Biology subjects

Ghimire, B.

Publications and source records attributed to Ghimire, B..

10 recordsLinked to original sources

bioRxiv2025

Critical spatial separation at the scale of V1 receptive fields determines motion segmentation

Integrating elements that belong to a single object while segregating overlapping objects is a fundamental challenge for the visual system, exemplified by the phenomenon of motion transparency. While the middle temporal (MT) cortex is central to motion processing, the role of V1 in motion transparency remains controversial. It is still unclear at what spatial scale segmentation for motion transparency occurs. To address these questions, we conducted human psychophysics experiments using locally paired-dot stimuli moving in two directions separated by 90{degrees}. Subjects performed a 3AFC task to report whether the visual stimulus had no motion, a single direction, or two distinct directions. We systematically manipulated the path length of the dots, and therefore, the spatial separation between the paired dots, and the retinal eccentricity of the visual stimulus. We found that as the spatial separation between the paired dots increased, subjects perception shifted from a single direction to two distinct directions. Critically, we found that the spatial separation required for this perceptual transition increased with the eccentricity and closely matched the known receptive field sizes of V1 neurons at those eccentricities. Direction segmentation occurred only when the spatial separation between motion components exceeded the V1 receptive field size. Conversely, direction integration occurred when the spatial separation was smaller than the V1 receptive field size. Our results demonstrate that the receptive field size of V1 neurons sets the critical spatial scale for direction segmentation and suggest that V1 plays a key role in motion transparency and, more generally, in motion segmentation.

neuroscience↗

bioRxiv2025

Mechanisms of Neural Representation and Segregation of Multiple Spatially Separated Visual Stimuli

Segregating objects from one another and the background is essential for scene understanding, object recognition, and visually guided action. In natural scenes, it is common to encounter spatially separated stimuli, such as distinct figure-ground regions, adjacent objects, and partial occlusions. Neurons in mid- and high-level visual cortex have large receptive fields (RFs) that often encompass multiple, spatially separated stimuli. It is unclear how neurons represent and segregate multiple stimuli within their RFs, and the role of spatial cues for such representation. To investigate these questions, we recorded neuronal responses in the middle temporal (MT) cortex of monkeys to spatially separated stimuli that moved simultaneously in two directions. We found that, across motion directions, response tuning to multiple stimuli was systematically biased toward the stimulus located at the more-preferred RF subregion of the neuron. The sign and magnitude of this spatial-location bias were correlated with the spatial preference of the neuron for single stimuli presented in isolation. We demonstrated that neuronal responses to multiple stimuli can be captured by an extended normalization model, which is a sum of the responses elicited by individual stimuli weighted by the spatial preference of the neuron. We also proposed a circuit implementation for the model. Our results indicate that visual neurons leverage spatial selectivity within their RFs to represent multiple spatially separated stimuli. The spatial-location bias in neuronal responses enables individual components of multiple stimuli to be represented by a population of neurons with different spatial preferences, providing a neural substrate for segregating multiple stimuli. Significance StatementElucidating how neurons represent multiple visual stimuli is crucial for understanding the principles and mechanisms of neural coding. We found that the neuronal response in MT to spatially separated moving stimuli can be captured by the well-known normalization model, with an important new extension: the responses elicited by the individual stimulus components are combined and weighted by the neurons spatial preference for single stimuli within its receptive field. Consequently, the response of a neuron to multiple stimuli can be substantially biased toward the stimulus at the neurons preferred spatial location. Our results revealed a previously unknown coding strategy for representing and segregating multiple spatially separated stimuli. Our proposed circuit implementation provides insight into the neural mechanisms underlying spatial preference-weighted normalization.

neuroscience↗

bioRxiv2024

Comprehensive multi-omics profiling of a healthy human cohort

Multi-omics approaches can offer powerful insights into personalized biomarker profiles relevant for disease diagnosis, prognosis, and therapeutics. However, separating meaningful biological variability from technical noise remains a major challenge. The EATRIS-Plus consortium analyzed blood samples from 127 healthy adults across six omics layers using twelve platforms, resulting in one of the most comprehensive multi-omics profiling datasets of healthy individuals available to date. We applied reproducible workflows to analyze and integrate these data, revealing several key findings. Sex significantly influenced all omics layers, emphasizing the importance of sex-balanced study designs. Age could be accurately predicted using epigenetic clocks, achieving high performance with our high-resolution enzymatic methylation sequencing data (R2 = 0.90), whereas candidate aging biomarkers were identified across all omics layers. The resulting dataset provides reference ranges in healthy individuals for abundance and variability of omics features, enabling robust power analyses, sample size estimations, and benchmarking of multi-omics integration methods. This resource can guide future biomarker discovery and personalized health research and was made FAIR-compliant and publicly available via the ClinData Portal (https://clindata.imtm.cz) and a Zenodo repository (https://doi.org/10.5281/zenodo.17514796).

bioinformatics↗

bioRxiv2023

α-Melanocyte-Stimulating Hormone Regulates Pathological Cardiac Remodeling by Activating Melanocortin 5 Receptor in Cardiomyocytes

Background-Melanocyte-stimulating hormone (-MSH) regulates diverse physiological functions by activating melanocortin receptors (MC-R). -MSH is predominantly expressed in the pituitary gland, but it is also found in several peripheral tissues such as the skin and heart. However, the role of -MSH and its possible target receptors in the heart remain completely unknown. Therefore, we sought to investigate whether -MSH could be involved in the regulation of pathological cardiac remodeling. MethodsTissue -MSH concentrations and the effects of chronic -MSH administration were investigated in mice subjected to transverse aortic constriction (TAC). Rat H9c2 cells, neonatal mouse ventricular myocytes and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) were used to study the effects of -MSH and selective MC-R agonists. Inducible cardiomyocyte-specific melanocortin 5 receptor (MC5-R) knockout mouse model was engineered to investigate the role of MC5-R in cardiac hypertrophy. Results-MSH was highly expressed in the mouse heart, particularly in the ventricles, and its level was reduced in the left ventricles of TAC-operated mice. Administration of a stable -MSH analogue protected mice against TAC-induced cardiac hypertrophy and systolic dysfunction. In vitro experiments revealed that cardiomyocytes serve as effector cells for the -MSH mediated antihypertrophic signaling and that selective activation of MC5-R mimics the actions of -MSH. In keeping with these findings, MC5-R was downregulated in the failing mouse heart and stressed hiPSC-CMs. Silencing of MC5-R in mouse cardiomyocytes induced hypertrophy and fibrosis markers in vitro and aggravated TAC-induced cardiac hypertrophy and fibrosis in vivo. Conversely, pharmacological activation of MC5-R improved systolic function and reduced cardiac fibrosis in TAC-operated mice. Conclusions-MSH is expressed in the heart and protects against pathological cardiac remodeling by activating MC5-R in cardiomyocytes. These results suggest that analogues of naturally occurring -MSH, that have been recently approved for clinical use and have agonistic activity at MC5-R, may be of benefit in treating heart failure.

physiology↗

bioRxiv2023

Neural coding of multiple motion speeds in visual cortical area MT

Motion speed provides a salient cue for visual segmentation, yet how the visual system represents and differentiates multiple speeds remains poorly understood. Here, we investigated the neural coding of multiple speeds. First, we characterized the perceptual capacity of human and macaque subjects to segment overlapping random-dot stimuli moving at different speeds. We then recorded from neurons in the middle temporal (MT) cortex of macaque monkeys to determine how multiple speeds are represented. We made a novel finding that the responses of MT neurons to two speeds showed a robust bias toward the faster speed component when both speeds were slow ([≤] 20{degrees}/s). This faster-speed bias emerged early in the neuronal response. It occurred regardless of whether the two speed components moved in the same or different directions, and even when attention was directed away from the receptive field. As stimulus speed increased, the faster-speed bias diminished. Our finding can be explained by a modified divisive normalization model, in which the weights for the speed components are proportional to the responses of a population of neurons, referred to as the weighting pool, elicited by the individual speeds. We suggest that the weighting pool include neurons with a broad range of speed preferences. We found that a classifier can differentiate the responses of MT neurons to two speeds versus a corresponding log-mean speed. We further showed that it was possible to decode two speeds from MT population response, supporting the theoretical framework of coding multiplicity of visual features in neuronal populations. The decoded speeds can account for the perceptual performance of segmenting two speeds with a large (x4) but not a small (x2) separation, raising questions for future investigations. Our findings help define the neural coding rule of multiple speeds. The faster-speed bias in MT at slow stimulus speeds could benefit important behavioral tasks such as figure-ground segregation, as figural objects tend to move faster than the background in the natural environment.

neuroscience↗

bioRxiv2022

Single-cell functional genomics of natural killer cell evasion in blood cancers

Natural killer (NK) cells are emerging as a promising therapeutic option in cancer. To better understand how cancer cells evade NK cells, we studied interacting NK and blood cancer cells using single-cell and genome-scale functional genomics screens. At single-cell resolution, interaction of NK and cancer cells induced distinct activation states in both cell types depending on the cancer cell lineage and molecular phenotype, ranging from more sensitive myeloid to more resistant B-lymphoid cancers. CRISPR screens uncovered cancer cell-intrinsic genes driving sensitivity and resistance, including antigen presentation and death receptor signaling mediators, adhesion molecules, protein fucosylation genes, and transcriptional regulators. CRISPR screens with a single-cell transcriptomic readout revealed how these cancer cell genes influenced the gene expression landscape of both cell types, including regulation of activation states in both cancer and NK cells by IFN{gamma} signaling. Our findings provide a resource for rational design of NK cell-based therapies in blood cancers. HIGHLIGHTSO_LITranscriptomic states of interacting NK cells and cancer cells depend on cancer cell lineage C_LIO_LIMolecular correlates of increased sensitivity of myeloid compared to B-lymphoid cancers include activating receptor ligands NCR3LG1, PVR, and ULBP1 C_LIO_LINew regulators of NK cell resistance from 12 genome-scale CRISPR screens include blood cancer-specific regulators SELPLG, SPN, and MYB C_LIO_LISingle-cell transcriptomics CRISPR screens targeting 65 genome-wide screen hits identify MHC-I, IFNy, and NF-{kappa}B regulation as underlying mechanisms C_LI

immunology↗

bioRxiv2020

Epidemiology of Dengue viral infection in Nepal: 2006-2019

BackgroundDengue is one of the newest emerging diseases in Nepal with increasing burden and geographic spread over the last 14 years. The main objective of this study was to explore the spatio-temporal epidemiological patterns of Dengue since its first report (2006) till 2019 in Nepal. MethodsThis study is a retrospective analysis of dengue data available from the Epidemiological Disease Control Division (EDCD) of Government of Nepal. The data in this study cover the last 14 years (2006-2019) of reported dengue cases in Nepal. Epidemiological trend and spatio-temporal analyses were performed. Maps of reported case incidence were created using QGIS version 3.4. ResultsSince the first report of dengue in a foreigner in 2004, Nepal reported a total of 17,992 dengue cases in 68 districts of Nepal in 2019. The incidence was approximately five times higher in 2018 (Incidence Rate Ratio (IRR): 4.8; 95% CI: 1.5 - 15.3) and over 140 times higher in 2019 (IRR: 141.6; CI: 45.8 - 438.4). Population density was not a statistically significant predictor of case incidence. Mean elevation had a negative association with case incidence. A one standard deviation increase in elevation was associated with a 90% decrease in reported case incidence (IRR: 0.10; CI: 0.01 - 0.20). However, the association with mean elevation varied across the years. In comparison to 2016, incidence was greater at higher elevations in 2018 (IRR: 22.7; CI: 6.0 - 86.1) and 2019 (IRR: 9.6; CI: 2.6 - 36.1). ConclusionThere is a high risk of dengue outbreak in the Terai region with increasing spread towards the mid-mountains and beyond as seen over the last 14 years. Urgent measures are required to increase the availability of diagnostics and resources to mitigate future dengue epidemics. Findings from this study can inform the spatio-temporal distribution of dengue and can help in resource allocation and priority setting for future epidemic. Author summaryDengue in humans is caused by four different serotypes (DENV-1, DENV-2, DENV-3 & DENV-4). Globally it is the most pervasive vector borne diseases with increasing number of cases in recent years. Dengue is one of the youngest emerging diseases in Nepal with increasing cases and spread from the tropical lowland to the highland (hilly) regions. We conducted a spatio-temporal analysis of national data to consolidate the information using QGIS to measure the dengue incidence at district levels of Nepal. Spatio-temporal analysis exploring the incidence and distribution of dengue cases aids in identification of high-risk areas which can ultimately enable national dengue programme to mobilize and allocate resources for the control and treatment. This study shows, the persistent high risk of dengue outbreak in lowland Terai region with annual rise in the risk of spread towards the mid-mountains and beyond. Urgent measures are required to increase the diagnostics and resources to mitigate the epidemic burden of dengue in Terai and peripheral regions.

microbiology↗

bioRxiv2020

Patient-tailored design of AML cell subpopulation-selective drug combinations

The extensive primary and secondary drug resistance in acute myeloid leukemia (AML) requires rational approaches to design personalized combinatorial treatments that exploit patient-specific therapeutic vulnerabilities to optimally target disease-driving AML cell subpopulations. However, the large number of AML-relevant drug combinations makes the testing impossible in scarce primary patient cells. This combinatorial problem is further exacerbated by the translational challenge of how to design such personalized and selective drug combinations that do not only show synergistic effect in overall AML cell killing but also result in minimal toxic side effects on non-malignant cells. To solve these challenges, we implemented a systematic computational-experimental approach for identifying potential drug combinations that have a desired synergy-efficacy-toxicity balance. Our mechanism-agnostic approach combines single-cell RNA-sequencing (scRNA-seq) with ex vivo single-agent viability testing in primary patient cells. The data integration and predictive modelling are carried out at a single-cell resolution by means of a machine learning model that makes use of compound-target interaction networks to narrow down the massive search space of potentially effective drug combinations. When applied to two diagnostic and two refractory AML patient cases, each having a different genetic background, our integrated approach predicted a number of patient-specific combinations that were shown to result not only in synergistic cancer cell inhibition but were also capable of targeting specific AML cell subpopulations that emerge in differing stages of disease pathogenesis or treatment regimens. Overall, 53% of the 59 predicted combinations were experimentally confirmed to show synergy, and 83% were non-antagonistic, as validated with viability assays, which is a significant improvement over the success rate of randomly guessing a synergistic drug combination (5%). Importantly, 67% of the predicted combinations showed low toxicity to non-malignant cells, as validated with flow-based population assays, suggesting their selective killing of AML cell populations. Our data-driven approach provides an unbiased means for systematic prioritization of patient-specific drug combinations that selectively inhibit AML cells and avoid co-inhibition of non-malignant cells, thereby increasing their likelihood for clinical translation. The approach uses only a limited number of patient primary cells, and it is widely applicable to hematological cancers that are accessible for scRNA-seq profiling and ex vivo compound testing.

systems biology↗

bioRxiv2019

Gametophytes and embryo ontogeny: understanding the reproductive calendar of Cypripedium japonicum Thunb. (Cypripedoideae, Orchidaceae)

Among the flowering plants, the gametophyte development and reproductive biology of orchids is particularly poorly understood. Cypripedium japonicum is a perennial herb, native to East Asia. Due to its limited distribution, the species is included in the Endangered category of the IUCN Red List. Light microscopy and SEM methods were used to study the development of the gametes and embryo. The complete reproductive cycle was developed based on our observations. Anther development begins under the soil and meiosis of pollen cells begins 3 weeks before anthesis, possibly during early April. The megaspore mother cells develop just after pollination in early May and mature in mid-late June. The pattern of embryo sac formation is bisporic and there are six nuclei. Triple fertilization results in the endosperm nucleus. A globular embryo is formed after multiple cell division and 9 weeks after pollination the entire embryo sac is occupied by embryo. Overall comparisons of the features of gametophyte and embryo development in C. japonicum suggest that previous reports on the embryology of Cypripedium are not sufficient to characterize the entire genus. Based on the available information a reproductive calendar showing the key reproductive events leading to embryo formation has been prepared.\n\nHighlightManual pollination, reproductive biology and seed development process in Cypripedium japonicum Thunb., a ladys slipper orchid endemic to East Asia

developmental biology↗

bioRxiv2018

Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease

Alzheimers disease (AD) results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling early intervention into the disease process would be highly valuable. As life style factors largely modulate the disease risk, we hypothesised that the disease associated DNA methylation signatures are detectable in the peripheral blood of discordant twin pairs. Reduced Representation Bisulfite Sequencing, single cell RNA-sequencing and gene array data were utilised to examine DNA methylation signatures and associated gene expression changes in blood and hippocampus, and targeted bisulfite sequencing in cross cohort validation. Our results reveal that discordant twin pairs have disease associated differences in their peripheral blood epigenomes. A subset of affected genes, e.g. ADARB2 contain differentially methylated sites also in anterior hippocampus. The DNA methylation differences seem to influence gene expression in brain rather than in blood cells. The affected genes are associated with neuronal functions and pathologies. These DNA methylation signatures are valuable disease marker candidates and may provide insights into the molecular mechanisms of pathogenesis.

genomics↗