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Topic Review
Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum)
Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5′-phosphosulfate-binding (5′ PSB) regions and a 3′-phosphate-binding (3′ PB) motif that are essential for sulfotransferase activities. The protein–protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants’ growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops.
  • 1.2K
  • 13 Dec 2021
Topic Review
Extended Myc Network
Among the first discovered and most prominent cellular oncogenes is MYC, which encodes a bHLH-ZIP transcription factor (Myc) that both activates and suppresses numerous genes involved in proliferation, energy production, metabolism and translation. Myc belongs to a small group of bHLH-ZIP transcriptional regulators (the Myc Network) that includes its obligate heterodimerization partner Max and six “Mxd proteins” (Mxd1–4, Mnt and Mga), each of which heterodimerizes with Max and largely opposes Myc’s functions.
  • 1.2K
  • 13 Apr 2022
Topic Review
Liquid Biopsies on Breast Cancer
Breast cancer is the most common cancer among women worldwide. In the clinic today, imaging techniques like mammography and tissue biopsies are used to diagnose breast cancer. Even though these methods are important in primary diagnosis, they have limitations when it comes to longitudinal monitoring of residual disease after treatment, disease progression, therapy responses, and disease recurrence. Circulating cancer-derived material, including circulating cancer cells (CTCs), circulating DNA (ctDNA), and biomolecules encapsulated in extracellular vesicles,  acquired through liquid biopsies are currently focus of research as diagnostic, prognostic, and predictive biomarkers in breast cancer.
  • 1.2K
  • 08 Jan 2021
Topic Review
EVs as Potential-Biomarkers in MS
       Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system and its pathophysiology is characterized by a progressive blood-brain barrier dysfunction accompanied by infiltration in the central nervous system of peripheral pathogenic immune cells and inflammatory mediators leading to demyelination, axonal damage, and dysfunction and/or loss of synapses. Accumulating evidence highlights blood and cerebrospinal fluid (CSF) derived extracellular vesicles (EVs) as potential biomarkers of MS disease stages and of response to treatment. In particular, EVs released from blood–brain barrier (BBB) endothelial cells, platelets, leukocytes, myeloid cells, astrocytes, and oligodendrocytes seem to be involved in the pathogenesis of MS and of its rodent model experimental autoimmune encephalomyelitis. Further research is necessary to validate these observations and the screening of specific EVs subsets based on their cargo and membrane compositions associated to specific MS pathophysiological mechanisms might help guiding MS diagnosis, prognosis, and response to therapy. 
  • 1.2K
  • 28 Sep 2021
Topic Review
Small Peptides of Marine Origin
Cancer is one of the leading causes of death in the world, and antineoplastic drug research continues to be a major field in medicine development. The marine milieu has thousands of biological species that are a valuable source of novel functional proteins and peptides, which have been used in the treatment of many diseases, including cancer. In contrast with proteins and polypeptides, small peptides (with a molecular weight of less than 1000 Da) have overwhelming advantages, such as preferential and fast absorption, which can decrease the burden on human gastrointestinal function. Besides, these peptides are only connected by a few peptide bonds, and their small molecular weight makes it easy to modify and synthesize them. Specifically, small peptides can deliver nutrients and drugs to cells and tissues in the body. These characteristics make them stand out in relation to targeted drug therapy. Nowadays, the anticancer mechanisms of the small marine peptides are still largely not well understood; however, several marine peptides have been applied in preclinical treatment. 
  • 1.2K
  • 10 Mar 2021
Topic Review
Oxidative-Stress Modulators in Hematological Malignancies
Among the different mechanisms involved in oxidative stress, protein carbonylation and lipid peroxidation are both important modifications associated with the pathogenesis of several diseases, including cancer. Hematopoietic cells are particularly vulnerable to oxidative damage, as the excessive production of reactive oxygen species and associated lipid peroxidation suppress self-renewal and induce DNA damage and genomic instability, which can trigger malignancy. A richer understanding of the clinical effects of oxidative stress might improve the prognosis of these diseases and inform therapeutic strategies. The most common protein carbonylation and lipid peroxidation compounds, including hydroxynonenal, malondialdehyde, and advanced oxidation protein products, have been investigated for their potential effect on hematopoietic cells in several studies.
  • 1.2K
  • 17 Jan 2021
Topic Review
Vitamin D for COVID-19 Vaccination
Severe acute respiratory syndrome coronavirus 2 is a new, highly pathogenic virus that has recently elicited a global pandemic called the 2019 coronavirus disease (COVID-19). COVID-19 is characterized by significant immune dysfunction, which is caused by strong but unregulated innate immunity with depressed adaptive immunity. Reduced and delayed responses to interferons (IFN-I/IFN-III) can increase the synthesis of proinflammatory cytokines and extensive immune cell infiltration into the airways, leading to pulmonary disease. The development of effective treatments for severe COVID-19 patients relies on our knowledge of the pathophysiological components of this imbalanced innate immune response. Strategies to address innate response factors will be essential. Significant efforts are currently underway to develop vaccines against SARS-CoV-2. COVID-19 vaccines, such as inactivated DNA, mRNA, and protein subunit vaccines, have already been applied in clinical use. Various vaccines display different levels of effectiveness, and it is important to continue to optimize and update their composition in order to increase their effectiveness. However, due to the continuous emergence of variant viruses, improving the immunity of the general public may also increase the effectiveness of the vaccines. Many observational studies have demonstrated that serum levels of vitamin D are inversely correlated with the incidence or severity of COVID-19. Extensive evidence has shown that vitamin D supplementation could be vital in mitigating the progression of COVID-19 to reduce its severity. Vitamin D defends against SARS-CoV-2 through a complex mechanism through interactions between the modulation of innate and adaptive immune reactions, ACE2 expression, and inhibition of the renin-angiotensin system (RAS). 
  • 1.2K
  • 07 Sep 2021
Biography
Abu Saim Mohammad Saikat
Abu Saim Mohammad Saikat is an enthusiastic and innovative individual with extensive experience in scientific research, leadership, team management, event planning, and social networking. He exhibits a high level of dedication, gets fully engaged, and has a clear vision of his goals. He does not get distracted, uses his energy entirely to manifest his dreams, and fully uses his resources. He wa
  • 1.2K
  • 10 Feb 2023
Topic Review
Magnetic-Assisted Treatment of Liver Fibrosis
Chronic liver injury can be induced by viruses, toxins, cellular activation, and metabolic dysregulation and can lead to liver fibrosis. Hepatic fibrosis still remains a major burden on the global health systems. Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are considered the main cause of liver fibrosis. Hepatic stellate cells are key targets in antifibrotic treatment, but selective engagement of these cells is an unresolved issue. 
  • 1.2K
  • 25 Jan 2022
Topic Review
Mimicking the Mammalian Plasma Membrane
Cell membranes are very complex biological systems including a large variety of lipids and proteins. Therefore, they are difficult to extract and directly investigate with biophysical methods.
  • 1.2K
  • 02 Mar 2021
Topic Review
Nucleases and Co-Factors in DNA Replication Stress Responses
DNA replication stress is a constant threat that cells must manage to proliferate and maintain genome integrity. DNA replication stress responses, a subset of the broader DNA damage response (DDR), operate when the DNA replication machinery (replisome) is blocked or replication forks collapse during S phase. There are many sources of replication stress, such as DNA lesions caused by endogenous and exogenous agents including commonly used cancer therapeutics, and difficult-to-replicate DNA sequences comprising fragile sites, G-quadraplex DNA, hairpins at trinucleotide repeats, and telomeres. Replication stress is also a consequence of conflicts between opposing transcription and replication, and oncogenic stress which dysregulates replication origin firing and fork progression. Cells initially respond to replication stress by protecting blocked replisomes, but if the offending problem (e.g., DNA damage) is not bypassed or resolved in a timely manner, forks may be cleaved by nucleases, inducing a DNA double-strand break (DSB) and providing a means to accurately restart stalled forks via homologous recombination. However, DSBs pose their own risks to genome stability if left unrepaired or misrepaired.  
  • 1.2K
  • 29 Mar 2022
Topic Review
HDL-Mediated Cholesterol Trafficking in the Central Nervous System
Alzheimer’s disease (AD) is characterized by the accumulation of extracellular amyloid beta (Aβ) and abnormally hyperphosphorylated intracellular tau filaments in neurons. Cholesterol metabolism has been extensively implicated in the pathogenesis of AD through biological, epidemiological, and genetic studies, with the APOE gene being the most reproducible genetic risk factor for the development of AD. The apolipoprotein E (ApoE) 4  genotype seems to be a disruptive element in high-density lipoprotein (HDL)-like-mediated cholesterol transport through the brain. 
  • 1.2K
  • 30 Aug 2022
Topic Review
Heteroelement Analogues of Benzoxaborole
Heteroelement analogues of benzoxaboroles constitute an interesting class of boracyclic compounds and may offer the opportunity for various applications while retaining high stability arising from the presence of a strong B-O bond in the ring structure. The replacement of a carbon atom in the boracycle or an adjacent benzene ring with a heteroatom may result in a significant change of structural behaviour. Moreover,  physicochemical properties, including solubility, lipophilicity, hydrolytic stability, boron Lewis acidity, and others, can be modified. The aim of this review is to highlight several emerging groups of boracyclic systems which comprise various heteroelement atoms such as another boron, silicon, tin, nitrogen, phosphorus, and iodine. The information on synthesis and properties of such systems is complemented by presentation of their practical potential encompassing especially organic synthesis and catalysis as as medicinal chemistry. 
  • 1.2K
  • 22 Sep 2021
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
Nrf2 in Wound Healing Process
Wound healing involves a series of cellular events in damaged cells and tissues initiated with hemostasis and finally culminating with the formation of a fibrin clot. However, delay in the normal wound healing process during pathological conditions due to reactive oxygen species, inflammation and immune suppression at the wound site represents a medical challenge. So far, many therapeutic strategies have been developed to improve cellular homeostasis and chronic wounds in order to accelerate wound repair. In this context, the role of Nuclear factor erythroid 2-related factor 2 (Nrf2) during the wound healing process has been a stimulating research topic for therapeutic perspectives. Nrf2 is the main regulator of intracellular redox homeostasis. It increases cytoprotective gene expression and the antioxidant capacity of mammalian cells. It has been reported that some bioactive compounds attenuate cellular stress and thus accelerate cell proliferation, neovascularization and repair of damaged tissues by promoting Nrf2 activation.
  • 1.2K
  • 23 Jun 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
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
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
Flavivirus Genomes
The flavivirus genome consists of a single positive-stranded RNA molecule with just one open reading frame (ORF) flanked by untranslated 5′ and 3′ regions. The ORF encodes a polyprotein that is processed to produce three structural and seven non-structural viral proteins. The RNA genome is endowed with a type I cap structure at the 5′ terminus and lacks a poly A tail at its 3′ end. To store all the information required for their successful propagation, flaviviruses use discrete structural genomic RNA elements to code for functional information by the establishment of dynamic networks of long-range RNA–RNA interactions that promote specific functional folding.
  • 1.2K
  • 20 Apr 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
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