Biology subjects

Ramaswami, G.

Publications and source records attributed to Ramaswami, G..

16 recordsLinked to original sources

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

Latitudinal patterns of flowering phenology of three widespread tropical species from public media repositories.

Plant phenology encompasses the study of periodic events in biological life cycles of plants and the influence of seasonal changes in weather and other environmental factors. In order to understand the role of the environment and the changing climate on the life cycle of plants, long-term records are required to establish baselines against which significant future deviations can be discerned. This study aims to analyze the spatial flowering pattern of the plant species -Bombax ceiba, Butea monosperma and Cassia fistula across India, through images uploaded on public media repositories like citizen science portals and social media. Citizen science is rapidly emerging as a reliable source of supplementary scientific information, and can be utilized to understand broad patterns of tree behavior. We found that for all three species, flowering period is longer, and begins earlier in southern latitudes as compared to the northern latitudes. We conclude that publicly available images of flowering trees and citizen science data can be used to supplement existing information on tree phenology across India.

ecology↗

bioRxiv2023

Unveiling Nesting Strategies: Investigating Visual Concealment and Nest-site Selection in Yellow-wattled Lapwings, Vanellus malabaricus (Boddaert, 1783)

Ground-nesting birds such as Yellow-wattled Lapwing, Vanellus malabaricus (Boddaert, 1783) employ several nesting and behavioral strategies to mitigate nest predation, which greatly influences their reproductive success and survival. Yet the breeding ecology of Yellow-wattled Lapwing has received relatively little research attention despite the species widespread presence in the Indian subcontinent. The objective of this study was to investigate the significance and impact of two visual concealment strategies commonly utilized by open ground-nesting birds: visual concealment through vegetative characteristics and camouflage using Yellow-wattled Lapwing as the model organism. We also assessed the nest-site selection of Yellow-wattled Lapwings in relation to vegetation cover and food availability, as well as their choice of nest substrate by using behavioral sampling, quadrat sampling, and digital image analysis techniques. We found that variation in hatching success could not be attributed to the analyzed camouflage mechanisms (disruptive markings and pattern complexity matching). Furthermore, the nesting pairs exhibited a preference for areas with high vegetation cover and low food availability while selecting nesting sites. We also showed that this species might exhibit an active behavioral preference for selecting nest substrates. It is important to note that this study was conducted during a single nesting season for the Yellow-wattled Lapwings, and further temporal replicates are necessary to validate and establish the findings over the long term.

ecology↗

bioRxiv2023

Environmental correlates of tree reproductive phenology in a tropical state of India - insights from a citizen science project

Tropical tree reproductive phenology is sensitive to changing climate, but inter-individual and interannual variability at the regional scale is poorly understood. While large-scale and long-term datasets of environmental variables are available, reproductive phenology needs to be measured in-site, limiting the spatiotemporal scales of the data. We leveraged a unique dataset assembled by SeasonWatch, a citizen-science phenology monitoring programme in India to assess the environmental correlates of flowering in three ubiquitous and economically important tree species - jackfruit, mango and tamarind - in the south-western Indian state of Kerala. We explored (i) seasonal patterns in the flowering status of trees (ii) environmental correlates of flowering onset considering only trees with consecutive observations and (iii) spatiotemporal patterns in these environmental correlates to aid future hypotheses for changing phenology patterns. We used 165006 phenology observations spread over 19591 individual trees over 9 years. We first used bootstrapped circular statistics that accounts for observation biases in time to examine consistency in seasonality of flowering status over the whole season, and flowering onset across years and trees. Similar to results from cohort-based tree monitoring, we demonstrate seasonality in flowering status and onset across species, but also report large interannual and inter-individual variability. We then used used generalized linear mixed models with remotely sensed observations (ERA5-LAND) to show that some of the interannual variation in flowering onset across individuals was associated with environmental variables. Soil moisture, minimum temperature and solar radiation had significant associations with the onset of flowering but these effects were heterogeneous across species and habitats across Kerala. Our results become increasingly important in the face of large spatiotemporal change in the climate of this landscape and other tropical regions. We demonstrate the potential and limitations of citizen- science observations in making and testing predictions at scale for predictive climate science in tropical landscapes. Open Research StatementData are not yet provided. Environmental data used in this manuscript are from publicly available sources. All SeasonWatch data, the phenology data used in the manuscript, is licensed under the open-access creative commons license CC BY 4.0: https://creativecommons.org/licenses/by/4.0/ and is available upon request. Processed data and code used in this manuscript will be made publicly accessible through Zenodo upon acceptance of the manuscript. This manuscript does not use any novel code.

ecology↗

bioRxiv2023

Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration

BackgroundMicroglia are the resident immune cells in the brain that play a key role in driving neuroinflammation, a hallmark of neurodegenerative disorders. Inducible microglia-like cells have been developed as an in vitro platform for molecular and therapeutic hypothesis generation and testing. However, there has been no systematic assessment of similarity of these cells to primary human microglia along with their responsiveness to external cues expected of primary cells in the brain. MethodsIn this study, we performed transcriptional characterization of commercially available human inducible pluripotent stem cell (iPSC)-derived microglia-like (iMGL) cells by bulk and single cell RNA sequencing to assess their similarity with primary human microglia. To evaluate their stimulation responsiveness, iMGL cells were treated with Liver X Receptor (LXR) pathway agonists and their transcriptional responses characterized by bulk and single cell RNA sequencing. ResultsBulk transcriptome analyses demonstrate that iMGL cells have a similar overall expression profile to freshly isolated human primary microglia and express many key microglial transcription factors and functional and disease-associated genes. Notably, at the single-cell level, iMGL cells exhibit distinct transcriptional subpopulations, representing both homeostatic and activated states present in normal and diseased primary microglia. Treatment of iMGL cells with LXR pathway agonists induces robust transcriptional changes in lipid metabolism and cell cycle at the bulk level. At the single cell level, we observe heterogeneity in responses between cell subpopulations in homeostatic and activated states and deconvolute bulk expression changes into their corresponding single cell states. ConclusionsIn summary, our results demonstrate that iMGL cells exhibit a complex transcriptional profile and responsiveness, reminiscent of in vivo microglia, and thus represent a promising model system for therapeutic development in neurodegeneration.

genomics↗

bioRxiv2022

Developmentally regulated alternate 3' end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage

Alternative polyadenylation (APA) generates transcript isoforms that differ in the position of the 3 cleavage site, resulting in the production of mRNA isoforms with different length 3UTRs. Although widespread, the role of APA in the biology of cells, tissues and organisms has been controversial. We identified over 500 Drosophila genes that express mRNA isoforms with a long 3UTR in proliferating spermatogonia but a short 3UTR in differentiating spermatocytes due to APA. We show that the stage-specific choice of the 3 end cleavage site can be regulated by the arrangement of a canonical polyadenylation signal (PAS) near the distal cleavage site but a variant or no recognizable PAS near the proximal cleavage site. The emergence of transcripts with shorter 3UTRs in differentiating cells correlated with changes in expression of the encoded proteins, either from off in spermatogonia to on in spermatocytes or vice versa. Polysome gradient fractionation revealed over 250 genes where the long 3UTR versus short 3UTR mRNA isoforms migrated differently, consistent with dramatic stage-specific changes in translation state. Thus, the developmentally regulated choice of an alternative site at which to make the 3end cut that terminates nascent transcripts can profoundly affect the suite of proteins expressed as cells advance through sequential steps in a differentiation lineage.

developmental biology↗

bioRxiv2020

Broad transcriptomic dysregulation across the cerebral cortex in ASD

Classically, psychiatric disorders have been considered to lack defining pathology, but recent work has demonstrated consistent disruption at the molecular level, characterized by transcriptomic and epigenetic alterations.1-3 In ASD, upregulation of microglial, astrocyte, and immune signaling genes, downregulation of specific synaptic genes, and attenuation of regional gene expression differences are observed.1,2,4-6 However, whether these changes are limited to the cortical association areas profiled is unknown. Here, we perform RNA-sequencing (RNA-seq) on 725 brain samples spanning 11 distinct cortical areas in 112 ASD cases and neurotypical controls. We identify substantially more genes and isoforms that differentiate ASD from controls than previously observed. These alterations are pervasive and cortex-wide, but vary in magnitude across regions, roughly showing an anterior to posterior gradient, with the strongest signal in visual cortex, followed by parietal cortex and the temporal lobe. We find a notable enrichment of ASD genetic risk variants among cortex-wide downregulated synaptic plasticity genes and upregulated protein folding gene isoforms. Finally, using snRNA-seq, we determine that regional variation in the magnitude of transcriptomic dysregulation reflects changes in cellular proportion and cell-type-specific gene expression, particularly impacting L3/4 excitatory neurons. These results highlight widespread, genetically-driven neuronal dysfunction as a major component of ASD pathology in the cerebral cortex, extending beyond association cortices to involve primary sensory regions.

neuroscience↗

bioRxiv2020

Using Citizen Science to build baseline data on tropical tree phenology

Large-scale and long-term understanding of the phenology of widespread tree species is lacking in the tropics, and particularly in the Indian subcontinent. In the absence of baseline information, the impacts of climate on tree phenology, and thus on trophic interactions downstream of tree phenology, are also poorly understood. Citizen scientists can help bridge this gap by contributing simple, technology-based information over large spatial scales and over the long term. In this study, we describe an India-wide citizen science initiative called SeasonWatch, with preliminary insights into contributor behaviour and species phenology. Over a period of 8 years, between 2011 and 2019, cumulative contributor numbers have increased every year, although consistent contribution remains constant and low. The phenological patterns in the 4 most-observed species (Jackfruit Artocarpus heterophyllus Lam., Mango Mangifera indica L., Tamarind Tamarindus indica L., and Indian Laburnum Cassia fistula L.) are described, with discernible seasonal peaks in flowering and fruiting. Seasonal peaks are influenced by tree phenology reported in the south Indian state of Kerala, which has the maximum number of contributors and most number of observations per contributor, comprising 89% of all observations. We look in detail at the flowering phenology of one particular species, Cassia fistula, which appears to show aberrant phenology, reflecting a potential shift away from historical baselines. Latitudinal patterns in the phenology of widespread species such as Mangifera indica are also discernible from 4 seasonal bioblitz events organised during 2018-19, with trees in lower latitudes exhibiting flowering and fruiting phenology earlier than the higher latitudes. We conclude that there are signs of shifts in phenological patterns, as in the case of C. fistula, and extend a call for action to sustain long-term interest and participation by contributors to develop a baseline for common tropical tree species that can be used to understand long-term consequences of climate change on tropical tree phenology.

ecology↗

bioRxiv2020

Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss. Multiple genetic risk factors have been identified, implicating RNA and protein metabolism and intracellular transport, among other biological mechanisms. To achieve a systems-level understanding of the mechanisms governing ALS pathophysiology, we built gene co-expression networks using RNA-sequencing data from control human spinal cord samples, identifying 13 gene co-expression modules, each of which represents a distinct biological process or cell type. Analysis of four RNA-seq datasets from a range of ALS disease-associated contexts reveal dysregulation in numerous modules related to ribosomal function, wound response, and leukocyte activation, implicating astrocytes, oligodendrocytes, endothelia, and microglia in ALS pathophysiology. To identify potentially causal processes, we partitioned heritability across the genome, finding that ALS common genetic risk is enriched within two specific modules, SC.M4, representing genes related to RNA processing and gene regulation, and SC.M2, representing genes related to intracellular transport and autophagy and enriched in oligodendrocyte markers. Top hub genes of this module include ALS-implicated risk genes such as KPNA3, TMED2, and NCOA4, the latter of which regulates ferritin autophagy, implicating this process in ALS pathophysiology. These unbiased, genome-wide analyses confirm the utility of a systems approach to understanding the causes and drivers of ALS.

genomics↗

bioRxiv2020

Alterations in retrotransposition, synaptic connectivity, and myelination implicated by transcriptomic changes following maternal immune activation in non-human primates

BackgroundMaternal immune activation (MIA) is a proposed risk factor for multiple neurodevelopmental and psychiatric disorders, including schizophrenia. However, the molecular and neurobiological mechanisms through which MIA imparts risk for these disorders remain poorly understood. A recently developed nonhuman primate model of exposure to the viral mimic poly:ICLC during pregnancy shows abnormal social and repetitive behaviors and elevated striatal dopamine, a molecular hallmark of human psychosis, providing an unprecedented opportunity for mechanistic dissection. MethodsWe performed RNA-sequencing across four psychiatrically-relevant brain regions (prefrontal cortex, anterior cingulate, hippocampus, and primary visual cortex) from 3.5-4-year old male MIA-exposed and control offspring--an age comparable to mid adolescence in humans. ResultsWe identify 266 unique genes differentially expressed (DE) in at least one brain region with the greatest number observed in hippocampus. Co-expression networks identified region-specific alterations in synaptic signaling and oligodendrocytes. Across regions, we observed temporal and regional differences, but transcriptomic changes were largely similar across 1st or 2nd trimester MIA exposures, including for the top DE genes--PIWIL2 and MGARP. In addition to PIWIL2, several other known regulators of retrotransposition, as well as endogenous transposable elements were dysregulated in MIA offspring. ConclusionsTogether, these results begin to elucidate the brain-level molecular mechanisms through which MIA may impart risk for psychiatric disease.

neuroscience↗

bioRxiv2020

The architecture of brain co-expression reveals the brain-wide basis of disease susceptibility

Gene networks have proven their utility for elucidating transcriptome structure in the brain, yielding numerous biological insights. Most analyses have focused on expression relationships within a circumspect number of regions - how these relationships vary across a broad array of brain regions is largely unknown. By leveraging RNA-sequencing in 864 samples representing 12 brain regions in a cohort of 131 phenotypically normal individuals, we identify 12 brain-wide, 114 region-specific, and 50 cross-regional co-expression modules. We replicate the majority (81%) of modules in regional microarray datasets. Nearly 40% of expressed genes fall into brain-wide modules corresponding to major cell classes and conserved biological processes. Region-specific modules comprise 25% of expressed genes and correspond to region-specific cell types and processes, such as oxytocin signaling in the hypothalamus, or addiction pathways in the nucleus accumbens. We further leverage these modules to capture cell-type-specific lncRNA and gene isoforms, both of which contribute substantially to regional synaptic diversity. We identify enrichment of neuropsychiatric disease risk variants in brain wide and multi-regional modules, consistent with their broad impact on cell classes, and highlight specific roles in neuronal proliferation and activity-dependent processes. Finally, we examine the manner in which gene co-expression and gene regulatory networks reflect genetic risk, including the recently framed omnigenic model of disease architecture.

genetics↗

bioRxiv2019

Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis

Adenosine-to-inosine (A-to-I) RNA editing catalyzed by ADAR enzymes occurs in double-stranded RNAs (dsRNAs). How the RNA sequence and structure (i.e., the cis-regulation) determine the editing efficiency and specificity is poorly understood, despite a compelling need towards functional understanding of known editing events and transcriptome engineering of desired adenosines. We developed a CRISPR/Cas9-mediated saturation mutagenesis approach to generate comprehensive libraries of point mutations near an editing site and its editing complementary sequence (ECS) at the endogenous genomic locus. We used machine learning to integrate diverse RNA sequence features and computationally predicted structures to model editing levels measured by deep sequencing and identified cis-regulatory features of RNA editing. As proof-of-concept, we applied this integrative approach to three editing substrates. Our models explained over 70% of variation in editing levels. The models indicate that RNA sequence and structure features synergistically determine the editing levels. Our integrative approach can be broadly applied to any editing site towards the goal of deciphering the RNA editing code. It also provides guidance for designing and screening of antisense RNA sequences that form dsRNA duplex with the target transcript for ADAR-mediated transcriptome engineering.

molecular biology↗

bioRxiv2019

Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

Autism spectrum disorder (ASD) is a phenotypically and genetically heterogeneous neurodevelopmental disorder. Despite this heterogeneity, previous studies have shown patterns of molecular convergence in post-mortem brain tissue from autistic subjects. Here, we integrate genome-wide measures of mRNA expression, miRNA expression, DNA methylation, and histone acetylation from ASD and control brains to identify a convergent molecular subtype of ASD with shared dysregulation across both the epigenome and transcriptome. Focusing on this convergent subtype, we substantially expand the repertoire of differentially expressed genes in ASD and identify a component of upregulated immune processes that are associated with hypomethylation. We utilize eQTL and chromosome conformation datasets to link differentially acetylated regions with their cognate genes and identify an enrichment of ASD genetic risk variants in hyperacetylated noncoding regulatory regions linked to neuronal genes. These findings help elucidate how diverse genetic risk factors converge onto specific molecular processes in ASD.

genomics↗

bioRxiv2018

Genetic control of gene expression and splicing in the developing human brain

Most genetic risk for human diseases lies within non-coding regions of the genome, which is predicted to regulate gene expression, often in a tissue and stage specific manner. This has motivated building of extensive eQTL resources to understand how human allelic variation affects gene expression and splicing throughout the body, focusing primarily on adult tissue. Given the importance of regulatory pathways during brain development, we characterize the genetic control of the developing human cerebral cortical transcriptome, including expression and splicing, in 201 mid-gestational human brains, to understand how common allelic variation affects gene regulation during development. We leverage expression and splice quantitative trait loci to identify genes and isoforms relevant to neuropsychiatric disorders and brain volume. These findings demonstrate genetic mechanisms by which early developmental events have a striking and widespread influence on adult anatomical and behavioral phenotypes, as well as the evolution of the human cerebral cortex.\n\nHighlightsO_LIGenome wide map of human fetal brain eQTLs and sQTLs provides a new view of genetic control of expression and splicing.\nC_LIO_LIThere is substantial contrast between genetic control of transcript regulation in mature versus developing brain.\nC_LIO_LIWe identify novel regulatory regions specific to fetal brain development.\nC_LIO_LIIntegration of eQTLs and GWAS reveals specific relationships between expression and disease risk for neuropsychiatric diseases and relevant human brain phenotypes.\nC_LI

neuroscience↗

bioRxiv2018

Widespread RNA editing dysregulation in Autism Spectrum Disorders

Autism spectrum disorder (ASD) is a genetically complex, clinically heterogeneous neurodevelopmental disease. Recently, our understanding of the molecular abnormalities in ASD has been expanded through transcriptomic analyses of postmortem brains. However, a crucial molecular pathway involved in synaptic development, RNA editing, has not yet been studied on a genome-wide scale. Here, we profiled the global patterns of adenosine-to-inosine (A-to-I) editing in a large cohort of post-mortem ASD brains. Strikingly, we observed a global bias of hypo-editing in ASD brains, common to different brain regions and involving many genes with known neurobiological functions. Through genome-wide protein-RNA binding analyses and detailed molecular assays, we show that the Fragile X proteins, FMRP and FXR1P, interact with ADAR proteins and modulate A-to-I editing. Furthermore, we observed convergent patterns of RNA editing alterations in ASD and Fragile X syndrome, thus establishing RNA editing as a molecular link underlying these two highly related diseases. Our findings support a role for RNA editing dysregulation in ASD and highlight novel mechanisms for RNA editing regulation.

neuroscience↗

bioRxiv2018

Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic forms of autism in postmortem human brain tissue.

Autism spectrum disorder (ASD) encompasses a collection of complex neuropsychiatric disorders characterized by deficits in social functioning, communication and repetitive behavior. Building on recent studies supporting a role for developmentally moderated regulatory genomic variation in the molecular etiology of ASD, we quantified genome-wide patterns of DNA methylation in 233 post-mortem tissues samples isolated from three brain regions (prefrontal cortex, temporal cortex and cerebellum) dissected from 43 ASD patients and 38 non-psychiatric control donors. We identified widespread differences in DNA methylation associated with idiopathic ASD (iASD), with consistent signals in both cortical regions that were distinct to those observed in the cerebellum. Individuals carrying a duplication on chromosome 15q (dup15q), representing a genetically-defined subtype of ASD, were characterized by striking differences in DNA methylation across a discrete domain spanning an imprinted gene cluster within the duplicated region. In addition to the dramatic cis-effects on DNA methylation observed in dup15q carriers, we identified convergent methylomic signatures associated with both iASD and dup15q, reflecting the findings from previous studies of gene expression and H3K27ac. Cortical co-methylation network analysis identified a number of co-methylated modules significantly associated with ASD that are enriched for genomic regions annotated to genes involved in the immune system, synaptic signalling and neuronal regulation. Our study represents the first systematic analysis of DNA methylation associated with ASD across multiple brain regions, providing novel evidence for convergent molecular signatures associated with both idiopathic and syndromic autism.

genomics↗