Electrochemically coupled CH4 and CO2 consumption driven by microbial processes.

The chemical transformations of methane (CH4) and carbon dioxide (CO2) greenhouse gases typically have high energy barriers. Here we present an approach of strategic coupling of CH4 oxidation and CO2 reduction in a switched microbial process governed by redox cycling of iron minerals under temperate conditions. The presence of iron minerals leads to an obvious enhancement of carbon fixation, with the minerals acting as the electron acceptor for CH4 oxidation and the electron donor for CO2 reduction, facilitated by changes in the mineral structure. The electron flow between the two functionally active microbial consortia is tracked through electrochemistry, and the energy metabolism in these consortia is predicted at the genetic level. This study offers a promising strategy for the removal of CH4 and CO2 in the natural environment and proposes an engineering technique for the utilization of major greenhouse gases.

Biochar aided priming of carbon and nutrient availability in three soil orders of India.

In recent years biochar (BC) has gained importance for its huge carbon (C) sequestration potential and positive effects on various soil functions. However, there is a paucity of information on the long-term impact of BC on the priming effect and nutrient availability in soil with different properties. This study investigates the effects of BC prepared from rice husk (RBC4, RBC6), sugarcane bagasse (SBC4, SBC6) and mustard stalk (MBC4, MBC6) at 400 and 600 °C on soil C priming and nitrogen (N), phosphorus (P), and potassium (K) availability in an Alfisol, Inceptisol, and Mollisol. BC properties were analyzed, and its decomposition in three soil orders was studied for 290 days in an incubation experiment. Post-incubation, available N, P, and K in soil were estimated. CO2 evolution from BC and soil alone was also studied to determine the direction of priming effect on native soil C. Increasing pyrolysis temperature enhanced pH and EC of most of the BC. The pyrolysis temperature did not show clear trend with respect to priming effect and nutrient availability across feedstock and soil type. MBC6 increased C mineralization in all the soil orders while RBC6 in Alfisol and SBC6 in both Inceptisol and Mollisol demonstrated high negative priming, making them potential amendments for preserving native soil C. Most of the BC showed negative priming of native SOC in long run (290 days) but all these BC enhanced the available N, P, and K in soil. SBC4 enhanced N availability in Alfisol and Inceptisol, RBC4 improved N and P availability in Mollisol and P in Alfisol and MBC6 increased K availability in all the soils. Thus, based on management goals, tailored BC or blending different BC can efficiently improve C sequestration and boost soil fertility.

DNA damage in inhabitants exposed to heavy metals near Hudiara drain, Lahore, Pakistan.

The current study was conducted on the inhabitants living in the area adjacent to the Hudiara drain using bore water and vegetables adjacent to the Hudiara drain. Toxic heavy metals badly affect human health because of industrial environmental contamination. Particularly hundreds of millions of individuals globally have faced the consequences of consuming water and food tainted with pollutants. Concentrations of heavy metals in human blood were elevated in Hudiara drainings in Lahore city, Pakistan, due to highly polluted industrial effluents. The study determined the health effects of high levels of heavy metals (Cd, Cu, Zn, Fe, Pb, Ni, Hg, Cr) on residents of the Hudiara draining area, including serum MDA, 8-Isoprostane, 8-hydroxyguanosine, and creatinine levels. An absorption spectrophotometer was used to determine heavy metals in wate water, drinking water, soil, plants and human beings blood sampleas and ELISA kits were used to assess the level of 8-hydroxyguanosine, MDA, 8-Isoprostane in plasma serum creatinine level. Waste water samples, irrigation water samples, drinking water samples, Soil samples, Plants samples and blood specimens of adult of different weights and ages were collected from the polluted area of the Hudiara drain (Laloo and Mohanwal), and control samples were obtained from the unpolluted site Sheiikhpura, 60 km away from the site. Toxic heavy metals in blood damage the cell membrane and DNA structures, increasing the 8-hydroxyguanosine, MDA, creatinine, and 8-Isoprostane. Toxic metals contaminated bore water and vegetables, resulting in increased levels of creatinine, MDA, Isoprostane, and 8-hydroxy-2-guanosine in the blood of inhabitants from the adjacent area Hudiara drain compared to the control group. In addition,. This study also investigated heavy metal concentrations in meat and milk samples from buffaloes, cows, and goats. In meat, cow samples showed the highest Cd, Cu, Fe and Mn concentrations. In milk also, cows exhibited elevated Cu and Fe levels compared to goats. The results highlight species-specific variations in heavy metal accumulation, emphasizing the need for targeted monitoring to address potential health risks. The significant difference between the two groups i.e., the control group and the affected group, in all traits of the respondents (weight, age, heavy metal values MDA, 8-Isoprostane, 8-hydroxyguaniosine, and serum creatinine level). Pearson's correlation coefficient was calculated. The study has shown that the level of serum MDA, 8-Isoprostane, 8-hydroxyguaniosine, or creatinine has not significantly correlated with age, so it is independent of age. This study has proved that in Pakistan, the selected area of Lahore in the villages of Laloo and Mohanwal, excess of heavy metals in the human body damages the DNA and increases the level of 8-Isoprostane, MDA, creatinine, and 8-hydroxyguaniosine. As a result, National and international cooperation must take major steps to control exposure to heavy metals.

Antioxidant capacity sources of soils under different land uses.

Antioxidants (AOX) in soils originate mainly from secondary plant metabolites and are pivotal in many redox processes in environment, maintaining soil quality. Still, little is known about the influence of land uses on their accumulation in soil. The aim of the paper was to determine the content of these redox-active compounds in the extracts of A horizons of abandoned fallows, arable and woodland soils. Total antioxidant capacity (TAC) of soils under various uses and vegetation was evaluated in different soil extracts using Folin-Ciocâlteu method. The contribution of humic acids to TAC was determined and antioxidant profiles estimated using the chromatographic GC-MS method. Forest soils exhibited the highest TAC (15.5 mg g-1) and AOX contents (4.34 mg g-1), which were positively correlated with soil organic carbon content. It was estimated that humic acids contribute to over 50% of TAC in soils. The main phenolics in woodland A horizons were isovanillic and p-hydroxybenzoic acid (p-HA), while esculetin and p-HA predominated in the abandoned fallows due to the prevalence of herbaceous vegetation. Cultivated soils were the most abundant in p-HA (56.42%). In the studied topsoils, there were considerable amounts of aliphatic organic matter, which role in redox processes should be further evaluated.

Occurrence, distribution, and ecological risk assessment of heavy metals in Chao Phraya River, Thailand.

Understanding heavy metals in rivers is crucial, as their presence and distribution impact water quality, ecosystem health, and human well-being. This study examined the presence and levels of nine heavy metals (Cd, Cr, Cu, Fe, Hg, Mn, Ni, Pb, and Zn) in 16 surface water samples along the Chao Phraya River, identifying Fe, Mn, Zn, and Cr as predominant metals. Although average concentrations in both rainy and dry seasons generally adhered to WHO guidelines, Mn exceeded these limits yet remained within Thailand's acceptable standards. Seasonal variations were observed in the Chao Phraya River, and Spearman's correlation coefficient analysis established significant associations between season and concentrations of heavy metals. The water quality index (WQI) demonstrated varied water quality statuses at each sampling point along the Chao Phraya River, indicating poor conditions during the rainy season, further deteriorating to very poor conditions in the dry season. The hazard potential index (HPI) was employed to assess heavy metal contamination, revealing that during the dry season in the estuary area, the HPI value exceeded the critical threshold index, indicating the presence of heavy metal pollution in the water and unsuitable for consumption. Using the species sensitivity distribution model, an ecological risk assessment ranked the heavy metals' HC5 values as Pb > Zn > Cr > Cu > Hg > Cd > Ni, identifying nickel as the most detrimental and lead as the least toxic. Despite Cr and Zn showing a moderate risk, and Cu and Ni posing a high risk to aquatic organisms, the main contributors to ecological risk were identified as Cu, Ni, and Zn, suggesting a significant potential ecological risk in the Chao Phraya River's surface water. The results of this study provide fundamental insights that can direct future actions in preventing and managing heavy metal pollution in the river ecosystem.

The association between C-reactive protein and coronary artery calcification: a systematic review and meta-analysis.

BACKGROUND: While coronary artery calcification (CAC) is recognized as a reliable marker for coronary atherosclerosis, the relationship between the concentration of C-reactive protein (CRP) and the incidence and progression of CAC remains controversial. METHOD: PubMed, Embase, Web of Science, and Scopus were systematically searched to identify relevant observational studies until October 2023. The methodological quality of the included studies was evaluated using the Newcastle-Ottawa Scale (NOS). A random-effects meta-analysis was employed to calculate pooled odd ratios (OR) and corresponding 95% confidence intervals, considering heterogeneity among the studies. RESULTS: Out of the 2545 records, 42 cross-sectional and 9 cohort studies were included in the systematic review. The meta-analysis on 12 eligible cross-sectional studies revealed no significant association between CAC and CRP [pooled OR: 1.03 (1.00, 1.06)]. Additionally, an insignificant association was found between CAC and CRP through meta-analysis on three eligible cohort studies [pooled OR: 1.05 (0.95, 1.15)] with no considerable heterogeneity across studies. Sensitivity analyses indicated that the meta-analysis models were robust. There was no evidence of publication bias. CONCLUSION: Based on the meta-analysis findings, elevated levels of CRP did not emerge as a valuable prognostic maker for CAC incidence and progression prediction.

Elevated ADH5 expression suggested better prognosis in kidney renal clear cell carcinoma (KIRC) and related to immunity through single-cell and bulk RNA-sequencing.

BACKGROUND: Despite the rapid advances in modern medical technology, kidney renal clear cell carcinoma (KIRC) remains a challenging clinical problem in urology. Researchers urgently search for useful markers to break through the therapeutic conundrum due to its high lethality. Therefore, the study explores the value of ADH5 on overall survival (OS) and the immunology of KIRC. METHODS: The gene expression matrix and clinical information on ADH5 in the TCGA database were validated using external databases and qRT-PCR. To confirm the correlation between ADH5 and KIRC prognosis, univariate/multivariate Cox regression analysis was used. We also explored the signaling pathways associated with ADH5 in KIRC and investigated its association with immunity. RESULTS: The mRNA and protein levels showed an apparent downregulation of ADH5 in KIRC. Correlation analysis revealed that ADH5 was directly related to histological grade, clinical stage, and TMN stage (p < 0.05). Univariate and multivariate Cox regression analysis identified ADH5 as an independent factor affecting the prognosis of KIRC. Enrichment analysis looked into five ADH5-related signaling pathways. The results showed no correlation between ADH5 and TMB, TNB, and MSI. From an immunological perspective, ADH5 was found to be associated with the tumor microenvironment, immune cell infiltration, and immune checkpoints. Lower ADH5 expression was associated with greater responsiveness to immunotherapy. Single-cell sequencing revealed that ADH5 is highly expressed in immune cells. CONCLUSION: ADH5 could be a promising prognostic biomarker and a potential therapeutic target for KIRC. Besides, it was found that KIRC patients with low ADH5 expression were more sensitive to immunotherapy.

The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling.

Plasma proteins are considered the most informative source of biomarkers for disease diagnosis and monitoring. Mass spectrometry (MS)-based proteomics has been applied to identify biomarkers in plasma, but the complexity of the plasma proteome and the extremely large dynamic range of protein abundances in plasma make the clinical application of plasma proteomics highly challenging. We designed and synthesized zeolite-based nanoparticles to deplete high-abundance plasma proteins. The resulting novel plasma proteomic assay can measure approximately 3000 plasma proteins in a 45 min chromatographic gradient. Compared to those in neat and depleted plasma, the plasma proteins identified by our assay exhibited distinct biological profiles, as validated in several public datasets. A pilot investigation of the proteomic profile of a hepatocellular carcinoma (HCC) cohort identified 15 promising protein features, highlighting the diagnostic value of the plasma proteome in distinguishing individuals with and without HCC. Furthermore, this assay can be easily integrated with all current downstream protein profiling methods and potentially extended to other biofluids. In conclusion, we established a robust and efficient plasma proteomic assay with unprecedented identification depth, paving the way for the translation of plasma proteomics into clinical applications.

Quantifying Disparities in Per- and Polyfluoroalkyl Substances (PFAS) Levels in Drinking Water from Overburdened Communities in New Jersey, 2019-2021.

BACKGROUND: Policymakers have become increasingly concerned regarding the widespread exposure and toxicity of per- and polyfluoroalkyl substances (PFAS). While concerns exist about unequal distribution of PFAS contamination in drinking water, research is lacking. OBJECTIVES: We assess the scope of PFAS contamination in drinking water in New Jersey (NJ), the first US state to develop regulatory levels for PFAS in drinking water. We test for inequities in PFAS concentrations by community sociodemographic characteristics. METHODS: We use PFAS testing data for community water systems (CWS) (n=491) from the NJ Department of Environmental Protection (NJDEP) from 2019 to 2021 and demographic data at the block group level from the US Census to estimate the demographics of the NJ population served by CWS. We use difference in means tests to determine whether CWSs serving "overburdened communities" (OBCs) have a statistically significant difference in likelihood of PFAS detections. OBCs are defined by the NJDEP to be census block groups in which: a) at least 35% of the households qualify as low-income, b) at least 40% of the residents identify as people of color, or c) at least 40% of the households have limited English proficiency. We calculate statewide summary statistics to approximate the relative proportions of sociodemographic groups that are served by CWSs with PFAS detections. RESULTS: We find that 63% of all CWSs tested by NJDEP from 2019 to 2021 had PFAS detections in public drinking water, collectively serving 84% of NJ's population receiving water from CWSs. Additionally, CWSs serving OBCs had a statistically significant higher likelihood of PFAS detection and a higher likelihood of exposure above state MCLs. We also find that a larger proportion of people of color lived in CWS service areas with PFAS detections compared to the non-Hispanic white population. DISCUSSION: These findings quantitatively identify disparities in PFAS contamination of drinking water by CWS service area and highlight the extent of PFAS drinking water contamination and the importance of PFAS remediation efforts for protecting environmental health and justice. https://doi.org/10.1289/EHP12787.

Soil organic carbon fractionation, carbon index, and microbial activity under different agroforestry systems in North Eastern Himalayas, India.

The potential of soil organic carbon fractions for agroforestry systems (AFSs) is not well understood. Five distinct AFSs were tested for its impact on soil organic carbon fractionation, carbon index, and microbial activity in North Eastern Himalayas, India. The mean labile carbon (LC) ranged from 4.55 to 5.43 kg soil-1 across the land use systems. Napier system observed the lowest very labile carbon (VLC) 12.36 kg soil-1 in 60-75-cm depth. The mean non labile carbon (NLC) ranged from 15.67 to 16.83 g kg soil-1 across the land use. Highest less labile carbon (LLC) was observed in agri-horti-silviculture (AHS) followed by agri-silvi-horticulture (ASH) land use system. The black gram + mandarin + Alnus nepalensis land use recorded higher lability index (1.66) followed by maize + Schima wallichii (1.65) in 0-15-cm depth. Among the different land use systems, carbon pool index increased in all the depths over buckwheat + mandarin. The mean carbon management index (CMI) value ranged from 167.02 to 210.12 among the land use system. The mean CMI was highest in black gram + mandarin + Alnus nepalensis (210.12) followed by soybean + Ficus hookerii + guava (191.56), maize + Schima wallichii (281.71), and lowest in buckwheat + mandarin (167.02). Among the AFSs, black gram + mandarin + Alnus nepalensis showed greater amount of carbon pool index, lability index, and carbon management index and, hence, considered the best sustainable agroforestry system to sequester more carbon in the Sikkim Himalaya. Such system also retained more different organic carbon fractions. The mean CMI value ranged from 167.02 to 210.12 among AFSs. Acid phosphatase activity was more during the rainy season followed by winter and summer season. Similar trends were followed by the urease activity in all the three seasons. Overall conclusion from this investigation is that SOC fractions, carbon index, and microbial activity levels are strongly influenced by the prevailing agroforestry systems.

Biomonitoring potentially toxic elements in atmospheric particulate matter of greater Dhaka region using leaves of higher plants.

In this study, four different plant species, namely Artocarpus heterophyllus, Mangifera indica, Psidium guajava, and Swietenia mahagoni, were selected from seven different locations to assess the feasibility of using them as a cost-effective alternative for biomonitoring air quality. Atmospheric coarse particulate matter (PM10), soil samples, and leaf samples were collected from residential, industrial, and traffic-congested sites located in the greater Dhaka region. The heavy metal concentrations (Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) in the leaves of the different species, PM10, and soil samples were analyzed. The highest Pb (718 ng/m3) and Zn (15,956 ng/m3) concentrations were found in PM10 of Kodomtoli which is an industrial area. On the other hand, the highest Fe (6,152 ng/m3) and Ni (61.1 ng/m3) concentrations were recorded in the PM10 of Gabtoli, a heavy-traffic area. A significant positive correlation (r = 0.74; p < 0.01) between Pb content in plant leaves and PM fraction was found which indicated that atmospheric PM-bound Pb may contribute to the uptake of Pb by plant leaves. The analysis of the enrichment factor (EF) revealed that soils were contaminated with Cd, Ni, Pb, and Zn. The abaxial leaf surfaces of Psidium guajava growing at the polluted site exhibited up to a 40% decrease in stomatal pores compared to the control site. Saet's summary index (Zc) demonstrated that Mangifera indica had the highest bioaccumulation capacity. The metal accumulation index (MAI) was also evaluated to assess the overall metal accumulation capacity of the selected plants. Of the four species, Swietenia mahagoni (3.05) exhibited the highest MAI value followed by Mangifera indica (2.97). Mangifera indica and Swietenia mahagoni were also found to accumulate high concentrations of Pb and Cr in their leaves and are deemed to be good candidates to biomonitor Pb and Cr contents in ambient air.

Paucibacter sediminis sp. nov., isolated from sediment in a freshwater pond.

A Gram-stain-negative, aerobic, oxidase-positive, weakly catalase-positive, motile by means of a single polar flagellum, rod-shaped bacterium designated as strain S2-9T was isolated from sediment sampled in Wiyang pond, Republic of Korea. Growth of this strain was observed at 10-40 °C (optimum, 35 °C) and pH 5.5-9.5 (optimum, pH 7.0-8.0) and in the presence of 0-0.5 % NaCl in Reasoner's 2A broth. The major fatty acids (>10 %) of strain S2-9T were C16 : 0 and summed feature 3 (comprising a mixture of C16 : 1 ω7c and/or C16 : 1 ω6c). Ubiquinone-8 was detected as the respiratory quinone. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Strain S2-9T showed the highest 16S rRNA gene sequence similarity to Paucibacter oligotrophus CHU3T (98.7 %), followed by 'Paucibacter aquatile' CR182 (98.4 %), all type strains of Pelomonas species (98.1-98.3 %), Mitsuaria chitosanitabida NBRC 102408T (97.9 %), Kinneretia asaccharophila KIN192T (97.8 %), Mitsuaria chitinivorans HWN-4T (97.4 %), and Paucibacter toxinivorans 2C20T (97.4 %). Phylogenetic trees based on the 16S rRNA gene and whole-genome sequences showed that strain S2-9T formed a tight phylogenetic lineage with Paucibacter species (CHU3T, CR182, and 2C20T). Average nucleotide identity and digital DNA-DNA hybridization values between strain S2-9T and Paucibacter strains were 76.6-79.3% and 19.5-21.5 %, respectively. The genomic DNA G+C content of strain S2-9T was 68.3 mol%. Notably, genes responsible for both sulphur oxidation and reduction and denitrification were found in the genome of strain S2-9T, suggesting that strain S2-9T is involved in the nitrogen and sulphur cycles in pond ecosystems. Based on the polyphasic taxonomic results, strain S2-9T represents a novel species of the genus Paucibacter, for which the name Paucibacter sediminis sp. nov. is proposed. The type strain is S2-9T (= KACC 22267T= JCM 34541T).

Two-Dimensional Gel Electrophoresis for Protein Separation of Plant Samples.

This chapter provides a description of the procedure for two-dimensional electrophoresis that can be performed for any given gel size and isoelectric focusing range. This will enable the operator to recognize critical steps and gain sufficient information to generate 2D images suitable for computer-assisted analysis of 2D-gel, as well as mass spectrometry analysis for protein identification and characterization.

Indophenol Blue Colorimetric Method to Determine Grain Protein Content of Cereal Plants.

Here, we propose a method to convert the organic nitrogen in maize kernels into ammonia in solution and then chlorinate it to prepare monochloride salts, which can form an oxidatively coupled blue-green mixture with sodium salicylate and sodium dichloroisocyanurate. The concentration of ammonium ions in the blue-green mixture can then be determined in the solution, and finally the protein content in maize kernels can be calculated from the nitrogen content.

One-Dimensional Acrylamide Gel Electrophoresis for Analysis of Plant Samples.

Polyacrylamide gel electrophoresis (PAGE) is a widely used technique for separating proteins from complex plant samples. Prior to the analysis, proteins must be extracted from plant tissues, which are rather complex than other types of biological material. Different protocols have been applied depending on the protein source, such as seeds, pollen, leaves, roots, and flowers. Total protein amounts must also be determined before conducting gel electrophoresis. The most common methodologies include PAGE under native or denaturing conditions. Both procedures are used consequently for protein identification and characterization via mass spectrometry. Additionally, various staining procedures are available to visualize protein bands in the gel, facilitating the software-based digital evaluation of the gel through image acquisition.

Monosaccharide Analysis After One-Pot Derivatization Followed by Reverse-Phase Liquid Chromatography Separation and UV/Vis Detection.

Derivatization of monosaccharides with 1-phenyl-3-methyl-5-pyrazolone (PMP) introduces two chromophores per sugar molecule. Their separation on a superficially porous C18 reverse-phase column, using common liquid chromatography equipment, results in short analysis times (under 20 min) and high sensitivity (limit of quantitation 1 nmol). This method allows for complex monosaccharide mixtures to be separated and quantified using a reasonably simple and safe derivatization procedure.

Sample Preparation and Phosphopeptide Enrichment for Plant Phosphoproteomics via Label-Free Mass Spectrometry.

Phosphopeptide enrichment is the main bottleneck of every phosphorylation study. Therefore, in this chapter, a general workflow tries to overbridge the hurdles of plant sample handling from sample collection to protein extraction, protein solubilization, enzymatic digestion, and enrichment step prior to mass spectrometry. The workflow provides information to perform global proteomics as well as phosphoproteomics enabling the researcher to use the protocol in both fields.

Identification of Volatiles in Tomato Fruit Using Headspace Solid-Phase-Micro-Extraction (HS-SPME) Coupled with Gas Chromatography-Mass Spectrometry (GC-MS).

Plant volatile organic compounds (VOCs) are organic chemicals that plants release as part of their natural biological processes. Various plant tissues produce VOCs, including leaves, stems, flowers, and roots. VOCs are essential in plant communication, defense against pests and pathogens, aroma and flavor, and attracting pollinators. The study of plant volatiles has become an increasingly important area of research in recent years, as scientists have recognized these compounds' important roles in plant physiology. As a result, there has been a growing interest in developing methods for collecting and analyzing plant VOCs. HS-SPME-GC-MS (headspace solid-phase microextraction-gas chromatography-mass spectrometry) is commonly used for plant volatile analysis due to its high sensitivity and selectivity. This chapter describes an efficient method for extracting and identifying volatile compounds by HS-SPME coupled with GC-MS in tomato fruits.