[Study of the genes correlated with cyst calcification in patients with cystic echinococcosis]

OBJECTIVE

To explore the genes (biomarkers) correlated with cyst calcification in patients with cystic echinococcosis (CE), and to provide the evidence for the judgment on the patients' prognosis at molecular level.

METHODS

The liver tissues from 32 patients with liver CE (10 cases for mRNA microarray and 22 cases for real-time PCR analysis) and 11 patients with hepatic cystadenoma were collected from three hospitals in Ningxia from June, 2013 to December, 2014. A comparison of the different gene-expressions between five patients with calcified lesions and five cases with no calcification was carried out using Significant Analysis of Microarrays (SAM) to select a subset of differentially expressed genes (DEGs) . Fold-change analysis was used to assess the changes of the expression quantity in the same genes between two groups. The verification was conducted among the liver tissues from 22 patients with liver CE (11 in the group of calcified or 11 in that of non-calcified) by real-time quantitative PCR (RT-qPCR). With GAPDH as a reference-gene and the liver tissues from 11 cases with hepatic cystadenoma as standardized control groups, the relative expressions of galecitin-4 (LGALS4) and acid ceramidase (ASAH1) in patients with calcified and non-calcified were calculated, respectively. The differences between two groups were compared using t'-test.

RESULTS

Five screened genes presented siginificantly different expressions all had showed the low-regulated expressions in the calcified group, with the most distinct low-regulation of LGALS4 and ASAH1 whose fold changes were 0.008 8, and 0.020 3, respectively. The verification by RT-qPCR illustrated that the relative expression of LGALS4 was showed at level of 0.49±0.27 amongst patients with calcified, and at level of 2.70±2.61 amongst non-calcified individuals,,indicating significant differences between two groups (t=-2.59, P=0.026); while the ASAH1 was relatively expressed at levels of 1.36±0.33 and of 1.68±0.67 amongst patients with calcified and non-calcified, respectively, showing insignificant changes statistically (t=-1.44, P=0.167). In the non-calcified group, both LGALS4 and ASAH1 genes expression quantities had a small fluctuation range, but with positively correlated trend (r=0.91, P=0.001), which indicated that a patient with the low LGALS4 expression quantity also had a relative low level of ASAH1 expression quantity.

CONCLUSIONS

Low expression quantity of LGALS4 and ASAH1 genes in patients with CE in the calcification might be potential biomarker for an indication of the disease self-healing.

Enhancing local luminescence in a hollow ZnO microcolumn by antiresonant reflecting

Hollow ZnO microcolumns with size induced photoluminescence and cathodoluminescence properties were prepared by a thermal chemical vapor transport and condensation method. It was found that the luminescence emission could be confined in the nano-sized hollow core and the wavelength dependent light intensity could be influenced by the geometric structure of the ZnO microcolumn, which can act as a hollow optical waveguide. Based on the antiresonant reflection in the optical waveguide, we established a theoretical model to address the field enhancement in the hollow ZnO microcolumn, which systematically clarifies the influence of the geometric structure of the microcolumn on the field enhancement. We report for the first time, the enhanced emission of the near ultraviolet light (working wavelength of 385 nm) along the axial direction of the ZnO microcolumn. The corresponding microsized light emitter has also been obtained. Experiments agree well with both theoretical predictions and computer simulations based on the finite-difference time-domain method with perfectly matched layer boundary conditions. These findings provide valuable information for the application of ZnO micro- and nanostructures in optoelectronic devices.

A MALDI-MS-based quantitative analytical method for endogenous estrone in human breast cancer cells

The level of endogenous estrone, one of the three major naturally occurring estrogens, has a significant correlation with the incidence of post-menopausal breast cancer. However, it is challenging to quantitatively monitor it owing to its low abundance. Here, we develop a robust and highly sensitive mass-assisted laser desorption/ionization mass spectrometry (MALDI-MS)-based quantitative platform to identify the absolute quantities of endogenous estrones in a variety of clinical specimens. The one-step modification of endogenous estrone provided good linearity (R(2) > 0.99) and significantly increased the sensitivity of the platform (limit of quantitation: 11 fmol). In addition, we could identify the absolute amount of endogenous estrones in cells of the breast cancer cell line MCF-7 (34 fmol/10(6) cells) by using a deuterated estrone as an internal standard. Finally, by applying the MALDI-MS-based quantitative method to endogenous estrones, we successfully monitored changes in the metabolic expression level of estrones (17.7 fmol/10(6) letrozole-treated cells) in MCF-7 cells resulting from treatment with an aromatase inhibitor. Taken together, these results suggest that this MALDI-MS-based quantitative approach may be a general method for the targeted metabolomics of ketone-containing metabolites, which can reflect clinical conditions and pathogenic mechanisms.

Metal removal and reduction potential of an exopolysaccharide produced by Arctic psychrotrophic bacterium Pseudomonas sp. PAMC 28620

Metal reducing potential of an exopolysaccharide (EPS) produced by Arctic glacier soil bacteriumPseudomonassp. PAMC 28620.

Cloning, molecular characterization, and expression analysis of a nucleoporin gene (rgNUP98-96) from Rehmannia glutinosa

Nucleoporin 98 (NUP98) and nucleoporin 96 (NUP96) are essential components of the nuclear pore complex (NPC) in eukaryote cells. However, there is a lack of available information about complete Rehmannia glutinosa NUP98-96 (rgNUP98-96) sequences. Here, the full-length cDNA sequence of rgNUP96-98 was isolated from R. glutinosa using rapid amplification of cDNA ends (RACE) technology, based on a cloned cDNA sequence (GenBank accession No. JZ483329). The identified rgNUP98-96 was 3476 bp, and it encoded a 1041-amino acid peptide. The BLAST search analysis of rgNUP98-96 showed an intermediate degree of similarity (60-79%) to the NUP98-96 protein sequences of 34 other plants, including the dicotyledons Erythranthe guttata, Genlisea aurea, Coffea canephora, Nicotiana benthamiana, Solanum lycopersicum, and Solanum tuberosum. The phylogenetic analysis of NUP96-98 sequences indicated that R. glutinosa and E. guttata sequences shared the closest homology. The calculated molecular mass and predicted isolectric point of the complex protein were 117.6 kDa and 4.99, respectively. The secondary and three-dimensional structure studies illustrated that the rgNUP96-98 protein folded into a channel motif comprised of 34 alpha-helices, nine beta-strands, and several long loops. Using quantitative real-time PCR, the spatio-temporal expression patterns of rgNUP98-96 were analyzed in R. glutinosa, and the results indicated that rgNUP98-96 was highly expressed at the early stage of R. glutinosa tuberous root expansion, which is associated with a higher expression pattern in roots. The study provides a valuable foundation for further investigation of rgNUP96-98 molecular functions in R. glutinosa.

Hypervalinemia and hyperleucine-isoleucinemia caused by mutations in the branched-chain-amino-acid aminotransferase gene

Valine, leucine, and isoleucine are essential branched chain amino acids (BCAAs). When BCAA metabolism is genetically impaired in human, serum levels of BCAA and/or their metabolites rise considerably, causing severe neurological dysfunction. The first step in BCAA catabolism is catalyzed by branched chain aminotransferase (BCAT). Hypervalinemia and hyperleucine-isoleucinemia caused by BCAT gene mutation in human have not been reported previously. A 25-year-old man presented with headache complaints and mild memory impairment for about six years. Brain MRI showed symmetric white matter abnormal signals. Metabolic studies revealed remarkably elevated plasma valine and leucine concentrations. Maple syrup urine disease (MSUD) diagnosis was not supported since all genes for the branched-chain α-keto acid dehydrogenase complex (BCKD) gene were normal. Interestingly, two heterogeneous BCAT2 gene mutations were found in the patient, including c.509G > A (p.Arg170Gln) and c.790G > A (p.Glu264Lys). In addition, c.509G > A (p.Arg170Gln) and c.790G > A (p.Glu264Lys) were found in his father and mother, respectively, suggesting an autosomal recessive disorder. BCAT2 functional studies demonstrated that the two BCAT2 gene mutations resulted in decreased BCAT2 enzyme activity. After treatment with vitamin B6, the levels of BCAA, especially valine were remarkably decreased and brain MRI lesions were improved. These findings suggest a new type of branched chain amino acid metabolism disorder. This rare case provides great insight into the further understanding of BCAA metabolism and its defect in human. BCAT2 gene mutations can cause hypervalinemia and hyperleucine-isoleucinemia, which are associated with brain white matter lesions.

Biotransformation of lysine into cadaverine using barium alginate-immobilized Escherichia coli overexpressing CadA

In this study, Escherichia coli cells overexpressing lysine decarboxylase (CadA) were used for cadaverine production. Barium alginate was selected as a matrix for immobilization of E. coli YH91. Free cells and immobilized cells (IC) were characterized for their physiochemical properties, and the optimum pH and temperature were determined as 6 and 37 °C, respectively. Immobilized cells were three times more thermally stable compared to free cells at the optimum temperature and had a half-life (t 1/2) of 131 h. The free cells lost most of lysine decarboxylase activity after nine cycles, but in contrast immobilized cells retained 56% of their residual activity even after the 18th cycle. The immobilized cells gave a maximum production of cadaverine (75.8 g/L) with 84% conversion.

Evolutionary analysis of the ubiquitin gene of baculovirus and insect hosts

Baculovirus is the only virus that has been found to encode the ubiquitin protein. In this study, ubiquitin sequences from 16 insects and 49 viruses were collected and compared. The resulting sequences were aligned with virus genomes. Then MAGE 5.0, k-estimated software, as well as other software programs were used for systemic evolutionary, selection pressure, and evolutionary distance analysis. The results of the pairwise ratio of non-synonymous to synonymous substitution values and evolutionary distances showed that ubiquitin from baculovirus and insect hosts have been under purifying selection during evolution and are thus evolutionarily conserved. Moreover, genes from insect hosts were more conserved than those in baculovirus. Analysis of the non-synonymous to synonymous substitution rates at each site and entropy calculations revealed the evolutionary status of every site in the ubiquitin genes of baculovirus and their hosts. Genome locations and phylogenetic trees indicated that granuloviruses and non-photosynthetic vegetation evolved, and granulovirus evolution was more similar to that of insect hosts. Our results suggest that the ubiquitin gene in baculovirus may have been acquired through horizontal transfer from the host.

Effects of lead contamination on the clonal propagative ability of Phragmites australis (common reed) grown in wet and dry environments

Clonal propagation is important for the survival and maintenance of the common reed Phragmites australis. Pot culture experiments were conducted to investigate the effects of lead (Pb) concentration (0, 500, 1500, 3000, 4500 mg·kg(-1) ) and water stress on the clonal reproductive ability of this species. The Pb concentration found in plant organs, in decreasing order, was roots >shoots >rhizomes. There was a negative relationship between the growth of clonal propagative modules (excluding axillary shoot buds) and Pb concentrations, which caused a decrease in biomass, rhizome growth and number of axillary and apical rhizome buds. Daughter axillary shoots exhibited a tolerance strategy, with no significant change in their number; the axillary and apical rhizome buds, daughter apical rhizome shoots and rhizomes exhibited compensatory growth during the late stage of Pb (excluding 4500 mg·kg(-1) ) treatment in a wet environment. Pb applications above 500 mg·kg(-1) reduced these parameters significantly in the drought treatment, except for the number of axillary shoot buds, which did not change. Our results indicate that clonal propagative resistance to Pb contamination can occur via tolerance strategies, compensatory growth and a Pb allocation strategy, enabling these reeds to maintain population stability in wet environments. However, clonal modular growth and reproductive ability were inhibited significantly by the interaction between drought and Pb, which would cause a decline in P. australis populations in a dry environment. Lead concentrations of 4500 and 500 mg·kg(-1) in soils might meet or exceed the Pb tolerance threshold of clonally propagated reeds in wet and dry environments, respectively.

Production of rapamycin in Streptomyces hygroscopicus from glycerol-based media optimized by systemic methodology

Rapamycin, produced by the soil bacterium Streptomyces hygroscopicus, has the ability to suppress the immune system and is used as an antifungal, anti-inflammatory, antitumor, and immunosuppressive agent. In an attempt to increase the productivity of rapamycin, mutagenesis of wild-type Streptomyces hygroscopicus was performed using ultraviolet radiation, and the medium composition was optimized using glycerol (which is one of the cheapest starting substrates) by applying Plackett-Burman design and response surface methodology. Plackett-Burman design was used to analyze 14 medium constituents: M100 (maltodextrin), glycerol, soybean meal, soytone, yeast extract, (NH4)2SO4, L-lysine, KH2PO4, K2HPO4, NaCl, FeSO4·7H2O, CaCO3, 2-(N-morpholino) ethanesulfonic acid, and the initial pH level. Glycerol, soytone, yeast extract, and CaCO3 were analyzed to evaluate their effect on rapamycin production. The individual and interaction effects of the four selected variables were determined by Box-Behnken design, suggesting CaCO3, soytone, and yeast extract have negative effects, but glycerol was a positive factor to determine rapamycin productivity. Medium optimization using statistical design resulted in a 45% (220.7 ± 5.7 mg/l) increase in rapamycin production for the Streptomyces hygroscopicus mutant, compared with the unoptimized production medium (151.9 ± 22.6 mg/l), and nearly 588% compared with wildtype Streptomyces hygroscopicus (37.5 ± 2.8 mg/l). The change in pH showed that CaCO3 is a critical and negative factor for rapamycin production.

LED light stress induced biomass and fatty acid production in microalgal biosystem, Acutodesmus obliquus

Microbial algal system can serve as a potential source for the production of much high value bioproducts and biofuels. The quality and intensity of light are the key elements to optimize the production of algal biomass and fatty acid contents. This study presents the effect of differential LED flashing light conditions on the growth of microalgae, Acutodesmus obliquus. The induced light stress was optimized for its biomass and fatty acid content. The microalgae are exposed to various frequency of intermittent LED flashing light (blue and red lights) at three different phases in the 18 day cell growth (log, lag and stationary phase). The frequency of light flashing rate was adjusted to 120, 10, 5, 3.75, and 1 times per min. The effect of light stress on growth and fatty acids composition of A. obliquus induced an increase in algae growth and fatty acid production. Different optimal timing for light stress was subjected to elucidate the effect of light stress on algae growth and fatty acid production. The results showed an increase in the algae growth (1.2mg/L of chl a content) under light stress condition at FT10 (flashing time, 10 times per min) from the initial day (log phase) compared with the control experiment (0.4 mg/L of chl a content). However, the total fatty acids (71 mg/g) and volumetric FAME production (9.4 ml/l) level was found to be significant under FT5 (flashing time, 5 times per min), adopting flashing light from day 10 (stationary phase). TEM studies also revealed the deposition of lipid to be largest in the 18 day old cells under flashing light (FT5) condition, representing maximum accumulation of lipids bodies (up to 770 nm diameter in particle size) occupying approximately 42% of the total area of the cell.

Mass spectrometry-based N-linked glycomic profiling as a means for tracking pancreatic cancer metastasis

The aberrant glycosylation profile on the surface of cancer cells has been recognized for its potential diagnostic value towards assessing tumor progression. In this study, we initially investigate N-glycan profiles on the surface of normal (HPDE) and cancerous (Capan-1, Panc-1, and MIA PaCa-2) pancreatic cell lines, which are from different sites of pancreatic tumor. The enzymatically deglycosylated total N-glycans are permethylated via a quantitative solid-phase method and then analyzed by using MALDI-TOF MS and MALDI-QIT-TOF MS. We demonstrate that the level of high-mannose type glycans is higher among Capan-1 cells-pancreatic cancer cells that have metastasized to the liver-than that observed among Panc-1 and MIA PaCa-2 cells-pancreatic cancer cells from the pancreas duct head and tail regions, respectively. Furthermore, the relative abundance of highly-branched sialyted N-glycans is significantly up-regulated on Panc-1 and MIA PaCa-2 pancreatic cancer cells compared to that of normal HPDE pancreas cells. Taken together, these results indicate that specific N-glycosylation profile changes in pancreatic cancer cells can be used to not only distinguish between normal and cancerous cells but also provide more information on their location and metastatic potential.

Comparative N-linked glycan analysis of wild-type and α1,3-galactosyltransferase gene knock-out pig fibroblasts using mass spectrometry approaches

Carbohydrate antigens expressed on pig cells are considered to be major barriers in pig-to-human xenotransplantation. Even after α1,3-galactosyltransferase gene knock-out (GalT-KO) pigs are generated, potential non-Gal antigens are still existed. However, to the best of our knowledge there is no extensive study analyzing N-glycans expressed on the GalT-KO pig tissues or cells. Here, we identified and quantified totally 47 N-glycans from wild-type (WT) and GalT-KO pig fibroblasts using mass spectrometry. First, our results confirmed the absence of galactose-alpha-1,3-galactose (α-Gal) residue in the GalT-KO pig cells. Interestingly, we showed that the level of overall fucosylated N-glycans from GalT-KO pig fibroblasts is much higher than from WT pig fibroblasts. Moreover, the relative quantity of the N-glycolylneuraminic acid (NeuGc) antigen is slightly higher in the GalT-KO pigs. Thus, this study will contribute to a better understanding of cellular glycan alterations on GalT-KO pigs for successful xenotransplantation.

Exopolysaccharide from psychrotrophic Arctic glacier soil bacterium Flavobacterium sp. ASB 3-3 and its potential applications

Exopolysaccharide from psychrotrophic Arctic glacier soil bacteriumFlavobacteriumsp. ASB 3-3.

Mutational analysis of podocyte genes in children with sporadic steroid-resistant nephrotic syndrome

Recent studies have demonstrated that mutations in 4 podocyte genes, NPHS1, NPHS2, CD2AP, and WT1, are associated with the pathogenesis of steroid-resistant nephrotic syndrome (SRNS). Systematic investigation of all 4 genes for sporadic SRNS in China has not been performed. We examined 10 Chinese children with sporadic SRNS who showed no response to immunosuppressive agents and 20 SRNS controls who exhibited a response to prolonged steroid or immunosuppressive treatment and achieved complete remission. We analyzed mutations in the 4 podocyte genes, NPHS1, NPHS2, CD2AP, and WT1. Mutational analysis was performed using polymerase chain reaction and direct sequencing. Of the 10 SRNS children who showed no response to immunosuppressive agents, the compound heterozygous NPHS1 mutations 2677A>G (T893A) and *142T>C were identified in 1 patient, while a heterozygous mutation in WT1, 1180C>T (R394W), was found in another patient. Of the 20 SRNS children showing complete remission who responded to prolonged steroid therapy or immunosuppressive agents, 4 heterozygous NPHS1 mutations, 928G>A, IVS8+30C>T, IVS21+14G>A, and IVS25-23C>T, were identified in 4 patients and a heterozygous CD2AP mutation, IVS7-135G>A, was identified in 1 patient. Our results indicate the necessity of genetic examination for mutations in podocyte genes in Chinese SRNS children who show no response to immunosuppressive agents.