Component analysis and network pharmacology of flavonoids in Sophora flavescens tissues at anthesis / 药学学报

italic>Sophora flavescens is a traditional Chinese medicine rich in flavonoids and has wide application potential in drug development and clinical practice. In this study, a total of 227 flavonoids were detected among five tissues of S. flavescens during anthesis using widely targeted metabolomics techniques. There were 137 flavonoids shared by five S. flavescens tissues and 18 root-specific flavonoids. There were 156, 155, 156 and 150 differentially accumulated metabolites identified in stem, leaf, flower, and young pod, respectively, compared with root. Forty-seven potentially active flavonoid components in S. flavescens were identified using the PubChem and SwissADME databases. The 58 potential target proteins for these potentially active components were predicted to be important in the treatment of type 2 diabetes mellitus (T2DM) based on the SwissTargetPrediction and GeneCards database. These 58 target proteins were used to construct a protein-protein interaction network through the STRING database, from which we performed GO and KEGG functional enrichment analysis. The mechanisms by which S. flavescens flavonoids may be useful in the treatment of T2DM was further explored in a multi-level and systematic way based on a "component-target-pathway" network. Finally, ten key potentially effective components were identified and found to be mainly distributed in the roots, flowers, and pods, and their content varied significantly between tissues. The results predict that the key targets of S. flavescens flavonoids in the treatment of T2DM are AKT1, ESR1, EGFR, PIK3R1, TNF and PTGS2, and that they play a hypoglycemic role through the regulation of endocrine resistance, AGE-RAGE, the PI3K-Akt signaling pathway, EGFR tyrosine kinase inhibitor resistance and other signaling pathways. This analysis of the tissue distribution and network pharmacology of S. flavescens flavonoids provides a theoretical basis for further studies on S. flavescens metabolites, the rational development and utilization of the S. flavescens aboveground parts, and initiates a comprehensive exploration of the mechanisms by which S. flavescens can be used in the treatment of T2DM.

Transcriptional regulation mechanism of differential accumulation of flavonoids in leaves and roots of Sarcandra glabra based on metabonomics and transcriptomics / 中国中药杂志

This study aims to explore the molecular regulation mechanism of the differential accumulation of flavonoids in the leaves and roots of Sarcandra glabra. Liquid chromatography-mass spectrometry(LC-MS) and high-throughput transcriptome sequencing(RNA-seq) were employed to screen out the flavonoid-related differential metabolites and differentially expressed genes(DEGs) encoding key metabolic enzymes. Eight DEGs were randomly selected for qRT-PCR verification. The results showed that a total of 37 flavonoid-related differential metabolites between the leaves and roots of S. glabra were obtained, including pinocembrin, phlorizin, na-ringenin, kaempferol, leucocyanidin, and 5-O-caffeoylshikimic acid. The transcriptome analysis predicted 36 DEGs associated with flavonoids in the leaves and roots of S. glabra, including 2 genes in the PAL pathway, 3 genes in the 4CL pathway, 2 genes in the CHS pathway, 4 genes in the CHI pathway, 2 genes in the FLS pathway, 1 gene in the DFR pathway, 1 gene in the CYP73A pathway, 1 gene in the CYP75B1 pathway, 3 genes in the PGT1 pathway, 6 genes in the HCT pathway, 2 genes in the C3'H pathway, 1 gene in the CCOAOMT pathway, 1 gene in the ANR pathway, 1 gene in the LAR pathway, 2 genes in the 3AT pathway, 1 gene in the BZ1 pathway, 2 genes in the IFTM7 pathway, and 1 gene in the CYP81E9 pathway. Six transcription factors, including C2H2, bHLH, and bZIP, were involved in regulating the differential accumulation of flavonoids in the leaves and roots of S. glabra. The qRT-PCR results showed that the up-or down-regulated expression of the 8 randomly selected enzyme genes involved in flavonoid synthesis in the leaves and roots of S. glabra was consistent with the transcriptome sequencing results. This study preliminarily analyzed the transcriptional regulation mechanism of differential accumulation of flavonoids in the leaves and roots of S. glabra, laying a foundation for further elucidating the regulatory effects of key enzyme genes and corresponding transcription factors on the accumulation of flavonoids in S. glabra.

Mechanism of Learning and Memory Impairment in Rats Exposed to Arsenic and/or Fluoride Based on Microbiome and Metabolome / 生物医学与环境科学（英文）

OBJECTIVE@#Arsenic (As) and fluoride (F) are two of the most common elements contaminating groundwater resources. A growing number of studies have found that As and F can cause neurotoxicity in infants and children, leading to cognitive, learning, and memory impairments. However, early biomarkers of learning and memory impairment induced by As and/or F remain unclear. In the present study, the mechanisms by which As and/or F cause learning memory impairment are explored at the multi-omics level (microbiome and metabolome).@*METHODS@#We stablished an SD rats model exposed to arsenic and/or fluoride from intrauterine to adult period.@*RESULTS@#Arsenic and/fluoride exposed groups showed reduced neurobehavioral performance and lesions in the hippocampal CA1 region. 16S rRNA gene sequencing revealed that As and/or F exposure significantly altered the composition and diversity of the gut microbiome，featuring the Lachnospiraceae_NK4A136_group, Ruminococcus_1, Prevotellaceae_NK3B31_group, [Eubacterium]_xylanophilum_group. Metabolome analysis showed that As and/or F-induced learning and memory impairment may be related to tryptophan, lipoic acid, glutamate, gamma-aminobutyric acidergic (GABAergic) synapse, and arachidonic acid (AA) metabolism. The gut microbiota, metabolites, and learning memory indicators were significantly correlated.@*CONCLUSION@#Learning memory impairment triggered by As and/or F exposure may be mediated by different gut microbes and their associated metabolites.

Dead heart of pith-decayed Scutellariae Radix: a study based on multi-omics / 中国中药杂志

Dead heart is an important trait of pith-decayed Scutellariae Radix. The purpose of this study was to clarify the scientific connotation of the dead heart using multi-omics. Metabolomics and transcriptomics combined with multivariate statistical analysis such as principal component analysis(PCA) and partial least squares discriminant analysis(PLS-DA) were used to systematically compare the differences in chemical composition and gene expression among phloem, outer xylem and near-dead xylem of pith-decayed Scutella-riae Radix. The results revealed significant differences in the contents of flavonoid glycosides and aglycones among the three parts. Compared with phloem and outer xylem, near-dead xylem had markedly lowered content of flavonoid glycosides(including baicalin, norwogonin-7-O-β-D-glucuronide, oroxylin A-7-O-β-D-glucuronide, and wogonoside) while markedly increased content of aglycones(including 3,5,7,2',6'-pentahydroxy dihydroflavone, baicalin, wogonin, and oroxylin A). The differentially expressed genes were mainly concentrated in KEGG pathways such as phenylpropanoid metabolism, flavonoid biosynthesis, ABC transporter, and plant MAPK signal transduction pathway. This study systematically elucidated the material basis of the dead heart of pith-decayed Scutellariae Radix with multiple growing years. Specifically, the content of flavonoid aglycones was significantly increased in the near-dead xylem, and the gene expression of metabolic pathways such as flavonoid glycoside hydrolysis, interxylary cork development and programmed apoptosis was significantly up-regulated. This study provided a theoretical basis for guiding the high-quality production of pith-decayed Scutellariae Radix.

Discovery of the mechanisms of acupuncture in the treatment of migraine based on functional magnetic resonance imaging and omics / 医学前沿

Migraine is one of the most prevalent and disabling neurological disease, but the current pharmacotherapies show limited efficacy and often accompanied by adverse effects. Acupuncture is a promising complementary therapy, but further clinical evidence is needed. The influence of acupuncture on migraine is not an immediate effect, and its mechanism remains unclear. This study aims to provide further clinical evidence for the anti-migraine effects of acupuncture and explore the mechanism involved. A randomized controlled trial was performed among 10 normal controls and 38 migraineurs. The migraineurs were divided into blank control, sham acupuncture, and acupuncture groups. Patients were subjected to two courses of treatment, and each treatment lasted for 5 days, with an interval of 1 day between the two courses. The effectiveness of treatment was evaluated using pain questionnaire. The functional magnetic resonance imaging (fMRI) data were analyzed for investigating brain changes induced by treatments. Blood plasma was collected for metabolomics and proteomics studies. Correlation and mediation analyses were performed to investigate the interaction between clinical, fMRI and omics changes. Results showed that acupuncture effectively relieved migraine symptoms in a way different from sham acupuncture in terms of curative effect, affected brain regions, and signaling pathways. The anti-migraine mechanism involves a complex network related to the regulation of the response to hypoxic stress, reversal of brain energy imbalance, and regulation of inflammation. The brain regions of migraineurs affected by acupuncture include the lingual gyrus, default mode network, and cerebellum. The effect of acupuncture on patients' metabolites/proteins may precede that of the brain.

Viscumalbum L. homeopathic mother tinctures: metabolome and antitumor activity

Viscum album L. is a semi-parasitic plant with antitumor activity attributed to theaqueous extracts. However, European V. album ethanolic extracts (VAE) have also demonstrated invitro activity in tumor models. Aims: Evaluate the metabolic profiles of fifty VAE harvested duringsummer and winter seasons and their antitumor activity through 2D and 3D models. Methodology:VAEwerepreparedbymacerationfrom:V.albumsubsp.albumgrowingonMalus domestica,Quercus sp.and Ulmus sp.; V. album subsp. austriacum from Pinus sylvestris; V. album subsp. abietis from Abies alba.Chemical analyses were performed through liquid chromatography coupled with high resolutionmass spectrometry and Partial Least Squares Discriminant Analysis (PLS-DA) was performed in theMetaboanalyst 4.0. The antitumor potential of the selected VAE was evaluated in 2D and 3D models(MDA-MB-231 cancer cells) by MTT, crystal violet and glycolytic pathway analysis. Results anddiscussion:Thefirst3principalcomponentsinPLS-DAexplained60%and40%ofdatavariationin positive andnegativemodesrespectively.Threegroupswereformedandshowedchemicalsimilarityamong V. album subspecies. The compounds responsible for group separation were tentativelyidentifiedas:pinobankasinornaringenin hexoside;isorhamnetin-3-hexoside,meglutolanddifferent aminoacids.ThesummerVAEat0.5%v/vinducedhighercytotoxicdamagethanthewinterpreparations, and Abies alba and Quercus sp. VAE promoted 49% and 42% reduction of tumorviability in 3D model (72h incubation), respectively. MDA-MB-231 glycolytic pathway in 2D modelshowed a decrease in the glucose consumption and extracellular lactate production. Also, PFK (6-phosphofructo-1-kinase)andPK(Pyruvatekinase)activitieswereinhibitedbyAbiesalbaandQuercus sp. VAE at 48h of incubation. Conclusion: VAE extracts showed different metabolomes andthe glycolytic pathway should be an important target involved in the inhibition of tumor growth bytheseextracts

Metabolomics based protective effect of Amygdalus mongolica on pulmonary fibrosis in rats / 药学学报

This study used pharmacology combined with metabolomics to explore the effect of Amygdalus mongolica total extract on bleomycin induced pulmonary fibrosis in rats. The rat model of pulmonary fibrosis was established by intratracheal injection of bleomycin and treated with the total extract of Amygdalus mongolica. The pathological changes of lung tissue were evaluated by hematoxylin and eosin (HE) and Masson staining, the contents of superoxide dismutase (SOD) and malondialdehyde (MDA) in lung tissue were detected, and transforming growth factor β1 (TGF-β1), Smad family member 3 (Smad3), α-smooth muscle actin (α-SMA) pathway index expression in lung tissue was detected by fluorescence quantitative PCR. UPLC-Q-TOF/MS was used to study serum metabolomics to explore the changing patterns of biomarkers and the metabolic pathways affected by them. The results showed that compared with the model group, the medium (1.5 g·kg-1) and high (3.0 g·kg-1) doses of Amygdalus mongolica total extract could significantly reduce the lung index, significantly increase the activity of SOD in serum and lung tissue, reduce the degree of alveolar inflammation and pulmonary fibrosis, and reduce MDA in serum and lung tissue, and significantly reduce TGF-β1, Smad3, α-SMA mRNA expression in lung tissue. Serum metabolomics profile analysis identified 25 significantly different metabolites, the Amygdalus mongolica total extract can participate in linoleic acid metabolism, glycerophospholipid metabolism and alpha-linolenic acid metabolism by reducing five key biomarkers: lysoPE(0∶0/22∶5(4Z,7Z,10Z,13Z,16Z)), lysoPC(20∶0/0∶0), PC(20∶5(5Z,8Z,11Z,14Z,17Z)/15∶0), 12,13-dihydroxy-9-octadecenoic acid (12,13-DHOME), 9,10-dihydroxy-12-octadecenoic acid (9,10-DHOME) to affect pulmonary fibrosis. This study preliminarily revealed the action mechanism of Amygdalus mongolica total extract against pulmonary fibrosis in rats, and provided a reference basis for the clinical application of Amygdalus mongolica. The animal experiments were approved by the Medical Ethics Committee of Baotou Medical College (No.20170315).

Mechanism study of rhubarb-peach kernel regulation of feces metabolic profile in mice with adenomyosis / 药学学报

This paper aims to investigate the regulatory mechanism of blood-activating and stasis-dissipating drugs on fecal metabolic characteristics of rhubarb-peach kernel in mice with adenomyosis (AM) using fecal metabolome method. Adenomyosis was modeled by pituitary transplantation, and after the end of modeling administration, fecal samples were collected from mice. Non-targeted metabolomics studies were performed using liquid chromatography-mass spectrometry (LC-MS) to compare the metabolic characteristics of the feces of mice in each group and to find intestinal differential metabolites and potential differential metabolic pathways. The results showed that compared with the normal group, 5-hydroxy-L-tryptophan, histidine, L-acetylcarnitine, 16-hydroxy hexadecanoic acid, thromboxane B2, etc. were significantly up-regulated, L-urobilin and prostaglandin D3 were down-regulated in the feces of the model group, and were reversed after treatment with the rhubarb-peach kernel. The results of metabolic pathway enrichment analysis showed that tryptophan metabolism and histidine metabolism were the main intervention pathways of the rhubarb-peach kernel on AM intestinal metabolism. This study found that the underlying mechanism of the rhubarb-peach kernel in the treatment of AM is related to the intervention of intestinal metabolism of tryptophan, histidine, bile acid, choline and arachidonic acid, and the regulation of pro-inflammatory microenvironment and fatty acid metabolic homeostasis. This study has been approved by the Experimental Animal Ethics Committee of China Three Gorges University (No. 20190801).

Research progress of metabolomics in citrin deficiency / 中华检验医学杂志

Citrin deficiency is an autosomal recessive disorder caused by mutation of the SLC25A13 gene, and is one of the most important causes of infant cholestasis in China. The metabolic mechanism of CD is complex, involving the urea cycle, the malate aspartate cycle, the citrate malate cycle, fatty acid metabolism, carbohydrate motabolism and other metabolic pathways. Metabolomics has some applications in CD by analyzing metabolite alterations. This article provides a review for research progress of metabolomics in CD.

Analysis of apple postharment damage under high CO₂ concentration by transcriptome combined with metabolome / 生物工程学报

The environmental gas concentration affects the storage period and quality of fruits and vegetables. High concentration CO₂ treating for a long time will cause damage to fruits, However, the specific molecular mechanism is unclear. To analyze the mechanism of CO₂ injury in apple, high-throughput sequencing technology of Illumina Hiseq 4000 and non-targeted metabolism technology were used to analyze the transcriptome sequencing and metabolomics analysis of browning flesh tissue of damage fruit and normal pulp tissue of the control group. A total of 6 332 differentially expressed genes were obtained, including 4 187 up-regulated genes and 2 145 down regulated genes. Functional analysis of the differentially expressed genes confirmed that the occurrence of CO₂ injury in apple was related to redox process, lipid metabolism, hormone signal transduction process and energy metabolism process. Twenty candidate browning genes were successfully screened, among which grxcr1 (md14g1137800) and gpx (md06g1081300) participated in the reactive oxygen species scavenging process, and pld1_ 2 (md15g1125000) and plcd (md07g1221900) participated in phospholipid acid synthesis and affected membrane metabolism. mdh1 (md05g1238800) participated in TCA cycle and affected energy metabolism. A total of 77 differential metabolites were obtained by metabolomic analysis, mainly organic acids, lipids, sugars and polyketones, including 35 metabolites related to browning. The metabolism of flavonoids was involved in the browning process of apple. Compared with the control tissue, the content of flavonoids such as catechin and quercetin decreased significantly in the damaged apple tissue, the antioxidant capacity of cells decreased, the redox state was unbalanced, and the cell structure was destroyed, resulting in browning. The results of this study further enrich the theoretical basis of CO₂ damage, and provide reference for the practical application of high concentration CO₂ preservation technology.

Application of omics technology in oleaginous microorganisms / 生物工程学报

Microbial oils are potential resources of fuels and food oils in the future. In recent years, with the rapid development of systems biology technology, understanding the physiological metabolism and lipid accumulation characteristics of oleaginous microorganisms from a global perspective has become a research focus. As an important tool for systems biology research, omics technology has been widely used to reveal the mechanism of high-efficiency production of oils by oleaginous microorganisms. This provides a basis for rational genetic modification and fermentation process control of oleaginous microorganisms. In this article, we summarize the application of omics technology in oleaginous microorganisms, introduced the commonly used sample pre-processing and data analysis methods for omics analysis of oleaginous microorganisms, reviewe the researches for revealing the mechanism of efficient lipid production by oleaginous microorganisms based on omics technologies including genomics, transcriptomics, proteomics (modification) and metabolomics (lipidomics), as well as mathematical models based on omics data. The future development and application of omics technology for microbial oil production are also proposed.

Analytical methods for assessing changes induced by gamma exposure in an animal model

SUMMARY OBJECTIVE: Ionizing radiation can cause radio-induced changes in the cellular metabolome due to the breakdown of DNA bonds. Our goal was to find the early tissue response to radiation exposure supported by distinct analytical methods. METHODS: Histological analyses were performed on the organs extracted from rats to search for microscopic changes. The histological slides stained with hematoxyline-eosin (HE) were analyzed in magnification (40x). Subsequently, the tissues were subjected to mass spectrometry that allowed molecular analysis and DESI-MSI that generated the molecular image of lipids, assessing changes in intensities, especially in the brain. RESULTS: The histological analysis found nonspecific inflammatory changes; no areas of fibrosis, necrosis, or apoptosis were identified, suggesting non-morphological tissue alterations. However, the DESI-MSI images of brain lipids allowed the observation of many radio-induced changes in the lipid's intensities. CONCLUSIONS: No early radio induced histological or mass weight changes in the radiation exposed rats could be observed at 5 Gy. However, early changes in the molecular level were observed in the DESI-MSI images of the brain lipids. The DESI-MSI method proved to be efficient and relevant, allowing a regional molecular analysis of the tissues, expanding a new field of study that is still in its infancy: radiometabolomics.

RESUMO OBJETIVO: Radiação ionizante pode causar alterações no metaboloma celular devido à quebra de ligações no DNA. O objetivo deste trabalho foi evidenciar a resposta aguda tecidual induzida pela exposição da radiação ionizante. MÉTODOS: Análises histológicas foram realizadas nos órgãos extraídos de ratos para análise de alterações microscópicas. As lâminas histológicas coradas com hematoxilina eosina (HE) foram analisadas em aumento (40x). Posteriormente, os tecidos foram submetidos a espectrometria de massa, que permitiu análise molecular e o Desi-MSI que gerou imagem molecular de lipídios, identificando alterações na intensidade, principalmente no cérebro. RESULTADOS: As análises histológicas encontraram alterações inflamatórias inespecíficas, nem áreas de fibrose, necrose ou apoptose, sugerindo ausência de alterações morfológicas. As imagens de lipídios cerebrais obtidas por Desi-MSI permitiram observar as inúmeras alterações na intensidade nas seções teciduais do encéfalo. CONCLUSÕES: Alterações agudas radioinduzidas de massa do órgão e histológicas nos órgãos dos ratos expostos não puderam ser observadas a 5 Gy. Entretanto, mudanças em nível molecular foram observadas nas imagens de Desi-MSI dos lipídios cerebrais. O método Desi-MSI mostrou-se eficiente e relevante, permitindo a análise molecular regi-onal dos tecidos no SNC, expandindo um novo campo de estudo que ainda está em sua infância: a radiometaboloma.

Expressão e atividade de sistemas de dois componentes (TCS) de Salmonella enterica sorovar Typhimurium no contexto do metaboloma intestinal humano / Expression and activity of two-component systems of Salmonella enterica sorovar Typhimurium in the context of the human intestinal metabolome

A interação entre membros do microbioma intestinal humano, células hospedeiras e patógenos invasores pode ocorrer de diversas formas, sendo uma delas através de pequenas moléculas chamadas metabólitos. A percepção e resposta efetiva de um microrganismo às diferentes condições encontradas em seu ambiente, incluindo metabólitos produzidos por outros microrganismos, são fatores importantes para sua adaptação, sobrevivência e disseminação. Os sistemas de dois componentes (TCS) permitem a percepção e resposta a mudanças ambientais, regulando a expressão de genes específicos. Nosso grupo mostrou anteriormente que um extrato orgânico de fezes humanas (EF), bem como o ácido 3,4-dimetilbenzoico (3,4-DMB), encontrado no EF, inibe a capacidade de Salmonella enterica sorovar Typhimurium de invadir células hospedeiras. O presente trabalho propôs investigar o impacto do microbioma intestinal humano, bem como de pequenas moléculas produzidas por Clostridium citroniae (membro deste microbioma) na expressão e atividade dos genes de TCS de Salmonella. Os metabólitos de EF e de culturas puras de C. citroniae foram extraídos com acetato de etila e adicionados a meio de cultura. O pH do meio foi ajustado (~ 7,4) e a solução foi esterilizada por filtragem. Salmonella foi cultivada na presença ou ausência do EF e do extrato de C. citroniae, bem como do ácido 3,4-DMB, em condições aeróbias e anaeróbias, até alcançar o meio da fase logarítmica de crescimento. O RNA foi extraído para a realização de PCR em Tempo Real utilizando iniciadores direcionados a quase todos os TCS de Salmonella. Nossos resultados mostraram que vários genes de TCS envolvidos na virulência de Salmonella (SsrAB, EnvZ-OmpR, QseCB, PhoQP, TorSR, TtrRS) foram regulados diferencialmente por esses metabólitos, tanto em condições aeróbias quanto anaeróbias. EnvZ-OmpR, PhoPQ e SsrAB estão diretamente envolvidos na regulação das Ilhas de Patogenicidade 1 e 2 de Salmonella. QseCB é crucial para a detecção de quorum em Salmonella, de hormônios hospedeiros e para a regulação da motilidade (swimming). Vários outros TCS também foram regulados, incluindo TorSR e TtrRS, envolvidos na regulação da respiração anaeróbica de N-óxido de trimetilamina (TMAO) e tetrationato, respectivamente. Esses compostos são importantes para a sobrevivência de Salmonella no ambiente anaeróbico do intestino humano. Nossos resultados de avaliação de expressão gênica global de Salmonella cultivada na presença de ácido 3,4-DMB (aerobiose e anaerobiose) bem como na presença do EF em anaerobiose, mostraram que genes condificados em SPI-1 e SPI-2, SPI-4 e alguns genes do TCS foram reprimidos, enquanto genes marR, marB e marA foram ativadas nessas condições. Adicionalmente, comparamos nossos resultados de RNAseq, de Salmonella cultivada na presença do ácido 3,4-DMB em aerobiose, com resultados disponíveis da base de dados Salmonella Compendium. Ainda, a capacidade de Salmonella de adentrar e sobreviver dentro de células fagocíticas (macrófagos RAW 264.7) parece ser afetada pelas três condições testadas neste trabalho. Nossos resultados mostram que importantes vias de sinalização da virulência de Salmonella podem ser moduladas pelos metabólitos presentes no microbioma intestinal humano e abrem caminhos para novas pesquisas sobre a sinalização intercelular microbioma-patógeno no ambiente intestinal.

The interaction between members of the human gut microbiome, host cells and invading pathogens often occurs through small molecules, also called metabolites. The perception and effective response of a microorganism to the different conditions found in its environment, including metabolites produced by other microbes, is important for its adaptation, survival and dissemination. Two-component systems (TCS) allow the perception and response to environmental changes by regulating the expression of specific genes. Our group previously showed that organic extracts of human feces (EF) as well as the specific metabolite 3,4-dimethylbenzoic acid (3,4-DMB) found within the EF, inhibit the ability of Salmonella enterica sorovar Typhimurium to invade host cells. In the present work, we investigated the impact of the human gut microbiome as well as small molecules produced by Clostridium citroniae (a member of this microbiome) on the expression and activity of Salmonella TCS genes. Metabolites (from feces or C. citroniae cultures) were extracted using ethyl acetate and added to culture medium. The pH of the medium was adjusted (~7.4), and the solution was filter sterilized. Salmonella was grown in the presence or absence of the organic extracts as well as 3,4-DMB acid under aerobic and anaerobic conditions until it reached mid-log growth. RNA was then extracted for Real-time PCR using primers targeting almost all Salmonella TCS. Our results showed that several TCS involved in Salmonella virulence (SsrAB, EnvZ-OmpR, QseCB, PhoQP, TorSR, TtrRS) were differentially regulated by these metabolites both in aerobic and anaerobic conditions. EnvZ-OmpR, PhoPQ, and SsrAB are directly involved in the regulation of Salmonella Pathogenicity Islands 1 and 2. QseCB is crucial for Salmonella =quorum sensing, sensing of host hormones and regulation of swimming motility. Several other TCS were also regulated, including TorSR and TtrRS, which are involved in the anaerobic respiration of trimethylamine N-oxide (TMAO) and tetrathionate, respectively. These compounds are important for Salmonella survival in the anaerobic environment of the human gut. Our results of the evaluation of global Salmonella gene expression grown in the presence of 3,4-DMB acid (aerobiosis and anaerobiosis) as well as in the presence of EF in anaerobiosis, showed that genes encoded in SPI-1 and SPI-2, SPI-4 and some TCS genes have been repressed, while multiple drug resistance genes, as well marR, marB and marA genes have been activated under these conditions. Besides, we compared our results of RNAseq, Salmonella was grown in the presence of 3,4-DMB acid in aerobiosis, with results available from the Salmonella Compendium database. Also, Salmonella's ability to enter and survive within phagocytic cells (macrophages RAW 264.7) appears to be affected by the three conditions tested in this work. Our results show that important Salmonella virulence signalling pathways can be modulated by the metabolites present in the human intestinal microbiome and open the way for further research on the microbiome-pathogen intercellular signalling in the intestinal environment.

Candidate genes involved in the biosynthesis of lignan in Schisandra chinensis fruit based on transcriptome and metabolomes analysis / 中国天然药物

Schisandra chinensis Turcz. (Baill.) is a plant species with fruits that have been well known in Far Eastern medicine for a long time. It has traditionally been used as a stimulating and fortifying agent in cases of physical exhaustion and to inhibit fatigue. The major bioactive compounds found in S. chinensis are lignans with a dibenzocyclooctadiene skeleton, but little is known about their biosynthesis in plants. S. chinensis is the ideal medicinal plant for studying the biosynthesis of lignans, especially the dibenzocyclooctadiene skeleton. Genomic information for this important herbal plant is unavailable. To better understand the lignan biosynthesis pathway, we generated transcriptome sequences from the fruit during ripening and performed de novo sequence assembly, yielding 136 843 unique transcripts with N50 of 1778 bp. Putative functions could be assigned to 41 824 transcripts (51.57%) based on BLAST searches against annotation databases including GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes). Furthermore, 22 candidate cytochrome P450 genes and 15 candidate dirigent proteins genes that were most likely involved in the lignan biosynthesis pathway were discovered based on transcriptome sequencing of S. chinensis. The genomic data obtained from S. chinensis, especially the identification of putative genes involved in the lignan biosynthesis pathway, will facilitate our understanding of lignan biosynthesis at the molecular level. The lignan metabolite profiles were analyzed by metabolomes, the accumulation patterns of 30 metabolites involved in the lignan pathway were studied. Co-expression network of lignan contents and transcriptional changes showed 355 strong correlations (correlation coefficient, R > 0.9) between 21 compounds and 153 transcripts. Furthermore, the comprehensive analysis and characterization of the genes involved in lignan pathways and the metabolite profiles of lignans are expected to provide better insight regarding the diversity of the chemical composition, synthetic characteristics, and regulatory mechanisms of this medical herb.

The regulatory effects of Chaihu-Shu-Gan-San on fecal metabolome and gut microbiota in depression model rats / 国际药学研究杂志

Objective: To investigate the regulatory effects of Chaihu-Shu-Gan-San(CSGS)on fecal metabolome and gut microbiota in depression model rats. Methods: The UPLC-Q-TOF/MS-based metabolomics approach was used to investigate the regulatory effect of CSGS on the depression- related 16 fecal metabolites, such as nicotinic acid and hupoxianthine. Meanwhile, the 16S rRNA analysis was performed to investigate the regulator effects of CSGS on the microbiota in 3 phylum levels(Firmicutes, Bacteroidetes, and Proteobacteria)and 11 genus levels(Candidatus arthromitus, Oscillibacter, etc.). Results: The change rate of body weight (P< 0.01), the number of rearing and crossing(P< 0.01)and the sucrose preference(P< 0.01)in the depression rat group presented a significant decrease compared with control group. While rats in the CSGS group and fluoxetine group showed a significant increase in the body weight(P< 0.01), the number of rearing and crossing(P< 0.01), and the sucrose preference(P< 0.01)compared with model group. In addition, the decreased level of Firmicutes was positively regulated by CSGS but not fluoxetine, and the increased Bacteroidetes and Proteobacteria levels were also down-regulated by CSGS. Meanwhile, the abnormal levels of 3 genera of the gut microbiota with high abundance of Oscillibacter and low abundance of Lactobacillus and Christensenella, were all regulated to a nearly normal level by CSGS. Conclusion: CSGS could reverse changes of fecal metabolome in depression model rats by positive regulation, and CSGS likely exerts its antidepressant effect via regulating the gut microbiota, at least partially, to alter the related metabolites.

Metabonome in Early Diagnosis of Renal Cell Carcinoma / 中国医学科学院学报

Renal cell carcinoma(RCC)is one of the most common malignant tumors in the urinary system.Many patients have already been in the advanced stage at the first medical consultation and the prognosis is dismal.Metabonomics searches for differential metabolomes through high-throughput analysis of endogenous metabolites showing high potential in the early diagnosis of RCC and the investigations on its pathophysiological mechanisms.Metabonomics techniques are also useful for identifying tumor markers,which will help to enable early diagnosis and improve clinical prognosis of RCC.

Metabolic Profiling of Plasma from Pancreatic Cancer Patients in Korea / 대한췌담도학회지

BACKGROUND/AIMS: Pancreatic cancer (PC) patients have poor prognoses because this cancer is typically diagnosed at an advanced stage and the therapeutic options are limited. We examined the potential of metabolic profiling for early diagnosis and identification of potential therapeutic targets. METHODS: Ten patients and 10 healthy volunteer controls older than 20 years of age were enrolled between May and December 2015. The patients were confirmed to have pancreatic ductal adenocarcinoma cytologically or histologically. Blood plasma samples were derivatized and analyzed by gas chromatography mass spectrometry (GC-MS). Untargeted GC-MS data were analyzed using statistical methods, including Wilcoxon rank-sum test and principal component analyses. RESULTS: L-lysine was 1.36-fold higher in patients than in healthy controls (p<0.05). L-leucine was 0.63-fold lower (p<0.01) and palmitic acid was 0.93-fold lower (p<0.5) in patients than in controls. Orthogonal partial least squared-discriminant analysis revealed significant differences between the patients and controls. CONCLUSIONS: This study suggests that the metabolic profiles of patients with PC are distinct from those of the healthy population. Further studies are required to develop methods for early diagnosis and identify therapeutic targets.

Eating behavior of schizophrenic patients / Comportamento alimentar de pacientes com esquizofrenia

ABSTRACT Objective To assess the eating behavior, food practices, nutritional and metabolic profiles of patients with schizophrenia undergoing treatment. Methods Cross-sectional exploratory descriptive qualitative study used a semi-structured questionnaire on the eating behavior, food practices, and perception of changes after the initiation of drug therapy and a quantitative method using anthropometric and body composition measurements, metabolic parameters, and 5-day dietary records to analyze nutrient ingestion of patients with schizophrenia in an outpatient clinic at a tertiary hospital (n=33). The qualitative data were analyzed and coded by three researchers and quantitative data were analyzed using descriptive exploratory statistics. Results The results of this study showed that schizophrenic patients presented high prevalence of excess weight (71.0%), metabolic syndrome (42.0%), dyslipidemia (62.0%), changes in appetite (76.0%), and increase in energy intake (74.2%), associated with important irregularities in eating behavior and food practices (such as irregularity of meals, emotional intake, high carbohydrate and fat intake, and low energy expenditure) and lifestyle (changes in social and work routines). Conclusion This eating profile may interact synergistically with psychotropic drugs to contribute to weight gain and metabolic changes in schizophrenia. Nutrition education may prevent and monitor the risk of metabolic and nutrition problems, irrespective of the medications used.

RESUMO Objetivo Avaliar o comportamento e as práticas alimentares, o perfil nutricional e metabólico de pacientes com esquizofrenia em tratamento ambulatorial de um hospital terciário. Métodos Trata-se de estudo descritivo exploratório transversal com abordagem qualitativa utilizando questionário semi-estruturado sobre comportamentos alimentares, práticas alimentares e percepção de mudanças após o início da terapia medicamentosa e abordagem quantitativa usando medidas antropométricas e de composição corporal, parâmetros metabólicos e registros alimentares por cinco dias para analisar a ingestão de nutrientes em pacientes com esquizofrenia (n=33). Os dados qualitativos foram analisados e codificados por três pesquisadores e os dados quantitativos foram analisados utilizando estatísticas exploratórias descritivas. Resultados Os resultados deste estudo mostraram que os pacientes com esquizofrenia apresentaram uma alta prevalência de excesso de peso (71,0%), síndrome metabólica (42,0%) e dislipidemia (62,0%), com alterações no apetite (76,0%), consumo excessivo de energia (74,2%), associado à irregularidades no comportamento alimentar e nas práticas alimentares (como a irregularidade das refeições, o consumo emocional, a ingestão elevada de carboidratos e gorduras e o baixo gasto de energia) e o estilo de vida (mudanças nas rotinas sociais e de trabalho). Conclusão Esse perfil alimentar pode interagir sinergicamente com às drogas psicotrópicas utilizadas o tratamento de esquizofrenia contribuindo com o ganho de peso e alterações metabólicas após o diagnóstico da doença. Nesse sentido, acredita-se que a educação nutricional pode prevenir e monitorar o risco de problema metabólico e nutricional, independentemente dos medicamentos utilizados.

Focus on diagnosis and treatment of genetic liver disorders / 中华肝脏病杂志

The advancement and popularization of molecular diagnostic techniques has challenged and redefined the traditional concept of genetic metabolic disease. Regardless of disease origin, all genetic defects that lead to hepatobiliary dysfunction or structural abnormalities are termed as genetic liver disorders. Online Mendelian Inheritance in Man (OMIM) is a database consisting 693 genetic diseases with clear molecular mechanism of liver related phenotypes. Moreover, the effective measures to control infectious liver disease have strengthened the importance of research in the field of (adult and children) genetic liver disorders at home and abroad by well-recognized hepatologists. Notably, all patients with unexplained hepatopathy and multiple system diseases involving liver and gallbladder needs screening for genetic liver disorders, except for factors such as infection, immunity, drug-related, and anatomical abnormalities. We hope more patients with complicated liver disorders will benefit from definitive diagnosis and effective treatment in the near future with clear explanation of clinical phenotype, genotype, and metabolomics.

Focus on diagnosis and treatment of genetic liver disorders / 中华肝脏病杂志

The advancement and popularization of molecular diagnostic techniques has challenged and redefined the traditional concept of genetic metabolic disease. Regardless of disease origin, all genetic defects that lead to hepatobiliary dysfunction or structural abnormalities are termed as genetic liver disorders. Online Mendelian Inheritance in Man (OMIM) is a database consisting 693 genetic diseases with clear molecular mechanism of liver related phenotypes. Moreover, the effective measures to control infectious liver disease have strengthened the importance of research in the field of (adult and children) genetic liver disorders at home and abroad by well-recognized hepatologists. Notably, all patients with unexplained hepatopathy and multiple system diseases involving liver and gallbladder needs screening for genetic liver disorders, except for factors such as infection, immunity, drug-related, and anatomical abnormalities. We hope more patients with complicated liver disorders will benefit from definitive diagnosis and effective treatment in the near future with clear explanation of clinical phenotype, genotype, and metabolomics.