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Biology subjects

Tiwari, M.

Publications and source records attributed to Tiwari, M..

23 records · Page 2Linked to original sources

Heterogeneous strains in tissue collagen show that high strains locally suppress degradation by collagenase

Collagen, the most abundant protein in mammals, contributes to the physical properties of different tissues during development, homeostasis, and disease. The adaptation of physical properties of tissues to mechanical stimuli is thus dependent on the control of tissue collagen levels by well-regulated synthesis and degradation of collagen. Importantly, how various molecular-level events within a tissue sustaining a range of mechanical strains contribute towards maintaining its collagen levels, remains unclear to date. Such molecular level processes in tissues are studied here in the case of isolated tendons consisting of collagen fibrils oriented along tissue loading-axis and beating embryonic hearts to gain understanding of mechanical load dependent tissue sculpting. Using a novel bioreactor design, starved mice tail tendon fascicles were used as a "cell-free" model and were subjected to heterogeneous and uniaxial deformation modes. Patterned photobleaching of fluorescent probes, a novel Aza-peptide or dye, on fascicles used to quantify tissue strains. Tissue microstructure was simultaneously imaged using second harmonic generation (SHG) signal to assess tissue collagen content while deformed fascicle samples were exposed to purified matrix metalloproteinase-1 (MMP-1) or bacterial collagenase (BC). A decrease in the degradation rate (relative to strain-free) was observed for physiological strain limits of tendon tissue (i.e. [~]5-8%) while at higher strains (i.e. pathological) the degradation rate was independent of strain magnitude changes. Interestingly, the strain dependence of degradation rate was independent of cleavage-site specificity of the collagenase molecules and the mode of tendon tissue deformation. Although spatially different within a tissue sample, the values of strain, degradation rate and collagen fiber organization with time during degradation of each tendon fascicle region were highly correlated. Tendon regions dominated by collagen fibers inclined to fascicle-axis were observed to follow non-affine deformation. The dependence of the degradation rate on mechanical strain is due to sequestration of collagen cleavage sites within fibrils. Permeation, tissue mass density and mobility of fluorescent collagenase and dextran are strain-independent for fascicle strains up to [~]5-8% while the degradation rate is positively correlated to unfolded triple-helical collagen content. Normal beating chick hearts subjected to [~]5% peak strain in a spatiotemporal coordinate contractile wave were observed to maintain their collagen mass until the beating strain is suppressed by inhibition of myosin-II. Based on the presence of exogeneous MMP inhibitors, endogenous MMPs within the non-beating hearts degrade the collagens immediately (in [~]30-60 mins). Both tissue systems under mechanical strains suggest degradative sculpting where mechanical strain-dependent collagen fibril architecture changes appear to play a key role in determining collagen lifetime within tissues. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=139 HEIGHT=200 SRC="FIGDIR/small/430141v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@17da11borg.highwire.dtl.DTLVardef@dbfb8forg.highwire.dtl.DTLVardef@6069b9org.highwire.dtl.DTLVardef@1bd273e_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Loss of clathrin heavy chain enhances actin-dependent stiffness of mouse embryonic stem cells

Mouse embryonic stem cells (mESCs) display unique mechanical properties, including low cell stiffness, and specific responses to features of the underlying substratum. Using atomic force microscopy (AFM), we demonstrate that mESCs lacking the clathrin heavy chain (Cltc), display higher Youngs modulus, indicative of greater cellular stiffness, in comparison to WT mESCs. We have previously shown that mESCs lacking Cltc display a loss of pluripotency, and an initiation of differentiation. The increased stiffness observed in these cells was accompanied by the presence of actin stress fibres and accumulation of the inactive, phosphorylated, actin binding protein, Cofilin. Treatment of Cltc knockdown mESCs with actin polymerization inhibitors resulted in a decrease in the Youngs modulus, to values similar to those obtained with WT mESCs. However, the expression profile of pluripotency factors was not rescued. This indicates that a restoration of mechanical properties, through modulation of the actin cytoskeleton, may not always be accompanied by a change in the expression of critical transcription factors that regulate the state of a stem cell, and that this may be dependent on the presence of active endocytosis in a cell.

cell biology↗

Investigating the genomic landscape in novel coronavirus (2019-nCoV) genomes to identify non-synonymous mutations for use in diagnosis and drug design

Novel coronavirus has wrecked medical and health care facilities claiming ~5% death tolls globally. All efforts to contain the pathogenesis either using inhibitory drugs or vaccines largely remained futile due to a lack of better understanding of the genomic feature of this virus. In the present study, we compared the 2019-nCoV with other coronaviruses, which indicated that bat-SARS like coronavirus could be a probable ancestor of the novel coronavirus. The protein sequence similarity of pangolin-hCoV and bat-hCoV with human coronavirus was higher as compared to their nucleotide similarity denoting the occurrence of more synonymous mutations in the genome. Phylogenetic and alignment analysis of 591 novel coronaviruses of different clades from Group I to Group V revealed several mutations and concomitant amino acid changes. Detailed investigation on nucleotide substitution unfolded 100 substitutions in the coding region of which 43 were synonymous and 57 were of non-synonymous type. The non-synonymous substitutions resulting into 57 amino acid changes were found to be distributed over different hCoV proteins with maximum on spike protein. An important diamino acid change RG to KR was observed in ORF9 protein. Additionally, several interesting features of the novel coronavirus genome have been highlighted in respect to various other human infecting viruses which may explain extreme pathogenicity, infectivity and simultaneously the reason behind failure of the antiviral therapies. SummaryThis study presents a comprehensive phylogenetic analysis of SARS-CoV2 isolates to understand discrete mutations that are occurring between patient samples. This analysis will provide an explanation for varying treatment efficacies of different inhibitory drugs and a future direction towards a combinatorial treatment therapies based on the kind of mutation in the viral genome.

genetics↗

Identification of miRNAs and their corresponding mRNA targets from chickpea root infected with M. ciceri and functional characterization of candidate miRNAs by overexpression in chickpea roots

O_LILegumes developed symbiotic associations with rhizobia to meet its nitrogen requirement. The nitrogen fixation takes place in root nodules which involves bacterial colonization, organogenesis and nitrogen fixation. C_LIO_LIOne microRNA and four parallel analysis of RNA ends (PARE) libraries were sequenced to unravel the miRNA mediated regulation of symbiosis in chickpea. C_LIO_LISequencing of microRNA library identified a set of 91 miRNAs comprising of 84 conserved and 7 novel miRNAs. Additionally, PARE library analysis revealed 564 genes being targeted by 85 miRNAs. C_LIO_LIPhylogenetic analysis of the precursor sequences of the 91 miRNAs clearly indicated a clustering of two distinct miRNAs in the same clade representing a close ancestral precursor. C_LIO_LIFurther, biogenesis of miRNAs was predicted using the miRNAs identified from different legume genomes. C_LIO_LIThe miRNA reads from the nodule library were also mapped onto bacterial genomes from which bacterial small RNA were predicted. C_LIO_LIThe antagonistic expression of some of the miRNA-target pairs was investigated and the negative co-related expression profiling proved the validity of the libraries and the miRNA-target pairs. Four miRNAs were selected based on the antagonistic expression profiling and were ectopically expressed in chickpea roots by hairy root transformation. C_LIO_LIThe overexpression lines showed significant change in nodule numbers. The target of miR171f (NRK), miR394 (HP) and miR1509 (AK) are novel ones being reported for the first time. This analysis opens a wide arena for investigation of the novel miRNAs and target pairs, polycistronic miRNAs and the bacterial derived smRNAs predicted in this study. C_LI

plant biology↗

Global analysis of Two Component System (TCS) member of chickpea and other legume genomes implicates its role in enhanced nodulation

Nodule organogenesis is governed primarily by phytohormone cytokinin. We observed the significant nodulation in chickpea at particular cytokinin concentration (2.5x10-7) which indicated the importance of cytokinin in nodule development. Cytokinin signaling is mediated through the Two Component System (TCS) which comprises of sensor histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs). Therefore, we analyzed the interconnection of cytokinin with TCS molecules during root nodule development through global analysis of TCS candidates in legumes with special consideration to cytokinin receptor and Type-B RR member. We have conducted an in depth global analysis of TCS family members in chickpea and other legumes, Medicago and pigeon pea. Higher number of TCS genes were found in Medicago (96), followed by pigeonpea (75) and chickpea (67). A good correlation between TCS members with their corresponding total number of genes were observed in all three-legume species. Collinearity analysis of TCS revealed phylogenetically closer proximity of Cicer to Medicago followed by Glycine than Cajanus. Comprehensive analysis of 3-dimensional structure, genomic organisation and domain arrangement showed a conservation of TCS members within species. In depth investigation showed that HKs were mainly conserved among TCS members in legumes and non-legumes while divergence occurred at level of RRs. Further, Type-B RRs were functionally most diversified in RRs based on phylogeny, syntenic and transcript analysis. Few numbers of segmentally duplicated pair of TCS showed difference in their transcriptional regulation suggesting the functional evolution. For functional characterization the cre1 mutants of (Medicago) were complemented with chickpea cytokinin responsive HKs and nodulation deficient phenotype of mutants were restored. A synchronous cytokinin-induced expression of chickpea cytokinin receptor HKs and CaNIN provides strong relation of cytokinin signaling during nodulation. Furthermore, interesting potential candidate CaRR13 was selected to deduce the underlying molecular mechanism of nodulation, chickpea in specific and legumes in general.

genomics↗