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Seminars in Radiation Oncology Apr 2022Ionizing radiation is used to create models of accelerated aging because the processes of aging and radiation injury share common elements. In this chapter we review the... (Review)
Review
Ionizing radiation is used to create models of accelerated aging because the processes of aging and radiation injury share common elements. In this chapter we review the biological processes of aging and the similarities and impact of ionizing radiation on those processes. The information draws on data from laboratory studies and from epidemiology studies of radiation exposure victims. The chapter reviews the effects of radiation on DNA, cells, and organs systems on aged adults. The science of aging and the effect of radiation on the aging process are areas of active research and our understanding is evolving.
Topics: Adult; Aging; Biological Phenomena; Humans; Middle Aged; Radiation Exposure; Radiation Injuries; Radiation, Ionizing
PubMed: 35307120
DOI: 10.1016/j.semradonc.2021.11.011 -
Cell Cycle (Georgetown, Tex.) Nov 2020Hippo pathway is a chain of kinases consists of a series of protein kinases and transcription factors. Meanwhile, oxidative stress is a condition of elevated... (Review)
Review
Hippo pathway is a chain of kinases consists of a series of protein kinases and transcription factors. Meanwhile, oxidative stress is a condition of elevated concentrations of reactive oxygen species (ROS) that cause molecular damage to vital structures and functions. Both of them are key regulators in cell proliferation, survival, and development. These processes are strictly regulated by highly coordinated mechanisms, including c-Jun n-terminal kinase (JNK) pathway, mTOR pathway and a number of extrinsic and intrinsic factors. Recently, emerging evidence suggests that Hippo pathway is involved in the responses to cellular stresses, including mechanic stress, DNA damage, and oxidative stress, to mediate biological process, such as apoptosis, pyroptosis, and metastasis. But the exact mechanism remains to be further explored. Therefore, the purpose of this review is to summarize recent findings and discuss how Hippo pathway, oxidative stress, and the crosstalk between them regulate some biological process which determines cell fate.
Topics: Animals; Biological Phenomena; Cell Differentiation; Cell Proliferation; Hippo Signaling Pathway; Humans; Oxidation-Reduction; Oxidative Stress; Signal Transduction
PubMed: 33016196
DOI: 10.1080/15384101.2020.1824448 -
International Journal of Molecular... Oct 2022The yeast has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular... (Review)
Review
The yeast has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular toolbox, and its strong conservation of basic eukaryotic biology also make it a prime model for eukaryotic cell biology and genetics. In this review, we discuss the characteristics that made yeast such an extensively used model organism and specifically focus on the DNA damage response pathway as a prime example of how research in helped elucidate a highly conserved biological process. In addition, we also highlight differences in the DNA damage response of and humans and discuss the challenges of using as a model system.
Topics: Biological Phenomena; Biology; Cell Cycle Checkpoints; DNA Damage; Eukaryotic Cells; Humans; Saccharomyces cerevisiae
PubMed: 36232965
DOI: 10.3390/ijms231911665 -
Bioresource Technology Sep 2020This review presents an emerging biorefinery platform for C bioalcohol production through chemical synthesis using the organic waste materials. Bioalcohols are the most... (Review)
Review
This review presents an emerging biorefinery platform for C bioalcohol production through chemical synthesis using the organic waste materials. Bioalcohols are the most commercialized carbon-neutral transportation fuels, compatible with existing an internal combustion (IC) engine. However, current bioalcohol fermentation processes have made from sugar-rich edible crops. Also, carbon loss from the fermentation process is substantial. To minimize carbon loss, volatile fatty acids (VFAs) can be utilized as a raw material for bioalcohol production. Thus, a two-step chemical upgrading of VFAs into C alcohols is summarized in comparison with current challenges of biological fermentation processes for bioalcohol production. This review also provides the prospect of the hybrid biological/chemical process, presenting the technical advantages of the system. Finally, economic viability of hybridized process for bioalcohol production is compared with the current biological process.
Topics: Biological Phenomena; Bioreactors; Carbohydrates; Fatty Acids, Volatile; Fermentation; Sewage; Waste Products
PubMed: 32467028
DOI: 10.1016/j.biortech.2020.123568 -
Liver International : Official Journal... Jan 2021Mature transfer RNAs (tRNA) charged with amino acids decode mRNA to synthesize proteins. Dysregulation of translational machineries has a fundamental impact on cancer...
BACKGROUND & AIMS
Mature transfer RNAs (tRNA) charged with amino acids decode mRNA to synthesize proteins. Dysregulation of translational machineries has a fundamental impact on cancer biology. This study aims to map the tRNAome landscape in liver cancer patients and to explore potential therapeutic targets at the interface of charging amino acid with tRNA.
METHODS
Resected tumour and paired tumour-free (TFL) tissues from hepatocellular carcinoma (HCC) patients (n = 69), and healthy liver tissues from organ transplant donors (n = 21), HCC cell lines, and cholangiocarcinoma (CC) patient-derived tumour organoids were used.
RESULTS
The expression levels of different mature tRNAs were highly correlated and closely clustered within individual tissues, suggesting that different members of the tRNAome function cooperatively in protein translation. Interestingly, high expression of tRNA-Lys-CUU in HCC tumours was associated with more tumour recurrence (HR 1.1; P = .022) and worse patient survival (HR 1.1; P = .0037). The expression of Lysyl-tRNA Synthetase (KARS), the enzyme catalysing the charge of lysine to tRNA-Lys-CUU, was significantly upregulated in HCC tumour tissues compared to tumour-free liver tissues. In HCC cell lines, lysine deprivation, KARS knockdown or treatment with the KARS inhibitor cladosporin effectively inhibited overall cell growth, single cell-based colony formation and cell migration. This was mechanistically mediated by cell cycling arrest and induction of apoptosis. Finally, these inhibitory effects were confirmed in 3D cultured patient-derived CC organoids.
CONCLUSIONS
The biological process of charging tRNA-Lys-CUU with lysine sustains liver cancer cell growth and migration, and is clinically relevant in HCC patients. This process can be therapeutically targeted and represents an unexplored territory for developing novel treatment strategies against liver cancer.
Topics: Biological Phenomena; Carcinoma, Hepatocellular; Humans; Liver Neoplasms; Lysine; Neoplasm Recurrence, Local; Transfer RNA Aminoacylation
PubMed: 33084231
DOI: 10.1111/liv.14692 -
Environmental Science and Pollution... Aug 2021
Topics: Biological Phenomena; Conservation of Natural Resources; Environmental Pollution
PubMed: 33712962
DOI: 10.1007/s11356-021-13372-0 -
PloS One 2009The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic...
BACKGROUND
The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known about interactions between higher order biological systems, such as biological pathways and processes. We propose a methodology for gleaning patterns of interactions between biological processes by analyzing protein-protein interactions, transcriptional co-expression and genetic interactions. At the heart of the methodology are the concept of Linked Processes and the resultant network of biological processes, the Process Linkage Network (PLN).
RESULTS
We construct, catalogue, and analyze different types of PLNs derived from different data sources and different species. When applied to the Gene Ontology, many of the resulting links connect processes that are distant from each other in the hierarchy, even though the connection makes eminent sense biologically. Some others, however, carry an element of surprise and may reflect mechanisms that are unique to the organism under investigation. In this aspect our method complements the link structure between processes inherent in the Gene Ontology, which by its very nature is species-independent. As a practical application of the linkage of processes we demonstrate that it can be effectively used in protein function prediction, having the power to increase both the coverage and the accuracy of predictions, when carefully integrated into prediction methods.
CONCLUSIONS
Our approach constitutes a promising new direction towards understanding the higher levels of organization of the cell as a system which should help current efforts to re-engineer ontologies and improve our ability to predict which proteins are involved in specific biological processes.
Topics: Algorithms; Biological Phenomena; Computational Biology; Databases, Protein; Gene Regulatory Networks; Protein Interaction Mapping; Proteins; Saccharomyces cerevisiae
PubMed: 19390589
DOI: 10.1371/journal.pone.0005313 -
Reproductive Sciences (Thousand Oaks,... Oct 2023Polycystic ovary syndrome (PCOS) is a common gynecological endocrine disordered disease, affecting the function of the ovaries in women of reproductive age. However,...
Polycystic ovary syndrome (PCOS) is a common gynecological endocrine disordered disease, affecting the function of the ovaries in women of reproductive age. However, there are limited curative therapies for PCOS due to lack of reliable candidates. Hence, this study aimed to identify hub pathogenic genes and potential therapeutic targets for PCOS using bioinformatics tools. We obtained the expression profiles of 29 PCOS samples and 24 normal samples from three Gene Expression Omnibus (GEO) datasets. Then, the differentially expressed genes (DEGs) were screened, which were subjected to functional enrichment analyses. Moreover, we found 30 ferroptosis-related genes out of the 89 DEGs. Among the top 10 significant ferroptosis-related DEGs, 8 genes showed good predictive performance. We constructed interaction network of top three ferroptosis-related DEGs (SLC38A1, ACO1, DDIT3). Finally, real-time PCR was performed to test the relative expression of these genes. In conclusions, we have identified ferroptosis-related DEGs as core genes and potential therapeutic targets of PCOS based on comprehensive bioinformatics analysis. The findings are conducive to understanding of the pathogenesis of PCOS and paving the way towards curative therapies.
Topics: Humans; Female; Polycystic Ovary Syndrome; Gene Regulatory Networks; Gene Expression Profiling; Computational Biology; Biological Phenomena
PubMed: 37171773
DOI: 10.1007/s43032-023-01259-z -
Mechanisms of Ageing and Development Sep 2022Ageing is a complex biological phenomenon representing the major risk factor for developing age-related diseases, such as cardiovascular pathologies, neurodegenerative...
Ageing is a complex biological phenomenon representing the major risk factor for developing age-related diseases, such as cardiovascular pathologies, neurodegenerative diseases, and cancer. Geroscience, the new vision of gerontology, identifies cellular senescence as an interconnected biological process that characterises ageing and age-related diseases. Therefore, many strategies have been employed in the last years to reduce the harmful effects of senescence, and among these, the most intriguing ones use nutraceutical compounds. Here we show that a pre-treatment with Quercetin, a bioactive flavonoid present in many fruits and vegetables, increasing cellular antioxidant defence, can alleviate Doxorubicin (Doxo)-induced cellular senescence in human normal WI-38 fibroblasts. Furthermore, our work demonstrates that Quercetin pre-treatment, reducing the number of senescent cells and the production of the senescence-associated secretory phenotype (SASP) factors, can decrease the pro-tumour effects of conditioned medium from Doxo-induced senescent fibroblasts on osteosarcoma cells. Overall, our findings are consistent with the hypothesis that targeting senescent cells can be an emerging strategy for cancer treatment, especially in elderly patients, in which senescent cells are already abundant in several tissues and organs.
Topics: Aged; Biological Phenomena; Cellular Senescence; Doxorubicin; Fibroblasts; Humans; Neoplasms; Quercetin
PubMed: 35728630
DOI: 10.1016/j.mad.2022.111689 -
Water Research Feb 2021Phenolic compounds are common ccontaminants in industrial effluents. In this study, a combined catalytic microbubble ozonation and biological process was developed and...
FeO@GAC catalyzed microbubble ozonation coupled with biological process for industrial phenolic wastewater treatment: Catalytic performance, biological process screening and microbial characteristics.
Phenolic compounds are common ccontaminants in industrial effluents. In this study, a combined catalytic microbubble ozonation and biological process was developed and applied for efficient industrial phenolic wastewater (PWW) treatment. Catalytic activity of an iron-oxides (FeO) doped granular activated carbon (GAC) catalyst (FeO@GAC) in microbubble ozonation for PWW treatment was investigated. The results demonstrated that the FeO@GAC catalyzed microbubble ozonation (O/FeO@GAC) obtained significantly higher reaction rate constant (k = 0.023 min) in TOC removal compared to the bare GAC catalyzed microbubble ozonation (O/GAC, k = 0.013 min) and ordinary microbubble ozonation (k = 0.008 min). Destruction rate constant of phenolic compounds (k) was improved from 0.014 min (ordinary microbubble ozonation) to 0.025 min (O/FeO@GAC). The 60-min pretreatment of PWW by O/FeO@GAC process enhanced BOD/COD ratio from 0.31 to 0.76 and reduced the acute bio-toxicity by 79.2%. Screening and characterization of biological post-treatment processes were conducted among activated sludge process (ASP), up-flow anaerobic sludge blanket (UASB) and membrane bioreactor (MBR). UASB and ASP showed limited phenolic compounds removal of 35.4% and 57.0% with lower bio-toxicity resistance than MBR (94.9% phenolic compounds removal). The combined process O/FeO@GAC-MBR was thus developed and achieved high COD removal (98.0%) and phenolic compounds degradation (99.4%). PWW pretreatment by O/FeO@GAC process decreased membrane fouling rate of MBR by 88.2% by reducing proteins/polysaccharides accumulation in both extracellular polymeric substances and soluble microbial products. 16S rRNA high-throughput sequencing revealed the predominance of phylum Proteobacteria, class Alphaproteobacteria and genera Mycobacterium, Gordonia, Pedomicrobium & Defluviimonas in biological PWW treatment bio-systems. Pearson correlation coefficient and ANOVA analysis verified that Mycobacterium possessed high bio-toxicity resistance and was the main contributor to the biodegradation of phenolic compounds.
Topics: Biological Phenomena; Bioreactors; Catalysis; Charcoal; Microbubbles; Ozone; RNA, Ribosomal, 16S; Wastewater; Water Pollutants, Chemical
PubMed: 33279753
DOI: 10.1016/j.watres.2020.116687