Biology subjects

Mishra, A. K.

Publications and source records attributed to Mishra, A. K..

28 records · Page 2Linked to original sources

bioRxiv2021

A tau class Glutathione-S-Transferase (OsGSTU5) acts as a negative regulator of VirE2 interaction with T-DNA during Agrobacterium infection in rice

During Agrobacterium-mediated transformation (AMT), T-DNA along with several virulence proteins like VirD2, VirE2, VirE3, VirD5, and VirF enter into the plant cytoplasm. VirE2 is supposed to serve as single-stranded DNA binding (SSB) protein and assist the cytoplasmic trafficking of T-DNA inside the host cell. In the present study, a rice glutathione-S-transferase (OsGSTU5) that interacts with VirE2 protein in plant cytoplasm has been identified. OsGSTU5 is observed to be involved in post-translational glutathionylation of VirE2 protein (gVirE2). In silico analysis revealed that gVirE2+ssDNA complex is structurally less stable than VirE2+ ssDNA complex. The gel shift activity confirms the attenuated SSB property of gVirE2 over VirE2 protein under in vitro condition. Moreover, knock-down and overexpression OsGSTU5 phenotypes of rice showed increased and decreased T-DNA expression, respectively after Agrobacterium infection. The present finding convincingly establishes the role of OsGSTU5 as defense protein in rice that can further serve as an important target for modulation of AMT efficiency in rice.

plant biology↗

bioRxiv2021

Homothorax Controls a Binary Rhodopsin Switch in Drosophila Ocelli

Visual perception of the environment is mediated by specialized photoreceptor (PR) neurons of the eye. Each PR expresses photosensitive opsins, which are activated by a particular wavelength of light. In most insects, the visual system comprises a pair of compound eyes that are mainly associated with motion detection, color or polarized light perception and a triplet of ocelli that are thought to be critical during flight to detect horizon and movements. It is widely believed that evolutionary diversification of compound eye and ocelli in insects occurred from an ancestral visual organ around 500 million years ago. Concurrently, opsin genes were also duplicated to provide distinct spectral sensitivities to different PRs of compound eye and ocelli. In the fruit fly Drosophila melanogaster, Rhodopsin1 (Rh1) and Rh2 are closely related opsins that are originated from the duplication of a single ancestral gene. However, in the visual organs, Rh2 is uniquely expressed in ocelli whereas Rh1 is uniquely expressed in outer PRs of the compound eye. It is currently unknown how this differential expression of Rh1 and Rh2 in the two visual organs is controlled to provide unique spectral sensitivities to ocelli and compound eyes. Here, we show that Homothorax (Hth) is expressed in ocelli and confers proper rhodopsin expression. We find that Hth controls a binary Rhodopsin switch in ocelli to promote Rh2 expression and repress Rh1 expression. Genetic and molecular analysis of rh1 and rh2 supports that Hth acts through their promoters to regulate Rhodopsin expression in the ocelli. Finally, we also show that when ectopically expressed in the retina, hth is sufficient to induce Rh2 expression only at the outer PRs in a cell autonomous manner. We therefore propose that the diversification of rhodpsins in the ocelli and retinal outer PRs occurred by duplication of an ancestral gene, which is under the control of Homothorax.

genetics↗

bioRxiv2020

Reproductive effort of intertidal tropical seagrass as an indicator of habitat disturbance

Habitat disturbance is one of the major causes of seagrass loss around the Andaman Sea in the Indian Ocean bioregion. Assessing the seagrass response to these disturbances is of utmost importance in planning effective conservation measures. Here we report about seagrass reproductive effort (RE) as an indicator to assess seagrass response to habitat disturbances. Quadrat sampling was used to collect seagrass samples at three locations (a disturbed and undisturbed site per location) of the Andaman and Nicobar Islands. The health of seagrass meadows was quantified based on density-biomass indices of the disturbed sites. A change ratio (D/U) was derived by contrasting the RE of disturbed (D) sites with the undisturbed (U) sites of all three locations. The relationship between RE and plant morphometrics were also quantified. Reproductive density of T. hemprichii was higher and significant at the three disturbed sites. The average reproductive density of T. hemprichii at the disturbed sites was 3.3-fold higher than the undisturbed sites. The reproductive density consisted around 52% of the total shoot density of T. hemprichii at the disturbed sites. In general, the increase in the plant RE was site-specific and was 4-fold higher at the three disturbed sites. Positive and significant correlations was observed between the change ratio of RE and the plant morphometrics, suggesting an active participation of seagrass morphometrics in the reproductive process. Increase in seagrass RE can contribute to the increase in population genetic diversity, meadow maintenance and various ecosystem functions under the influence of anthropogenic disturbance scenarios.

ecology↗

bioRxiv2019

A Simplest Bioinformatics Pipeline for Whole Transcriptome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis.

Recent advances in next generation sequencing (NGS) technologies have heralded the genomic research. From the good-old inferring differentially expressed genes (DEG) using microarray to the current adage NGS-based whole transcriptome or RNA-Seq pipelines, there have been advances and improvements. With several bioinformatics pipelines for analysing RNA-Seq on rise, inferring the candidate DEGs prove to be a cumbersome approach as one may have to reach consensus among all the pipelines. To Check this, we have benchmarked the well known cufflinks-cuffdiff pipeline on a set of datasets and outline it in the form of a protocol where researchers interested in performing whole transcriptome shotgun sequencing and its downstream analysis can better disseminate the analysis using their datasets.

bioinformatics↗

bioRxiv2019

Ecological association between seagrass and mangrove ecosystems increases seagrass population longevity in island ecosystem

We report for first time about tropical seagrass meadows association with mangrove ecosystems and its effect on seagrass population dynamics off India in Andaman Sea. Two sites of Neil island, i.e. site 1, associated with mangroves and site 2 without mangroves were selected. Quadrat sampling (n=5) were used to collect sediment and seagrass samples. Reconstruction techniques were used to derive population age structure. T. hemprichii population was found mostly with sandy substrate at both sites, with silt consisting very low fraction at site 1. Density, biomass, productivity and morphometric features of T. hemprichii were significantly higher at site1. Reproductive density was higher at site 1, whereas reproductive effort to produce fruits were higher at site 2. The rhizome (vertical+ horizontal) production rates were higher at site 1 and the vertical elongation rate was higher at site 2. Plastochrome interval for site1 and 2 were 25.49 and 26.80 days respectively leading to formation of 14.31 and 13.62 leaves per year. T. hemprichii population at site 1 had four years of longevity and higher younger plants compared to site 2. The long-term average recruitment and present recruitment rate were higher at site 1 compared to site 2, resulting in steady state growth of the overall population at site 1. Higher number of younger plants suggests fitness of the T. hemprichii population at site 1, which increases the ecological significance of mangrove ecosystems have on seagrass population dynamics. This association should be considered for better management and conservation practices of coastal seascapes under global change scenarios.

ecology↗

bioRxiv2019

Boat anchors not OK: Loss of Dugong grass (Halophila ovalis) population structure in Havelock island of Andaman and Nicobar Islands, India

Anthropogenic disturbance due to deployment of boat anchors and loss of seagrass ecosystem is not well understood in India. So, we used Govind Nagar beach of Havelock Island of Andaman and Nicobar Islands (ANI)to assess the impacts of boat anchors from traditional fishing and recreational activities on the seagrass Halophila ovalis population structure. H. ovalis density, biomass, morphometrics, canopy height and percentage cover were estimated from two stations of Govind Nagar beach i.e., one highly impacted from boat anchors (Station1) and a sheltered station (Station 2). A clear evidence in reduction of shoot density of H. ovalis was observed at station 1, exception was similar apex densities between both stations. H. ovalis morphometrics, such as number of leaves per shoot, leaf length, width and horizontal rhizome length were observed with significant lower values at station 1 compared to the sheltered station 2. Reduction in seagrass morphometrics also resulted in the loss of seagrass canopy height and percentage cover. A clear evidence of loss of seagrass population structure under the influence of physical disturbances caused by boat anchors were observed. We report for the first time the impacts of boat anchors on seagrass ecosystems of India and our results pitch for wider studies across India. The impact of boat anchors is small-scale, but in long-term loss of seagrass ecosystem services will have dire consequences on fish habitat and carbon storage. Therefore, proper management and conservation measures should be taken to prevent the loss of important dugong grass habitats of ANI.\n\nHighlightsO_LIPhysical disturbances caused by boat anchors decreased the shoot density of H. ovalis by 1.2-fold.\nC_LIO_LI1 to 2-fold reduction in canopy height and the morphological features of individual plants were observed due to damage caused by boat anchors\nC_LIO_LIHabitat disturbance reduced 1.6-fold percentage cover of H. ovalis at Havelock Island of Andaman and Nicobar Islands, India\nC_LI

ecology↗

bioRxiv2018

Population dynamics of Cymodocea nodosa under future ocean scenarios.

Rising carbon dioxide (CO2) concentrations in the atmosphere will increase the average pCO2 level in the world oceans, which will have a knock-on effect on the marine ecosystem. Coastal seagrass communities are predicted to benefit from the increase in CO2 levels, but long-term effects of elevated CO2 on seagrass communities are less understood. Population reconstruction techniques were used to investigate the population dynamics of Cymodocea nodosa meadows, exposed to long term elevated CO2 at volcanic seeps off Greece and Italy. Effect of elevated CO2 was noticed on the growth, morphometry, density, biomass and age structure at CO2 seeps than reference sites. Above to below ground biomass ratio of C. nodosa were higher at CO2 seeps. The shoot age and shoot longevity of plants were lower at seeps. The present recruitment (sampled year) of the seagrass were higher than long-term average recruitment of the communities near the seeps. Carbon to nitrogen ratios (%DW) and annual leaf production of C. nodosa were higher in leaves at seeps. This study suggests under long-term CO2 enrichment C. nodosa production increases, but the plant survival rate decreases because of other co-factors such as nutrient availability and trace metal toxicity. Therefore, along with high CO2 other factors must be taken into consideration while predicting effects of future CO2 concentrations.

ecology↗

bioRxiv2018

Andaman mangrove sediments: source of nutrients and sink of heavy metals

Andaman Islands (AI) of India is a biodiversity hotspot of mangroves but biogeochemical dynamics of AI is less understood. We collected sediment samples of four AI mangrove sites and one site without mangroves for nutrients and trace metal analysis. Samples were collected from each site at the inlet of seawater (Zone A) and the other 500m into the mangrove creek (Zone B). Nutrients (sulphate, ammonium, nitrite and nitrate) levels, organic matter (OM) and carbon content were higher at Zone B of mangrove ecosystem due to the higher OM content from mangrove leaf litter decomposition and microbial degradation. Metal (Pb &Cd) content of zones with and without mangroves were similar and Igeo values indicated moderate contamination of mangrove zones of AI due to lack of anthropogenic pollution. Our results suggest mangrove ecosystems of AI are uncontaminated from heavy metals and are source of nutrients to the oligotrophic coastal ecosystems of Andaman Sea.

ecology↗

bioRxiv2018

Elevated trace elements in Posidonia oceanica and Cymodocea nodosa at six Mediterranean volcanic seeps

Seagrasses form important habitats around shallow marine CO2 seeps, providing opportunities to assess trace element (TE) accumulation along gradients in seawater pH. Here we assessed Cd, Cu, Hg, Ni, Pb and Zn levels in sediment and seagrasses at six CO2 seeps and reference sites off Italy and Greece. Some seep sediments had much higher concentrations of TEs, the extreme example being Cd at 43-fold above reference levels. Sediment Quality Guideline (SQG) scores indicated that three seeps had sediment TEs levels likely to have \"Adverse impacts\" on marine biota; namely Vulcano (for Hg), Ischia (for Cu) and Paleochori (for Cd and Ni). SQG indicated seep sediments of Italian seeps were adversely affected by Cu and Hg, whereas Greek CO2 seeps were affected by Cd and Ni. An increase in sediment TEs levels positively corelated with higher levels of TEs in seagrass roots of Posidonia oceanica (Zn and Ni) and Cymodocea nodosa (Zn). Differences in the bioavailability and possible toxicity of TEs helps explain why seagrasses were abundant at some CO2 seeps but not others.

ecology↗

bioRxiv2018

Overexpression of Arabidopsis ubiquitin ligase AtPUB46 enhances tolerance to drought and oxidative stress

The U-Box E3 ubiquitin ligase, AtPUB46, functions in the drought response: T-DNA insertion mutants of this single paralogous gene are hypersensitive to water- and oxidative stress (Adler et al. BMC Plant Biology 17:8, 2017). Here we analyze the phenotype of AtPUB46 overexpressing (OE) plants. AtPUB46-OE show increased tolerance to water stress and have smaller leaf blades and reduced stomatal pore area and stomatal index compared with wild type (WT). Despite this, the rate of water loss from detached rosettes is similar in AtPUB46-OE and WT plants. Germination of AtPUB46-OE seeds was less sensitive to salt than WT whereas seedling greening was more sensitive. We observed a complex response to oxidative stress applied by different agents: AtPUB46-OE plants were hypersensitive to H2O2 but hyposensitive to methyl viologen. AtPUB46-GFP fusion protein is cytoplasmic, however, in response to H2O2 a considerable proportion translocates to the nucleus. We conclude that the differential stress phenotype of the AtPUB46-OE does not result from its smaller leaf size but from a change in the activity of a stress pathway(s) regulated by a degradation substrate of the AtPUB46 E3 and also from a reduction in stomatal pore size and index.\n\nAccession NumbersSequence data for this article can be found in: The Arabidopsis Information Resource database (http://www.arabidopsis.org) under accession numbers At5G18320 (PUB46).

plant biology↗