Biology subjects

Sampath, K.

Publications and source records attributed to Sampath, K..

8 recordsLinked to original sources

bioRxiv2025

An Integrated Decarbonising Approach to Mitigate Methane Emissions and Enhance Productivity in Rice Cultivation

Flooded rice paddies contribute approximately 12% of global anthropogenic methane emissions, accounting for 1.5% of the total warming effect from all greenhouse gases. With the rising global demand for rice due to population growth, the need for effective methane mitigation strategies in rice cultivation is increasingly critical. This study investigates the combined impact of irrigation methods, fertiliser combinations, and varietal differences on productivity, water use and methane emissions in rice. Field trials were conducted across five land parcels covering 8 Ha in the Sathyamangalam region of Tamil Nadu, India, from October 2024 to January 2025. Results revealed that drip irrigation significantly reduced seasonal methane emissions by up to 68% (128 kg/ha/season) compared to continuous flood irrigation (402.32 kg/ha/season) offering a sustainable solution to address climate change. Furthermore, our modified package of practices coupled with tailored fertiliser combination, led to a 28% reduction in methane emissions (222 kg/ha/season) relative to continuous flooding methods used by the farmers in the region (309 kg/ha/season). Methane emission differences of up to 23.8% were also evident across rice varieties ADT-45 (229.7 kg/ha/season and BPT-5204 (301.7 kg/ha/season) for. Although flood irrigation yielded a 5-6% higher grain productivity than drip irrigation, the TLL fertiliser package under flood irrigation still provided distinct benefits with a yield increase of 5.4%. Notably, water usage under drip irrigation was 42.5% lower on average across the five locations, with minimal impact on yield, resulting in a marked improvement in water use efficiency (0.62 kg.m-3 under drip vs. 0.39 kg.m-3 under flood irrigation). Our findings highlight the value of integrating modern irrigation techniques, optimizing fertiliser management, and appropriate varietal selection with higher environmental sustainability and improved farm productivity to mitigate climate impact in rice cultivation.

plant biology↗

bioRxiv2025

In toto imaging of germ plasm dynamics reveals an essential role for early distribution of germ granules in germline development

A fundamental question in developmental biology is how the fertilized egg gives rise to all the different cell types of an organism. The traditional view is that the different cell types are specified either by intrinsic factors such as cell fate determinants or via intercellular signaling. In some animals a cytoplasmic determinant-like substance called germplasm specifies the germline. In zebrafish eggs, germplasm is dispersed in form of mRNP complexes called germ granules, which are enriched at the animal pole. After fertilization the distribution of germ granules changes dramatically. The germ granules accumulate in the corners of the first two cleavage furrows of the embryo, to form four large masses that are essential for germline development. Although germ granule movement has been linked to the network dynamics of the microtubular and actin cytoskeleton, a clear mechanistic understanding of the process is currently lacking. Fundamental questions about germplasm dynamics, including "What is the main driving force?" have not been answered yet. To address this gap, we performed careful quantitative analysis of germ granule dynamics relative to dynamic cytoskeletal reorganization in early zebrafish embryos by live-imaging. We identified stereotypic signatures of germ granule dynamics across different regions of the early embryo. Interestingly, we find that the timing of large-scale germ granule movements contrasts prevailing models for the mechanism of germ granule aggregation during cleavage divisions, and rather points to cytokinetic apparatus itself. Using zebrafish mutants affecting the RNA-binding protein Ybx1 (Y-box binding-protein 1), we show that the timing and dynamics of germ granule accumulation in the blastodisc is a crucial factor for appropriate later aggregation into cleavage furrows and eventual distribution to PGCs. Germplasm accumulation in the cleavage furrows is reduced and ectopic aggregates form at the blastoderm margin of ybx1 mutant embryos. Our work establishes Ybx1 as a novel factor with crucial functions in germplasm distribution and suggests that additional factors drive normal germplasm dynamics.

developmental biology↗

bioRxiv2025

Measuring morphogen transport over multiple spatial scales in live zebrafish embryos

Morphogenesis is controlled by signalling morphogens that form gradients across the embryo. The gradient formation requires that the low molecular weight morphogens slow down their diffusion by at least one order of magnitude. However, the precise slow-down of diffusion across the relevant micrometre scales has not been directly observed. Here, we develop and employ Single-Plane Illumination Microscope based spatial Fluorescence Cross-Correlation Spectroscopy (SPIM-sFCCS) to directly measure the diffusion coefficient of the morphogen Squint in early zebrafish embryos as a function of topography and length scale. We show that Squints diffusion coefficient changes on length scales that are commensurate with the diameter of the intercellular spaces in the embryo and that the slow-down is regulated by receptor binding. The slowdown can be reduced by either the knockdown of Activin receptor 2b, a receptor for Squint, or the overexpression of Lefty2, an inhibitor of Squint. Based on our results and supporting simulations, we propose an interstitial space-dependent transient receptor binding and diffusing mechanism to explain this slowdown, which is crucial for gradient formation and embryonic patterning.

developmental biology↗

bioRxiv2024

Structure and physiological investigation of arginylated actin

Actin is an evolutionarily conserved cytoskeletal protein with crucial roles in cell polarity, division, migration, and muscle contraction. Actin function is regulated in part by posttranslational modifications. One such modification in non-muscle cells is arginylation, in which an arginine residue is added to the N-terminus of {beta}-actin. What is the structure of arginylated {beta}-actin (R-{beta}-actin), are its interactions with other proteins altered and what phenotypes result when R-{beta}-actin is the sole actin isoform present in the cell? Here we report the 4.2 [A] structure of ADP-bound human R-{beta}-actin filaments, the overall structure of which is nearly identical to the filaments made of non-arginylated actin. In vitro functional assays using isoform-pure actins with defined post-translational modifications reveal that the interaction between myosin-II and actin is altered upon actin arginylation, due to frequent detachment of myosin-II from R-actin filaments. In vivo, we find that replacement of the only actin gene in Schizosaccharomyces pombe with a synthetic gene encoding R-Sp-actin reduces Arp2/3-based actin patches while thickening the formin-induced actin. Furthermore, consistent with altered interactions between myosin-II and R-actin filaments, the assembly and constriction of cytokinetic actomyosin ring are perturbed in the R-Sp-actin cells. Thus, despite the overall structural similarity of arginylated and non-arginylated actin filaments, actin arginylation affects actin filament assortment into distinct subcellular structures and its interaction with myosin II.

biochemistry↗

bioRxiv2023

Translational control of furina by an RNA regulon is essential for heart morphogenesis and cardiac valve function

Heart development is a complex process, starting from specification of cardiac precursors and formation of a linear tube to gradual progression to a functional beating organ. For normal heart development, many processes, including asymmetric positioning of the heart along the left-right (L/R) axis, cardiac growth, and cardiac valve morphogenesis must be completed successfully. Although heart development has been studied extensively, the mechanisms that control heart morphogenesis and valve formation are not fully understood. The pro-convertase FurinA is a key protein that functions in heart development in many vertebrates including zebrafish. How FurinA activity is regulated during heart development is not known. Through computational analysis of the zebrafish transcriptome, we identified a short sequence and structure RNA motif in a variant transcript of FurinA harbouring a long 3untranslated region (3UTR). The alternative 3UTR furina isoform is expressed at embryonic stages preceding organ positioning. Reporter localization and RNA-binding assays show that the furina 3UTR forms complexes with the conserved RNA-binding protein and translational repressor Ybx1. Conditional mutant zebrafish embryos affecting ybx1 show premature and increased Furin reporter protein expression, abnormal cardiac morphogenesis and heart looping defects. Our mutant ybx1 hearts have an expanded atrioventricular canal, abnormal sino-atrial valves and many mutant embryos show retrograde blood flow from the ventricle to the atrium. This is similar to human heart valve regurgitation patients. Our findings show an essential function for the 3UTR element/Ybx1 regulon in translational repression of FurinA, revealing a new upstream regulatory mechanism that controls embryonic heart development, and demonstrates the ybx1 mutant as a model to study cardiac valve development and function.

developmental biology↗

bioRxiv2020

The RNA-binding protein Igf2bp3 is critical for embryonic and germline development in zebrafish

The ability to reproduce is essential in all branches of life. In metazoans, this process is initiated by formation of the germline, a group of cells that are destined to form the future gonads, the tissue that will produce the gametes. The molecular mechanisms underlying germline formation differs between species. In zebrafish, development of the germline is dependent on the specification, migration and proliferation of progenitors called the primordial germ cells (PGCs). PGC specification is dependent on a maternally provided cytoplasmic complex of ribonucleoproteins (RNPs), the germplasm. Here, we show that the conserved RNA-binding protein (RBP), Igf2bp3, has an essential role during germline development. Loss of Igf2bp3 leads to reduced germline RNA expression, and mis-regulated germline development. Maternal mutants affecting igf2bp3 exhibit abnormal PGC movement, maintenance and migration, and adult igf2bp3 mutants show a male biased sex ratio. Therefore, Igf2bp3 is required for germplasm components, and maintains correct development of the germline.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2019

Expanding the Zebrafish Genetic Code through Site-Specific Introduction of Diazirine-lysine, Bicyclononyne-lysine and Azido-lysine

Site-specific incorporation of un-natural amino acids (UNAA) is a powerful approach to engineer and understand protein function [1-4]. Site-specific incorporation of UNAAs is achieved through repurposing the amber codon (UAG) as a sense codon for the UNAA, a tRNACUA that base pairs with an UAG codon in the mRNA and an orthogonal amino-acyl tRNA synthetase (aaRS) that charges the tRNACUA with the UNAA [5, 6]. Here, we report expansion of the zebrafish genetic code to incorporate the UNAAs, Azido-lysine (AzK), bicyclononyne-lysine (BCNK), and Diazirine-lysine (AbK) into green fluorescent protein (GFP) and Glutathione-S-transferase (GST). We also present proteomic evidence for UNAA incorporation into GFP. Our work sets the stage for the use of UNAA mutagenesis to investigate and engineer protein function in zebrafish.

synthetic biology↗

bioRxiv2018

The effector of Hippo signaling, Taz, is required for formation of the micropyle and fertilization in zebrafish

The mechanisms that ensure fertilization of eggs by a single sperm are not fully understood. In all teleosts, a channel called the micropyle is the only route of entry for sperm to enter and fertilize the egg. The micropyle forms by penetration of the developing vitelline envelope by a single specialized follicle cell, the micropylar cell, which subsequently degenerates. The mechanisms underlying micropylar cell specification and micropyle formation are poorly understood. Here, we show that an effector of the Hippo signaling pathway, the Transcriptional co-activator with a PDZ-binding domain (Taz), plays crucial roles in micropyle formation and fertilization in zebrafish. Genome editing mutants affecting taz can grow to adults, however, eggs from homozygous taz females are not fertilized even though oocytes in mutant females are histologically normal with intact animal-vegetal polarity, complete meiosis and proper ovulation. However, taz mutant eggs have no micropyle. We show that Taz protein is specifically enriched from mid-oogenesis onwards in two follicle cells located at the animal pole of the oocyte, and co-localizes with the actin and tubulin cytoskeleton. Taz protein and micropylar cell are not detected in taz mutant ovaries. Our work identifies a novel role for the Hippo/Taz pathway in micropylar cell specification in zebrafish, and uncovers the molecular basis of micropyle formation in teleosts.

developmental biology↗