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Dalal, A.

Publications and source records attributed to Dalal, A..

30 records · Page 2Linked to original sources

Precision phenotyping of a barley diversity set reveals distinct drought response strategies

Plants exhibit a wide array of responses and adaptive mechanisms to drought. During drought, the trade-off between water loss and CO2 uptake for growth is mediated by the regulation of stomatal aperture in response to soil water content (SWC), among other factors. We earlier identified, in a few reference varieties of barley that differed by the SWC at which transpiration was curtailed, two divergent water use strategies: water-saving ("isohydric") and water-spending ("anisohydric"). We proposed that an isohydric strategy may reduce risk from early droughts in climates where the probability of precipitation increases during the growing season, whereas an anisohydric strategy is consistent with environments having terminal droughts, or with those where dry periods are short and show little seasonal variation. Here, we have examined drought response in an 81-line barley diversity set that spans 20th century European barley breeding and identified a several lines with a third, dynamic transpirational response to drought. We found a strong positive correlation between vigor and transpiration, the dynamic group being highest for both. However, these lines curtailed daily transpiration at a higher SWC than the isohydric group. While the dynamic lines, particularly cv Hydrogen and Baronesse, were not the most resilient in terms of restoring initial growth rates, their strong initial vigor and high return to initial transpiration rates meant that their growth nevertheless surpassed more resilient lines during recovery from drought. The results will be of use for defining barley physiological ideotypes suited to future climate scenarios.

plant biology↗

Heritable intraspecific variation among prey in size and movement interact to shape predation risk and potential natural selection

O_LIPredator and prey traits are important determinants of the outcomes of trophic interactions. In turn, the outcomes of trophic interactions shape the evolution of predator and prey traits. How species traits are likely to respond to selection from trophic interactions depends crucially on whether and how heritable species traits are and their genetic correlations. Of the many traits potentially influencing the outcomes of trophic interactions, body size and movement traits have emerged as universally key traits. Yet, how these traits shape and are shaped by trophic interactions is generally unclear, as few studies have simultaneously measured the impacts of these traits on the outcomes of trophic interactions, their heritability, and their correlations within the same system. C_LIO_LIWe used outcrossed and then clonally propagated lines of the ciliate protist Paramecium caudatum from natural populations to examine variation in morphology and movement behavior, the extent to which this variation was heritable, and how intraspecific differences among lines altered Paramecium susceptibility to predation by the copepod Macrocyclops albidus. C_LIO_LIWe found that the Paramecium lines exhibited heritable variation in body size and movement traits. In contrast to expectations from interspecific allometric relationships, body size and movement speed showed little covariance among clonal lines. The proportion of Paramecium consumed by copepods was positively associated with Paramecium body size and velocity, however, we also found evidence of an interaction such that greater velocities led to greater predation risk for large body-sized paramecia but did not alter predation risk for smaller body-sized paramecia. The proportion of paramecia consumed was not related to copepod body size. These patterns of predation risk and heritable trait variation in paramecia suggest that copepod predation may act as a selective force operating independently on movement and body size and generating the strongest selection against large, high-velocity paramecia. C_LIO_LIOur results illustrate how the interactions between ecology and genetics can shape the potential natural selection on prey traits through the outcomes of trophic interactions. Further simultaneous measures of predation outcomes, traits, and their quantitative genetic characteristics will provide insights into the evolutionary ecology of species interactions and their eco-evolutionary consequences. C_LI

ecology↗

Structure-guided engineering of biased-agonism in the human niacin receptor via single amino acid substitution

The Hydroxycarboxylic acid receptor 2 (HCA2), also known as the niacin receptor or GPR109A, is a prototypical G protein-coupled receptor that plays a central role in the inhibition of lipolytic and atherogenic activities in our body. Interestingly, GPR109A activation also results in vasodilation that is linked to the side-effect of flushing associated with dyslipidemia drugs such as niacin. This receptor continues to be a key target for developing novel pharmacophores and lead compounds as potential therapeutics in dyslipidemia with minimized flushing response, however, the lack of structural insights into agonist-binding and receptor activation has limited the efforts. Here, we present five different cryo-EM structures of the GPR109A-G-protein complexes with the receptor bound to dyslipidemia drugs, niacin or acipimox, non-flushing agonists, MK6892 or GSK256073, and recently approved psoriasis drug, monomethyl fumarate (MMF). These structures allow us to visualize the binding mechanism of agonists with a conserved molecular interaction network, and elucidate the previously lacking molecular basis of receptor activation and transducer-coupling. Importantly, cellular pharmacology experiments, guided by the structural framework determined here, elucidate pathway-selective biased signaling elicited by the non-flushing agonists. Finally, taking lead from the structural insights, we successfully engineered receptor mutants via single amino acid substitutions that either fail to elicit agonist-induced transducer-coupling or exhibits G-protein signaling bias. Taken together, our study provides previously lacking structural framework to understand the agonist-binding and activation of GPR109A, and opens up the possibilities of structure-guided novel drug discovery targeting this therapeutically important receptor.

biochemistry↗

A tale of two pumps: Blue light and ABA alter Arabidopsis leaf hydraulics via bundle sheath cells H+-pumps and channels

This study focuses on the cellular mechanism underlying the co-regulation of the leaf hydraulic conductance (Kleaf) by blue light (BL) and the stress hormone ABA in Arabidopsis thaliana. Our previous work has demonstrated that (1) Kleaf increased by BL signaling within the leaf bundle sheath cells (BSCs), which activated their plasmalemma (PM) H+-ATPase (AHA2), acidifying the xylem sap; (2) external acidification enhanced the BSCs Kleaf and their osmotic water permeability (Pf); (3) ABA decreased both Kleaf and Pf by reducing the BSCs PM aquaporins activity. We now show, using pH and EM (membrane potential) probes combined with H+-pumps inhibitors and manipulations of cytosolic and external Ca2+ concentrations ([Ca2+]CYT, [Ca2+]EXT, respectively), that, in the BSCs: (a) under BL, ABA inhibits AHA2, depolarizing the BSCs and alkalinizing the xylem sap, (b) ABA stimulates the BSCs vacuolar H+-ATPase (VHA), alkalinizing their cytosol; (c) each pump stimulation, AHA2 by BL and VHA by ABA, requires [Ca2+]CYT elevation. ABA-effect-mimicking conditions in patch-clamp experiments activate the BSCs K+-release channels (SKOR and/or GORK). ABA decreased the Kleaf of skor mutants less than WTs, while during water deprivation stress, skor plants transpired more and their leaves lost relatively less K+ than WT. This suggests a role for SKOR in water conservation under drought.

plant biology↗

Drought and recovery in barley: key gene networks and retrotransposon response.

O_LIDuring drought, plants close their stomata at a critical soil water content (SWC), together with diverse physiological, developmental, and biochemical responses. C_LIO_LIUsing precision-phenotyping lysimeters, we imposed pre-flowering drought on four barley varieties (Arvo, Golden Promise, Hankkija 673 and Morex) and followed their physiological responses. For Golden Promise, we carried out RNA-seq on leaf transcripts before and during drought, and during recovery, also examining retrotransposon BARE1 expression. Transcriptional data were subjected to network analysis. C_LIO_LIThe varieties differed by their critical SWC, Hankkija 673 responding at the highest and Golden Promise at the lowest. Pathways connected to drought and salinity response were strongly upregulated during drought; pathways connected to growth and development were strongly downregulated. During recovery, growth and development pathways were upregulated; altogether 117 networked genes involved in ubiquitin-mediated autophagy were downregulated. The differential response to SWC suggests adaptation to distinct rainfall patterns. C_LIO_LIWe identified several strongly differentially expressed genes not earlier associated with drought response in barley. BARE1 transcription is strongly transcriptionally upregulated by drought and downregulated during recovery unequally between the investigated cultivars. The downregulation of networked autophagy genes suggests a role for autophagy in drought response; its importance to resilience should be further investigated. C_LI

plant biology↗

Stress is basic: ABA alkalinizes both the xylem sap and the cytosol of Arabidopsis vascular bundle sheath cellsby inhibiting their P-type H+-ATPaseand stimulating their V-type H+-ATPase

BACKGROUND AND HYPOTHESIS* Under water deprivation, in many perennial species, the stress hormone, ABA, appears in the xylem sap in the shoot (including leaf) veins and the xylem sap pH (pHEXT) increases. This study aimed to test the hypothesis that ABA is the signal for an altered proton balance of the leaf-vein-enwrapping bundle sheath cells (BSCs). METHODS* Plant Material. We used a few Arabidopsis thaliana (L.) Heynh. genotypes: wildtype (WT) of two accessions, Landsberg erecta (Ler) and Columbia (Col), and a few mutants and transformants in these backgrounds. * H+-Pumps activities. We monitored ABA effects on the H+-pump activities in the BSCs cytosol-delimiting membranes (plasma membrane and tonoplast) by monitoring the cytosol and the xylem pH, and the membrane potential (EM), by imaging the fluorescence of pH- and membrane potential (EM)-reporting probes: (a) the BSCs pHEXT - with the ratiometric fluorescent dye FITC-dextran petiole-fed into detached leaves in unbuffered xylem perfusion solution (XPS), (b) the BSCs pHCYT - with the ratiometric dye SNARF1 loaded into BSCs isolated protoplasts, and (c) the BSCs EM - with the ratiometric dye di- 8-ANEPPS. RESULTS* ABA increased the pHEXT; this response was abolished in an abi1-1 mutant with impaired signaling via a PP2C (ABI1) and in an aha2-4 mutant with knocked-down AHA2; * ABA depolarized the WT BSCs; * ABA increased pHCYT irrespective of AHA2 activity (i.e., whether or not AHA was inhibited by vanadate, or in the aha2-4 mutant); * The ABA-induced cytosol alkalinization was abolished in the absence of VHA activity (i.e., when VHA was inhibited by bafilomycin A1, or in the vha-a2 vha-a3 double mutant with inactive VHA); * All these results resemble the ABA effect on GCs; * In contrast to GCs, AHA2 and not AHA1 is the ABA major target in BSCs; * Blue light (BL) enabled the response of the BSCs VHA to ABA; * The ABA- and BL-signaling pathways acting on both BSCs pumps, AHA2 and VHA, are likely to be BSCs autonomous, based on (a) the presence in the BSCs of many genes of the ABA- and BL-signaling pathways and (b) ABA responses (depolarization and pHCYT elevation) demonstrated under BL in isolated protoplasts. SIGNIFICANCE STATEMENTWe reveal here an alkalinizing effect of the plant drought-stress hormone ABA on the pH on both sides of the plasmalemma of the vein-enwrapping bundle sheath cells (BSCs), due to ABA inhibition of the BSCs AHA2, the plasmalemma H+- ATPase and stimulation of VHA, their vacuolar H+-ATPase. Since pH affects the BSCs selective regulation of solute and water fluxes into the leaf, these H+- pumps may be attractive targets for manipulations aiming to improve plant drought response.

plant biology↗

Flagellin triggers mesophyll dehydration: An early PTI defense against bacterial establishment in intercellular spaces

Plants have evolved various mechanisms to defend themselves against pathogens. Many pathogens induce the formation of water-soaked lesions during early infection under conditions of high atmospheric humidity. These water-soaked spots are caused by the disruption of the plasma membrane or cell wall integrity due to various activities of effector proteins during infection. We hypothesized that bacterial PAMP-flagellin plays a role in modulating the cell-membrane permeability that controls the availability of water in the apoplast, to prevent bacterial establishment on the cell wall during the early stages of the PAMP-triggered immunity (PTI) response. Our results revealed that the conductivity of hydraulic pathways in the leaf was reduced in response to flagellin22 (flg22). The cellular osmotic water permeability (Pf) of both mesophyll cells and bundlesheath cells was dramatically reduced in response to flg22 treatment. Moreover, the whole-leaf hydraulic conductance (Kleaf) was also reduced in response to flg22 treatment. The fact that the Pf of mesophyll cells of an aquaporin (AQP) mutant was not affected by the flg22 treatment suggests the involvement of AQP channels in the flg22-induced Pf reduction signal transduction pathway. We conclude that the binding of flagellin to their receptors elicits signals to close AQPs, consequently reducing the water content of the cell wall and intercellular spaces and leading to a more negative water potential. This serves as an early PTI response to pathogen attack, which, in turn, might decrease the rate of bacterial growth and establishment in the apoplast. Significance statementWe report that the membrane osmotic water permeability of both leaf mesophyll and vascular bundle-sheath cells is reduced in response to treatment with flagellin22. We suggest that this mechanism for cell dehydration may serve as an apoplastic defense response, to limit the chances of bacterial pathogens becoming established on the walls of leaf mesophyll cells.

plant biology↗

PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak

The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium has achieved its initial goal of completing the sequencing of 1000 SARS-CoV-2 genomes from nasopharyngeal and oropharyngeal swabs collected from individuals testing positive for COVID-19 by Real Time PCR. The samples were collected across 10 states covering different zones within India. Given the importance of this information for public health response initiatives investigating transmission of COVID-19, the sequence data is being released in GISAID database. This information will improve our understanding on how the virus is spreading, ultimately helping to interrupt the transmission chains, prevent new cases of infection, and provide impetus to research on intervention measures. This will also provide us with information on evolution of the virus, genetic predisposition (if any) and adaptation to human hosts. One thousand and fifty two sequences were used for phylodynamic, temporal and geographic mutation patterns and haplotype network analyses. Initial results indicate that multiple lineages of SARS-CoV-2 are circulating in India, probably introduced by travel from Europe, USA and East Asia. A2a (20A/B/C) was found to be predominant, along with few parental haplotypes 19A/B. In particular, there is a predominance of the D614G mutation, which is found to be emerging in almost all regions of the country. Additionally, mutations in important regions of the viral genome with significant geographical clustering have also been observed. The temporal haplotype diversities landscape in each region appears to be similar pan India, with haplotype diversities peaking between March-May, while by June A2a (20A/B/C) emerged as the predominant one. Within haplotypes, different states appear to have different proportions. Temporal and geographic patterns in the sequences obtained reveal interesting clustering of mutations. Some mutations are present at particularly high frequencies in one state as compared to others. The negative estimate Tajimas D (D = -2.26817) is consistent with the rapid expansion of SARS-CoV-2 population in India. Detailed mutational analysis across India to understand the gradual emergence of mutants at different regions of the country and its possible implication will help in better disease management.

genomics↗

A High Throughput Gravimetric Phenotyping Platform for Real Time Physiological Screening of Plant Environment Dynamic Responses

Food security for the growing global population is a major concern. The data provided by genomic tools far exceeds the supply of phenotypic data, creating a knowledge gap. To meet the challenge of improving crops to feed the growing global population, this gap must be bridged. Physiological traits are considered key functional traits in the context of responsiveness or sensitivity to environmental conditions. Many recently introduced high-throughput phenotyping techniques are based on remote sensing or imaging and are capable of directly measuring morphological traits, but measure physiological parameters only indirectly. This paper describes a method for direct physiological phenotyping that has several advantages for the functional phenotyping of plant-environment interactions. It aims to help users overcome the many challenges encountered in the use of load-cell gravimetric systems and pot experiments. The suggested techniques will enable users to distinguish between soil weight, plant weight and soil water content, providing a method for continuous and simultaneous measurement of dynamic soil, plant and atmosphere conditions, alongside key physiological traits. This method allows researchers to closely mimic field stress scenarios while taking into consideration the environments effect on the plants physiology. This method also minimizes pot effects, which are one of the major problems in pre-field phenotyping. It includes a feedback fertigation system that enables a truly randomized experimental design with a field-like plant density. This system detects the soil-water content limiting threshold ({theta}) and allows for the translation of data into knowledge through the use of a real-time analytic tool and an online statistical resource. This method for the rapid and direct measurement of the physiological responses of multiple plants to a dynamic environment has great potential for use in screening for beneficial traits associated with responses to abiotic stress, in the context of pre-field breeding and crop improvement. SUMMARYThis high-throughput, whole-plant water relations gravimetric phenotyping method enables direct and simultaneous real-time measurements and analysis of multiple yield-related physiological traits involved in dynamic plant-environment interactions.

plant biology↗

A High-Throughput Physiological Functional Phenotyping System for Time- and Cost-Effective Screening of Potential Biostimulants

The improvement of crop productivity under abiotic stress is one of the biggest challenges faced by the agricultural scientific community. Despite extensive research, the research-to-commercial transfer rate of abiotic stress-resistant crops remains very low. This is mainly due to the complexity of genotype{square}x{square}environment interactions and in particular, the ability to quantify the dynamic plant physiological response profile to a dynamic environment.\n\nMost existing phenotyping facilities collect information using robotics and automated image acquisition and analysis. However, their ability to directly measure the physiological properties of the whole plant is limited. We demonstrate a high-throughput functional phenotyping system (HFPS) that enables comparing plants dynamic responses to different ambient conditions in dynamic environments due to its direct and simultaneous measurement of yield-related physiological traits of plants under several treatments. The system is designed as one-to-one (1:1) plant-[sensors+controller] units, i.e., each individual plant has its own personalized sensor, controller and irrigation valves that enable (i) monitoring water-relation kinetics of each plant-environment response throughout the plants life cycle with high spatiotemporal resolution, (ii) a truly randomized experimental design due to multiple independent treatment scenarios for every plant, and (iii) reduction of artificial ambient perturbations due to the immobility of the plants or other objects. In addition, we propose two new resilience-quantifying-related traits that can also be phenotyped using the HFPS: transpiration recovery rate and night water reabsorption.\n\nWe use the HFPS to screen the effects of two commercial biostimulants (a seaweed extract--ICL-SW, and a metabolite formula--ICL-NewFo1) on Capsicum annuum under different irrigation regimes. Biostimulants are considered an alternative approach to improving crop productivity. However, their complex mode of action necessitates cost-effective pre-field phenotyping. The combination of two types of treatment (biostimulants and drought) enabled us to evaluate the precision and resolution of the system in investigating the effect of biostimulants on drought tolerance. We analyze and discuss plant behavior at different stages, and assess the penalty and trade-off between productivity and survivability. In this test case, we suggest a protocol for the screening of biostimulants physiological mechanisms of action.

plant biology↗

Vascular bundle sheath and mesophyll regulation of leaf water balance in response to chitin

Plants can detect pathogen invasion by sensing pathogen-associated molecular patterns (PAMPs). This sensing process leads to the induction of defense responses. Most PAMP mechanisms of action have been described in the guard cells. Here, we describe the effects of chitin, a PAMP found in fungal cell walls, on the cellular osmotic water permeability (Pf) of the leaf vascular bundle-sheath (BS) and mesophyll cells and its subsequent effect on leaf hydraulic conductance (Kleaf).\n\nThe BS is a parenchymatic tissue that tightly encases the vascular system. BS cells have been shown to control Kleaf through changes in their Pf, for example, in response to ABA. It was recently reported that, in Arabidopsis, the chitin receptors chitin elicitor receptor kinase 1 (CERK1) and LYSINE MOTIF RECEPTOR KINASE 5 (LYK5) are highly expressed in the BS, as well as the neighboring mesophyll. Therefore, we studied the possible impact of chitin on these cells.\n\nOur results revealed that both BS cells and mesophyll cells exhibit a sharp decrease in Pf in response to chitin treatment. In addition, xylem-fed chitin decreased Kleaf and led to stomatal closure. However, an Atlyk5 mutant showed none of these responses. Complimenting AtLYK5 specifically in the BS cells (using the SCARECROW promoter) and transient expresion in mesophyll cells each resulted in a response to chitin that was similar to that observed in the wild type. These results suggest that BS and mesophyll cells each play a role in the perception of apoplastic chitin and in initiating chitin-triggered immunity.\n\nSignificance StatementPAMP perception by plant receptors triggers various defense responses important for plant immunity. Here we provide new insights into a topic that has received a great deal of previous attention, revealing that a chitin immune response is present in additional leaf tissues other than the stomata. Chitin perception by the bundle sheath cells enwrapping the whole leaf vascular system decrease its cellular osmotic permeability and leaf hydraulic conductance. This in turn, leads to hydraulic signals being sent to the stomata and regulates whole-leaf water balance in response to chitin application and, perhaps, during fungal infection. Emphasizing the dynamic role of the BS in chitin-sensing and water balance regulation.

plant biology↗

Whole exome sequencing reveals a mutation in ARMC9 as a cause of mental retardation, ptosis and polydactyly

Intellectual disability (ID) refers to deficits in mental abilities, social behaviour and motor skills to perform activities of daily living as compared to peers. Numerous genetic and environmental factors may be responsible for ID. We report on identification of a novel gene for syndromic ID, using homozygosity mapping followed by exome sequencing in a family with mental retardation, ptosis and polydactyly. The analysis revealed a synonymous mutation c.879G>A which leads to a splicing defect in ARMC9 gene. The variant is present in conserved region of ARM domain of ARMC9 protein which is predicted to form a platform for protein interaction. This domain is likely to be altered in patients due to splicing defect caused by this synonymous mutation. Our study was helpful in elucidation of molecular basis of mental retardation, ptosis and polydactyly phenotype and addition of ARMC9 to group of genes leading to syndromic ID.

genetics↗