Biology subjects

Chaudhary, A.

Publications and source records attributed to Chaudhary, A..

27 records · Page 2Linked to original sources

bioRxiv2020

Cell wall damage attenuates root hair cell patterning and tissue morphogenesis mediated by the Arabidopsis receptor kinase STRUBBELIG.

Cell wall remodeling is essential for the control of growth and development as well as the regulation of stress responses. However, the underlying cell wall monitoring mechanisms remain poorly understood. Regulation of root hair fate and flower development in Arabidopsis thaliana requires signaling mediated by the atypical receptor kinase STRUBBELIG (SUB). Furthermore, SUB is involved in cell wall integrity signaling and regulates the cellular response to reduced levels of cellulose, a central component of the cell wall. Here, we show that continuous exposure to sub-lethal doses of the cellulose biosynthesis inhibitor isoxaben results in altered root hair patterning and floral morphogenesis. Genetically impairing cellulose biosynthesis also results in root hair patterning defects. We further show that isoxaben exerts its developmental effects through the attenuation of SUB signaling. Our evidence indicates that down-regulation of SUB is a multi-step process and involves changes in SUB complex architecture at the plasma membrane, enhanced removal of SUB from the cell surface, and downregulation of SUB transcript levels. The results provide molecular insight into how the cell wall regulates cell fate and tissue morphogenesis.

plant biology↗

bioRxiv2020

Ageratina adenophora and Lantana camara in Kailash Sacred Landscape, India: Current distribution and future climatic scenarios through modeling

The Himalayan region is one of the global biodiversity hotspots. However, its biodiversity and ecosystems are threatened due to abiotic and biotic drivers. One of the major biotic threats to biodiversity in this region is the rapid spread of invasive alien species (IAS). Natural forests and grasslands are increasingly getting infested by IAS affecting regeneration of native species and decline in availability of bio-resources. Assessing the current status of IAS and prediction of their future spread would be vital for evolving specific species management interventions. Keeping this in view, we conducted an in-depth study on two IASs, viz., Ageratina adenophora and Lantana camara in the Indian part of Kailash Sacred Landscape (KSL), Western Himalaya. Intensive field surveys were conducted to collect the presence of A. adenophora (n = 567) and L. camara (n = 120) along an altitudinal gradient between 300 and 3000 m a.s.l. We performed Principle Component Analysis to nullify the multi-colinearity effects of the environmental predictors following MaxEnt species distribution model in the current and future climatic scenarios for both the species. All current and future model precision (i.e. Area Under the Curve; AUC) for both species was higher than 0.81. It is predicted that under the current rate of climate change and higher emission (i.e. RCP8.5 pathway), A. adenophora will spread 45.3% more than its current distribution and is likely to reach up to 3029 m a.s.l. Whereas, L. camara will spread 29.8% more than its current distribution range and likely to reach up to 3018 m a.s.l. Our results will help in future conservation planning and participatory management of forests and grasslands in the KSL- India.

ecology↗

bioRxiv2020

Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines

Ebola virus (EBOV) glycoprotein (GP) can be recognized by neutralizing antibodies (NAbs) and is the main target for vaccine design. Here, we first investigate the contribution of the stalk and heptad repeat 1-C (HR1C) regions to GP metastability. Specific stalk and HR1C modifications in a mucin-deleted form (GP{Delta}muc) increase trimer yield, whereas alterations of HR1C exert a more complex effect on thermostability. Crystal structures are determined to validate two rationally designed GP{Delta}muc trimers in their unliganded state. We then display a modified GP{Delta}muc trimer on reengineered nanoparticles that encapsulate a layer of locking domains (LD) and a cluster of helper T-cell epitopes. In mice and rabbits, GP trimers and nanoparticles elicit cross-ebolavirus NAbs, as well as non-NAbs that enhance pseudovirus infection. Repertoire sequencing reveals quantitative profiles of vaccine-induced B-cell responses. This study demonstrates a promising vaccine strategy for filoviruses, such as EBOV, based on GP stabilization and nanoparticle display.

microbiology↗

bioRxiv2019

DRD2 TaqI A polymorphism in Eastern Uttar Pradesh population

Dopamine receptor D2 (DRD2) encoded by DRD2 gene, is located on chromosome 11q22-23. Dopamine plays the central role in motivation, cognition, and reward seeking behaviour. Its dysfunction is implicated in numerous neurological and psychiatric disorders including drug abuse, schizophrenia, ADHD etc. The TaqI A polymorphism is localized 9.8 kb downstream from DRD2 gene in exon 8 of protein kinase gene (ANKK1). It is a SNP demonstrated to cause Glutamate to Lysine substitution at 713 amino acid residue in putative binding domain of ANKK1. Due to the central role of dopamine in reward seeking behavior, DRD2 TaqI A loci is a suitable candidate for investigation of molecular basis of addiction. The aim of the present study is to evaluate the frequency of DRD2 TaqI A polymorphism in Eastern Uttar Pradesh population. 3ml blood samples were collected from 50 individuals randomly selected from Eastern UP. Written informed consent along with profile detail was taken from each subject prior to blood sample collection. DRD2 TaqI A polymorphism analysis was done by PCR-RFLP method. Genomic DNA was extracted from each collected blood samples and amplified using DRD2 Taq1 region specific primers. PCR amplification produced 310bp long amplicon which was digested with Taq I enzyme for polymorphism analysis. In case of A2 allele, Taq1 enzyme cleaved 310bp long fragment into two fragments of 180bp and 130bp. In case of A1 allele, a C to T substitution demolished the restriction site of Taq1, so amplicon of A1 allele remained uncut. In total 50 sample analyzed in present study, A2/A2, A2/A1 and A1/A1 genotype were found in 12, 32 and 06 samples respectively. The genotypic frequencies of mutant homozygous (A1/A1) is 0.12, heterozygous (A2/A1) is 0.64 and normal homozygous (A2/A2) is 0.24. The allelic frequency of A1 is 0.44 and of A2 is 0.56. In conclusion, the results of present study suggests that in TaqI A polymorphism of DRD2 gene, the frequency of allele A2 is higher than that of A1 allele in population of Eastern Uttar Pradesh.

neuroscience↗

bioRxiv2019

The Arabidopsis receptor kinase STRUBBELIG regulates the response to cellulose deficiency

Plant cells are encased in a semi-rigid cell wall of complex build. As a consequence, cell wall remodeling is essential for the control of growth and development as well as the regulation of abiotic and biotic stress responses. Plant cells actively sense physico-chemical changes in the cell wall and initiate corresponding cellular responses. However, the underlying cell wall monitoring mechanisms remain poorly understood. In Arabidopsis the atypical receptor kinase STRUBBELIG (SUB) mediates tissue morphogenesis. Here, we show that SUB-mediated signal transduction also regulates the cellular response to a reduction in the biosynthesis of cellulose, a central carbohydrate component of the cell wall. SUB signaling affects early increase of intracellular reactive oxygen species, stress gene induction as well as ectopic lignin and callose accumulation upon exogenous application of the cellulose biosynthesis inhibitor isoxaben. Moreover, our data reveal that SUB signaling is required for maintaining cell size and shape of root epidermal cells and the recovery of root growth after transient exposure to isoxaben. SUB is also required for root growth arrest in mutants with defective cellulose biosynthesis. Genetic data further indicate that SUB controls the isoxaben-induced cell wall stress response independently from other known receptor kinase genes mediating this response, such as THESEUS1 or MIK2. We propose that SUB functions in a least two distinct biological processes: the control of tissue morphogenesis and the response to cell wall damage. Taken together, our results reveal a novel signal transduction pathway that contributes to the molecular framework underlying cell wall integrity signaling.\n\nAuthor SummaryPlant cells are encapsulated by a semi-rigid and biochemically complex cell wall. This particular feature has consequences for multiple biologically important processes, such as cell and organ growth or various stress responses. For a plant cell to grow the cell wall has to be modified to allow cell expansion, which is driven by outward-directed turgor pressure generated inside the cell. In return, changes in cell wall architecture need to be monitored by individual cells, and to be coordinated across cells in a growing tissue, for an organ to attain its regular size and shape. Cell wall surveillance also comes also into play in the reaction against certain stresses, including for example infection by plant pathogens, many of which break through the cell wall during infection, thereby generating wall-derived factors that can induce defense responses. There is only limited knowledge regarding the molecular system that monitors the composition and status of the cell wall. Here we provide further insight into the mechanism. We show that the cell surface receptor STRUBBELIG, previously known to control organ development in Arabidopsis, also promotes the cells response to reduced amounts of cellulose, a main component of the cell wall.

plant biology↗

bioRxiv2018

Tissue morphogenesis mediated by the Arabidopsis receptor kinase STRUBBELIG involves a clathrin-dependent process

HighlightThe Arabidopsis receptor kinase STRUBBELIG is internalized by clathrin-mediated endocytosis and affects clathrin-dependent processes in a tissue-dependent manner.\n\nAbstractSignaling mediated by cell surface receptor kinases is central to the coordination of growth patterns during organogenesis. Receptor kinase signaling is in part controlled through endocytosis and subcellular distribution of the respective receptor kinase. For the majority of plant cell surface receptors the underlying trafficking mechanisms are not characterized. In Arabidopsis, tissue morphogenesis relies on the atypical receptor kinase STRUBBELIG (SUB). Here, we approach the endocytic mechanism of SUB. Our data reveal that a functional SUB:EGFP fusion is ubiquitinated in vivo. We further show that plasma membrane-bound SUB:EGFP becomes internalized in a clathrin-dependent fashion. We also find that SUB:EGFP associates with the trans-Golgi network and accumulates in multivesicular bodies and the vacuole. Coimmunoprecipitation experiments reveal that SUB:EGFP and clathrin are present within the same protein complex. Our genetic analysis shows that SUB and CLATHRIN HEAVY CHAIN 2 promote root hair patterning. By contrast, SUB behaves as a negative regulator of a clathrin-dependent process during floral development. Taken together, the data indicate that SUB undergoes clathrin-mediated endocytosis, that this process does not dependent on stimulation of SUB signaling by an exogenous agent, and that SUB genetically interacts with clathrin-dependent pathways in a tissue-specific manner.

plant biology↗

bioRxiv2018

Taxa-driven functional shifts associated with stormflow in an urban stream microbial community

Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single stormflow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. Results demonstrated general trends present in the stream under stormflow vs. baseflow conditions across years and seasons and also highlighted the significant influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study provided evidence of stormflow impacts on an urban stream microbiome from an environmental and public health perspective.\n\nImportanceUrban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and stormflow events represent one such source of complex physical, chemical and biological perturbations. Microorganisms are important components of these streams from both ecological and public-health perspectives, and analyzing the effect of such perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced stormflow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high rainfall event, with potential environment and public health implications. Previous work in this area has been limited to specific genes/organisms or has not assessed immediate stormflow impact.

microbiology↗

bioRxiv2017

Biodiversity loss under future global socio-economic and climate scenarios

Efficient forward-looking mitigation measures are needed to halt the global biodiversity decline. These require spatially explicit scenarios of expected changes in multiple indicators of biodiversity under future socio-economic and environmental conditions. Here we link five future (2050 and 2100) global gridded maps (0.25{degrees} x 0.25{degrees} resolution) available from the land use harmonization (LUH) database that represent alternative representative concentration and shared socio-economic pathways (RCP-SSP) with the countryside species-area relationship model to project the future land use change driven rates of species extinctions and phylogenetic diversity loss (in million years) for mammals, birds and amphibians in each of the 804 terrestrial ecoregions and 176 countries and compare them to the current (1900-2015) and past (850-1900) rates of biodiversity loss. Future land-use changes are projected to commit an additional 209-818 endemic species and 1190-4402 million years of evolutionary history to extinction by 2100 depending upon the scenario, equivalent to 20-80% of the number committed to extinction under current (2015) land use extent. Results show that hotspots of future biodiversity loss differ depending upon the scenario, taxon and metric considered. The most aggressive climate mitigation scenario (RCP2.6 SSP-1), representing a world shifting towards a radically more sustainable path including increasing crop yields, reduced meat production and reduced tropical deforestation coupled with high trade, projects the lowest land use change driven global biodiversity loss followed by RCP8.5 SSP-5, RCP6.0 SSP-4 and RCP7.0 SSP-3. Interestingly, the scenario with the second most aggressive climate target (RCP3.4 SSP-4) projected the highest biodiversity loss among the five scenarios tested. This is because it represents a world with continued high consumption in rich countries and increased land clearing for crop production in species rich, low-income countries such as Indonesia, Madagascar, Tanzania, Philippines and DR Congo. These contrasting results illustrate that the strategies to prevent climate change could simultaneously contribute to reduction in current high rates of biodiversity loss, but only if habitat preservation is incorporated into national and global sustainable development plans.

ecology↗

bioRxiv2017

Evolutionary Isolation And Phylogenetic Diversity Loss Under Random Extinction Events

The extinction of species at the present leads to the loss of phylogenetic diversity (PD) from the evolutionary tree in which these species lie. Prior to extinction, the total PD present can be divided up among the species in various ways using measures of evolutionary isolation (such as fair proportion and equal splits). However, the loss of PD when certain combinations of species become extinct can be either larger or smaller than the cumulative loss of the isolation values associated with the extinct species. In this paper, we show that for trees generated under neutral evolutionary models, the loss of PD under a null model of random extinction at the present can be predicted from the loss of the cumulative isolation values, by applying a non-linear transformation that is independent of the tree. Moreover, the error in the prediction provably converges to zero as the size of the tree grows, with simulations showing good agreement even for moderate sized trees (n = 64).

evolutionary biology↗