Biology subjects

Gupta, N.

Publications and source records attributed to Gupta, N..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Non-autonomy of age-related morphological changes in the C. elegans germline stem cell niche

Declines in tissue renewal and repair due to alterations in tissue stem cells is a hallmark of aging. Many stem cell pools are maintained morphologically complex niches. Using the C. elegans hermaphrodite germline stem cell system, we analyzed age-related changes in the morphology of the niche, the distal tip cell (DTC), and identified a molecular mechanism that promotes a subset of these changes. We found decreases in the number and length of long DTC processes with age. We also found that a long-lived daf-2 mutant exhibits a daf-16-dependent maintenance of long DTC processes. Surprisingly, the tissue requirement for daf-16(+) is non-autonomous, and daf-16(+) in body wall muscle is both necessary and sufficient. In addition, after a delay, pre-formed DTC processes deteriorate upon premature germline differentiation, but not upon cell cycle inhibition. We propose a reciprocal DTC-germline interaction model and speculate how reduced daf-2 activity both delays stem cell exhaustion and maintains DTC processes. These studies establish the C. elegans DTC as a powerful in vivo model for understanding age-related changes in cellular morphology and their consequences in stem cell systems. SUMMARYThe C. elegans germline stem cell niche morphology is markedly altered with age and is regulated non-autonomously from the muscle by insulin/IGF-like signaling. Results suggest reciprocal niche-germline regulation.

cell biology↗

bioRxiv2025

Wilms tumor 1 impairs apoptotic clearance of fibroblasts in distal fibrotic lung lesions

Idiopathic pulmonary fibrosis (IPF) is a fatal fibrotic lung disease characterized by impaired fibroblast clearance and excessive extracellular matrix (ECM) protein production. Wilms Tumor 1 (WT1), a transcription factor, is selectively upregulated in IPF fibroblasts. However, the mechanisms by which WT1 contributes to fibroblast accumulation and ECM production remain unknown. Here, we investigated the heterogeneity of WT1-expressing mesenchymal cells using single-nucleus RNA sequencing of distal lung tissues from IPF patients and control donors. WT1 was selectively upregulated in a subset of IPF fibroblasts that co-expressed several pro- survival and ECM genes. The results of both loss-of-function and gain-of-function studies are consistent with a role for WT1 as a positive regulator of pro-survival genes to impair apoptotic clearance and promote ECM production. Fibroblast-specific overexpression of WT1 augmented fibroproliferation, myofibroblast accumulation, and ECM production during bleomycin-induced pulmonary fibrosis in young and aged mice. Together, these findings suggest that targeting WT1 is a promising strategy for attenuating fibroblast expansion and ECM production during fibrogenesis.

pathology↗

bioRxiv2025

New Insight Into the Neuroimmune Interplay In Pseudomonas aeruginosa Keratitis

PurposeThe miR-183/96/182 cluster (miR-183C) is required for normal functions of sensory neurons (SN) and various immune cells, including myeloid cells (MC). This research aims to reveal the roles of miR-183C of SN in the interplay of corneal sensory nerves (CSN) and MC during Pseudomonas aeruginosa (PA) keratitis. MethodsDouble-tracing mice with SN-specific (SNS) conditional knockout of miR-183C (CKO) and age-and sex-matched wild type (WT) controls were used. Their CSN are labeled with Red Fluorescent Protein (RFP); MC with Enhanced Green (EG)FP. The left corneas were scarified and infected with ATCC19660 PA. Corneal flatmounts were prepared at 3, 6, and 12 hours post-infection (hpi) and 1, 3, and 5 days (d)pi for confocal microscopy. Myeloperoxidase (MPO) assay and plate count were performed at 1 dpi. ResultsIn WT mice, CSN began to degenerate as early as 3 hpi, starting from the fine terminal CSN in the epithelial/subepithelial layers, most prominently in the central region. By 1 dpi, CSN in the epithelium/subepithelial layer were nearly completely destroyed, while stromal nerves persisted. From 3 dpi, CSN were obliterated in both layers. In CKO vs WT mice, CNS followed a slightly slower pace of degeneration. CSN density was decreased at 3 and 6 hpi. However, at 3 dpi, residual large-diameter stromal CSN were better preserved. MC were decreased in the central cornea at 3 and 6 hpi, but increased in the periphery. Both changes were more prominent in CKO vs WT mice. At 12 hpi, densely packed MC formed a ring-shaped band circling a "dark" zone nearly devoid of MC, colocalizing with CSN most degenerated zone in the central cornea. In CKO vs WT, the ring center was larger with fewer MC. At 1 dpi, the entire cornea was filled with MC; however, MC density was lower in CKO mice. An MPO assay showed decreased neutrophils in PA-infected cornea of CKO mice. This led to a decreased severity of PA keratitis at 3 dpi. ConclusionsThis double-tracing model reveals the interplay between CSN and MC during PA keratitis with greater clarity, providing new insights into PA keratitis. CSN-imposed modulation on innate immunity is most impressive within 24 hours after infection. Functionally, the miR-183C in CSN modulates CSN density and the dynamics of MC fluxes-a neuroimmune interaction in display.

immunology↗

bioRxiv2025

Effect of perchlorate on biocementation capable bacteria and Martian bricks

With the recent discovery of perchlorate (0.5-1%) in Martian regolith, more experiments related to the impact of perchlorate on microbial life are crucial to understanding the possibility of earth life forms that could sustain on the Martian terrain. While we are familiar with the idea of bioconsolidated Martian bricks made via Microbially Induced Calcite Precipitation (MICP), studies on the effect of perchlorate on Martian bricks & biocementation capable microbes have been obscure. In this work, we investigated the effect of perchlorate (MgClO4- salt) on a lab-isolated biocementation capable bacteria & Martian bricks bioconsolidated by the same, with 1% perchlorate in Mars Global Simulant-1 (MGS-1). The screening of biocementation-capable bacteria involved phenol red assay for urease activity followed by Scanning Electron Microscopy (SEM) and X-ray diffraction (XRD) study of the precipitate formed through MICP via ureolytic pathway. The biocementation capable bacterium SI_IISc_isolate was found phylogenetically closest to Sporosarcina pasteurii strain S2135, its draft genome being approximately 3.69 Mb. To understand the effect of perchlorate on SI_IISc_isolate, we majorly relied on Gram-staining & SEM. The negative effect of perchlorate stress on the isolate was evident by its decreased growth in the presence of varying concentrations of perchlorate through plate assays, growth curve studies in broth & live-dead staining. Gram-staining study and SEM both revealed that perchlorate induces the release of extracellular matrix (ECM) and promotes clustering of cells by the bacteria, which we termed as multicellularity-like behavior. Further, we constructed Martian bricks with Martian Global Simulant (MGS-1) along with 1% perchlorate, utilizing the microbially induced calcite precipitation ability of the Sporosarcina sp. strain SI_IISc_isolate via ureolysis, following an established protocol at our lab. The bioconsolidation experiments showed that in the presence of a natural adhesive - guar gum, perchlorate tends to significantly improve the compressive strength of Martian bricks. However, the end result eventually relies on the overall effect of various additives in the regolith.

bioengineering↗

bioRxiv2025

Inhibiting fibronectin assembly in the breast tumor microenvironment increases cell death and improves response to doxorubicin

PurposeEffective therapies for solid tumors, including breast cancers, are hindered by several roadblocks that can be largely attributed to the fibrotic extracellular matrix (ECM). Fibronectin (FN) is a highly upregulated ECM component in the fibrotic tumor stroma and is associated with poor patient prognosis. This study aimed to investigate the therapeutic potential of an anti-fibrotic peptide that specifically targets FN and blocks the fibrillar assembly of FN. MethodsTo target FN, we used PEGylated Functional Upstream Domain (PEG-FUD), which binds to the 70 kDa N-terminal region of FN with high affinity, localizes to mammary tumors, and potently inhibits FN assembly in vitro and in vivo. Here, we used the 4T1 tumor model to investigate the efficacy and mechanisms of PEG-FUD to inhibit tumor growth. ResultsOur data demonstrates that PEG-FUD monotherapy reduces tumor growth without systemic toxicity. Analysis of the tumor microenvironment revealed that PEG-FUD effectively inhibited FN matrix assembly within tumors and reduced adhesion-mediated signaling through 5 integrin and FAK leading to enhanced tumor cell death. Notably, signaling through FAK has been associated with resistance mechanisms to doxorubicin (DOX). Therefore, we tested the combination of PEG-FUD and Dox, which significantly reduced tumor growth by 60% compared to vehicle control and 30% compared to Dox monotherapy. ConclusionsOur findings demonstrate that PEG-FUD significantly modifies the peritumoral ECM of breast cancer, leading to increased tumor cell death, and potentiates the efficacy of conventional breast cancer therapy.

cancer biology↗

bioRxiv2025

Inducible re-epithelialization of cancer cells increases autophagy and DNA damage: implications for breast cancer dormancy

Epithelial lineage differentiation is pivotal to mammary gland development and it can pause metastasis of breast cancer (BC) by inducing tumor dormancy. To simulate this, we expressed epithelial genes in mesenchymal BC cells. Inducible expression of the epithelial OVOL genes in metastatic BC cells suppressed proliferation and migration. We found that C1ORF116, an OVOLs target, is susceptible to genetic and epigenetic aberrations in BC. It is regulated by steroids and functions as a putative autophagy receptor that inhibits antioxidants like thioredoxin. Accordingly, boosting epithelialization lowered glutathione, elevated reactive oxygen species and increased both DNA oxidation and double strand breaks. Epithelialization also associated with redistribution of NRF2 and an altered interplay among p38, ATM, and the other kinases regulating the DNA damage response. Hence, hormonal regulation of OVOLs and chronic stress might permit epithelial differentiation and retard exit from dormancy, while altering redox homeostasis and permitting DNA damage accumulation, which may awaken dormant tumors.

cancer biology↗

bioRxiv2025

TMPRSS2-ERG confers resistance to antiandrogens: mechanism and therapeutic implications

Approximately 50% of prostate cancer (PCa) patients harbor fusions involving the TMPRSS2 and ERG genes. Despite this, tailored therapies targeting the fused gene, tERG, remain undeveloped. Our study analyzed biopsy samples from two clinical trials assessing the efficacies of androgen receptor (AR) signaling inhibitors (ARSIs). The results revealed that tERG promotes resistance to ARSIs and is associated with elevated levels of the glucocorticoid receptor (GR). Subsequent assays showed that GR directly interacts with tERG, alleviates allosteric autoinhibition and prevents chemotherapy-induced tERG degradation. In PCa models, either inhibiting GR or lowering cortisol levels suppressed tumor growth in tERG-positive models, but not in fusion-negative models. In addition, patient-derived fusion-positive xenografts displayed enhanced sensitivity to combined GR and AR inhibitors. Collectively, these findings highlight TMPRSS2-ERG as a new biomarker and propose that simultaneous inhibition of GR and AR may specifically benefit tERG-positine patients. However, GR stimulatory corticosteroid therapies may not be advisable for this patient subgroup.

cancer biology↗

bioRxiv2025

MLC1 alteration in iPSCs give rise to disease-like cellular vacuolation phenotype in the astrocyte lineage

BackgroundMegalencephalic leukoencephalopathy with subcortical cysts (MLC), a rare and progressive neurodegenerative disorder involving the white matter, is not adequately recapitulated by current disease models. Somatic cell reprogramming, along with advancements in genome engineering, may allow the establishment of in-vitro human models of MLC for disease modeling and drug screening. In this study, we utilized cellular reprogramming and gene-editing techniques to develop induced pluripotent stem cell (iPSC) models of MLC to recapitulate the cellular context of the classical MLC-impacted nervous system. MethodsSomatic cell reprogramming of peripheral patient-derived blood mononuclear cells (PBMCs) was used to develop iPSC models of MLC. CRISPR-Cas9 system-based genome engineering was also utilized to create the MLC1 knockout model of the disease. Directed differentiation of iPSCs to neural stem cells (NSCs) and astrocytes was performed in a 2D cell culture format, followed by various cellular and molecular biology approaches, to characterize the disease model. ResultsMLC iPSCs established by somatic cell reprogramming and genome engineering were well characterized for pluripotency. iPSCs were subsequently differentiated to disease-relevant cell types: neural stem cells (NSCs) and astrocytes. RNA sequencing profiling of MLC NSCs revealed a set of differentially expressed genes related to neurological disorders and epilepsy, a common clinical finding within MLC disease. This gene set can serve as a target for drug screening for the development of a potential therapeutic for this disease. Upon differentiation to the more disease relevant cell type-astrocytes, MLC-characteristic vacuoles were clearly observed, which were distinctly absent from controls. This emergence recapitulated a distinguishing phenotypic marker of the disease. ConclusionThrough the creation and analyses of iPSC models of MLC, our work addresses a critical need for relevant cellular models of MLC for use in both disease modeling and drug screening assays. Further investigation can utilize MLC iPSC models, as well as generated transcriptomic data sets and analyses, to identify potential therapeutic interventions for this debilitating disease.

cell biology↗

bioRxiv2025

Biopolymers can be used for consolidation of lunar and Martian regoliths

Creating long-term extraterrestrial habitats to support continuous human occupation requires structures that can bear load, while remaining resilient to large temperature fluctuations. Exploiting locally available regolith is part of a paradigm termed in situ resource utilization (ISRU) that advocates minimal dependence on terrestrial supplies via local resource exploitation for construction. In this work, we report on a consolidation method for making load-bearing structures out of lunar and Martian regolith simulants using biopolymer binders. We quantify the compressive and tensile strength of the final brick-like structures, termed biopolymer regolith composites, and investigate their dependence on biopolymer concentration and chemistry. A pressure-assisted die casting process is developed that can produce bricks with compressive strengths of [~] 15 MPa and tensile strengths of around 2 MPa, from regolith simulants. We finally report on the performance of these bricks under large temperature and pressure variations and find that their strengths remain unchanged. We believe that this makes biopolymer regolith composite bricks suitable candidates for use in harsh extraterrestrial environments, while adhering to the guidelines of the ISRU paradigm. Keyword: Lunar regolith; Martian regolith; Space habitation; Extraterrestrial construction; Biopolymers; Regolith simulant

bioengineering↗

bioRxiv2024

Salt-induced reduction of hyperswarming motility in Bacillus cereus MHS is associated with reduced flagellation, reduced nanotube formation and reduction in expression of quorum sensing regulator

Bacteria have been known to thrive in challenging environmental niches through diverse phenomena. Swarming is one such favourable adaptation that could help bacteria survive extreme conditions. Therefore, targeting swarming is crucial for improving our understanding of bacterial motility and preventing related infections. Bacillus cereus, which causes food poisoning, has been shown to perform swarming, and salts like NaCl can act as a food preservative to control bacterial growth. In order to explore the possible alterations in the swarming of Bacillus cereus in the presence of salt, the present study encompasses the effect of NaCl on the swarming characteristics of a natural bacterial isolate, Bacillus cereus MHS, with a hyperswarming phenotype. Here we report that the presence of an increased amount of NaCl in growth media could induce a reduction in swarming motility and swarming pattern of MHS on Luria agar plates and the observed reduction in swarming was associated with the reduced flagellation and reduction in bacterial nanotube formation. Gene expression studies supported the phenotypic and ultrastructure observations as the expressions of bfla and ymdb genes, involved in formations of flagella and nanotubes respectively, were found to be reduced in the swarming MHS cells in the presence of increased NaCl in swarm media. It was also observed that the salt-induced reduction in swarming of MHS is associated with the reduced expression of the quorum sensing regulator gene plcR. This study first time reports the bacterial nanotubes in a Bacillus cereus strain and indicates a possible link between the bacterial nanotube formation and hyperswarming phenotype in Bacillus cereus MHS.

microbiology↗

bioRxiv2024

Ex vivo Model of Functioning Human Lymph Node Reveals Pivotal Role for Innate Lymphoid Cells and Stromal Populations in Response to Vaccine Adjuvant

Immunological processes that underpin the administration of therapeutics and vaccines are poorly defined due to a lack of models which faithfully recapitulate human immune responses. Inbred mice lack the diversity inherent to people, while the microanatomical organisation of human tissue is lost in isolated cell suspensions. We describe precision-cut human lymph node (LN) slices as architecturally-preserved, functioning lymphoid tissue model system, and explore early inflammatory responses to a potent vaccine liposomal adjuvant containing a TLR4-agonist and QS21 saponin. Combining scRNA-seq, multiplexed immunofluorescence and secretome analysis, we dissect direct and indirect signalling pathways in both leukocytes and stromal cells to reveal communication networks linking innate and adaptive immunity. Application of molecular inhibitors reveals that secretion of IL-1{beta}, but not IL-18, is TLR4-dependent in human LN. Retaining donor-to-donor immune variation, this ex vivo LN model system enables the study of pathways previously difficult to observe in humans, paving the way towards precision medicine.

immunology↗

bioRxiv2024

Immunomodulatory Role of the Stem Cell Circadian Clock in Muscle Repair

The circadian clock orchestrates vital physiological processes such as metabolism, immune function, and tissue regeneration, aligning them with the optimal time of day. This study identifies an intricate interplay between the circadian clock within muscle stem cells (SCs) and their capacity to modulate the immune microenvironment during muscle regeneration. We uncover that the SC clock provokes time of day-dependent induction of inflammatory response genes following injury, particularly those related to neutrophil activity and chemotaxis. These responses are driven by rhythms of cytosolic regeneration of the signaling metabolite NAD+. We demonstrate that genetically enhancing cytosolic NAD+ regeneration in SCs is sufficient to induce robust inflammatory responses that significantly influence muscle regeneration. Furthermore, using mononuclear single-cell sequencing of the regenerating muscle niche, we uncover a key role for the cytokine CCL2 in mediating SC-neutrophil crosstalk in a time of day-dependent manner. Our findings highlight a crucial intersection between SC metabolic shifts and immune responses within the muscle microenvironment, dictated by the circadian rhythms, and underscore the potential for targeting circadian and metabolic pathways to enhance tissue regeneration.

developmental biology↗

bioRxiv2024

A benchmark comparison of CRISPRn guide-RNA design algorithms and generation of small single and dual-targeting libraries to boost screening efficiency

Genome-wide CRISPR sgRNA libraries have emerged as transformative tools to systematically probe gene function. While these libraries have been iterated over time to be more efficient, their large size limits their use in some applications. Here, we benchmarked publicly available genome-wide single-targeting sgRNA libraries and evaluated dual targeting as a strategy for pooled CRISPR loss-of-function screens. We leveraged this data to design two minimal genome-wide human CRISPR-Cas9 libraries that are 50% smaller than other libraries and that preserve specificity and sensitivity, thus enabling broader deployment at scale.

molecular biology↗

bioRxiv2024

Therapeutic Activity of Resolvin D1 (RvD1) in Murine MASH

Background and AimsRecent studies have highlighted the beneficial effect of resolvin D1 (RvD1), a DHA-derived specialized pro-resolving mediator, on metabolic dysfunction-associated steatohepatitis (MASH), but the underlying mechanisms are not well understood. Our study aims to determine the mechanism by which RvD1 protects against MASH progression. MethodsRvD1 was administered to mice with experimental MASH, followed by bulk and single-cell RNA sequencing analysis. Primary cells including bone marrow-derived macrophages (BMDMs), Kupffer cells, T cells, and primary hepatocytes were isolated to elucidate the effect of RvD1 on inflammation, cell death, and fibrosis regression genes. ResultsHepatic tissue levels of RvD1 were decreased in murine and human MASH, likely due to an expansion of pro-inflammatory M1-like macrophages with diminished ability to produce RvD1. Administering RvD1 reduced inflammation, cell death, and liver fibrosis. Mechanistically, RvD1 reduced inflammation by suppressing the Stat1-Cxcl10 signaling pathway in macrophages and prevented hepatocyte death by alleviating ER stress-mediated apoptosis. Moreover, RvD1 induced Mmp2 and decreased Acta2 expression in hepatic stellate cells (HSCs), and promoted Mmp9 and Mmp12 expression in macrophages, leading to fibrosis regression in MASH. ConclusionsRvD1 reduces Stat1-mediated inflammation, mitigates ER stress-induced apoptosis, and promotes MMP-mediated fibrosis regression in MASH. This study highlights the therapeutic potential of RvD1 to treat MASH. Impact and implicationsMetabolic dysfunction-associated steatohepatitis (MASH) is an increasing healthcare burden worldwide. Current treatments for MASH and its sequelae are very limited. Recent studies highlighted the therapeutic benefit of specialized pro-resolving mediators (SPMs), including resolvin D1 (RvD1), in liver diseases. However, the mechanisms underlying these beneficial effects are not well understood. Based on unbiased transcriptomic analyses using bulk and single-cell RNA sequencing in RvD1-treated MASH livers, we show that RvD1 suppresses Stat1-mediated inflammatory responses and ER stress-induced apoptosis, and induces gene expression related to fibrosis regression. Our study provides new mechanistic insight into the role of RvD1 in MASH and highlights its therapeutic potential to treat MASH. HighlightsO_LILiver RvD1 levels are decreased in MASH patients and MASH mice C_LIO_LIRvD1 administration suppresses Stat1-mediated inflammatory response C_LIO_LIRvD1 administration alleviates ER stress-induced apoptosis C_LIO_LIRvD1 administration induces fibrosis regression gene expression C_LI

pharmacology and toxicology↗

bioRxiv2023

G6PD deficiency mediated impairment of iNOS and lysosomal acidification affecting phagocytotic clearance in microglia in response to SARS-CoV-2

The glucose-6-phosphate dehydrogenase (G6PD) deficiency is X-linked and is the most common enzymatic deficiency disorder globally. It is a crucial enzyme for the pentose phosphate pathway and produces NADPH, which plays a vital role in the regulation of oxidative stress of many cell types. The deficiency of G6PD causes hemolytic anemia, diabetes, cardiovascular and neurological disorders. Notably, the patient with G6PD deficiency was severely affected by SARS-CoV-2 and showed prolonged COVID-19 symptoms, neurological impacts, and high mortality. However, the mechanism of COVID-19 severity in G6PD deficient patients is still ambiguous. Here, using a CRISPR-edited G6PD deficient human microglia cell culture model, we observed a significant reduction in NADPH and an increase in basal reactive oxygen species (ROS) in microglia. Interestingly, the deficiency of the G6PD-NAPDH axis impairs induced nitric oxide synthase (iNOS) mediated nitric oxide (NO) production which plays a fundamental role in inhibiting viral replication. Surprisingly, we also observed that the deficiency of the G6PD-NADPH axis reduced lysosomal acidification, which further abrogates the lysosomal clearance of viral particles. Thus, impairment of NO production and lysosomal acidification as well as redox dysregulation in G6PD deficient microglia altered innate immune response, promoting the severity of SARS-CoV-2 pathogenesis.

cell biology↗

bioRxiv2023

Olfactory system structure and function in newly hatched and adult locusts

An important question in neuroscience is how sensory systems change as animals grow and interact with the environment. Exploring sensory systems in animals as they develop can reveal how networks of neurons process information as the neurons themselves grow and the needs of the animal change. Here we compared the structure and function of peripheral parts of the olfactory pathway in newly hatched and adult locusts. We found that populations of olfactory sensory neurons (OSNs) in hatchlings and adults responded with similar tunings to a panel of odors. The morphologies of local neurons (LNs) and projection neurons (PNs) in the antennal lobes (ALs) were very similar in both age groups, though they were smaller in hatchlings, they were proportional to overall brain size. The odor evoked responses of LNs and PNs were also very similar in both age groups, characterized by complex patterns of activity including oscillatory synchronization. Notably, in hatchlings, spontaneous and odor-evoked firing rates of PNs were lower, and LFP oscillations were lower in frequency, than in the adult. Hatchlings have smaller antennae with fewer OSNs; removing antennal segments from adults also reduced LFP oscillation frequency. Thus, consistent with earlier computational models, the developmental increase in frequency is due to increasing intensity of input to the oscillation circuitry. Overall, our results show that locusts hatch with a fully formed olfactory system that structurally and functionally matches that of the adult, despite its small size and lack of prior experience with olfactory stimuli.

neuroscience↗

bioRxiv2023

ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction

Since the release of ModelSEED in 2010, the systems biology research community has used the ModelSEED genome-scale metabolic model reconstruction pipeline to build over 200,000 draft metabolic reconstructions that support hundreds of publications. Here we describe the first comprehensive update to this reconstruction tool, with new features such as (i) a dramatically improved representation of energy metabolism, which ensures that models produce accurate amounts of ATP per mol of nutrient consumed; (ii) a new template for Archaea model reconstruction; and (iii) a significantly improved curation of all metabolic pathways with mappings to RAST subsystems annotations. We applied the improved pipeline to build and analyze core and genome-scale models for Archaea and Bacteria genomes in KEGG. The new ModelSEED pipeline generates larger models that possess more reactions and genes and require fewer gap-filled reactions. In addition, we see conserved patterns in the ATP biosynthesis mechanism across phylogeny, and identify clades where our understanding of energy biosynthesis is still poor. ModelSEED v2 is available through KBase and the ModelSEED website (https://modelseed.org/), which supports reconstruction, gap-filling, flux balance analysis and model export through a modern web interface.

systems biology↗

bioRxiv2023

Information- and Communication-Centric Approach in Cell Metabolism for Analyzing Behavior of Microbial Communities

Microorganisms naturally form community ecosystems to improve fitness in diverse environments and conduct otherwise intractable processes. Microbial communities are therefore central to biogeochemical cycling, human health, agricultural productivity, and technologies as nuanced as nanotechnology-enabled devices; however, the combinatorial scaling of exchanges with the environment that predicate community functions are experimentally untenable. Several computational tools have been presented to capture these exchanges, yet, no attempt has been made to understand the total information flow to a community from its environment. We therefore adapted a recently developed model for singular organisms, which blends molecular communication and the Shannon Information theory to quantify information flow, to communities and exemplify this expanded model on idealized communities: one of Escherichia coli (E. coli) and Pseudomonas fluorescens to emulate an ecological community and the other of Bacteroides thetaiotaomicron (B. theta) and Kleb Ciella to emulate a human microbiome interaction. Each of these sample communities exhibit critical syntrophy in certain environmental conditions, which should be evident through our community mutual information model. We further explored alternative frameworks for constructing community genome-scale metabolic models (GEMs) - mixed-bag and compartmentalized. Our study revealed that information flow is greater through communities than isolated models, and that the mixed-bag framework conducts greater information flow than the compartmentalized framework for community GEMs, presumably because the latter is encumbered with transport reactions that are absent in the former. This community Mutual Information model is furthermore wrapped as a KBase Application (Run Flux Mutual Information Analysis, RFMIA) for optimum accessibility to biological investigators. We anticipate that this unique quantitative approach to consider information flow through metabolic systems will accelerate both basic and applied discovery in diverse biological fields. Author SummaryMicroorganisms frequently communicate information via information-bearing molecules, which must be fundamentally understood to engineer biological cells that properly engage with their environments, such as the envisioned Internet of Bio-NanoThings. The study of these molecular communications has employed information and communication theory to analyze the exchanged information via chemical reactions and molecular transport. We introduce an information- and communication-centric computational approach to estimate the information flow in biological cells and its impacts on the behavior of single organisms and communities. This study complements our previous work of cell metabolism by developing an end-to-end perspective of molecular communication based on enzyme-regulated reactions. We explore the mutual information using Shannon information theory, measured in bits, between influential nutrients and cellular growth rate. The developed RFMIA computational tool is deployed in the U.S. Department of Energys Systems Biology Knowledgebase, where it quantitatively estimates information flow in both organism and community metabolic networks and extends recent developments in computer communications to explore and explain a new biology for the open-source community.

bioinformatics↗