The biological functions and metabolic pathways of valine in swine

Valine is an essential amino acid and a type of branched-chain amino acid. Due to the involvement of branchedchain amino acids in various metabolic pathways, there has been a surge of interests in valine nutrition and its role in animal physiology. In pigs, the interactions between valine and other branched-chain amino acids or aromatic amino acids are complex. In this review, we delve into the interaction mechanism, metabolic pathways, and biological functions of valine. Appropriate valine supplementation not only enhances growth and reproductive performances, but also modulates gut microbiota and immune functions. Based on past observations and interpretations, we provide recommended feed levels of valine for weaned piglets, growing pigs, gilts, lactating sows, barrows and entire males. The summarized valine nutrient requirements for pigs at different stages offer valuable insights for future research and practical applications in animal husbandry.

Effects of different doses of glucose and fructose on central metabolic pathways and intercellular wireless communication networks in humans

Fructose and glucose are often widely used in food processing and may contribute to many metabolic diseases.To observe the effects of different doses of glucose and fructose on human metabolism and cellular communication,volunteers were given low,medium,and high doses of glucose and fructose.Serum cytokines,glucose,lactate,nicotinamide adenine dinucleotide(NADH)and metabolic enzymes were assayed,and central carbon metabolic pathway networks and cytokine communication networks were constructed.The results showed that the glucose and fructose groups basically maintained the trend of decreasing catabolism and increasing anabolism with increasing dose.Compared with glucose,low-dose fructose decreased catabolism and increased anabolism,significantly enhanced the expression of the inflammatory cytokine interferon-γ(IFN-γ),macrophage-derived chemokine(MDC),induced protein-10(IP-10),and eotaxin,and significantly reduced the activity of isocitrate dehydrogenase(ICDH)and pyruvate dehydrogenase complexes(PDHC).Both medium and high doses of fructose increase catabolism and anabolism,and there are more cytokines and enzymes with significant changes.Furthermore,multiple cytokines and enzymes show strong relevance to metabolic regulation by altering the transcription and expression of enzymes in central carbon metabolic pathways.Therefore,excessive intake of fructose should be reduced to avoid excessive inflammatory responses,allergic reactions and autoimmune diseases.

Ambient Light Alters Gene Expression Pattern of Enzymes and Transcription Factors Involved in Phenylpropanoid Metabolic Pathway in Potato under Chilling Stress

[Objective] Expressions of key enzymatic genes involved in phenyl-propanoid metabolic pathway in potato and StR2R3-MYB and StTGA transcripters were investigated in the present study. [Method] The primitive cultivar Yan was the materials for replicated trials and total RNA extracted from tissues of seedlings. Re-al-time florescent quantification PCR, multiple intervals of air temperature, light-il umi-nation and time-duration were factors of treatments in the experiment. Data on gene expressions were obtained and proceed to asses and compare effects based on statistical analysis. [Result] The results showed negative correlations between tem-perature degrees and expressions of StPAL, StDFR and StR2R3-MYB genes but not StTGA. Positive correlations, however, were derived between those of StCHS, StDFR and StR2R3-MYB and light-intensity. Significant interactive effects between expressions of StPAL and StDFR and treatments, light intensity and temperature degree, along the phenylpropanoid pathway were observed. Transcription regulator of StR2R3-MYB showed significant positive effect on the expression of StCHS of potato. StTGA transcription factor, on the other hand, gave significant negative ef-fects on the expression of StDFR. [Conclusion] Results from present study reveal the role of environmental factors and complicate interactions between such condi-tions as temperature-light il umination and mRNA function of target genes.

Protective effects of Zuogui Jiangtang Jieyu Formula on hippocampal neurons in rats of diabetes complicated with depression via the TRP/KYN metabolic pathway

Objective To explore the protective effects and mechanism of Zuogui Jiangtang Jieyu Formula(左归降糖解郁方,ZGJTJYF)on hippocampal neurons in rats of diabetes complicated with depression(DD)via the TRP/KYN metabolic pathway.Methods(i)In vivo experiments:60 specified pathogen free(SPF)grade male Sprague-Dawley(SD)rats were randomly divided into six groups with 10 rats in each groups:control,DD model,positive(1.8 mg/kg fluoxetine+0.18 g/kg metformin),high-dose ZGJTJYF(ZGJTJYFH,40.500 g/kg ZGJTJYF),middle-dose ZGJTJYF(ZGJTJYF-M,20.250 g/kg ZGJTJYF),and lowdose ZGJTJYF(ZGJTJYF-L,10.125 g/kg ZGJTJYF)groups.Except for the control group,other groups were established DD model by high-fat emulsion intake with single tail vein streptozotocin(STZ)and four weeks of chronic unpredictable mild stress(CUMS).All drug administration groups were treated by gavage during CUMS modeling,and the control and model groups were given equal amount of distilled water.After four weeks,the serum levels of blood glucose and glycosylated hemoglobin were measured to determine the hypoglycemic effect of ZGJTJYF.Moreover,the open field test and Morris water maze test were performed to evaluate the antidepressant effect of ZGJTJYF.Changes in 5-hydroxytryptamine(5-HT)level were detected via high-performance liquid chromatography with electrochemical detection(HPLC-ECD);the levels of tryptophan(TRP),kynurenine(KYN),and indoleamine 2,3-dioxygenase(IDO)in the hippocampus were detected using enzyme-linked immunosorbent assay(ELISA);the protein expression levels of synaptophysin(SYN)and postsynaptic density material-95(PSD-95)were detected via immunohistochemistry(IHC);and the protein expression levels of N-methyl-D-aspartate receptor(NR)2 A and NR2 B were detected using Western blot.(ii)In vitro experiments:five SPF grade SD pregnant rats(E16–18)were used to obtain primary hippocampal neurons(Ne),six SD new-born rats were used to collected primary astrocytes(As)and microglia(MG),and to establish a Ne-As-MG co-culture system.All co-culture systems were divided into six groups:control(PBS),model[150 mmol/L glucose+200μmol/L corticosterone(G&P)+PBS],blank(G&P+blank serum),positive(G&P+positive drug-containing serum),ZGJTJYF(G&P+ZGJTJYF serum),and 1-methyl-D-tryptophan(1-MT,IDO inhibitor)(G&P+1-MT)groups.After 18 h of intervention by corresponding treatment,immunofluorescence was used to analyze the protein expression levels of SYN,PSD-95,NR2 A,and NR2 B;ELISA was performed to measure the levels of interleukin(IL)-1β,IL-6,tumor necrosis factor(TNF)-α,and TRP/KYN metabolic pathway-related factors[TRP,KYN,kynurenine acid(KYNA),quinolinic acid(QUIN)].Results(i)In vivo experimental results showed that ZGJTJYF-M and ZGJTJYF-L significantly improved the elevated blood glucose state of DD rats(P<0.01 and P<0.05,respectively);ZGJTJYF-H,ZGJTJYF-M,and ZGJTJYF-L increased their autonomous activity,learning,and memory ability(P<0.01,P<0.01,and P<0.05,respectively).Moreover,the levels of 5-HT and TRP were significantly increased(P<0.01),and the levels of KYN and IDO were significantly decreased in the hippocampus(P<0.01)of rats after ZGJTJYF-M treatment.The protein expression levels of SYN and PSD-95 were significantly upregulated in hippocampal neurons(P<0.01),while the abnormal activation of NR2A and NR2B was markedly inhibited in hippocampus(P<0.05)of rats after ZGJTJYF-M treatment.(ii)In vitro experimental results showed that ZGJTJYF-containing serum significantly increased the protein expression levels of SYN and PSD-95 in hippocampal neurons(P<0.01),decreased the levels of IL-1β(P<0.01),IL-6(P<0.05),TNF-α(P<0.01),IDO(P<0.05),KYN(P<0.05),and QUIN(P<0.01),and increased the levels of TRP and KYNA(P<0.01)in the simulated DD state.ZGJTJYF also had an significantly inhibitory effect on the abnormal activation of NR2A and NR2B in neurons(P<0.05)in a stimulated DD state.Conclusion ZGJTJYF can effectively improve 5-HT deficiency in the hippocampus of rats by inhibiting IDO expression and regulating the TRP/KYN metabolic pathway,and it has a favorable protective effect on hippocampal neuron injury caused by DD.Therefore,ZGJTJYF is an effective potential therapeutic drug for the prevention and treatment of DD.

Recent Advances on Key Enzyme Genes in Metabolic Pathways Related to the Synthesis of Aroma Compounds in Tobacco

This article summarized three main kinds of metabolic pathways related to the synthesis of aroma compounds in plants, concluded the roles and expres- sion patterns of key enzyme genes catalyzing the formation of major intermediate products in phenylpropanoid metabolic pathway, isoprene metabolic pathway and alkaloid biosynthetic pathway respectively, highlighted the latest developments of these key enzyme genes in tobacco, and accordingly proposed that in-depth study at the protein level and analysis of metabolic network interaction should be carried out in tobacco besides the expression regulation and transgenic crop improvement at the genetic level. Based on the above analysis, further improvement of tobacco aroma quality through metabolic engineering and its application prospect in agricultural production were prospected.

Analysis of the key networks,metabolic pathways,and regulation substances of hypoxia based on the omics and zebrafish model

OBJECTIVE Hypoxia is associated with many complicated pathophysiological and biochemical processes that integrated and regulated via the key gene,protein and endogenous metabolite levels.Up to date,the exact molecular mechanism of hypoxia still remains unclear.In this work,we further explore the molecular mechanism of hypoxia and adaption to attenuate the damage in zebrafish model that have potential to resist hypoxic environment.METHODS The hypoxic zebrafish model was established in different concentration of oxygen with 3%,5%,10%,21%in water.The brain tissue was separated and the RNA-seq was used to identify the differentially expressed genes.The related endogenous metabolites profiles were obtained by LC-HDMS,and the multivariate statistics was applied to discover the important metabolites candidates in hypoxic zebrafish.The candidates were searched in HMDB,KEGG and Lipid Maps databases.RESULTS The zebrafish hypoxic model was successfully constructed via the different concentration of oxygen,temperature and hypoxic time.The activities of the related hypoxic metabolic enzymes and factors including HIF-1a,actate dehydrogenase(LDH)and citrate synthase(CS)were evaluated.Significant differences(P<0.05 and fold change>2)in the expression of 422 genes were observed between the normal and 3% hypoxic model.Among them,201 genes increased depended on the lower concentration of oxygen.53 metabolites were identified that had significant difference between the hypoxia and control groups(P<0.05,fold change>1.5 and VIP>1.5).The ten key metabolites were increased gradually while six compounds were decreased.The endogenous hypoxic metabolites of phenylalanine,D-glucosamine-6P and several important lipids with the relevant hub genes had similar change in hypoxic model.In addition,the metabolic pathways of phenylalanine,glutamine and glycolipid were influenced in both the levels of genes and metabolites.CONCLUSION The up-regulation of phenylalanine,D-glucosamine-6P and lipid may have further understanding of protective effect in hypoxia.Our data provided an insight to further reveal the hypoxia and adaptation mechanism.

Apocynum venetum Feed Affects the Serum Metabolism of Tan-sheep through the Amino Acid and Glycolipid Metabolic Pathways

[Objective]The paper was to explore the effects of Apocynum venetum diet on nutritional metabolism of Tan sheep.[Method]Forty Ningxia Tan sheep were randomly divided into 4 groups(A,B,C and D),with 10 sheep in each group.The sheep were fed with different contents of A.venetum granule feedstuff(0%,5%,10%and 15%).Blood samples were collected from jugular vein on the 20th,40th and 60th day of the experimental period.Serum samples were prepared and analyzed for differential metabolites by UPLC-Q-TOF/MS technique and annotated to the KEGG pathway.[Result](1)The differential metabolites increased with the extension of feeding time.The up-regulated metabolites in Tan sheep serum were more than the down-regulated ones,and reached the maximum on the 40th day.The up-regulated differential metabolites included 2 amino acids(valine and alanine),7 organic acids(β-hydroxybutyric acid,fumarate,ethylmalonic acid,hydroxyphenylacetic acid,gentiolic acid,protocatechuic acid,and oxycholic acid),pyrocatechol and taurochenocholate.The down-regulated differential metabolite was only p-chlorophenol.(2)With the increase of A.venetum content in pelleted diet,the differential metabolites in the serum of Tan sheep also increased,and the serum metabolic level gradually stabilized after the 10%concentration level.Similarly,the up-regulated metabolites were far more than the down-regulated metabolites.The up-regulated differential metabolites included 3 organic acids(β-hydroxybutyric acid,oxycholic acid and gentiolic acid),2 amino acids(alanine and valine)and catechol,and the down-regulated differential metabolite was only taurochenocholate.(3)The metabolic pathways involving in differential metabolites were mainly tricarboxylic acid cycle,tyrosine metabolism,taurine and bile acid pathway.[Conclusion]The results will provide a scientific basis for the green breeding of Tan sheep.

Advances in Single Nucleotide Polymorphisms of Vitamin D Metabolic Pathway Genes and Respiratory Diseases

Vitamin D is a fat-soluble vitamin.It is an essential vitamin for human body.It has a classical effect on regulating calcium and phosphorus metabolism.Participate in cellular and humoral immune processes by regulating the growth,differentiation and metabolism of immune cells.A large number of studies in recent years have shown that vitamin D deficiency increases the incidence of respiratory diseases.Respiratory diseases mainly include bronchial asthma,chronic obstructive pulmonary disease,tuberculosis,acute upper respiratory tract infection and pneumonia.Vitamin D metabolic pathway genes play a very important regulatory role in the transformation of vitamin D into active vitamin D,including CYP2R1,CYP27B1,CYP24A1,VDBP,VDR five genes.Genetic polymorphism of genes is the molecular basis of individual differences and disease development.Therefore,this paper summarizes the research on single nucleotide polymorphism of vitamin D metabolic pathway gene and respiratory diseases.In order to provide a new idea for future treatment.

Effect of the modified wendan decoction on hippocampal astrocyte neurotrophy by regulating the TRP-KYN metabolic pathway in depression-model rats

Objective:To observe the effect of the modified Wendan decoction on the neurotrophic function of hippocampal astrocytes by regulating the tryptophan-kynurenine(TRP-KYN)neuroprotective metabolic pathway in depression-model rats.Methods:A total of 96 Sprague Dawley(SD)rats were randomly divided into the blank group,model group,sham surgery group,neurotoxicity blocker group(blocker 1 for short)group,decoction group,fluoxetine group,blocker 1 plus decoction group,and blocker 1 plus fluoxetine group.Depression in rats of all groups,except for the blank group,was generated by isolation combined with chronic unpredictable mild stress.After corresponding treatments of the rats in each group,the sucrose preference test was performed to evaluate the depressive behaviors of the rats.Serum levels of tryptophan(TRP),kynurenine(KYN),and kynurenic acid(KYNA)were detected via enzyme-linked immunosorbent assay(ELISA);the mRNA/protein expression of hippocampal astrocyte markers,glial fibrillary acidic protein(GFAP)and S100β,was detected via reverse transcription-polymerase chain reaction(RT-PCR)and immunohistochemistry.ELISA and RT-PCR were carried out to detect the levels/mRNA expressions of brain-derived neurotrophic factor(BDNF)and glial-cell-line-derived neurotrophic factor(GDNF),the nutrient secretions of hippocampal astrocytes in rats.Results:Compared to the blank group,the number of activities of rats was significantly reduced,and the GFAP expression in the hippocampus was significantly increased while the BDNF and GDNF expressions were significantly decreased in the model group.With the intervention of the modified Wendan decoction,the depression of rats was significantly improved,and the BDNF and GDNF expressions in the hippocampus were increased while the GFAP expression was decreased significantly in the model group.Conclusion:The modified Wendan decoction may improve the neurotrophic function of rats’hippocampal astrocytes by enhancing the neuroprotective function of the TRP-KYN pathway,thereby exerting an antidepressant effect.

Research Progress on the Relationship between Polymorphism and SLE of Vitamin D Metabolic Pathway Related Gene

Vitamin D is a class of hormones necessary to maintain normal physiological activities of the body.A large number of studies have shown that vitamin D,as a fat-soluble vitamin,is not only related to calcium and phosphorus metabolism,but also closely related to immune regulation,humoral regulation,cell cycle and so on.Systemic Lupus erythema-Tosus(SLE)is a specific autoimmune diffuse connective tissue disease that causes tissue and organ damage under the joint action of multiple factors such as environment and heredity.Among many factors,the vitamin D metabolism pathway gene is particularly important for its influence.Some literature has shown that the genetic polymorphism of vitamin D metabolic pathway genes is correlated with SLE.Therefore,by referring to relevant literature,this paper summarized the progress in the research on the mechanism of genetic polymorphism of vitamin metabolism pathway genes and the development of SLE.

Serum Metabolomic Indicates Potential Biomarkers and Metabolic Pathways of Pediatric Kashin-Beck Disease

Objective To explore potential serum biomarkers of children with Kashin-Beck Disease(KBD)and the metabolic pathways to which the biomarkers belong.Methods A two-stage metabolomic study was employed.The discovery cohort included 56 patients,51 internal controls,and 50 external controls.The metabolites were determined by HPLC-(Q-TOF)-MS and confirmed by Human Metabolome Databases(HMDB)and Metlin databases.MetaboAnalyst 3.0 and the Kyoto Encyclopedia of Genes and Genomes(KEGG)database were used to analyze the metabolic pathways of the candidate metabolites.The use of HPLC-(Q-TRAP)-MS enabled quantitative detection of the target metabolites which were chosen using the discovery study and verified in another independent verification cohort of 31 patients,41 internal controls,and 50 external controls.Results Eight candidate metabolites were identified out in the discovery study,namely kynurenic acid,N-α-acetylarginine,6-hydroxymelatonin,sphinganine,ceramide,sphingosine-1 P,spermidine,and glycine.These metabolites exist in sphingolipid,glutathione,and tryptophan metabolic pathways.In the second-stage study,five candidate metabolites were validated,including kynurenic acid,N-α-acetylarginine,sphinganine,spermidine,and sphingosine-1 P.Except for spermidine,all substances exhibited low expression in the case group compared with the external control group,and the difference in levels of sphinganine,spermidine,and sphingosine-1 P was statistically significant.Conclusion The direction of change of levels of sphinganine,spermidine,and sphingosine-1 P in the two-stage study cohorts was completely consistent,and the differences were statistically significant.Therefore,these substances can be used as potential biomarkers of KBD.Furthermore,these results raise the possibility that sphingolipid metabolic pathways may be closely related to KBD.

Metabolic and proteostatic differences in quiescent and active neural stem cells

Adult neural stem cells are neurogenesis progenitor cells that play an important role in neurogenesis.Therefore,neural regeneration may be a promising target for treatment of many neurological illnesses.The regenerative capacity of adult neural stem cells can be chara cterized by two states:quiescent and active.Quiescent adult neural stem cells are more stable and guarantee the quantity and quality of the adult neural stem cell pool.Active adult neural stem cells are chara cterized by rapid proliferation and differentiation into neurons which allow for integration into neural circuits.This review focuses on diffe rences between quiescent and active adult neural stem cells in nutrition metabolism and protein homeostasis.Furthermore,we discuss the physiological significance and underlying advantages of these diffe rences.Due to the limited number of adult neural stem cells studies,we refe rred to studies of embryonic adult neural stem cells or non-mammalian adult neural stem cells to evaluate specific mechanisms.

Metagenomic analysis revealing the metabolic role of microbial communities in the free amino acid biosynthesis of Monascus rice vinegar during fermentation

Free amino acid(FAA)is the important component of vinegar that infl uences quality perception and consumer acceptance.FAA is one of the major metabolites produced by microorganisms;however,the microbial metabolic network on FAA biosynthesis remains unclear.Through metagenomic analysis,this work aimed to elucidate the roles of microbes in FAA biosynthesis during Monascus rice vinegar fermentation.Taxonomic profiles from functional analyses showed 14 dominant genera with high contributions to the metabolism pathways.The metabolic network for FAA biosynthesis was then constructed,and the microbial distribution in different metabolic pathways was illuminated.The results revealed that 5 functional genera were closely involved in FAA biosynthesis.This study illuminated the metabolic roles of microorganisms in FAA biosynthesis and provided crucial insights into the functional attributes of microbiota in vinegar fermentation.

Chromatin Remodeling Factor SMARCA5 is Essential for Hippocampal Memory Maintenance via Metabolic Pathways in Mice

Gene transcription and new protein synthesis regulated by epigenetics play integral roles in the formation of new memories.However,as an important part of epigenetics,the function of chromatin remodeling in learning and memory has been less studied.Here,we showed that SMARCA5(SWI/SNF related,matrix-associated,actin-dependent regulator of chromatin,subfamily A,member 5),a critical chromatin remodeler,was responsible for hippocampus-dependent memory maintenance and neurogenesis.Using proteomics analysis,we found protein expression changes in the hippocampal dentate gyrus(DG)after the knockdown of SMARCA5 during contextual fear conditioning(CFC)memory maintenance in mice.Moreover,SMARCA5 was revealed to participate in CFC memory maintenance via modulating the proteins of metabolic pathways such as nucleoside diphosphate kinase-3(NME3)and aminoacylase 1(ACY1).This work is the first to describe the role of SMARCA5 in memory maintenance and to demonstrate the involvement of metabolic pathways regulated by SMARCA5 in learning and memory.

High-throughput metabolomics reveals the perturbed metabolic pathways and biomarkers of Yang Huang syndrome as potential targets for evaluating the therapeutic effects and mechanism of geniposide

High-throughput metabolomics can clarify the underlying molecular mechanism of diseases via the qualitative and quantitative analysis of metabolites.This study used the established Yang Huang syndrome(YHS)mouse model to evaluate the efficacy of geniposide(GEN).Urine metabolic data were quantified by ultraperformance liquid chromatography-tandem mass spectrometry.The non-target screening of the massive biological information dataset was performed,and a total of 33 metabolites,including tyramine glucuronide,aurine,and L-cysteine,were identified relating to YHS.These differential metabolites directly participated in the disturbance of phase I reaction and hydrophilic transformation of bilirubin.Interestingly,they were completely reversed by GEN.While,as the auxiliary technical means,we also focused on the molecular prediction and docking results in network pharmacological and integrated analysis part.We used integrated analysis to communicate the multiple results of metabolomics and network pharmacology.This study is the first to report that GEN indirectly regulates the metabolite“tyramine glucuronide”through its direct effect on the target heme oxygenase 1 in vivo.Meanwhile,heme oxygenase-1,a prediction of network pharmacology,was the confirmed metabolic enzyme of phase I reaction in hepatocytes.Our study indicated that the combination of high-throughput metabolomics and network pharmacology is a robust combination for deciphering the pathogenesis of the traditional Chinese medicine(TCM)syndrome.

Insights into simultaneous anammox and denitrification system with short-term pyridine exposure: Process capability, inhibition kinetics and metabolic pathways

In-depth knowledge on the role of pyridine as a bottleneck restricting the successful application of anammox-based process treating refractory coking wastewater remains unknown.In this study,the effect of short-term pyridine addition on a simultaneous anammox and denitrification(SAD)system fed with 25–150 mg/L pyridine was explored.The short-term operation showed that the highest total nitrogen(TN)removal efficiency was achieved at 25–50 mg/L of pyridine.As the pyridine addition increased,the contribution of the anammox pathway in nitrogen removal decreased from 99.3%to 79.1%,while the denitrification capability gradually improved.The specific anammox activity(SAA)at 150 mg/L pyridine decreased by 56.7%of the maximum SAA.The modified non-competitive inhibition model indicated that the 50%inhibitory concentration(IC_(50))of pyridine on anammox was 84.18 mg/L and the substrate inhibition constant(Ki)of pyridine for self-degradation was 135.19 mg/L according to the Haldane model.Moreover,high-throughput sequencing confirmed the abundance of Candidatus Kuenenia as the amount of anammox species decreased,while the amounts of denitrifiers and pyridine degraders significantly increased as the pyridine stress increased.Finally,the possible pathways of nitrogen bioconversion and pyridine biodegradation in the SAD system were elucidated through metagenomic analysis and gas chromatography/mass spectrometry results.The findings of this study enlarge the understanding of the removal mechanisms of complex nitrogenous pyridinecontaining wastewater treated by the SAD process.

Metabolic pathway databases and moot repositories

Background： The number of biological Knowledge bases/databases storing metabolic pathway information and models has been growing rapidly. These resources are diverse in the type of information/data, the analytical tools, and objectives. Here we present a review of the most popular metabolic pathway databases and model repositories, focusing on their scope, content including reactions, enzymes, compounds, and genes, and applicability. The review aims to help researchers choose a suitable database or model repository according to the information and data required, by providing an insight look of each pathway resource. Results： Four pathways databases and three model repositories were selected on the basis of popularity and diversity. Our review showed that the pathway resources vary in many aspects, such as their scope, content, access to data and the tools. In addition, inconsistencies have been observed in nomenclature and representation of database entities. The three model repositories reviewed do not offer a brief description of the models＇ characteristics such as simulation conditions. Conclusions： The inconsistencies among the databases in representing their contents may hamper the maximal use of the knowledge accumulated in these databases in particular and the area of systems biology＇ at large. Therefore, it is strongly recommended that the database creators and the metabolic network models developers should follow international standards for the nomenclature of reactions and metabolites. Besides, computationally generated models that could be obtained from model repositories should be utilized with manual curations as they lack some important components that are necessary for full functionality of the models.

The anthocyanin's role on the food metabolic pathways,color and drying processes:An experimental and theoretical approach

This review is intended to cover the works related to the anthocyanin behavior in food that is subjected to drying.Both experimental and theoretical results available in scientific literature are discussed.An increase in anthocyanin concentration has been observed upon thermal processing.Nevertheless,a conclusive explanation is still unavailable.The accessible studies suggest an increase in concentration during maturations,which could be related to the enzymatic activity.The possible enzymes involved in such a procedure have also been covered,including their role played in the process.The possible activation mechanisms and the related factors such as temperature,pH,oxygen contents and the presence of UV-light irradiation were also considered.Moreover,the metabolic pathways were also explored including experimental evaluation and theoretical models based on atomistic methodologies such as density functional theory(DFT).This review is aimed to provide a comprehensive overview of the probable mechanisms behind the increase of anthocyanin concentration during drying.

The global integrative network:integration of signaling and metabolic pathways

The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes.The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis.However,current databases use distinct structures to present signaling and metabolic pathways,which leads to the chaos in the integrated networks.Moreover,for the metabolic pathways,the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes,which hinders the topological analysis of the integrated networks.Here,we propose a novel“meta-pathway”structure,which uses the uniformed structure to display the signaling and metabolic pathways,and resolves the difficulty in linking the metabolic enzymes to the reactions topologically.We compiled a comprehensive collection of global integrative networks(GINs)by merging the meta-pathways of 7077 species.We demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species—human,mouse,Arabidopsis,and rice.Almost all of the nodes were assembled into one major network for each of the four species,which provided opportunities for robust crosstalk and topological analysis,and knowledge graph construction.

Transcriptome-based analysis of key genes and pathways affecting the linoleic acid content in chickens

Linoleic acid is an essential polyunsaturated fatty acid that cannot be synthesized by humans or animals themselves and can only be obtained externally.The amount of linoleic acid present has an impact on the quality and flavour of meat and indirectly affects consumer preference.However,the molecular mechanisms influencing the deposition of linoleic acid in organisms are not clear.As the molecular mechanisms of linoleic acid deposition are not well understood,to investigate the main effector genes affecting the linoleic acid content,this study aimed to screen for hub genes in slow-type yellow-feathered chickens by transcriptome sequencing(RNA-Seq)and weighted gene coexpression network analysis(WGCNA).We screened for candidate genes associated with the linoleic acid content in slow-type yellow-feathered broilers.A total of 399 Tiannong partridge chickens were slaughtered at 126 days of age,fatty acid levels were measured in pectoral muscle,and pectoral muscle tissue was collected for transcriptome sequencing.Transcriptome sequencing results were combined with phenotypes for WGCNA to screen for candidate genes.KEGG enrichment analysis was also performed on the genes that were significantly enriched in the modules with the highest correlation.A total of 13310 genes were identified after quality control of transcriptomic data from 399 pectoral muscle tissues.WGCNA was performed,and a total of 26 modules were obtained,eight of which were highly correlated with the linoleic acid content.Four key genes,namely,MDH2,ATP5B,RPL7A and PDGFRA,were screened according to the criteria|GS|>0.2 and|MM|>0.8.The functional enrichment results showed that the genes within the target modules were mainly enriched in metabolic pathways.In this study,a large-sample-size transcriptome analysis revealed that metabolic pathways play an important role in the regulation of the linoleic acid content in Tiannong partridge chickens,and MDH2,ATP5B,RPL7A and PDGFRA were screened as important candidate genes affecting the linoleic acid content.The results of this study provide a theoretical basis for selecting molecular markers and comprehensively understanding the molecular mechanism affecting the linoleic acid content in muscle,providing an important reference for the breeding of slow-type yellowfeathered broiler chickens.