Biology subjects

Parajuli, R.

Publications and source records attributed to Parajuli, R..

4 recordsLinked to original sources

bioRxiv2025

Botanical nursing by a dwarf shrub as a nature-based approach to plant biodiversity conservation in the Nepal Himalayas

Plant-plant positive interactions are among the main drivers of plant community structure, especially in stressful environments. While the ecological dynamics of facilitation are increasingly understood, studies evaluating the importance of nurse plants in preserving phylogenetic diversity and protecting species of medicinal value and conservation concern are still limited. Here, we investigated the nurse effects of a Himalayan endemic shrub, Berberis angulosa, in promoting taxonomic richness, composition and phylogenetic diversity of overall and highly valued species in the high-elevation mountain landscape of Langtang National Park, Nepal. Using pair-wise sampling design, we recorded plant communities within the patches of Berberis shrubs and in open gaps at three altitudinal belts. Compared to adjacent open areas, Berberis patches were found to harbor compositionally distinct and phylogenetically diverse plant communities with significantly higher average overall and human-valued species richness. Relative interaction indices showed clear patterns along elevation gradient with the strongest facilitation observed at highest elevation. Similarly, Net Relatedness Indices (NRI) were significantly different between nursed vs open habitats for both overall and human-valued species, with lower mean NRI within Berberis patches indicating higher phylogenetic diversity of communities within the nursed habitats. Facilitation by Berberis enhanced community-level richness by 40% (39 species; total = 97), including 19 human-valued species ([~]36%; total = 53) that occurred exclusively within shrub canopies. Many medicinal, endemic and conservation priority species were either shrub specialists or had significant association with Berberis patches, illustrating the protective role of the nurse shrub. Our results demonstrate that the facilitative effect of Berberis is not only crucial in maintaining plant communities with diverse evolutionary histories but also equally contributing to local beta and landscape-scale gamma biodiversity, sustaining valuable ecosystem services and benefits to human communities in the Himalayas. These findings suggest that appropriate management of such nurse plants may constitute a nature-based approach to biodiversity conservation, that should be considered in policies for sustainability, resilience and ecosystem functioning in this and similar alpine systems.

ecology↗

bioRxiv2023

A spatially resolved single cell genomic atlas of the adult human breast

The adult human breast comprises an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue. While previous studies have mainly focused on the breast epithelial system, many of the non-epithelial cell types remain understudied. Here, we constructed a comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics data profiled 535,941 cells from 62 women, and 120,024 nuclei from 20 women, identifying 11 major cell types and 53 cell states. These data revealed abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Our spatial mapping using three technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells in the ducts and lobules, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide an unprecedented reference of adult normal breast tissue for studying mammary biology and disease states such as breast cancer.

genomics↗

bioRxiv2023

3D Confinement-enabled Priming of Synaptic Activation Promotes Primary T Cell Expansion

The success of autologous cell therapy, which depends highly on T lymphocyte expansion efficiency, is often hindered by suboptimal interactions between T-cell receptors and peptide-MHC molecules. Here, we demonstrate 3D confinement-enabled priming of T cell-MHC immune synapse junctions based on cytoskeletal forces within minutes, which is 200-fold faster than conventional 24 h bulk shaking method. Using T cell-Dynabead binding skeletons in the starting culture, two- to six-fold greater T cell expansion was achieved over the conventional T cell expansion approach without inducing excessive cell exhaustion. Under 3D force-confinement, T-cell division (G1, S, and G2 phases) was increased to be twice as fast. Creating 3D T cell-Dynabead skeletons as the "booster" material enables highly efficient T cell expansion, without requiring complex surface modification of antigen-presenting cells. This method can be modularly adapted to existing T cell expansion processes for a wide range of applications including adoptive cell therapies. Teaser3D confinement-enabled priming of synaptic activation enables radically faster autologous cell production.

immunology↗

bioRxiv2021

Pre-neoplastic stromal cells drive BRCA1-mediated breast tumorigenesis

Women with germline mutations in BRCA1 (BRCA1+/mut) have increased risk for developing hereditary breast cancer1, 2. Cancer initiation in BRCA1+/mut is associated with pre-malignant changes in the breast epithelium including altered differentiation3-5, proliferative stress6 and genomic instability7. However, the role of the epithelium- associated stromal niche during BRCA1-driven tumor initiation remains unclear. Here, we show that the pre-malignant stromal niche promotes epithelial proliferation and BRCA1- driven cancer initiation in trans. Using single-cell RNAseq (scRNAseq) analysis of human pre-neoplastic BRCA1+/mut and control breast tissues, we show that stromal cells provide numerous pro-proliferative paracrine signals inducing epithelial proliferation. We identify a subpopulation of pre-cancer associated fibroblasts (pre-CAFs) that produces copious amounts of pro-tumorigenic factors including matrix metalloproteinase 3 (MMP3)8, 9, and promotes BRCA1-driven tumorigenesis in vivo. Our gene-signature analysis and mathematical modeling of epithelial differentiation reveals that stromal-induced proliferation leads to the accumulation of luminal progenitor cells with altered differentiation, and thus contributes to increased breast cancer risk in BRCA1+/mut. Our results demonstrate how alterations in cell-cell communication can induce imbalances in epithelial homeostasis ultimately leading to cancer initiation. We anticipate our results to form the foundation for novel disease monitoring and therapeutic strategies to improve patient management in hereditary breast cancer. For example, pre-CAF specific proteins may serve as biomarkers for pre-cancerous disease initiation to inform whether radical bilateral mastectomy is needed. In addition, MMP inhibitors could be re-indicated for primary cancer prevention treatment in women with high-risk BRCA1 mutations.

cancer biology↗