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1.
Microorganisms ; 12(4)2024 Mar 29.
Article in English | MEDLINE | ID: mdl-38674640

ABSTRACT

Neboviruses (NeVs) from the Caliciviridae family have been linked to enteric diseases in bovines and have been detected worldwide. As viruses rely entirely on the cellular machinery of the host for replication, their ability to thrive in a specific host is greatly impacted by the specific codon usage preferences. Here, we systematically analyzed the codon usage bias in NeVs to explore the genetic and evolutionary patterns. Relative Synonymous Codon Usage and Effective Number of Codon analyses indicated a marginally lower codon usage bias in NeVs, predominantly influenced by the nucleotide compositional constraints. Nonetheless, NeVs showed a higher codon usage bias for codons containing G/C at the third codon position. The neutrality plot analysis revealed natural selection as the primary factor that shaped the codon usage bias in both the VP1 (82%) and VP2 (57%) genes of NeVs. Furthermore, the NeVs showed a highly comparable codon usage pattern to bovines, as reflected through Codon Adaptation Index and Relative Codon Deoptimization Index analyses. Notably, yak NeVs showed considerably different nucleotide compositional constraints and mutational pressure compared to bovine NeVs, which appear to be predominantly host-driven. This study sheds light on the genetic mechanism driving NeVs' adaptability, evolution, and fitness to their host species.

2.
Arch Virol ; 169(5): 102, 2024 Apr 17.
Article in English | MEDLINE | ID: mdl-38630315

ABSTRACT

A highly divergent bovine calicivirus was identified in an Indian calf with enteritis. The whole genome of this virus was sequenced, revealing distinct amino acid motifs in the polyprotein encoded by open reading frame 1 (ORF1) that are unique to caliciviruses. Phylogenetic analysis showed that it was related to members of the genus Nebovirus of the family Caliciviridae. Although it showed only 33.7-34.2% sequence identity in the VP1 protein to the nebovirus prototype strains, it showed 90.6% identity in VP1 to Kirklareli virus, a nebovirus detected in calves with enteritis in Turkey in 2012. An in-house-designed and optimized reverse transcription polymerase chain reaction (RT-PCR) assay was used to screen 120 archived bovine diarrhoeic fecal samples, 40 each from the Indian states of Uttar Pradesh, Haryana, and Himachal Pradesh, revealing frequent circulation of these divergent caliciviruses in the bovine population, with an overall positivity rate of 64.17% (77/120). This underscores the importance of conducting a comprehensive investigation of the prevalence of these divergent caliciviruses and assessing their associations with other pathogens responsible for enteritis in India.


Subject(s)
Caliciviridae , Enteritis , RNA Viruses , Cattle , Animals , Phylogeny , Caliciviridae/genetics , India/epidemiology
3.
Curr Diabetes Rev ; 2024 Mar 18.
Article in English | MEDLINE | ID: mdl-38500279

ABSTRACT

BACKGROUND: Diabetes mellitus remains a global health challenge, demanding innovative therapeutic strategies. Herbal remedies have garnered attention for their potential in diabetes management, and recent advancements in nanotechnology have enabled the development of herbal nanoformulations with enhanced efficacy and bioavailability. OBJECTIVE: This review aimed to comprehensively analyze the mechanisms, formulations, and clinical impact of herbal nanoformulations in managing diabetes mellitus. METHOD: A systematic literature search was conducted to identify relevant studies exploring the mechanisms of action, various formulations, and clinical outcomes of herbal nanoformulations in diabetes management. RESULT: Herbal nanoformulations exert their anti-diabetic effects through multiple mechanisms, including enhanced bioavailability, improved tissue targeting, and potentiation of insulin signaling pathways. Various herbal ingredients, such as bitter melon, fenugreek, and Gymnema sylvestre, have been encapsulated into nanocarriers, like liposomes, polymeric nanoparticles, and solid lipid nanoparticles, to enhance their therapeutic potential. Clinical studies have demonstrated promising results, showing improvements in glycemic control, lipid profile, and antioxidant status with minimal adverse effects. CONCLUSION: Herbal nanoformulations represent a promising avenue for the management of diabetes mellitus, offering improved therapeutic outcomes compared to conventional herbal preparations. Further research is warranted to optimize formulation strategies, elucidate long-term safety profiles, and explore the potential synergistic effects of herbal nanoformulations in combination therapies for diabetes management.

4.
Article in English | MEDLINE | ID: mdl-38551059

ABSTRACT

The article has been withdrawn at the request of the authors of the journal "Central Nervous System Agents in Medicinal Chemistry" as a conflict has arisen among the authors in adding another author at the later stage of publicationBentham Science apologizes to the readers of the journal for any inconvenience this may have caused.The Bentham Editorial Policy on Article Withdrawal can be found at https://benthamscience.com/editorial-policies-main.php BENTHAM SCIENCE DISCLAIMER: It is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere. Furthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained. Plagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered. By submitting a manuscript the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.

5.
Matrix Biol ; 128: 39-64, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38387749

ABSTRACT

Collagen type XVIII (COL18) is an abundant heparan sulfate proteoglycan in vascular basement membranes. Here, we asked (i) if the loss of COL18 would result in blood-brain barrier (BBB) breakdown, pathological alterations of small arteries and capillaries and neuroinflammation as found in cerebral small vessel disease (CSVD) and (ii) if such changes may be associated with remodeling of synapses and neural extracellular matrix (ECM). We found that 5-month-old Col18a1-/- mice had elevated BBB permeability for mouse IgG in the deep gray matter, and intravascular erythrocyte accumulations were observed brain-wide in capillaries and arterioles. BBB permeability increased with age and affected cortical regions and the hippocampus in 12-month-old Col18a1-/- mice. None of the Col18a1-/- mice displayed hallmarks of advanced CSVD, such as hemorrhages, and did not show perivascular space enlargement. Col18a1 deficiency-induced BBB leakage was accompanied by activation of microglia and astrocytes, a loss of aggrecan in the ECM of perineuronal nets associated with fast-spiking inhibitory interneurons and accumulation of the perisynaptic ECM proteoglycan brevican and the microglial complement protein C1q at excitatory synapses. As the pathway underlying these regulations, we found increased signaling through the TGF-ß1/Smad3/TIMP-3 cascade. We verified the pivotal role of COL18 for small vessel wall structure in CSVD by demonstrating the protein's involvement in vascular remodeling in autopsy brains from patients with cerebral hypertensive arteriopathy. Our study highlights an association between the alterations of perivascular ECM, extracellular proteolysis, and perineuronal/perisynaptic ECM, as a possible substrate of synaptic and cognitive alterations in CSVD.


Subject(s)
Cerebral Small Vessel Diseases , Collagen Type XVIII , Neuroinflammatory Diseases , Animals , Humans , Infant , Mice , Cerebral Small Vessel Diseases/genetics , Cerebral Small Vessel Diseases/metabolism , Collagen Type XVIII/genetics , Collagen Type XVIII/metabolism , Endostatins , Extracellular Matrix/metabolism , Heparan Sulfate Proteoglycans/metabolism , Mice, Knockout
6.
J Biomol Struct Dyn ; : 1-19, 2024 Jan 04.
Article in English | MEDLINE | ID: mdl-38174578

ABSTRACT

After the emergence of the COVID-19 pandemic in late 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has undergone a dynamic evolution driven by the acquisition of genetic modifications, resulting in several variants that are further classified as variants of interest (VOIs), variants under monitoring (VUM) and variants of concern (VOC) by World Health Organization (WHO). Currently, there are five SARS-CoV-2 VOCs (Alpha, Beta, Delta, Gamma and Omicron), two VOIs (Lambda and Mu) and several other VOIs that have been reported globally. In this study, we report a natural compound, Curcumin, as the potential inhibitor to the interactions between receptor binding domain (RBD(S1)) and human angiotensin-converting enzyme 2 (hACE2) domains and showcased its inhibitory potential for the Delta and Omicron variants through a computational approach by implementing state of the art methods. The study for the first time revealed a higher efficiency of Curcumin, especially for hindering the interaction between RBD(S1) and hACE-2 domains of Delta and Omicron variants as compared to other lead compounds. We investigated that the mutations in the RBD(S1) of VOC especially Delta and Omicron variants affect its structure compared to that of the wild type and other variants and therefore altered its binding to the hACE2 receptor. Molecular docking and molecular dynamics (MD) simulation analyses substantially supported the findings in terms of the stability of the docked complexes. This study offers compelling evidence, warranting a more in-depth exploration into the impact of these alterations on the binding of identified drug molecules with the Spike protein. Further investigation into their potential therapeutic effects in vivo is highly recommended.Communicated by Ramaswamy H. Sarma.

7.
Anal Methods ; 15(40): 5268-5285, 2023 Oct 19.
Article in English | MEDLINE | ID: mdl-37800698

ABSTRACT

Fluorescent and colourimetric probes for small analytes (cations, anions and neutral molecules) have drawn significant attention in recent years. These probes interact with analytes and induce spectral change due to the variations in the photo-physical properties of the fluorophore/chromophore used. Among several photo-physical mechanisms, ESIPT (excited state intramolecular proton transfer) based probes are more advantageous due to their photo-physical properties viz. solvent polarity effect, large spectral shift with multi-channel fluorescence, high quantum yield etc. In recent years, ESIPT-based probes have shown several promising applications, especially monitoring small analytes in biological samples, smartphone app-assisted heavy metal detection in environmental samples, inkless writing, anti-counterfeiting applications etc. Therefore, this review is dedicated to recently reported ESIPT-based probes for small analytes. We have highlighted the organic units responsible for the ESIPT mechanism, their photo-physical parameters, selectivity and sensitivity properties and recent advances in their applications.

8.
Article in English | MEDLINE | ID: mdl-37608651

ABSTRACT

Epilepsy is the most general, extensive, and severe neurological disorder, affecting more than 50 million individuals globally. Initially, conventional medicines and simple salts like potassium bromide were employed as antiepileptic medication candidates. Nowadays, many anticonvulsant drugs have been discovered as first-generation and second-generation and newer drugs and are still in development phases. The pharmacophore-based drug design process includes pharmacophore modeling and validation, pharmacophore-based virtual screening, virtual hits profiling, and lead identification with special reference. This comprehensive article reviews recently developed anticonvulsant derivatives on the basis of pharmacophoric approaches. A literature survey was performed using various search engines like Google Scholar, Scopus, Sci Finder, ScienceDirect, Science gate, Scilit, PubMed, NINDS database of NIH, Bentham Sciences, and other online and print journals and scientific databases. The presented review discusses such kinds of newer drugs that are in the market as well as in clinical trial phases. Detailed outcomes of pharmacophoric modeling have been discussed for newly derived derivatives like targets involved in Epilepsy, lead molecules etc., for the treatment of epilepsy. This exhaustive review will assist the researchers in the further development of potential antiepileptic agents.

9.
Science ; 380(6644): 543-551, 2023 05 05.
Article in English | MEDLINE | ID: mdl-37141366

ABSTRACT

The ability to form precise, episodic memories develops with age, with young children only able to form gist-like memories that lack precision. The cellular and molecular events in the developing hippocampus that underlie the emergence of precise, episodic-like memory are unclear. In mice, the absence of a competitive neuronal engram allocation process in the immature hippocampus precluded the formation of sparse engrams and precise memories until the fourth postnatal week, when inhibitory circuits in the hippocampus mature. This age-dependent shift in precision of episodic-like memories involved the functional maturation of parvalbumin-expressing interneurons in subfield CA1 through assembly of extracellular perineuronal nets, which is necessary and sufficient for the onset of competitive neuronal allocation, sparse engram formation, and memory precision.


Subject(s)
Hippocampus , Memory, Episodic , Mice , Animals , Hippocampus/physiology , Neurons/physiology , Interneurons , Mice, Inbred C57BL
10.
Biology (Basel) ; 12(4)2023 Apr 21.
Article in English | MEDLINE | ID: mdl-37106829

ABSTRACT

Hippocampal local field potentials (LFP) are highly related to behavior and memory functions. It has been shown that beta band LFP oscillations are correlated with contextual novelty and mnemonic performance. Evidence suggests that changes in neuromodulators, such as acetylcholine and dopamine, during exploration in a novel environment underlie changes in LFP. However, potential downstream mechanisms through which neuromodulators may alter the beta band oscillation in vivo remain to be fully understood. In this paper, we study the role of the membrane cationic channel TRPC4, which is modulated by various neuromodulators through G-protein-coupled receptors, by combining shRNA-mediated TRPC4 knockdown (KD) with LFP measurements in the CA1 region of the hippocampus in behaving mice. We demonstrate that the increased beta oscillation power seen in the control group mice in a novel environment is absent in the TRPC4 KD group. A similar loss of modulation was also seen in the low-gamma band oscillations in the TRPC4 KD group. These results demonstrate that TRPC4 channels are involved in the novelty-induced modulation of beta and low-gamma oscillations in the CA1 region.

11.
Cell Mol Life Sci ; 80(4): 82, 2023 Mar 05.
Article in English | MEDLINE | ID: mdl-36871239

ABSTRACT

Neurotrypsin (NT) is a neuronal trypsin-like serine protease whose mutations cause severe mental retardation in humans. NT is activated in vitro by Hebbian-like conjunction of pre- and postsynaptic activities, which promotes the formation of dendritic filopodia via proteolytic cleavage of the proteoglycan agrin. Here, we investigated the functional importance of this mechanism for synaptic plasticity, learning, and extinction of memory. We report that juvenile neurotrypsin-deficient (NT-/-) mice exhibit impaired long-term potentiation induced by a spaced stimulation protocol designed to probe the generation of new filopodia and their conversion into functional synapses. Behaviorally, juvenile NT-/- mice show impaired contextual fear memory and have a sociability deficit. The latter persists in aged NT-/- mice, which, unlike juvenile mice, show normal recall but impaired extinction of contextual fear memories. Structurally, juvenile mutants exhibit reduced spine density in the CA1 region, fewer thin spines, and no modulation in the density of dendritic spines following fear conditioning and extinction in contrast to wild-type littermates. The head width of thin spines is reduced in both juvenile and aged NT-/- mice. In vivo delivery of adeno-associated virus expressing an NT-generated fragment of agrin, agrin-22, but not a shorter agrin-15, elevates the spine density in NT-/- mice. Moreover, agrin-22 co-aggregates with pre- and postsynaptic markers and increases the density and size of presynaptic boutons and presynaptic puncta, corroborating the view that agrin-22 supports the synaptic growth.


Subject(s)
Long-Term Potentiation , Peptide Hydrolases , Humans , Animals , Mice , Aged , Agrin , Dendritic Spines , Memory Disorders
12.
Cells ; 12(5)2023 02 25.
Article in English | MEDLINE | ID: mdl-36899880

ABSTRACT

Our previous studies demonstrated that enzymatic removal of highly sulfated heparan sulfates with heparinase 1 impaired axonal excitability and reduced expression of ankyrin G at the axon initial segments in the CA1 region of the hippocampus ex vivo, impaired context discrimination in vivo, and increased Ca2+/calmodulin-dependent protein kinase II (CaMKII) activity in vitro. Here, we show that in vivo delivery of heparinase 1 in the CA1 region of the hippocampus elevated autophosphorylation of CaMKII 24 h after injection in mice. Patch clamp recording in CA1 neurons revealed no significant heparinase effects on the amplitude or frequency of miniature excitatory and inhibitory postsynaptic currents, while the threshold for action potential generation was increased and fewer spikes were generated in response to current injection. Delivery of heparinase on the next day after contextual fear conditioning induced context overgeneralization 24 h after injection. Co-administration of heparinase with the CaMKII inhibitor (autocamtide-2-related inhibitory peptide) rescued neuronal excitability and expression of ankyrin G at the axon initial segment. It also restored context discrimination, suggesting the key role of CaMKII in neuronal signaling downstream of heparan sulfate proteoglycans and highlighting a link between impaired CA1 pyramidal cell excitability and context generalization during recall of contextual memories.


Subject(s)
Calcium-Calmodulin-Dependent Protein Kinase Type 2 , Heparitin Sulfate , Animals , Mice , Ankyrins/metabolism , Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism , Heparin Lyase/metabolism , Heparin Lyase/pharmacology , Heparitin Sulfate/metabolism , Hippocampus/metabolism
13.
ACS Omega ; 8(1): 98-126, 2023 Jan 10.
Article in English | MEDLINE | ID: mdl-36643462

ABSTRACT

Biothiols (cysteine, homocysteine, and glutathione) are an important class of compounds with a free thiol group. These biothiols plays an important role in several metabolic processes in living bodies when present in optimum concentration. Researchers have developed several probes for the detection and quantification of biothiols that can absorb in UV, visible, and near-infrared (NIR) regions of the electromagnetic spectrum. Among them, NIR organic probes have attracted significant attention due to their application in in vivo and in vitro imaging. In this review, we have summarized probes for these biothiols, which could work in the NIR region, and discussed their sensing mechanism and potential applications. Along with focusing on the pros and cons of the reported probes we have classified them according to the fluorophore used and summarized their photophysical and sensing properties (emission, response time, limit of detection).

14.
EMBO J ; 42(4): e112453, 2023 02 15.
Article in English | MEDLINE | ID: mdl-36594364

ABSTRACT

Synaptic dysfunction caused by soluble ß-amyloid peptide (Aß) is a hallmark of early-stage Alzheimer's disease (AD), and is tightly linked to cognitive decline. By yet unknown mechanisms, Aß suppresses the transcriptional activity of cAMP-responsive element-binding protein (CREB), a master regulator of cell survival and plasticity-related gene expression. Here, we report that Aß elicits nucleocytoplasmic trafficking of Jacob, a protein that connects a NMDA-receptor-derived signalosome to CREB, in AD patient brains and mouse hippocampal neurons. Aß-regulated trafficking of Jacob induces transcriptional inactivation of CREB leading to impairment and loss of synapses in mouse models of AD. The small chemical compound Nitarsone selectively hinders the assembly of a Jacob/LIM-only 4 (LMO4)/ Protein phosphatase 1 (PP1) signalosome and thereby restores CREB transcriptional activity. Nitarsone prevents impairment of synaptic plasticity as well as cognitive decline in mouse models of AD. Collectively, the data suggest targeting Jacob protein-induced CREB shutoff as a therapeutic avenue against early synaptic dysfunction in AD.


Subject(s)
Alzheimer Disease , Animals , Mice , Alzheimer Disease/genetics , Alzheimer Disease/metabolism , Amyloid beta-Peptides/metabolism , Mice, Transgenic , Neurons/metabolism , Synapses/metabolism
15.
Proteins ; 91(6): 798-806, 2023 06.
Article in English | MEDLINE | ID: mdl-36629264

ABSTRACT

Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to evolve carrying flexible amino acid substitutions in the spike protein's receptor binding domain (RBD). These substitutions modify the binding of the SARS-CoV-2 to human angiotensin-converting enzyme 2 (hACE2) receptor and have been implicated in altered host fitness, transmissibility, and efficacy against antibody therapeutics and vaccines. Reliably predicting the binding strength of SARS-CoV-2 variants RBD to hACE2 receptor and neutralizing antibodies (NAbs) can help assessing their fitness, and rapid deployment of effective antibody therapeutics, respectively. Here, we introduced a two-step computational framework with 3-fold validation that first identified dissociation constant as a reliable predictor of binding affinity in hetero- dimeric and trimeric protein complexes. The second step implements dissociation constant as descriptor of the binding strengths of SARS-CoV-2 variants RBD to hACE2 and NAbs. Then, we examined several variants of concerns (VOCs) such as Alpha, Beta, Gamma, Delta, and Omicron and demonstrated that these VOCs RBD bind to the hACE2 with enhanced affinity. Furthermore, the binding affinity of Omicron variant's RBD was reduced with majority of the RBD-directed NAbs, which is highly consistent with the experimental neutralization data. By studying the atomic contacts between RBD and NAbs, we revealed the molecular footprints of four NAbs (GH-12, P2B-1A1, Asarnow_3D11, and C118)-that may likely neutralize the recently emerged Omicron variant-facilitating enhanced binding affinity. Finally, our findings suggest a computational pathway that could aid researchers identify a range of current NAbs that may be effective against emerging SARS-CoV-2 variants.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Consensus , Antibodies, Neutralizing
16.
Viruses ; 14(12)2022 12 12.
Article in English | MEDLINE | ID: mdl-36560768

ABSTRACT

The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of the initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track the virus's genetic changes that drive the early evolutionary dynamics of the Omicron. Based on the Omicron dataset chosen for the improved temporal signals and sampled globally between November 2021 and January 2022, the most recent common ancestor (tMRCA) and substitution rates for BA.1 were estimated to be that of 18 September 2021 (95% highest posterior density (HPD), 4 August-22 October 2021) and 1.435 × 10-3 (95% HPD = 1.021 × 10-3 - 1.869 × 10-3) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September-28 November 2021) and 1.074 × 10-3 (95% HPD = 6.444 × 10-4 - 1.586 × 10-3) substitution/site/year were estimated for the BA.2 sub-lineage. The findings of this study suggest that the Omicron BA.1 and BA.2 sub-lineages originated independently and evolved over time. Furthermore, we identified multiple sites in the spike protein undergoing continued diversifying selection that may alter the neutralization profile of BA.1. This study sheds light on the ongoing global genomic surveillance and Bayesian molecular dating analyses to better understand the evolutionary dynamics of the virus and, as a result, mitigate the impact of emerging variants on public health.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Bayes Theorem , Mutation , Phylogeny , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus
17.
Comput Struct Biotechnol J ; 20: 6467-6472, 2022.
Article in English | MEDLINE | ID: mdl-36467582

ABSTRACT

The structural information of a protein is pivotal to comprehend its functions, protein-protein and protein-ligand interactions. There is a widening gap between the number of known protein sequences and that of experimentally determined structures. The protein structure prediction has emerged as an efficient alternative to deliver the reliable structural information of proteins. However, it remains a challenge to identify the best model among the many predicted by one or a few structure prediction methods. Here we report ProFitFun-Meta, a neural network based pure single model scoring method for assessing the quality of predicted model structures by an effective combination structural information of various backbone dihedral angle and residue surface accessibility preferences of amino acid residues with other spatial properties of protein structures. The performance of ProFitFun-Meta was validated and benchmarked against current state-of-the-art methods on the extensive datasets, comprising a Test Dataset (n = 26,604), an External Dataset (n = 40,000), and CASP14 Dataset (n = 1200). The comprehensive performance evaluation of ProFitFun-Meta demonstrated its reliability and efficiency in terms of Spearman's (ρ) and Pearson's (r) correlation coefficients, GDT-TS loss (g), and absolute loss (d). An improved performance over the current state-of-the-art methods and leading performers of CASP14 experiment in quality assessment category demonstrated its potential to become an integral component of computational pipelines for protein modeling and design. The minimal dependencies, high computational efficiency, and portability to various Linux and Windows OS provide an additional edge to ProFitFun-Meta for its easy implementation and applications in various regimes of computational protein folding.

18.
Cells ; 11(13)2022 06 27.
Article in English | MEDLINE | ID: mdl-35805117

ABSTRACT

Understanding changes in the expression of genes involved in regulating various components of the neural extracellular matrix (ECM) during aging can provide an insight into aging-associated decline in synaptic and cognitive functions. Hence, in this study, we compared the expression levels of ECM-related genes in the hippocampus of young, aged and very aged mice. ECM gene expression was downregulated, despite the accumulation of ECM proteoglycans during aging. The most robustly downregulated gene was carbohydrate sulfotransferase 3 (Chst3), the enzyme responsible for the chondroitin 6-sulfation (C6S) of proteoglycans. Further analysis of epigenetic mechanisms revealed a decrease in H3K4me3, three methyl groups at the lysine 4 on the histone H3 proteins, associated with the promoter region of the Chst3 gene, resulting in the downregulation of Chst3 expression in non-neuronal cells. Cluster analysis revealed that the expression of lecticans-substrates of CHST3-is tightly co-regulated with this enzyme. These changes in ECM-related genes were accompanied by an age-confounded decline in cognitive performance. Despite the co-directional impairment in cognitive function and average Chst3 expression in the studied age groups, at the individual level we found a negative correlation between mRNA levels of Chst3 and cognitive performance within the very aged group. An analysis of correlations between the expression of ECM-related genes and cognitive performance in novel object versus novel location recognition tasks revealed an apparent trade-off in the positive gene effects in one task at the expense of another. Further analysis revealed that, despite the reduction in the Chst3 mRNA, the expression of CHST3 protein is increased in glial cells but not in neurons, which, however, does not lead to changes in the absolute level of C6S and even results in the decrease in C6S in perineuronal, perisynaptic and periaxonal ECM relative to the elevated expression of its protein carrier versican.


Subject(s)
Epigenesis, Genetic , Proteoglycans , Aging/genetics , Animals , Cognition , Mice , RNA, Messenger , Sulfotransferases , Carbohydrate Sulfotransferases
19.
Environ Res ; 212(Pt C): 113303, 2022 09.
Article in English | MEDLINE | ID: mdl-35460633

ABSTRACT

Understanding the origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a highly debatable and unresolved issue for scientific communities all over the world. Understanding the mechanism of virus entry to the host cells is crucial to deciphering the susceptibility profiles of animal species to SARS-CoV-2. The interaction of SARS-CoV-2 ligands (receptor-binding domain on spike protein) with its host cell receptor, angiotensin-converting enzyme 2 (ACE2), is a critical determinant of host range and cross-species transmission. In this study, we developed and implemented a rigorous computational approach for predicting binding affinity between 299 ACE2 orthologs from diverse vertebrate species and the SARS-CoV-2 spike protein. The findings show that the SARS-CoV-2 spike protein can bind to a wide range of vertebrate species carrying evolutionary divergent ACE2, implying a broad host range at the virus entry level, which may contribute to cross-species transmission and further viral evolution. Furthermore, the current study facilitated the identification of genetic determinants that may differentiate susceptible from resistant host species based on the conservation of ACE2-spike protein interacting residues in vertebrate host species known to facilitate SARS-CoV-2 infection; however, these genetic determinants warrant in vivo experimental confirmation. The molecular interactions associated with varied binding affinity of distinct ACE2 isoforms in a specific bat species were identified using protein structure analysis, implying the existence of diversified bat species' susceptibility to SARS-CoV-2. The current study's findings highlight the importance of intensive surveillance programmes aimed at identifying susceptible hosts, especially those with the potential to transmit zoonotic pathogens, in order to prevent future outbreaks.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Angiotensin-Converting Enzyme 2 , Animals , Humans , Peptidyl-Dipeptidase A/chemistry , Peptidyl-Dipeptidase A/genetics , Peptidyl-Dipeptidase A/metabolism , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Vertebrates/metabolism
20.
Phys Chem Chem Phys ; 24(8): 5083-5093, 2022 Feb 23.
Article in English | MEDLINE | ID: mdl-35147154

ABSTRACT

Green and sustainable energy production through renewable sources is an enormously exciting field of research. Herein, we report an A-site lanthanum doped oxygen excess ruthenate (predominantly Ru5+-ions) double perovskite system, CaLaScRuO6+δ (CLSR), as an excellent photocatalyst for water splitting. The well characterized polycrystalline compound shows canted antiferromagnetic (AFM) behavior due to the existence of disordered Ru-ions at the B-site. Based on density functional theory + U (Hubbard U) calculations, we have estimated various magnetic exchange interactions and found that the ground state is antiferromagnetic in nature which is in perfect agreement with our experimental results. Detailed analysis of the electronic structure further reveals that the present system belongs to the family of charge transfer semiconductors with an energy gap of ∼0.45 eV. Finally, the material is found to proficiently work for the oxygen evolution reaction (OER) via visible-light driven water splitting at neutral pH in an ecofriendly manner.

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