Association of Altered Plasma Lipidome with Disease Severity in COVID-19 Patients.

The severity of COVID-19 is linked to an imbalanced immune response. The dysregulated metabolism of small molecules and bioactive lipids has also been associated with disease severity. To promote understanding of the disease biochemistry and provide targets for intervention, we applied a range of LC-MS platforms to analyze over 100 plasma samples from patients with varying COVID-19 severity and with detailed clinical information on inflammatory responses (>30 immune markers). This is the third publication in a series, and it reports the results of comprehensive lipidome profiling using targeted LC-MS/MS. We identified 1076 lipid features across 25 subclasses, including glycerophospholipids, sterols, glycerolipids, and sphingolipids, among which 531 lipid features were dramatically changed in the plasma of intensive care unit (ICU) patients compared to patients in the ward. Patients in the ICU showed 1.3-57-fold increases in ceramides, (lyso-)glycerophospholipids, diglycerides, triglycerides, and plasmagen phosphoethanolamines, and 1.3-2-fold lower levels of a cyclic lysophosphatidic acid, sphingosine-1-phosphates, sphingomyelins, arachidonic acid-containing phospholipids, lactosylceramide, and cholesterol esters compared to patients in the ward. Specifically, phosphatidylinositols (PIs) showed strong fatty acid saturation-dependent behavior, with saturated fatty acid (SFA)- and monosaturated fatty acid (MUFA)-derived PI decreasing and polystaturated (PUFA)-derived PI increasing. We also found ~4000 significant Spearman correlations between lipids and multiple clinical markers of immune response with |R| ≥ 0.35 and FDR corrected Q < 0.05. Except for lysophosphatidic acid, lysophospholipids were positively associated with the CD4 fraction of T cells, and the cytokines IL-8 and IL-18. In contrast, sphingosine-1-phosphates were negatively correlated with innate immune markers such as CRP and IL-6. Further indications of metabolic changes in moderate COVID-19 disease were demonstrated in recovering ward patients compared to those at the start of hospitalization, where 99 lipid species were altered (6 increased by 30-62%; 93 decreased by 1.3-2.8-fold). Overall, these findings support and expand on early reports that dysregulated lipid metabolism is involved in COVID-19.

Global transcriptome analysis reveals Salmonella Typhimurium employs nitrate metabolism to combat bile stress.

Salmonella Typhimurium is an enteric pathogen that is highly tolerant to bile. Next-generation mRNA sequencing was performed to analyze the adaptive responses to bile in two S. Typhimurium strains: wild type (WT) and a mutant lacking cold shock protein E (ΔcspE). CspE is an RNA chaperone which is crucial for survival of S. Typhimurium during bile stress. This study identifies transcriptional responses in bile-tolerant WT and bile-sensitive ΔcspE. Upregulation of several genes involved in nitrate metabolism was observed, including fnr, a global regulator of nitrate metabolism. Notably, Δfnr was susceptible to bile stress. Also, complementation with fnr lowered reactive oxygen species and enhanced the survival of bile-sensitive ΔcspE. Importantly, intracellular nitrite amounts were highly induced in bile-treated WT compared to ΔcspE. Also, the WT strain pre-treated with nitrate displayed better growth with bile. These results demonstrate that nitrate-dependent metabolism promotes adaptation of S. Typhimurium to bile.

A comparison between different human hepatocyte models reveals profound differences in net glucose production, lipid composition and metabolism in vitro.

Hepatocytes are responsible for maintaining a stable blood glucose concentration during periods of nutrient scarcity. The breakdown of glycogen and de novo synthesis of glucose are crucial metabolic pathways deeply interlinked with lipid metabolism. Alterations in these pathways are often associated with metabolic diseases with serious clinical implications. Studying energy metabolism in human cells is challenging. Primary hepatocytes are still considered the golden standard for in vitro studies and have been instrumental in elucidating key aspects of energy metabolism found in vivo. As a result of several limitations posed by using primary cells, a multitude of alternative hepatocyte cellular models emerged as potential substitutes. Yet, there remains a lack of clarity regarding the precise applications for which these models accurately reflect the metabolic competence of primary hepatocytes. In this study, we compared primary hepatocytes, stem cell-derived hepatocytes, adult donor-derived liver organoids, immortalized Upcyte-hepatocytes and the hepatoma cell line HepG2s in their response to a glucose production challenge. We observed the highest net glucose production in primary hepatocytes, followed by organoids, stem-cell derived hepatocytes, Upcyte-hepatocytes and HepG2s. Glucogenic gene induction was observed in all tested models, as indicated by an increase in G6PC and PCK1 expression. Lipidomic analysis revealed considerable differences across the models, with organoids showing the closest similarity to primary hepatocytes in the common lipidome, comprising 347 lipid species across 19 classes. Changes in lipid profiles as a result of the glucose production challenge showed a variety of, and in some cases opposite, trends when compared to primary hepatocytes.

Tackling municipal solid waste crisis in India: Insights into cutting-edge technologies and risk assessment.

Municipal Solid Waste (MSW) management is a pressing global concern, with increasing interest in Waste-to-Energy Technologies (WTE-T) to divert waste from landfills. However, WTE-T adoption is hindered by financial uncertainties. The economic benefits of MSW treatment and energy generation must be balanced against environmental impact. Integrating cutting-edge technologies like Artificial Intelligence (AI) can enhance MSW management strategies and facilitate WTE-T adoption. This review paper explores waste classification, generation, and disposal methods, emphasizing public awareness to reduce waste. It discusses AI's role in waste management, including route optimization, waste composition forecasting, and process parameter optimization for energy generation. Various energy production techniques from MSW, such as high-solids anaerobic digestion, torrefaction, plasma pyrolysis, incineration, gasification, biodegradation, and hydrothermal carbonization, are examined for their advantages and challenges. The paper emphasizes risk assessment in MSW management, covering chemical, mechanical, biological, and health-related risks, aiming to identify and mitigate potential adverse effects. Electronic waste (E-waste) impact on human health and the environment is thoroughly discussed, highlighting the release of hazardous substances and their contribution to air, soil, and water pollution. The paper advocates for circular economy (CE) principles and waste-to-energy solutions to achieve sustainable waste management. It also addresses complexities and constraints faced by developing nations and proposes strategies to overcome them. In conclusion, this comprehensive review underscores the importance of risk assessment, the potential of AI and waste-to-energy solutions, and the need for sustainable waste management to safeguard public health and the environment.

Evaluation of the Moonlighting Histone H3 Specific Protease (H3ase) Activity and the Dehydrogenase Activity of Glutamate Dehydrogenase (GDH).

The N-terminus of Histone H3 is proteolytically processed in aged chicken liver. A histone H3 N-terminus specific endopeptidase (named H3ase) has been purified from the nuclear extract of aged chicken liver. By sequencing and a series of biochemical methods including the demonstration of H3ase activity in bacterially expressed GDH, it was established that the H3ase activity was a moonlighting protease activity of glutamate dehydrogenase (GDH). However, the active site for the H3ase in the GDH remains elusive. Here, using cross-linking studies of the homogenously purified H3ase, we show that the GDH and the H3ase remain in the same native state. Further, the H3ase and GDH activities could be uncoupled by partial denaturation of GDH, suggesting strong evidence for the involvement of different active sites for GDH and H3ase activities. Through densitometry of the H3ase clipped H3 products, the H3ase activity was quantified and it was compared with the GDH activity of the chicken liver nuclear GDH. Furthermore, the H3ase mostly remained distributed in the perinuclear area as demonstrated by MNase digestion and immuno-localization of H3ase in chicken liver nuclei, as well as cultured mouse hepatocyte cells, suggesting that H3ase demonstrated regulated access to the chromatin. The present study thus broadly compares the H3ase and GDH activities of the chicken liver GDH.

Development of targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry method for acyl-Coenzyme A covering short- to long-chain species in a single analytical run.

Acyl-CoAs play a significant role in numerous physiological and metabolic processes making it important to assess their concentration levels for evaluating metabolic health. Considering the important role of acyl-CoAs, it is crucial to develop an analytical method that can analyze these compounds. Due to the structural variations of acyl-CoAs, multiple analytical methods are often required for comprehensive analysis of these compounds, which increases complexity and the analysis time. In this study, we have developed a method using a zwitterionic HILIC column that enables the coverage of free CoA and short- to long-chain acyl-CoA species in one analytical run. Initially, we developed the method using an LC-QTOF instrument for the identification of acyl-CoA species and optimizing their chromatography. Later, a targeted HILIC-MS/MS method was created in scheduled multiple reaction monitoring mode using a QTRAP MS detector. The performance of the method was evaluated based on various parameters such as linearity, precision, recovery and matrix effect. This method was applied to identify the difference in acyl-CoA profiles in HepG2 cells cultured in different conditions. Our findings revealed an increase in levels of acetyl-CoA, medium- and long-chain acyl-CoA while a decrease in the profiles of free CoA in the starved state, indicating a clear alteration in the fatty acid oxidation process.

Development of a targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry based lipidomics platform applied to a coronavirus disease severity study.

The importance of lipids seen in studies of metabolism, cancer, the recent COVID-19 pandemic and other diseases has brought the field of lipidomics to the forefront of clinical research. Quantitative and comprehensive analysis is required to understand biological interactions among lipid species. However, lipidomic analysis is often challenging due to the various compositional structures, diverse physicochemical properties, and wide dynamic range of concentrations of lipids in biological systems. To study the comprehensive lipidome, a hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS)-based screening method with 1200 lipid features across 19 (sub)classes, including both nonpolar and polar lipids, has been developed. HILIC-MS/MS was selected due to its class separation property and fatty acyl chain level information. 3D models of class chromatographic retention behavior were established and evaluations of cross-class and within-class interferences were performed to avoid over-reporting these features. This targeted HILIC-MS/MS method was fully validated, with acceptable analytical parameters in terms of linearity, precision, reproducibility, and recovery. The accurate quantitation of 608 lipid species in the SRM 1950 NIST plasma was achieved using multi-internal standards per class and post-hoc correction, extending current databases by providing lipid concentrations resolved at fatty acyl chain level. The overall correlation coefficients (R2) of measured concentrations with values from literature range from 0.64 to 0.84. The applicability of the developed targeted lipidomics method was demonstrated by discovering 520 differential lipid features related to COVID-19 severity. This high coverage and targeted approach will aid in future investigations of the lipidome in various disease contexts.

Functional Characterization of Salmonella Typhimurium Encoded YciF, a Domain of Unknown Function (DUF892) Family Protein, and Its Role in Protection during Bile and Oxidative Stress.

YciF (STM14_2092) is a member of the domain of unknown function (DUF892) family. It is an uncharacterized protein involved in stress responses in Salmonella Typhimurium. In this study, we investigated the significance of YciF and its DUF892 domain during bile and oxidative stress responses of S. Typhimurium. Purified wild-type YciF forms higher order oligomers, binds to iron, and displays ferroxidase activity. Studies on the site-specific mutants revealed that the ferroxidase activity of YciF is dependent on the two metal binding sites present within the DUF892 domain. Transcriptional analysis displayed that the ΔcspE strain, which has compromised expression of YciF, encounters iron toxicity due to dysregulation of iron homeostasis in the presence of bile. Utilizing this observation, we demonstrate that the bile mediated iron toxicity in ΔcspE causes lethality, primarily through the generation of reactive oxygen species (ROS). Expression of wild-type YciF, but not the three mutants of the DUF892 domain, in ΔcspE alleviate ROS in the presence of bile. Our results establish the role of YciF as a ferroxidase that can sequester excess iron in the cellular milieu to counter ROS-associated cell death. This is the first report of biochemical and functional characterization of a member of the DUF892 family. IMPORTANCE The DUF892 domain has a wide taxonomic distribution encompassing several bacterial pathogens. This domain belongs to the ferritin-like superfamily; however, it has not been biochemically and functionally characterized. This is the first report of characterization of a member of this family. In this study, we demonstrate that S. Typhimurium YciF is an iron binding protein with ferroxidase activity, which is dependent on the metal binding sites present within the DUF892 domain. YciF combats iron toxicity and oxidative damage caused due to exposure to bile. The functional characterization of YciF delineates the significance of the DUF892 domain in bacteria. In addition, our studies on S. Typhimurium bile stress response divulged the importance of comprehensive iron homeostasis and ROS in bacteria.

Application of soil amendments mitigates phytotoxic effects on Solanum melongena L. and Lycopersicon esculentum L. seedlings exposed to chlorpyrifos and dimethoate pesticides.

This field study was done to study the effects of pesticides chlorpyrifos and dimethoate singly and in combination with soil amendments like chemical fertilizer (CF), farmyard manure (FM), and 50% CF + 50% FM (CM) on various indices of growth, physio-biochemical parameters of brinjal, and their residual effect in tomato seedlings. As compared to the control, the decrease of 9.5 and 5.5%, 8.9 and 5.0% in fresh weight, dry weight respectively was recorded in the pesticide-only treatment in the brinjal crop. Pesticides when applied in combination with soil amendments depicted the highest growth of 105.4 and 118.2%, 104.1 and 115.1% in pesticides + CF treatment, 72.7 and 85.1%, 68.1 and 78.1% in pesticides + CM treatment, and 64.4 and 74.0%, 62.7 and 65.7% in pesticides + FM treatment compared to control. In tomato seedlings, the pesticides + CF treatment exhibited the lowest growth indices (25.5 and 31.9%, 26.4 and 28.8%) across the combined treatments while pesticide-only treatment depicted minimum growth compared to the control. In the case of photosynthesis rate and antioxidant activity, the combined treatments showed the trend as pesticides + CF > pesticides + CM > pesticides + FM in the brinjal crop; however, the trend became somewhat reversed in the tomato crop. The results indicated that soil-amended practices modulated pesticide-induced damage by upregulating photosynthetic performance, chlorophyll a fluorescence, and antioxidant balancing which might be associated with the mitigation of ROS-induced pesticide toxicity, and the effect was more pronounced with CM. Furthermore, our study was supported by non-metric-multidimensional scaling (NMDS)-constructed ordination plots by showing spatial patterns in different variables. The study might help in taking management decision to design mitigation actions for government and non-government agency at the farmers' level.

Large survey dataset of rice production practices applied by farmers on their largest farm plot during 2018 in India.

This dataset provides detailed information on rice production practices being applied by farmers during 2018 rainy season in India. Data was collected through computer-assisted personal interview of farmers using the digital platform Open Data Kit (ODK). The dataset, n = 8355, covers eight Indian states, viz., Andhra Pradesh, Bihar, Chhattisgarh, Haryana, Odisha, Punjab, Uttar Pradesh and West Bengal. Sampling frames were constructed separately for each district within states and farmers were selected randomly. The survey was deployed in 49 districts with a maximum of 210 interviews per district. The digital survey form was available on mobile phones of trained enumerators and was designed to minimize data entry errors. Each survey captured approximately 225 variables around rice production practices of farmers' largest plot starting with land preparation, establishment method, crop variety and planting time through to crop yield. Detailed modules captured fertilizer application, irrigation, weed management, biotic and abiotic stresses. Additional information was gathered on household demographics and marketing. Geo-points were recorded for each surveyed plot with an accuracy of <10 m. This dataset is generated to bridge a data-gap in the national system and generates information about the adoption of technologies, as well as enabling prediction and other analytics. It can potentially be the basis for evidence-based agriculture programming by policy makers.

Implementing the Practice of Birth Companion in Labor During the COVID-19 Pandemic: A Quality Improvement Endeavor in India.

Objective We aim to implement the practice of birth companions (BC) (from 0% to 90%) during labor to provide respectful maternity care (RMC) during the coronavirus disease 2019 (COVID-19) pandemic. Methods This was a prospective quality improvement (QI) study conducted in the Department of Obstetrics and Gynecology at All India Institute of Medical Sciences (AIIMS), Rishikesh, India. The methodology given by the World Health Organization (WHO)'s Point of Care Continuous Quality Improvement (POCQI) manual was followed, and standard tools of quality improvement were used to attain the objective. Results The QI team conducted a cause and effect analysis to understand the reasons why birth companions were not allowed during childbirth. The Pareto principle derived at three most important causes of the problem: absence of a defined policy, ignorance of guidelines promoting BC even during the pandemic, and relatives could enter wards only after a negative reverse transcriptase polymerase chain reaction (RTPCR) report, which could take up to 48 hours. Multiple change ideas were tested by means of Plan-Do-Study-Act (PDSA) cycles that were successful in bringing about desired change and improvement in the delivery of quality healthcare. Conclusion QI methodology was effective in promoting and achieving more than 90% birth companionship in labor and thus helpful in providing respectful maternity care even during the COVID-19 pandemic.

COVID-19 lockdown-driven changes in the Ganga River ecosystem in response to human perturbations.

We examined 10 subsurface water, 5 benthic water and 19 sediment (02 cm) samples along a 518 km of the middle segment of the Ganga River to assess the possible improvements that resulted from the industrial shutdown during the COVID-19 pandemic. The sites included the main stem river, tributary confluences, and two point sources, one of which releases metal-rich effluents and the other flushes municipal sewage. We found significant declines in the carbon, nutrient and metal concentrations in both the water and sediment. Even the most polluted zones did not show hypoxia (dissolve oxygen; DO < 2.0 mg L-1) that had been observed in the previous year. Despite a significant decline in carbon and nitrogen as substrates, the activities of extracellular enzymes (EEs), such as ß-D-glucosidase, FDAase and protease in sediment (0-2 cm depth), increased significantly (p < 0.05) in response to the declining metal concentrations resulting from the industrial shutdown. We found strong negative correlations between EE activity and the concentrations of metal pollutants measured in 2019, but the correlations between these variables appeared poor in 2020 (lockdown period). Also, we found large variances (low stability coefficients) during the period of strong anthropogenic effects (2019). The study indicates that industrial sources are important contributors of metal pollution in the Ganga River and has relevance exploring river ecosystem recovery windows for management decisions.

Evaluation of pregnancy outcomes using medroxyprogesterone acetate versus gonadotropin-releasing hormone antagonist in ovarian stimulation: A retrospective cohort study.

Background: Limited studies have compared pregnancy outcomes with medroxyprogesterone acetate (MPA) vs. gonadotropin-releasing hormone antagonist (GnRH antagonist) in ovarian stimulation protocols. The results show heterogeneity. Objective: This study aims to assess pregnancy outcomes with the use of MPA instead of GnRH antagonist for ovarian stimulation in donor-recipient cycles. Materials and Methods: This retrospective study was carried out from June 2016 to May 2019. The study included 250 donors receiving ovarian stimulation with 2 different protocols: group 1 (n = 109) receiving GnRH antagonist (0.25 mg/day) from the 5 th or 6 th day of menses and group 2 (n = 141) receiving MPA (10 mg/day) from the second day of menses. In 384 recipients, 2 good-quality blastocysts were transferred after endometrial preparation. The primary endpoint was live birth in recipients. Results: The results showed that live birth was comparable in both recipient groups (59% vs. 60%, OR: 0.63, 95% CI: 0.13-2.99, p = 0.559). The number of live-born fetuses (adjusted OR: 0.57, 95% CI: 0.31-1.05, p > 0.01) showed no significant difference in both groups. However, the implantation rate with twin sacs was significantly lower in group 2 (adjusted OR: 0.57, 95% CI: 0.33-0.99, p = 0.05). The regression analysis for good-quality blastocyst proportion was comparable (OR: 0.63, 95% CI: -4.33-5.60, p = 0.802) in both donor groups. The mean stimulation cost in group 2 was less than in group 1. Conclusion: MPA had a comparable live birth and embryological outcomes in both groups. Oral administration makes it convenient, acceptable, and patient-friendly. Its cost-effectiveness and convenience open new possibilities in ovarian stimulation protocols.

Effects of COVID-19 lockdown on water quality, microbial extracellular enzyme activity, and sediment-P release in the Ganga River, India.

This study investigates possible improvement in water quality and ecosystem functions in the Ganga River as influenced by COVID-19 lockdown in India. A total of 132 samples were collected during summer-2020 low flow (coinciding COVID-19 lockdown) for water (sub-surface and sediment-water interface) and 132 samples separately for sediment (river bottom and land-water interface) considering 518-km main river stem including three-point sources (one releases urban sewage and the other two add metal-rich industrial effluents) and a pollution-impacted tributary. Parameters such as dissolved oxygen deficit and the concentrations of carbon, nutrients (N and P), and heavy metals were measured in water. Sediment P-release was measured in bottom sediment whereas extracellular enzymes (EE; alkaline phosphatase, FDAase, protease, and ß-D-glucosidase) and CO2 emission were measured at land-water interface to evaluate changes in water quality and ecosystem functions. The data comparisons were made with preceding year (2019) measurements. Sediment-P release and the concentrations of carbon, nutrients, and heavy metals declined significantly (p<0.05) in 2020 compared to those recorded in 2019. Unlike the preceding year, we did not observe benthic hypoxia (DO <2.0 mg L-1) in 2020 even at the most polluted site. The EE activities, which declined sharply in the year 2019, showed improvement during the 2020. The stability coefficient and correlative evidences also showed a large improvement in the water quality and functional variables. Positive changes in functional attributes indicated a transient recovery when human perturbations withdrawn. The study suggests that timing the ecosystem recovery windows, as observed here, may help taking management decision to design mitigation actions for rivers to recover from anthropogenic perturbations.

Microbial amelioration of salinity stress in HD 2967 wheat cultivar by up-regulating antioxidant defense.

An experiment was conducted to investigate the potential of Piriformospora indica and plant growth-promoting bacteria (PGPB) to ameliorate salinity stress in HD 2967 wheat cultivar. Plants were treated with four different levels of salinity viz. 0, 50, 100 and 200 mM NaCl (electrical conductivity value 0.01, 5.84, 11.50 and 21.4 mS cm-1, respectively) under greenhouse conditions, using a completely randomized design experiment. Plants inoculated with PGPB and P. indica showed decrease in lipid peroxidation, relative membrane permeability and lipoxygenase enzyme (LOX) activity as compared to uninoculated plants. The result of this study showed that PGPB and P. indica inoculated HD 2967 wheat plants accumulated higher content of proline, α-tocopherol and carotenoid as compared to uninoculated plants. The HD 2967 wheat plants either inoculated with PGPB or P. indica showed significantly higher activities of antioxidant enzymes viz. superoxide dismutase, catalase and ascorbate peroxidase than that of the uninoculated plants. Moreover, PGPB inoculated plants showed greater activity of antioxidant enzymes than the plants inoculated with P. indica. Salinity stress tolerance was more pronounced in the PGPB inoculated than P. indica inoculated plants. This study revealed the potentiality of PGPB and P. indica as bio-ameliorator under salinity stress, and suggests that this plant microbial association could be a promising biotechnological tool to combat the deleterious effects of salinity stress.