Fatty Acid Degradation Research Articles

FAMS-A Targeted Fatty Acid Mass Spectrometry Method for Monitoring Free Fatty Acids from Polysorbate Hydrolysis.

Polysorbates are the predominant surfactants used to stabilize protein formulations. Unfortunately, polysorbates can undergo hydrolytic degradation, which releases fatty acids that can accumulate to form visible particles. The detection and quantitation of these fatty acid degradation products are critical for assessing the extent of polysorbate degradation and the associated risks of particle formation. We previously developed a user-friendly mass spectrometric method called Fatty Acids by Mass Spectrometry (FAMS) to quantify the free fatty acids. The FAMS method was validated according to ICH Q2 (R1) guidelines and is suitable for a wide range of products, buffers and protein concentrations. The end-to-end workflow can be automated from sample preparation to data analysis. To broaden method accessibility, the QDa detector selected for fatty acid measurement does not require specific mass spectrometry experience. We provide here a detailed procedure for both manual and automated sample preparation for high-throughput analysis. In addition, we highlight in this protocol the critical operational details, procedural watchouts and troubleshooting tips to support the successful execution of this method in another laboratory.

Deciphering Antibiotic-Targeted Metabolic Pathways in Acinetobacter baumannii: Insights from Transcriptomics and Genome-Scale Metabolic Modeling.

In the ongoing battle against antibiotic-resistant infections, Acinetobacter baumannii has emerged as a critical pathogen in healthcare settings. To understand its response to antibiotic-induced stress, we integrated transcriptomic data from various antibiotics (amikacin sulfate, ciprofloxacin, polymyxin-B, and meropenem) with metabolic modeling techniques. Key metabolic pathways, including arginine and proline metabolism, glycine-serine and threonine metabolism, glyoxylate and dicarboxylate metabolism, and propanoate metabolism, were significantly impacted by all four antibiotics across multiple strains. Specifically, biotin metabolism was consistently down-regulated under polymyxin-B treatment, while fatty acid metabolism was perturbed under amikacin sulfate. Ciprofloxacin induced up-regulation in glycerophospholipid metabolism. Validation with an independent dataset focusing on colistin treatment confirmed alterations in fatty acid degradation, elongation, and arginine metabolism. By harmonizing genetic data with metabolic modeling and a metabolite-centric approach, our findings offer insights into the intricate adaptations of A. baumannii under antibiotic pressure, suggesting more effective strategies to combat antibiotic-resistant infections.

Hydrogen sulfide attenuates chilling injury in loquat fruit by alleviating oxidative stress and maintaining cell membrane integrity

The effects of hydrogen sulfide (H2S) on chilling injury (CI), reactive oxygen species (ROS) metabolism, sugar metabolism, pentose phosphate pathway (PPP), and membrane lipid metabolism in loquat fruit throughout the refrigerated period were investigated in this study. The findings indicated that H2S application restrained the increase in internal browning (IB), malondialdehyde (MDA) content, and electrolyte leakage, while sustaining higher total phenolic and total flavonoid levels, and lower soluble quinone content in loquat fruit. Besides, H2S promoted antioxidant accumulation and increased antioxidant enzyme activities by the regulation of ROS metabolism, along with increasing fructose and glucose levels and reducing power by activating sugar metabolism and PPP. Furthermore, H2S treatment retarded the degradation of phospholipids and fatty acids in loquat fruit by modulating membrane lipid metabolism relevant enzyme activities. These findings indicated that H2S application mitigated CI in loquat fruit by alleviating oxidative stress and maintaining cell membrane structural integrity.

Integrated ultrasensitive metabolomics and single-cell transcriptomics identify crucial regulators of sheep oocyte maturation and early embryo development in vitro

IntroductionDevelopmental competence of oocytes matured in vitro is limited due to a lack of complete understanding of metabolism and metabolic gene expression during oocyte maturation and embryo development. Conventional metabolic analysis requires a large number of samples and is not efficiently applicable in oocytes and early embryos, thereby posing challenges in identifying key metabolites and regulating their in vitro culture system. ObjectivesTo enhance the developmental competence of sheep oocytes, this study aimed to identify and supplement essential metabolites that were deficient in the culture systems. MethodsThe metabolic characteristics of oocytes and embryos were determined using ultrasensitive metabolomics analysis on trace samples and single-cell RNA-seq. By conducting integrated analyses of metabolites in cells (oocytes and embryos) and their developmental microenvironment (follicular fluid, oviductal fluid, and in vitro culture systems), we identified key missing metabolites in the in vitro culture systems. In order to assess the impact of these key missing metabolites on oocyte development competence, we performed in vitro culture experiments. Furthermore, omics analyses were employed to elucidate the underlying mechanisms. ResultsOur findings demonstrated that betaine, carnitine and creatine were the key missing metabolites in vitro culture systems and supplementation of betaine and L-carnitine significantly improved the blastocyst formation rate (67.48% and 48.61%). Through in vitro culture experiments and omics analyses, we have discovered that L-carnitine had the potential to promote fatty acid oxidation, reduce lipid content and lipid peroxidation level, and regulate spindle morphological grade through fatty acid degradation pathway. Additionally, betaine may participate in methylation modification and osmotic pressure regulation, thereby potentially improving oocyte maturation and early embryo development in sheep. ConclusionTogether, these analyses identified key metabolites that promote ovine oocyte maturation and early embryo development, while also providing a new viewpoint to improve clinical applications such as oocyte maturation or embryo culture.

Comparative analysis of edible oil quality in fish nugget frying: Vacuum vs. atmospheric conditions

Consumer awareness about safe and nutritional fried food leads to the development of vacuum frying which overcomes major limitations of traditional frying. In this study effect of vacuum (120◦C, 40kPa) and atmospheric frying (180°C) on the fried fish nuggets quality and frying oil was compared. Oils used for frying (soyabean and mustard oil) were repeatedly used for 25 h without any replenishment. Vacuum frying (VF) oils and fish nuggets show a slower degradation of polyunstaurated fatty acids (PUFA), lesser transfatty acid (TFA) formation and a low C18:2/C16:0 ratio as compared to atmospheric frying (AF). Soyabean oil used for vacuum frying fish nuggets show an increase from 2.14 % to 3.11 %, decrease from 45.25 % to 38.29 %, while as AF fish nuggets show an increase from 2.14 % to 5.48 % and decrease from 45.25 % to 22.19 % in TFA content and PUFA content respectively after 25 h of frying. Oil uptake was also found lower (34.89 %) in VF fish nuggets as compared to AF(37.45 %), while as water loss was higher in AF chips than VF nuggets by 1.42-fold after 10 minutes of frying. Sensory analysis revealed that VF fish nuggets show a higher retention of sensory attributes and overall acceptability but they were less crispy then AF fish nuggets. Overall, vacuum frying results in the production of safe and nutritious fried fish nuggets.

Omega-3 PUFAs slow organ aging through promoting energy metabolism

Energy metabolism disorder, mainly exhibiting the inhibition of fatty acid degradation and lipid accumulation, is highly related with aging acceleration. However, the intervention measures are deficient. Here, we reported Omega-3 polyunsaturated fatty acids (Omega-3 PUFAs), especially EPA, exerted beneficial effects on maintaining energy metabolism and lipid homeostasis to slow organ aging. As the endogenous agonist of peroxisome proliferator–activated receptor α (PPARα), Omega-3 PUFAs significantly boosted fatty acid β-oxidation and ATP production in multiple aged organs. Consequently, Omega-3 PUFAs effectively inhibited age-related pathological changes, preserved organ function, and retarded aging process. The beneficial effects of Omega-3 PUFAs were also testified in mfat-1 transgenic mice, which spontaneously generate abundant endogenous Omega-3 PUFAs. In conclusion, our study innovatively demonstrated Omega-3 PUFAs administration in diet slow aging through promoting energy metabolism. The supplement of Omega-3 PUFAs or fat-1 transgene provides a promising therapeutic approach to promote healthy aging in the elderly.

TSA attenuates the progression of c-Myc-driven hepatocarcinogenesis by pAKT-ADH4 pathway

Hepatocellular carcinoma (HCC) is the primary malignant tumor of the liver. c-Myc is one of the most common oncogenes in clinical settings, and amplified levels of c-Myc are frequently found in HCC. Histone deacetylase inhibitors (HDACi), such as Trichostatin A (TSA), hold enormous promise for the treatment of HCC. However, the potential and mechanism of TSA in the treatment of c-Myc-induced HCC are unclear. In this study, we investigated the effects of TSA treatment on a c-Myc-induced HCC model in mice. TSA treatment delayed the development of HCC, and liver function indicators such as ALT, AST, liver weight ratio, and spleen weight ratio demonstrated the effectiveness of TSA treatment. Oil red staining further demonstrated that TSA attenuated lipid accumulation in the HCC tissues of mice. Through mRNA sequencing, we identified that TSA mainly affected cell cycle and fatty acid degradation genes, with alcohol dehydrogenase 4 (ADH4) potentially being the core molecular downstream target. QPCR, immunohistochemistry, and western blot analysis revealed that ADH4 expression was repressed by c-Myc and restored after TSA treatment both in vitro and in vivo. Furthermore, we observed that the levels of total NAD+ and NADH, NAD+, NAD+/NADH, and ATP concentration increased after c-Myc transfection in liver cells but decreased after TSA intervention. The levels of phosphorylated protein kinase B (p-AKT) and p-mTOR were identified as targets regulated by TSA, and they governed the ADH4 expression and the downstream regulation of total NAD+ and NADH, NAD+, NAD+/NADH, and ATP concentration. Overall, our study suggests that TSA has a therapeutic effect on c-Myc-induced HCC through the AKT-mTOR-ADH4 pathway. These findings provide valuable insights into the potential treatment of HCC using TSA and shed light on the underlying molecular mechanisms involved.

Enhancing bioremediation of petroleum-contaminated soil by sophorolipids-modified biochar: Combined metagenomic and metabolomic analyses

In this study, sophorolipids (SLs)-modified biochar (BC-SLs) was used to enhance the bioremediation of petroleum hydrocarbons (PHs) contaminated soil. The biodegradation rate of petroleum hydrocarbons (PHs) by BC-SLs and BC treatments were 62.86 % and 52.64 % after 60 days of remediation experiments, respectively, higher than non-biochar treatment group (24.09 %). The metagenomic analysis showed that the abundance of petroleum-degrading bacteria Actinobacteria and Proteobacteria were increased by 3.8 % and 5.3 %, respectively in BC-SLs treatment, and the abundance of functional genes for PHs degradation, such as alkB, nidA and pcaG, were significantly increased by 12.85 %, 30.08 % and 21.01 %, respectively. The metabolomic analysis showed that BC-SLs facilitated the metabolic process of PHs, the microbial metabolism of petroleum hydrocarbons (PHs) became more active. Fatty acid degradation and polycyclic aromatic hydrocarbons (PAHs) degradation were up-regulated, indicating the promoting effect of the BC-SLs for PHs metabolism. The combined metagenomic and metabolomic analysis demonstrated the strong positive correlations between PHs metabolites and PHs-degrading bacteria, such as lauric acid vs. Actinobacteria, benzoic vs. Proteobacteria. The strong positive correlations between PHs metabolites and PHs-degrading genes were also observed, such as o-ehyltoluene vs. nahD, 4-isopropylbenzoic acid vs. etbAa. The modification of biochar with SLs increased the oxygen-containing functional groups on the surface of biochar. Meanwhile, the emulsification and solubilization of SLs promoted the bioavailability of PHs. The effects of BC-SLs on the nitrogen cycle during PHs remediation showed that it facilitated the accumulation of nitrogen-fixing genes, promoted nitrification but inhibited denitrification process. This study confirms that the application of BC-SLs is an effective remediation of PHs contamination and a sustainable method for controlling agricultural waste resources.

Multiomics reveals blood differential metabolites and differential genes in the early onset of ketosis in dairy cows

Ketosis—a metabolic state characterized by elevated levels of ketone bodies in the blood or urine—reduces the performance and health of dairy cows and causes substantial economic losses for the dairy industry. Currently, beta-hydroxybutyric acid is the gold standard for determining ketosis in cows; however, as this method is only applicable postpartum, it is not conducive to the early intervention of ketosis in dairy cows. In this study, the sera of dry, periparturient, postpartum ketotic, and healthy cows were analyzed by both transcriptomics and metabolomics techniques. Moreover, changes of gene expression and metabolites were observed, and serum physiological and biochemical indexes were detected by ELISA. The purpose was to screen biomarkers that can be used to detect the incidence of dry or periparturient ketosis in cows. The results showed that ketotic cows had increased levels of glycolipid metabolism indexes, oxidizing factors, and inflammatory factors during dry periods and liver damage, which could be used as early biomarkers to predict the onset of ketosis. Transcriptomic results yielded 20 differentially expressed genes (DEGs) between ketotic and healthy cows during dry, peripartum, and postpartum periods. GO and KEGG enrichment analyses indicated that these DEGs were involved in amino acid metabolism, energy metabolism, and disease-related signaling pathways. The metabolomics sequencing results showed that ketotic cows mainly showed enrichment in tricarboxylic acid cycle, butyric acid metabolism, carbon metabolism, lysine degradation, fatty acid degradation, and other signaling pathways. Metabolites differed between ketotic and healthy cows in dry, pre-parturition, and post-parturition periods. Combined transcriptomics and metabolomics analyses identified significant enrichment in the glucagon signaling pathway and the lysine degradation signaling pathway in dry, periparturient, and postpartum ketotic cows. PRKAB2 and SETMAR—key DEGs of the glucagon signaling pathway and lysine degradation signaling pathway, respectively—can be used as key marker genes for determining the early onset of ketosis in dairy cows.

Gut dysbiosis of Rana zhenhaiensis tadpoles after lead (Pb) exposure based on integrated analysis of microbiota and gut transcriptome

Lead (Pb) is a ubiquitously detected heavy metal pollutant in aquatic ecosystems. Previous studies focused mainly on the response of gut microbiota to Pb stress, with less emphasis on gene expression in intestine, thereby limiting the information about impacts of Pb on intestinal homeostasis in amphibians. Here, microbial community and transcriptional response of intestines in Rana zhenhaiensis tadpoles to Pb exposure were evaluated. Our results showed that 10 μg/L Pb significantly decreased bacterial diversity compared to the controls by the Simpson index. Additionally, 1000 μg/L Pb exposure resulted in a significant reduction in the abundance of Fusobacteriota phylum and Cetobacterium genus but a significant expansion in Hafnia-Obesumbacterium genus. Moreover, transcriptome analysis revealed that about 90 % of the DEGs (8458 out of 9450 DEGs) were down-regulated in 1000 μg/L Pb group, mainly including genes annotated with biological functions in fatty acid degradation, and oxidative phosphorylation, while up-regulated DEGs involved in metabolism of xenobiotics by cytochrome P450. The expression of Gsto1, Gsta5, Gstt4, and Nadph showed strong correlation with the abundance of genera Serratia, Lactococcus, and Hafnia-Obesumbacterium. The findings of this study provide important insights into understanding the influence of Pb on intestinal homeostasis in amphibians.

The aroma formation from fresh tea leaves of Longjing 43 to finished Enshi Yulu tea at an industrial scale.

Enshi Yulu tea (ESYL) is the most representative of steamed green tea in China, but its aroma formation in processing is unclear. Thus, the ESYL volatiles during the whole industrial processing were investigated using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. A total of 134 volatiles were identified. Among these, 31 differential volatiles [P < 0.05 and variable importance in projection (VIP) > 1] and 25 key volatiles [relative odor activity value (rOAV) and/or the ratio of each rOAV to the maximum rOAV (ROAV) > 1.0] were screened out, wherein β-ionone and nonanal were the most key odorants. Besides, the sensory evaluation combined with multivariate statistical analysis of volatiles pinpointed spreading, fixation, first drying, and second drying as the key processing steps that have a pronounced influence on the aroma quality of ESYL. Furthermore, the oxidative degradation of unsaturated fatty acids, synthesis of monoterpenes, and degradation of carotenoids were the main metabolic pathway for the formation of key odorants. The study provides comprehensive insights into the volatile characteristics during the industrial processing of ESYL and promote our understanding of the aroma formation in steamed green teas. © 2024 Society of Chemical Industry.

TetR-like regulator BP1026B_II1561 controls aromatic amino acid biosynthesis and intracellular pathogenesis in Burkholderia pseudomallei.

Burkholderia pseudomallei (Bp) causes the tropical disease melioidosis that afflicts an estimated 165,000 people each year. Bp is a facultative intracellular pathogen that transits through distinct intracellular stages including attachment to host cells, invasion through the endocytic pathway, escape from the endosome, replication in the cytoplasm, generation of protrusions towards neighboring cells, and host cell fusion allowing Bp infection to spread without exiting the intracellular environment. We have identified a TetR-like transcriptional regulator, BP1026B_II1561, that is up-regulated during the late stages of infection as Bp protrudes toward neighboring cells. We have characterized BP1026B_II1561 and determined that it has a role in pathogenesis. A deletional mutant of BP1026B_II1561 is attenuated in RAW264.7 macrophage and BALB/c mouse models of infection. Using RNA-seq, we found that BP1026B_II1561 controls secondary metabolite biosynthesis, fatty acid degradation, and propanoate metabolism. In addition, we identified that BP1026B_II1561 directly controls expression of an outer membrane porin and genes in the shikimate biosynthetic pathway using ChIP-seq. Transposon mutants of genes within the BP1026B_II1561 regulon show defects during intracellular replication in RAW264.7 cells confirming the role of this transcriptional regulator and the pathways it controls in pathogenesis. BP1026B_II1561 also up-regulates the majority of the enzymes in shikimate and tryptophan biosynthetic pathways, suggesting their importance for Bp physiology. To investigate this, we tested fluorinated analogs of anthranilate and tryptophan, intermediates and products of the shikimate and tryptophan biosynthetic pathways, respectively, and showed inhibition of Bp growth at nanomolar concentrations. The expression of these pathways by BP1026b_II1561 and during intracellular infection combined with the inhibition of Bp growth by fluorotryptophan/anthranilate highlights these pathways as potential targets for therapeutic intervention against melioidosis. In the present study, we have identified BP1026B_II1561 as a critical transcriptional regulator for Bp pathogenesis and partially characterized its role during host cell infection.

Refractory wastewater shapes bacterial assembly and key taxa during long-term acclimatization

Bacterial assembly and key taxa during long-term acclimatization in refractory wastewater treatment systems is of paramount importance for optimizing system performance and improving management strategies. Therefore, this study employed high-throughput sequencing, coupled with machine learning models and statistical analysis approaches, to comprehensively elucidate key features of bacterial communities and assembly processes in pesticide wastewater treatment systems. A nine-month monitoring showed substantial variation in diversity and composition of bacterial community between two interconnected biological treatment units (designated as BA and PA). Dynamics of bacterial communities in both units were similar. Moreover, water quality played crucial roles in regulating the bacterial community structure of activated sludge, which were primarily driven by deterministic patterns. Homogeneous selection contributed to 62.85 % and 64.43 % of the variations in BA and PA samples, respectively. Additionally, network analysis revealed significant modularity in bacterial compositions in both groups. Linear regression analysis identified major bacterial modules associated with metabolism and degradation functions. Notably, Module 2 in PA samples has significant positive correlations with functions related to metabolism of nucleotide, amino acid, and xenobiotics, as well as benzoate degradation. Furthermore, key taxa in ecological modules identified by Random Forest model, such as Pseudomonas, Sphingobium, and PHOS-HE28, were dominant populations with metabolism and degradation functions. Particularly, Sphingobium, appeared to be a potential multifunctional degrading bacterium, related to amino acid and xenobiotics metabolism, as well as fatty acid, valine, leucine, isoleucine, fluorobenzoate, and aminobenzoate degradation. These findings are important for developing operating strategies to maintain stable system performance during refractory wastewater treatment.

Characterization, sources, and formation processes of dicarboxylic acids, oxocarboxylic acids and α-dicarbonyls in PM2.5 aerosols in New Delhi

Daytime and nighttime fine aerosol (PM2.5) samples were collected during a heavy pollution episode in November 2020, January 2021, and also during clean event (August 2020) in New Delhi. These samples (n = 20) were analyzed for water-soluble dicarboxylic acids (diacids) and related compounds, carbonaceous components, and inorganic ions to identify their sources and atmospheric processing in different episodes/seasons. Among the measured organics, oxalic acid (C2) was found to be the most abundant species followed by terephthalic (tPh), succinic (C4), phthalic (Ph), and azelaic (C9) acids. Such high abundance of tPh were different from those in other Asian cities where C3 is generally the second or third dominant species. tPh very well correlated with OC, Cl− and K+, indicating combustion of biomass and plastic-containing waste may be the possible sources. Significant high contents of diacids, oxoacids, and dicarbonyls were observed during heavy pollution episode, implying an enhanced emission and/or atmospheric processing of these species. Additionally, two important secondary formation pathways for C2 diacid were discussed in New Delhi, i.e. (i) biomass burning derived (biogenic) volatile organic precursors lead to formation of C2 diacid through transformation of oxoacids and dicarbonyls by oxidation, and (ii) oxidative degradation of the unsaturated fatty acids results in formation of C5 and C4 which subsequently decompose to C2 diacid. This study demonstrated that both primary emissions in clean event and secondary production during polluted event are important sources of aerosols in New Delhi.

Targeted lipidomics-based study of radiation-induced metabolite profiles changes in plasma of total body irradiation cases

Purpose Lipidomics is an important tool for triaging exposed individuals, and helps early adoption of prevention and control strategies. The purpose of this study was to screen significantly perturbed lipids between pre- and post-irradiation of human plasma samples after total body irradiation (TBI) and explore potential radiation biomarkers for early radiation classification. Methods Plasma samples were collected before and after irradiation from 22 hospitalized cases of acute myeloid leukemia (AML) prepared for bone marrow transplantation. Acute total-body γ irradiation was performed at doses of 0, 4, 8, and 12 Gy. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) with multiple reaction monitoring (MRM) method was utilized. Self-paired studies before and after irradiation were performed to screen potential lipid categorization markers and markers of dose-response relationships for radiation perturbation in humans. Based on the screened potential markers, a human TBI dose estimation model was developed. Results In total, 426 individual lipids from 14 major classes were quantified and 152 potential biomarkers with categorical characteristics were screened. A total of 80 lipids (32 TGs, 29 SMs, 9 FAs, 5 CEs, 5 PIs) were upregulated at 4 Gy, and a total of 91 lipids (39 SMs, 18 TGs, 15 HexCers, 7 CEs, 6 Cers, 3 LacCers, 2 LPEs, 1 PI) were upregulated at 12 Gy. Comparison of the ROC curves between the non-exposed and exposed groups at different doses showed AUC values ranging from 0.807 to 0.876. The metabolic pathways of potential lipid markers are mainly sphingolipid and glycerolipid metabolism, unsaturated fatty acid biosynthesis, fatty acid degradation and biosynthesis. Among the 13 dose-dependent radiosensitive lipids, CE (20:5), CE (18:1) and PI (18:2/18:2) were gradually incorporated into the TBI dose estimation model. Conclusion This study suggested that it was feasible to acquire quantitative lipid biomarker panels using targeted lipidomics platforms for rapid, high-throughput triage. Lipidomics strategies for radiation biodosimetry in humans were established with lipid biomarkers with good dose-response relationship.

Multi-omics integrated analysis reveals the physiological response of large yellow croaker (Larimichthys crocea) to starvation and refeeding during overwintering

This study aimed to investigate the physiological response to starvation and refeeding during the overwintering period of large yellow croaker (Larimichthys crocea) using physiological and biochemical assays, microbiomics and transcriptomics. Fish were sampled at the beginning of starvation (Fa0 group), after 8 weeks (Fa8 group), after 16 weeks (Fa16 group), and after 8 weeks of refeeding (Fe group). Results indicated that compared to the Fa0 group, the viscerosomatic index (VSI) and intestinal digestive enzyme activities (trypsin, lipase, and amylase) significantly decreased in the Fa8 and Fa16 groups (P < 0.05), but these indicators recovered in the Fe group. Prolonged starvation significantly reduced triglyceride (TG) levels in both serum and liver, but these levels rebounded after 8 weeks of refeeding. Chronic starvation also led to a notable increase in serum low-density lipoprotein (LDL) levels, accompanied by a significant decrease in liver LDL content. As the duration of starvation increasing, the antioxidant and immune capabilities in the serum total antioxidant capacity (T-AOC), superoxide dismutase (SOD), lysozyme (LZM), alkaline phosphatase (AKP), acid phosphatase (ACP) significantly enhanced (P < 0.05), and these indicators significantly declined in the Fe group (P < 0.05). Intestinal flora analysis showed that the Alpha diversity gradually decreased with the prolongation of starvation but recovered after 8 weeks of refeeding, with the abundance of Akkermansia muciniphila significantly increasing (P < 0.05) in the Fa16 group compared to the other groups. Liver transcriptomic analysis revealed that upregulated genes enriched in pathways such as "Ribosome biogenesis in eukaryotes", "Proteasome", "RNA transport", "Biosynthesis of unsaturated fatty acids", "Fatty acid metabolism", "Fatty acid degradation", and "PPAR signaling pathway" (P < 0.05), while downregulated genes significantly enriched in "metabolic pathways" (P < 0.05) in the Fa16 group. Genes related to immune responses were significantly downregulated (P < 0.05) in the Fe group. The correlation analysis of intestinal flora and transcriptome revealed LOC104925398 (complement C3-like) and LOC113745439 (heat shock 70 kDa protein) exhibited significant positive correlations with Levilactobacillus brevis, unclassified Lachnoclostridium, Escherichia coli, and Akkermansia muciniphila (P < 0.05). In conclusion, prolonged starvation was more advantageous to the safe overwintering of large yellow croaker. Our study revealed the physiological response of large yellow croaker to starvation and refeeding during the overwintering period, providing a theoretical foundation for the formulation of safe overwintering strategies.

Characterizing seed dormancy in Epimedium brevicornu Maxim.: Development of novel chill models and determination of dormancy release mechanisms by transcriptomics

PurposeEpimedium brevicornu Maxim. is a perennial persistent C3 plant of the genus Epimedium Linn. in the family Berberaceae that exhibits severe physiological and morphological seed dormancy.We placed mature E. brevicornu seeds under nine stratification treatment conditions and explored the mechanisms of influence by combining seed embryo growth status assessment with related metabolic pathways and gene co-expression analysis.ResultsWe identified 3.9 °C as the optimum cold-stratification temperature of E. brevicornu seeds via a chilling unit (CU) model. The best treatment was variable-temperature stratification (10/20 °C, 12/12 h) for 4 months followed by low-temperature stratification (4 °C) for 3 months (4-3). A total of 63801 differentially expressed genes were annotated to 2587 transcription factors (TFs) in 17 clusters in nine treatments (0-0, 0-3, 1-3, 2-3, 3-3, 4-3, 4-2, 4-1, 4-0). Genes specifically highly expressed in the dormancy release treatment group were significantly enriched in embryo development ending in seed dormancy and fatty acid degradation, indicating the importance of these two processes. Coexpression analysis implied that the TF GRF had the most reciprocal relationships with genes, and multiple interactions centred on zf-HD and YABBY as well as on MYB, GRF, and TCP were observed.ConclusionIn this study, analyses of plant hormone signal pathways and fatty acid degradation pathways revealed changes in key genes during the dormancy release of E. brevicornu seeds, providing evidence for the filtering of E. brevicornu seed dormancy-related genes.

Biokinetic and microbial insights into regulatory mechanisms of long-chain fatty acid degradation during food waste-lipid co-digestion within anaerobic membrane bioreactor

This study investigated the effects of varying lipid ratios on the anaerobic co-digestion of high-lipid food waste (FW) in a mesophilic anaerobic membrane bioreactor (AnMBR). At a lipid concentration of 5 %, optimal biogas production (3.84 L/L/d) and lipid removal efficiency (78 %) were achieved; however, increasing lipid concentrations resulted in significant accumulations of long-chain fatty acids (LCFAs) and volatile fatty acids (VFAs). Batch tests further demonstrated the impact of various types of LCFAs, with stearic acid showing the slowest microbial growth rate (0.033d-1), confirming its role in the accumulation of acetate-dominated VFAs, potentially limiting the methanogenesis process at elevated lipid levels. Furthermore, at 8 % lipid content, the downregulation of key LCFA degradation enzymes and dominance of hydrogenotrophic methanogens indicated adverse conditions. The importance of the intricate interplay between LCFA degradation kinetics and microbial community for the system efficiency was evidenced, offering insights for optimizing and managing high-lipidic wastes.

Proteomic Profiling of Cocos nucifera L. Zygotic Embryos during Maturation of Dwarf and Tall Cultivars: The Dynamics of Carbohydrate and Fatty Acid Metabolism.

There is a limited number of studies analyzing the molecular and biochemical processes regulating the metabolism of the maturation of Cocos nucifera L. zygotic embryos. Our research focused on the regulation of carbohydrate and lipid metabolic pathways occurring at three developmental stages of embryos from the Mexican Pacific tall (MPT) and the Yucatan green dwarf (YGD) cultivars. We used the TMT-synchronous precursor selection (SPS)-MS3 strategy to analyze the dynamics of proteomes from both embryos; 1044 and 540 proteins were determined for the MPT and YGD, respectively. A comparison of the differentially accumulated proteins (DAPs) revealed that the biological processes (BP) enriched in the MPT embryo included the glyoxylate and dicarboxylate metabolism along with fatty acid degradation, while in YGD, the nitrogen metabolism and pentose phosphate pathway were the most enriched BPs. Findings suggest that the MPT embryos use fatty acids to sustain a higher glycolytic/gluconeogenic metabolism than the YGD embryos. Moreover, the YGD proteome was enriched with proteins associated with biotic or abiotic stresses, e.g., peroxidase and catalase. The goal of this study was to highlight the differences in the regulation of carbohydrate and lipid metabolic pathways during the maturation of coconut YGD and MPT zygotic embryos.

Molecular Insights into the Defense of Dioscorea opposita Cultivar Tiegun Callus Against Pathogenic and Endophytic Fungal Infection Through Transcriptome Analysis.

Dioscorea opposita cultivar Tiegun is an economically important crop with high nutritional and medicinal value. Plants can activate complex and diverse defense mechanisms after infection by pathogenic fungi. Moreover, endophytic fungi can also trigger the plant immune system to resist pathogen invasion. However, the study of the effects of endophytic fungi on plant infection lags far behind that of pathogenic fungi, and the underlying mechanism is not fully understood. Here, the black spot pathogen Alternaria alternata and the endophytic fungus Penicillium halotolerans of Tiegun were identified and used to infect calli. The results showed that A. alternata could cause more severe membrane lipid peroxidation, whereas P. halotolerans could rapidly increase the activity of the plant antioxidant enzymes superoxide dismutase, peroxidase, and catalase; thus, the degree of damage to the callus caused by P. halotolerans was weaker than that caused by A. alternata. RNA sequencing analysis revealed that various plant defense pathways, such as phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and the mitogen-activated protein kinase signaling pathway, play important roles in triggering the plant immune response during fungal infection. Furthermore, the tryptophan metabolism, betalain biosynthesis, fatty acid degradation, flavonoid biosynthesis, tyrosine metabolism, and isoquinoline alkaloid biosynthesis pathways may accelerate the infection of pathogenic fungi, and the ribosome biogenesis pathway in eukaryotes may retard the damage caused by endophytic fungi. This study lays a foundation for exploring the infection mechanism of yam pathogens and endophytic fungi and provides insight for effective fungal disease control in agriculture.