Abundant Enzyme Research Articles

New insights into the inhibition performance and mechanisms of sodium dodecyl benzene sulfonate (SDBS) on nitrogen removal in activated sludge-biofilm system

To investigate the effect of sodium dodecyl benzene sulfonate (SDBS) on nitrogen (N) removal performance and biological mechanisms, a gradient of SDBS concentrations was introduced into a set of sequencing batch biofilm reactors (SBBRs). The results indicated that a negative correlation was observed between SDBS concentration and the removal efficiencies of chemical oxygen demand (COD), ammonia nitrogen (NH4+-N), and nitrate nitrogen (NO3−-N). Compared to the control group, their removal efficiencies were the lowest (decreases of 11.83 %, 12.15 %, and 8.11 %) when SDBS concentration was 1.67 mg (g MLSS) -1 (5 mg L−1). High-throughput sequencing showed that the abundance of Proteobacteria remained stable with SDBS addition, while the abundances of Patescibacteria and Actinobacteria decreased by 0.67–0.70 % and 0.69–3.06 %, respectively. Moreover, SDBS reduced both microbial diversity and richness and hindered the interspecific relationships among microorganisms. It also inhibited N metabolic activities and led to a decrease in the expression of key functional genes involved in N transformation (nifD, nifH, nasA, norB, norC, and nosZ). Additionally, the abundances of key enzymes (EC:1.7.99.1, EC:1.7.2.4, and EC:1.1.1.42) in the N and tricarboxylic acid (TCA) cycles decreased following the addition of SDBS. This study provided insights into the effects of SDBS on N removal in activated sludge-biofilm systems and the adaptive responses of microbial communities to SDBS exposure.

Age-dependent changes in cytochrome P450 abundance and composition in human liver.

Cytochrome P450 (CYP) superfamily represents the major drug metabolizing enzymes responsible for metabolizing over 65% of therapeutic drugs, including those for pediatric use. CYP-ontogeny based physiologically-based pharmacokinetic (PBPK) models have emerged as useful tools to mechanistically extrapolate adult pharmacokinetic data to children. However, these models integrate physiological differences in pediatric population including age-dependent differences in the abundances of CYP enzymes. Conventionally, developmental changes in CYP enzymes have been reported using protein abundance and activity data from subcellular fractions such as microsomes, which is prone to high technical variability. Similarly, the available pediatric pharmacokinetic data suffer from the lack of specific CYP substrates, especially in younger children. In the present study, we utilized viable hepatocytes from 50 pediatric (age, day 1- 18 yr) and 8 adult human donors and carried out global proteomics-based quantification of all major hepatic CYP enzymes, including orphan enzymes that have not been studied previously. While CYPs 2B6, 3A5, 4A11, 4F3, and 4V2 did not show significant association with age, all other quantified isoforms either increased or decreased with age. CYPs 1A2, 2C8, 2C18, and 2C19 were absent or barely detected in the neonatal group, while CYP3A7 was the highest in this group. The >1-2 yr age-group showed the highest total abundance of all CYP enzymes. The age-dependent differences in CYP enzymes reported in this study can be used to develop ontogeny-based PBPK models, which in turn can help improve pediatric dose-prediction based on adult dosing, leading to safer drug pharmacology in children. Significance Statement We quantified age-dependent differences in the abundances of hepatic CYP enzymes using a large set of viable pediatric and adult hepatocytes using quantitative global proteomics. We report for the first time the ontogeny in the abundance of CYP enzymes in human hepatocytes, especially, orphan CYPs 20A1, 27A1, 51A1, 7B1, and 8B1 and the CYP4 subfamily of enzymes. Our study provides important data about CYP ontogeny that can be used for the better prediction of pediatric pharmacokinetics using physiologically-based pharmacokinetic modeling.

Seasonal Controls on Microbial Depolymerization and Oxidation of Organic Matter in Floodplain Soils.

Floodplain soils are vast reservoirs of organic carbon often attributed to anaerobic conditions that impose metabolic constraints on organic matter degradation. What remains elusive is how such metabolic constraints respond to dynamic flooding and drainage cycles characteristic of floodplain soils. Here we show that microbial depolymerization and respiration of organic compounds, two rate-limiting steps in decomposition, vary spatially and temporally with seasonal flooding of mountainous floodplain soils (Gothic, Colorado, USA). Combining metabolomics and -proteomics, we found a lower abundance of oxidative enzymes during flooding coincided with the accumulation of aromatic, high-molecular weight compounds, particularly in surface soils. In subsurface soils, we found that a lower oxidation state of carbon coincided with a greater abundance of chemically reduced, energetically less favorable low-molecular weight metabolites, irrespective of flooding condition. Our results suggest that seasonal flooding temporarily constrains oxidative depolymerization of larger, potentially plant-derived compounds in surface soils; in contrast, energetic constraints on microbial respiration persist in more reducing subsurface soils regardless of flooding. Our work underscores that the potential vulnerability of these distinct anaerobic carbon storage mechanisms to changing flooding dynamics should be considered, particularly as climate change shifts both the frequency and extent of flooding in floodplains globally.

Enlightening the toxinological dark matter of spider venom enzymes

Spiders produce highly adapted venoms featuring a complex mixture of biomolecules used mainly for hunting and defense. The most prominent components are peptidic neurotoxins, a major focus of research and drug development, whereas venom enzymes have been largely neglected. Nevertheless, investigation of venom enzymes not only reveals insights into their biological functions, but also provides templates for future industrial applications. Here we compared spider venom enzymes validated at protein level contained in the VenomZone database and from all publicly available proteo-transcriptomic spider venom datasets. We assigned reported enzymes to cellular processes and known venom functions, including toxicity, prey pre-digestion, venom preservation, venom component activation, and spreading factors. Our study unveiled extensive discrepancy between public databases and publications with regard to enzyme coverage, which impedes the development of novel spider venom enzyme-based applications. Uncovering the previously unrecognized abundance and diversity of venom enzymes will open new avenues for spider venom biodiscovery.

187 Exploring deep shotgun sequencing to understand the rumen microbial function in Angus bulls with divergent RFI EPD

Abstract We investigated the rumen microbiome of Angus bulls selected for Residual Feed Intake-Expected Progeny Difference (RFI-EPD) utilizing deep shotgun metagenomic sequencing. Negative RFI-EPD bulls (NegRFI: n = 10; RFI-EPD = -0.3883 kg/d) and Positive RFI-EPD bulls (PosRFI: n = 10; RFI-EPD = 0.2935 kg/d) were selected from a group of 59 Angus bulls [average body weight (BW) = 427.81 ± 18.77 kg] fed a high-forage total mixed ration after a 59-d testing period. At the end of the 59-d period, rumen fluid samples were collected for bacterial DNA extraction and subsequent shotgun metagenomic sequencing. Results of the metagenome analysis revealed greater gene richness in NegRFI bulls compared with PosRFI. Analysis of similarity revealed a significant difference (P = 0.05) in the rumen microbial community between the NegRFI and PosRFI. Linear Discriminant Analysis effect size (Lefse) was used to identify the differentially abundant taxa. The Lefse results showed that class Fibrobacteria (LDA = 5.1) and genus Fibrobacter (LDA = 4.8) were the most differentially enriched markers in NegRFI bulls, compared with PosRFI bulls. Relative abundance of the carbohydrate-active enzymes was also compared using lefse analysis. The results showed greater relative abundance of glycoside hydrolases and carbohydrate-binding modules such as GH5, CBM86, CBM35, GH43, and CBM6 (LDA > 3.0) in NegRFI bulls whereas GH13 and GT2 were greater in PosRFI. The distinct metabolic and microbial profiles observed in NegRFI, compared with PosRFI bulls, characterized by greater gene richness and specific taxa such as Fibrobacter, and variations in carbohydrate-active enzymes, underscore the potential genetic and functional differences in their rumen microbiome. These findings contribute to a deeper understanding of the interplay between host genetics, microbiota, and feed efficiency in Angus bulls, opening avenues for targeted interventions and advancements in livestock management practices.

Hydrochloric acid-modified biochar enhances nitrogen retention and microbial diversity in mollisols

The annual decline in the quality of China's mollisols and associated nitrogen loss necessitates effective interventions. This study investigates the effects of hydrochloric acid-modified biochar (BC-H700), derived from corn straw, on nitrogen retention and microbial diversity in mollisols through pot experiments. Through 100 days of continuous study found the application of 6 % BC-H700 significantly improved soil properties, increasing pH by 18.60 %, organic matter by 1.6 %, ammonium nitrogen by 26.96 %, and nitrate nitrogen by 23.04 %. By inquiring impact of BC-H700 on microbial enzyme activities in 60-day revealing BC-H700 also enhanced the activities of key nitrogen-transforming enzymes (AMO, NOR, NOS) and functional genes (nirK, norB, nosZ) while reducing narG gene abundance and NR enzyme activity. These changes indicate that BC-H700 promotes nitrification, inhibits denitrification, enhances nitrogen retention, and reduces N2O emissions. Furthermore, BC-H700 improved microbial diversity, increasing the abundance of beneficial bacteria such as Actinobacteria, Proteobacteria, Nitrospirae, and Gemmatimonadetes. The main environmental factors affecting soil bacterial community structure were identified as organic matter, NO3-, NO2-, AMO, NOR, and NOS. Overall, BC-H700 facilitates nitrogen transformation and retention through complex interactions with soil properties and microbes. This study contributes to understanding biochar's role in soil nitrogen management and offers practical insights for improving mollisol health.

Different bioaugmentation regimes that mitigate ammonium/salt inhibition in repeated batch anaerobic digestion: Generic converging trend of microbial communities

Bioaugmentation regimes (i.e., dosage, repetition, and timing) in AD must be optimized to ensure their effectiveness. Although previous studies have investigated these aspects, most have focused exclusively on short-term effects, with some reporting conflicting conclusions. Here, AD experiments of three consecutive repeated batches were conducted to determine the effect of bioaugmentation regimes under ammonium/salt inhibition conditions. A positive correlation between reactor performance and inoculum dosage was confirmed in the first batch, which diminished in subsequent batches for both inhibitors. Moreover, a diminishing marginal effect was observed with repeated inoculum introduction. While the bacterial community largely influenced the reactor performance, the archaeal community exhibited only a minor impact. Prediction of the key enzyme abundances suggested an overall decline in different AD steps. Overall, repeated batch experiments revealed that a homogeneous bacterial community deteriorated the AD process during long-term operation. Thus, a balanced bacterial community is key for efficient methane production.

10-Gingerol Increases Antioxidant Enzymes and Attenuates Lipopolysaccharide-Induced Inflammation by Modulating Adipokines in 3T3-L1 Adipocytes.

Obesity increases reactive oxygen species production and alters adipokines levels, resulting in a low-grade chronic inflammation state, which contributes to tissue metabolic dysfunction. 10-gingerol, a phenol present in ginger, has shown potential anti-obesogenic effects in vitro. However, the antioxidant and anti-inflammatory properties of 10-gingerol have not been approached. The aim of this study was to investigate the effects of 10-gingerol on antioxidant enzymes' expression and adipokine production in 3T3-L1 adipocytes in response to lipopolysaccharide (LPS)-induced inflammation. 10-gingerol antioxidant capacity was assessed through Oxygen Radical Absorbance Capacity (ORAC) , Ferric Reducing Antioxidant Power (FRAP), and radical scavenging activity of 2,2-diphenyl-2-picrylhydrazyl (DPPH) assays. 3T3-L1 cells were differentiated and stimulated with 100 ng/mL LPSs. Then, 15 µg/mL 10-gingerol was added for 48 h. The mRNA expression and protein abundance of antioxidant enzymes were evaluated by qPCR and Western blot, respectively. Adipokine levels were determined by ELISA. 10-gingerol showed low FRAP and DPPH values but a moderate ORAC value. Moreover, 10-gingerol increased Gpx1 and Sod1 but downregulated Cat expression. Additionally, 10-gingerol significantly increased CAT and GPx1 levels but not SOD-1. Finally, adiponectin and leptin concentrations were increased while resistin and tumor necrosis factor alpha (TNFα) were decreased by 10-gingerol. 10-gingerol presented antioxidant potential by increasing antioxidant enzymes and attenuated LPS-induced inflammation by modulating adipokines in 3T3-L1 adipocytes.

Upcycling of nutrients from kitchen waste: Integration of anaerobic digestion system and microbial protein production system

To upcycle the nutrients from kitchen waste (KW), an integrated system consisting of anaerobic digestion (AD) reactor and microbial protein (MP) production reactor was established in this study. The subsystem I (AD system) demonstrated an efficient bio-energy production (282.37 mL CH4/g VS), with 553.54 mg/L of NH4+-N remained in the digestate. The subsystem II (MP production system) utilized the nitrogenous constituents of the digestate, with 2.04 g/L MP production. In order to further enhance the recovery efficiency, C/N ratio in the subsystem II was studied. NH4+-N recovery efficiency was 23.08% higher after C/N ratio optimization along with 0.24 g/L increment on MP production. Over 0.7 g/L of essential amino acids was obtained, according with the qualitative necessary for the feeds. Also, the key enzyme abundance of CO2 releasing and amino acid biosynthesis was obviously increased with max. 55.21%. Meanwhile, the integrated system was profitable via a simplified economic assessment.

Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.

Excess body fat elevates colorectal cancer risk. While bariatric surgery (BRS) induces significant weight loss, its effects on the fecal stream and colon biology are poorly understood. Specifically, limited data exist on the impact of bariatric surgery (BRS) on fecal secondary bile acids (BA), including lithocholic acid (LCA), a putative promotor of colorectal carcinogenesis. This cross-sectional case-control study included 44 patients with obesity; 15 pre-BRS (controls) vs. 29 at a median of 24.1months post-BRS.We examined the fecal concentrations of 11 BA by liquid chromatography and gene abundance of BA-metabolizing bacterial enzymes through fecal metagenomic sequencing. Differences were quantified using non-parametric tests for BA levels and linear discriminant analysis (LDA) effect size (LEfSe) for genes encoding BA-metabolizing enzymes. Total fecal secondary BA concentrations trended towards lower levels post- vs. pre-BRS controls (p = 0.07). Individually, fecal LCA concentrations were significantly lower post- vs. pre-BRS (8477.0 vs. 11,914.0 uM/mg, p < 0.008). Consistent with this finding, fecal bacterial genes encoding BA-metabolizing enzymes, specifically 3-betahydroxycholanate-3-dehydrogenase (EC 1.1.1.391) and 3-alpha-hydroxycholanate dehydrogenase (EC 1.1.1.52), were also lower post- vs. pre-BRS controls (LDA of - 3.32 and - 2.64, respectively, adjusted p < 0.0001). Post-BRS fecal BA concentrations showed significant inverse correlations with weight loss, a healthy diet quality, and increased physical activity. Concentrations of LCA, a secondary BA, and bacterial genes needed for BA metabolism are lower post-BRS. These changes can impact health and modulate the colorectal cancer cascade. Further research is warranted to examine how surgical alterations and the associated dietary changes impact bile acid metabolism.

Spatial and temporal dynamics of microbes and genes in drinking water reservoirs: Distribution and potential for taste and odor generation

Numerous reservoirs encounter challenges related to taste and odor issues, often attributed to odorous compounds such as geosmin (GSM) and 2-methylisoborneol (2-MIB). In this study, two large reservoirs located in northern and southern China were investigated. The Jinpen (JP) reservoir had 45.99 % Actinomycetes and 14.82 % Cyanobacteria, while the Xikeng (XK) reservoir contained 37.55 % Actinomycetes and 48.27 % Cyanobacteria. Most of the 2-MIB produced in surface layers of the two reservoirs in summer originated from Cyanobacteria, most of the 2-MIB produced in winter and in the bottom water originated from Actinomycetes. Mic gene abundance in the XK reservoir reached 5.42 × 104 copies/L in winter. The abundance of GSM synthase was notably high in the bottom layer and sediment of both reservoirs, while 2-MIB synthase was abundant in the surface layer of the XK reservoir, echoing the patterns observed in mic gene abundance. The abundance of odor-producing enzymes in the two reservoirs was inhibited by total nitrogen, temperature significantly influenced Actinomycetes abundance in the JP reservoir, whereas dissolved oxygen had a greater impact in the XK reservoir. Overall, this study elucidates the molecular mechanisms underlying odor compounding, providing essential guidance for water quality management strategies and the improvement of urban water reservoir quality.

Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity.

Entomopathogenic fungi belonging to the Order Hypocreales are renowned for their ability to infect and kill insect hosts, while their endophytic mode of life and the beneficial rhizosphere effects on plant hosts have only been recently recognized. Understanding the molecular mechanisms underlying their different lifestyles could optimize their potential as both biocontrol and biofertilizer agents, as well as the wider appreciation of niche plasticity in fungal ecology. This study describes the comprehensive whole genome sequencing and analysis of one of the most effective entomopathogenic and endophytic EPF strains, Metarhizium brunneum V275 (commercially known as Lalguard Met52), achieved through Nanopore and Illumina reads. Comparative genomics for exploring intraspecies variability and analyses of key gene sets were conducted with a second effective EPF strain, M. brunneum ARSEF 4556. The search for strain- or species-specific genes was extended to M. brunneum strain ARSEF 3297 and other species of genus Metarhizium, to identify molecular mechanisms and putative key genome adaptations associated with mode of life differences. Genome size differed significantly, with M. brunneum V275 having the largest genome amongst M. brunneum strains sequenced to date. Genome analyses revealed an abundance of plant-degrading enzymes, plant colonization-associated genes, and intriguing intraspecies variations regarding their predicted secondary metabolic compounds and the number and localization of Transposable Elements. The potential significance of the differences found between closely related endophytic and entomopathogenic fungi, regarding plant growth-promoting and entomopathogenic abilities, are discussed, enhancing our understanding of their diverse functionalities and putative applications in agriculture and ecology.

Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway.

The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase motor domains, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of native structures of Cdc48 affinity purified from budding yeast lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data uncover elements of Shp1-Cdc48 interactions and support a 'hand-over-hand' mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by the D2 motor in substrate translocation/unfolding.

Genomic Exploration of a Chitinolytic Streptomyces albogriseolus PMB5 Strain from European mantis (Mantis religiosa).

The genus Streptomyces is renowned not only for its natural antibiotic production but also for its abundant chitinolytic enzymes, which break down stubborn chitin into chitooligosaccharides. Despite this, there have been limited studies utilizing whole-genome sequencing to explore the repertoire of chitin degradation and utilization genes in Streptomyces. A particularly compelling source of novel antimicrobials and enzymes lies in the microbiota of insects, where bacterial symbionts produce antimicrobials to protect against opportunistic pathogens and enzymes to adapt to the environment. In this study, we present the chitinolytic strain Streptomyces albogriseolus PMB5, isolated from the insectivorous Mantis religiosa (European mantis). Whole-genome sequencing revealed that PMB5 harbors a linear chromosome of 7,211,961 bp and a linear plasmid of 327,989 bp. The genome comprises 6683 genes, including 6592 protein-coding sequences and 91 RNA genes. Furthermore, genome analysis revealed 19 biosynthetic gene clusters covering polyketides, terpenes, and RiPPs, with 10 clusters showing significant gene similarity (>80%) to known clusters like antimycin, hopene, and geosmin. In the genome of S. albogriseolus PMB5, we were able to identify several antibiotic resistance genes; these included cml (resistance to phenicol), gimA (resistance to macrolides), parY (resistance to aminocoumarin), oleC/oleD (resistance to macrolides), novA (resistance to aminocoumarin) and bla/blc (resistance to beta-lactams). Additionally, three clusters displayed no similarity to known sequences, suggesting novel bioactive compound discovery potential. Remarkably, strain PMB5 is the first reported S. albogriseolus capable of thriving on a medium utilizing chitin as a carbon source, with over 50 chitin-utilizing genes identified, including five AA10 family LPMOs, five GH18 chitinases, and one GH19 chitinase. This study significantly enhances the genomic understanding of S. albogriseolus, a species previously underrepresented in research, paving the way to further exploration of the biotechnological potential of the species.

Proteomic insights into adventitious root formation in Larix kaempferi

The adventitious root formaton (ARF) in excised plant parts is essential for the survival of isolated plant fragments. In this study, we explored the complex mechanisms of ARF in Larix kaempferi by conducting a comprehensive proteomic analysis across three distinct stages: the induction of adventitious root primordia (C1, 0–25 d), the formation of adventitious root primordia (C2, 25–35 d), and the elongation of adventitious roots (C3, 35–45 d). We identified 1976 proteins, with 263 and 156 proteins exhibiting increased abundance in the C2/C1 and C3/C2 transitions, respectively. In contrast, a decrease in the abundance of 106 and 132 proteins suggests a significant demand for metabolic processes during the C2/C1 phase. The abundance of IAA-amino acid hydrolase and S-adenosylmethionine synthase were increased in the C2/C1 phase, underscoring the role of auxin in adventitious root induction. The decrease in abundance of photosynthesis-related proteins during the C2/C1 phase highlights the significance of initial light conditions in adventitious root induction. Moreover, variation in cell wall synthesis and metabolic proteins in the C2/C1 and C3/C2 stages suggests that cell wall metabolism is integral to adventitious root regeneration. Gene Ontology enrichment analysis revealed pathways related to protein modification enzymes, including deubiquitinases and kinases, which are crucial for modulating protein modifications to promote ARF. Furthermore, the increased abundance of antioxidant enzymes, such as peroxidases and glutathione peroxidases, indicates a potential approach for enhancing ARF by supplementing the culture medium with antioxidants. Our study provides insights into metabolic changes during ARF in L. kaempferi, offering strategies to enhance adventitious root regeneration. These findings have the potential to refine plant propagation techniques and expedite breeding processes. SignficanceThe main challenge in the asexual reproduction technology of Larix kaempferi lies in adventitious root formation (ARF). While numerous studies have concentrated on the efficiency of ARF, proteomic data are currently scarce. In this study, we collected samples from three stages of ARF in L. kaempferi and subsequently performed proteomic analysis. The data generated not only reveal changes in protein abundance but also elucidate key metabolic processes involved in ARF. These insights offer a novel perspective on addressing the challenge of adventurous root regeneration.

Screening and Identification of Protease-Producing Microorganisms in the Gut of Gryllotalpa orientalis (Orthoptera: Gryllotalpidae).

The insect gut harbors a diverse array of functional microorganisms that warrant further exploration and utilization. However, there is currently a paucity of research reports on the discovery of protease-producing microorganisms with industrial application value in the gut. Here, we employed microbial culturing to screen and identify the protease-producing microorganisms in the gut extract of Gryllotalpa orientalis. Based on morphological, physiological, and biochemical characterization, 16S rRNA sequencing, as well as ANI and dDDH values of whole genome, the protease-producing strains isolated from the insect gut were identified as Priestia aryahattai DBM-1 and DX-4, P. megaterium DX-3, and Serratia surfactantfaciens DBM-5. According to whole-genome analysis, strain DBM-5, which exhibited the highest enzyme activity, possesses abundant membrane transport genes and carbohydrate metabolism enzymes. In contrast, strains DX-3 and DX-4 not only have the ability to hydrolyze proteins but also demonstrate the capability to hydrolyze plant materials. Furthermore, strains that are closely related tend to have similar metabolic product gene clusters in their genomes. The screening and identification of protease resources are essential for the subsequent development and utilization of gut functional microorganisms and genetic resources in insects.

Glycerol Handling in Paired Visceral and Subcutaneous Adipose Tissues in Women with Normal Weight and Upper-Body Obesity.

In adipose tissue, reduced expression of the glycerol channel aquaporin 7 (AQP7) has been associated with increased accumulation of triglyceride. The present study determines the relative protein abundances of lipolytic enzymes, AQP7, and cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C) in paired mesenteric and omental visceral adipose tissue (VAT) and abdominal and femoral subcutaneous adipose tissue (SAT) in women with either normal weight or upper-body obesity. No differences in the expression of hormone-sensitive lipase (HSL) or AQP7 were found between the two groups in the four depots. The expression of adipocyte triglyceride lipase (ATGL) and HSL were higher in omental VAT and femoral SAT than in mesenteric VAT in both groups of women. Similarly, AQP7 expression was higher in omental VAT than in mesenteric VAT. The expression of PEPCK-C was lower in omental VAT than in femoral SAT. No correlation between the expression of AQP7 and the mean adipocyte size was observed; however, the expression of PEPCK-C positively correlated with the mean adipocyte size. In conclusion, a depot-specific protein expression pattern was found for ATGL, HSL, AQP7, and PEPCK-C. The expression pattern supports that the regulation of AQP7 protein expression is at least in part linked to the lipolytic rate. Furthermore, the results support that the synthesis of glycerol-3-phosphate via glyceroneogenesis contributes to regulating triglyceride accumulation in white adipose tissue in women.

Developmental Expression of Drug Transporters and Conjugating Enzymes Involved in Enterohepatic Recycling: Implication for Pediatric Drug Dosing.

Around 50% of the drugs used in children have never been tested for safety and efficacy in this vulnerable population. Immature drug elimination pathways can lead to drug toxicity when pediatric doses are determined using empirical methods such as body-surface area or body-weight-normalized adult dosing. In the absence of clinical data, physiologically-based pharmacokinetic (PBPK) modeling has emerged as a useful tool to predict drug pharmacokinetics in children. These models utilize developmental physiological data, including age-dependent differences in the abundance of drug-metabolizing enzymes and transporters (DMET), to mechanistically extrapolate adult pharmacokinetic data to children. The reported abundance data of hepatic DMET proteins in subcellular fractions isolated from frozen tissue are prone to high technical variability. Therefore, we carried out the proteomics-based quantification of hepatic drug transporters and conjugating enzymes in 50 pediatric and 8 adult human hepatocyte samples. Out of the 34 studied proteins, 28 showed a significant increase or decrease with age. While MRP6, OAT7, and SULT1E1 were highest in < 1-year-old samples, the abundance of P-gp and UGT1A4 was negligible in < 1-year-old samples and increased significantly after 1 year of age. Incorporation of the age-dependent abundance data in PBPK models can help improve pediatric dose prediction, leading to safer drug pharmacotherapy in children.

Insight into the autochthonous lactic acid bacteria as starter culture for improving the quality of Sichuan radish paocai: Changes in microbial diversity and metabolic profiles

Paocai is a traditional Chinese fermented vegetable product popular in Asian countries. Recently, functional starters were used to control the fermentation process and improve the quality of paocai. In this study, three autochthonous lactic acid bacteria including Lactiplantibacillus plantarum LB6, Lactiplantibacillus pentosus LB3, and Weissella cibaria W51 were selected as starters and the effect of the starters on the fermentation of paocai was investigated. The results suggested that the inoculated fermentation led to a lower nitrite peak and more pronounced changes in pH and total titratable acid in the early stage of fermentation, compared with natural fermentation. Analysis of the flavor compounds indicated that the total content of volatile organic compounds of paocai through natural fermentation was significantly lower than that in inoculated fermentation. As for free amino acids, in the early stage of fermentation, the types and contents of free amino acids in the inoculated fermentation paocai were higher than those in the blank group. In the later stage of fermentation, the contents of amino acids representing umami and sweet tastes were also higher than those in the blank group. The bacterial community analysis showed that Lactobacillus and Lactococcus were the dominant bacteria in both inoculated fermentation and natural fermentation. Then, the correlations among physicochemical properties, microbial community and flavor compounds were revealed, and it was found that the dominant bacteria such as Lactococcus, Leuconostoc, Lactobacillus and Weissella displayed a considerable impact on the physical and chemical properties and flavor of paocai. In addition, the metabolic pathways involved in flavor formation and the abundance of related enzymes were elucidated. The abundance of enzymes involved in generating prephenic acid, 2-methylbutanoic acid, L-lactic acid, D-lactic acid, butanoic acid, etc., and in the pathway of producing flavor substances (His, Met, ethyl hexanoate, etc.) was up-regulated in the inoculated fermentation. Results presented in this study may provide a reference for the development of paocai starters and further guidance for the flavor improvement of Sichuan paocai.

Application of fungal inoculants enhances colonization of secondary bacterial degraders during in situ paddy straw degradation: a genomic insights into cross-domain synergism.

Rice cultivation generates huge amounts of on farm residues especially under mechanical harvesting. Paddy straw being recalcitrant hinders sowing of upcoming rabi crops like wheat and mustard. Non-environmental sustainable practice of on-farm burning of the paddy residues is being popularly followed for quick disposal of the agro-residues and land preparation. However, conservation agriculture involving in situ residue incorporation can be a sustainable option to utilize the residues for improvement of soil biological health. However, low temperature coupled with poor nitrogen status of soil reduces the decomposition rate of residues that may lead to nitrogen immobilization and hindrance in land preparation. In this direction, ecological impact of two approaches viz priming with urea and copiotrophic fungus-based bioformulation (CFB) consisting of Coprinopsis cinerea LA2 and Cyathus stercoreus ITCC3745 was studied for in situ degradation of residues. Succession of bacterial diversity was deciphered through high throughput whole metagenomic sequencing along with studies on dynamics of soil microbial enzymes. Treatments receiving CFB (T1) and urea (T2) when compared with bulk soil (absolute control) showed an increase in richness of the microbial diversity as compared to control straw retained treatment control (T3). The β diversity indices also indicated sufficient group variations among the treatments receiving CFB and urea as compared to only straw retained treatment and bulk soil. Priming of paddy straw with CFB and urea also induced significant rewiring of the bacterial co-occurrence networks. Quantification of soil ligno-cellulolytic activity as well as abundance of carbohydrate active enzymes (CAZy) genes indicated high activities of hydrolytic enzymes in CFB primed straw retention treatment as compared to urea primed straw retention treatment. The genomic insights on effectiveness of copiotrophic fungus bioformulation for in situ degradation of paddy straw will further help in developing strategies for management of crop residues in eco-friendly manner.