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1.
Talanta ; 275: 126089, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38608343

ABSTRACT

Water, although an important part of everyday life, is acts as one of the most significant contaminants in various applications such as biomedical monitoring, chemical production, petroleum-based fuel and food processing. In fact, the presence of water in other solvents is a huge concern. For the quantification of trace water content, different methods such as Karl-Fischer, electrochemical, nuclear magnetic resonance, chromatography, and thermogravimetric analysis have been used. Although every technique has its own benefit, each one suffers from several drawbacks that include high detection costs, lengthy procedures and specialized operations. Nowadays, the development of fluorescence-based chemical probes has become an exciting area of research for the quick and accurate estimation of water content in organic solvents. A variety of chemical processes such as hydrolysis reaction, metal ions promoted oxidation reaction, suppression of the -C═N isomerization, protonation and deprotonation reactions, and molecular aggregation have been well researched in the last few years for the fluorescent detection of trace water. These chemical processes eventually lead to different photophysical events such as aggregation-induced emission (AIE), aggregation-induced emission enhancement (AIEE), aggregation-caused quenching (ACQ), fluorescent resonance energy transfer (FRET), charge transfer, photo-induced electron transfer (PET), excited state intramolecular proton transfer (ESIPT) that are responsible for the detection. This review presents a summary of the fluorescence-based chemosensors reported in recent years. The design of water sensors, sensing mechanisms and their potential applications are reviewed and discussed.

2.
Spectrochim Acta A Mol Biomol Spectrosc ; 313: 124143, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38471309

ABSTRACT

A sensitive and selective relay-based scheme for the detection of salicylaldehyde, Hg2+, and folic acid (FA) has been demonstrated using fluorescent ovalbumin functionalized gold nanoclusters (OVA-AuNCs, λem = 655 nm) in this article. The OVA-AuNCs were conjugated to salicylaldehyde via an imine linkage to form Salic_OVA-AuNCs conjugate. The molecular docking study reveals that multiple functional groups and amino acid residues are involved in the interaction between salicylaldehyde and the OVA-AuNCs. The coupling of salicylaldehyde with OVA-AuNCs results in fluorescence quenching at 655 nm and concomitant formation of an emission band at 500 nm, which have leveraged to detect salicylaldehyde down to 2.02 µM. Following that, the Salic_OVA-AuNCs has been used for the detection of Hg2+ and FA. Several processes, such as internal charge transfer (ICT), photoinduced electron transfer (PET) and metallophilic interactions, are involved between the Salic_OVA-AuNCs nanoprobe and the analytes, which allowed to detect Hg2+ and FA down to 0.13 nM and 0.11 nM, respectively. The Salic_OVA-AuNCs nanoprobe has an additional naked-eye utility when applied to paper-strip sensing strategy for Hg2+ and FA detection.


Subject(s)
Aldehydes , Mercury , Metal Nanoparticles , Ovalbumin , Gold/chemistry , Folic Acid , Molecular Docking Simulation , Metal Nanoparticles/chemistry , Spectrometry, Fluorescence/methods , Mercury/chemistry , Fluorescent Dyes/chemistry
3.
Indian J Otolaryngol Head Neck Surg ; 76(1): 1335-1340, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38440520

ABSTRACT

Collision tumours, characterized by the simultaneous occurrence of two distinct neoplasms within the same anatomical site, are exceedingly rare in oral pathology. This case report presents an uncommon collision tumour involving desmoplastic ameloblastoma and squamous odontogenic tumour in the anterior maxilla of a 52-year-old male from the Indian population. Desmoplastic ameloblastoma is a variant of ameloblastoma known for its unique histopathological features, while squamous odontogenic tumour is a benign epithelial odontogenic tumour with distinctive clinical behaviour. The rarity of this occurrence emphasizes the need for accurate diagnosis and effective treatment strategies. This report discusses the clinical presentation, radiographic findings, and histopathological characteristics of this collision tumour. Through the presentation of this case, we aim to contribute to the understanding of these rare entities and their management considerations.

4.
Autophagy ; 20(3): 697-698, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37953605

ABSTRACT

Mycobacterium tuberculosis (Mtb) employs a multifaceted arsenal to elude host defense mechanisms, including those associated with autophagy and lysosome function. Within the realm of host-pathogen interactions, NCOR1, a well-recognized transcriptional co-repressor, is known to associate with a multitude of protein complexes to effect the repression of a diverse spectrum of genes. However, its role in regulating macroautophagy/autophagy, lysosome biogenesis, and, by extension, Mtb pathogenesis remains unexplored. The depletion of NCOR1 assumes a pivotal role in the control of the AMPK-MTOR-TFEB signaling axis, thereby fine-tuning cellular ATP homeostasis. This finely orchestrated adjustment further alters the profile of proteins involved in autophagy and lysosomal biogenesis through its master regulator, TFEB, culminating in the increased Mtb survival within the host milieu. Furthermore, the treatment of NCOR1-depleted cells with either rapamycin, antimycin A, or metformin demonstrates a capacity to restore the TFEB activity and LC3-II levels, consequently restoring the capacity of host cells to clear Mtb. Additionally, exogenous NCOR1 expression rescues the AMPK-MTOR-TFEB signaling axis and essentially the autophagic induction machinery. Overall, these findings demonstrate a crucial role of NCOR1 in regulating Mtb pathogenesis within myeloid cells and sheds light toward its involvement in the development of novel host-directed therapies.


Subject(s)
Mycobacterium tuberculosis , Mycobacterium tuberculosis/metabolism , Autophagy/genetics , AMP-Activated Protein Kinases/metabolism , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism , Transcription Factors/metabolism , TOR Serine-Threonine Kinases/metabolism , Lysosomes/metabolism
5.
Front Plant Sci ; 14: 1273355, 2023.
Article in English | MEDLINE | ID: mdl-38107012

ABSTRACT

Sap from the fresh seaweed Kappaphycus alvarezii (KA) has been reported to improve crop growth, quality, and stress alleviation. However, limited studies are reported for the minimally processed aqueous homogenates (MPHs) derived from dry seaweeds. The present investigation was envisaged to characterize the MPHs from the red seaweed KA and a brown seaweed Sargassum wightii (SW) and also assess the effect of foliar application on maize (Zea mays) crop performance when applied alone or in proportions ranging from 0% to 100%. Two doses (0.35% and 0.7%) were compared with control. Both the MPHs contained several compounds like retronecine, tyrosyl-glycine, hexyl 2-furoate, 1-phosphatidyl-1D-myo-inositol, 12-(2,3-dihydroxycyclopentyl)-2-dodecanone, and trihomomethionine and many others that have known bioactivity for enhancing plant growth and providing stress tolerance. Both doses of MPHs enhanced crop growth and yield; however, the best response was in general observed at a lower dose. The MPH of SW at 100% gave the highest seed yield at a lower dose, which was also on par with that obtained under a lower dose of 100% KA. Other combinations, 80:20 and 40:60 KA : SW, were also found to give comparable yields. The highest dose of 100% MPH of SW was found on par with control, a phenomenon that was investigated in detail with respect to metabolites and antioxidant profile in leaves as well as membrane modeling. Higher ROS and certain sugar and organic acids were observed in 100% MPH of SW at a higher dose, although none of the antioxidant enzymes were significantly affected, nor was there any change in membrane characteristics of the leaf with respect to control as well as lower dose. Improvements in the seed yield were attributed to improved photosynthate production on account of higher dry matter accumulation in the MPH-treated plants, which may also be attributed to the presence of bioactive compounds in the biostimulants. In the future, it is imperative to direct scientific investigations towards the quantification and identification of the most effective concentrations of these compounds within MPHs to optimize plant responses. The study indicated the beneficial use of the MPHs towards increasing crop production by employing optimum dose as foliar spray to crops.

6.
J Am Chem Soc ; 145(33): 18549-18559, 2023 Aug 23.
Article in English | MEDLINE | ID: mdl-37579341

ABSTRACT

Organic-inorganic metal hybrids with their tailorable lattice dimensionality and intrinsic spin-splitting properties are interesting material platforms for spintronic applications. While the spin decoherence process is extensively studied in lead- and tin-based hybrids, these systems generally show short spin decoherence lifetimes, and their correlation with the lattice framework is still not well-understood. Herein, we synthesized magnetic manganese hybrid single crystals of (4-fluorobenzylamine)2MnCl4, ((R)-3-fluoropyrrolidinium)MnCl3, and (pyrrolidinium)2MnCl4, which represent a change in lattice dimensionality from 2D and 1D to 0D, and studied their spin decoherence processes using continuous-wave electron spin resonance spectroscopy. All manganese hybrids exhibit nanosecond-scale spin decoherence time τ2 dominated by the symmetry-directed spin exchange interaction strengths of Mn2+-Mn2+ pairs, which is much longer than lead- and tin-based metal hybrids. In contrast to the similar temperature variation laws of τ2 in 2D and 0D structures, which first increase and gradually drop afterward, the 1D structure presents a monotonous rise of τ2 with the temperatures, indicating the strong correlation of spin decoherence with the lattice rigidity of the inorganic framework. This is also rationalized on the basis that the spin decoherence is governed by the competitive contributions from motional narrowing (prolonging the τ2) and electron-phonon coupling interaction (shortening the τ2), both of which are thermally activated, with the difference that the former is more pronounced in rigid crystalline lattices.

7.
PLoS Biol ; 21(8): e3002231, 2023 08.
Article in English | MEDLINE | ID: mdl-37590294

ABSTRACT

Mycobacterium tuberculosis (Mtb) defends host-mediated killing by repressing the autophagolysosome machinery. For the first time, we report NCoR1 co-repressor as a crucial host factor, controlling Mtb growth in myeloid cells by regulating both autophagosome maturation and lysosome biogenesis. We found that the dynamic expression of NCoR1 is compromised in human peripheral blood mononuclear cells (PBMCs) during active Mtb infection, which is rescued upon prolonged anti-mycobacterial therapy. In addition, a loss of function in myeloid-specific NCoR1 considerably exacerbates the growth of M. tuberculosis in vitro in THP1 differentiated macrophages, ex vivo in bone marrow-derived macrophages (BMDMs), and in vivo in NCoR1MyeKO mice. We showed that NCoR1 depletion controls the AMPK-mTOR-TFEB signalling axis by fine-tuning cellular adenosine triphosphate (ATP) homeostasis, which in turn changes the expression of proteins involved in autophagy and lysosomal biogenesis. Moreover, we also showed that the treatment of NCoR1 depleted cells by Rapamycin, Antimycin-A, or Metformin rescued the TFEB activity and LC3 levels, resulting in enhanced Mtb clearance. Similarly, expressing NCoR1 exogenously rescued the AMPK-mTOR-TFEB signalling axis and Mtb killing. Overall, our data revealed a central role of NCoR1 in Mtb pathogenesis in myeloid cells.


Subject(s)
Mycobacterium tuberculosis , Nuclear Receptor Co-Repressor 1 , Animals , Humans , Mice , AMP-Activated Protein Kinases , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors , Leukocytes, Mononuclear , Myeloid Cells , TOR Serine-Threonine Kinases , Nuclear Receptor Co-Repressor 1/metabolism
8.
J Appl Phycol ; 35(3): 983-996, 2023.
Article in English | MEDLINE | ID: mdl-37249919

ABSTRACT

Gracilaria edulis is one of the most studied agarophytes, especially in tropical regions like India because of its natural abundance. Apart from the Indian peninsula, it is widely distributed in tropical and subtropical regions. The taxonomy of G. edulis is evolving; currently G. edulis is the taxonomically accepted name, however several phylogenetic and morphological investigations supported its inclusion in the genus Hydropuntia. In addition to the conventional farming methods like the tube net and raft methods which use clonally propagated seed material, spore-based planting materials like carpospores have been employed to cultivate G. edulis. Co-cultivation with shrimp farm wastewater has also been practised to make the cultivation economically viable and environmentally sustainable as the seaweed could provide an efficient ecosystem service by up taking nitrogen from the shrimp waste. Like other seaweed cultivation systems, farming of G. edulis is also infested by various epiphytes like Ulva, Cladophora, Ceramium, Centroceras, Hypnea and Padina as well as grazed by fishes like Monodactylus, Pelates and Pteroscirtes which decrease the growth and ultimately result in low yield of agar, seaweed sap and other value added products. Food grade agar produced by this seaweed is an important resource and the current review focusses on the latest extraction technologies. Further, there also is evidence based application of plant bio-stimulant derived from G. edulis feedstock which has proven to be highly effective in enhancing the yield by 10-33% in field trials of nine cash crops. Supplementary Information: The online version contains supplementary material available at 10.1007/s10811-023-02955-8.

9.
Microbiol Spectr ; 11(3): e0286322, 2023 06 15.
Article in English | MEDLINE | ID: mdl-37014250

ABSTRACT

The peptidoglycan (PG) layer, a crucial component of the tripartite E.coli envelope, is required to maintain cellular integrity, protecting the cells from mechanical stress resulting from intracellular turgor pressure. Thus, coordinating synthesis and hydrolysis of PG during cell division (septal PG) is crucial for bacteria. The FtsEX complex directs septal PG hydrolysis through the activation of amidases; however, the mechanism and regulation of septal PG synthesis are unclear. In addition, how septal PG synthesis and hydrolysis are coordinated has remained unclear. Here, we have shown that overexpression of FtsE leads to a mid-cell bulging phenotype in E.coli, which is different from the filamentous phenotype observed during overexpression of other cell division proteins. Silencing of the common PG synthesis genes murA and murB reduced bulging, confirming that this phenotype is due to excess PG synthesis. We further demonstrated that septal PG synthesis is independent of FtsE ATPase activity and FtsX. These observations and previous results suggest that FtsEX plays a role during septal PG hydrolysis, whereas FtsE alone coordinates septal PG synthesis. Overall, our study findings support a model in which FtsE plays a role in coordinating septal PG synthesis with bacterial cell division. IMPORTANCE The peptidoglycan (PG) layer is an essential component of the E.coli envelope that is required to maintain cellular shape and integrity. Thus, coordinating PG synthesis and hydrolysis at the mid-cell (septal PG) is crucial during bacterial division. The FtsEX complex directs septal PG hydrolysis through the activation of amidases; however, its role in regulation of septal PG synthesis is unclear. Here, we demonstrate that overexpression of FtsE in E.coli leads to a mid-cell bulging phenotype due to excess PG synthesis. This phenotype was reduced upon silencing of common PG synthesis genes murA and murB. We further demonstrated that septal PG synthesis is independent of FtsE ATPase activity and FtsX. These observations suggest that the FtsEX complex plays a role during septal PG hydrolysis, whereas FtsE alone coordinates septal PG synthesis. Our study indicates that FtsE plays a role in coordinating septal PG synthesis with bacterial cell division.


Subject(s)
Escherichia coli Proteins , Escherichia coli , Escherichia coli/metabolism , ATP-Binding Cassette Transporters/genetics , ATP-Binding Cassette Transporters/chemistry , ATP-Binding Cassette Transporters/metabolism , Peptidoglycan/metabolism , Cell Cycle Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Protein Binding , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Amidohydrolases/metabolism , Adenosine Triphosphatases/metabolism , Nucleotides/metabolism , Cystic Fibrosis Transmembrane Conductance Regulator/genetics
10.
Front Plant Sci ; 14: 1097682, 2023.
Article in English | MEDLINE | ID: mdl-36875593

ABSTRACT

The usage of seaweed extracts in cropping systems is gaining attention nowadays due to their distinct bioactive properties. This study aims to assess how saffron (Crocus sativus L.) corm production was affected by seaweed extract through different application modes. The study was conducted at the CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP, India, during the autumn-winter agricultural cycle. Five treatments using a combination of Kappaphycus and Sargassum seaweed extracts were replicated five times in a randomized block design. Treatments that were examined include T1: Control, T2: Corm dipping @ 5% seaweed extract, T3: Foliar spray @ 5% seaweed extract, T4: Drenching @ 5% seaweed extract, and T5: Corm dipping + foliar spray @ 5% seaweed extract. Seaweed extract, when applied to saffron plants (T5: Corm dipping + foliar spray @ 5% seaweed extract) resulted in significantly higher growth parameters along with the higher dry weight of stem, leaves, corms, and total roots per corm. Corm production, viz., the number of daughter corms and corm weight per m2 was significantly affected by seaweed extract application, with the maximum value recorded with treatment T5. Biochemical parameters chlorophyll, carotenoids, and photosynthetic rate were higher in T5, while nutrient concentration was lowest in this treatment. Seaweed extracts improved corm production, making it a feasible alternative to limiting the application of conventional fertilizers, attenuating the effects on the environment, and enhancing corm number and weight.

11.
ACS Omega ; 7(50): 46646-46652, 2022 Dec 20.
Article in English | MEDLINE | ID: mdl-36570225

ABSTRACT

Lipopeptide (LP) biosurfactants from microbes have the potential to gradually replace chemical synthetic surfactants and fit the contemporary green and sustainable industrial production concept. However, their active participation is comparatively low in the global market pertaining to their low yield in microbial broth and costly downstream processes arising due to tedious isolation and purification methods. Herein, an efficient extraction method is developed that utilizes an aqueous biphasic system (ABS) comprising ionic liquids and polypropylene glycol 400 (PPG) to selectively extract a mixture of cyclic lipopeptides, namely, surfactin and fengycin from the culture broth of Bacillus amyloliquefaciens 5NPA-1, isolated from the halophyte Salicornia brachiata Roxb. Out of four different ABSs, the ABS composed of 2-hydroxyethyl ammonium formate and PPG displayed a maximum extraction efficiency of 82.30%. PPG-rich phase containing lipopeptides exhibited excellent antimicrobial and mosquito larvicidal properties with no toxic effect on plants. The developed method is simple, novel and accelerates the application of cyclic lipopeptides produced by the microbial source.

12.
FASEB J ; 36(10): e22566, 2022 10.
Article in English | MEDLINE | ID: mdl-36165231

ABSTRACT

CMTM6, a type 3 transmembrane protein, is known to stabilize the expression of programmed cell death ligand 1 (PD-L1) and hence facilitates the immune evasion of tumor cells. Recently, we demonstrated that CMTM6 is a major driver of cisplatin resistance in oral squamous cell carcinomas (OSCC). However, the detailed mechanism of how CMTM6 rewires cisplatin resistance in OSCC is yet to be explored. RNA sequencing analysis of cisplatin-resistant OSCC lines stably expressing Nt shRNA and CMTM6 shRNA revealed that CMTM6 might be a potential regulator of the ribosome biogenesis network. Knocking down CMTM6 significantly inhibited transcription of 47S precursor rRNA and hindered the nucleolar structure, indicating reduced ribosome biogenesis. When CMTM6 was ectopically over-expressed in CMTM6KD cells, almost all ribosomal machinery components were rescued. Mechanistically, CMTM6 induced the expression of C-Myc, which promotes RNA polymerase I mediated rDNA transcription. In addition to this, CMTM6 was also found to regulate the AKT-mTORC1-dependent ribosome biogenesis and protein synthesis in cisplatin-resistant lines. The nude mice and zebrafish xenograft experiments indicate that blocking ribosome synthesis either by genetic inhibitor (CMTM6KD) or pharmacological inhibitor (CX-5461) significantly restores cisplatin-mediated cell death in chemoresistant OSCC. Overall, our study suggests that CMTM6 is a major regulator of the ribosome biogenesis network and targeting the ribosome biogenesis network is a viable target to overcome chemoresistance in OSCC. The novel combination of CX-5461 and cisplatin deserves further clinical investigation in advanced OSCC.


Subject(s)
Carcinoma, Squamous Cell , Head and Neck Neoplasms , Mouth Neoplasms , Animals , B7-H1 Antigen , Carcinoma, Squamous Cell/genetics , Cell Death , Cell Line, Tumor , Cisplatin/pharmacology , DNA, Ribosomal , Humans , Ligands , Mechanistic Target of Rapamycin Complex 1 , Mice , Mice, Nude , Mouth Neoplasms/drug therapy , Mouth Neoplasms/pathology , Proto-Oncogene Proteins c-akt , RNA Polymerase I , RNA, Small Interfering , Ribosomes , Squamous Cell Carcinoma of Head and Neck , Zebrafish/genetics
14.
Front Microbiol ; 13: 856913, 2022.
Article in English | MEDLINE | ID: mdl-35847066

ABSTRACT

The emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a serious pandemic has altered the global socioeconomic dynamics. The wide prevalence, high death counts, and rapid emergence of new variants urge for the establishment of research infrastructure to facilitate the rapid development of efficient therapeutic modalities and preventive measures. In agreement with this, SARS-CoV-2 strains were isolated from patient swab samples collected during the first COVID-19 wave in Odisha, India. The viral isolates were adapted to in vitro cultures and further characterized to identify strain-specific variations in viral growth characteristics. The neutralization susceptibility of viral isolates to vaccine-induced antibodies was determined using sera from individuals vaccinated in the Government-run vaccine drive in India. The major goal was to isolate and adapt SARS-CoV-2 viruses in cell culture with minimum modifications to facilitate research activities involved in the understanding of the molecular virology, host-virus interactions, drug discovery, and animal challenge models that eventually contribute toward the development of reliable therapeutics.

15.
Mol Omics ; 18(6): 490-505, 2022 07 11.
Article in English | MEDLINE | ID: mdl-35506682

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown alterations in nasopharyngeal (NP) microbial diversity, enrichment of opportunistic pathogens and their role in co-infections during respiratory infections. Therefore, we hypothesized that microbial diversity changes, with increase in the population of opportunistic pathogens, during SARS-CoV2 infection in the nasopharynx, which may be involved in co-infection in COVID-19 patients. The 16S rRNA variable regions, V1-V9, of NP samples of control and COVID-19 (symptomatic and asymptomatic) patients were sequenced using the Oxford Nanopore™ technology. Comprehensive bioinformatics analysis for determining alpha/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index were used to analyze the control and COVID-19-specific NP microbiomes. We observed significant dysbiosis in the COVID-19 NP microbiome with an increase in the abundance of opportunistic pathogens at genus and species levels in asymptomatic/symptomatic patients. The significant abundance of Mycobacteria spp. and Mycoplasma spp. in symptomatic patients suggests their association and role in co-infections in COVID-19 patients. Furthermore, we found strong correlation of enrichment of Mycobacteria and Mycoplasma with the occurrences of chest pain and fever in symptomatic COVID-19 patients. This is the first study from India to show the abundance of Mycobacteria and Mycoplasma opportunistic pathogens in non-hospitalized COVID-19 patients and their relationship with symptoms, indicating the possibility of co-infections.


Subject(s)
COVID-19 , Coinfection , Mycobacterium , Mycoplasma , Coinfection/epidemiology , Dysbiosis , Humans , Nasopharynx , RNA, Ribosomal, 16S/genetics , RNA, Viral , SARS-CoV-2
17.
Nucleic Acids Res ; 50(3): 1551-1561, 2022 02 22.
Article in English | MEDLINE | ID: mdl-35048970

ABSTRACT

During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.


Subject(s)
Evolution, Molecular , Genetic Variation/genetics , Genome, Viral/genetics , Host-Pathogen Interactions/genetics , SARS-CoV-2/genetics , APOBEC-1 Deaminase/genetics , Adenosine Deaminase/genetics , Animals , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , Chlorocebus aethiops , Coronavirus RNA-Dependent RNA Polymerase/genetics , Databases, Genetic , Immune Evasion/genetics , India/epidemiology , Phylogeny , RNA-Binding Proteins/genetics , SARS-CoV-2/classification , SARS-CoV-2/growth & development , Spike Glycoprotein, Coronavirus/genetics , Vero Cells
18.
Front Immunol ; 12: 733539, 2021.
Article in English | MEDLINE | ID: mdl-34899693

ABSTRACT

The response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely impacted by the level of virus exposure and status of the host immunity. The nature of protection shown by direct asymptomatic contacts of coronavirus disease 2019 (COVID-19)-positive patients is quite intriguing. In this study, we have characterized the antibody titer, SARS-CoV-2 surrogate virus neutralization, cytokine levels, single-cell T-cell receptor (TCR), and B-cell receptor (BCR) profiling in asymptomatic direct contacts, infected cases, and controls. We observed significant increase in antibodies with neutralizing amplitude in asymptomatic contacts along with cytokines such as Eotaxin, granulocyte-colony stimulating factor (G-CSF), interleukin 7 (IL-7), migration inhibitory factor (MIF), and macrophage inflammatory protein-1α (MIP-1α). Upon single-cell RNA (scRNA) sequencing, we explored the dynamics of the adaptive immune response in few representative asymptomatic close contacts and COVID-19-infected patients. We reported direct asymptomatic contacts to have decreased CD4+ naive T cells with concomitant increase in CD4+ memory and CD8+ Temra cells along with expanded clonotypes compared to infected patients. Noticeable proportions of class switched memory B cells were also observed in them. Overall, these findings gave an insight into the nature of protection in asymptomatic contacts.


Subject(s)
Adaptive Immunity/immunology , COVID-19/immunology , Genomics/methods , SARS-CoV-2/immunology , Single-Cell Analysis/methods , Adaptive Immunity/genetics , Adult , Antibodies, Viral/immunology , COVID-19/genetics , COVID-19/virology , Cytokines/immunology , Cytokines/metabolism , Female , Gene Expression Profiling/methods , Humans , Male , Memory B Cells/immunology , Memory B Cells/metabolism , Memory B Cells/virology , Middle Aged , SARS-CoV-2/physiology , Sequence Analysis, RNA/methods , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , T-Lymphocytes/virology , Young Adult
19.
Arch Microbiol ; 204(1): 72, 2021 Dec 24.
Article in English | MEDLINE | ID: mdl-34951686

ABSTRACT

Kappaphycus alvarezii seaweed extract (KSWE) is known to enhance crop productivity and impart stress tolerance. Close to one quarter of foliar spray applied to maize falls on the soil, either as drift or from leaf as drip. It was hypothesized that the drift spray would profoundly influence soil microbes under stress. An experiment was conducted with five treatments, with or without KSWE application at critical stages of maize grown under soil moisture stress and compared with an irrigated control. An Illumina platform was employed for the analysis of the V3-V4 region of 16S rRNA gene from the soil metagenome. A total of 345,552 operational taxonomic units were generated which were classified into 55 phyla, 152 classes, 240 orders, 305 families and 593 genera. Shannon's index and Shannon's equitability indicated increased soil bacterial diversity after multiple KSWE applications under conditions of abiotic duress. The abundance of the genera Alicyclobacillus, Anaerolinea, Bacillus, Balneimonas, Nitrospira, Rubrobacter and Steroidobacter decreased (49-79%) under drought imposed at the V5,10 and 15 stages of maize over the irrigated control, while it significantly improved when followed by KSWE application under drought. Flavobacterium, Nitrosomonas, Nitrosovibrio, Rubrobacter genera and several other bacterial taxa which are important for plant growth promotion and nutrient cycling were found to be enriched by KSWE application under drought conditions. Treatments having enriched microbial abundance due to KSWE application under stress recorded higher soil enzymatic activities and plant cob yield, suggesting the contribution of altered soil ecology mediated by KSWE as one of the reasons for improvement of yield.


Subject(s)
Fertilizers , Metagenomics , Seaweed , Soil Microbiology , RNA, Ribosomal, 16S/genetics , Soil
20.
Indian J Thorac Cardiovasc Surg ; 37(6): 623-630, 2021 Nov.
Article in English | MEDLINE | ID: mdl-34776660

ABSTRACT

BACKGROUND: For risk stratifying patients undergoing coronary artery bypass graft (CABG), the Society of Thoracic Surgeons (STS) risk score and the European System for Cardiac Operative Risk Evaluation (EuroSCORE) are currently used. However, the superiority of one over the other in the context of Indian patients has not been assessed. The aim of this study was to compare these 2 scoring systems in Indian patients undergoing CABG. METHODOLOGY: This was a retrospective analysis of prospectively collected data between January 2015 and September 2020 of all patients undergoing CABG. Observed mortality in the cohort was compared with the predicted mortality using the STS and the EuroSCORE II. Sensitivity and specificity were calculated for both the scores. Receiver operating characteristic (ROC) curves were constructed for both the STS and the EuroSCORE II and area under the ROC curve (AUC) was calculated. RESULTS: A total of 4895 patients were included in the study. The overall observed mortality in the entire cohort was 74 (1.5%). The EuroSCORE II-predicted mortality was 1.9 ± 2.5 whereas the STS score-predicted mortality was 1.2 ± 1.8. The observed to predicted mortality ratio for EuroSCORE was 0.79 and 1.25 for the STS score. The discriminative ability for operative mortality of the STS score was 0.72 (0.71 to 0.74) and 0.713 for the EuroSCORE, suggesting satisfactory discriminatory power. There was no difference between the STS score and the EuroSCORE in terms of discriminatory power (p = 0.58) and a difference in the AUC being 0.01. The discriminatory power of the EuroSCORE and the STS score was best in the high-risk category. CONCLUSIONS: Both the EuroSCORE and the STS scores had satisfactory and similar discriminatory power. However, in the Indian population, while the EuroSCORE II overestimated mortality, the STS score underestimated it to a similar degree of error.

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