Biology subjects

Kasinathan, S.

Publications and source records attributed to Kasinathan, S..

9 recordsLinked to original sources

bioRxiv2026

Phenology of 50 tree species across 9 years in a South Asian tropical rainforest indicates complex influence of climate, traits, and phylogeny

In relatively aseasonal tropical rainforests, few studies have explored long-term phenological patterns of a high diversity of tree species in relation to climate, phylogeny, and functional traits. In these systems, short-duration seasonal pulses of irradiance and water deficit are expected to provide narrower windows for leafing and flowering and wider windows for fruiting across prolonged wet seasons, potentially mediated by functional traits and phylogenetic relatedness. Here, we document leafing, flowering, and fruiting phenology of 50 tree species (920 - 1077 trees, 10 - 42 trees/species) monitored monthly over an 9-y period (2017 - 26) in a relatively aseasonal south Asian tropical rainforest in the Anamalai Hills, Western Ghats, India. We examined correlations between climatic variables (irradiance, daylength, temperature, precipitation) and tree phenology and Mantel correlations among similarity in monthly phenology, functional traits (wood density, seed size, and maximum height), and phylogenetic relatedness. We then investigated the phylogenetic signal of phenological traits (frequency, amplitude, duration, and peak month) using Pagels {lambda}. Leaf flushing and flowering showed distinct seasonality and negative associations with daylength and precipitation, whereas fruiting showed greater temporal spread and weaker associations with climate. Functional traits or phylogeny did not significantly influence leaf flushing and flowering, whereas dissimilarity in fruiting was correlated with phylogenetic distance and peak fruiting month showed a significant phylogenetic signal ({lambda} = 0.96). The results indicate that in relatively aseasonal tropical rainforests, proximate climatic cues more strongly influence leaf flushing and flowering, whereas phylogenetic constraints affect timing of fruiting and may cause lineage-specific vulnerabilities to climate change.

ecology↗

bioRxiv2024

Distribution models predict climate-related range alteration or extinction of eleven threatened tropical rainforest trees in the Western Ghats

Evidence for climate-change related alteration in distributions and ranges of forest trees is accumulating, but information from Asian tropical forests, particularly for threatened and endemic species, remains limited. Here, we examine landscape-level distribution-abundance patterns of 11 endemic and threatened tropical rainforest tree species in the Anamalai Hills and model their distribution and responses to future climate scenarios in the Southern Western Ghats (SWG), India. Six of the primarily low- and mid-elevation species were more abundant in protected reserves than forest fragments. Occurrence data from the Anamalais and SWG (N = 3004, range: 41 - 706 per species) were used to model distributions using maximum entropy (maxent) species distribution modelling in R. Maxent model performances indicated excellent fits for 9 of 11 species (AUC>0.90) with precipitation and temperature variables showing higher permutation importance. There was high interspecies variability in range size (197 - 12,221 km2) and niche width (0.04 - 0.50). Models of distribution under future climate in 2061 - 2080 predict range reductions in six species (including near-extinction for two species), increases for three species, and no substantial change for two species. Predicted southward and westward shifts in ranges and persistence in parts of the SWG indicate the importance of identifying and conserving micro-climatic zones or refugia to ensure the persistence of tree species under anticipated climate change.

ecology↗

bioRxiv2023

Effects of sampling methodology on phenology indices: insights from sites across India and modelling

Plant phenology is the study of timing and extent of leaf, flower, and fruit production. Phenology data are used to study drivers of cyclicity and seasonality of plant life-history stages, interactions with organisms such as pollinators, and effects of global change factors. Indices such as timing of phenological events, proportion of individuals in a particular phenophase, seasonality, and synchrony have often been used to summarise plant phenology data. However, these indices have specific utilities and limitations and may be sensitive to sampling methodology, making cross-site comparisons challenging, particularly when data collection methods vary in terms of sample size, observation frequency, and the resolution at which phenophase intensity scores/values are recorded. We use fruiting phenology data from tropical trees across five sites in India to study the effects of sampling methodology on two indices: an index of population-level synchrony (overlap), and an index of seasonality. We supplement these results with simulations of fast- and slow-changing phenologies to test for the effects of sampling methodology on these indices. We found that the overlap index is sensitive to the phenophase intensity measurement resolution--with coarser intensity measures leading to overestimation of the overlap index. The seasonality index, on the other hand, was not affected by intensity resolution. Simulations indicated that finer intensity resolution is more important than frequency of observation to accurately estimate population synchrony and seasonality for fast- and slow-changing phenophases. Based on our findings, we provide recommendations for study design of future tropical tree phenology research, particularly for long-term or cross-site studies.

ecology↗

bioRxiv2023

Structure and dynamics of secondary and mature rainforests: insights from South Asian long-term monitoring plots

We assessed tree community and carbon dynamics over 5 years in two 1-ha long-term ecosystem monitoring plots, one each in mature tropical rainforests (MR) and 10-year post-agroforestry secondary rainforests (SR) in Indias Western Ghats mountains. Both plots were established in 2017 and monitored annually six times. We expected (1) higher tree diversity, distinct species composition, and greater carbon stock in MR; (2) higher carbon sequestration rates in SR; and (3) carbon dynamics shaped by growth and mortality in SR and MR, respectively. The SR plot had fewer species (67 vs. 84), stored substantially less carbon (76 vs. 193 Mg), and comprised a distinct community with fewer late-successional species than MR. SR gained 5.8 Mg carbon, due to tree growth exceeding losses from mortality, while in MR mortality exceeded growth and recruitment resulting in a 3.3 Mg carbon decline over five years. While MR had higher tree diversity, carbon stocks and relatively intact composition, the high rates of biodiversity and carbon accrual in SR highlight the conservation and climate significance of post-agroforestry secondary forests. Moderate carbon losses noted here in MR, as in other mature South Asian tropical forests, is a cause for concern under ongoing climate change.

ecology↗

bioRxiv2022

Sensitive multimodal profiling of native DNA by transposase-mediated single-molecule sequencing

We present SMRT-Tag: a multiplexable, PCR-free approach for constructing low-input, single-molecule Pacific Biosciences (PacBio) sequencing libraries through Tn5 transposition. As proof-of-concept, we apply SMRT-Tag to resolve human genetic and epigenetic variation in gold-standard human reference samples. SMRT-Tag requires 1-5% as much input material as existing protocols (15,000 - 50,000 human cell equivalents) and enables highly-sensitive and simultaneous detection of single nucleotide variants, small insertions / deletions, and CpG methylation comparable to the current state-of-the-art. We further combine SMRT-Tag with in situ adenine methyltransferase footprinting of nuclei (SAMOSA-Tag) to facilitate joint analysis of nucleosome repeat length, CTCF occupancy, and CpG methylation on individual chromatin fibers in osteosarcoma cells. SMRT-Tag promises to enable basic and clinical research by offering scalable, sensitive, and multimodal single-molecule genomic and epigenomic analyses in rare cell populations.

genomics↗

bioRxiv2021

Single-fiber nucleosome density shapes the regulatory output of a mammalian chromatin remodeling enzyme

ATP-dependent chromatin remodelers regulate the DNA accessibility required of virtually all nuclear processes. Biochemical studies have provided insight into remodeler action at the nucleosome level, but how these findings translate to activity on chromatin fibers in vitro and in vivo remains poorly understood. Here, we present a massively multiplex single-molecule platform allowing high-resolution mapping of nucleosomes on fibers assembled on mammalian genomic sequences. We apply this method to distinguish between competing models for chromatin remodeling by the essential ISWI ATPase SNF2h: linker-length-dependent dynamic positioning versus fixed-linker-length static clamping. Our single-fiber data demonstrate that SNF2h operates as a density-dependent, length-sensing chromatin remodeler whose ability to decrease or increase DNA accessibility depends on single-fiber nucleosome density. In vivo, this activity manifests as different regulatory modes across epigenomic domains: at canonically-defined heterochromatin, SNF2h generates evenly-spaced nucleosome arrays of multiple nucleosome repeat lengths; at SNF2h-dependent accessible sites, SNF2h slides nucleosomes to increase accessibility of motifs for the essential transcription factor CTCF. Overall, our generalizable approach provides molecularly-precise views of the processes that shape nuclear physiology. Concurrently, our data illustrate how a mammalian chromatin remodeling enzyme can effectively sense nucleosome density to induce diametrically-opposed regulatory effects within the nucleus.

genomics↗

bioRxiv2020

MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis

Male germ cell production is a metabolically-driven and apoptosis-prone process. Here we show that the glucose-sensing transcription factor MLX, and its binding partner MondoA, are both required for male fertility in the mouse, as well as survival of human tumor cells derived from the male germ line. Loss of Mlx results in altered metabolism as well as activation of multiple stress pathways and germ cell apoptosis in the testes. This is concomitant with dysregulation of the expression of male-specific germ cell transcripts and proteins, manifesting as oligoasthenoteratozoospermia (OAT). Our genomic and functional analyses identify loci directly bound by MLX involved in these processes, including metabolic targets, apoptotic effectors and obligate components of male-specific germ cell development. These in vivo and in vitro studies implicate MLX and other members of the proximal MYC network, such as MNT, in regulation of metabolism and differentiation, as well as in suppression of intrinsic and extrinsic death signaling pathways in both spermatogenesis and male germ cell tumors. Highlights- The MAX-like bHLHLZ protein MLX is required for male fertility, but not embryonic development. - MLX and its heterodimeric partner MondoA are each required for both male fertility and survival of male germ cell tumors. - Genomic analysis identifies direct MLX targets associated with metabolism, stress and male germ cell development. - Loss of MLX alters MYC network genome occupancy and transcriptional output.

developmental biology↗

bioRxiv2020

Massively multiplex single-molecule oligonucleosome footprinting

Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present the single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput single-molecule sequencing method that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencing to natively and nondestructively measure nucleosome positions on individual chromatin fibres. SAMOSA data allows unbiased classification of single-molecular states of nucleosome occupancy on individual chromatin fibres. We leverage this to estimate nucleosome regularity and spacing on single chromatin fibres genome-wide, at predicted transcription factor binding motifs, and across both active and silent human epigenomic domains. Our analyses suggest that chromatin is comprised of a diverse array of both regular and irregular single-molecular oligonucleosome patterns that differ subtly in their relative abundance across epigenomic domains. This irregularity is particularly striking in constitutive heterochromatin, which has typically been viewed as a conformationally static entity. Our proof-of-concept study provides a powerful new methodology for studying nucleosome organization at a previously intractable resolution, and offers up new avenues for modeling and visualizing higher-order chromatin structure. 1-sentence summaryHigh-throughput single-molecule real-time footprinting of chromatin arrays reveals heterogeneous patterns of oligonucleosome occupancy.

genomics↗

bioRxiv2017

Non-B-form DNA structures mark centromeres

Animal and plant centromeres are embedded in repetitive \"satellite\" DNA, but are thought to be epigenetically specified. To define genetic characteristics of centromeres, we surveyed satellite DNA from diverse eukaryotes and identified variation in <10-bp dyad symmetries predicted to adopt non-B-form conformations. Organisms lacking centromeric dyad symmetries had binding sites for sequence-specific DNA binding proteins with DNA bending activity. For example, human and mouse centromeres are depleted for dyad symmetries, but are enriched for non-B DNA and are associated with binding sites for the conserved DNA-binding protein CENP-B, which is required for artificial centromere function but is paradoxically non-essential. We also detected dyad symmetries and predicted non-B-form DNA structures at neocentromeres, which form at ectopic loci. We propose that centromeres form at non-B-form DNA because of dyad symmetries or are strengthened by sequence-specific DNA binding proteins. Our findings resolve the CENP-B paradox and provide a general basis for centromere specification.

evolutionary biology↗