Biology subjects

Ramaswamy, S.

Publications and source records attributed to Ramaswamy, S..

26 records · Page 2Linked to original sources

bioRxiv2020

Whole genome and phylogenetic analysis of SARS-CoV-2 strains from the index and early patients with COVID-19 in Dubai, United Arab Emirates, 29 January to 18 March 2020

International travel played a significant role in the early global spread of SARS-CoV-2. Understanding transmission patterns from different regions of the world will further inform global dynamics of the pandemic. Using data from Dubai in the United Arab Emirates (UAE), a major international travel hub in the Middle East, we establish SARS-CoV-2 full genome sequences from the index and early COVID-19 patients in the UAE. The genome sequences are analysed in the context of virus introductions, chain of transmissions, and possible links to earlier strains from other regions of the world. Phylogenetic analysis showed multiple spatiotemporal introductions of SARS-CoV-2 into the UAE from Asia, Europe, and the Middle East during the early phase of the pandemic. We also provide evidence for early community-based transmission and catalogue new mutations in SARS-CoV-2 strains in the UAE. Our findings contribute to the understanding of the global transmission network of SARS-CoV-2.

genomics↗

bioRxiv2019

Aneuploidy and deregulated DNA damage response define haploinsufficiency in breast tissues of BRCA2 mutation carriers

Women harboring heterozygous germline mutations of BRCA2 have a 50-80% risk of developing breast cancer, yet the early pathogenesis of these cancers is poorly understood. We sought to reveal early steps in BRCA2-associated carcinogenesis through analysis of sorted cell populations from freshly-isolated, non-cancerous breast tissues among a cohort of BRCA2 mutation carriers and matched controls. Single-cell whole-genome sequencing demonstrates that >25% of BRCA2 carrier (BRCA2mut/+) luminal progenitor (LP) cells exhibit sub-chromosomal copy number variations (CNVs), which are rarely observed in non-carriers. Correspondingly, primary BRCA2mut/+ breast epithelia exhibit spontaneous and replication stress-induced DNA damage together with attenuated replication checkpoint and apoptotic responses, associated with an age-associated expansion of the LP compartment in human carrier tissues. These phenotypes are not associated with loss of wild-type BRCA2. Collectively, these findings provide evidence for BRCA2 haploinsufficiency and associated DNA damage in vivo that precede histologic abnormalities. These results provide unanticipated opportunities for new cancer risk assessment and prevention strategies in high-risk patients.

cancer biology↗

bioRxiv2019

Data-driven integration of hippocampal CA1 synapse physiology in silico

The anatomy and physiology of synaptic connections in rodent hippocampal CA1 have been exhaustively characterized in recent decades. Yet, the resulting knowledge remains disparate and difficult to reconcile. Here, we present a data-driven approach to integrate the current state-of-the-art knowledge on the synaptic anatomy and physiology of rodent hippocampal CA1, including axo-dendritic innervation patterns, number of synapses per connection, quantal conductances, neurotransmitter release probability, and short-term plasticity into a single coherent resource. First, we undertook an extensive literature review of paired-recordings of hippocampal neurons and compiled experimental data on their synaptic anatomy and physiology. The data collected in this manner is sparse and inhomogeneous due to the diversity of experimental techniques used by different labs, which necessitates the need for an integrative framework to unify these data. To this end, we extended a previously developed workflow for the neocortex to constrain a unifying in silico reconstruction of the synaptic physiology of CA1 connections. Our work identifies gaps in the existing knowledge and provides a complementary resource towards a more complete quantification of synaptic anatomy and physiology in the rodent hippocampal CA1 region.

neuroscience↗

bioRxiv2019

Estimating the Readily-Releasable Vesicle Pool Size at Synaptic Connections in a Neocortical Microcircuit

Previous studies based on the Quantal Model for synaptic transmission suggested that neurotransmitter release is mediated by a single release site at individual synaptic contacts in the neocortex. However, recent studies seem to contradict this hypothesis and indicate that multi-vesicular release (MVR) could better explain the synaptic response variability observed in vitro. In this study we present a novel method to estimate the number of release sites per synapse, also known as the size of the readily-releasable pool (NRRP), from paired whole-cell recordings of layer 5 thick tufted pyramidal cell (L5_TTPC) connections in the somatosensory neocortex. Our approach extends the work of Loebel and colleagues to take advantage of a recently reported data-driven biophysical model of neocortical tissue. Using this approach, we estimated NRRP to be between two to three for connections between L5-TTPC. To constrain NRRP values for other connections in the microcircuit, we developed and validated a generalization approach using data on post-synaptic potential (PSP) coefficient of variations (CVs) from literature and matching to in silico experiments. Our study shows that synaptic connections in the neocortex generally are mediated by MVR and provides a data-driven approach to constrain the MVR model parameters of the microcircuit.

neuroscience↗

bioRxiv2018

A computational model of loss of dopaminergic cells in Parkinson’s disease due to glutamate-induced excitotoxicity

Parkinsons disease (PD) is a neurodegenerative disease associated with progressive and inexorable loss of dopaminergic cells in Substantia Nigra pars compacta (SNc). A full understanding of the underlying pathogenesis of this cell loss is unavailable, though a number of mechanisms have been indicated in the literature. A couple of these mechanisms, however, show potential for the development of radical and promising PD therapeutics. One of these mechanisms is the peculiar metabolic vulnerability of SNc cells by virtue of their excessive energy demands; the other is the excitotoxicity caused by excessive glutamate release onto SNc by an overactive Subthalamic Nucleus (STN). To investigate the latter hypothesis computationally, we developed a spiking neuron network model of the SNc-STN-GPe system. In the model, prolonged stimulation of SNc cells by an overactive STN leads to an increase in a stress variable; when the stress in a SNc neuron exceeds a stress threshold the neuron dies. The model shows that the interaction between SNc and STN involves a positive feedback due to which, an initial loss of SNc cells that crosses a threshold causes a runaway effect that leads to an inexorable loss of SNc cells, strongly resembling the process of neurodegeneration. The model further suggests a link between the two aforementioned PD mechanisms: metabolic vulnerability and glutamate excitotoxicity. Our simulation results show that the excitotoxic cause of SNc cell loss in PD might be initiated by weak excitotoxicity mediated by energy deficit, followed by strong excitotoxicity, mediated by a disinhibited STN. A variety of conventional therapies are simulated in the model to test their efficacy in slowing down or arresting SNc cell loss. Among the current therapeutics, glutamate inhibition, dopamine restoration, subthalamotomy and deep brain stimulation showed superior neuroprotective effects in the proposed model.

neuroscience↗

bioRxiv2018

Objective Classification of Neocortical Pyramidal Cells

A consensus on the number of morphologically different types of pyramidal cells (PCs) in the neocortex has not yet been reached, despite over a century of anatomical studies. This is because of a lack of agreement on the subjective classifications of neuron types, which is based on expert analyses of neuronal morphologies: the shapes of somata, dendrites, and axons. Even for neurons that are visually different to non-experts, there is no common ground to consistently distinguish morphological types. We found that objective classification is possible with methods from algebraic topology, and that the dendritic arbor is sufficient for reliable identification of distinct types of PCs. We also provide a solution for the more challenging problem of whether two similar neurons belong to different types or to a continuum of the same type. Using this scheme, we objectively identify seventeen types of PCs in the rat somatosensory cortex. Our topological classification does not require expert input, is stable, and helps settle the long-standing debate on whether cell-types are discrete or continuous morphological variations of each other.

neuroscience↗

bioRxiv2018

Data-driven modeling of cholinergic modulation of neural microcircuits: bridging neurons, synapses, and network states

1Neuromodulators, such as acetylcholine (ACh), control information processing in neural microcircuits by regulating neuronal and synaptic physiology. Computational models and simulations enable predictions on the potential role of ACh in reconfiguring network states. As a prelude into investigating how the cellular and synaptic effects of ACh collectively influence emergent network dynamics, we developed a data-driven framework incorporating phenomenological models of the anatomy and physiology of cholinergic modulation of the neocortex. The first-draft models were integrated into a biologically detailed tissue model of neocortical microcircuitry to predict how ACh affects different types of neurons and synapses, and consequently alters global network states. Preliminary simulations not only corroborate the long-standing notion that ACh desynchronizes network activity, but also reveal a potentially finegrained control over a spectrum of neocortical states. We show that low levels of ACh, such as those during sleep, drive microcircuit activity into slow oscillations and network synchrony, whereas high ACh concentrations, such as those during wakefulness, govern fast oscillations and network asynchrony. In addition, network states modulated by ACh levels shape spike-time cross-correlations across distinct neuronal populations in strikingly different ways. These effects are likely due to the differential regulation of neurons and synapses caused by increasing levels of ACh that enhances cellular excitability by increasing neuronal activity and decreases the efficacy of local synaptic transmission by altering neurotransmitter release probability. We conclude by discussing future directions to refine the biological accuracy of the framework, which will extend its utility and foster the development of hypotheses to investigate the role of neuromodulation in neural information processing.

neuroscience↗

bioRxiv2017

Inferring critical points of ecosystem transitions from spatial data

Ecosystems can undergo abrupt transitions from one state to an alternative stable state when the driver crosses a threshold or a critical point. Dynamical systems theory suggests that systems take long to recover from perturbations near such transitions. This leads to characteristic changes in the dynamics of the system, which can be used as early warning signals of imminent transitions. However, these signals are qualitative and cannot quantify the critical points. Here, we propose a method to estimate critical points quantitatively from spatial data. We employ a spatial model of vegetation that shows a transition from vegetated to bare state. We show that the critical point can be estimated as the ecosystem state and the driver values at which spatial variance and autocorrelation are maximum. We demonstrate the validity of this method by analysing spatial data from regions of Africa and Australia that exhibit alternative vegetation biomes.

ecology↗