From genome to evolution: investigating type II methylotrophs using a pangenomic analysis.

A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway, Methylooceanibacter marginalis lacked serine hydroxymethyltransferase (SHMT), and Methylobacterium variabile exhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably, Methylobrevis sp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway. Methylovirgula sp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, and Methylocapsa sp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications. IMPORTANCE: Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.

Comparative Study of Chromium Phytoremediation by Two Aquatic Macrophytes.

Chromium (Cr) occurs in several oxidation states from trivalent to hexavalent. However, hexavalent forms are more toxic and mainly produced by anthropogenic activities. A hydroponic experiment was conducted to analyse the comparative remediation of Cr by Marsilea minuta and Pistia stratiotes. Plants were exposed to four concentrations of Cr (0.5, 1.0, 1.5, and 2.0 mM) for 3 days. The highest accumulation of Cr was seen at the 1.5 mM concentration after 3 days in Marsilea (11.96 mg/g) and Pistia (18.78 mg/g). Dry weights decreased and malondialdehyde (MDA) levels increased in response to increasing Cr concentrations. Results indicate that both macrophytes are suitable candidates for Cr phytoremediation. Antioxidant-enzyme activity as a function of metal tolerance is imperative for a coherent understanding of plant physiology under metal stress.

Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria.

The growth and survival of an organism in a particular environment is highly depends on the certain indispensable genes, termed as essential genes. Sulfate-reducing bacteria (SRB) are obligate anaerobes which thrives on sulfate reduction for its energy requirements. The present study used Oleidesulfovibrio alaskensis G20 (OA G20) as a model SRB to categorize the essential genes based on their key metabolic pathways. Herein, we reported a feedback loop framework for gene of interest discovery, from bio-problem to gene set of interest, leveraging expert annotation with computational prediction. Defined bio-problem was applied to retrieve the genes of SRB from literature databases (PubMed, and PubMed Central) and annotated them to the genome of OA G20. Retrieved gene list was further used to enrich protein-protein interaction and was corroborated to the pangenome analysis, to categorize the enriched gene sets and the respective pathways under essential and non-essential. Interestingly, the sat gene (dde_2265) from the sulfur metabolism was the bridging gene between all the enriched pathways. Gene clusters involved in essential pathways were linked with the genes from seleno-compound metabolism, amino acid metabolism, secondary metabolite synthesis, and cofactor biosynthesis. Furthermore, pangenome analysis demonstrated the gene distribution, where 69.83% of the 116 enriched genes were mapped under "persistent," inferring the essentiality of these genes. Likewise, 21.55% of the enriched genes, which involves specially the formate dehydrogenases and metallic hydrogenases, appeared under "shell." Our methodology suggested that semi-automated text mining and network analysis may play a crucial role in deciphering the previously unexplored genes and key mechanisms which can help to generate a baseline prior to perform any experimental studies.

Insight into Tumor Hypoxia: Radionuclide-based Biomarker as Diagnostic Tools.

The radiolabeled tracers have been extensively utilized to access various physiological and pathological conditions non-invasively, such as cancers, inflammation, and organ-specific imaging. These tracers demonstrate and study tumor hypoxia in several malignancies. Hypoxia is commonly seen in solid tumors. Tumor Hypoxia is a non-physiological condition of reduced oxygen concentration in the tumor. Hypoxia is associated with adverse outcomes such as treatment resistance and metastases in solid tumors. Tumor hypoxia may result in resistance to radiation therapy and chemotherapy, leading to a poor prognosis. It is one of the clinically paramount factors in treatment planning. Various chemical scaffolds are labeled with compatible radioisotopes for imaging hypoxia by Single-photon emission computed tomography (SPECT) and Positron emission tomography (PET). Radionuclides, such as [18F]Flourine, [99mTc]Technetium, [131I]Iodine, [124I] Iodine, and [64Cu]Copper are used for incorporation into different chemical scaffolds.Among them, [18F]Flourine and [64Cu]Copper tagged radiopharmaceuticals are most explored, such as [18F]FMISO, [18F]FAZA, [18F]FETNIM, and N4-methyl thiosemicarbazone [64Cu][Cu (ATSM)]. Some of the promising scaffolds for imaging hypoxia are [18F]EF1, [18F]EF5, [18F]EF3, and [18F]HX4. This review is focused on developing radiochemistry routes to synthesize different radiopharmaceuticals for imaging hypoxia in clinical and preclinical studies, as described in the literature. The chemist and radiochemist exerted enormous efforts to overcome these obstacles. They have successfully formulated multiple radiopharmaceuticals for hypoxia imaging. Radionuclide incorporation in high selectivity and efficiency (radiochemical yield, specific activity, purity, and radio-scalability) is a need for application perspective. Versatile chemistry, including nucleophilic and electrophilic substitutions, allows the direct or indirect introduction of radioisotopes into molecules of interest. This review will discuss the chemical routes for synthesizing and utilizing different precursors for radiolabeling with radionuclides.We will briefly summaries these radio-labeled tracers' application and biological significance.

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow.

A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text. We present a text mining workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) from literature databases (e.g., PubMed and PMC). This semi-automatic workflow is built with the Named Entity Recognition (NER) method and Convolutional Neural Network (CNN) model. With PubMed and PMCID as inputs, the workflow identified 227 genes belonging to several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment and biological network analysis was performed using UniprotKB and STRING-DB, respectively. The GO analysis showed that metal ion binding, sulfur binding, and electron transport were among the principal molecular functions. Furthermore, the biological network analysis generated three interlinked clusters containing genes involved in metal ion binding, cellular respiration, and electron transfer, which suggests the involvement of the extracted gene set in biocorrosion. Finally, the dataset was validated through manual curation, yielding a similar set of genes as our workflow; among these, hysB and hydA, and sat and dsrB were identified as the metal ion binding and sulfur metabolism genes, respectively. The identified genes were mapped with the pangenome of 63 SRB genomes that yielded the distribution of these genes across 63 SRB based on the amino acid sequence similarity and were further categorized as core and accessory gene families. SRB's role in biocorrosion involves the transfer of electrons from the metal surface via a hydrogen medium to the sulfate reduction pathway. Therefore, genes encoding hydrogenases and cytochromes might be participating in removing hydrogen from the metals through electron transfer. Moreover, the production of corrosive sulfide from the sulfur metabolism indirectly contributes to the localized pitting of the metals. After the corroboration of text mining results with SRB biocorrosion mechanisms, we suggest that the text mining framework could be utilized for genes/proteins extraction and significantly reduce the manual curation time.

Chemical characterization of PM10 and PM2.5 combusted firecracker particles during Diwali of Lucknow City, India: air-quality deterioration and health implications.

Urban air pollution is a growing menace leading to human discomfort, increased hospitalizations, morbidity, and mortality. This study deals with deteriorated air quality due to firecracker bursting during Diwali in Lucknow. Inhalable particulates and gaseous pollutants were monitored during Diwali 2020 using air samplers. Elements, ions, and surface morphology of particles were analyzed using ICP-MS, ion chromatograph, and SEM-EDX, respectively. PM10, PM2.5, SO2, and NO2 were 558, 352, 44, and 86 µg/m3 during Diwali night and 233, 101, 17, and 40 µg/m3 on pre-Diwali night while 241, 122, 24, and 43 µg/m3 on Diwali day. Concentrations surged for PM10: 139% and 132%, PM2.5: 249% and 189%, SO2: 159% and 83%, and NO2: 115% and 100% on Diwali night compared to pre-Diwali night and corresponding Diwali day, respectively. Al, K, Ba, and B showed dominance in PM10 whereas Zn, Al, Ba, and K in PM2.5 on Diwali night. The order of metal abundance in PM2.5 was Cd < Co < Ag < As < Cr < Ni < Cu < Bi < Pb < Mn < Sr < Fe < B < Zn < Al < Ba < K. Cations NH4+, K+, Mg2+, Ca2+, and anions F-, Cl-, NO3-, Br-, NO2-, SO4-2, PO43- showed a 2-8 fold increase on Diwali night relative to pre-Diwali night. Average metal concentrations varied by 2.2, 1.6, and 0.09 times on Diwali than pre-Diwali in residential, commercial, and industrial areas, respectively. PM10 concentration increased by 458% and 1140% while PM2.5, 487%, and 2247% than respective NAAQS and WHO standards. Tiny firecracker particles vary in toxicity as compared to vehicular emissions and have enhanced bioavailability leading to severe threat in terms of LRI, COPD, and atherosclerosis for city dwellers. It is imperative to recognize the present status of ambient air quality and implement regulatory strategies for emission reduction.

Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b.

Particulate methane monooxygenase (pMMO), a membrane-bound enzyme having three subunits (α, ß, and γ) and copper-containing centers, is found in most of the methanotrophs that selectively catalyze the oxidation of methane into methanol. Active sites in the pMMO of Methylosinus trichosporium OB3b were determined by docking the modeled structure with ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene. The docking energy between the modeled pMMO structure and ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene was -5.2, -5.7, -4.2, and -3.8 kcal/mol, respectively, suggesting the existence of more than one active site within the monomeric subunits due to the presence of multiple binding sites within the pMMO monomer. The evaluation of tunnels and cavities of the active sites and the docking results showed that each active site is specific to the radius of the substrate. To increase the catalysis rates of methane in the pMMO of M. trichosporium OB3b, selected amino acid residues interacting at the binding site of ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene were mutated. Based on screening the strain energy, docking energy, and physiochemical properties, five mutants were downselected, B:Leu31Ser, B:Phe96Gly, B:Phe92Thr, B:Trp106Ala, and B:Tyr110Phe, which showed the docking energy of -6.3, -6.7, -6.3, -6.5, and -6.5 kcal/mol, respectively, as compared to the wild type (-5.2 kcal/mol) with ethylbenzene. These results suggest that these five mutants would likely increase methane oxidation rates compared to wild-type pMMO.

Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20.

Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, Desulfovibrio alaskensis G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.

Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion.

Sulfate-reducing bacteria (SRB) have a unique ability to respire under anaerobic conditions using sulfate as a terminal electron acceptor, reducing it to hydrogen sulfide. SRB thrives in many natural environments (freshwater sediments and salty marshes), deep subsurface environments (oil wells and hydrothermal vents), and processing facilities in an industrial setting. Owing to their ability to alter the physicochemical properties of underlying metals, SRB can induce fouling, corrosion, and pipeline clogging challenges. Indigenous SRB causes oil souring and associated product loss and, subsequently, the abandonment of impacted oil wells. The sessile cells in biofilms are 1,000 times more resistant to biocides and induce 100-fold greater corrosion than their planktonic counterparts. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation and corrosion. Here, we examine the critical genes involved in biofilm formation and microbiologically influenced corrosion and categorize them into various functional categories. The current effort also discusses chemical and biological methods for controlling the SRB biofilms. Finally, we highlight the importance of surface engineering approaches for controlling biofilm formation on underlying metal surfaces.

Establishing the [18F]-FDG Production via Two Different Automated Synthesizers for Routine Clinical Studies: Our Institutional Experiences of 4 years.

INTRODUCTION: [18F]-Fluorodeoxyglucose ([18F]-FDG) is the most widely used positron-emission tomography tracer used for imaging in clinical studies such as early detection of cancer or its malignancies, quantifications, staging, and restaging of several malignancies. For clinical application, routine production of this tracer is mandatory in compliance to regulatory guidelines. Several dedicated commercial synthesizers are currently used for producing[18F]-FDG for clinical usage. Being at hospital radiopharmacy, it is our responsibility and duty to support the clinical service with uninterrupted production and supply of [18F]-FDG. This document describes the production of [18F]-FDG using two different automated synthesizers in terms of its production yield, time of synthesis, and analyze the quality control (QC) of the produced [18F]-FDG. MATERIALS AND METHODS: The precursor, mannose triflate ultra-pure, authentic nonradioactive standard FDG and [18O]-water were obtained from ABX, Germany. Solvents and reagents were purchased from Sigma Aldrich India Ltd. and Fisher Scientific India Ltd., (Mumbai, Maharashtra, India). RESULTS: The protocol developed for the synthesis with MPS-100 synthesizer yield of [18F]-FDG is approximate about 45% End of Bombardment (EOB) with synthesis time of around 35 min, whereas with F300E synthesizer it is around 60% with synthesis time of 25 min. The quality of the tracer produced by both synthesizers is at par with the QC parameter for clinical applications. CONCLUSIONS: Finally, we have developed the production using two automated synthesis modules which have the capability to produce [18F]-FDG, to do the patient studies in good yield and purity. Our protocol is simple, reproducible, and robust.

An Exposition of 11C and 18F Radiotracers Synthesis for PET Imaging.

The development of new radiolabeled Positron emission tomography tracers has been extensively utilized to access the increasing diversity in the research process and to facilitate the development in research methodology, clinical usage of drug discovery and patient care. Recent advances in radiochemistry, as well as the latest techniques in automated radio-synthesizer, have encouraged and challenged the radiochemists to produce the routinely developed radiotracers. Various radionuclides like 18F, 11C, 15O, 13N 99mTc, 131I, 124I and 64Cu are used for incorporating into different chemical scaffolds; among them, 18F and 11C tagged radiotracers are mostly explored such as 11C-Methionine, 11C-Choline, 18F-FDG, 18F-FLT, and 18F-FES. This review is focused on the development of radiochemistry routes to synthesize different radiotracers of 11C and 18F for clinical studies.

Adaptive Enrichment of a Thermophilic Bacterial Isolate for Enhanced Enzymatic Activity.

The mimicking of evolution on a laboratory timescale to enhance biocatalyst specificity, substrate utilization activity, and/or product formation, is an effective and well-established approach that does not involve genetic engineering or regulatory details of the microorganism. The present work employed an evolutionary adaptive approach to improve the lignocellulose deconstruction capabilities of the strain by inducing the expression of laccase, a multicopper oxidase, in Geobacillus sp. strain WSUCF1. This bacterium is highly efficient in depolymerizing unprocessed lignocellulose, needing no preprocessing/pretreatment of the biomasses. However, it natively produces low levels of laccase. After 15 rounds of serially adapting this thermophilic strain in the presence of unprocessed corn stover as the selective pressure, we recorded a 20-fold increase in catalytic laccase activity, at 9.23 ± 0.6 U/mL, in an adapted yet stable strain of Geobacillus sp. WSUCF1, compared with the initial laccase production (0.46 ± 0.04 U/mL) obtained with the unadapted strain grown on unprocessed corn stover before optimization. Chemical composition analysis demonstrated that lignin removal by the adapted strain was 22 wt.% compared with 6 wt.% removal by the unadapted strain. These results signify a favorable prospect for fast, cost competitive bulk production of this thermostable enzyme. Also, this work has practical importance, as this fast adaptation of the Geobacillus sp. strain WSUCF1 suggests the possibility of growing industrial quantities of Geobacillus sp. strain WSUCF1 cells as biocatalysts on reasonably inexpensive carbon sources for commercial use. This work is the first application of the adaptive laboratory evolution approach for developing the desired phenotype of enhanced ligninolytic capability in any microbial strain.

Rhenium(I)-based Double-heterostranded Helicates.

Rhenium(I)-based supramolecular coordination complexes were obtained using Re2(CO)10, (2-hydroxyphenyl)benzimidazole-derived bis-chelating N∩O donors and a benzimidazolyl-derived ditopic monodentate N-donor possessing Troger's base spacer in a one-pot approach.

Effect of vitamin D supplementation during pregnancy on neonatal mineral homeostasis and anthropometry of the newborn and infant.

Hypovitaminosis D is common in India. In the present prospective partially randomised study of vitamin D (D3) supplementation during pregnancy, subjects were randomised in the second trimester to receive either one oral dose of 1500 µg vitamin D3 (group 1, n 48) or two doses of 3000 µg vitamin D3 each in the second and third trimesters (group 2, n 49). Maternal 25-hydroxyvitamin D (25(OH)D) at term, cord blood (CB) alkaline phosphatase (ALP), neonatal serum Ca and anthropometry were measured in these subjects and in forty-three non-supplemented mother-infant pairs (usual care). Median maternal 25(OH)D at term was higher in group 2 (58·7, interquartile range (IQR) 38·4-89·4 nmol/l) v. group 1 (26·2, IQR 17·7-57·7 nmol/l) and usual-care group (39·2, IQR 21·2-73·4 nmol/l) (P = 0·000). CB ALP was increased (>8.02 µkat/l or >480 IU/l) in 66·7 % of the usual-care group v. 41·9 % of group 1 and 38·9 % of group 2 (P = 0·03). Neonatal Ca and CB 25(OH)D did not differ significantly in the three groups. Birth weight, length and head circumference were greater and the anterior fontanelle was smaller in groups 1 and 2 (3·08 and 3·03 kg, 50·3 and 50·1 cm, 34·5 and 34·4 cm, 2·6 and 2·5 cm, respectively) v. usual care (2·77 kg, 49·4, 33·6, 3·3 cm; P = 0·000 for length, head circumference and fontanelle and P = 0·003 for weight). These differences were still evident at 9 months. We conclude that both 1500 µg and two doses of 3000 µg vitamin D3 had a beneficial effect on infant anthropometry, the larger dose also improving CB ALP and maternal 25(OH)D.

Vitamin D deficiency in rural girls and pregnant women despite abundant sunshine in northern India.

CONTEXT: Vitamin D deficiency is common in urban Indians despite living in the tropics and its public health consequences are enormous. However, 70% of India is rural, and data from rural subjects, who are expected to have good sun exposure, are scant. OBJECTIVES: To determine the population prevalence of vitamin D deficiency in rural pregnant women and adolescent girls, compare serum 25-hydroxyvitamin D (25OHD) status in adolescent boys from the same families, and determine seasonal differences in serum 25OHD. DESIGN: A cross-sectional study conducted over 18 months. SUBJECTS: A random selection of 121 adolescent girls from a survey of a population of 8270 in a rural low socioeconomic community; 139 pregnant women in the second trimester; and a subset of 28 adolescent girls compared with 34 brothers. MEASUREMENTS: Serum 25OHD, serum alkaline phosphatase (AP), sun exposure, and dietary calcium intake. RESULTS: The age-adjusted community prevalence of vitamin D deficiency (25OHD < 50 nmol/l) in adolescent girls was 88.6%. Seventy-four per cent of pregnant women had vitamin D deficiency. Mean +/- SD 25OHD in girls and women in summer was 55.5 +/- 19.8 nmol/l compared to 27.3 +/- 12.3 nmol/l in winter (P < 0.001). Winter serum 25OHD in boys (67.5 +/- 29.0 nmol/l) was higher than that in their sisters (31.3 +/- 13.5 nmol/l, P < 0.001). CONCLUSION: We report a high prevalence of vitamin D deficiency among pregnant women and adolescent girls from a rural Indian community. Boys are relatively protected. Seasonal variation in serum 25OHD is significant at latitude 26 degrees N.