Vitamin E alleviates chlorpyrifos induced glutathione depletion, lipid peroxidation and iron accumulation to inhibit ferroptosis in hepatocytes and mitigate toxicity in zebrafish.

Organophosphates, a widely used group of pesticides, can cause severe toxicity in human beings and other non-target organisms. Liver, being the primary site for xenobiotic metabolism, is extremely vulnerable to xenobiotic-induced toxicity. Considering the numerous vital functions performed by the liver, including xenobiotic detoxification, protecting this organ from the ubiquitous pesticides in our food and environment is essential for maintaining homeostasis. In this study, we have investigated the impact of the organophosphate pesticide, Chlorpyrifos (CPF), on zebrafish liver at a concentration (300 µg/L) which is environmentally realistic. We have also demonstrated the role of dietary supplementation of α-tocopherol or Vitamin E (Vit E) (500 mg/kg feed) in mitigating pesticide-induced liver toxicity. Mechanistically, we showed that Vit E resulted in significant elevation of the Nrf2 and its downstream antioxidant enzyme activities and gene expressions, especially that of GST and GPx, resulting in reduction of CPF-induced intracellular lipid ROS and hepatic LPO. Further interrogation, such as analysis of GSH: GSSG ratio, intracellular iron concentration, iron metabolizing genes, mitochondrial dysfunction etc. revealed that CPF induces ferroptosis which can be reversed by Vit E supplementation. Ultimately, reduced concentration of CPF in zebrafish serum and flesh highlighted the role of Vit E in ameliorating CPF toxicity.

Low-latency gravitational wave alert products and their performance at the time of the fourth LIGO-Virgo-KAGRA observing run.

Multimessenger searches for binary neutron star (BNS) and neutron star-black hole (NSBH) mergers are currently one of the most exciting areas of astronomy. The search for joint electromagnetic and neutrino counterparts to gravitational wave (GW)s has resumed with ALIGO's, AdVirgo's and KAGRA's fourth observing run (O4). To support this effort, public semiautomated data products are sent in near real-time and include localization and source properties to guide complementary observations. In preparation for O4, we have conducted a study using a simulated population of compact binaries and a mock data challenge (MDC) in the form of a real-time replay to optimize and profile the software infrastructure and scientific deliverables. End-toend performance was tested, including data ingestion, running online search pipelines, performing annotations, and issuing alerts to the astrophysics community. We present an overview of the low-latency infrastructure and the performance of the data products that are now being released during O4 based on the MDC. We report the expected median latency for the preliminary alert of full bandwidth searches (29.5 s) and show consistency and accuracy of released data products using the MDC. We report the expected median latency for triggers from early warning searches (-3.1 s), which are new in O4 and target neutron star mergers during inspiral phase. This paper provides a performance overview for LIGO-Virgo-KAGRA (LVK) low-latency alert infrastructure and data products using theMDCand serves as a useful reference for the interpretation of O4 detections.

Assessing combinatorial diversity of aureochrome bZIPs through genome-wide screening.

Aureochromes are unique blue light-responsive LOV (Light Oxygen Voltage) photoreceptors cum basic leucine zipper (bZIP) transcription factors (TFs), present exclusively in photosynthetic marine stramenopiles. Considering the availability of the complete genome sequence, this study focuses on aureochromes from Ectocarpus siliculosus. Aureochromes mediate light-regulated developmental responses in this brown photosynthetic algae. Both the LOV sensor and the bZIP effector shows overall sequence-structure conservation. The structurally similar LOV+bZIP modules of aureochrome homologs/paralogs prefer a dimeric state. Besides a heterogeneous linker connecting the sensor-effector and a flexible N-terminal region, the sequence composition of both domains is vital. Aureochromes execute diverse cellular responses in different photosynthetic stramenopiles - though their activities can vary even within a given algal species. Therefore, it is important to understand whether aureochromes select dimerization partners from the same family or interact with other bZIPs as well. To regulate multifarious biological activities, it is possible that aureochromes activate the global TF interaction network. Following homo/heterodimer modeling, we address the compatibility of dimerization partners by screening through heptad repeats. We evaluate the dimer interface area in terms of gain in solvation energy and the number of hydrogen bonds/salt bridge interactions. We further explore the relative stability of these structures from a graph-theoretic perspective through well-studied measures such as the energy of the graph, average participation coefficient, and betweenness centrality. Furthermore, we also conduct an information-theoretic analysis using hitherto understudied measures such as network information centrality and Kullback-Leibler divergence. We find that all our investigations into the relative stability of the dimers using diverse methods from bioinformatics, network science, and, information theory are in harmonious agreement. Coupling preferences of monomers in aureochromes can be further translated to design novel optogenetic tools useful for understanding human development and disease.

Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1.

Ample evidence indicates that the gut microbiome is a tumor-extrinsic factor associated with antitumor response to anti-programmed cell death protein-1 (PD-1) therapy, but inconsistencies exist between published microbial signatures associated with clinical outcomes. To resolve this, we evaluated a new melanoma cohort, along with four published datasets. Time-to-event analysis showed that baseline microbiota composition was optimally associated with clinical outcome at approximately 1 year after initiation of treatment. Meta-analysis and other bioinformatic analyses of the combined data show that bacteria associated with favorable response are confined within the Actinobacteria phylum and the Lachnospiraceae/Ruminococcaceae families of Firmicutes. Conversely, Gram-negative bacteria were associated with an inflammatory host intestinal gene signature, increased blood neutrophil-to-lymphocyte ratio, and unfavorable outcome. Two microbial signatures, enriched for Lachnospiraceae spp. and Streptococcaceae spp., were associated with favorable and unfavorable clinical response, respectively, and with distinct immune-related adverse effects. Despite between-cohort heterogeneity, optimized all-minus-one supervised learning algorithms trained on batch-corrected microbiome data consistently predicted outcomes to programmed cell death protein-1 therapy in all cohorts. Gut microbial communities (microbiotypes) with nonuniform geographical distribution were associated with favorable and unfavorable outcomes, contributing to discrepancies between cohorts. Our findings shed new light on the complex interaction between the gut microbiome and response to cancer immunotherapy, providing a roadmap for future studies.

Mass Testing and Proactiveness Affect Epidemic Spreading.

The detection and management of diseases become quite complicated when pathogens contain asymptomatic phenotypes amongst their ranks, as evident during the recent COVID-19 pandemic. Spreading of diseases has been studied extensively under the paradigm of susceptible-infected-recovered-deceased (SIRD) dynamics. Various game-theoretic approaches have also addressed disease spread, many of which consider S , I , R , and D as strategies rather than as states. Remarkably, most studies from the above approaches do not account for the distinction between the symptomatic or asymptomatic aspect of the disease. It is well-known that precautionary measures like washing hands, wearing masks and social distancing significantly mitigate the spread of many contagious diseases. Herein, we consider the adoption of such precautions as strategies and treat S , I , R , and D as states. We also attempt to capture the differences in epidemic spreading arising from symptomatic and asymptomatic diseases on various network topologies. Through extensive computer simulations, we examine that the cost of maintaining precautionary measures as well as the extent of mass testing in a population affects the final fraction of socially responsible individuals. We observe that the lack of mass testing could potentially lead to a pandemic in case of asymptomatic diseases. Network topology also seems to play an important role. We further observe that the final fraction of proactive individuals depends on the initial fraction of both infected as well as proactive individuals. Additionally, edge density can significantly influence the overall outcome. Our findings are in broad agreement with the lessons learnt from the ongoing COVID-19 pandemic.

Network approach to mutagenesis sheds insight on phage resistance in mycobacteria.

MOTIVATION: A rigorous yet general mathematical approach to mutagenesis, especially one capable of delivering systems-level perspectives would be invaluable. Such systems-level understanding of phage resistance is also highly desirable for phage-bacteria interactions and phage therapy research. Independently, the ability to distinguish between two graphs with a set of common or identical nodes and identify the implications thereof, is important in network science. RESULTS: Herein, we propose a measure called shortest path alteration fraction (SPAF) to compare any two networks by shortest paths, using sets. When SPAF is one, it can identify node pairs connected by at least one shortest path, which are present in either network but not both. Similarly, SPAF equalling zero identifies identical shortest paths, which are simultaneously present between a node pair in both networks. We study the utility of our measure theoretically in five diverse microbial species, to capture reported effects of well-studied mutations and predict new ones. We also scrutinize the effectiveness of our procedure through theoretical and experimental tests on Mycobacterium smegmatis mc2155 and by generating a mutant of mc2155, which is resistant to mycobacteriophage D29. This mutant of mc2155, which is resistant to D29 exhibits significant phenotypic alterations. Whole-genome sequencing identifies mutations, which cannot readily explain the observed phenotypes. Exhaustive analyses of protein-protein interaction network of the mutant and wild-type, using the machinery of topological metrics and differential networks does not yield a clear picture. However, SPAF coherently identifies pairs of proteins at the end of a subset of shortest paths, from amongst hundreds of thousands of viable shortest paths in the networks. The altered functions associated with the protein pairs are strongly correlated with the observed phenotypes. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Gut Microbiome Directs Hepatocytes to Recruit MDSCs and Promote Cholangiocarcinoma.

Gut dysbiosis is commonly observed in patients with cirrhosis and chronic gastrointestinal disorders; however, its effect on antitumor immunity in the liver is largely unknown. Here we studied how the gut microbiome affects antitumor immunity in cholangiocarcinoma. Primary sclerosing cholangitis (PSC) or colitis, two known risk factors for cholangiocarcinoma which promote tumor development in mice, caused an accumulation of CXCR2+ polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC). A decrease in gut barrier function observed in mice with PSC and colitis allowed gut-derived bacteria and lipopolysaccharide to appear in the liver and induced CXCL1 expression in hepatocytes through a TLR4-dependent mechanism and an accumulation of CXCR2+ PMN-MDSCs. In contrast, neomycin treatment blocked CXCL1 expression and PMN-MDSC accumulation and inhibited tumor growth even in the absence of liver disease or colitis. Our study demonstrates that the gut microbiome controls hepatocytes to form an immunosuppressive environment by increasing PMN-MDSCs to promote liver cancer. SIGNIFICANCE: MDSCs have been shown to be induced by tumors and suppress antitumor immunity. Here we show that the gut microbiome can control accumulation of MDSCs in the liver in the context of a benign liver disease or colitis.See related commentary by Chagani and Kwong, p. 1014.This article is highlighted in the In This Issue feature, p. 995.

Human NK cells prime inflammatory DC precursors to induce Tc17 differentiation.

Adaptive immune responses are acknowledged to evolve from innate immunity. However, limited information exists regarding whether encounters between innate cells direct the generation of specialized T-cell subsets. We aim to understand how natural killer (NK) cells modulate cell-mediated immunity in humans. We found that human CD14+CD16- monocytes that differentiate into inflammatory dendritic cells (DCs) are shaped at the early stages of differentiation by cell-to-cell interactions with NK cells. Although a fraction of monocytes is eliminated by NK-cell-mediated cytotoxicity, the polarization of interferon-γ (IFN-γ) at the NKp30-stabilized synapses triggers a stable IFN-γ signature in surviving monocytes that persists after their differentiation into DCs. Notably, NK-cell-instructed DCs drive the priming of type 17 CD8+ T cells (Tc17) with the capacity to produce IFN-γ and interleukin-17A. Compared with healthy donors, this cellular network is impaired in patients with classical NK-cell deficiency driven by mutations in the GATA2 gene. Our findings reveal a previously unrecognized connection by which Tc17-mediated immunity might be regulated by NK-cell-mediated tuning of antigen-presenting cells.

Residue interaction dynamics in Vaucheria aureochrome1 light-oxygen-voltage: Bridging theory and experiments.

Allosteric communication is the basis of signaling and information transfer. Collective interactions between amino acid residues, which are spatially distributed in the three dimensional structure of a protein molecule, form the basis of allosteric network. While the construction of residue interaction graphs (RIG) is based on static crystal structures of proteins, it is important to extract information on protein dynamics to understand allostery. Therefore, quantitative analysis of RIG based on the framework of differential network (DN), is immensely helpful in identifying key amino acid residue interactions within such communication pathways. While the simultaneous availability of protein structures from two different states is essential for DN, there are additional challenges. Crystallographic artifacts like nonbiological dimeric arrangements within the crystal lattice automatically influence the construction and eventually the interpretation of RIG. Therefore, experimental validation of predictions from the analyses of RIG is naturally scarce in the literature. Herein, we study the photo sensor domain of the signaling photoreceptor transcription factor, aureochrome1, to understand light-driven signaling. We perform direct experiments to verify the predictions from RIG using the machinery of DN. However, the agreement leaves scope for improvement. We then discuss the notion of quaternary structure alignment to obtain a biologically meaningful dimer. Thence, we reconstruct the RIG and reanalyze the modified structure. Results of these reanalyses render far superior agreement with experiments. Therefore, this notion of addressing crystallographic biases provides a fresh yet general approach for reconciliation of theory and experiments. It is applicable beyond the present case to all signaling proteins in general.

Modeling Phage-Bacteria Dynamics.

Phage-bacteria interaction is a classic example of competitive coevolution in nature. Mathematical modeling of such interactions furnishes new insight into the dynamics of phage and bacteria. Besides its intrinsic value, a somewhat underutilized aspect of such insight is that it can provide beneficial inputs toward better experimental design. In this chapter, we discuss several modeling techniques that can be used to study the dynamics between phages and their host bacteria. Monte Carlo simulations and differential equations (both ordinary and delay differential equations) can be used to successfully model phage-bacteria dynamics in well-mixed populations. The presence of spatial restrictions in the interaction media significantly affects the dynamics of phage-bacteria interactions. For such cases, techniques like cellular automata and reaction-diffusion equations can be used to capture these effects adequately. We discuss details of the modeling techniques with specific examples.

Role of a 19S Proteasome Subunit- PSMD10Gankyrin in Neurogenesis of Human Neural Progenitor Cells.

PSMD10Gankyrin, a proteasome assembly chaperone, is a widely known oncoprotein which aspects many hall mark properties of cancer. However, except proteasome assembly chaperon function its role in normal cell function remains unknown. To address this issue, we induced PSMD10Gankyrin overexpression in HEK293 cells and the resultant large-scale changes in gene expression profile were analyzed. We constituted networks from microarray data of these differentially expressed genes and carried out extensive topological analyses. The overrecurring yet consistent theme that appeared throughout analysis using varied network metrics is that all genes and interactions identified as important would be involved in neurogenesis and neuronal development. Intrigued we tested the possibility that PSMD10Gankyrin may be strongly associated with cell fate decisions that commit neural stem cells to differentiate into neurons. Overexpression of PSMD10Gankyrin in human neural progenitor cells facilitated neuronal differentiation via ß-catenin Ngn1 pathway. Here for the first time we provide preliminary and yet compelling experimental evidence for the involvement of a potential oncoprotein - PSMD10Gankyrin, in neuronal differentiation.

Monte Carlo study with reweighting of uniaxial nematic liquid crystals composed of biaxial molecules.

We present a high accuracy Monte Carlo simulation study of the uniaxial nematic (N_{U}) to isotropic (I) phase transition of a lattice dispersion model of uniaxial nematics composed of biaxial molecules. The N_{U}-I coexistence curve terminating at the Landau critical point has been determined using the multiple histogram reweighting technique. A close investigation reveals a sharp departure in the nature of the N_{U}-I coexistence curve in the temperature-biaxiality parameter phase diagram in comparison to the earlier theoretical (either mean-field or computer simulation) predictions. The coexistence curve shows a change in curvature with increasing value of the degree of molecular biaxiality.

Pressure-induced phase transitions in liquid crystals: A molecular field approach.

A rigorous microscopic treatment of a nematic fluid system based on a pairwise interaction potential is immensely complex. For studying such systems molecular field theories are often the standard method of choice. In this paper we have chosen a simple effective potential U=u_{4}/v^{4}-u_{2}/v^{2}-Au_{2}/v^{2}〈P_{2}〉P_{2}(cosϑ) to study an isothermal-isobaric ensemble describing a liquid crystalline system. Using this we have studied in particular the pressure dependence of liquid crystalline phase transitions.

Modeling Bacteria-Phage Interactions and Its Implications for Phage Therapy.

Bacteriophages are more abundant than any other organism on our planet. The interaction of bacteriophages and bacteria and their coevolution is well known. In this chapter, we describe various aspects of modeling such systems and their dynamics. We explore their interaction in: (i) liquid media, which leads to well-mixed populations and (ii) solid media, where their interaction is spatially restricted. Such modeling, when used in conjunction with experiments would not only shed deep insight into the underlying dynamics but also provide useful clues toward potential therapeutic applications.

Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells.

Primary liver tumors and liver metastasis currently represent the leading cause of cancer-related death. Commensal bacteria are important regulators of antitumor immunity, and although the liver is exposed to gut bacteria, their role in antitumor surveillance of liver tumors is poorly understood. We found that altering commensal gut bacteria in mice induced a liver-selective antitumor effect, with an increase of hepatic CXCR6+ natural killer T (NKT) cells and heightened interferon-γ production upon antigen stimulation. In vivo functional studies showed that NKT cells mediated liver-selective tumor inhibition. NKT cell accumulation was regulated by CXCL16 expression of liver sinusoidal endothelial cells, which was controlled by gut microbiome-mediated primary-to-secondary bile acid conversion. Our study suggests a link between gut bacteria-controlled bile acid metabolism and liver antitumor immunosurveillance.

Assessment of In vivo Antiviral Potential of Datura metel Linn. Extracts against Rabies Virus.

OBJECTIVE: The soxhlet, cold, and ayurvedic extracts of Datura metel Linn. were evaluated for in vivo antirabies activity. MATERIALS AND METHODS: Soxhlet and cold extraction method were used to extract Datura (fruit and seed) extracts, and ayurvedic extraction of Datura was prepared. In vivo toxicity assay was performed as per the OECD 420. LD50 dose was calculated by Reed and Muench method. The in vivo antirabies activity was screened in Swiss albino mice with the virus challenge dose of 10 LD50 (intracerebrally) in both preexposure (PE) and postexposure treatment with oral administration of Datura extracts in Swiss albino mice and observed for 21 days. The virus load in the mice brain was evaluated by TCID50 titration method. RESULTS: Datura (ayurvedic preparation) was found to be nontoxic up to 2000 mg/kg in Swiss albino mice, i.e., 60 mg/30 g of mice, when administered (0.5 ml) orally and observed till 21 days. Up to 20% survival rate on the test group (PE of Datura extracts) up to 14 days postinfection as compared to the virus control group (10 LD50) was observed. No survival rate was observed in the postexposure group of Datura extract; however, the survival time was increased by 4 days as compared to the virus control group. Viral load of the infected mice brain sample was estimated in vero cell line, and 3 log reduction in the virus titer was observed in text group as compared to the virus control, suggesting that Datura extract has an in vivo antirabies activity. CONCLUSION: To the best of our knowledge, this is the first study of in vivo antiviral activity of an ayurvedic preparation of D. metel Linn. against rabies virus. Datura extracts have a potential in vivo antirabies activity. SUMMARY: In the present study, Datura metel Linn. (ayurvedic preparation) extract exhibited survival (20%) in the preexposure (PE) of the virus and the survival time was increased in the postexposure treatment where the disease was established. The mortality was observed, and the viral load was determined by titration method. Abbreviation Used: TCID50: tissue culture infectious dose 50; LD50: lethal dose 50; RV CVS: Rabies virus challenge virus standard; PE: Pre exposure; IC: intracerebral; PI: post infection; FITC: Fluorescein isothiocyanate.

Magnetic Nanoparticle Mediated Steroid Delivery Mitigates Cisplatin Induced Hearing Loss.

Cisplatin (cis-diamminedichloroplatinum) is widely used as a chemotherapeutic drug for genitourinary, breast, lung and head and neck cancers. Though effective in inducing apoptosis in cancer cells, cisplatin treatment causes severe hearing loss among patients. Steroids have been shown to mitigate cisplatin-induced hearing loss. However, steroids may interfere with the anti-cancer properties of cisplatin if administered systemically, or are rapidly cleared from the middle and inner ear and hence lack effectiveness when administered intra-tympanically. In this work, we deliver prednisolone-loaded nanoparticles magnetically to the cochlea of cisplatin-treated mice. This magnetic delivery method substantially reduced hearing loss in treated animals at high frequency compared to control animals or animals that received intra-tympanic methylprednisolone. The method also protected the outer hair cells from cisplatin-mediated ototoxicity.

Use of rapid fluorescent focus inhibition test (RFFIT) for in vitro evaluation of anti-rabies activity.

Even in the twenty-first century, rabies remains one of the most dreaded diseases in many parts of the world. An effective chemotherapeutic still remains elusive. The present study was aimed at in vitro evaluation of crude extracts of Allamanda cathartica and Cynodon dactylon for their potential anti-rabies activity based on the principle of immunofluorescence. The extracts were tested for cytotoxicity and screened for the presence of phytochemicals. While A. cathartica extracts were found to be non-toxic, the CC50 of C. dactylon (water and methanol) cold extracts were found to be 8.17 and 9.20 mg/mL respectively on BHK-21 cell line. Rapid Fluorescent Focus Inhibition Test (RFFIT) was used to evaluate anti-rabies activities of these plants against the rabies challenge virus standard strain. We observed 50% inhibition of 10 TCID50 CVS at 5 mg/mL (IC50) whereas florescence (no inhibition) was observed with A. cathartica extracts. The present study highlights the use of modified RFFIT as a method of choice for testing anti-rabies activity over assays based on evaluation of cytopathic effect.