Biology subjects

Maharjan, R.

Publications and source records attributed to Maharjan, R..

7 recordsLinked to original sources

bioRxiv2026

Systemic delivery of drug-free polymeric nanoparticles reprograms innate immunity in a sex-dependent manner after spinal cord injury

Sex differences influence distinct inflammatory responses after spinal cord injury (SCI), yet their impact on immune-modulating nanotherapeutics remains unclear. Here, we investigated the sex-dependent effects of drug-free poly(lactic-co-glycolic acid) (PLGA)-based nanoparticles (NPs) following SCI. Systemic NP administration enhanced locomotor recovery in both sexes and eliminated the functional gap observed in controls. Mechanistically, NPs engaged distinct immune pathways between sexes. Females accumulated more NPs in the spleen, leading to reduced monocyte-derived macrophage infiltration, whereas males showed greater NP accumulation at the lesion and attenuated microglial activation. Transcriptomic analysis showed preferential modulation of eicosanoid-related pathways in females and NF-{kappa}B-linked signaling in males. These sex-specific, yet convergent NPs-induced immunomodulatory effects reduced fibrotic scarring and enhanced remyelination, with females showing greater Schwann cell-mediated repair and males exhibiting marked suppression of microglial activation. Collectively, these findings demonstrate that NPs promote comparable functional recovery in both sexes through distinct, sex-influenced immune mechanisms and establish a translational framework for sex-informed immune targeting and nanotherapeutic design in SCI and other inflammation-mediated diseases. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/709912v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@5af2ecorg.highwire.dtl.DTLVardef@1027071org.highwire.dtl.DTLVardef@12449ceorg.highwire.dtl.DTLVardef@169a327_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Structures of MmpL complexes reveal the assembly and mechanism of this family of transporters

We co-expressed the MmpL5 transporter and MmpS5 adaptor proteins in Mycobacterium smegmatis and defined their structures from these detergent-solubilized crude membranes. Data generated from these samples allowed us to simultaneously solve three distinct classes of membrane protein complexes to high resolutions. We observed that MmpL5 presents as a monomer in complex with the cytosolic meromycolate extension acyl carrier protein M (AcpM) in a molar ratio of 1:1, where these AcpM-MmpL5 complexes closely pack together to generate regular two-dimensional arrays. We also identified MmpL5 as a trimer that interacts with MmpS5 and AcpM in a molar ratio of 3:3:3 to assemble the tripartite complex AcpM-MmpL5-MmpS5 that spans both the inner and outer membranes of the mycobacterium. In addition, we discovered that MmpL5 and AcpM are able to form the trimeric AcpM-MmpL5 complex in a molar ratio of 3:3. The structural data reveal that the full-length MmpL5 trimer is capable of spanning the entire mycobacterial cell envelope to transport substrates. However, this assembly requires the presence of MmpS5 to stabilize secondary structural features of the MmpL5 periplasmic subdomains.

microbiology↗

bioRxiv2025

Lepidoptera Diversity, Richness, and Distribution in Semi-Urban Farmland and other Habitats around Lumbini, Rupandehi

This study comprehensively examined Lepidoptera diversity in the semi-urban agricultural landscapes of Lumbini, Nepal, documenting 30 moth species from six families and 39 butterfly species from five families over 14 days. Field methods included moth traps with 50 Watts LED lights inside a box with egg cartons for moth trapping and butterfly transect surveys across various habitats--grasslands, shrublands, and agricultural areas for recording butterfly species. The Erebidae family dominated moth populations, while Nymphalidae led butterfly diversity, showing resilience in disturbed habitats influenced by environmental factors such as weather patterns, lunar phases, and habitat characteristics. Statistical analyses using Simpsons Diversity Index, Shannon-Wiener Diversity Index, Pielous Evenness Index, and Margalefs Richness Index revealed that shrubland and agricultural habitats supported the highest species richness and evenness, while grasslands hosted fewer species. The study highlighted the importance of agricultural and shrubland ecosystems for biodiversity, emphasizing ongoing monitoring to understand how Lepidoptera populations respond to environmental changes, offering essential insights for future conservation efforts.

zoology↗

bioRxiv2023

Regulation of RNA methylation by therapy treatment, promotes tumor survival

Our data previously revealed that chemosurviving cancer cells translate specific genes. Here, we find that the m6A-RNA-methyltransferase, METTL3, increases transiently in chemotherapy-treated breast cancer and leukemic cells in vitro and in vivo. Consistently, m6A increases on RNA from chemo-treated cells, and is needed for chemosurvival. This is regulated by eIF2 phosphorylation and mTOR inhibition upon therapy treatment. METTL3 mRNA purification reveals that eIF3 promotes METTL3 translation that is reduced by mutating a 5'UTR m6A-motif or depleting METTL3. METTL3 increase is transient after therapy treatment, as metabolic enzymes that control methylation and thus m6A levels on METTL3 RNA, are altered over time after therapy. Increased METTL3 reduces proliferation and anti-viral immune response genes, and enhances invasion genes, which promote tumor survival. Consistently, overriding phospho-eIF2 prevents METTL3 elevation, and reduces chemosurvival and immune-cell migration. These data reveal that therapy-induced stress signals transiently upregulate METTL3 translation, to alter gene expression for tumor survival. One sentence summarym6A enzyme translation upon therapy stress, promotes tumor survival

molecular biology↗

bioRxiv2020

The molecular basis of Acinetobacter baumannii cadmium toxicity and resistance

Acinetobacter species are ubiquitous Gram-negative bacteria that can be found in water, soil and as commensals of the human skin. The successful inhabitation of Acinetobacter species in diverse environments is primarily attributable to the expression of an arsenal of stress resistance determinants, which includes an extensive repertoire of metal ion efflux systems. Although metal ion homeostasis in the hospital pathogen Acinetobacter baumannii is known to contribute to pathogenesis, insights into its metal ion transporters for environmental persistence are lacking. Here, we studied the impact of cadmium stress on A. baumannii. Our functional genomics and independent mutant analyses revealed a primary role for CzcE, a member of the cation diffusion facilitator (CDF) superfamily, in resisting cadmium stress. Further, we show that the CzcCBA heavy metal efflux system also contributes to cadmium efflux. Analysis of the A. baumannii metallome under cadmium stress showed zinc depletion and copper enrichment, which are likely to influence cellular fitness. Overall, this work expands our understanding of the role of membrane transporters in A. baumannii metal ion homeostasis. IMPORTANCECadmium toxicity is a widespread problem, yet the interaction of this heavy metal with biological systems is poorly understood. Some microbes have evolved traits to proactively counteract cadmium toxicity, which includes Acinetobacter baumannii. Here we show that A. baumannii utilises a dedicated cadmium efflux protein in concert with a system that is primarily attuned to zinc efflux, to efficiently overcome cadmium stress. The molecular characterization of A. baumannii under cadmium stress revealed how active cadmium efflux plays a key role in preventing the dysregulation of bacterial metal ion homeostasis, which appeared to be the primary means by which cadmium exerts toxicity upon the bacterium.

microbiology↗

bioRxiv2020

SFPQ intron retention, reduced expression and aggregate formation in central nervous system tissue are pathological features of amyotrophic lateral sclerosis

BackgroundSplicing factor proline and glutamine rich (SFPQ, also known as polypyrimidine tract-binding protein-associated-splicing factor, PSF) is a RNA-DNA binding protein with roles in key cellular pathways such as DNA transcription and repair, RNA processing and paraspeckle formation. Dysregulation of SFPQ is emerging as a common pathological feature of multiple neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Increased retention of SFPQ intron nine and nuclear loss of the protein have been linked to multiple genetic subtypes of ALS. Consequently, SFPQ dysregulation has been hypothesised to be a common pathological feature of this highly heterogeneous disease. MethodsThis study provides a comprehensive assessment of SFPQ pathology in large ALS patient cohorts. SFPQ gene expression and intron nine retention were examined in multiple neuroanatomical regions and blood from ALS patients and control individuals using RNA sequencing (RNA-Seq) and quantitative PCR (RT-qPCR). SFPQ protein levels were assessed by immunoblotting of patient and control motor cortex and SFPQ expression pattern was examined by immunofluorescent staining of patient and control spinal cord sections. Finally, whole-genome sequencing data from a large cohort of sporadic ALS patients was analysed for genetic variation in SFPQ. ResultsSFPQ intron nine retention was significantly increased in ALS patient motor cortex. Total SFPQ mRNA expression was significantly downregulated in ALS patient motor cortex but not ALS patient blood, indicating tissue specific SFPQ dysregulation. At the protein level, nuclear expression of SFPQ in both control and patient spinal motor neurons was highly variable and nuclear depletion of SFPQ was not a consistent feature in our ALS cohort. However, we did observe SFPQ-positive cytoplasmic ubiquitinated protein aggregates in ALS spinal motor neurons. In addition, our genetic screen of ALS patients identified two novel, and two rare sequence variants in SFPQ not previously reported in ALS. ConclusionsThis study shows that dysregulation of SFPQ is a feature of ALS patient central nervous system tissue. These findings confirm SFPQ pathology as a feature of ALS and indicate that investigations into the functional consequences of this pathology will provide insight into the biology of ALS.

neuroscience↗

bioRxiv2019

Phytolacca americana PaGT2 is an ambidextrous polyphenol glucosyltransferase

The health benefits of polyphenols have attracted their use as potential therapeutic agents, food additives, and cosmetics. However, low water solubility of polyphenols limits their cell absorbability, obscuring further exploration. Glycosylation is known to enhance the solubility of polyphenols preserving their pharmacological properties. Here, we show that a uridine diphosphate (UDP) glucosyltransferase from Phytolacca americana (PaGT2) regioselectively catalyzes the transfer of glucose from UDP-glucose to stilbenoids such as piceatannol and flavonoids such as kaempferol. To understand the structure-function relationship of PaGT2, we determined the crystal structure of PaGT2 as well as PaGT2 complexed with donor analogue UDP-2-fluoro glucose and stilbenoid acceptor analogues. While only one conserved histidine residue is recognized as a catalytic residue in known UGTs, the crystal structures of PaGT2 suggested the presence of two catalytically active residues (His18 and His81) at two sides of the catalytic pocket. Although the single catalytic residue mutant His18Ala or His81Ala did not completely impair the glucosylation activity of the enzyme, the double mutant His18Ala/His81Ala failed to form glucoside products. These results showed that both catalytic residues in PaGT2 actively and independently catalyze glucosylation, hence we called PaGT2 as an ambidextrous UGT. The information from PaGT2 will be advantageous for the engineering of efficient biocatalysts for production of therapeutic polyphenols.

biochemistry↗