Biology subjects

Kurup, S.

Publications and source records attributed to Kurup, S..

11 recordsLinked to original sources

bioRxiv2026

A Bayesian approach for identifying similar transcript dynamics using curve registration

Changes in gene expression over time can provide valuable insights into developmental processes and responses to the environment. Differences in expression may be indicative of potential differences in regulation. Comparing transcript dynamics may help identify correspondences between developmental stages within and between species, differences in the timing of key events during development, and transcriptional response to treatments or perturbations. A straightforward comparison between the dynamics is, however, hindered by measurements that were taken at different time points and over different timescales. To address this, we developed a statistical approach that seeks the optimal alignment between two time series as a function of a temporal shift and stretch. We validated our approach using simulated data and applied it to several transcriptome datasets, including comparisons between different plant species. Our development facilitates knowledge transfer from model systems to less studied species, the identification of modules of co-regulated genes, and the discovery of condition-specific, temporally differentially-expressed genes. The method is provided freely available as an R package.

bioinformatics↗

bioRxiv2026

A Suite of Eight Toxoplasma gondii Effectors Cooperates to Activate the Non-canonical NF-κB Pathway

As a master of host-cell reprogramming, Toxoplasma gondii (T. gondii) tachyzoites manipulate diverse signaling networks to establish a niche permissive for long-term infection. While the parasites subversion of canonical NF-{kappa}B signaling (p65/p50) is well established, how infection impacts the non-canonical NF-{kappa}B pathway has been largely unexplored. Here, we report that T. gondii infection induces robust nuclear accumulation of the non-canonical NF-{kappa}B subunits RelB and p52 in both human and murine cells. This activation follows a gradual kinetic profile and is conserved across both Type I and Type II parasite genetic backgrounds. We demonstrate that this reprogramming is strictly dependent on the MYR1-dependent export of dense granule effectors. Mechanistically, T. gondii infection drives the depletion of the negative regulator TRAF3, leading to the stabilization of NF-{kappa}B-inducing kinase (NIK), phosphorylation of p100, and its subsequent processing into p52. Utilizing a panel of combinatorial knockout parasites, we reveal that no single effector is responsible for this phenotype. Instead, a suite of eight MYR1-dependent effectors, IST, NSM, HCE1/TEEGR, GRA16, GRA18, GRA24, GRA28, and GRA84, functions through a collaborative, additive network to trigger the non-canonical response. These findings highlight a distributed regulatory strategy used by the parasite to overcome host transcriptional robustness and shape host signaling. ImportanceToxoplasma gondii infects nearly one-third of the global population and establishes infection by extensively rewiring host immune signaling. While decades of work have focused on how the parasite modulates canonical NF-{kappa}B activity, whether it also engages the alternative, non-canonical arm of this pathway has remained unclear. Here, we show that T. gondii tachyzoites activate non-canonical NF-{kappa}B signaling, driving nuclear accumulation of RelB/p52 through MYR1-dependent effector export. Unexpectedly, no single effector is responsible. Instead, eight secreted proteins act cooperatively to enable NIK stabilization and engage the alternative NF-{kappa}B cascade, revealing a networked mode of immune control. This discovery highlights a regulatory logic evolved by the parasite to overcome host transcriptional robustness. Together, these findings identify non-canonical NF-{kappa}B activation as a new axis of host-parasite interaction and expand our understanding of how T. gondii reprograms central immune signaling circuits through multi-effector networks.

microbiology↗

bioRxiv2025

Associative transcriptomics in Brassica napus suggests a role for Arabidopsis Response Regulator orthologs in seedling vigour

Background and AimsOptimal seedling vigour determines successful crop establishment and its ability to overcome abiotic and biotic threats. Seedling vigour is regulated by several different factors, genetic, physiological, environmental, post-harvest storage, making it challenging to fully elucidate. The aim of this study was to dissect the genetic basis of post-germinative seedling traits and its implications in seedling establishment success in Brassica napus. MethodsA B. napus diversity set panel was used to phenotype seedling establishment traits in the soil including days to emergence, days to appearance of first and second true leaves, and days to reach 25% and 50% cotyledon expansion. An associative transcriptomics analysis was performed to identify the genetic factors regulating seedling establishment. Key ResultsThe study of different phenotypic traits highlighted the relevance of scoring more than one trait to determine good performers. Gene expression markers significantly associated with the studied traits were associated with the cytokinin signalling pathway and photomorphogenesis. Gene expression markers for orthologues of Arabidopsis thaliana RESPONSE REGULATOR 4 and 5 (ARR4, ARR5) were significantly associated with days to appearance of second leaf. SUPPRESSOR OF PHYA-105 1 (SPA1) orthologues were associated with cotyledon area, meanwhile ALTERED SEED GERMINATION 7 (ASG7) and PSEUDO-RESPONSE REGULATOR 7 (PRR7) orthologues were associated with days to emergence, suggesting a complex and interconnected regulatory pathway controlling several traits of seedling establishment. ConclusionsThese results uncovered promising genes that appear to work in a complex and interconnected manner controlling several post-germinative seedling traits affecting final seedling establishment speed.

plant biology↗

bioRxiv2025

Mutations in components of the TREX-2 complex result in misexpression of the Kelch-domain F-Box protein KFB39 promoter in Arabidopsis thaliana

Arabidopsis thaliana gene At2g44130 encodes a Kelch-like domain F-box protein designated KFB39 and was previously shown to be specifically expressed on exposure to the oxylipin cis-jasmone. In order to better understand the regulation of At2g44130, a forward genetic screen was carried out to identify mutants in which a promoter-GUS fusion was expressed in the absence of the inducer, cis-jasmone. Two mutants were recovered, showing mis-expression of the promoter-GUS fusion and surprisingly both were found to be in components (SAC3B, THP1) of the TREX-2 nuclear pore complex. Genetic analysis of sac3 mutants in Arabidopsis revealed additive impairments to growth and development as well as reduced capacity for nuclear export. Promoter-GUS fusions of the Arabidopsis SAC3 and THP1 genes revealed a discrete expression pattern that was non-overlapping with KFB39. A link between the expression of KFB39 and the TREX-2 complex is not obvious, but we note that previously, unrelated forward genetic screens using promoter-reporter fusions have also recovered sac3b and thp1 mutants. We consider some possible explanations for these shared occurrences.

plant biology↗

bioRxiv2023

FOXC1 and FOXC2 maintain mitral valve endothelial cell junctions, extracellular matrix, and lymphatic vessels to prevent myxomatous degeneration

BackgroundMitral valve (MV) disease including myxomatous degeneration is the most common form of valvular heart disease with an age-dependent frequency. Genetic evidence indicates mutations of the transcription factor FOXC1 are associated with MV defects, including mitral valve regurgitation. In this study, we sought to determine whether murine Foxc1 and its closely related factor, Foxc2, are required in valvular endothelial cells (VECs) for the maintenance of MV leaflets, including VEC junctions and the stratified trilaminar extracellular matrix (ECM). MethodsAdult mice carrying tamoxifen-inducible, endothelial cell (EC)-specific, compound Foxc1;Foxc2 mutations (i.e., EC-Foxc-DKO mice) were used to study the function of Foxc1 and Foxc2 in the maintenance of mitral valves. The EC-mutations of Foxc1/c2 were induced at 7 - 8 weeks of age by tamoxifen treatment, and abnormalities in the MVs of EC-Foxc-DKO mice were assessed via whole-mount immunostaining, immunohistochemistry, and Movat pentachrome/Massons Trichrome staining. ResultsEC-deletions of Foxc1 and Foxc2 in mice resulted in abnormally extended and thicker mitral valves by causing defects in regulation of ECM organization with increased proteoglycan and decreased collagen. Notably, reticular adherens junctions were found in VECs of control MV leaflets, and these reticular structures were severely disrupted in EC-Foxc1/c2 mutant mice. PROX1, a key regulator in a subset of VECs on the fibrosa side of MVs, was downregulated in EC-Foxc1/c2 mutant VECs. Furthermore, we determined the precise location of lymphatic vessels in murine MVs, and these lymphatic vessels were aberrantly expanded in EC-Foxc1/c2 mutant mitral valves. ConclusionsOur results indicate that Foxc1 and Foxc2 are required for maintaining the integrity of the MV, including VEC junctions, ECM organization, and lymphatic vessels to prevent myxomatous mitral valve degeneration.

cell biology↗

bioRxiv2023

Harnessing genetic variations improving seedling vigor for successful crop establishment in deep sown direct-seeded rice

Improving seedling vigour remains key objective for breeders working with direct-seeded rice (DSR). To understand the genetic control of seedling vigour in deep sown DSR, combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes was performed. Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 3.79 Mb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The potential candidate gene, LOC_Os07g25150 codes for Myb-30-related transcription factor. The LOC_Os07g25150 codes for Myb 30-related transcription factor, LOC_Os07g17689 annotated as protein translation factor, LOC_Os07g17770 as tryptophanyl-tRNA synthetase, LOC_Os07g15440 as alanyl-tRNA synthetase family protein, LOC_Os07g24100 as retrotransposon protein and the remaining others as expressed proteins. The antagonistic relationship between Myb-30 and ethylene-mediated signalling (EIN-3) in regulating mesocotyl elongation have been observed. The functional characterization and knocking of LOC_Os07g25150 codes for Myb 30-related transcription factor may provide better understanding of the mechanism behind mesocotyl elongation. The four promising introgression lines with longer mesocotyl length, longer root length and semi-dwarf plant height have been identified.

genomics↗

bioRxiv2022

The palisade-specific gene IQD22 enhances photosynthetic capacity by phenocopying sun leaf architecture

The world requires a rise in crop production which needs to be increased significantly in order to satisfy demand by 20501. However traditional plant breeding approaches are anticipated to fall short in delivering the increases in yield required and therefore targeted manipulation of plant metabolism is increasingly being pursued with the aim to achieve this goal2. Improving photosynthetic efficiency is predicted to have a significant influence on enhancing crop productivity and several ambitious genetic engineering projects are currently under way to achieve higher photosynthetic rates in crops3,4. A naturally evolved adaptive trait which allows plants to increase photosynthetic efficiency specifically under high light is the differentiation of sun leaves which are characterised by an increase in palisade cell layers and more elongated cells within this layer5. These morphological changes allow a more efficient distribution of light within the leaf and provide an increased cell surface to which chloroplasts can relocate thereby increasing the capacity for CO up-take6. Here we show that, surprisingly, this complex morphological trait can be phenocopied by the modulation of the expression of a single palisade specific gene, IQD22, in Arabidopsis. Furthermore, we could show that the architectural changes were reflected in an increase of photosynthetic rate of 30%. The simplicity with which we could enhance photosynthesis by phenocopying sun leave traits is in stark contrast to the complex and challenging metabolic engineering approaches currently being pursued.

plant biology↗

bioRxiv2021

A point mutation in the kinase domain of CRK10 leads to xylem vessel collapse and activates defence responses

Cysteine-rich receptor-like kinases (CRKs) are a large family of plasma membrane-bound receptors ubiquitous in higher plants. They are transcriptionally regulated by a wide variety of environmental cues and stresses, however their precise biological roles remain largely unknown. Here we report a novel mutant isolated for the CYSTEINE-RICH RECEPTOR-LIKE KINASE 10 (CRK10) of Arabidopsis thaliana which harbours the substitution of alanine 397 by a threonine in the C-helix of its kinase domain and which we registered as crk10-A397T in the community database. In situ phosphorylation assays with the His-tagged wild type (WT) and crk10-A397T versions of the CRK10 kinase domain revealed that both alleles are active kinases capable of auto-phosphorylation with the newly introduced threonine acting as an additional phosphorylation site in crk10-A397T. Phenotypically the mutant is a dwarf and the analysis of thin cross sections with light and transmission electron microscopy revealed that collapsed xylem vessels in roots and hypocotyls are very likely the cause for this reduction in stature. Transcriptomic analysis of WT and mutant hypocotyls revealed that predominantly biotic and abiotic stress-responsive genes are constitutively up-regulated in the mutant. Root-infection assays with the vascular pathogen Fusarium oxysporum demonstrated that the crk10-A397T mutant has enhanced resistance to this pathogen compared to WT plants. Taken together our results suggest that crk10-A397T is a gain-of-function allele of CRK10 and open up new avenues for the investigation of this elusive receptor-like kinase family.

plant biology↗

bioRxiv2021

Bayesian optimisation for yield in high-dimensional trait-space identifies crop ideotypes in Oil Seed Rape

The improvement of crop yield has long been a major breeding target and is increasingly becoming a goal in many areas of plant research. Yield has been shown to be a complex trait, depending on multiple genes, plant architecture and plant-environment interactions. This complexity is frequently reduced by focussing on contributing factors to yield (yield traits). However, a quantitative understanding of the interplay between yield traits, and the effect of these relationships on yield is largely unexplored. Consequently, the extent to which crop varieties achieve their optimal morphology in a given environment and how this impacts on seed yield is unknown. Here we use causal inference to model the hierarchically structured effects of 27 macro and micro yield traits on each other over the course of plant development, and on seed yield in Spring and Winter oilseed rape plants. We perform Bayesian optimisation on the modelled yield potential, identifying the morphology of ideotype plants which are expected to be higher yielding than the existing varieties in the studied panels. We find that existing Spring varieties occupy the optimal regions of trait-space, but that potentially high yielding strategies are unexplored in extant Winter varieties. In addition to concrete recommendations for varietal improvement in oilseed rape, this work provides a novel, general methodological framework for the study of crop breeding as an optimisation problem.

plant biology↗

bioRxiv2020

Uncovering the ideal plant ideotype for maximising seed yield in Brassica napus

Seed yield is a complex trait for many crop species including oilseed rape (Brassica napus), the second most important oilseed crop worldwide. Studies have focused on the contribution of distinct factors in seed yield such as environmental cues, agronomical practices, growth conditions or specific phenotypic traits at the whole plant level, such as number of pods in a plant. However, in spite of the immense economic importance of oilseeds, none of these studies have comprehensively analysed individual traits and their combined contribution to seed yield. Here, we describe the analysis and contribution of 33 phenotypic traits within a B. napus diversity set population and their trade-offs on seed yield not only at the whole plant level but also the less studied female reproductive traits. Our results revealed that both winter and spring oilseed rape; the two more economically important oilseed rape groups in terms of oil production; were found to share a common dominant reproductive strategy for seed yield. In this strategy the main inflorescence is the principal source of seed yield, producing a good number of ovules, a large number of long pods with a concomitantly high number of seeds per pod. We observed that winter oilseed rape opted for more reproductive strategies than spring oilseed rape, presenting more environmental flexibility to maximise seed yield. Overall, we conclude that, oilseed rape adopts a similar strategy that is key for maximal seed yield and propose an ideal ideotype highlighting crucial phenotypic traits that could be potential targets for breeding. One sentence summaryThe main florescence is the principal source of seed yield in winter and spring oilseed rape, with winter oilseed rape following several reproductive strategies to maximise seed yield.

plant biology↗

bioRxiv2019

Big data from small tissues: extraction of high-quality RNA for different plant tissue types during oilseed Brassica spp. seed development for RNA-Sequencing

Obtaining high-quality RNA for gene expression analyses from different seed tissues is challenging due to the presence of various contaminants, such as polyphenols, polysaccharides and lipids which interfere with RNA extraction methods. At present, the available protocols for extracting RNA from seeds require high amounts of tissue and are mainly focused on extracting RNA from whole seeds. However, extracting RNA at the tissue level enables more detailed studies regarding tissue specific transcriptome during development. Seeds from heart stage embryo to mature developmental stages of Brassica napus and B. oleracea were sampled for isolation of the embryo, endosperm and seed coat tissues. Ovules and gynoecia wall tissue were also collected at the pre-fertilization stage. After testing several RNA extraction methods, E.Z.N.A. Plant RNA Kit and Picopure RNA Isolation kit extraction methods with some modifications, as well as the use of PVPP for seed coats and endosperms at green stages, resulted in high RNA concentrations with clear 28S and 18S bands and high RIN values. Here, we present efficient and reliable RNA extraction methods for different genotypes of Brassica spp for different tissue types during seed development. The high-quality RNA obtained by using these methodologies is suitable for RNA-Sequencing and gene expression analyses.

plant biology↗