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Topic Review
Effect of G-Quadruplexes on DNA Mismatch Repair Pathway
DNA G-quadruplexes (G4s) are known to be an integral part of the complex regulatory systems in both normal and pathological cells. Here we studied the effect of G4s on the DNA mismatch repair pathway. To assess the role of the distance between G4 and DNA mismatch on the functioning of the key mismatch repair protein, MutS, from E. coli on G4-containing substrates, a set of DNA duplexes with an embedded intramolecular parallel G4 structure and a monomethylated recognition site for the MutH endonuclease was prepared; the distance between the mismatched G/T pair and the G4 structure varied from 18 to 3 bp. It has been shown that this non-B form structure is not perceived by the E. coli system as damage that needs to be repaired; at the same time, it does not prevent activation of DNA mismatch repair, even when the G4 structure and G/T pair are at the distance of 3 bp. Thus, the preferential binding of MutS to G4 does not correlate with DNA mismatch repair activity, suggesting an unexpected role of these DNA-protein interactions in genome maintenance.
  • 1.2K
  • 09 Oct 2021
Topic Review
Didymo
Didymosphenia geminata diatoms, or Didymo, was first found to be an invasive species that could have negative impacts on the environment due to the aggressive growth of its polysaccharide-based stalks.
  • 1.2K
  • 08 Nov 2021
Topic Review
Gene annotation for 'Flaviviridae' genomes
Responding to the ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and Zika, demands a greater understanding of how these viruses emerge and spread. Updated phylogenies are central to this understanding. Most cladograms of Flaviviridae focus on specific lineages and ignore outgroups, thus hampering the efficacy of the analysis to test ingroup monophyly and relationships. This is due to the lack of annotated Flaviviridae genomes, which has gene content variation among genera. This variation makes analysis without partitioning difficult. Therefore, we developed an annotation pipeline for the genera of Flaviviridae (Flavirirus, Hepacivirus, Pegivirus, and Pestivirus), named “Fast Loci Annotation of Viruses” (FLAVi: flavi-web.com), that combines ab initio and homology-based strategies. FLAVi recovered 100% of the genes in Flavivirus and Hepacivirus genomes. In Pegivirus and Pestivirus, annotation efficiency was 100% except for one partition each. There were no false positives. The combined phylogenetic analysis of multiple genes made possible by annotation has clear impacts over the tree topology compared to phylogenies that we inferred without outgroups or data partitioning. The final tree is largely congruent with previous hypotheses and adds evidence supporting the close phylogenetic relationship between dengue and Zika.
  • 1.2K
  • 27 Oct 2020
Topic Review
Histone Lysine Methylation
The level and state of histone lysine methylation depends not only on the activity of histone methyltransferases (KMTs) but also on the counteracting activity of histone lysine demethylases (KDMs). The variety of methylation sites and differentially methylated states describes the level of complexity of signaling mediated by histone lysine methylation, which is involved in transcription regulation, gene silencing, genome stability and RNA processing.
  • 1.2K
  • 10 Feb 2021
Topic Review
The Zinc-Sensing Receptor GPR39
GPR39, also known as ZnR (zinc sensing receptor), is a member of a large family A of 7-transmembrane (7-TM) containing G protein-coupled receptors (GPCRs).
  • 1.2K
  • 05 May 2021
Topic Review
Role of Coenzyme Q
Coenzyme Q is a unique lipidic molecule highly conserved in evolution and essential to maintaining aerobic metabolism. It is endogenously synthesized in all cells by a very complex pathway involving a group of nuclear genes that share high homology among species. This pathway is tightly regulated at transcription and translation, but also by environment and energy requirements. Dysfunction in CoQ synthesis produces mitochondrial diseases that can partially reverted by CoQ supplementation. The main function of CoQ10 in human metabolism and antioxidant protection of membranes against oxidation and ferroptosis makes CoQ10 as an essential factor in many metabolic, chronic diseases and also in aging.
  • 1.2K
  • 29 Mar 2022
Topic Review
A Paraoxonase for All Seasons
Paraoxonases (PON) are a multigene family consisting of three enzymes, PON1, PON2, and PON3, located on human chromosome 7 (7q21.3–22.1). All three PONs have been shown to act as antioxidants and consequently have anti-inflammatory effects in various disease states such as atherosclerosis and cardiovascular diseases.
  • 1.2K
  • 12 Apr 2022
Topic Review
Green Tea Catechins in Fatty Liver Disease
Epigallocatechin-3-gallate (EGCG) is a polyphenol green tea catechin with potential health benefits and therapeutic effects in non-alcoholic fatty liver disease (NAFLD), a common liver disorder that adversely affects liver function and lipid metabolism. 
  • 1.2K
  • 14 Apr 2022
Topic Review
Tumor-Associated Macrophages (TAMs)
Tumor-associated macrophages (TAMs) are a major component of the immune cells of the TME. They play a prominent role by secreting cytokines and chemokines and coordinating with inflammatory mechanisms to promote tumor development, invasion, metastasis, immunosuppression, angiogenesis, and drug tolerance. Different subtypes of TAMs have different functions, which can be dynamically changed in response to various signals from cancer cells or the TME.
  • 1.2K
  • 18 Aug 2021
Topic Review
Epigenetics of Atrial Fibrillation
Atrial fibrillation (AF) is known to be the most common supraventricular arrhythmia affecting up to 1% of the general population. Its prevalence exponentially increases with age and could reach up to 8% in the elderly population. The management of AF is a complex issue that is addressed by extensive ongoing basic and clinical research. AF centers around different types of disturbances, including ion channel dysfunction, Ca2+-handling abnormalities, and structural remodeling. 
  • 1.2K
  • 15 Nov 2022
Topic Review
Non-Coding RNAs in Nervous System
Oxidative stress (OS) is defined as an imbalance between free radicals biogenesis and the cell antioxidant capacity to eliminate them. In neurodegenerative diseases, OS play a central role altering mitochondrial metabolism, protein synthesis, and inducing cellular malfunctioning. Most part of the human genome encodes for non-coding protein genes, which are transcribed into non-coding RNA (ncRNA). Most of these ncRNAs are involved transcriptional and post-transcriptional regulation of gene and their deregulation has been linked to diverse neurodegenerative disorders. In this review we compiled most recent evidences reporting a role of main types of ncRNAs in the regulation and management of oxidative stress in Alzheimer's disease, Parkinson's disease, Huntington's disease and Amyotrophic Lateral Sclerosis. 
  • 1.2K
  • 19 Nov 2020
Topic Review
Amyloidogenic Regions in bPaS1
Bacterial S1 protein is a functionally important ribosomal protein. It is a part of the 30S ribosomal subunit and is also able to interact with mRNA and tmRNA. An important feature of the S1 protein family is a strong tendency towards aggregation. 
  • 1.2K
  • 20 Jul 2021
Topic Review
Resveratrol in Human Male Fertility
Resveratrol (RSV) (3,4′,5 trihydroxystilbene) is a natural, non-flavonoid polyphenol widely present in the Mediterranean diet and, particularly, in grapes, peanuts, berries, and red wine.
  • 1.2K
  • 13 May 2021
Topic Review
EVs, Substance Abuse, and HIV
While extracellular vesicles (EVs) have been shown to play a role in CNS disorders, the intersection of EVs, drug use, and HIV is of particular interest. The interactions of HIV and drugs of abuse are a growing concern given the increasing incidence of HIV transmission via shared needles in illicit drug use. As a drug commonly taken through shared needles, METH is being investigated due to its role in exacerbating HIV-mediated inflammation through both increased vesicular shedding and extracellular release. In vivo experiments have shown that cocaine-induced EV release impacts synaptic plasticity through noncoding RNA. Nicotine studies have also highlighted how the differential packaging of antioxidant enzyme cargoes into EVs affects nicotine-mediated HIV pathogenesis. Additionally, studies of both morphine and heroin have demonstrated differences in the miRNA cargoes of EVs, potentially impacting gene expression and exacerbating HIV. Studies of alcohol use in combination with HIV have shown that EV cargoes such as cytokines are affected in HIV-infected subjects who use alcohol. Investigating EV cargo alterations in all forms of substance abuse studies may allow the EV, HIV, and addiction fields to progress towards diagnosis and remedies for substance-abuse-induced toxicity in HIV patients.
  • 1.2K
  • 27 Sep 2020
Topic Review
Lysosomal Calcium Channels
Ca2+ is pivotal intracellular messenger that coordinates multiple cell functions such as fertilization, growth, differentiation, and viability. Intracellular Ca2+ signaling is regulated by both extracellular Ca2+ entry and Ca2+ release from intracellular stores. Apart from working as the cellular recycling center, the lysosome has been increasingly recognized as a significant intracellular Ca2+ store that provides Ca2+ to regulate many cellular processes. The lysosome also talks to other organelles by releasing and taking up Ca2+. In lysosomal Ca2+-dependent processes, autophagy is particularly important, because it has been implicated in many human diseases including cancer.
  • 1.2K
  • 27 Apr 2021
Topic Review
Hypoxia-Inducible Factors and the Regulation of Lipid Metabolism
Oxygen deprivation or hypoxia characterizes a number of serious pathological conditions and elicits a number of adaptive changes that are mainly mediated at the transcriptional level by the family of hypoxia-inducible factors (HIFs). The HIF target gene repertoire includes genes responsible for the regulation of metabolism, oxygen delivery and cell survival. Although the involvement of HIFs in the regulation of carbohydrate metabolism and the switch to anaerobic glycolysis under hypoxia is well established, their role in the control of lipid anabolism and catabolism remains still relatively obscure. Recent evidence indicates that many aspects of lipid metabolism are modified during hypoxia or in tumor cells in a HIF-dependent manner, contributing significantly to the pathogenesis and/or progression of cancer and metabolic disorders. 
  • 1.2K
  • 23 May 2022
Topic Review
Rab Proteins in Mitophagy
Mitochondrial dysfunction and vesicular trafficking alterations have been implicated in the pathogenesis of several neurodegenerative diseases. It has become clear that pathogenetic pathways leading to neurodegeneration are often interconnected. Indeed, growing evidence suggests a concerted contribution of impaired mitophagy and vesicles formation in the dysregulation of neuronal homeostasis, contributing to neuronal cell death. Among the molecular factors involved in the trafficking of vesicles, Ras analog in brain (Rab) proteins seem to play a central role in mitochondrial quality checking and disposal through both canonical PINK1/Parkin-mediated mitophagy and novel alternative pathways. In turn, the lack of proper elimination of dysfunctional mitochondria has emerged as a possible causative/early event in some neurodegenerative diseases.
  • 1.2K
  • 14 Apr 2023
Topic Review
Cancer Chemoprevention
Carcinogenesis is a multistep process characterized by a progression of molecular changes that ultimately transform a cell to undergo uncontrolled proliferation.
  • 1.2K
  • 02 Apr 2021
Topic Review
Formaldehyde Measurement in Biological Samples
Formaldehyde (FA) is the simplest aldehyde present both in the environment and in living organisms. FA is an extremely reactive compound capable of protein crosslinking and DNA damage. However, FA is a product of normal cellular metabolism, and it plays an important role in many biochemical processes. Different methods initially used for non-biological objects have been adapted for biological samples. In addition, numerous approaches, including chemically-synthesized probes and genetically encoded FA-sensors for in cellulo and in vivo FA monitoring, were developed. 
  • 1.2K
  • 05 Jul 2022
Topic Review
E3s That Target Wild-Type p53
p53 plays a role in different biological processes such as proliferation, invasion, pluripotency, metabolism, cell cycle control, ROS (reactive oxygen species) production, apoptosis, inflammation and autophagy. In the nucleus, p53 functions as a bona-fide transcription factor which activates and represses transcription of a number of target genes. In the cytoplasm, p53 can interact with proteins of the apoptotic machinery and by this also induces cell death. Despite being so important for the fate of the cell, expression levels of p53 are kept low in unstressed cells and the protein is largely inactive. 
  • 1.2K
  • 27 Feb 2023
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