Biology subjects

Koirala, P.

Publications and source records attributed to Koirala, P..

9 recordsLinked to original sources

bioRxiv2026

Activation of PPARγ redirects fibro-adipogenic progenitors to replace ectopic bone with fat in models of fibrodysplasia ossificans progressiva and trauma-induced heterotopic ossification

The pathologic, osteogenic differentiation of fibroadipogenic progenitor cells (FAPs) is the primary recognized contributor to ectopic bone formation in fibrodysplasia ossificans progressiva (FOP) and trauma-induced heterotopic ossification (HO). Both conditions are characterized by up-regulated BMP signaling - the former by a gene mutation rendering the BMP receptor ACVR1 susceptible to activation by inflammatory ligands (Activin A), and the latter by up-regulated presence of BMP2 ligand in the setting of unmutated BMP receptor. We performed an unbiased assessment of FDA-approved therapies which would optimally target the transcriptional aberrations observed in developing FOP and HO lesions based on publicly-available datasets. This analysis uncovered rosiglitazone, a peroxisome proliferator-activated receptor gamma (PPAR{gamma}) agonist as the highest scoring therapeutic option across three data sets for both conditions. Rosiglitazone treatment eliminated ectopic bone lesions in a mouse model of FOP, and replaced these lesions with ectopic adipose tissue; similarly, systemic and local rosiglitazone treatment eliminated ectopic bone lesions in a mouse model of trauma-induced HO and replaced these lesions with ectopic adipose tissue. Our findings were corroborated by a single case report from 2010 showing positive results with rosiglitazone in a non-diabetic patient with FOP, with no subsequent studies. Overall, our findings suggest that a previously FDA-approved therapeutic is likely to be a successful therapeutic agent for both FOP and trauma-induced HO, both conditions for which current therapeutic options remain inadequate. One Sentence SummaryWe show that a previously FDA-approved therapeutic known to induce adipogenesis reduces ectopic bone and induces ectopic fat formation in diseases of heterotopic ossification.

cell biology↗

bioRxiv2026

A closed-loop cell therapy engineered to autonomously secrete Activin A inhibitor protects from fibrodysplasia ossificans progressiva

Engineered cell therapies present an opportunity for endogenous, site-specific production of therapeutic agents. Here we describe a closed-loop cell therapy which secretes an inhibitor of Activin A, ActR2A-Fc, upon exposure to Activin A. We demonstrate in vivo therapeutic efficacy of this approach in a mouse model of fibrodysplasia ossificans progressiva (FOP), a morbid condition in which patients develop extensive heterotopic bony lesions in response to aberrant sensitivity to Activin A through a mutation in the type I BMP receptor ACVR1 (ACVR1 R206H). To blunt Activin A activity, we designed a transposon plasmid containing the transgene encoding ActR2A-Fc, with expression controlled by the BMP-responsive element (BRE). In cells containing the causative mutation, the BRE is pathologically activated upon exposure to Activin A. FOP-derived marrow cells modified with the BRE-ActR2AFc plasmid exhibited the desired closed-loop functionality, with increased ActR2A-Fc expression upon exposure to Activin A and reduced expression upon withdrawal of Activin A. Engineered marrow cells secreted bioactive ActR2A-Fc, and bone marrow transplantation of FOP marrow cells engineered with the BRE-ActR2AFc transposon into same-sex FOP mice resulted in absence of heterotopic bony lesions. Experiments with labeled, engineered FOP marrow cells verified trafficking of the therapeutic cells to sites at risk for FOP. These data provide proof-of-concept for the therapeutic utility of engineered cell therapy for the treatment of FOP. Significance statementIn this study, we describe our development of an autologous, closed-loop cell therapy which can migrate to sites of tissue injury and locally secreting an inhibitor of Activin A. Through our use of an Activin A-responsive promoter to drive expression of the recombinant Activin A inhibitor, this engineered cell therapy exhibits closed-loop behavior and effectively prevents heterotopic bone formation in a mouse model of fibrodysplasia ossificans progressiva (FOP). We believe that the findings in this manuscript impactful beyond FOP, and provide a blueprint for the development of marrow-derived cell therapies across the disease spectrum.

cell biology↗

bioRxiv2025

A method for creating custom 3D-printed molds to facilitate zebrafish imaging studies, including of cardiac development.

Embryo mounting is one of the technical challenges researchers encounter when undertaking an imaging project. Embryos need to be oriented in a reproducible manner such that the tissue of interest is accessible to a microscope objective for the entire imaging period. To overcome this challenge researchers can embed embryos in viscous media or create specialized dishes and casts to hold embryos in a desired orientation during imaging. Here we describe a method for using a cheap stereolithographic (SLA) 3D-printer to manufacture re-usable molds that create agarose wells in which embryos can be mounted for imaging. These agarose wells provide a reliable means for orienting multiple embryos for imaging. This method includes a design framework that can be easily customized for a variety of tissues, organisms and imaging challenges. Using this method we have created molds for imaging cardiac development in zebrafish for both upright and inverted microscopes. By utilizing materials and equipment that are accessible this method allows researchers to easily create molds specific to their mounting needs. SUMMARYHere we describe a method that uses a cheap stereolithographic (SLA) 3D printer to create molds to facilitate the reproducible mounting of zebrafish embryos for imaging studies. Using this method, weve created molds for imaging cardiac morphogenesis in zebrafish embryos.

developmental biology↗

bioRxiv2024

Naturalistic language comprehension engages a cascade of widespread brain networks in the one second following comprehension

Language comprehension (LC) is a cornerstone of human cognition, enabling the extraction of meaning from written and spoken communication with remarkable efficiency. Decades of neuroimaging research have identified the brain networks associated with LC, but limitations in spatial and temporal resolution have hindered a comprehensive characterization of the whole-brain (millimeter scale), real-time (millisecond precision) dynamics underlying this process. To overcome these constraints, we applied a fusion of multimodal brain imaging techniques (fMRI and EEG) in healthy adults (n = 30) to map the spatiotemporal progression of neural network engagement during LC in the one second following comprehension. Our findings reveal a cascade of brain network activations, beginning with the occipitotemporal perceptual word processing network (250 ms), followed by the temporoparietal semantic retrieval network (400 ms), the posterior default mode inferential network (500 ms), the frontotemporal semantic integration network (600 ms), and finally, a distributed goal-directed comprehension network (700 ms). Crucially, inferential processing emerged as a "hinge point," linking early word processing to later higher-order networks. Efficient LC was associated with greater mediation by this inferential network and reduced reliance on top-down semantic integration. These findings provide evidence that naturalistic LC relies on rapid, dynamic interactions across widespread brain networks, with individual differences in LC reflecting specific subnetwork interactions. This work offers a framework for investigating the temporal evolution of distributed brain network dynamics in complex cognition across domains and clinical populations.

neuroscience↗

bioRxiv2023

Regulation of an antibiotic resistance efflux pump by quorum sensing and a TetR-family repressor in Chromobacterium subtsugae

The soil bacterium Chromobacterium substugae uses a single LuxI-R-type quorum-sensing system, CviI-R, to regulate genes in a cell density-dependent manner. CviI synthesizes the signal N-hexanoyl-homoserine lactone (C6-HSL) and CviR is a C6-HSL-responsive cytoplasmic transcription regulator. C6-HSL-bound CviR activates dozens of genes, for example the cdeAB-oprM cluster coding for an efflux pump conferring antibiotic resistance. The cdeAB-oprM genes are also regulated by an antibiotic-responsive transcription factor, CdeR, which represses expression of these genes. We are interested in understanding how C. subtsugae integrates different environmental cues to regulate antibiotic resistance. In this study, we sought to delineate the mechanism of regulation of the cdeAB-oprM genes by CviR and CdeR. In recombinant E. coli, the cdeA promoter is activated by CviR and repressed by CdeR. We identify non-overlapping sequence elements in the cdeA promoter that are required for CviR activation and CdeR repression, respectively. We also examined the role of CdeR in modulating cdeA activation by C6-HSL in C. subtsugae. We show that CviR and CdeR can independently modulate transcription from the cdeA promoter in C. subtsugae, consistent with the conclusion that CviR and CdeR regulate the cdeAB-oprM genes by interacting directly with different binding sites in the cdeA promoter. These results contribute to a molecular understanding of how the cdeAB-oprM genes are regulated and provide new insight into how C. subtsugae integrates different environmental cues to regulate antibiotic resistance. ImportanceMany bacteria regulate antibiotic resistance in response to antibiotics and other cues from the environment. In many cases the regulatory mechanisms are best understood in the context of clinical isolates where mutations frequently emerge in resistance regulation pathways. However, an understanding of the role of antibiotic resistance regulators in integrating environmental information is less well understood. In the soil bacterium Chromobacterium subtsugae, an antibiotic-resistance gene cluster is regulated by population density and antibiotics through two different transcription factors; the quorum sensing signal receptor CviR and an antibiotic-responsive transcription factor CdeR. In this study, we show that these factors independently modulate the transcription of the antibiotic resistance genes and coordinate to ensure sensitive responses to changes in cell density. The results give new insight into antibiotic resistance regulation in C. subtsugae and contribute to a broader understanding of how bacteria optimize the regulation of antibiotic resistance in response to changes in the environment.

microbiology↗

bioRxiv2023

The myocardium utilizes Pdgfra-PI3K signaling to steer towards the midline during heart tube formation

Coordinated cell movement is a fundamental process in organ formation. During heart development, bilateral myocardial precursors collectively move towards the midline (cardiac fusion) to form the primitive heart tube. Along with extrinsic influences such as the adjacent anterior endoderm which are known to be required for cardiac fusion, we previously showed that the platelet-derived growth factor receptor alpha (Pdgfra) is also required. However, an intrinsic mechanism that regulates myocardial movement remains to be elucidated. Here, we uncover an essential intrinsic role in the myocardium for the phosphoinositide 3-kinase (PI3K) intracellular signaling pathway in directing myocardial movement towards the midline. In vivo imaging reveals that in PI3K-inhibited zebrafish embryos myocardial movements are misdirected and slower, while midline-oriented dynamic myocardial membrane protrusions become unpolarized. Moreover, PI3K activity is dependent on and genetically interacts with Pdgfra to regulate myocardial movement. Together our findings reveal an intrinsic myocardial steering mechanism that responds to extrinsic cues during the initiation of cardiac development.

developmental biology↗

bioRxiv2022

Cross-species activation of hydrogen cyanide production by a promiscuous quorum-sensing receptor promotes Chromobacterium subtsugae competition in a dual-species model

Many saprophytic bacteria have LuxR-I-type acyl-homoserine lactone (AHL) quorum-sensing systems that may be important for competing with other bacteria in complex soil communities. LuxR AHL receptors specifically interact with cognate AHLs to cause changes in expression of target genes. Some LuxR-type AHL receptors have relaxed specificity and are responsive to non-cognate AHLs. These promiscuous receptors might be used to sense and respond to AHLs produced by other bacteria by eavesdropping. We are interested in understanding the role of eavesdropping during interspecies competition. The soil saprophyte Chromobacterium subtsugae has a single AHL circuit, CviR-I, which produces and responds to N-hexanoyl-HSL (C6-HSL). The AHL receptor CviR can respond to a variety of AHLs in addition to C6-HSL. In prior studies we have utilized a coculture model with C. subtsugae and another soil saprophyte Burkholderia thailandensis. Using this model, we previously showed that promiscuous activation of CviR by B. thailandensis AHLs provides a competitive advantage to C. subtsugae. Here, we show that B. thailandensis AHLs activate transcription of dozens of genes in C. subtsugae, including the hcnABC genes coding for production of hydrogen cyanide. We show that hydrogen cyanide production is population density-dependent and demonstrate that the cross-induction of hydrogen cyanide by B. thailandensis AHLs provides a competitive advantage to C. subtsugae. Our results provide new information on C. subtsugae quorum sensing and are the basis for future studies aimed at understanding the role of eavesdropping in interspecies competition. IMPACT STATEMENTIn quorum sensing, population density-dependent changes in gene regulation are the result of a cytoplasmic transcription regulator binding to a quorum sensing signal. The signal-receptor interaction is considered to be specific to ensure fidelity of the system. However, some quorum-sensing receptor proteins have relaxed specificity and can recognize and respond to a range of signals. These promiscuous receptors might provide some benefit by enabling interspecies activation of quorum sensing by "eavesdropping," although the potential benefits of eavesdropping are not well studied. The current study utilizes a dual-species laboratory competition model, where one species has a promiscuous signal receptor and can respond to signals produced by the other species. In our study, we identify the signals that enable quorum sensing cross talk and show that cross talk promotes competition by inducing hydrogen cyanide production. Our results highlight how quorum sensing-enabled interspecies cross talk might provide an advantage during competition and provide a new basis for understanding how receptor-signal pairs might evolve in natural environments. DATA SUMMARYThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2020

Neuroimaging Correlates of Emotional Response-Inhibition Discriminate Between Young Depressed Adults With and Without Sub-threshold Bipolar Symptoms

BackgroundA significant number of subjects with major depression (MDD) exhibit subthreshold mania symptoms (MDD+). This study investigated, for the first time, using emotional inhibition tasks, whether the neurobiology of MDD+ subjects is more akin to bipolar disorder depression (BDD) or to MDD subjects without any subthreshold bipolar symptoms (MDD-). MethodThis study included 118 medication-free young adult subjects (16 - 30 yrs.): 20 BDD, 28 MDD+, 41 MDD-, and 29 HC subjects. Participants underwent fMRI during emotional and non-emotional Go/No-go tasks during which they responded for Go stimuli and inhibited response for happy, fear, emotional (happy + fear) and non-emotional (gender) faces No-go stimuli. Linear mixed effects (LME) analysis for group effects and Gaussian Process Classifier (GPC) analyses was conducted. ResultsMDD- group compared to both the BDD and MDD+ groups, exhibited significantly lower activation in parietal, temporal and frontal regions (cluster-wise corrected p <0.05) for emotional inhibition conditions vs. non-emotional condition. No significant differences were found between BDD and MDD+ groups. GPC classification of emotional vs non-emotional response-inhibition activation pattern showed good discrimination between BDD and MDD- subjects (AUC: 0.70; balanced accuracy: 70% (p = 0.006)) as well as MDD+ and MDD- subjects (AUC: 0.72; balanced accuracy: 67% (p = 0.015)) but less efficient discrimination between BDD and MDD+ groups (AUC: 0.68; balanced accuracy: 61% (p = 0.091)). Notably, classification of the MDD- group was weighted for left amygdala activation pattern. ConclusionUsing an fMRI emotional Go-Nogo task, MDD- subjects can be discriminated from BDD subjects and MDD+.

neuroscience↗

bioRxiv2019

Risk factors associated with Avian Influenza subtype H9 outbreaks on poultry farms in Kathmandu valley, Nepal

Poultry sector contributes to four percent in national GDP of Nepal. However, this sector is under threat with periodic outbreaks of Avian Influenza (AI) subtypes H5 and H9 since 2009. This has been both a both public health threat and an economic issue. Since last three years, outbreaks of AI subtype H9 has caused huge economic losses in major poultry producing areas of Nepal. However, the risk factors associated with these outbreaks have not been assessed. A retrospective case-control study was conducted from April 2018 to May 2019 in Kathmandu Valley to understand the risk factors associated with AI subtype H9 outbreaks. Out of 100 farms selected, 50 were \"case\" farms, confirmed positive to H9 at Central Veterinary Laboratory, Kathmandu, and other 50 farms were \"control\" farms, matched for farm size and locality within a radius of three km from the case farm. Each farm was visited to collect information using semi-structured questionnaire. Nineteen potential risk factors were included in the questionnaire under the broad categories: birds and farm characteristics, management aspects and biosecurity status of the farms. Univariable and multivariable logistic regression analysis were conducted to calculate corresponding odds ratios. Identified risk factors associated with AI subtype H9 outbreaks in Kathmandu valley were: \"Birds of age 31-40 days\" (OR= 11.31, 95% CI: 1.31-98.02, p=0.028), \"Older farms operating for >5 years\" (OR= 10.9, 95% CI: 1.76-66.93, p=0.01), \"Commercial layers farms\" (OR=36.0, 95% CI: 0.97-1332.40, p=0.052), \"Used stream water to water birds (OR= 5.7, 95% CI: 1.10-30.13, p=0.039)\", \"Farms without practice of fumigation after each batch of poultry (OR= 4, 95% CI: 1.44-13.13, p=0.009)., \"Farm with previous history of AI (OR= 13.8, 95% CI: 1.34-143.63, p = 0.028), \"Did not applied farm boots (OR= 2.58, 95% CI: 0.98-6.80, p= 0.055), \"Visitors allowed to enter the farms (OR= 2.5, 95% CI: 1.011-6.17, p = 0.047) and \"No foot bath at entry of farms (OR= 3.3, 95% CI: 1.29-8.38, p = 0.013). This study depicts that outbreaks of AI subtype H9 in Kathmandu valley was related to poor management practices and biosecurity in the poultry farms. We suggest improving management practices and increase biosecurity in the farms to reduce incidences of AI subtype H9 outbreaks in Kathmandu valley.

scientific communication and education↗