Biology subjects

Yadav, S.

Publications and source records attributed to Yadav, S..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Zinc nano-fertilization enhances wheat productivity and biofortification

Zinc (Zn) malnutrition has emerged as one of the major health challenges in developing nations across the globe. Development of Zn management protocols in staple food crops using modern scientific tools to enhance Zn concentration in grains along with augmented crop yields became utmost necessary. In this context a 2-year experiment was carried out to assess the effects of zinc oxide nanoparticles (ZnO-NPs) vis-a-vis bulk zinc sulfate (ZnSO4) on wheat growth, yield and Zn concentration in plant parts. Four levels of application of ZnO-NPs (0, 20, 25 and 30 mg kg-1) were compared with ZnSO4 (equal to Zinc concentration in ZnO-NPs). Results revealed that seed vigor was significantly (p <0.05) higher under 25 and 30 mg kg-1 soil ZnO-NPs treatments over ZnSO4. Among the crop yield parameters such as tillers (plant-1), grain weight (plant-1), biomass (plant-1) and grain yield were significantly (p <0.05) higher under ZnO-NPs 25 mg kg-1 treated soil as compared to any other treatment. Zinc concentration in grains increased with dose of ZnO-NPs and it was significantly more than ZnSO4 treated soil at each treatment level. ZnO-NPs and ZnSO4 treatments did not affect photosynthetic rate and chlorophyll (SPAD) content significantly. In conclusion, 25 mg kg-1 ZnO-NPs application could be recommended in wheat cultivation to improve growth, yield and grain Zn biofortification.

plant biology↗

bioRxiv2022

Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane

Mate-allocation in breeding programs can improve progeny performance by exploiting non-additive effects. Breeding decisions in the mate-allocation approach are based on predicted progeny merit rather than parental breeding value. This is particularly attractive when non-additive effects are significant, and the best-predicted progeny can be clonally propagated, for example sugarcane. We compared mate-allocation strategies that leverage non-additive and heterozygosity effects to maximise sugarcane clonal performance to schemes that use only additive effects to maximise breeding value. We used phenotypes and genotypes from a population of 2,909 clones phenotyped in Australias sugarcane breeding programs final assessment trials for three traits: tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and fibre. The clones from the last generation of this data set were used as parents to simulate families from all possible crosses (1,225), each with 50 progenies. The breeding and clonal values of progeny were predicted using GBLUP (considering only additive effects) and the e-GBLUP model (incorporating additive, non-additive and heterozygosity effects). Integer linear programming was used to identify the optimal mate-allocation among the selected parents. Compared to the breeding value, the predicted progeny value of allocated crossing pairs based on clonal performance (e-GBLUP) increased by 57%, 12%, and 16% for TCH, CCS, and fibre, respectively. In our study, the mate-allocation strategy exploiting non-additive and heterozygosity effects resulted in better clonal performance. However, there was a noticeable decline in additive gain, particularly for TCH, which might have been caused by the presence of large epistatic effects. When crosses were chosen based on clonal performance for TCH, progenies inbreeding coefficients were found significantly lower than for random mating, indicating that utilising non-additive and heterozygosity effects has advantages for controlling inbreeding depression. Therefore, mate-allocation is recommended in clonal crops to improve clonal performance and reduce inbreeding.

genomics↗

bioRxiv2022

MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root

Plants deposit lignin in the secondary cell wall as a common response to drought and pathogen attacks. Cell wall localized multicopper oxidase family enzymes LACCASES (LACs) catalyze the formation of monolignol radicals and facilitate lignin formation. We show an upregulation of the expression of several LAC genes and a downregulation of microRNA397 (CamiR397) in response to natural drought in chickpea roots. CamiR397 was found to target LAC4 and LAC17L out of twenty annotated LACs in chickpea. CamiR397 and its target genes are expressed in root. Overexpression of CamiR397 reduced expression of LAC4 and LAC17L and lignin deposition in chickpea root xylem causing reduction in xylem diameter. Downregulation of CamiR397 activity by expressing a short tandem target mimic (STTM397) construct increased root lignin deposition in chickpea. CamiR397-overexpressing (miR397OX) and STTM397 chickpea lines showed sensitivity and tolerance, respectively, to drought. Infection with a fungal pathogen Macrophomina phaseolina, responsible for dry root rot disease in chickpea, induced local lignin deposition and LAC gene expression. CamiR397-overexpressing and STTM397 chickpea lines showed more sensitivity and tolerance, respectively, to dry root rot. Our results demonstrated the regulatory role of CamiR397 in root lignification during drought and dry root rot in an agriculturally important crop chickpea.

plant biology↗

bioRxiv2022

Computational investigations in inhibition of alcohol/aldehyde dehydrogenase in lignocellulosic hydrolysates

Second generation alcoholic biofuels synthesis from lignocellulosic biomass (LB) consists three steps viz., pre-treatment, detoxification, and fermentation. This dilute acid pre-treatment process generates several compounds like acids, aldehydes, ketones, oxides and their phenolic derivatives that are potential inhibitors of some of the crucial enzymes in the metabolic pathway of ABE fermentation. With application of hybrid quantum mechanics/ molecular mechanics (QM/MM) approach, our aim is to discern the molecular mechanism of inhibition of key AADs across solventogenic species. The objectives of present study are: (1) identification and homology modelling of key AADs; (2) validation, quality assessment and physiochemical characterization of the modelled enzymes; (3) identification, construction and optimization of chemical structure of potent microbial inhibitors in LH; and (4) applications of hybrid QM/MM simulations to profile the molecular interactions between microbial inhibitors and key AADs. Our computational investigation has revealed various important facets of inhibition of the AAD enzymes, which could guide structural biologist in designing efficient and robust enzymes. Moreover, our methodology also provides a general framework which could applied for deciphering the molecular mechanism of inhibition behaviour of other enzymes. HighlightsO_LIHomology modelling of 7 alcohol/aldehyde dehydrogenase (AAD) in solventogenic Clostridia C_LIO_LIIdentification and structural optimization of potent microbial inhibitors in lignocellulosic hydrolysates C_LIO_LIQM/MM simulations to profile the molecular interactions between 10 inhibitors and 7 AADs C_LIO_LIDiscernment of the molecular mechanism of inhibition of key alcohol/aldehyde dehydrogenase C_LIO_LIA methodological framework for deciphering the molecular mechanism of enzyme inhibition C_LI

bioinformatics↗

bioRxiv2022

Single-cell imaging based prognosis prediction identifies new breast cancer survival subtypes

Quantitative models that explicitly capture single-cell resolution cell-cell interaction features to predict patient survival at population scale are currently missing. Here, we computationally extracted hundreds of features describing single-cell based cell-cell interactions and cellular phenotypes from a large, published cohort of cyto-images of breast cancer patients. We applied these features to a neural-network based Cox-nnet survival model and obtained high accuracy in predicting patient survival in test data (Concordance Index > 0.8). We identified seven survival subtypes using the top survival features, which present distinct profiles of epithelial, immune, fibroblast cells, and their interactions. We identified atypical subpopulations of TNBC patients with moderate prognosis (marked by GATA3 over-expression) and Luminal A patients with poor prognosis (marked by KRT6 and ACTA2 over-expression and CDH1 under-expression). These atypical subpopulations are validated in TCGA-BRCA and METABRIC datasets. This work provides important guidelines on bridging single-cell level information towards population-level survival prediction. STATEMENT OF TRANSLATIONAL RELEVANCEOur findings from a breast cancer population cohort demonstrate the clinical utility of using the single-cell level imaging mass cytometry (IMC) data as a new type of patient prognosis prediction marker. Not only did the prognosis prediction achieve high accuracy with a Concordance index score greater than 0.8, it also enabled the discovery of seven survival subtypes that are more distinguishable than the molecular subtypes. These new subtypes present distinct profiles of epithelial, immune, fibroblast cells, and their interactions. Most importantly, this study identified and validated atypical subpopulations of TNBC patients with moderate prognosis (GATA3 over-expression) and Luminal A patients with poor prognosis (KRT6 and ACTA2 over-expression and CDH1 under-expression), using multiple large breast cancer cohorts.

bioinformatics↗

bioRxiv2022

Fine-scale variability in coral bleaching and mortality during a marine heatwave

Coral bleaching and mortality can show significant spatial and taxonomic heterogeneity at local scales, highlighting the need to understand the fine-scale drivers and impacts of thermal stress. In this study, we used structure-from-motion photogrammetry to track coral bleaching, mortality, and changes in community composition during the 2019 marine heatwave in K[a]ne ohe Bay, Hawai i. We surveyed 30 shallow reef patches every 3 weeks for the duration of the bleaching event (August-December) and one year after, resulting in a total of 210 large-area, high-resolution photomosaics that enabled us to follow the fate of thousands of coral colonies through time. We also measured environmental variables such as temperature, sedimentation, depth, and wave velocity at each of these sites, and extracted estimates of habitat complexity (rugosity R and fractal dimension D) from digital elevation models to better understand their effects on patterns of bleaching and mortality. We found that up to 80% of corals experienced moderate to severe bleaching in this period, with peak bleaching occurring in October when heat stress (DHW) reached its maximum. Mortality continued to accumulate as bleaching levels dropped, driving large declines in more heat-susceptible species (77% loss of Pocillopora cover) and moderate declines in heat-tolerant species (19% and 23% for Porites compressa and Montipora capitata, respectively). Declines in live coral were accompanied by a rapid increase in algal cover across the survey sites. Spatial differences in bleaching were significantly linked to habitat complexity and coral species composition, with reefs that were dominated by Pocillopora experiencing the most severe bleaching. Mortality was also influenced by species composition, fractal dimension, and site-level differences in thermal stress. Our results show that spatial heterogeneity in the impacts of bleaching are driven by a mix of environmental variation, habitat complexity, and differences in assemblage composition.

ecology↗

bioRxiv2022

Probing Action Potential Generation and Timing under Multiplexed Basal Dendritic Computations Using Two-photon 3D Holographic Uncaging

Basal dendrites of layer 5 cortical pyramidal neurons exhibit Na+ and NMDAR spikes, and are uniquely poised to influence somatic output. Nevertheless, due to technical limitations, how multibranch basal dendritic integration shapes action-potential output remains poorly mapped. Here, we combine 3D two-photon holographic transmitter-uncaging, whole-cell dynamic-clamp, and biophysical modeling, to reveal how synchronously activated synapses (distributed and clustered) across multiple basal dendritic branches impacts action-potential generation - under quiescent and in vivo like conditions. While dendritic Na+ spikes promote milli-second precision, distributed inputs and NMDAR spikes modulate firing rates via axo-somatic persistent sodium channel amplification. Action-potential precision, noise-enhanced responsiveness, and improved temporal resolution, were observed under high conductance states, revealing multiplexed dendritic control of somatic output amidst noisy membrane-voltage fluctuations and backpropagating spikes. Our results unveil a critical multibranch integration framework in which a delicate interplay between distributed synapses, clustered synapses, and axo-somatic subthreshold conductances, dictates somatic spike precision and gain.

neuroscience↗

bioRxiv2022

Lithography-less, frugal and long-term diffusion-based static gradient generating microfluidic device for high-throughput drug testing

Drug testing is a vital step in identification of the potential efficacy of any new/existing drug and/or combinations of drugs. The conventional methods of testing the efficacy of new drugs using multi-well plates are time consuming, prone to evaporation loss and manual error. Microfluidic devices with automated generation of concentration gradient provide a promising alternative. The implementation of such microfluidic devices is still limited owing to the additional expertise and facilities required to fabricate and run these devices. Conventional microfluidic devices also need pumps, tubings, valves, and other accessories, making them bulky and nonportable. To address these problems, we have developed a method for fabricating microfluidic structures using a nonconventional technique by exploiting the Saffman-Taylor instability in lifted Hele-Shaw cell. Multi-channel structure molds with varying dimensions were fabricated by shaping ceramic polymer slurry and retaining the shape. Further using the mold thus made, polydimethyl siloxane (PDMS) devices offering static, stable, diffusion-based gradient were casted using soft lithography. We have demonstrated with COMSOL simulation, as well as using Fluorescein isothiocyanate (FITC), a fluorescent dye, that the concentration gradient can be generated in this device, which remains stable for at least 5 days. Using this multichannel device, in vitro drug efficacy was validated with two drugs namely-Temozolomide (TMZ) and Curcumin, one FDA approved and one under research, on glioblastoma cells (U87MG). The resulting IC50 values were consistent with those reported in literature. We have also demonstrated the possibility of conducting molecular assays post-drug testing in the device by microtubule staining after curcumin treatment on cervical cancer cells (HeLa). In summary, we have demonstrated a i) user-friendly, ii) portable, static drug testing platform that iii) does not require further accessories and can create iv) a stable gradient for long duration. Such a device can reduce the time, manual errors, fabrication and running expenditure, and resources to a great extent in drug testing. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/505813v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@e1f648org.highwire.dtl.DTLVardef@f029d7org.highwire.dtl.DTLVardef@14afd68org.highwire.dtl.DTLVardef@42b888_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

Scalable large-area mesh-structured microfluidic gradient generator for drug testing applications

Microfluidic concentration gradient generators are useful in drug testing. drug screening, and other cellular applications to avoid manual errors, save time, and labor. However, expensive fabrication techniques make such devices prohibitively costly. Here, in the present work, we developed a microfluidic concentration gradient generator (CGG) using a recently proposed non-conventional photolithography-less method. In this method, ceramic suspension fluid was shaped into a square mesh by controlling Saffman Taylor instability in a Multiport Lifted Hele-Shaw Cell (MLHSC). Using the shaped ceramic structure as template, the microfluidic concentration gradient generator (CGG) was prepared by soft lithography. The concentration gradient was characterized and effect of the flow rates were studied usingCOMSOL simulations. The simulation result was further validated by creating fluorescein dye (Fluorescein isothiocanate, FITC) gradient in the fabricated CGG. To demonstrate the use of this device for drug testing, we created various concentrations of an anticancer drug - curcumin - using the device and determined its inhibitory concentration on cervical cancer cell-line HeLa. We found that the IC50 of curcumin for HeLa to be 28.6 {+/-} 6.1 M which matched well with the conventional muti-well drug testing method (34.9 {+/-} 1.7 M). This method of CGG fabrication has multiple advantages over conventional photolithography such as: i) the channel layout and inlet-outlet arrangements can be changed by simply wiping the ceramic fluid before it solidifies, (ii) it is cost effective, (iii) large area patterning is easily achievable, and (iv) the method is scalable. This technique can be utilised to achieve broad range of concentration gradient to be used for various biological and non-biological applications. Table of Content O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/500002v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@d0bb65org.highwire.dtl.DTLVardef@1bef09dorg.highwire.dtl.DTLVardef@a6ebe8org.highwire.dtl.DTLVardef@c9dd17_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

Neurodevelopmental disorder associated mutations in TAOK1 reveal its function as a plasma membrane remodeling kinase

Mutations in TAOK1, a serine-threonine kinase encoding gene are strongly associated with both autism spectrum disorder (ASD) and neurodevelopmental delay (NDD). However, molecular function of this evolutionarily conserved kinase and the mechanisms through which TAOK1 mutations lead to neuropathology are unknown. Here, we showed that TAOK1 is highly expressed in neurons within the brain, and has a functional role in remodeling the plasma membrane through direct association with phosphoinositides. We characterized four NDD-associated TAOK1 mutations, and demonstrated that these mutations render TAOK1 catalytically dead. Kinase dead TAOK1 mutants were aberrantly trapped in membrane-bound state, which induced exuberant membrane protrusions. Expression of TAOK1 disease mutants in hippocampal neurons led to abnormal growth of the dendritic arbor. The coiled-coil region C-terminal to the kinase domain are predicted to fold into a triple helix. We showed that this triple helix directly bound phospholipids, and was required for both TAOK1 membrane association and induction of aberrant protrusions. Further, TAOK1 mutants were rescued from their membrane-trapped state by exogenous expression of the isolated kinase domain. Utilizing mass-spectrometry, we identified critical residues in the triple helix phosphorylated by TAOK1 that autoregulated its plasma membrane association. These findings define a previously unknown function of TAOK1 as a unique plasma membrane remodeling kinase, and reveal the underlying mechanisms through which TAOK1 dysfunction leads to neurodevelopmental disorders.

neuroscience↗

bioRxiv2022

Imaging the structure and dynamic activity of retinal microglia and macrophage-like cells in the living human eye

PurposeWe recently showed how a refined sequential detection pattern and image processing pipeline for multi-offset adaptive optics scanning light ophthalmoscopy (AOSLO) can increase the contrast of weakly scattering inner retinal structures, including microglia. However, sequential detection was still time-consuming, preventing dynamics from being monitored over short intervals (< 3 mins). Here we show that simultaneous fiber-bundle (FB) detection can overcomes this limitation to reveal the structure and dynamic activity of microglia and macrophage-like cells in healthy and diseased retinae. MethodsWe designed and implemented a custom 7-fiber optical FB with one central confocal fiber and six larger fibers for multi-offset detection in AOSLO at a single focal plane. We imaged the ganglion cell layer at several locations at multiple timepoints (from minutes to weeks) in 8 healthy participants and in 4 patients with ocular infections or inflammation, including ocular syphilis and posterior uveitis. Microglia and immune cells were manually segmented to quantify cell morphometry and motility. ResultsFiber-bundle detection reduced single acquisition time to 20-30 seconds, enabling imaging over larger areas and monitoring of dynamics over shorter intervals. Presumed microglia in healthy retinas had an average diameter of 12.8 m and with a spectrum of morphologies including circular cells and elongated cells with visible processes. We also detected the somas of putative macroglia, potentially astrocytes, near the optic nerve head. Microglia moved slowly in normal eyes (0.02m/sec, on average) but speed increased in patients with active infections or inflammation (up to 2.37m/sec). Microglia activity was absent in a patient with chronic uveitis that was quiescent but apparent over short intervals in an active uveitis retina. In a patient with ocular syphilis imaged at multiple timepoints during treatment, macrophage-like cells containing granular internal structures were seen. Decreases in the quantity and motility of these immune cells were correlated with improvements to vision and other structural and systemic biomarkers. ConclusionsFB-AOSLO enable simplified optical setup with easy alignment and implementation. We imaged the fine-scale structure and dynamics of microglia and macrophage-like cells during active infection and inflammation in the living eye for the first time. In healthy eyes we also detected putative glia cell near the optic nerve head. FB-AOSLO offers promise as a powerful tool for detecting and monitoring retinal inflammation and infection in the living eye over short response to treatment.

bioengineering↗

bioRxiv2022

Proteomic identification of phosphorylation dependent Septin 7 interactors that drive dendritic spine formation

Septins are a family of cytoskeletal proteins that regulate several important aspects of neuronal development. Septin 7 (Sept7) is enriched at the base of dendritic spines in excitatory neurons and mediates both spine formation and spine-synapse maturation. Phosphorylation at a conserved C-terminal tail residue of Sept7 mediates its translocation into the dendritic spine head to allow spine-synapse maturation. The mechanistic basis for postsynaptic stability and compartmentalization conferred by phosphorylated Sept7, however, is not known. We report herein the proteomic identification of Sept7 phosphorylation dependent neuronal interactors. Using Sept7 C-terminal phosphopeptide pulldown and biochemical assays, we show that the 14-3-3 family of proteins specifically interact with Sept7 when phosphorylated at the T426 residue. Biochemically, we validate the interaction between Sept7 and 14-3-3 isoform gamma, and show that 14-3-3 gamma is also enriched in mature dendritic spine head. Further, we demonstrate that interaction of phosphorylated Sept7 with 14-3-3 protects it from dephosphorylation, as expression of a 14-3-3 antagonist significantly decreases phosphorylated Sept7 in neurons. This study identifies 14-3-3 proteins as an important physiological regulator of Sept7 function in neuronal development.

neuroscience↗

bioRxiv2021

Single-cell genetic heterogeneity linked to immune infiltration in glioblastoma.

Glioblastoma (GBM) is the most aggressive brain tumor with a median survival of ~15 months. Targeted approaches have not been successful in this tumor type due to the large extent of intratumor heterogeneity. Mosaic amplification of oncogenes suggests that multiple genetically distinct clones are present in each tumor. To uncover the relationships between genetically diverse subpopulations of GBM cells and their native tumor microenvironment, we employed highly multiplexed spatial protein profiling, coupled with single-cell spatial mapping of fluorescence in situ hybridization (FISH) for EGFR, CDK4, and PDGFRA. Single-cell FISH analysis of a total of 35,843 single nuclei (~2,100 per tumor) revealed that tumors in which amplifications of EGFR and CDK4 more frequently co-occur in the same cell exhibit higher infiltration of CD163+ immunosuppressive macrophages. Our results suggest that high throughput assessment of genomic alterations at the single cell level could provide a measure for predicting the immune state of GBM.

cancer biology↗

bioRxiv2021

Bacterial keratitis: similar bacterial and clinical outcomes in female versus male New Zealand White rabbits infected with Serratia marcescens

Females and males respond differently to a number of systemic viral infections. Differences between females and males with respect to the severity of keratitis caused by Gram-negative bacteria such as Serratia marcescens are less well established. In this study we injected female and male New Zealand White rabbit corneas with a keratitis isolate of S. marcescens and evaluated the eyes after 48 hours for a number of clinical and microbiological parameters. No statistical differences in bacterial burden and corneal scores were recorded between female and male rabbits although there was a non-significant trend toward a higher frequency of female rabbits demonstrating hypopyons. This data suggests that for experimental bacterial keratitis studies involving Gram-negative rods, a single sex or mixed group of rabbit is sufficient for evaluating pathology and bacterial burdens. This will reduce the number of animals used for subsequent studies.

microbiology↗

bioRxiv2021

Development of a transboundary model of livestock disease in Europe

Epidemiological models of notifiable livestock disease are typically framed at a national level and targeted for specific diseases. There are inherent difficulties in extending models beyond national borders as details of the livestock population, production systems and marketing systems of neighbouring countries are not always readily available. It can also be a challenge to capture heterogeneities in production systems, control policies, and response resourcing across multiple countries, in a single transboundary model. In this paper we describe EuFMDiS, a continental-scale modelling framework for transboundary animal disease, specifically designed to support emergency animal disease planning in Europe. EuFMDiS simulates the spread of livestock disease within and between countries and allows control policies to be enacted and resourced on per-country basis. It provides a sophisticated decision support tool that can be used to look at the risk of disease introduction, establishment and spread; control approaches in terms of effectiveness and costs; resource management; and post-outbreak management issues.

bioinformatics↗

bioRxiv2021

TAOK2 is an ER-localized Kinase that Catalyzes the Dynamic Tethering of ER to Microtubules

The endoplasmic reticulum (ER) depends on extensive association with the microtubule cytoskeleton for its structure, function and mitotic inheritance. The identity of molecular tethers that mediate ER-microtubule coupling, and mechanisms through which dynamic tethering is regulated are poorly understood. Here, we identify, Thousand And One amino acid Kinase 2 (TAOK2) as a pleiotropic protein kinase that mediates tethering of ER to microtubules. We show that TAOK2 is a unique multipass membrane spanning serine/threonine kinase localized in distinct ER domains via four transmembrane and amphipathic helices. Using in vitro and cellular assays, we find that TAOK2 directly binds microtubules with high affinity. We define the minimal TAOK2 determinants that induce ER-microtubule tethering, and delineate the mechanism for its autoregulation. While ER membrane dynamics are increased in TAOK2 knockout cells, the movement of ER along growing microtubule plus-ends is disrupted. We show that ER-microtubule tethering is tightly regulated by catalytic activity of TAOK2 in both interphase and mitotic cells, perturbation of which leads to profound defects in ER morphology and cell division. Our study identifies TAOK2 as an ER-microtubule tether, and reveals a kinase-regulated mechanism for control of ER dynamics critical for cell growth and division.

cell biology↗

bioRxiv2021

Auxin-responsive (phospho)proteome analysis reveals regulation of cell cycle and ethylene signaling during rice crown root development

The rice root system, which primarily consists of adventitious/crown roots (AR/CR) developed from the coleoptile base, is an excellent model system for studying shoot-to-root trans-differentiation process. We reveal global changes in protein and metabolite abundance, and protein phosphorylation in response to an auxin stimulus during CR development. Global proteome and metabolome analyses of developing crown root primordia (CRP) and emerged CRs uncovered that the biological processes associated with chromatin conformational change, gene expression, and cell cycle were translationally regulated by auxin signaling. Spatial gene expression pattern analysis of differentially abundant proteins disclosed their stage-specific dynamic expression pattern during CRP development. Further, our tempo-spatial gene expression and functional analyses revealed that auxin creates a regulatory feedback module during CRP development and activates ethylene biosynthesis exclusively during CRP initiation. Ethylene signaling promotes CR formation by repressing the cytokinin response regulator, OsRR2. Additionally, the (phospho)proteome analysis identified differential phosphorylation of the Cyclin-dependent kinase G-2 (OsCDKG;2), and cell wall proteins, in response to auxin signaling, suggesting that auxin-dependent phosphorylation may be required for cell cycle activation, and cell wall synthesis during root organogenesis. Thus, our study provides evidence for the translational and post-translational regulation during CRP trans-differentiation downstream of the auxin signaling pathway. HighlightGlobal (phospho)proteome and metabolic profiling of rice CRP and CRs uncover differential proteins and metabolites associated with gene expression, cell cycle, ethylene signaling and cell wall synthesis during CR development.

plant biology↗

bioRxiv2021

Response of rhizobial strains on biochemical traits and nutrient uptake in Mungbean (Vigna radiata L. Wilczek) under moisture stress

The present study was conducted to assess the biochemical responses and nutrient uptake in response to rhizobial inoculations in mungbean, and to screen the rhizobial isolates for drought tolerance. A field experiment was designed in randomized block design and replicated thrice during kharif 2016 at Crop Physiology Field Area, CCS, Hisar. The experiment consisted of two levels of treatments (1) without inoculation (only RDF) and (2) with inoculation (RDF with combination of five rhizobial strains viz. Vigna 703 + PSB strain P-36, MR 63, MR 54, MB 17a and MH 8b2) and two environments i.e. rainfed (no post sowing irrigation) and irrigated. Membrane stability index, leghaemoglobin content, chlorophyll content reduced by 17.7 %, 24.5% and 2.9% resp. under rainfed conditions while the plants inoculated with rhizobial isolate MR63 and MB 17a showed greater chlorophyll content (20.2% and 16.2%), LHb (29.1% and 22.9%) and MSI (19.4% and 17.9%) and enhanced nutrient uptake over RDF.

physiology↗