Search bioRxiv⌕ Search

Biology subjects

Ramesh, R.

Publications and source records attributed to Ramesh, R..

11 recordsLinked to original sources

Physiological learning involves intrasynaptic reorganization of GluA1-containing AMPA receptors

Learning and memory formation depend on persistent modifications of excitatory synaptic transmission in the hippocampus through changes in AMPA receptor (AMPAR) content and properties at potentiated synapses. However, directly demonstrating such changes after physiological, behavior-driven learning in the intact brain has remained technically difficult. Using SDS-digested freeze-fracture replica labeling (SDS-FRL), we examined the density and nanoscale localization of AMPAR subunits GluA1, GluA2, and GluA3 in the mouse hippocampal CA1 pyramidal cells. GluA2 density was higher than GluA1 and GluA3 densities at both synaptic and extrasynaptic sites, consistent with previous studies showing that AMPARs in CA1 pyramidal cells mostly contain GluA2. The extrasynaptic density of GluA3 was substantially lower than those of GluA1 and GluA2, pointing to distinct trafficking mechanisms. GluA1- and GluA2-containing receptors were enriched at synaptic peripheries, whereas GluA3 was more centrally localized and clustered, a subunit-specific intrasynaptic organization consistent with differential roles in plasticity. To investigate learning-induced reorganization, we combined the inhibitory avoidance, hippocampus-dependent contextual learning paradigm with SDS-FRL in the CA1 stratum radiatum. Learning induced a selective increase in synaptic GluA1 density accompanied by a concurrent decrease in GluA2 density, consistent with a compositional shift toward higher-conductance GluA1-containing receptors, specifically in the proximal CA1 area. Strikingly, we found a redistribution of GluA1 from the synaptic periphery toward the center, accompanied by increased clustering. These findings reveal intrasynaptic receptor redistribution alongside subunit composition change, a nanoscale molecular signature at CA3-CA1 synapses, which may constitute a mechanism of hippocampal memory formation in physiological learning.

neuroscience↗

Kinase-specific phosphorylation of tau outside the amyloid core encodes fibril fold selection

Tauopathies are defined by the accumulation of filamentous tau assemblies that adopt disease-specific molecular conformations, or tau strains. Although tau is extensively hyperphosphorylated in Alzheimers disease, how phosphorylation patterns influence tau folding and strain selection remains unclear. Here, we show that site-specific phosphorylation of 0N3R tau by extracellular signal-regulated kinase 2 (ERK2), occurring predominantly within the proline-rich region and largely excluding the microtubule-binding domain, is sufficient to direct tau assembly into a structurally homogeneous fibril conformation. Residue-resolved NMR spectroscopy identifies a defined and quantifiable ERK2 phosphorylation pattern in the proline-rich region of tau. Cryo-electron microscopy at 3.0 [A] resolution reveals that ERK2-phosphorylated 3R tau assembles into filaments with an ordered cross-{beta} fold adopting an Alzheimers disease PHF fold, despite the absence of phospho-sites within the fibril core. These filaments exhibit robust seeding activity in tau biosensor cells. Together, these results demonstrate that kinase-specific phosphorylation outside the amyloid core can be sufficient to bias tau toward a defined fibril structure, establishing a direct mechanistic link between kinase specificity, post-translational modification, and tau strain formation.

molecular biology↗

NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation

Transcription factor (TF) coordination plays a key role in target gene (TG) regulation via protein-protein interactions (PPIs) and DNA co-binding to regulatory elements. Single-cell technologies facilitate gene expression measurement for individual cells and cell-type identification, yet the connection between TF coordination and TG regulation of various cell types remains unclear. To address this, we have developed a novel computational approach, Network Regression Embeddings (NetREm), to reveal cell-type TF-TF coordination activities for TG regulation. NetREm leverages network-constrained regularization using prior knowledge of direct and/or indirect PPIs among TFs to analyze single-cell gene expression data. We test NetREm by simulation data and benchmark its performance in 4 real-world applications that have gold standard TF-TG networks available: mouse (mESCs) and simulated human (hESCs) embryonic stem (ESCs), human hematopoietic stem (HSCs), and mouse dendritic (mDCs) cells. Further, we showcase NetREms ability to prioritize valid novel TF-TF coordination links in human Peripheral Blood Mononuclear cell (PBMC) sub-types. We apply NetREm to analyze various cell types in both central (CNS) and peripheral (PNS) nerve system (NS) (e.g. neuronal, glial, Schwann cells (SCs)) as well as in Alzheimers disease (AD). Our findings uncover cell-type coordinating TFs and identify new TF-TG candidate links. We validate our top predictions using Cut&Run and knockout loss-of-function expression data in rat/mouse models and compare results with additional functional genomic data, including expression quantitative trait loci (eQTL) and Genome-Wide Association Studies (GWAS) to link genetic variants (single nucleotide polymorphisms (SNPs)) to TF coordination. NetREm is open-source available on GitHub as a software package.

bioinformatics↗

Investigating miRNA signatures in metastatic breast cancer: An in silico analysis.

miRNAs are small non-coding RNAs that regulate most cellular processes. Tumorigenesis disrupts the normal balance in the cell, which leads to changes in the cell cycle, cell signalling, activation of growth factors, miRNA deregulation, etc. Thus, the variations in miRNA expression between normal and tumor stages can be used to predict, diagnose, detect and identify different cancer stages, thereby suggesting the potential use of the miRNAs as biomarkers or potential therapeutic targets for cancer. In this study we aim to identify differentially expressed miRNAs which could serve as potential biomarkers or therapeutic targets for breast cancer. Microarray-based expression analysis was performed on tissue samples from patients with early and locally advanced breast cancer and nCounter analysis was performed to detect differentially expressed miRNA. Additionally, functional enrichment analysis, miRNA linked gene prediction, and in silico analysis for miRNA expression in cancer databases were carried out. This analysis revealed increased expression of Hsa-miR-199a and b. Further these miRs had increased expression levels across various cancer. Importantly, genes such as CALR, SSR2, and YWHAZ predicted as miRs target were highly expressed in breast cancer. However, these genes lack therapeutic drugs targeting them. Overall, our study identified previously unexplored miRNAs and their gene targets, which could be exploited as potential targets for future therapeutic interventions.

cancer biology↗

OpenMEA: Open-Source Microelectrode Array Platform for Bioelectronic Interfacing

Bioelectronic interfaces have the potential to revolutionize the treatment of medical disorders and augment physiology. Implantable devices such as pacemakers and deep brain stimulators have already been deployed to control activity in diseases including Parkinsons disease and epilepsy. These devices typically operate by delivering electrical stimulation at pre-programmed intervals (known as open-loop stimulation). Recent advances in machine learning and low-power integrated circuits have led to the emergence of personalized medical devices that monitor the users state and stimulate in response to measured biological activity (known as closed-loop stimulation). There are two key questions that require fundamental research to achieve breakthroughs in personalized devices: 1) What biomarkers and algorithms are best suited to detecting biological states (e.g. seizures in epilepsy)? and 2) What types of electrical stimuli are optimal for controlling these states? The answer to these questions can be explored in vitro using multielectrode array (MEA) systems that interface with biological tissue with reduced experimental complexity, better reproducibility, and fewer confounding variables present in whole organisms. However, existing MEA systems have functional limitations and closed-source designs that prevent researchers from developing improvements. This paper introduces OpenMEA, an open-source platform for closed-loop bioelectronics research. OpenMEA includes designs for the components necessary to build a benchtop in vitro laboratory, including electrophysiological recording and stimulation electronics, a microfluidic perfusion system, and physical designs for multielectrode arrays. The system is demonstrated with the electrical recording and stimulation of epileptogenic human and rodent brain slices. The aim of OpenMEA is to democratize bioelectronic research tools to accelerate the deployment of devices for the treatment of disorders and beyond.

bioengineering↗

A Single-Cell Molecular Atlas of White Adipose Tissue Shows Differences in Myeloid and Lymphoid Cell Polarization in Type 2 Diabetes and HIV Infection

Subcutaneous adipose tissue (SAT) is a critical regulator of systemic metabolic homeostasis. Persons with HIV (PWH) have an increased risk of metabolic diseases and significant alterations in the SAT immune environment compared with the general population. We generated a comprehensive SAT atlas to characterize cellular compositional and transcriptional changes in 59 PWH with a spectrum of metabolic health. Glucose intolerance was associated with increased lipid-associated macrophages and CD4+ and CD8+ T effector memory cells, and decreased perivascular macrophages. We observed a coordinated intercellular regulatory program which enriched for genes related to inflammation and lipid-processing across multiple cell types as glucose intolerance increased. Increased CD4+ effector memory tissue resident cells most strongly associated with altered expression of adipocyte genes critical for lipid metabolism and cellular regulation. Many of these findings were present in a separate group of 32 diabetic HIV-negative persons, suggesting these changes are not specific to HIV.

immunology↗

JUN Regulation of Injury-induced Enhancers in Schwann Cells

Schwann cells play a critical role after peripheral nerve injury by clearing myelin debris, forming axon-guiding Bands of Bungner, and re-myelinating regenerating axons. Schwann cells undergo epigenomic remodeling to differentiate into a repair state that expresses unique genes, some of which are not expressed at other stages of Schwann cell development. We previously identified a set of enhancers that are activated in Schwann cells after nerve injury, and we determined if these enhancers are pre-programmed into the Schwann cell epigenome as poised enhancers prior to injury. Poised enhancers share many attributes of active enhancers, such as open chromatin, but are marked by repressive H3K27 trimethylation (H3K27me3) rather than H3K27ac. We find that most injury-induced enhancers are not marked as poised enhancers prior to injury indicating that injury-induced enhancers are not pre-programmed in the Schwann cell epigenome. Injury-induced enhancers are enriched with AP-1 binding motifs, and the c-JUN subunit of AP-1 had been shown to be critical to drive the transcriptional response of Schwann cells after injury. Using in vivo ChIP-seq analysis we find that c-JUN binds to a subset of injury-induced enhancers. To test the role of specific injury-induced enhancers, we focused on c-JUN-binding enhancers upstream of the Sonic Hedgehog (Shh) gene, which is only upregulated in repair Schwann cells compared to other stages of Schwann cell development. We confirm that c-JUN regulates these enhancers and also show that the enhancers are required for robust induction of the Shh gene after injury. Significance StatementThe pro-regenerative actions of Schwann cells after nerve injury depends on upon profound reprogramming of the epigenome. The repair state is directed by injury-induced transcription factors, like JUN, which is uniquely required after nerve injury. In this study, we test whether the injury program is pre-programmed into the epigenome as poised enhancers and define which enhancers bind JUN. Finally, we test the roles of these enhancers by performing CRISPR-mediated deletion of JUN-bound injury enhancers in the Sonic hedgehog gene. While many long range enhancers drive expression of Sonic hedgehog at different developmental stages of specific tissues, these studies identify an entirely new set of enhancers that are required for Sonic hedgehog induction in Schwann cells after injury.

neuroscience↗

Viral genome-capsid core senses host environments to prime RNA release

Viruses are metastable macromolecular assemblies containing a nucleic acid core packaged by capsid proteins that are primed to disassemble in host-specific environments leading to genome release and replication. The mechanism of how viruses sense environmental changes associated with host entry to prime them for disassembly is unknown. We have applied a combination of mass spectrometry, cryo-EM, and simulation-assisted structure refinement to Turnip crinkle virus (TCV), which serves as a model non-enveloped icosahedral virus (Triangulation number = 3, 180 copies/icosahedron). Our results reveal genomic RNA tightly binds a subset of viral coat proteins to form a stable RNA-capsid core which undergoes conformational switching in response to host-specific environmental changes. These changes include: i) Depletion of Ca2+ which triggers viral particle expansion ii) Increase in osmolytes further disrupt interactions of outer coat proteins from the RNA-capsid core to promote complete viral disassembly. A cryo-EM structure of the expanded particle shows that RNA is asymmetrically extruded from a single 5-fold axis during disassembly. The genomic RNA:capsid protein interactions confer metastability to the TCV capsid and drive release of RNA from the disassembling virion within the plant host cell. AUTHOR SUMMARYRNA viruses including coronaviruses, dengue, influenza, and HIV are a significant threat to human health. These viral particles are finely tuned to undergo complex conformational changes that allow for response to varied environments. Turnip crinkle virus (TCV) serves as an excellent model for studying RNA virus dynamics. Since TCV is non-enveloped and has no post-translational modifications, we can specifically investigate the contributions of RNA to viral dynamics. Genomic RNA is not a passive entity but plays a crucial and previously uncharacterized role in viral disassembly. Our results reveal that the genomic RNA-capsid core serves as an environmental sensor and undergoes conformational switching in response to host cell conditions.

plant biology↗

Early embryonic heat shock induces long-term epigenetic memory by affecting the transition to zygotic independence

Early-life stress can generate persistent life-long effects that impact adult health and disease risk, but little is known of how such programming is established and maintained. Previous use of the Drosophila strain wm4h show that an early embryonic heat shock result in stable epigenetic alteration in the adult fly. To investigate the potential role of small non-coding RNA (sncRNA) in the initiation of such long-term epigenetic effects, we here generated a fine timeline of sncRNA expression during the first 5 stages of Drosophila embryogenesis in this strain. Building on this, we show that (1) miRNA is increased following early embryonic heat shock, and (2) the increased miRNA is coming from two separate sources, maternal and zygotic. By performing long RNA sequencing on the same single embryo, we found that a subgroup of miRNA with maternal origin, had a strong negative correlation with a group of early zygotic transcripts. Critically, we found evidence that one such early zygotic transcript, the insulator binding factor Elba1, is a Su(var) for wm4h. The findings provide insights of the dynamics and stress-sensitivity of sncRNA during the first embryonic stages in Drosophila and suggest an interplay between miRNA, Elba1 and long-term epigenetic alteration. HIGHLIGHTSO_LIWe provide a high-resolution timeline for sncRNA for Drosophila stage 1-5 embryos C_LIO_LIHeat shock before midblastula transition (MBT) results in a massive upregulation of miRNA at cellularization C_LIO_LIHeat shock-induced miRNAs negatively associate with downregulation of a specific subset of pre-MBT genes C_LIO_LIElba1 is a position-effect-variegation (PEV) modifier for wm4h C_LIO_LIHeat shock-induces an "leaky" expression of genes that overlap with Elba 1-3 binding sites C_LI

developmental biology↗

Nutritional dependence of sperm mitochondrial metabolism and small RNA biogenesis

A wide spectrum of exogenous factors, including diet, environmental pollutants, stress, and seasonal changes have major impact on sperm quality and function. The molecular basis, however, that explains this susceptibility remains largely unknown. Using a combination of proteomics and small RNA (sRNA) sequencing, we show that Drosophila sperm display rapid molecular changes in response to dietary sugar, both in terms of metabolic/redox proteins and sRNA content, particularly miRNA and mitochondria derived sRNA (mt-sRNA). Thus, results from two independent omics point at the dynamics of mitochondria as the central aspect in rapid metabolic adjustments in sperm. Using specific stains and in vivo redox reporter flies, we show that diet indeed rapidly alters the production of mitochondrial derived reactive oxygen species (ROS). Quenching ROS via supplementation of N acetyl cysteine reduces diet-upregulated miRNA, but not mitochondrial-sRNA. Together, these results open new territories in our search for the mechanistic understanding of sperm health and disease. HighlightsO_LIDiet rapidly changes the proteomic and sRNA profiles in sperm C_LIO_LIDiet sensitive sperm proteins are found in human infertility studies C_LIO_LISperm mitochondrial ROS levels are modulated by diet C_LIO_LIdme-miR-10 regulation is secondary to diet-induced ROS C_LIO_LIDiet, but not diet-induced ROS, alters the expression of mitochondrial small RNA, especially tsRNA C_LI

molecular biology↗

A computational model that explores the effect of environmental geometries on grid cell representations

Grid cells are a special class of spatial cells found in the medial entorhinal cortex (MEC) characterized by their strikingly regular hexagonal firing fields. This spatially periodic firing pattern was originally considered to be invariant to the geometric properties of the environment. However, this notion was contested by examining the grid cell periodicity in environments with different polarity (Krupic et al 2015) and in connected environments (Carpenter et al 2015). Aforementioned experimental results demonstrated the dependence of grid cell activity on environmental geometry. Analysis of grid cell periodicity on practically infinite variations of environmental geometry imposes a limitation on the experimental study. Hence we analyze the grid cell periodicity from a computational point of view using a model that was successful in generating a wide range of spatial cells, including grid cells, place cells, head direction cells and border cells. We simulated the model in four types of environmental geometries such as: 1) connected environments, 2) convex shapes, 3) concave shapes and 4) regular polygons with varying number of sides. Simulation results point to a greater function for grid cells than what was believed hitherto. Grid cells in the model code not just for local position but also for more global information like the shape of the environment. The proposed model is interesting not only because it was able to capture the aforementioned experimental results but, more importantly, it was able to make many important predictions on the effect of the environmental geometry on the grid cell periodicity.

neuroscience↗