Biology subjects

Swain, S.

Publications and source records attributed to Swain, S..

11 recordsLinked to original sources

bioRxiv2025

Agentic Lab: An Agentic-physical AI system for cell and organoid experimentation and manufacturing

Reproducibility in biological research and manufacturing remains constrained by the complexity of multi-step protocols, fragmented data-analysis pipelines, and the intrinsic variability of experimental execution. Here, we present Agentic Lab, an agentic-physical AI platform that unifies large language model and vision language model (LLMs/VLMs)-driven reasoning with real-world laboratory operations. Agentic Lab uses multi-agent orchestration architecture, comprising of specialized subagents for knowledge retrieval, protocol design, multimodal data analysis, and training-free segmentation and representation learning for intrinsically explainable single-cell and organoid phenotyping. These agents operate under the orchestration of a virtual principal investigator MolAgent that is linked to an augmented reality (AR)-based physical AI interface, which can bridge digital reasoning with human physical execution. Agentic Lab perceives real-world experimental activities, provides context-aware instructions, identifying procedural errors in real time for humans to correct, and continuously evolves with its long-term memory database expanding through the accumulation of experimental data logs from human scientists. This interaction allows scientists and AI agents to collaborate and co-evolve dynamically, closing the loop between planning, action, and analysis in the traditional cell and organoid research lifecycle. We demonstrate Agentic Lab in organoid differentiation from human pluripotent stem cells, where it autonomously generates protocols, monitors culture procedures, and identifies subtle morphological heterogeneity linked to growth conditions. The system interprets these phenotypes, grounds them in literature, and proposes targeted instructions for improving differentiation efficiency. By combining multi-agent reasoning with physical laboratory awareness, Agentic Lab transforms experimentation and biomanufacturing from a static workflow into an adaptive, feedback-driven, bidirectional process that integrates agentic AI into the research lifecycle. This framework establishes a foundation for intelligent laboratories that integrate design, execution, and interpretation within a unified agentic-physical system.

bioengineering↗

bioRxiv2023

Aeroplane wing, a new recessive autosomal phenotypic marker in malaria vector, Anopheles stephensi Liston

A novel and distinct mutant, with an aeroplane wing (ae) phenotype, is reported for the first time in the urban malaria vector, Anopheles stephensi. The mutant mosquitoes exhibit extended wings that are easily visible to naked eyes in both sexes. This mutant was first observed in a nutritionally stressed experimental isofemale line and characterized for its genetic inheritance and other related parameters. Meticulous and strategic genetic crosses revealed that the ae gene is an autosomal, recessive, non-sex-linked and monogenic trait with full penetrance and uniform expression in the adult stage. Cytogenetic study of the ovarian polytene chromosome revealed an inversion on the 3L chromosome (3Li) in both the ae mutant and its parent line. No significant differences in wing venation and other parameters were observed in ae mutants compared to their normal parental lines. This ae mutant would be an excellent marker that can be used by researchers to study the function of related genes within the genome. Author summaryIn the present study, we have established and describe the inheritance of an unusual novel aeroplane (ae) winged mutant in Anopheles stephensi, an urban malaria vector in India. The ae mutant lines exhibit three open-wing orientations in both the sexes of adults viz. left (LW), right (RW) and double wing (DW) during its resting phase. Through various inbreeding crosses we demonstrated the mode of inheritance of the ae gene to be autosomal, recessive and monogenic in nature. The morphometric studies of eggs and wings revealed that mutant lines are on par with their parental lines. Cytogenetic study of polytene chromosome of ae mutant revealed the presence of heterogenic inversion on the 3L chromosome arm, which might help in adaptation mechanism. We strongly believe that ae phenotypic markers have great applications bridging both basic and applied genetic research such as constructing linkage maps, identifying loci of quantitative and/or qualitative traits and as guides for insect transformation studies.

genetics↗

bioRxiv2023

Pooled effector library screening in protoplasts rapidly identifies novel Avr genes

Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance (R) gene cloning and stacking has accelerated in recent years 1-3, the identification of corresponding avirulence (Avr) genes in many pathogens is hampered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts for rapid identification of interacting R/Avr pairs. We validated this platform by isolating known and novel Avr genes from wheat stem rust (Puccinia graminis f. sp. tritici) by screening a designed library of putative effectors against individual R genes. Rapid Avr gene identification provides molecular tools to understand and track pathogen virulence evolution by genotype surveillance and optimise R gene deployment and stacking strategies. This screening platform is broadly applicable to many crop pathogens, whilst also adaptable for screening genes involved in other protoplast-selectable traits.

plant biology↗

bioRxiv2022

Enrichment of phenotype among biological forms of Anopheles stephensi Liston through establishment of isofemale lines

The success of vector management programs relies on knowledge of the biology and genetic make-up of mosquitoes so that they can be interlaced with modern tools for developing suitable intervention strategies. There are many reports available for rearing varied species of mosquito vectors. However, there are limited studies addressing the development of isofemale lines among mosquitoes to homogenize the population to obtain both high-quality genome assemblies and enrichment of phenotype. Anopheles stephensi, an urban malaria vector, is one of the major invasive vectors of malaria distributed throughout the Indian subcontinent, Middle East, and has recently been expanding its range in Africa. With the existence of three biological forms, distinctly identifiable based on the number of ridges on eggs with varying vectorial competence, An. stephensi is a perfect species for developing a method for the successful establishment of isofemale lines, which can be tested for retention of the expected vectorial competence for the various forms. We describe the key steps in the establishment and validation of isofemale lines, which include monitoring the transgenerational fitness traits, morphometrics of eggs, and adult wing size during every generation. After the initial inbreeding depression, as proof of the tedious selection process, no significant morphometric differences were observed in the wings and egg size between the parental and their respective isofemale lines. We observed a significant change in the vectorial competence between the respective isofemale and parental lines enriching expected differential susceptibility towards malaria parasites by the type and intermediate forms. Interestingly, IndCh and IndInt strains showed variations in resistance to different insecticides belonging to all the four major classes. These variant lines have been characterized for their levels of homozygosity both at the phenotype and genotype levels and can be used as a standard reference or as a biological resource for other studies related to urban malaria research. Author summaryIsofemale lines can be a valuable resource for characterizing and enhancing several genotypic and phenotypic traits. This is the first detailed report of the establishment of two isofemale lines of type and intermediate biological forms in Anopheles stephensi. The work encompasses the characterization of fitness traits among the two lines through a transgenerational study. Further, isofemale colonies were established and used to characterize insecticide susceptibility and vector competence. The study provides valuable insights into the differential susceptibility status of the parental and isofemale to different insecticides belonging to the same class. Corroborating with the earlier hypothesis we exemplify the high vector competence in type form than the intermediate from using homozygous isofemale lines. Using these isofemale lines it is now possible to study host-parasite interactions and identify factors that might be responsible for altered susceptibility and increased vector competence in An. stephensi biological forms that would also pave way for developing better vector management strategies.

genetics↗

bioRxiv2022

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. An. stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, have been reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a TNF-like gene, which is the homolog of the eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of wengen (wgn) and grindelwald (grnd) genes in IndInt, which are known to be the receptors for eiger in Drosophila. We have identified all the genes in IndInt required for eiger-mediated signaling by analogy to TNF-TNFR system, suggesting the presence of a functionally active eiger signaling pathway present in IndInt. Comparative genomics of high-quality genome assemblies of the three type-forms with that of IndInt, reveals structurally disruptive mutations in eiger gene in all three strains of the type-form, alluding to compromised innate immunity in the type-form as the cause of high vectorial capacity in these strains. This is the first report of the presence of an intact evolutionarily-conserved TNF-TNFR signaling system in malaria vectors, with a potential role in Plasmodium resistance.

genomics↗

bioRxiv2022

A Novel High-Throughput Single B-Cell Cloning Platform for Isolation and Characterization of High-Affinity and potent SARS-CoV-2 Neutralizing Antibodies

Monoclonal antibodies (mAbs) that are specific to SARS-CoV-2 can be useful in diagnosing, preventing, and treating the coronavirus (COVID-19) illness. Strategies for the high-throughput and rapid isolation of these potent neutralizing antibodies are critical toward the development of therapeutically targeting COVID-19 as well as other infectious diseases. In the present study, a single B-cell cloning method was used to screen SARS-CoV-2 receptor-binding domain (RBD) specific, high affinity, and neutralizing mAbs from patients blood samples. An RBD-specific antibody, SAR03, was discovered that showed high binding (ELISA and SPR) and neutralizing activity (competitive ELISA and pseudovirus-based reporter assay) against Sars-CoV-2. Mechanistic studies on human cells revealed that SAR03 competes with the ACE-2 receptor for binding with the RBD domain (S1 subunit) present in the spike protein of Sars-CoV-2. This study highlights the potential of the single B cell cloning method for the rapid and efficient screening of high-affinity and effective neutralizing antibodies for Sars-CoV-2 and other emerging infectious diseases. HighlightsO_LISingle B-cell cloning is a high-throughput and efficient method of generating high affinity neutralizing antibodies C_LIO_LISingle B-cell cloning method was used to screen SARS-CoV-2 receptor-binding domain (RBD) specific, high affinity, and neutralizing monoclonal antibodies from patients blood samples. C_LIO_LIAn RBD-specific antibody, SAR03, was discovered that showed high binding and neutralizing activity against SARS-CoV-2. C_LI

immunology↗

bioRxiv2021

The genome trilogy of Anopheles stephensi, an urban malaria vector, reveals structure of a locus associated with adaptation to environmental heterogeneity

BackgroundAnopheles stephensi is the most menacing malaria vector to watch for in newly urbanizing parts of the world. The fitness is reported to be a direct consequence of the vector adapting to laying eggs in over-head water tanks with street-side water puddles polluted by oil and sewage. Large frequent inversions of malaria vectors are implicated in adaptation. ResultsWe report the assembly of a strain of An. stephensi of the type-form, collected from a construction site from Chennai (IndCh) in 2016. The genome completes the trilogy with respect to a 16 Mbp inversion (2Rb) in An. stephensi associated with adaptation to environmental heterogeneity. Comparative genome analysis revealed breakpoint structure and allowed extraction of 22,650 segregating SNPs for typing this inversion. Using whole genome sequencing of 82 individual mosquitoes, we conclude that one third of both wild and laboratory populations maintain heterozygous genotype of 2Rb. The large number of SNPs are tailored to assign inversion genotype directly from 1740 exonic SNPs 80% of which are expressed in various developmental stages. ConclusionsThe genome trilogy approach accelerates study of fine structure and typing of important inversions in malaria vectors putting the genome resources for the much understudied An. stephensi, on par with the extensively studied malaria vector, Anopheles gambiae. We argue that the IndCh genome is relevant for field translation work compared to those reported earlier by showing that individuals from diverse populations cluster with IndCh pointing to significant commerce between cities, perhaps, allowing for survival of the fittest strain.

genomics↗

bioRxiv2021

Comparative performance analysis of mulberry silkworm (Bombyx mori L.) races for integration of superior yield and maximize profit in West Bengal

India has a prosperous and glorious history in silk production and its silk trade dates back to 15th century. Sericulture is practiced in many regions of India, where West Bengal ranks third in mulberry silk production. About 2000 villages are engaged in mulberry cultivation with plantation area of 37,883 acres. But nowadays, farmers have lack their interest in this sector due to low cost benefit ratio, high investment cost in terms of silk worm rearing, land uses and lack of proper knowledge on different races of Bombyx mori. Therefore, the present study has been aiming to find out the comparative performance of bivoltine, multivoltine, and F1 variety of B. mori by analysed the cocoon, post-cocoon characters, and silk related traits for identifying the best superior races of B. mori. The results showed that feeding habits of silkworm larvae of three races had significant effect on cocoon parameters. The average weight of ten 5th instar larvae of bivoltine was higher in comparison with multivoltine and F1 variety. Similar trends were obtained in the average length of silk thread from a single cocoon in bivoltine races, higher by 30% and 77.14% from F1 and multivoltine, respectively (P<0.05). We also inquired about capital investment and profit-making of three varieties. Net profit for bivoltine was significantly increased by 15.65% and 10.21% than multivoltine and F1 varieties, respectively.The heatmap analysis revealed that the bivoltine races of B. mori were separately clustered based on the positive correlation of measured variables mostly length of silk thread, renditta, dry cocoon weight, the average weight of larvae, present market price, leaves for rearing, net profit and selling price of cocoon per acre farmland; whereas, the multivoltine and F1 variety clustered in a separate group. From our findings, it is clear that the culture of bivoltine is preferable for the farmers who dont have enough landed property and also profitable in terms of cocoon, post cocoon and silk traits. Therefore, it is recommended that the farming of bivoltine silkworm is more gainfulcompared to F1 and multivoltine variety, and capable of more income generation than other traditional agricultural crops. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/436391v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1bb1e89org.highwire.dtl.DTLVardef@1d1bb69org.highwire.dtl.DTLVardef@6727f3org.highwire.dtl.DTLVardef@6ff918_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig.C_FLOATNO Graphical abstract represents the comparative performance of bivoltine, multivoltine and F1 races of B. mori on the aspect of biological and economic traits in tropical climate condition. C_FIG

zoology↗

bioRxiv2021

Assessment of Polarized Piezoelectric SrBi4Ti4O15 Nanoparticles as an alternative antibacterial agent

Strontium bismuth titanate nanoparticles (SrBi4Ti4O15/SBT NPs,) and their polarized counterparts were prepared to assess their antibacterial efficacy on biomaterials. The structural properties of the SBT NPs were performed by X-ray diffraction and the antibacterial efficacy was evaluated against Staphyllococcus aureus (S. aureus) pathogenic bacteria. Significant antibacterial activity of polarized SBT specimen was observed against S. aureus bacteria. Results presented in this work confirmed that polarized SBT can effectively combat bacterial growth and prevent biofilm formation activity of pathogenic bacteria and hence they can be used as alternative antimicrobial agents.

bioengineering↗

bioRxiv2021

Fabrication of silver doped nano hydroxyapatite-carrageenan hydrogels for articular cartilage applications

It can be found from the results that nano hydroxyapatite- silver -3.0 wt% carageenan (nHA-Ag-CG3.0) improved the mechanical properties of the as-formed hydrogel scaffold after incorporation of higher CG concentration. The Youngs modulus of hydroxyapatite- silver - 1.5wt% carageenan (nHA-Ag-CG1.5) was found to be 0.36 {+/-} 0.07 MPa that increased in case of nHA-Ag-CG3.0 demonstrating better interfacial compatibility of their matrix with respect to the reinforcement. This increase in reinforcement concentration resulted in higher stiffness that dissipated energy. The higher swelling ratio is envisaged to induce better cell adhesion and proliferation. The biodegradability test was performed in phosphate buffered saline at body temperature for 3 weeks. The biodegradability rate of nHA-Ag-CG1.5 was found to be equivalent to nHA-Ag-CG3.0 hydrogels at day 7 while it increased faster in nHA-Ag-CG3.0 on days 14 and 21 that may be ascribed to the possible interaction of nHA and Ag with their CG matrix. The bacterial cell viability of Staphylococcus aureus (S. aureus) was performed after 10 h, 20 h and 30 h of culture. The nHA-Ag-CG1.5 exhibited restrained growth of S. aureus as compared to nHA-Ag-CG3.0 and these results were validated by CLSM analysis. Hence, nHA-Ag-CG3.0 may be considered to have more cytocompatibility than nHA-Ag-CG 1.5.

bioengineering↗

bioRxiv2019

DIMR, a Yeast-Based Synthetic Reporter System for Probing Oligomeric Transcription Factor DNA Binding

Transcription factors (TFs) are fundamental components of biological regulation, facilitating the basal and differential gene expression necessary for life. TFs exert transcriptional regulation through interactions with both DNA and other TFs, ultimately influencing the action of RNA polymerase at a genomic locus. Current approaches are proficient at identification of binding site requirements for individual TFs, but few methods have been adapted to study oligomeric TF complexes. Further, many approaches that have been turned toward understanding DNA binding of TF complexes, such as electrophoretic mobility shift assays, require protein purification steps that can be burdensome or scope-limiting when considering more exhaustive experimental design. In order to address these shortfalls and to facilitate a more streamlined approach to understanding DNA binding by TF complexes, we developed the DIMR (Dynamic, Interdependent TF binding Molecular Reporter) system, a modular, yeast-based synthetic transcriptional activity reporter. As a proof of concept, we focused on the NUCLEAR FACTOR-Y (NF-Y) family of obligate heterotrimeric TFs in Arabidopsis thaliana. The DIMR system was able to reproduce the strict DNA-binding requirements of an experimentally validated NF-YA2/B2/C3 complex with high fidelity, including recapitulation of previously characterized mutations in subunits that either break NF-Y complex interactions or are directly involved in DNA binding. The DIMR system is a novel, powerful, and easy-to-use approach to address questions regarding the binding of oligomeric TFs to DNA.\n\nOne sentence summaryThe DIMR system provides an accessible and easy-to-use platform to elucidate DNA binding and transcriptional regulatory capacity of oligomeric transcription factor complexes

synthetic biology↗