological conditions (Kell et al. 2005). In view of these, the changes at the cellular or subcellular level due to impacting influence of environmental stimulus can be more precisely understood through omics technologies (Figure 12.2).
Biochemical Markers in Ophthalmology
Published in Ching-Yu Cheng, Tien Yin Wong, Ophthalmic Epidemiology, 2022
Abdus Samad Ansari, Pirro G. Hysi
Epigenetic and specifically DNA methylation are among the mechanisms that control mRNA production and the transcriptional profile of each cell. Transcriptomics is the field of science that aims at studies and characterizes transcription in healthy physiological states as well as in relation to human disease.
Morroniside ameliorates glucocorticoid-induced osteoporosis and promotes osteoblastogenesis by interacting with sodium-glucose cotransporter 2
Published in Pharmaceutical Biology, 2023
Hou-Zhi Yang, Runbei Dong, Yutao Jia, Yuqiao Li, Gan Luo, Tianhao Li, Yao Long, Shuang Liang, Shanshan Li, Xin Jin, Tianwei Sun
We acknowledge that the biological effects of MOR on the transcriptional level are not completely clear at present. Therefore, in a future study, we intend to investigate the transcriptomic changes following MOR treatment using the high-throughput gene expression profiling technique. In addition, zebrafish is a well-established animal model for in vivo screening drugs that promote bone development (Busse et al. 2020). It shares many similarities but distinct differences in their anatomy, phylogenetic information and physiological properties compared to humans. Another limitation in our study is the lack of confirming the effects of MOR in the bone marrow-derived mesenchymal stem cells (MSCs). Therefore, our study cannot completely rule out the possibility of differences between osteoblastic precursors and osteoblast cells regarding the responses to MOR. Although the MC3T3-E1 cell line is one of the most common osteoblast-like cell lines for studying osteoblast proliferation and differentiation, further studies using MSCs and murine models are required to validate the present results and to develop MOR into a potential therapeutic agent for glucocorticoid induced-OP. Moreover, limited by our cell line and zebrafish model, we did not study MOR’s effect on glucose metabolism in osteoblasts and bone tissue, nor did we measure the changes in intracellular glucose concentration. Therefore, the specific mechanism of the effect of MOR on glucose production in osteoblasts needs to be studied in the near future.
Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside
Published in Expert Review of Proteomics, 2021
Lauren C Beck, Claire L Granger, Andrea C Masi, Christopher J Stewart
Given the importance of identifying underlying mechanisms and biomarkers for many GI pediatric diseases, gene expression studies represent yet another crucial field. Transcriptomics is the comprehensive study of all RNA transcripts transcribed by the genome, usually in a specific cell, at a given developmental stage, or under a specific set of conditions [40]. This includes both coding and non-coding RNA transcripts. Transcriptome profiling studies, therefore, are a very powerful way of dissecting specific transcriptional signatures of disease by allowing the identification of differentially expressed genes between healthy and diseased patients. The transcriptome of a patient can be captured using similar methods to those used for screening genetic content, for example, by RNA-microarrays or RNA-sequencing [41]. RNA-sequencing offers a more comprehensive analysis of the transcriptome than microarray experiments and does not require a priori knowledge [41].
Approaching complexity: systems biology and ms-based techniques to address immune signaling
Published in Expert Review of Proteomics, 2020
Joseph Gillen, Caleb Bridgwater, Aleksandra Nita-Lazar
Transcriptomics as a field covers a wide range of techniques all meant to investigate the RNA transcripts in a cell. Methods like microarrays and RNAseq can provide insight into the set of RNA molecules transcribed and present in a single cell or across biological sample. This provides hints into the genome expression in different types of cells. Microarrays function by the matching of an array of predefined complementary probes to transcripts to quantify their abundance. Using sample probes from the target organism, a transcriptional profile can be made by arraying RNA probes together. RNAseq works by creating a cDNA library, from the RNA sample, then addition of sequence adaptors followed by high throughput sequencing of the sample [3]. These techniques are effective, quick, and inform the mechanics of drug treatments or disease states on the genome. Major drawbacks of transcriptomic approaches are the loose association between mRNA levels and actual protein expression, as well as the lack of information on proteoforms or other regulatory mechanisms not encoded in the transcriptome. Microarrays and RNAseq are attractive to researchers due to their relatively low cost and high throughput abilities and many labs will successfully continue to incorporate transcriptomics into their research [4].