Evaluation of N Fertilizers Effects on Grape Based on the Expression of N Metabolic Genes

In order to study the influence of different types of N fertilizers on grapevine(Vitis labruscana ‘Black Summer') trees were used as experiment materials and fertilizers foliar application trails were conducted in the flowering and veraison stages. The expression levels of five grapevine N metabolic genes, including Vv GHD, Vv Ni R, Vv NR, Vv GS and Vv AS, were analyzed, some physiological traits including the flower and fruit dropping rate, leaves and shoots growth rate, chlorophyll content and the fruit size of grape berry were also investigated. The results showed that,in general, the expression levels of the five N metabolic genes were increased after foliar applied different types of N fertilizers in the two periods.N metabolic genes showed similar expression patterns toward the same type of fertilizer in the two periods, whereas foliar applied different types of N fertilizers, their expression patterns changed. Moreover, the N fertilizer which had stronger and longer influence on the N metabolic genes could enhance the physiology traits more dramatically. Given the gene expression levels and the changes of physiology traits, we conclude that urea and ammonium nitrate have the best effect on grapevine; calcium nitrate can help to reduce the flower and berry dropping rate; ammonium sulphate and sodium nitrate have relatively poor effects on grapevine.

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.

The Later Effects of DHA in Diet on Regulating Transcription of Lipid Genes of Broiler

The effect of docosahexaenoic acid （DHA） on lipid metabolism in broiler were studied in order to provide test results for polyunsaturated fatty acids （PUFA） regulating fatty deposition. 1-wk-old Arbor Acres （AA） broiler were fed with DHA microalgae and slaughtered after 2 wk. The tissues were stored for isolating total RNA. RT-PCR was used to analyze the expression changes of genes. DHA microalgae significantly increased average body gain and feed conversion rates, reduced the levels of total cholesterol （TC）, total glycerin （TG）, and low-density lipoprotein cholesterol （LDL-C） in serum and increased the content of high-density lipoprotein cholesterol. 1 wk later, the effects were still remained. In liver tissue, DHA microalgae increased the expression of PPARα and carnitine palmitoyltransferase-1 （CPT-1）. 1 wk later, it was observed that DHA up-regulated the expression of fatty acid synthase （FAS）, acetyl CoA carboxylase （ACC）, lipoprotein lipase （LPL） and carnitine palmitoyltransferase-1 （CPT-1）. 2 wk later, it still increased the expressions of FAS and CPT-1, but a converse result was observed for ACC and LPL. In adipose tissue, DHA microalgae suppressed the expression of PPARα and LPL, up-regulated the expression of ACC, FAS, and CPT-1. After withdrawal, the expression of genes in test group was significantly lower than that in control group （P0.01）. In the muscle of chest, DHA microalgae significantly inhibited the gene expression （P0.01）. 1 wk later, the expressions of FAS, LPL and CPT-1 in test group were significantly higher than that in control group （P0.05）. 2 wk later, it was shown that DHA significantly inhibited fat synthesis and decomposition. In the leg, there was not any PPARα expression being detected, probably because of the less expression in muscle tissues or the regulation of PPARα had no relation to the case. DHA microalgae promote fat synthesis in the liver and inhibit in adipose and muscle tissues. It still has effects after 1 wk of withdrawal.

Meta-analysis of ADH1B and ALDH2 polymorphisms and esophageal cancer risk in China

AIM: To evaluate whether alcohol dehydrogenase-1B (ADH1B) His47Arg and aldehyde dehydrogenase-2 (ALDH2) Glu487Lys polymorphism is involved in the esophageal squamous cell carcinoma (ESCC) risk in Chinese Han population. METHODS: Seven studies of ADH1B and ALDH2 genotypes in Chinese Han population in 1450 cases and 2459 controls were included for meta-analysis. Stratified analyses were carried out to determine the genealcohol and gene-gene interaction with ESCC risk. Potential sources of heterogeneity between studies were explored, and publication bias was also evaluated. RESULTS: Individuals with ADH1B arginine (Arg)/Arg genotype showed 3.95-fold increased ESCC risk in the recessive genetic model [Arg/Arg vs Arg/histidine (His) + His/His: odds ratio (OR) = 3.95, 95% confidence in- terval (CI): 2.76-5.67]. Signif icant association was found in the dominant model for ALDH2 lysine (Lys) allele [glutamate (Glu)/Lys + Lys/Lys vs Glu/Glu: OR = 2.00,95% CI: 1.54-2.61]. Compared with the non-alcoholics, Arg/Arg (OR = 25.20, 95% CI: 10.87-53.44) and Glu/ Lys + Lys/Lys (OR = 21.47, 95% CI: 6.44-71.59) were found to interact with alcohol drinking to increase the ESCC risk. ADH1B Arg+ and ALDH2 Lys+ had a higher risk for ESCC (OR = 7.09, 95% CI: 2.16-23.33). CONCLUSION: The genetic variations of ADH1B His47Arg and ALDH2 Glu487Lys are susceptible loci for ESCC in Chinese Han population and interact substantially with alcohol consumption. The individuals carrying both risky genotypes have a higher baseline risk of ESCC.

DNA polymorphism and risk of esophageal squamous cell carcinoma in a population of North Xinjiang,China

AIM:To investigate the role of metabolic enzyme and DNA repair genes in susceptibility of esophageal squamous cell carcinoma(ESCC). METHODS:A case-control study was designed with 454 samples from 128 ESCC patients and 326 gender, age and ethnicity-matched control subjects.Genotypes of 69 single nucleotide polymorphisms(SNPs)of metabolic enzyme(aldehyde dehydrogenase-2,ALDH2; alcohol dehydrogenase-1 B,ADHB1;Cytochrome P450 2A6,CYP2A6)and DNA repair capacity genes(excision repair cross complementing group 1,ERCC1; O 6-methylguanine DNA methyltransferase,MGMT; xeroderma pigmentosum group A,XPA;xeroderma pigmentosum group A,XPD)were determined by the Sequenom MassARRAY system,and results were analyzed using unconditional logistic regression adjusted for age,gender. RESULTS:There was no association between the variation in the ERCC1,XPA,ADHB1 genes and ESCC risk.Increased risk of ESCC was suggested in ALDH2 for frequency of presence C allele of SNP [Rs886205:1.626(1.158-2.284)],XPD for C allele [Rs50872:1.482(1.058-2.074)],and MGMT for A allele[Rs11016897:1.666(1.245-2.228)].Five variants of MGMT were associated with a protective effect on ESCC carcinogenesis,including C allele [Rs7069143:0.698(0.518-0.939)],C allele[Rs3793909: 0.6 5 3(0.4 2 9-0.9 9 5)],A a l l e l e[R s 1 2 7 7 1 8 8 2: 0.719(0.524-0.986)],C allele[Rs551491:0.707 (0.529-0.945)],and A allele[Rs7071825:0.618 (0.506-0.910)].At the genotype level,increased risk of ESCC carcinogenesis was found in homozygous carriers of the ALDH2 Rs886205[CC vs TT,odds ratios(OR): 3.116,95%CI:1.179-8.234],MGMT Rs11016879(AA vs GG,OR:3.112,95%CI:1.565-6.181),Rs12771882 (AA vs GG,OR:2.442,95%CI:1.204-4.595),and heterozygotes carriers of the ALDH2 Rs886205 (CT vs TT,OR:3.930,95%CI:1.470-10.504), MGMT Rs11016879(AG vs GG,OR:3.933,95%CI: 2.216-6.982)and Rs7075748(CT vs CC,OR:1.949, 95%CI:1.134-3.350),respectively.Three variants were associated with a protective effect on ESCC carcinogenesis,carriers of the MGMT Rs11016878(AG vs AA,OR:0.388,95%CI:0.180-0.836),Rs7069143(CT vs CC,OR:0.478,95%CI:0.303-0.754)and Rs7071825(GG vs AA,OR:0.493,95%CI:0.266-0.915). Increased risk of ESCC metastasis was indicated in MGMT for frequency of presence C allele[Rs7068306: 2.204(1.244-3.906)],A allele[Rs10734088:1.968 (1.111-3.484)]and C allele[Rs4751115:2.178(1.251-3.791)].Two variants in frequency of presence C allele of CYP2A6[Rs8192720:0.290(0.099-0.855)] and A allele of MGMT[Rs2053139:0.511(0.289-0.903)] were associated with a protective effect on ESCC progression.Increased risk of ESCC metastasis was found in heterozygote carriers of the MGMT Rs7068306 (CG vs CC,OR:4.706,95%CI:1.872-11.833).CONCLUSION:Polymorphic variation in ALDH2,XPD and MGMT genes may be of importance for ESCC susceptibility.Polymorphic variation in CYP2A6 and MGMT are associated with ESCC metastasis.

Implication of proliferation gene biomarkers in pulmonary hypertension

Objective/Background:Proliferation is a widely recognized trigger for pulmonary hypertension(PH),a life-threatening,progressive disorder of pulmonary blood vessels.This study was aimed to identify some proliferation associated genes/targets for better comprehension of PH pathogenesis.Methods:Human pulmonary arterial smooth muscle cells(hPASMCs)were cultured in the presence or absence of human recombinant platelet derived growth factor(rhPDGF)-BB.Cells were collected for metabolomics or transcriptomics study.Gene profiling of lungs of PH rats after hypoxia exposure or of PH patients were retrieved from GEO database.Results:90 metabolites(VIP score>1,fold change>2 or<0.5 and p<.05)and 2701 unique metabolism associated genes(MAGs)were identified in rhPDGF-BB treated hPASMCs compared to control cells.In addition,1151 differentially expressed genes(313 upregulated and 838 downregulated)were identified in rhPDGF-BB treated hPASMCs compared to control cells(fold change>2 or<0.5 and p<.05).152 differentially expressed MAGs were then determined,out of which 9 hub genes(IL6,CXCL8,CCL2,CXCR4,CCND1,PLAUR,PLAU,HBEGF and F3)were defined as core proliferation associated hub genes in protein proten interaction analysis.In addition,the hub gene-based LASSO model can predict the occurrence of PH(AUC=0.88).The expression of CXCR4,as one of the hub genes,was positively correlated to immune cell infiltrates.Conclusion:Our findings revealed some key proliferation associated genes in PH,which provide the crucial information concerning complex metabolic reprogramming and inflammatory modulation in response to proliferation signals and might offer therapeutic gains for PH.

A Point Mutation in an F-Box Domain-Containing Protein Is Responsible for Brown Hull Phenotype in Rice

The accumulation of pigments affects the color of rice hulls while only limited information is known about its underlying mechanisms. In the present study, a rice brown hull 6（bh6） mutant was isolated from an ethane methyl sulfonate（EMS）-induced IR64 mutant bank. Brown pigments started to accumulate in bh6 rice hulls after heading and reached a higher level in mature seeds. Some major agronomic traits including panicle length and 1000-grain weight in bh6 were significantly lower than those in its corresponding wild type IR64, while other agronomic traits such as plant height, growth duration and seed-setting rate were largely similar between the two genotypes. The analysis of pigment content showed that the contents of total flavonoids and anthocyanin in bh6 hulls were significantly higher than those in IR64 hulls. Our results showed that the brown hull phenotype in bh6 was controlled by a single recessive gene which locates on the long arm of chromosome 9. Sequencing analysis detected a single base substitution（G/A） at position 1013 of the candidate gene（LOC_Os09g12150） encoding an F-box domain-containing protein（FBX310）. Functional complementation experiment using the wild type allele can rescue the phenotype in bh6. Thus, we named this mutated gene as Os FBX310^（bh6）, an allele of OsFBX310 functioning as an inhibitor of brown hull. The isolation of Os FBX310^（bh6） and its wild type allele can provide useful experimental materials and will facilitate the studies on revealing the mechanisms of flavonoid metabolism in monocot plants.

Effect of an Ilex asprella root decoction on the related genes of lipid metabolism from chronic stress and hyperlipidemic fatty liver in rats

Background The gradually increasing changes in a human hyperlipidemic diet along with chronic stress might play an important role in the increased numbers of fatty liver. This study investigated the effects of Ilex asprella root decoction on related genes of lipid metabolism in chronic stress in hyperlipidemic fatty liver in rats. Methods Forty-eight male Wistar rats were randomly divided into four groups： normal control group, model control group, simvastatin group, and Ilex asprella root group. To establish chronic stress and hyperlipidemic fatty liver models in rats, the levels of serum lipids, glucose, liver index, insulin （INS）, insulin resistant （IR） index, adiponectin, superoxide dismutase （SOD）, glutathione peroxidase （GSH-pX）, glutathione （GSH）, liver X receptor （LXR）, and sterol responsive element binding protein （$REBP）-lc in rats were measured. Results When compared to the normal control group, the levels of serum lipids, glucose, liver index, INS, IR index, and GSH in the model control group significantly increased （P 〈0.01）. The protein levels of LXRa and SREBP-lc increased （P 〈0.05）, and the serum adiponectin and the SOD and GSH-pX decreased significantly （P 〈0.01）. When compared to the model control group, the levels of serum lipids, glucose, liver index, INS, IR index, SOD, and GSH-pX in the simvastatin group and Ilex asprella root group increased in varying degrees （P 〈0.01 or 0.05）; the serum adiponectin and GSH decreased （P 〈0.05）, while the protein levels of LXRa and SREBP-lc decreased in varying degrees （P 〈0.01 or 0.05）. When compared to the simvastatin group, the IR index and protein levels of LXRa in the Ilex asprella root group decreased （P 〈0.05）, and the serum adiponectin and SOD increased （P 〈0.05）. Conclusion The Ilex asprella root decoction has some protective effects on regulating the related genes of lipid metabolism caused by chronic stress and hyperlipidemic fatty liver in rats.

Polymorphisms of estrogen-metabolizing genes and breast cancer risk: a multigenic study

Background Endogenous estrogen plays a very important role in the carcinogenesis and progression of breast cancer. The enzymes involved in the biosynthesis and metabolism of estrogen have been proposed to contribute to this effect. To examine this hypothesis, we conducted a case-control study to investigate the relationship between polymorphisms of genes responsible for estrogen biosynthesis （CYP17, cytochrome P450c17a and CYP19, aromatase cytochrome P450） and estrogen sulfation of inactivation （ SULT1 A1, sulfotransferasel A1 ） and the risk of breast cancer in Chinese women. Methods This study involved 213 breast cancer patients and 430 matched controls. PCR-based restriction fragment length polymorphism （RFLP） and short tandem repeat polymorphism （STRP） assays were used to detect the mononucleotide transition of CYP17 and SULT1A1 and tandem repeat polymorphism of CYP19. Logistic regression analyses were used to determine OR and 95% CI of each and all three high-risk genotypes, of all three genotypes combined, and of estrogen exposure factbrs. The relationship between each high-risk genotype and clinicalpathological characteristics were also assessed. Results The frequency of A2 allele of CYP17 was 49.8% in cases and 49. 1% in controls （P =0. 82）. The frequency of His allele of SULT1A1 was significantly higher in cases （ 13.6% ） than in controls （9. 5% ） （P 〈 0. 05 ）. There was also significant difference of the （TTTA）10 allele of CYP19 which was 12. 4% in cases and 8.2% in controls （P 〈0. 05）. When the CYP17 A2 allele, CYP19 （TITA）1o and SULT1A1 His allele were considered as the “putative high-risk” genotype, there was an increased risk of breast cancer with the number of high-risk genotypes in a dose-response effect （trend, P = 0. 05 ）. In multivariate analysis, the SULT1A1 genotype remained the most significant determinant for breast cancer, with OR =2. 37 （95% CI 1.23 - 4. 74） , followed by CYP19, with OR = 1.75 （95% CI 1.27 - 3.56）. The （TTTA）10 allele of CYP19 was associated with tumor size, and the His allele of SULT1 A1 associated with status of lymph node metastasis. Conclusions This study supports the hypothesis that breast cancer can be initiated by estrogen exposure and that estrogen metabolizing genes are involved in this mechanism. This multigenic model is useful for identifying individuals who are at higher risks of breast cancer.

The association of olanzapine-induced metabolic disturbance related measures with TCF7L2 gene expression

Objective To investigate the relationship between olanzapine induced metabolic disturbance related measures and TCF7L2 gene expression.Methods Thirty adult C57BL/61 mice,in accordance with the random number table,were divided into 3 groups that were

Global regulation of fungal secondary metabolism in Trichoderma reesei by the transcription factor Ypr1,as revealed by transcriptome analysis

Trichoderma reesei Rut-C-30 is a well-known robust producer of cellulolytic enzymes,which are used to degrade lignocellulosic biomass for the sustainable production of biofuels and biochemicals.However,studies of its sec-ondary metabolism and regulation remain scarce.Ypr1 was previously described as a regulator of the biosynthesis of the yellow pigment sorbicillin(a bioactive agent with great pharmaceutical interest)in T.reesei and several other fungi.However,the manner in which this regulator affects global gene transcription has not been explored.In this study,we report the effect of Ypr1 on the regulation of both the secondary and primary metabolism of T.reesei Rut-C30.A global gene transcription profile was obtained using a comparative transcriptomic analysis of the wild-type strain T.reesei Rut-C-30 and its ypr1 deletion mutant.The results of this analysis suggest that,in addition to its role in regulating sorbicillin and the major extracellular(hemi)cellulases,Ypr1 also affects the transcription of genes encoding several other secondary metabolites.Although the primary metabolism of T.reeseiΔypr1 became less active compared with that of T.reesei Rut-C-30,several gene clusters involved in its secondary metabolism were activated,such as the gene clusters for the biosynthesis of specific polyketides and non-ribosomal peptides,together with the“sorbicillinoid-cellulase”super cluster,indicating that specific secondary metabolites and cellulases may be co-regulated in T.reesei Rut-C-30.The results presented in this study may benefit the development of genetic engineering strategies for the production of sorbicillin by T.reesei Rut-C-30,and provide insights for enhancing sorbicillin production in other filamentous fungal producers.

A Novel Vibriophage vB_VcaS_HC Containing Lysogeny-Related Gene Has Strong Lytic Ability against Pathogenic Bacteria

To avoid the negative effects of antibiotics,using phage to prevent animal disease becomes a promising method in aquaculture.Here,a lytic phage provisionally named vB_Vca S_HC that can infect the pathogen(i.e.,Vibrio campbellii 18)of prawn was isolated.The phage has an isometric head and a non-contractile tail.During phage infection,the induced host mortality in 5.5 h reached ca.96%,with a latent period of 1.5 h and a burst size of 172 PFU/cell.It has an 81,566 bp circular ds DNA genome containing 121 open reading frames(ORFs),and ca.71%of the ORFs are functionally unknown.Comparative genomic and phylogenetic analysis revealed that it is a novel phage belonging to Delepquintavirus,Siphoviridae,Caudovirales.In the phage genome,besides the ordinary genes related to structure assembly and DNA metabolism,there are 10 auxiliary metabolic genes.For the first time,the pyruvate phosphate dikinase(PPDK)gene was found in phages whose product is a key rate-limiting enzyme involving Embden-Meyerhof-Parnas(EMP)reaction.Interestingly,although the phage has a strong bactericidal activity and contains a potential lysogeny related gene,i.e.,the recombinase(Rec A)gene,we did not find the phage turned into a lysogenic state.Meanwhile,the phage genome does not contain any bacterial virulence gene or antimicrobial resistance gene.This study represents the first comprehensive characterization of a lytic V.campbellii phage and indicates that it is a promising candidate for the treatment of V.campbellii infections.

Occurrence and biosynthesis of plant sesterterpenes (C25), a new addition to terpene diversity

Terpenes,the largest group of plant-specialized metabolites,have received considerable attention for their highly diverse biological activities.Monoterpenes(C10),sesquiterpenes(C15),diterpenes(C20),and triterpenes(C30)have been extensively investigated at both the biochemical and molecular levels over the past two decades.Sesterterpenes(C25),an understudied terpenoid group,were recently described by plant scientists at the molecular level.This review summarizes the plant species that produce sesterterpenes and describes recent developments in the field of sesterterpene biosynthesis,placing a special focus on the catalytic mechanism and evolution of geranylfarnesyl diphosphate synthase and sesterterpene synthase.Finally,we propose several questions to be addressed in future studies,which may help to elucidate sesterterpene metabolism in plants.

Epigenetic control of autophagy in women’s tumors:role of non-coding RNAs

Cancer remains the second leading cause of death worldwide and a major public health and economic issue.To reduce the burden,new approaches are necessary to diagnose the disease at early stages and improve clinical outcomes of cancer patients,for which understanding the molecular mechanisms of carcinogenesis is crucial.Autophagy is a pro-survival pathway that ensures the removal and renewal of cellular macromolecular structures,thus playing a crucial role in the maintenance of cellular homeostasis.Dysregulation of autophagy can favor chemoresistance and survival of dormant cancer cells,thus favoring cancer progression and relapse.Several studies report dysregulated expression of long non-coding RNAs and micro-RNAs acting as tumor suppressors or tumor promoters by targeting genes involved in the autophagy pathway.Here,we focus on the role played by non-coding RNAs-mediated regulation of autophagy in development and progression of cancers in women.Understanding how epigenetics can impact autophagy might open novel therapeutic strategies in the fight against cancers in women.

Gene expression changes in blood RNA after swimming in a chlorinated pool

Exposure to disinfection by-products（DBP） such as trihalomethanes（THM） in swimming pools has been linked to adverse health effects in humans, but their biological mechanisms are unclear. We evaluated short-term changes in blood gene expression of adult recreational swimmers after swimming in a chlorinated pool. Volunteers swam 40 min in an indoor chlorinated pool. Blood samples were drawn and four THM（chloroform,bromodichloromethane, dibromochloromethane and bromoform） were measured in exhaled breath before and after swimming. Intensity of physical activity was measured as metabolic equivalents（METs）. Gene expression in whole blood m RNA was evaluated using Illumina Human HT-12v3 Expression-Bead Chip. Linear mixed models were used to evaluate the relationship between gene expression changes and THM exposure. Thirty-seven before-after pairs were analyzed. The median increase from baseline to after swimming were： 0.7 to 2.3 for MET, and 1.4 to 7.1 μg/m^3 for exhaled total THM（sum of the four THM）.Exhaled THM increased on average 0.94 μg/m^3 per 1 MET. While 1643 probes were differentially expressed post-exposure. Of them, 189 were also associated with exhaled levels of individual/total THM or MET after False Discovery Rate. The observed associations with the exhaled THM were low to moderate（Log-fold change range：-0.17 to 0.15）. In conclusion, we identified short-term gene expression changes associated with swimming in a pool that were minor in magnitude and their biological meaning was unspecific. The high collinearity between exhaled THM levels and intensity of physical activity precluded mutually adjusted models with both covariates. These exploratory results should be validated in future studies.

Unraveling the interaction between soil microbiomes and their potential for restoring polluted soils

Soils are not exempt from anthropogenic pollution,which can eventually cause disturbance of the microbial communities and areas without any kind of productivity.Among soil microbiota,bacteria play an important role in pollutant degradation,enabling them to thrive in contaminated sites.Given this,several techniques have been used to increase the number of pollutantdegrading bacteria in situ or for subsequent addition.Additionally,bacteriophages exhibit a high tolerance to pollutants and enhance bacterial metabolic activity through phage-encoded auxiliary metabolic genes(AMGs),thereby augmenting their skills for nutrient assimilation,resistance to phage infection,antibiotic resistance,heavy metal resistance,and degradation of pesticides and xenobiotics,among others.Several phage-encoded AMGs have been described during the last few years,but their diversity,distribution,and function have not been extensively explored,warranting further studies.Here,we highlight soil microbiome interactions,especially bacterium and phage interactions to understand this unexplored world with a high potential for restoring polluted soils.