Biology subjects

Poudel, A.

Publications and source records attributed to Poudel, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Genome-wide identification and characterization of the NAC transcription factor family in Cynodon dactylon and their expression during abiotic stresses

Common bermudagrass (Cynodon dactylon) is a highly resilient and cosmopolitan grass widely used for turf, forage, and soil stabilization. Although its genome has been sequenced, little study has focused on characterizing genes underlying its resilience, including the NAC transcription factor family, which is well known for its physiological and stress-related functions. This study aimed to systematically characterize NAC TF genes in the bermudagrass genome and assess their potential roles in abiotic stress tolerance. A total of 237 CdNAC genes were identified and phylogenetically classified into 14 groups, including 40 members in the NAM/NAC1 class, which is associated with plant growth and development, and 23 members in the SNAC class, which is associated with stress responses. Tissue-specific RNA-seq analysis indicated that about one-fourth of CdNAC genes were expressed across all tissues, whereas 13 genes showed relatively higher expression in roots and 9 in inflorescence, suggesting both essential and specialized functions. Stress-responsive expression profiling revealed that 35 CdNAC genes were upregulated in response to drought, 43 to heat, 10 to salt, and 42 to submergence stress. Notably, CdNAC122, 149, and 155, the members of SNAC class, were consistently upregulated across all stress conditions, while others exhibited stress-specific expression, such as CdNAC37, 130, 145, and 199 in drought, CdNAC7, 12, 18, and 29 in heat, CdNAC46 and 151 in salt, and CdNAC9 and 31 in submergence. In contrast, 53 genes were downregulated during different stresses, with most belonging to NAM/NAC1, TERN, or OsNAC7 classes, possibly reflecting suppression of photosynthesis and development-related processes under stress. These results provide the first comprehensive characterization of CdNAC genes, reveal their distinct regulatory roles in abiotic stress responses, and establish a foundation for future functional validation and applications in breeding of stress-resilient bermudagrass.

bioinformatics↗

bioRxiv2026

Dengue serotype-1 virus like particles induce antibody responses following HeLa cell expression

Dengue disease remains a significant global health threat, with current vaccines exhibiting variable efficacy and safety concerns. Virus-like particles (VLPs) offer a promising alternative by mimicking native virus structures without infectious genomes. We engineered a mammalian expression plasmid encoding Dengue-1 prM and E proteins, optimized for secretion using Japanese Encephalitis virus signal sequences, and transiently expressed it in HeLa cells. Purified VLPs exhibited spherical morphology ([~]39 nm diameter) consistent with native virions, as confirmed by transmission electron microscopy. Immunization of mice with these VLPs elicited robust Dengue-1 specific IgG antibody responses. Our study demonstrates production of immunogenic Dengue-1 VLPs in HeLa cells, highlighting their potential as a vaccine candidate and a tool for serodiagnosis. Further characterization of VLP epitopes and protective efficacy is warranted to advance vaccine development. ImportanceDengue remains a significant global health challenge, with serotype 1 being one of the dominant strains causing recurrent outbreaks in Nepal. Existing vaccines demonstrate limited efficacy and pose significant safety concerns, particularly in seronegative populations. To address these limitations, this study explores virus-like particles (VLPs) as a safer alternative vaccine platform. VLPs elicit robust immunogenicity by mimicking the structure of native virus while completely lacking genetic components. This study combines DENV1 structural proteins with optimized expression systems to enhance immunogenicity. This work is particularly significant as the first dengue vaccine research conducted in Nepal, directly addressing antigenic mismatches between existing commercial vaccines and locally circulating viral strains. Furthermore, the study provides scalable platform for developing region-specific dengue vaccines for other serotypes and flaviviruses.

immunology↗

bioRxiv2026

Rapid Isolation and Genomic Characterization of Sewage-Derived Bacteriophages Targeting Multidrug-Resistant Avian Pathogenic Escherichia coli in Poultry

Antimicrobial resistance (AMR) in Escherichia coli is a major threat to global poultry production, particularly for controlling colibacillosis caused by avian pathogenic E. coli (APEC). Intensive antibiotic use has accelerated the emergence of multidrug-resistant (MDR) strains, undermining treatment efficacy and facilitating zoonotic transmission of resistance genes. This study evaluated bacteriophage therapy as a targeted, antibiotic-independent strategy to control MDR E. coli in Nepalese poultry systems. Seventeen E. coli isolates were obtained from commercial broiler and local-breed chicken farms. Using the double-layer agar method, 18 lytic phages were isolated from three urban sewage samples, infecting eight isolates. Real Time PCR screening revealed extensive AMR profiles in six isolates; one broiler-derived strain (EcI8) harbored 30 resistance genes, including carbapenemases, ESBLs, aminoglycoside, quinolone, and last-resort antibiotic determinants associated with class 1 and 3 integrons. Purified phages were whole-genome sequenced and all of them belonged to the genera Tequatrovirus, Phapecoctavirus, Vequintavirus, and Gamaleyavirus--lineages previously used in veterinary and human phage therapy. Several exhibited broad host ranges (up to seven isolates) and lacked detectable virulence or resistance genes; they also encoded potent lytic enzymes, including endolysins, holins, spanins, and transglycosylases. Notably, one Phapecoctavirus (PG7) showed close similarity to established APEC-infecting phages. These findings demonstrate that sewage can be a readily accessible source of safe, therapeutically relevant phages targeting highly resistant poultry E. coli. Phage cocktails and derived enzybiotics delivered through drinking water or feed offer a scalable alternative for preventing and treating colibacillosis, reducing antibiotic dependence, and mitigating zoonotic AMR risks. This study establishes a rapid, reproducible pipeline for local phage isolation and genomic validation, supporting field deployment of tailored phage-based interventions in resource-limited poultry systems.

microbiology↗

bioRxiv2026

Shaping hydrogel bioinks into 3D, multiscale, perfusable models using multimodal printing

Despite technological advances, the fabrication of multiscale, multi-material, and topologically complex 3D structures using soft hydrogel bioinks remains a challenge due to the inherent trade-offs between print size/resolution, bioink properties, and design complexity. In this work, we combine additive (macroscale) digital light projection (DLP) mode with subtractive (microscale) two-photon ablation (TPA) mode with multi-material exchange capability. We identify ideal hydrogel bioink formulations that are compatible with both DLP and TPA modes of processing. Technical challenges related to multimodal fabrication such as alignment of multiscale topologies to facilitate seamless media perfusion, soft-hard multi-material printing to facilitate handling of mechanically weak hydrogel constructs, and hydrogel swelling during printing, were resolved. To highlight the novelty of this hybrid platform, we fabricated centimeter-scale bioink constructs with embedded microscale perfusable topologies that cannot be achieved by isolated use of either DLP or TPA modes. This includes simpler microfluidic chips with independently perfusable microchannels to more complex 3D constructs with embedded, multiscale, perfusable dual-fluidic circuits that mimic the alveoli-capillary interface, or microfluidic chips with endothelialized microchannels. The unique ability of this multimodal platform to mimic in vivo-like multiscale complexities can be potentially used to develop next-generation organ-on-chips.

bioengineering↗

bioRxiv2026

Artificial capillaries-on-a-chip with modular control over lumen size, architecture, in situ modifications and co-culture conditions.

Currently in vitro models of microvascular biology rely on self-assembly of vascular cells in compatible gels. However, the stochastic nature of this process results in large variations in lumen sizes, perfusion continuity, and shear stresses making systematic and reproducible analysis challenging. Here, we report a new technology to generate artificial capillaries on a chip with custom control over lumen sizes and architectures using a combination of femtosecond laser cavitation and collagen casting within multi-chambered microfluidic chips. The design allows seeding of endothelial cells within capillary-sized microchannels and seeding of stromal cells within top-open silos, with independent control over seeding sequence and media compositions. Results show that endothelialized microchannels, coined as artificial capillaries, exhibit excellent barrier function with reproducible control over lumen sizes ({phi}=8-35{micro}m) and their architectures (straight, curvatures, tapered, branched). The physical flow parameters measured across the lumen (namely, flow shear) and at the channel outlets (flow velocities) have been validated against high-fidelity numerical assessments from the Large Eddy Simulation scheme within the digitized versions of the microchannels. The experiment-computation compatibility enabled us to predict changes in regional velocity and wall shear stresses within artificial capillaries, for various capillary architectures. We also show that in situ editing of artificial capillaries in the form of adding new branches or adding occlusions is possible. Lastly, we developed a co-culture model which enables the study of stromal cells with artificial capillaries using conventional imaging methods. We envision that acellular chips with two seeding ports can be readily shipped worldwide and could potentially be adopted as a new technology to study microvascular biology in a reproducible manner.

bioengineering↗

bioRxiv2025

4-1BB expression and signaling regulates MAIT cell activation and effector functions

Mucosal associated invariant T (MAIT) cells are abundant unconventional T cells that recognize microbe-derived riboflavin metabolites presented by MR1. Upon recognition, they become activated, produce proinflammatory cytokines, chemokines and cytotoxic molecules. MAIT cells are also activated by cytokines independently of T cell receptor (TCR) engagement, however these two signals can also act in concert to finetune MAIT cell functions. Additionally, multiple other co-stimulatory signals have also been reported that can boost MAIT cell effector responses to TCR or cytokine stimulation. However, a comprehensive study exploring the role of surface bound TNF receptor superfamily (TNFRSF) molecule 4-1BB, well known for its co-stimulatory function during conventional T cell activation, is lacking in the context of MAIT cells. In this study, we show that 4-1BB is the earliest and most highly expressed TNFRSF co-stimulatory molecule on MAIT cells upon activation by Escherichia coli, with expression seen as early as six hours where it was predominantly MR1 mediated. 4-1BB expression on MAIT cells following late activation was due to both TCR signaling and cytokine signaling. We found marked differences in MAIT cell activation and cytokine expression between 4-1BB+ and 4-1BB- MAIT cells suggesting 4-1BB expression on MAIT cells is associated with functional superiority. By blocking 4-1BB signaling or co-culturing with a 4-1BBL overexpressing cell line we demonstrated an important role of co-stimulation via 4-1BB in MAIT cells during activation. Expression and signaling via 4-1BB also enhanced T-bet and Blimp1 expression. In summary, our study confirms a role for 4-1BB signaling during MAIT cell activation.

immunology↗

bioRxiv2025

A high-throughput microbial glycomics platform for prebiotic development

The mammalian intestine contains diverse carbohydrate pools that govern the gut microbiome composition. Structurally distinct polysaccharides, also called glycans, are differentially consumed by gut microbial subsets and direct their abundance by controlling gene expression and metabolite production. Therefore, identifying gut microbial accessible carbohydrates (MACs) is necessary to develop new prebiotics that beneficially manipulate the gut microbiome. However, no methods exist to efficiently examine MACs in biologically-derived mixtures. Here, we present a high-throughput platform to detect MACs from various plant, animal, and microbial sources using a genome-wide library of engineered Bacteroides thetaiotaomicron (Bt) strains that harness their endogenous glycan detection machinery. We demonstrate that this platform exhibits specific and sensitive responses to glycan mixtures and use bacterially-encoded proteins to characterize a previously unknown MAC from yeast. Expanding this technology across gut Bacteroides species will generate a broadly applicable approach to characterize heterogeneous glycan mixtures and identify prebiotic substrates.

molecular biology↗

bioRxiv2025

3D osteocyte networks under Pulsatile Unidirectional Fluid Flow Stimuli (PUFFS)

Although osteocytes are known to play a key role in skeletal mechano-adaptation, few in vitro models have investigated how pulsatile mechanical stimuli influence the properties of 3D osteocyte networks. Here we design and develop a microfluidic based in vitro model to study 3D osteocyte networks cultured under Pulsatile Unidirectional Fluid Flow Stimuli (PUFFS). Digital light projection stereolithography was used to design and fabricate a three-chambered PDMS microfluidic chip. Model osteocytes (murine MLO-Y4) were encapsulated in collagen matrix within the chip to form self-assembled three-dimensional (3D) cell networks. Daily stimulus in the form of PUFFS was then applied for upto 21 days. A combination of experiments, computational simulation and analytical modeling was used to characterize the mechanical environment experienced by embedded cells during PUFFS. Viability, morphology, cell-connectivity, expression of key proteins, and gene expression, and real-time calcium signaling within 3D osteocyte networks were characterized at select time-points and compared to static conditions. Results show that PUFFS stimulation at 0.33 and 1.66 Hz can initiate mechanotransduction via calcium signals that are propagated across the network of collagen encapsulated osteocytes via Cx43 junctions. Furthermore, osteocytes cultured in these devices maintain expression of several key osteocyte genes for up to 21d. Taken together, this model can potentially serve as a testbed to study how 3D osteocyte networks respond to dynamic mechanical stimulation relevant to skeletal tissues.

bioengineering↗

bioRxiv2024

CELLNET technology: Spatially organized, functional 3D networks at single cell resolution

Cells possess the remarkable ability to generate tissue-specific 3D interconnected networks and respond to a wide range of stimuli. Understanding the link between the spatial arrangement of individual cells and their networks emergent properties is necessary for the discovery of both fundamental biology as well as applied therapeutics. However, current methods spanning from lithography to 3D photo-patterning to acoustofluidic devices are unable to generate interconnected and organized single cell 3D networks within native extracellular matrix (ECM). To address this challenge, we report a novel technology coined as CELLNET. This involves the generation of crosslinked collagen within multi-chambered microfluidic devices followed by femtosecond laser ablation of 3D microchannel networks and cell seeding. Using model cells, we show that cell migrate within ablated networks within hours, self-organize and form viable, interconnected, 3D networks in custom architectures such as square grid, concentric circle, parallel lines, and spiral patterns. Heterotypic CELLNETs can also be generated by seeding multiple cell types in side-chambers of the devices. The functionality of cell networks can be studied by monitoring the real-time calcium signaling response of individual cells and signal propagation within CELLNETs when subjected to flow stimulus alone or a sequential combination of flow and biochemical stimuli. Furthermore, user-defined disrupted CELLNETs can be generated by lethally injuring target cells within the 3D network and analyzing the changes in their signaling dynamics. As compared to the current self-assembly based methods that exhibit high variability and poor reproducibility, CELLNETs can generate organized 3D single-cell networks and their real-time signaling responses to a range of stimuli can be accurately captured using simple cell seeding and easy-to-handle microfluidic devices. CELLNET, a new technology agnostic of cell types, ECM formulations, 3D cell-connectivity designs, or location and timing of network disruptions, could pave the way to address a range of fundamental and applied bioscience applications. TeaserNew technology to generate 3D single cell interconnected and disrupted networks within natural extracellular matrix in custom configurations.

bioengineering↗

bioRxiv2024

Vimentin promotes collective cell migration through collagen networks via increased matrix remodeling and spheroid fluidity

The intermediate filament (IF) protein vimentin is associated with many diseases with phenotypes of enhanced cellular migration and aggressive invasion through the extracellular matrix (ECM) of tissues, but vimentins role in in-vivo cell migration is still largely unclear. Vimentin is important for proper cellular adhesion and force generation, which are critical to cell migration; yet the vimentin cytoskeleton also hinders the ability of cells to squeeze through small pores in ECM, resisting migration. To identify the role of vimentin in collective cell migration, we generate spheroids of wide-type and vimentin-null mouse embryonic fibroblasts (mEFs) and embed them in a 3D collagen matrix. We find that loss of vimentin significantly impairs the ability of the spheroid to collectively expand through collagen networks and remodel the collagen network. Traction force analysis reveals that vimentin null spheroids exert less contractile force than their wild-type counterparts. In addition, spheroids made of mEFs with only vimentin unit length filaments (ULFs) exhibit similar behavior as vimentin-null spheroids, suggesting filamentous vimentin is required to promote 3D collective cell migration. We find the vimentin-mediated collective cell expansion is dependent on matrix metalloproteinase (MMP) degradation of the collagen matrix. Further, 3D vertex model simulation of spheroid and embedded ECM indicates that wild-type spheroids behave more fluid-like, enabling more active pulling and reconstructing the surrounding collagen network. Altogether, these results signify that VIF plays a critical role in enhancing migratory persistence in 3D matrix environments through MMP transportation and tissue fluidity.

biophysics↗

bioRxiv2024

RelQ-mediated alarmone signaling regulates growth, sporulation, and stress-induced biofilm formation in Clostridioides difficile

The bacterial stringent response (SR) is a conserved transcriptional reprogramming pathway mediated by the nucleotide signaling alarmones, (pp)pGpp. The SR has been implicated in antibiotic survival in Clostridioides difficile, a biofilm- and spore-forming pathogen that causes resilient, highly recurrent C. difficile infections. The role of the SR in other processes and the effectors by which it regulates C. difficile physiology are unknown. C. difficile RelQ is a clostridial alarmone synthetase. Deletion of relQ dysregulates C. difficile growth in unstressed conditions, affects susceptibility to antibiotic and oxidative stressors, and drastically reduces biofilm formation. While wild-type C. difficile displays increased biofilm formation in the presence of sub-lethal stress, the {Delta}relQ strain cannot upregulate biofilm production in response to stress. Deletion of relQ slows spore accumulation in planktonic cultures but accelerates it in biofilms. This work establishes biofilm formation and sporulation as alarmone-mediated processes in C. difficile and reveals the importance of RelQ in stress-induced biofilm regulation.

microbiology↗

bioRxiv2024

A Functional Analysis of a Resorbable Citrate-based Composite Tendon Anchor

Orthopaedic fixation seeks solutions to the challenges of non-union, reconstructive surgery, and soft tissue injuries by providing stability and tissue alignment during the healing process. Risks associated with fixation devices such as peri-implant resorption, implant loosening and sub-optimal device resorption remain a significant challenge in the development of transient fixation devices. Osteomimetic biomaterials, and in particular, bio-resorbable polymer composites designed to match the mineral phase content of native bone have been shown to exhibit osteoinductive and osteoconductive properties in vivo and have been used in bone fixation for the past 2 decades. However, the specific signalling pathways driving the osteogenic response to these biomaterials remain largely unknown. In this study a resorbable, bioactive, and mechanically robust citrate-based composite, formulated from poly(octamethylene citrate) (POC) and hydroxyapatite (HA) (POC-HA) was investigated as a potential orthopedic biomaterial. In vitro analysis with human Mesenchymal Stem Cells (hMSCs) indicated that POC-HA composite materials supported cell adhesion, growth, and proliferation and increased calcium deposition, alkaline phosphatase production, the expression of osteogenic specific genes and activation of canonical pathways leading to osteoinduction and osteoconduction. Further in vivo evaluation of a POC-HA tendon fixation device in a sheep metaphyseal model indicated the regenerative and remodelling potential of this citrate-based composite material in orthopedic applications.

bioengineering↗

bioRxiv2023

Droplet bioprinting of acellular and cell-laden structures at high-resolutions

Advances in Digital Light Processing (DLP) based (bio) printers have made printing of intricate structures at high resolution possible using a wide range of photosensitive bioinks. A typical setup of a DLP bioprinter includes a vat or reservoir filled with liquid bioink, which presents challenges in terms of cost associated with bioink synthesis, high waste, and gravity-induced cell settling, contaminations, or variation in bioink viscosity during the printing process. Here, we report a vat-free, low-volume, waste-free droplet bioprinting method capable of rapidly printing 3D soft structures at high resolution using model bioinks. A multiphase many-body dissipative particle dynamics (mDPD) model was developed to simulate the dynamic process of droplet-based DLP printing and elucidate the roles of surface wettability and bioink viscosity. Process variables such as light intensity, photo-initiator concentration, and bioink formulations were optimized to print 3D soft structures ([~]0.4 to 3 kPa) with an XY resolution of 38 {+/-} 1.5 m and Z resolution of 237{+/-}5.4 m. To demonstrate its versatility, droplet bioprinting was used to print a range of acellular 3D structures such as a lattice cube, a Mayan pyramid, a heart-shaped structure, and a microfluidic chip with endothelialized channels. Droplet bioprinting, performed using model C3H/10T1/2 cells, exhibited high viability (90%) and cell spreading. Additionally, microfluidic devices with internal channel network lined with endothelial cells showed robust monolayer formation while osteoblast-laden constructs showed mineral deposition upon osteogenic induction. Overall, droplet bioprinting could be a low-cost, no-waste, easy-to-use, method to make customized bioprinted constructs for a range of biomedical applications.

bioengineering↗

bioRxiv2023

Meniscus-enabled Projection Stereolithography (MAPS)

Light-based additive manufacturing methods have been widely used to print high-resolution 3D structures for applications in tissue engineering, soft robotics, photonics, and microfluidics, among others. Despite this progress, multi-material printing with these methods remains challenging due to constraints associated with hardware modifications, control systems, cross-contaminations, waste, and resin properties. Here, we report a new printing platform coined Meniscus-enabled Projection Stereolithography (MAPS), a vat-free method that relies on generating and maintaining a resin meniscus between a crosslinked structure and bottom window and to print lateral, vertical, discrete, or gradient multi-material 3D structures with little-to-no cross-contamination or waste. We also show that MAPS is compatible with a wide range of resins and can print complex multi-material 3D structures without requiring specialized hardware, software, or complex washing protocols. MAPSs ability to print structures with microscale variations in mechanical stiffness, opacity, surface energy, cell densities, and magnetic properties provides a generic method to make advanced materials for a broad range of applications.

bioengineering↗

bioRxiv2023

Poor biosafety and biosecurity practices and haphazard antibiotics usage in poultry farms in Nepal hindering antimicrobial stewardship

Poultry industry in Nepal has experienced remarkable growth in the last decade, but farm biosafety and biosecurity measures are often overlooked by farmers due to lack of knowledge or to save cost. As a result, farms often suffer from sporadic and regular outbreaks of many zoonotic diseases such as highly pathogenic avian influenza (HPAI), impacting production and creating public health challenges. Poor farm management practices, including overuse of antibiotics for prophylaxis and therapeutics, can complicate the spread of poultry diseases by creating and enhancing antimicrobial resistance (AMR) that is threating to both, poultry, and human health. We assessed biosafety, biosecurity risks and AMR stewardship in sixteen poultry farms located in four districts (Ramechhap, Nuwakot, Sindhupalchowk, and Kavre) surrounding densely populated Kathmandu valley. Risk assessment and AMR stewardship evaluation questionnaire were administered to formulate biosafety and biosecurity compliance matrix (BBCM). Risk assessment checklist assessed facility operations, personnel and standard operating procedures, water supply, cleaning and maintenance, rodent/pest control and farm record keeping. Oral and cloacal samples from the poultry were collected, pooled, and screened for eight poultry pathogens using Polymerase Chain Reaction (PCR) tests. Based on BBCM, we identified one of the farms in Sindhupalchowk (Farm 4) having the most (BBCM score= 67%) and a farm in Kavre (Farm 3) to having the least (BBCM score= 12%) biosafety and biosecurity compliance. Although most of the farms (61.6%) followed general poultry farming practices, only half had clean and well-maintained farms. Personal safety standard procedure compliance (BBCM score = 42.4%) and rodent control (BBCM score = 3.1%) were the biggest gaps. At least one of either bacterial or viral pathogen was detected in all farms. Mycoplasma gallisepticum was the most common disease detected in all but one farm, followed by Mycoplasma synoviae. Although more than half of the farmers considered AMR a threat, over 26% of them used antibiotics as a preventive measure and 81% did not consider withdrawal period for antibiotics prior to processing of their meat products. Additionally, antibiotics classified as Watch and Restrict by the WHO were frequently used by the farmers to treat bacterial infections in their farms. Lack of awareness and inadequate enforcement of regulations have exacerbated the risk of disease transmission in farms and compromised antimicrobial stewardship.

microbiology↗

bioRxiv2023

Printing double network tough hydrogels using Temperature-Controlled Projection Stereolithography (TOPS)

We report a new method to shape double-network (DN) hydrogels into customized microscale 3D structures that exhibit superior mechanical properties in both tension and compression. A one-pot prepolymer formulation containing photo-cross-linkable acrylamide and thermo-reversible sol-gel {kappa}-carrageenan with a suitable crosslinker, and photo-initiator/absorbers are optimized. A new TOPS system is utilized to photo-polymerize the primary acrylamide network into a 3D structure above the sol-gel transition of {kappa}-carrageenan (80{degrees}C), while cooling down generates the secondary physical {kappa}-carrageenan network to realize tough DN hydrogel structures. 3D structures, printed with high lateral (37m) and vertical (180m) resolutions and superior 3D design freedoms (internal voids), exhibit ultimate stress and strain of 200 kPa and 2400% respectively under tension, and simultaneously exhibit high compression stress of 15 MPa with a strain of 95%, both with high recovery rates. The roles of swelling, necking, self-healing, cyclic loading, dehydration, and rehydration on the mechanical properties of printed structures are also investigated. To demonstrate the potential of this technology to make mechanically reconfigurable flexible devices, we print an axicon lens and show that a Bessel beam can be dynamically tuned via user-defined tensile stretching of the device. This technique can be broadly applied to other hydrogels to make novel smart multifunctional devices for a range of applications.

bioengineering↗

bioRxiv2023

One Health Assessment of an Urban Temporary Settlement Reveals Gut Microbiome Serving as Antimicrobial Resistance Gene Reservoir

Antimicrobial resistance (AMR) is an emerging and growing global health challenge that could result in 10.2 million deaths annually by 2050. The unrestricted and haphazard use of antibiotics is contributing to the rapid emergence and spread of AMR, and the problem is exacerbated by release of untreated waste water from high-risk sources like hospitals into rivers. Bacteria often develop resistance through horizontal gene transfer mechanism and gut flora can act as a source for new Antimicrobial Resistance Genes (ARG). Upcoming methods like metagenomics can identify the resistance profile (AMR) of gut microbiome, and detect bacterial infections that otherwise go unnoticed. Our study focused on understanding the presence of AMR mutations and gene transfer dynamics in human, animal and environmental samples collected in one of the temporary settlements of Kathmandu (Nepal) using One Health approach. Current AMR reporting based on clinical cases is limited and does not provide information on specific pathogen and associated AMR genes-our study is an effort to contribute information to fulfill this gap. Twenty-one samples were collected from a temporary settlement in Thapathali (Kathmandu), which included fecal samples from birds (n=3) and humans (n=14), and environmental samples (n=4). Microbiological assessment was carried out based on 16S sequence metagenomic analysis using MiSeq (Illumina, USA). Taxonomic classification on obtained 16S sequences were determined by using Metaphlan 2 and Qiime 2 bioinformatics tools. ShortBRED was used to classify ARG and virulence factors, and WAFFLE was used for horizontal gene transfer event prediction. The network analysis was carried out using Gephi v0.9 and the ResistoXplorer web tool to identify ARG in the collected samples. Prevotella spp. was the dominant gut microbiome in humans. We detected diverse phages and viruses, including Stx-2 converting phages. 72 virulence factors and 53 ARG subtypes were detected, with poultry samples having the highest number of subtypes. The cluster and network analysis showed a strong association between gut microbiome and ARG, which was also supported by Horizontal Gene Transfer (HGT) analysis. One-Health interface showed ARG dynamics and revealed gut microbiomes of humans and animals serving as a reservoir for the circulating ARG.

genomics↗

bioRxiv2022

Screening Avian Pathogens in Eggs from Commercial Hatcheries in Nepal- an Effective Poultry Disease Surveillance Tool

BackgroundCommercial hatcheries play an important role in the overall poultry value chain-providing small to large poultry farmers with day old chicks. Any outbreak in such hatcheries can spread diseases to other farms. Regular screening of major avian pathogens, along with strict bio-security measures, can prevent spread of diseases in hatcheries. Newcastle Disease Virus (NDV), Infectious Bronchitis Virus (IBV), Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), Infectious Bursal Disease Virus (IBDV) and Influenza A Virus (IAV) are among the most prevalent poultry diseases which can be detected in egg albumin. MethodWe retrospectively (August 2020-August 2021, except October 2020) analyzed diagnostic results for six selected avian pathogens (NDV, IBV, MS, MG, IBDV and IAV) on eggs (n=4343) received from eleven major commercial poultry hatcheries located in the five adjoining districts of Kathmandu, Nepal. Albumin from 10% randomly selected eggs from each hatchery were tested for the six avian pathogens using multiplex PCR. ResultMajority (7/11, 64%) of the poultry hatcheries had at least one of the six pathogens present. We detected at least one avian pathogen in nine out of eleven months (82%) of screening. Except for IBDV, we found one or more of the other major avian pathogens-Influenza A (IAV) (n=4 times) and Mycoplasma gallisepticum (MG) (n=4 times) were detected the most, followed by Newcastle Virus (NDV) (n=3 times). Infectious bronchitis virus (IBV) were detected twice, and Mycoplasma synoviae (MS) was detected once. ConclusionIn a resource strapped country like Nepal, poultry disease outbreak investigation in particular and surveillance in general are challenging. Meanwhile, poultry production is highly impacted by disease outbreaks often triggered by poor bio-security and lack of pathogen screening practices. Our molecular screening tests have picked up major poultry pathogens present throughout the year in eggs collected from hatcheries. Influenza A was detected at 4 different incidences throughout the year, which is of concern to both human and animal health. Quick systematic screening of eggs at key distribution points (hatcheries) for major avian pathogens is an effective surveillance tool for early disease detection and containment of outbreaks.

microbiology↗