Variants of SARS-CoV-2, their effects on infection, transmission and neutralization by vaccine-induced antibodies.

OBJECTIVE: The current study reviewed Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) variants for their effects on infection, transmission and neutralization by vaccine-induced antibodies. MATERIALS AND METHODS: The research articles for the current study were searched over PubMed, Google Scholar, EMBASE and Web of Science online databases. The keywords used were: (("SARS-CoV-2" OR "COVID-19") AND ("mutation" OR "variant") AND ("death" OR "hospitalization" OR "infection" OR "transmission") AND ("antibody" OR "neutralize" OR "vaccine")). A total of 333 research articles were retrieved through online-database search. These articles were further scrutinized for their relevancy. Additionally, searches were performed to find the latest relevant information over Google search engine and relevant news browsers. Finally, around 35 germane articles were considered for scripting the current report. RESULTS: The mutations have changed amino acids at key positions in spike protein viz. S477N, E484K, Q677H, E484Q, L452R, K417T, K417N and N501Y. These mutations are relevant for different characteristics and are present in newly evolved strains of SARS-CoV-2 like E484K in B.1.526, B.1.525, P.2, B.1.1.7, P.1 and B.1.351. Mutations have increased the immune escape potential leading to 3.5-6.5-folds decrease in neutralization of antibodies (Pfizer and Moderna vaccines). The variant, B.1.617 circulating in India and many other countries (double variant) having E484Q and L452R mutations, has raised the infection rate and decreased the neutralization capacity of the vaccine-induced antibodies. Deadly K417N+E484K+N501Y triplet mutations found in B.1.351 and P.1 have increased the transmission ability of these strains by 50% leading to greater COVID-19 hospitalization, ICU admissions and deaths. CONCLUSIONS: The new SARS-CoV-2 variants have compromised the neutralization potential of the currently used vaccines, but still, they have considerable efficacy to reduce infection and mortality. GRAPHICAL ABSTRACT: https://www.europeanreview.org/wp/wp-content/uploads/Graphical_Abstract.jpg.

Defect mediated magnetic transitions in Fe and Mn doped MoS2.

We report single-phase syntheses of undoped 2H-MoS2 as well as Mn and Fe doped MoS2 by a facile hydrothermal route. The formation of the 2H-MoS2 phase was confirmed by XRD and was corroborated with Raman spectra. The morphology of the doped and undoped MoS2 nanostructures comprised sheets, as revealed by TEM and STEM images. The fine granular structure was observed by high resolution TEM micrographs. The STEM-EDS results show dopant concentrations of ∼1 atom% corresponding to Mn and Fe in doped MoS2. The undoped MoS2 revealed diamagnetic behavior at room temperature and paramagnetic behavior in the range (100 to 300 K). The Mn-MoS2 sample displayed ferromagnetism below 20 K with a coercive field of ∼50 Oe. Such a sample may be utilized for magnetic switching purposes at low temperatures. The onset of the antiferromagnetic interaction was observed below 145 K in Fe-MoS2 samples. They have been understood in terms of long-range magnetic interactions amongst the dipole moments mediated via surface defects as well as the interaction between the dipoles and the surface charges. The findings are corroborated with the help of EPR studies.

Cumulative Risk of Metabolic Syndrome Correlated with the Coexistence of (-1306C/T) and Altered Circulating MMP2 level.

BACKGROUND: Interindividual genetic variations and environmental factors both play pivotal roles in the pathogenesis of metabolic syndrome (MetS). The rationale of this study conducted was to analyze the association of Matrix Metalloproteinase (MMP) gene variants, MMP-1 (-1607 1G/2G) and MMP-2 (-1306 C/T) with susceptibility to MetS and its effect on serum MMP level. METHODS: Study involved 370 subjects with 1:1 distribution of cases and controls. Patients were recruited according to modified NCEP-ATP III criteria for MetS. Clinical, biochemical analysis, PCR-RFLP and ELISA methods were employed for genotyping and estimation of serum MMP level. RESULTS: Significantly (p<0.001) higher Serum MMP-2 (39.13±19.96 ng/ml) was detected in cases as compared to controls. The MMP-2 (-1306 C/T) was significantly associated with the risk of MetS. The variant genotype TT was significantly associated with increased risk of MetS. (p=0.032; OR=2.31; 95%CI=1.07-4.97). No significant association of MMP-1(-1607 1G/2G) was found with risk of MetS. CONCLUSION: Our study concluded that presence of MMP-2 (-1306 C/T) might be associated the risk of MetS. Serum MMP2 level was significantly higher in patients and correlated with clinical parameters of MetS. Clinical implication of the work may help to identify the individuals with high risk of MetS and further complications.

Association of death receptor 4, Caspase 3 and 5 gene polymorphism with increased risk to bladder cancer in North Indians.

PURPOSE: Perturbed apoptosis due to missense alterations in candidate tumor suppressor gene Death receptor 4 (DR4) and in caspases (Casp) lead to deregulated cell proliferation and cancer predisposition. Some data indicate that normal variations within the sequence of apoptotic genes may lead to suboptimal apoptotic capacity and therefore increased cancer risk. To test our proposal we examined whether six single nucleotide polymorphisms (SNPs) of the DR4 and Casp3, 5 genes contrive the risk of bladder cancer (BC) in a North Indian population. MATERIALS AND METHODS: Genotyping was performed in 200 BC patients and 225 controls by Allele-specific PCR and by polymerase chain reaction-restriction fragment length polymorphism. RESULTS: In DR4 Arg141His, BC patients having AA genotype (p = 0.036; OR = 2.51. In Casp5Leu13Phe G > C, significant association was observed with GC (p = 0.025; OR = 1.78) and also in GC + CC (p = 0.026; OR = 1.68). C allele carriers in Casp5Ala90Thr T > C showed low risk of BC (p = 0.036; OR = 0.83). While in Casp3 G > A, AG (p = 0.003; OR = 2.11), GG (p = 0.050; OR = 2.18), G allele (p < 0.001; OR = 1.85) and its carrier AG + GG (p = 0.001; OR = 2.12) have shown significant BC risk. Significant association between DR4 Ala228Glu polymorphism and smoking was observed in BC risk. Haplotype analysis demonstrated that DR4 (Thr209Arg-Arg141His-Ala228Glu) C-G-C is associated with 1.8 folds (OR = 1.85; p = 0.033) risk. GG genotype of Casp3 G > A polymorphism showed increased risk of recurrence (p = 0.009; HR = 5.20). CONCLUSION: This study provided new support for the association of DR4 and Casp3, 5 in BC development, the tumorigenic effect of which was observed to be more enhanced in case of smoking exposure.

Dielectric relaxation in a single tryptophan protein.

Although dielectric relaxation can significantly affect the intrinsic fluorescence properties of a protein, usually it is fast compared to fluorescence timescales and needs to be slowed down by adding viscogens or lowering temperature before its impact on fluorescence can be studied. We report here a remarkable blue shift in fluorescence upon bimolecular quenching in the single-tryptophan thermostable protein Bj2S, the 2S seed albumin from Brassica juncea, at ambient temperature and viscosity. The magnitude of the blue shift ( approximately 5 nm at 50% quenching by acrylamide) is striking in a single-tryptophan protein and is attributed to a slowly relaxing dielectric environment in Bj2S from red edge excitation, steady-state polarization and time-resolved fluorescence experiments. Our results have important implications on interpretation of fluorescence of proteins with highly constrained backbones and in designing model systems for studying slow protein solvation dynamics using Trp fluorescence as the reporter probe.

Cloning and sequencing of an apparently recombinant promoter for napin gene from Brassica campestris genomic library and its evolutionary significance.

From a genomic library of Brassica campestris (brown sarson cv. B54), we have cloned and sequenced about 2 kb of upstream regulatory region from one of the 2S albumin-coding gene family. The sequence has several seed-specific promoter motifs. A sequence alignment of the 5' flanking regions of the available Brassica 2S storage protein genes showed that our sequence is a double crossover recombinant product of the two members of the napin gene family. A possible explanation of this fact is that Brassica species evolved through gene duplication and recombination from a common ancestor with fewer number of chromosomes and genes.

Characterization of MboI satellites in Cirrhina mrigala and Clarias batrachus (Pisces).

We have cloned and characterized two highly reiterated, tandemly repeated, and A+T rich MboI DNA fragments, one in Cirrhina mrigala (Cyprinidae), with a monomer size of 266 bp, and one in Clarias batrachus (Clariidae), with a monomer size of 227 bp. The MboI fragment in C. mrigala is species-specific and absent in other carps, such as Catla catla and Labeo rohita. The MboI fragment in C. batrachus was also present in two other catfishes tested, namely Clarias gariepinus and Heteropneustes fossilis. In C, mrigala x C. catla and C. mrigala x L. rohita hybrids, the C. mrigala specific MboI fragment is inherited uniparentally. In the reciprocal hybrids of C. batrachus x H. fossilis, the satellite ladder contains the bands of both parental species. The MboI satellite of carp may be useful in genetic introgression analysis and that of catfish in distinguishing between gynogenetic progeny and true hybrids.

Deduced amino acid sequence of 2S storage protein from Brassica species and their conserved structural features.

2S seed storage albumin coding regions from five Brassica species, namely Brassica campestris, B. oleracea, B. nigra, B. juncea, and B. carinata have been cloned by PCR amplification of genomic DNA using oligonucleotide primers and their nucleotide sequences have been determined. These sequences showed more than 85% homology amongst themselves and considerable homology with some other crucifer 2S protein coding sequences. The deduced amino acid sequences showed more homology due to some inconsequential mutations in codons without changing the amino acids. Computer analysis of the protein sequences for possible secondary structure revealed a high degree of conservation of hydrophilic and hydrophobic domains and the invariant positions of cysteine residues. Unrooted phylogenic tree based on the coding region of 2S albumin from different Brassica species cloned by us and published sequences from other Cruciferae indicated that these genes originated before the evolutionary divergence of different Brassica species and were conserved due to some stringent structural and functional features required for seed metabolism.

Bypassing successive cloning of two fragments by one step cloning using polymerase chain reaction.

The polymerase chain reaction (PCR) was used for bringing together two DNA fragments present in two different plasmids. This helped avoiding the difficulties of two successive subcloning in the same plasmid and uncertainities of obtaining rightly oriented constructs. Two different fragments of DNA present in different plasmid were digested with the same enzyme and then ligated. The ligation mixture was used for the PCR using two oligo primers; one was specific for the 5' end of the other fragment and the other one was for the 3' end of the other fragment. The desired amplified fragment was separated by gel electrophoresis, eluted and was cloned in plasmid pBluescript KS(+). The same procedure is also applicable for one step cloning of more than two fragments in desired orientation.

Cloning and sequencing of 5' flanking sequence from the gene encoding 2S storage protein, from two Brassica species.

Using oligodeoxyribonucleotide primers and the polymerase chain reaction, we have cloned and sequenced about 1.2 kb of upstream sequences from two members of the 2S seed storage protein-encoding gene family from Brassica juncea and B. oleracea. The two sequences bear more than 90% homology and have characteristic seed-specific promoter motifs. The high degree of sequence conservation indicates that this napin-encoding gene family evolved earlier than the divergence of the three primary Brassica species and their amphidiploids, and the sequences have been conserved due to some metabolic constraints in seed development.

Characterisation of 2S albumin with nutritionally balanced aminoacid composition from the seeds of Chenopodium album and its antigenic homology with seed proteins of some Chenopodiaceae and Amaranthaceae species.

The low molecular weight 2S albumin protein of Chenopodium album seeds has been isolated and characterized with respect to its subunit structure by SDS-PAGE and antigenic homology with low molecular weight seed storage proteins of several other phylogenetically related species by immunoprecipitation and Western blotting. These studies revealed the existence of antigenically homologous proteins of similar molecular weights in seeds of some other members of Chenopodiaceae and Amaranthaceae. However, Chenopodium 2S albumin is antigenically unrelated to low mol.wt. albumins of dicots belonging to other families. It has a nutritionally balanced aminoacid composition in respect of essential aminoacids.

Characterization of 2S seed storage protein of Brassica campestris and its antigenic homology with seed proteins of other Cruciferae.

The low molecular weight seed storage protein of Brassica campestris has been isolated and its amino acid composition determined. Antibody raised against this low molecular weight protein has been used to compare the antigenic similarity between the low molecular weight storage proteins of different Cruciferae seeds by immunoprecipitation and Western blotting. These studies revealed the existence of antigenically homologous proteins of identical molecular weights in seeds of other Cruciferae but absent in some other dicots like mung bean and tobacco seeds.

Organization and size class homogeneity of ribosomal RNA genes of catfish Heteropneustes fossilis.

The ribosomal RNA genes of catfish Heteropneustes fossilis Bloch were examined by Southern blot analysis of genomic DNA digested with restriction enzymes and probed with labelled catfish ribosomal RNA. The major repeat length is 12 kb and about 300 copies per haploid genome are tandemly arranged. The repeat lengths are homogeneous in size in different tissues and individuals. A restriction site polymorphism exists in some of the repeats.

Cloning and characterization of a highly repetitive fish nucleotide sequence.

We have cloned and sequenced a highly repetitive HindIII fragment of DNA from the common carp Cyprinus carpio. It represents a tandemly repeated sequence with a monomeric unit of 245 bp and comprises 8% of the fish genome. Higher units of this monomer appear as a ladder in Southern blots. The monomeric unit has been sequenced; it is A + T-rich with some direct and some inverse-repeat nucleotide clusters.