Biology subjects

Rana, A.

Publications and source records attributed to Rana, A..

11 recordsLinked to original sources

bioRxiv2026

A translational checkpoint couples proline sensing to mitochondrial proline catabolism in Candida glabrata

Proline catabolism represents a central metabolic and regulatory hub integrating nutrient sensing, stress adaptation, and energy production across diverse organisms. Despite its biological importance, the regulatory mechanisms controlling proline catabolism remain poorly understood in eukaryotic microbes. Here, we describe the transcriptional and translational coordination to catabolize the proline to maintain the cellular homeostasis under stress in the human fungal pathogen Candida glabrata. We identified proline utilisation trigger global translation repression to activates the stress-sensing kinase Gcn2, which phosphorylates eIF2, thereby promoting the activation of the transcription factor Gcn4. Activated Gcn4 upregulates the transcription factor Put3 and the proline transporter Put4. Put3 orchestrates expression of the mitochondrial catabolic enzymes Put1 and Put2, ensuring efficient proline utilization, mitochondrial function, and redox balance. Genetic disruption of PUT3 abolishes proline utilization, impairs mitochondrial function, and severely compromises cellular fitness. Importantly, Put3-mediated proline catabolism is also critical for C. glabrata survival within macrophages and for virulence in systemic infection models. These findings reveal a mechanistic link between proline catabolism, translational regulation, and amino acid sensing in C. glabrata. We propose a regulatory cascade wherein Gcn2-Gcn4-Put3 signaling aligns translational reprogramming with metabolic demands to optimize proline utilization. Thus, this study establishes proline catabolism as a signaling-driven adaptive mechanism essential for fungal metabolism and persistence, rather than merely a nutritional pathway. AUTHOR SUMMARYProline is a versatile amino acid that is essential for cellular metabolism, signaling, stress adaptation, and redox equilibrium. Proline catabolism has been implicated in cancer biology and is increasingly recognized as a key determinant of virulence in diverse pathogens. Although the enzymatic processes of proline use are well characterized, the regulatory mechanisms that sense proline availability and coordinate its metabolic integration remain poorly understood. Here, we identify a hitherto unknown regulatory axis linking proline catabolism to translational reprogramming in Candida glabrata, which seems to be similarly present in numerous fungi. We demonstrate that proline utilization triggers global translational repression via Gcn2-dependent phosphorylation of eIF2, thereby activating the transcription factor Gcn4. Gcn4 is essential for proline utilization, as it controls the expression of PUT3 and PUT4. Notably, PUT3 has no known human counterpart. Our findings establish proline as a metabolic signal that couples translational control to virulence, revealing new opportunities for antifungal intervention.

microbiology↗

bioRxiv2025

Morphological variations in external genitalia do not explain the interspecific reproductive isolation in Nasonia species complex (Hymenoptera: Pteromalidae)

External genitalia play a crucial role in the successful copulation of conspecific partners in insects. Due to their structural specificity, external genitalia have often been used for distinguishing closely related species in different insects. However, in the young Pteromalid species complex Nasonia, these structures have not received much attention. Nasonia is a genus of parasitoid wasps, that lays eggs and completes its life cycle in dipteran pupae. All behavioral studies (including this study) conducted on this genus indicate that varied prezygotic isolation operates among these recently diverged ([~]1 million years) species. Whether such prezygotic isolation is caused by the incompatibility in their reproductive organs is not known. Here, we studied the internal male reproductive system of the four species and show that all four species have a similar organisation and thus ruling it out as a potential barrier. Furthermore, to investigate the role of male external genitalia as a prezygotic barrier, we also examined the ultrastructural details, including aedeagal length, aedeagal aperture length, and digital spines. We show that all these parameters and sperm length show variations across the four species. However, these variations do not correlate with the female acceptance of the heterospecific males. Therefore, we conclude that there must be other olfactory or behavioral isolating mechanisms and spatial or temporal factors that maintain the reproductive isolation of these four species.

zoology↗

bioRxiv2024

Parasite-induced replacement of host microbiota- Impact of Xenos gadagkari parasitization on the microbiota of Polistes wattii

AbstractO_ST_ABSBackgroundC_ST_ABSThe study of microbiota of social insects under different ecological conditions can provide important insights into the role of microbes in their biology and behaviour. Polistes is one of the most widely distributed and extensively studied genera of social wasps, yet the microbiota of any species of Polistes or any primitively eusocial wasp is still unknown. Polistes wattii is an abundantly distributed Asian wasp which hibernates in winter and exhibits a unique biannual nest founding strategy. It is often parasitized by the strepsipteran endoparasite Xenos gadagkari, which changes the morpho-physiology and behaviour of their hosts. In this study we employ 16S rRNA amplicon sequencing, using the Oxford Nanopore platform, to study the microbial community associated with P. wattii and compared the microbiota of the unparasitized male and female P. wattii with their parasitized counterparts. ResultsThe microbiota of females from preemergence solitary foundress nests differs from the females from the late colony phase of multiple foundress nests. The males and females also differ in their microbiota. To estimate the effect of strepsipteran parasitism on the microbiota of P. wattii, we compared the unparasitized wasps with that of the female and male X. gadagkari parasitoids and parasitized wasps. We show that the microbiota of the parasitoids and the parasitized wasps are dominated by Wolbachia and Providencia. {beta}-diversity differences indicated that the parasitoid replaces and homogenizes the microbiota of P. wattii. Although the normal microbiota of P. wattii resembles that of highly eusocial vespid wasps, we show X. gadagkari parasitization replaces the microbiota of P. wattii and it becomes more like the microbiota of strepsipterans. Therefore, it appears that X. gadagkari and other such strepsipteran parasitoids may have a bigger impact on the biology of their hosts, than previously thought. ConclusionThis is the first study of microbiota of any primitively eusocial Polistine wasp and any strepsipteran parasitoid associated with a hymenopteran species. Although strepsipteran parasitoids are commonly found in hymenopteran insects, the change on the microbiota of the host due to the parasitism was not known before. This study shows the drastic impact of the parasitoid on the microbiota of the host.

microbiology↗

bioRxiv2024

Lysosomes cell autonomously regulate myeloid cell states and immune responses

Myeloid cells maintain tissue homeostasis via the recognition, engulfment, and lysosomal clearance of dying cells and cellular debris, which is often accompanied by changes from homeostatic to reactive states. While a role for phagocytic receptors in gating these transitions has been described1,2, less is known about if and how lysosomes can contribute to transcriptional and functional plasticity. To determine how lysosomal health impacts myeloid cell states, we evaluated microglia and macrophages deficient for progranulin (encoded by Grn), a lysosomal protein with pleiotropic functions whose loss is associated with several neurodegenerative diseases3-8. Single-cell RNA-sequencing of the aged mouse brain identified a Grn knockout (KO)-specific microglial subpopulation marked by high GPNMB expression that displays hallmarks of lysosomal dysfunction, including lipofuscin accumulation. Epigenetic analysis of aged microglia revealed MITF/TFE transcription factors as key mediators of the transcriptional states associated with Grn deficiency. In addition to identifying a core myeloid cell transcriptional response to diverse lysosomal stressors, targeted perturbations of various lysosomal properties in vitro uncovered a cell autonomous, TREM2- independent, response to lysosomal deacidification (via v-ATPase or VPS34 loss of function) that overlaps with Grn KO microglia phenotypes, including the induction of a lysosomal gene program, increased proliferation, and secretion of pro-inflammatory cytokines. Compound loss-of-function approaches established GPNMB upregulation upon lysosomal stress is required for the compensatory response to enhance lysosomal function via promoting acidification. Finally, pharmacological endolysosomal reacidification through sodium/proton exchanger inhibition partially rescued Grn KO microglia phenotypes. Overall, these data establish a fundamental link between lysosomal health and myeloid cell epigenetic, transcriptional, and functional states observed in neurodegeneration models.

neuroscience↗

bioRxiv2024

Novel high-content and open-source image analysis tools for profiling mitochondrial morphology in neurological cell models

Mitochondria undergo dynamic morphological changes depending on cellular cues, stress, genetic factors, or disease. The structural complexity and disease-relevance of mitochondria have stimulated efforts to generate image analysis tools for describing mitochondrial morphology for therapeutic development. Using high-content analysis, we measured multiple morphological parameters and employed unbiased feature clustering to identify the most robust pair of texture metrics that described mitochondrial state. Here, we introduce a novel image analysis pipeline to enable rapid and accurate profiling of mitochondrial morphology in various cell types and pharmacological perturbations. We applied a high-content adapted implementation of our tool, MitoProfilerHC, to quantify mitochondrial morphology changes in i) a mammalian cell dose response study and ii) compartment-specific drug effects in primary neurons. Next, we expanded the usability of our pipeline by using napari, a Python-powered image analysis tool, to build an open-source version of MitoProfiler and validated its performance and applicability. In conclusion, we introduce MitoProfiler as both a high-content-based and an open-source method to accurately quantify mitochondrial morphology in cells, which we anticipate to greatly facilitate mechanistic discoveries in mitochondrial biology and disease.

cell biology↗

bioRxiv2024

Morphology, biology and phylogeny of Xenos gadagkari sp.nov. (Strepsiptera: Xenidae): an endoparasite of Polistes wattii (Hymenoptera: Vespidae).

We report the morphology, biology and phylogeny of a new strepsipteran endoparasitic species: Xenos gadagkari, from the primitively eusocial wasp Polistes wattii from Punjab, India. We report a high abundance of the endoparasite in P. wattii population of our study area and provide the morphological description of adult males, male puparium and neotenic females. This species is sufficiently different from other Xenos sp reported from various social wasps and therefore, constitutes a new species, X. gadagkari Sen and Nain, sp. nov. Although there are a few reports of Strepsipteran parasites from India, this is the first confirmational report with a thorough description of a Xenos species from the Indian population of P. wattii and underscores the need for further investigation of the diversity and distribution of this group in India. Our findings contribute to the growing body of knowledge on Xenos and provide a foundation for future behavioural, microbial and molecular studies on this enigmatic group of insects.

zoology↗

bioRxiv2023

Divergent proinflammatory immune responses associated with the differential susceptibility of cattle breeds to Tuberculosis

Tuberculosis (TB) in the bovine is one of the most predominant chronic debilitating infectious diseases primarily caused by Mycobacterium bovis. Besides, the incidence of TB in humans due to M. bovis, and that in bovines due to M. tuberculosis-indicates cattle as a major reservoir of zoonotic TB. While India accounts for the highest global burden of both TB and multidrug-resistant TB in humans, systematic evaluation of bovine TB (bTB) prevalence in India is largely lacking. Recent reports emphasized markedly greater bTB prevalence in exotic and crossbred cattle compared to indigenous cattle breeds that represent more than one-third of the total cattle population in India, which is the largest globally. This study aimed at elucidating the immune responses underlying the differential bTB incidence in prominent indigenous (Sahiwal), and crossbred (Sahiwal x Holstein Friesian) cattle reared in India. Employing the standard Single Intradermal Tuberculin Test (SITT), and mycobacterial gene-targeting single as well as multiplex-PCR-based screening revealed higher incidences of bovine tuberculin reactors as well as Mycobacterium tuberculosis Complex specific PCR positivity amongst the crossbred cattle. Further, ex vivo mycobacterial infection in cultures of bovine peripheral blood mononuclear cells (PBMC) from SITT, and myco-PCR negative healthy cattle exhibited significantly higher intracellular growth of M. bovis BCG, and M. tuberculosis H37Ra in the crossbred cattle PBMCs compared to native cattle. In addition, native cattle PBMCs induced higher pro-inflammatory cytokines and signaling pathways, such as interferon-gamma (IFN-{gamma}), interleukin-17 (IL-17), and tank binding kinase-1 (TBK-1) upon exposure to live mycobacterial infection in comparison to PBMCs from crossbred cattle that exhibited higher expression of IL-1{beta} transcripts. Together, these findings highlight that differences in the innate immune responses of these cattle breeds might be contributing to the differential susceptibility to TB infection, and the resultant disparity in bTB incidence amongst indigenous, and crossbred cattle.

immunology↗

bioRxiv2022

A diverse network of pericoerulear neurons control arousal states

As the primary source of norepinephrine (NE) in the brain, the locus coeruleus (LC) regulates arousal, avoidance and stress responses1,2. However, how local neuromodulatory inputs control LC function remains unresolved. Here we identify a population of transcriptionally, spatially and functionally diverse GABAergic neurons in the LC dendritic field that receive distant inputs and modulate modes of LC firing to control global arousal levels and arousal-related processing and behaviors. We define peri-LC anatomy using viral tracing and combine single-cell RNA sequencing with spatial transcriptomics to molecularly define both LC-NE and peri-LC cell types. We identify several neuronal cell types which underlie peri-LC functional diversity using a series of complementary neural circuit approaches in behaving mice. Our findings indicate that LC and peri-LC neurons are transcriptionally, functionally, and anatomically heterogenous neuronal populations which modulate arousal and avoidance states. Defining the molecular, cellular, and functional diversity of the LC and peri-LC provides a road map for understanding the neurobiological basis of arousal, motivation and neuropsychiatric disorders.

neuroscience↗

bioRxiv2021

Mitochondrial DNA metabolism is coupled with 20S proteasome function via regulation of deoxyribonucleotide homeostasis in Saccharomyces cerevisiae

The synthesis of mitochondrial DNA (mtDNA) is not coupled with cell cycle. Previous studies have shown that the size of deoxyribonucleoside triphosphate (dNTP) pools plays an important role in regulating mtDNA replication and amplification. In yeast, dNTPs are synthesized by the cytosolic ribonucleotide reductase (RNR). It is currently poorly understood as to how RNR activity is regulated in non-dividing or quiescent cells to finely tune mtDNA metabolism to cope with different metabolic states. Here, we show that defect in the 20S proteasome drastically destabilizes mtDNA. The mtDNA instability phenotype in 20S proteasome mutants is suppressed by overexpression of RNR3 or by the deletion of SML1, encoding a minor catalytic subunit and an intrinsic inhibitor of RNR respectively. We found that Sml1 is stabilized in the 20S proteasomal mutants, suggesting that 20S affects mtDNA stability by stabilizing Sml1. Interestingly, defect in the regulatory 19S proteasomal function has only subtle effect on mtDNA stability, supporting a role of the 20S proteasome in dNTP homeostasis independent of 19S. Finally, we found that when cells are transitioned from glycolytic to oxidative growth, Sml1 level is reduced in a 20S-dependent manner. In summary, our study establishes a link between cellular proteostasis and mtDNA metabolism through the regulation of dNTP homeostasis. We propose that increased degradation of Sml1 by the 20S proteasome under respiratory conditions provides a mechanism to stimulate dNTP synthesis and promote mtDNA amplification.

genetics↗

bioRxiv2019

Flossing DNA in a Dual Nanopore Device

Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single molecule data. Here we present an active control technique termed \"flossing\" that uses a dual nanopore device to trap a protein-tagged DNA molecule and perform up to 100s of back-and-forth electrical scans of the molecule in a few seconds. The protein motifs bound to 48 kb{lambda} DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multi-scan data to produce averaged inter-tag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.

biophysics↗

bioRxiv2018

KRASG12D and TP53R167H Cooperate to Induce Pancreatic Ductal Adenocarcinoma in Sus Scrofa Pigs

Although survival has improved in recent years, the prognosis of patients with advanced pancreatic ductal adenocarcinoma (PDAC) remains poor. Despite substantial differences in anatomy, physiology, genetics, and metabolism, the overwhelming majority of preclinical testing relies on transgenic mice. Hence, while mice have allowed for tremendous advances in cancer biology, they have been a poor predictor of drug performance/toxicity in the clinic. Given the greater similarity of sus scrofa pigs to humans, we engineered transgenic sus scrofa expressing a LSL-KRASG12D-TP53R167H cassette. By applying Adeno-Cre to pancreatic duct cells in vitro, cells self-immortalized and established tumors in immunocompromised mice. When Adeno-Cre was administered to the main pancreaticduct in vivo, pigs developed extensive PDAC at the injection site hallmarked by excessive proliferation and desmoplastic stroma. This serves as the first large animal model of pancreatic carcinogenesis, and may allow for insight into new avenues of translational research not before possible in rodents.

cancer biology↗