Biology subjects

Narayanan, P.

Publications and source records attributed to Narayanan, P..

8 recordsLinked to original sources

bioRxiv2026

Rapid evolution and comparative analysis of piRNA clusters in D.simulans

Eukaryotic genomes are ubiquitously occupied by mobile genetic elements termed transposons, which are silenced via a specialized class of small RNA called piRNA. The small RNA is produced from the transposons themselves when they occupy specialized regions of the genome termed piRNA clusters. The formation of these specialized regions, or their evolution over time, is not well understood. Recent work has suggested that they are extremely variable even within a single species such as Drosophila melanogaster. We were interested in taking a comparative approach to piRNA cluster evolution to ask the question - what processes are unique to D. melanogaster and which are shared? Shared phenomena are more likely to be fundamental aspects of piRNA formation and evolution compared to those that are more labile. Using five high-quality long-read genome assemblies and five genotype-specific piRNA libraries, we approach this question from a population genetics standpoint. We annotate piRNA clusters, transposons, and structural variants in each of these five genomes. We found extensive variation in piRNA clusters across strains, with smaller piRNA clusters more likely to be limited to a single genotype. By and large, our results are consistent with a model of piRNA cluster evolution in which piRNA clusters are rapidly formed and lost, with a small subset increasing in frequency and length over time. However, we find that the TEs which nucleate the formation of small piRNA clusters are entirely distinct in D. simulans compared to D. melanogaster, and likely reflect its invasion history rather than any inherent property of the transposon to nucleate clusters. Therefore, while large common clusters can act as traps as has been posited for piRNA clusters, there are also numerous small clusters that are born and lost rapidly within a species.

evolutionary biology↗

bioRxiv2025

Atypical p38 Kinase Signaling in Retinal Vascular Damage and Recovery

Despite the life-changing impact of anti-VEGF therapies, vascular retinopathies continue to affect millions of patients worldwide. To better understand disease progression, it is essential to define alternative mechanisms that contribute to retinal vascular dysregulation. Mitogen-activated protein kinase (MAPK) p38 plays a significant role in regulating vascular homeostasis, angiogenesis, and retinal disease progression, yet effective therapeutic targeting remains elusive. An alternative atypical p38 signaling pathway is mediated by interaction with the adaptor protein TGF-beta activated kinase 1, binding protein 1 (TAB1). Atypical p38 can be activated by ischemia or by inflammatory G protein-coupled receptors (GPCRs) to regulate inflammation and vascular homeostasis. However, atypical signaling has not been investigated in the context of vascular retinopathies, specifically oxygen-induced retinopathy (OIR). Here, we utilized a genetic knock-in mouse to block atypical p38 activity (Tab1KI) to explore retinal damage during OIR. We report that Tab1KI mice display significantly reduced vaso-obliteration and limited neovascularization relative to wild-type C57BL6 controls. Retinal RNAseq analysis revealed distinct transcriptional regulation in the Tab1KI mouse. Suppression of atypical p38 reduced Mef2c signaling, which in turn enhanced microglial activation and inflammation. Despite the upregulation of proangiogenic markers, the increase in endothelial markers does not correlate with the dysregulated growth of blood vessels. Instead, Mef2c suppression reduces pathological angiogenesis, while increasing physiological vascular regrowth. The combined data suggest that the selective inhibition of atypical p38 signaling could block the enhanced pathogenic neovascular tuft formation without impacting blood vessel repair. Further investigation will clarify how atypical p38 controls neovascular responses, potentially revealing new treatment strategies for vascular retinopathies. NEW AND NOTEWORTHYMAPK p38 drives ocular injury and inflammation, but the contribution of Tab1-dependent atypical p38 in retinal injury has not been investigated. Using a mouse genetic knock-in model to block atypical p38 during oxygen-induced retinal injury, we show that atypical p38 enhances vascular damage and neovascular tufting. Blockade of atypical p38 protects mice from retinal vascular damage.

cell biology↗

bioRxiv2024

Lipid composition differentiates ferroptosis sensitivity between in vitro and in vivo systems

Ferroptosis is a regulated non-apoptotic cell death process characterized by iron-dependent lipid peroxidation. This process has recently emerged as a promising approach for cancer therapy. Peroxidation of polyunsaturated fatty acid-containing phospholipids (PUFA-PLs) is necessary for the execution of ferroptosis. Ferroptosis is normally suppressed by glutathione peroxidase 4 (GPX4), which reduces lipid hydroperoxides to lipid alcohols. Some evidence indicates that GPX4 may be a useful target for drug development, yet factors that govern GPX4 inhibitor sensitivity in vivo are poorly understood. We find that pharmacological and genetic loss of GPX4 function was sufficient to induce ferroptosis in multiple adherent ("2D") cancer cell cultures. However, reducing GPX4 protein levels did not affect tumor xenograft growth when these cells were implanted in mice. Furthermore, sensitivity to GPX4 inhibition was markedly reduced when cells were cultured as spheroids ("3D"). Mechanistically, growth in 3D versus 2D conditions reduced the abundance of PUFA-PLs. 3D culture conditions upregulated the monounsaturated fatty acid (MUFA) biosynthetic gene stearoyl-CoA desaturase (SCD). SCD-derived MUFAs appear to protect against ferroptosis in 3D conditions by displacing PUFAs from phospholipids. Various structurally related long chain MUFAs can inhibit ferroptosis through this PUFA-displacement mechanism. These findings suggest that growth-condition-dependent lipidome remodeling is an important mechanism governing GPX4 inhibitor effects. This resistance mechanism may specifically limit GPX4 inhibitor effectiveness in vivo.

cancer biology↗

bioRxiv2023

Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s

During the last few centuries D. melanogaster populations were invaded by several transposable elements, the most recent of which was thought to be the P-element between 1950 and 1980. Here we describe a novel TE, which we named Spoink, that has invaded D. melanogaster. It is a 5216nt LTR retrotransposon of the Ty3/gypsy superfamily. Relying on strains sampled at different times during the last century we show that Spoink invaded worldwide D. melanogaster populations after the P-element between 1983 and 1993. This invasion was likely triggered by a horizontal transfer from the D. willistoni group, much as the P-element. Spoink is probably silenced by the piRNA pathway in natural populations and about 1/3 of the examined strains have an insertion into a canonical piRNA cluster such as 42AB. Given the degree of genetic investigation of D. melanogaster it is surprising that Spoink was able to invade unnoticed.

evolutionary biology↗

bioRxiv2023

Intracellular Cytomatrix, Immobilized Biocatalysis, Matrix Micromechanics and The Warburg Effect: Entanglement of Two Age-Old Mysteries of the Normal and Malignant Cell

For decades cancer studies have focused on molecular genetics while the role of the cytoplasm has remained obscure. Separation of the viscous fluid cytosol and elastic-solid cytomatrix has offered an opportunity to solve an age-old mystery in biochemistry; how millions of complex chemical reactions can occur simultaneously within the cell cytoplasm. The cytomatrix contains structural proteins, ribosomes, and metabolome enzymes responsible for unique biosynthetic pathways that involve immobilized biocatalysis. Immobilizing these catalytic complexes overcomes the spatial limitations for biochemical processes and allows integration of the intracellular and extracellular matrices and receptors with nuclear processes. Together, the cytosol and cytomatrix produce an interconnected synergistic network that maintains the operational flexibility of healthy cells as well as the survival of malignant cells. The cytomatrix is also responsible for cellular micromechanics and cytoplasmic motion. The combination of mechanical and biocatalytic processes triggered by extracellular signals and gene mutations in malignant cells requires additional energy. Cancer cells, consequently, utilize aerobic glycolysis, the Warburg effect, to meet the energy demands of the matrix mechanics that arise in response to imbalanced signaling and excessive biocatalytic activity. Clinical cancer is a rare event despite a high frequency of mutations, as clinical cancer is limited by the requirement for alterations that result in a high energy production state. Without these transformations, potential cancers can only survive in the quiescent state or will be eliminated. Survival of cancer cells indicates that the cancer cells were able to synchronize energy output for matrix mechanics supplying sufficient energy for tumor growth. Thus, the Warburg effect connects genetic aberrations and intracellular matrix mechanics with the ability to provide the energy supply required for the unprecedented complexity of tumor growth.

cancer biology↗

bioRxiv2021

Low mammalian species richness increases Kyasanur Forest Disease outbreak risk in deforested landscapes in the Western Ghats, India

Kyasanur forest disease virus (KFDV) is a rapidly expanding tick-borne zoonotic virus with natural foci in the forested region of the Western Ghats of South India. The Western Ghats is one of the worlds most important biodiversity hotspots and, like many such areas of high biodiversity, is under significant pressure from anthropogenic landscape change. The current study sought to quantify mammalian species richness using ensemble models of the distributions of a sample of species extant in the Western Ghats and to explore its association with KFDV outbreaks, as well as the modifying effects of deforestation on this association. Species richness was quantified as a composite of individual species distributions, as derived from ensembles of boosted regression tree, random forest, and generalised additive models. Species richness was further adjusted for the potential biotic constraints of sympatric species. Both species richness and forest loss demonstrated strong positive associations with KFDV outbreaks, however forest loss substantially modified the association between species richness and outbreaks. High species richness was associated with increased KFDV risk but only in areas of low forest loss. In contrast, lower species richness was associated with increased KFDV risk in areas of greater forest loss. This relationship persisted when species richness was adjusted for biotic constraints at the taluk-level. In addition, the taluk-level species abundances of three monkey species (Macaca radiata, Semnopithecus hypoleucus, and Semnopithecus priam) were also associated with outbreaks. These results suggest that increased monitoring of wildlife in areas of significant habitat fragmentation may add considerably to critical knowledge gaps in KFDV epidemiology and infection ecology and should be incorporated into novel One Health surveillance development for the region. In addition, the inclusion of some primate species as sentinels of KFDV circulation into general wildlife surveillance architecture may add further value. HighlightsO_LILocal mammalian species richness is estimated across the entire Western Ghats region C_LIO_LILow species richness is associated with high KFDV risk in deforested landscapes C_LIO_LIThis work identifies key landscapes for wildlife disease surveillance development C_LI

ecology↗

bioRxiv2020

The atlas of RNase H antisense oligonucleotide distribution and activity in the CNS of rodents and non-human primates following central administration

Antisense oligonucleotides (ASOs) have emerged as a new class of drugs to treat a wide range of diseases, including neurological indications. Spinraza, an ASO that modulates splicing of SMN2 RNA, has shown profound disease modifying effects in Spinal Muscular Atrophy (SMA) patients, energizing the field to develop ASOs for other neurological diseases. While SMA specifically affects spinal motor neurons, other neurological diseases affect different central nervous system (CNS) regions, neuronal, and non-neuronal cells. Therefore, it is critically important to characterize ASO distribution and activity in all major CNS structures and cell types to have a better understanding of which neurological diseases are amenable to ASO therapy. Here we present for the first time the atlas of ASO distribution and activity in the CNS of mice, rats, and non-human primates (NHP), species commonly used in preclinical therapeutic development. Following central administration of an ASO to rodents, we observe widespread distribution and robust activity throughout the CNS in neurons, oligodendrocytes, astrocytes, and microglia. This is also the case in NHP, despite a larger CNS volume and more complex neuroarchitecture. Our results demonstrate that ASO drugs are well suited for treating a wide range of neurological diseases for which no effective treatments are available.

neuroscience↗

bioRxiv2017

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is important to elucidate the general principles governing their thermodynamics/folding mechanisms. Here, we combine experiments and simulations to examine the folding/unfolding pathways of the VPK pseudoknot, a variant of the Mouse Mammary Tumor Virus (MMTV) PK involved in ribosomal frameshifting. Fluorescent nucleotide analogs (2-aminopurine and pyrrolocytidine) placed at different stem/loop positions in the PK, and laser temperature-jump approaches serve as local probes allowing us to monitor the order of assembly of VPK with two helices with different intrinsic stabilities. The experiments and molecular simulations show that at 50 mM KCl the dominant folding pathway populates only the more stable partially folded hairpin. As the salt concentration is increased a parallel folding pathway emerges, involving the less stable hairpin structure as an alternate intermediate. Notably, the flux between the pathways is modulated by the ionic strength. The findings support the principle that the order of PK structure formation is determined by the relative stabilities of the hairpins, which can be altered by sequence variations or salt concentrations. Our study not only unambiguously demonstrates that PK folds by parallel pathways, but also establishes that quantitative description of RNA self-assembly requires a synergistic combination of experiments and simulations.\n\nSIGNIFICANCEThe assembly mechanism of RNA, vital to describing their functions, depends on both the sequence and the metal ion concentration. How the latter influences the folding trajectories remains an important unsolved problem. Here, we examine the folding pathways of an RNA pseudoknot (PK) with key functional roles in transcription and translation, using a combination of experiments and simulations. We demonstrate that the PK, consisting of two helices with differing stabilities, folds by parallel pathways. Surprisingly, the flux between them is modulated by monovalent salt concentration. Our work shows that the order of assembly of PKs is determined by the relative stability of the helices, implying that the folding landscape can be controlled by sequence and ion concentration.

biophysics↗