Preparation of trehalase inhibitor validoxylamine A by biocatalyzed hydrolysis of validemycin a with honeybee (Apis cerana fabr.) β-glucosidase

Validoxylamine A is structurally similar to trehalose and acts a potent competivive inhibitor of trehalase. It has recently been receiving increased attention as a potential material for the development of new insecticides or drugs. In this study, β-glucosidase extracted from honeybees (Apis cerana Fabr.) was used as a catalyst to produce validoxylamine A through enzymatic hydrolysis of validamycin A. β-Glucosidase was separated and purified from honeybees, and its characteristics were examined. The results showed that β-glucosidase was stable across a range of temperatures from 30 to 40°C and across a relatively wide range of pH values from 5.0 to 7.5. Investigation of the biocatalyzed hydrolysis process from validamycin A to validoxylamine A with β-glucosidase revealed that both the substrate (validamycin A) and the product (validoxylamine A) inhibited β-glucosidase activity. The inhibition constant of the substrate K value was 5.01 mM, and that of the product K _ip value was 1.32 mM. This product inhibition was competitive.     

Purification and Characterization of the Glucoside 3-Dehydrogenase Produced by a Newly Isolated Sphingobacterium faecium ZJF-D6 CCTCC M 2013251

A soluble glucoside 3-dehydrogenase (G3DH) was purified from a newly isolated Sphingobacterium faecium ZJF-D6 CCTCC M 2013251. The enzyme was purified to 35.71-fold with a yield of 41.91 % and was estimated by sodium dodecyl sulphate–polyacrylamide gel electrophoresis with a molecular mass of 62 kDa. The sequences of two peptides of the enzyme were all contained in a GMC family oxidoreductase (EFK55866) by mass spectrometry analysis. The optimal pH of the enzyme was around 6.2. The enzyme was stable within a pH range of 5.0–6.6 and was sensitive to heat. G3DH from S. faecium exhibited extremely broad substrate specificity and well regioselectivity to validoxylamine A. The enzyme was completely inhibited by Hg₂Cl₂ and partly inhibited by Cu²⁺, Fe²⁺, Ca²⁺, and Cd²⁺. The apparent K _m values for D-glucose, sucrose, and validoxylamine were calculated to be 1.1, 1.7, and 2.1 mM, respectively. With this purified enzyme, 3-keto sucrose was prepared at pH 5.0, 30 °C for 10 h with a yield of 28.7 %.     

Radiochemical analysis of the polar agrochemicals validamycin and the metabolite melamine by ion-exchange chromatography

Suitable analytical methods to determine the radiochemical purity of validamycin and melamine are not described in the literature. High performance ion-exchange chromatography for the detection of underivatized validamycin and melamine has been proposed. The compounds were separated on HPLC using a styrene-divinylbenzene copolymer based cation-exchanger. For the separation of validamycin a resin in the hydrogen-form has given a good separation and for melamine in the Na⁺-form. For the first time an ion-exchange separation of validamycin is described allowing the separation of at least four components of commercial validamycin: validamycin A, validamycin B or G, validoxylamine A and validoxylamine B or G without prior derivatization. The methods were applied to determine the radiochemical purity of ¹⁴C- or ³H labeled compounds.This revised version was published online in November 2005 with corrections to the Cover Date.     

Intramolecular direct aldol reactions of sugar diketones: syntheses of valiolamine and validoxylamine G

A new and stereoselective intramolecular direct aldol reaction of diketones derived from carbohydrates has been developed to construct carbocycles with D-gluco-, D-galacto-, D-manno-, and L-ido-configurations. The stereochemical outcome of the aldol reaction of the diketone is dependent on the base used. Transformation of D-gluco-aldols readily affords valiolamine which also constitutes a formal synthesis of voglibose. Facile conversion of D-gluco-cyclohexanones into validoxylamine G has been achieved in 12 steps with 15.1% overall yield from D-glucose.     

Biosynthesis of the validamycins: identification of intermediates in the biosynthesis of validamycin A by Streptomyces hygroscopicus var. limoneus.

To study the biosynthesis of the pseudotrisaccharide antibiotic, validamycin A (1), a number of potential precursors of the antibiotic were synthesized in (2)H-, (3)H-, or (13)C-labeled form and fed to cultures of Streptomyces hygroscopicus var. limoneus. The resulting validamycin A from each of these feeding experiments was isolated, purified and analyzed by liquid scintillation counting, (2)H- or (13)C NMR or selective ion monitoring mass spectrometry (SIM-MS) techniques. The results demonstrate that 2-epi-5-epi-valiolone (9) is specifically incorporated into 1 and labels both cyclitol moieties. This suggests that 9 is the initial cyclization product generated from an open-chain C(7) precursor, D-sedoheptulose 7-phosphate (5), by a DHQ synthase-like cyclization mechanism. A more proximate precursor of 1 is valienone (11), which is also incorporated into both cyclitol moieties. The conversion of 9 into 11 involves first epimerization to 5-epi-valiolone (10), which is efficiently incorporated into 1, followed by dehydration, although a low level of incorporation of 2-epi-valienone (15) is also observed. Reduction of 11 affords validone (12), which is also incorporated specifically into 1, but labels only the reduced cyclitol moiety. The mode of introduction of the nitrogen atom linking the two pseudosaccharide moieties is not clear yet. 7-Tritiated valiolamine (8), valienamine (2), and validamine (3) were all not incorporated into 1, although each of these amines has been isolated from the fermentation, with 3 being most prevalent. Demonstration of in vivo formation of [7-(3)H]validamine ([7-(3)H]-3) from [7-(3)H]-12 suggests that 3 may be a pathway intermediate and that the nonincorporation of [7-(3)H]-3 into 1 is due to a lack of cellular uptake. We thus propose that 3, formed by amination of 12, and 11 condense to form a Schiff base, which is reduced to the pseudodisaccharide unit, validoxylamine A (13). Transfer of a D-glucose unit to the 4'-position of 13 then completes the biosynthesis of 1. Other possibilities for the mechanism of formation of the nitrogen bridge between the two pseudosaccharide units are also discussed.     

不相交主成分分析(PCA)和遗传算法(GA)用于差异表达基因的识别

建立了一种基于不相交主成分分析(Disjoint PCA)和遗传算法(GA)的特征变量选择方法, 并用于从基因表达谱(Gene expression profiles)数据中识别差异表达的基因. 在该方法中, 用不相交主成分分析评估基因组在区分两类不同样品时的区分能力; 用GA寻找区分能力最强的基因组; 所识别基因的偶然相关性用统计方法评估. 由于该方法考虑了基因间的协同作用更接近于基因的生物过程, 从而使所识别的基因具有更好的差异表达能力. 将该方法应用于肝细胞癌(HCC)样品的基因芯片数据分析, 结果表明, 所识别的基因具有较强的区分能力, 优于常用的基因芯片显著性分析(Significance analysis of microarrays, SAM)方法.     

Utilization of Rosmarinic and Ascorbic Acids for Maturation Culture Media in Order to Increase Sow Oocyte Quality Prior to IVF

The beneficial effect of antioxidant supplementation in maturation culture media of sow oocytes was evaluated by the expression quantification of apoptotic genes and the genes that ensure stability of germ cells during fertilization. The oocytes were cultivated for 44 h in conventional medium (C) or in medium supplemented with 105 µM rosmarinic acid (R) and 0.5 mM ascorbic acid (A) and classified into three quality classes by morphological observation from which the total RNA was isolated. The gene expression of Ptx3 and the apoptotic regulator p53, Bax and BCL-2 were evaluated by quantitative PCR technique. The decreased expression of the Bax gene in the A and R groups, compared to the control, indicates a protective role of antioxidants in the cells. Cell homeostasis was maintained, as reflected in the ratio of Bax/Bcl-2 in class I COCs (cumulus-oocyte complex) regardless of the experimental group, indicating minimum cellular stress. The expression of p53 genes was higher in all class III COC, but in A1 and R1 the expression was lower than in C1, and a similar Ptx-3 gene decreased significantly in groups A1, A2, A3 and R1 compared with control groups. Antioxidant supplementation showed beneficial effects on all morphological classes of pig COCs.     

Clinicopathological value and underlying molecular mechanism of annexin A2 in 992 cases of thyroid carcinoma

BackgroundThyroid carcinoma (THCA) is one of the most frequent endocrine cancers and has increasing morbidity. Annexin A2 (ANXA2) has been found to be highly expressed in various cancers; however, its expression level and potential mechanism in THCA remain unknown. This study investigated the clinicopathological value and primary molecular machinery of ANXA2 in THCA.Material and MethodsPublic RNA-sequencing and microarray data were obtained and analyzed with ANXA2 expression in THCA and corresponding non-cancerous thyroid tissue. A Pearson correlation coefficient calculation was used for the acquisition of ANXA2 coexpressed genes, while edgR, limma, and Robust Rank Aggregation were employed for differentially expressed gene (DEG) in THCA. The probable mechanism of ANXA2 in THCA was predicted by gene ontology and pathway enrichment. A dual-luciferase reporter assay was employed to confirm the targeting relationships between ANXA2 and its predicted microRNA (miRNA).ResultsExpression of ANXA2 was significantly upregulated in THCA tissues with a summarized standardized mean difference of 1.09 (P < 0.0001) based on 992 THCA cases and 589 cases of normal thyroid tissue. Expression of ANXA2 was related to pathologic stage. Subsequently, 1442 genes were obtained when overlapping 4542 ANXA2 coexpressed genes with 2248 DEGs in THCA; these genes were mostly enriched in pathways of extracellular matrix-receptor interaction, cell adhesion molecules, and complement and coagulation cascades. MiR-23b-3p was confirmed to target ANXA2 by dual-luciferase reporter assay.ConclusionsUpregulated expression of ANXA2 may promote the malignant biological behavior of THCA by affecting the involving pathways or being targeted by miR-23b-3p.     

Gene-expression profiling in gill and liver of zebrafish exposed to produced water

The effects of produced water (a by-product of oil and gas extraction) on gene expression were studied in gills and liver tissues of zebrafish. Adult, non-breeding zebrafish were exposed to control (freshwater mixed with 5% seawater) or produced water (freshwater mixed with 5% of produced water from the Oceberg C Oil Platform in the North Sea). A zebrafish library was used to make a microarray that consisted of 15,806 unique genes. The results indicate that 27 genes in the gills and 55 genes in the liver show significantly altered expression (greater than two-fold change). More than 70% of these gene sequences have not been annotated in the Gene Ontology (GO) database, making it difficult to characterize the affected genes. CYP1A displayed the greatest upregulation in the gills (eightfold, verified with quantitative real-time PCR). This study illustrates the utility of microarray approaches in investigations of environmental effects of toxicants.     

Biosynthesis and compositional regulation of poly[(3-hydroxybutyrate)-co-(3-hydroxyhexanoate)] in recombinant ralstonia eutropha expressing mutated polyhydroxyalkanoate synthase genes

A new strategy for bacterial polyhydroxyalkanoate (PHA) production by recombinant Ralstonia eutropha PHB(-)4 harboring mutated PHA synthase genes (phaC(Ac)) from Aeromona caviae was investigated. The strain harboring wild-type phaC(Ac) gene produced a PHA copolymer consisting of (R)-3-hydroxybutyrate and (R)-3-hydroxyhexanoate [P(3HB-co-3HHx)] with 3.5 mol-% of 3HHx fraction from soybean oil. When the mutants of phaC(Ac) gene were applied to this production system, 3HHx fraction in copolymers was varied in the range of 0-5.1 mol-%. Thus, the regulation of PHA copolymer compositions has been achieved by the use of mutated PHA synthase genes.     

Synthesis and Evaluation as Glycosidase Inhibitors of Carbasugar‐Derived Spirodiaziridines,Spirodiazirines, and Spiroaziridines

The spirodiaziridines 6 and 9 , potential inhibitors of α‐ and β‐glucosidases, were prepared from the validoxylamine A‐derived cyclohexanone 5 . The trimethylsilyl protecting groups of 5 are crucial for the formation of 6 in good yields. Oxidation of 6 gave 7 . The diaziridine 6 (pK_HA=2.6) and the diazirine 7 did not inhibit the β‐glucosidases from almonds, the β‐glucosidase from Caldocellum saccharolyticum, and the α‐glucosidase from yeast. The N‐benzyl diaziridine 9 is a very weak inhibitor of the α‐glucosidase, but did not inhibit the β‐glucosidases. To see whether the weak inhibition is due to the low basicity of the diaziridines or to geometric factors, we prepared the spiro‐aziridines 21 and 25 and 1‐epivalidamine ( 32 ). The known cyclohexanone 10 was methylenated and epoxidised to 16 and 17 . Azide opening of 16 and 17 , mesylation, LiAlH₄ reduction, and deprotection gave the aziridines 21 and 25 respectively. 1‐Epivalidamine ( 32 ) was prepared from the known carba‐glucose 29 . The aziridine 25 (pK_HA=6.8) is a weak irreversible inhibitor of the β‐glucosidase from Caldocellum saccharolyticum and a weak reversible inhibitor of the α‐glucosidase from yeast, but did not inhibit the β‐glucosidases from almonds. The poorly stable aziridine 21 weakly inhibited the three enzymes. Similarly, 1‐epivalidamine (pK_HA=8.4) proved only a weak inhibitor. The known cyclopentylamine 34 (pK_HA=7.9), however, is a micromolar inhibitor of these enzymes. The much stronger inhibition by 34 is related to the pseudoaxial orientation of its amino group.     

DNA methylation-regulated microRNA pathways in ovarian serous cystadenocarcinoma: A meta-analysis

Epigenetic regulation has been linked to the initiation and progression of cancer. Aberrant expression of microRNAs (miRNAs) is one such mechanism that can activate or silence oncogenes (OCGs) and tumor suppressor genes (TSGs) in cells. A growing number of studies suggest that miRNA expression can be regulated by methylation modification, thus triggering cancer development. However, there is no comprehensive in silico study concerning miRNA regulation by direct DNA methylation in cancer. Ovarian serous cystadenocarcinoma (OSC) was therefore chosen as a tumor model for the present work.Twelve batches of OSC data, with at least 35 patient samples in each batch, were obtained from The Cancer Genome Atlas (TCGA) database. The Spearman rank correlation coefficient (SRCC) was used to quantify the correlation between the CpG DNA methylation level and miRNA expression level. Meta-analysis was performed to reduce the effects of biological heterogeneity among different batches. MiRNA-target interactions were also inferred by computing SRCC and meta-analysis to assess the correlation between miRNA expression and cancer-associated gene expression and the interactions were further validated by a query against the miRTarBase database.A total of 26 potential epigenetic-regulated miRNA genes that can target OCGs or TSGs in OSC were found to show biological relevance between DNA methylation and miRNA gene expression. Furthermore, some of the identified DNA-methylated miRNA genes; for instance, the miR-200 family, were previously identified as epigenetic-regulated miRNAs and correlated with poor survival of ovarian cancer. We also found that several miRNA target genes, BTG3, NDN, HTRA3, CDC25A, and HMGA2 were also related to the poor outcomes in ovarian cancer.The present study proposed a systematic strategy to construct highly confident epigenetic-regulated miRNA pathways for OSC. The findings are validated and are in line with the literature. The inclusion of direct DNA methylated miRNA events may offer another layer of explanation that along with genetics can give a better understanding of the carcinogenesis process.     

High-performance liquid chromatography/nano-electrospray ionization tandem mass spectrometry, two-dimensional difference in-gel electrophoresis and gene microarray identification of lymphatic metastasis-associated biomarkers

The potential biomarkers for the lymphatic metastatic process of mouse hepatocarcinoma were investigated by using two-dimensional difference in-gel electrophoresis (2D DIGE), high-performance liquid chromatography/nano-electrospray ionization tandem mass spectrometry (HPLC/nESI-MS/MS) and GeneChip. 2D DIGE was performed to screen and quantify the differentially expressed proteins between two well-established mouse hepatocarcinoma cell lines, Hca-F with 75% and Hca-P with 25% metastasis rate of lymph node potentials. The protein spots in the gel were visualized by the highly sensitive Deep Purple (GE Healthcare) fluorescent stain. Protein identification was obtained for gel spots by HPLC/nESI-MS/MS analysis with high quality. GeneChip microarray was performed to identify genes differentially expressed at the mRNA level. Seventeen genes including the chloride intracellular channel l, caspase 3, fructose bisphosphatase 2, glutamate dehydrogenase 1, V-crk sarcoma virus CT10 oncogene homolog, N-myc downstream regulated gene1, villin2, gelsolin, enoyl coenzyme A hydratase 1, transketolase, vimentin, annexins A5 and A7, keratin complex2 basic gene7 and gene8, lactamase (bata 2) and Ero1-like protein were found abnormally regulated and expressed concordantly both at the protein and mRNA levels between the two cell lines. More than half of these genes were for the first time revealed to be involved directly in hepatocarcinoma due to the lymphatic metastasis. The interdisciplinary combination of HPLC/nESI-MS/MS with 2D DIGE and GeneChip techniques opens up the possibility for the biomarker discovery of disease with high confidence.     

Biomic study of human myeloid leukemia cells differentiation to macrophages using DNA array,proteomic, and bioinformatic analytical methods

A biomic approach by integrating three independent methods, DNA microarray, proteomics and bioinformatics, is used to study the differentiation of human myeloid leukemia cell line HL-60 into macrophages when induced by 12-O-tetradecanoyl-phorbol-13-acetate (TPA). Analysis of gene expression changes at the RNA level using cDNA against an array of 6033 human genes showed that 5950 (98.6%) of the genes were expressed in the HL-60 cells. A total of 624 genes (10.5%) were found to be regulated during HL-60 cell differentiation. Most of these genes have not been previously associated with HL-60 cells and include genes encoded for secreted proteins as well as genes involved in cell adhesion, signaling transduction, and metabolism. Protein analysis using two-dimensional gel electrophoresis showed a total of 682 distinct protein spots; 136 spots (19.9%) exhibited quantitative changes between HL-60 control and macrophages. These differentially expressed proteins were identified by mass spectrometry. We developed a bioinformatics program, the Bulk Gene Search System (BGSS, http://www.sinica.edu.tw:8900/perl/genequery.pl) to search for the functions of genes and proteins identified by cDNA microarrays and proteomics. The identified regulated proteins and genes were classified into seven groups according to subcellular locations and functions. This powerful holistic biomic approach using cDNA microarray, proteomics coupled to bioinformatics can provide in-depth information on the impact and importance of the regulated genes and proteins for HL-60 differentiation.     

Cloning and sequence analysis of the poly(3-hydroxyalkanoic acid)-synthesis genes ofPseudomonas acidophila

Pseudomonas acidophila can grow with CO₂ as a sole carbon source by the possession of a recombinant plasmid that clones genes that confer chemolithoautotrophic growth ability derived from the H₂-oxidizing bacteriumAlcaligenes hydrogenophilus. H₂-oxidizing bacteria produce poly(3-hydroxybutyric acid) (PHB) from CO₂, but recombinant P.acidophila can produce the more useful biopolymer poly(3-hydroxyalkanoic acid) (PHA). In this study, thepha genes ofP. acidophila were cloned and a sequence analysis was carried out. A gene library was constructed using the cosmid vector pVK102. A recombinant cosmid carrying thepha genes was selected by the complementation of a PHB-negative mutant ofAlcaligenes eutrophus H16. The resulting recombinant cosmid pIK7 contained a 14.8-kb DNA insert. Subcloning was done, and the recombinant plasmid pEH74 was selected by hybridization with theA. eutrophus H16pha genes.Escherichia coli possessing pEH74 produced PHB, indicating that pEH74 contained thepha genes ofP. acidophila. The nucleotide sequences of the PHA-synthesis genesphaA (3-ketothiolase),phaB (acetoacetyl-CoA reductase), andphaC (PHA synthase) in pEH74 were determined. The homologies ofphaA, phaB, andphaC betweenP. acidophila andA. eutrophus H16 were 64.7, 76.1, and 56.6%, respectively.

     

Expression of early genes in light-induced chloroplast differentiation of cultured plant cells.

The objective of this study was to identify genes, preferentially of the plastid, which are rapidly expressed during the initial phase of blue-light-induced chloroplast development in suspension-cultured cells (Chenopodium rubrum L.) and to analyse the encoded proteins. A cDNA library (lambda gt 10) was constructed using total RNA from plastid preparations of dark-grown cells exposed to blue light for 3, 6 and 12 h. By differential screening, at least three clones were identified which correspond to rapidly light-induced plastid genes. For these and a number of nuclear genes represented by other clones, a temporary accumulation of the specific mRNA was observed between 12 and 48 h of blue-light exposure. With regard to their nucleotide sequence and derived amino-acid sequence they seem to represent a novel group of genes distinctive in structure and encoded product.     

Whole-Genome Analysis of Acinetobacter baumannii Strain AB43 Containing a Type I-Fb CRISPR-Cas System: Insights into the Relationship with Drug Resistance

The CRISPR-Cas system is a bacterial and archaea adaptive immune system and is a newly recognized mechanism for controlling antibiotic resistance gene transfer. Acinetobacter baumannii (A. baumannii) is an important organism responsible for a variety of nosocomial infections. A. baumannii infections have become problematic worldwide because of the resistance of A. baumannii to multiple antibiotics. Thus, it is clinically significant to explore the relationship between the CRISPR-Cas system and drug resistance in A. baumannii. This study aimed to analyze the genomic characteristics of the A. baumannii strain AB3 containing the type I-Fb CRISPR-Cas system, which was isolated from a tertiary care hospital in China, and to investigate the relationship between the CRISPR-Cas system and antibiotic resistance in this strain. The whole-genome sequencing (WGS) of the AB43 strain was performed using Illumina and PacBio sequencing. The complete genome of AB43 consisted of a 3,854,806 bp chromosome and a 104,309 bp plasmid. The specific characteristics of the CRISPR-Cas system in AB43 are described as follows: (1) The strain AB43 carries a complete type I-Fb CRISPR-Cas system; (2) Homology analysis confirmed that the cas genes in AB43 share high sequence similarity with the same subtype cas genes; (3) A total of 28 of 105 A. baumannii AB43 CRISPR spacers matched genes in the bacteriophage genome database and the plasmid database, implying that the CRISPR-Cas system in AB43 provides immunity against invasive bacteriophage and plasmids; (4) None of the CRISPR spacers in A. baumannii AB43 were matched with antimicrobial resistance genes in the NCBI database. In addition, we analyzed the presence of antibiotic resistance genes and insertion sequences in the AB43 strain and found that the number of antibiotic resistance genes was not lower than in the “no CRISPR-Cas system” strain. This study supports the idea that the CRISPR-Cas system may inhibit drug-resistance gene expression via endogenous gene regulation, except to the published mechanism that the CRISPR-Cas system efficiently limits the acquisition of antibiotic resistance genes that make bacteria sensitive to antibiotics.     

Conversion from arenes having a benzene ring to those having a picolinic acid by simple growing cell reactions using Escherichia coli that expressed the six bacterial genes involved in biphenyl catabolism

The comprehensive bioconversion of aromatic compounds with a benzene ring to a picolinic acid was achieved with a recombinant Escherichia coli strain that expressed the six genes involved in biphenyl catabolism, these being the bphA1(2072)A2A3A4 genes encoding the evolved biphenyl dioxygenase, the bphB gene encoding dihydrodiol dehydrogenase, and the bphC gene encoding catechol 2,3-dioxygenase.     

Biosynthesis of the polyene antifungal antibiotic nystatin in Streptomyces noursei ATCC 11455: analysis of the gene cluster and deduction of the biosynthetic pathway

BACKGROUND: The polyene macrolide antibiotic nystatin produced by Streptomyces noursei ATCC 11455 is an important antifungal agent. The nystatin molecule contains a polyketide moiety represented by a 38-membered macrolactone ring to which the deoxysugar mycosamine is attached. Molecular cloning and characterization of the genes governing the nystatin biosynthesis is of considerable interest because this information can be used for the generation of new antifungal antibiotics. RESULTS: A DNA region of 123,580 base pairs from the S. noursei ATCC 11455 genome was isolated, sequenced and shown by gene disruption to be involved in nystatin biosynthesis. Analysis of the DNA sequence resulted in identification of six genes encoding a modular polyketide synthase (PKS), genes for thioesterase, deoxysugar biosynthesis, modification, transport and regulatory proteins. One of the PKS-encoding genes, nysC, was found to encode the largest (11,096 amino acids long) modular PKS described to date. Analysis of the deduced gene products allowed us to propose a model for the nystatin biosynthetic pathway in S. noursei. CONCLUSIONS: A complete set of genes responsible for the biosynthesis of the antifungal polyene antibiotic nystatin in S. noursei ATCC 11455 has been cloned and analyzed. This represents the first example of the complete DNA sequence analysis of a polyene antibiotic biosynthetic gene cluster. Manipulation of the genes identified within the cluster may potentially lead to the generation of novel polyketides and yield improvements in the production strains.