Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank.

MOTIVATION: Glycans play a central role in many essential biological processes. Glycan Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files containing glycans through the automatic detection and annotation of sugars and glycosidic linkages between sugar units and to proteins, all based on atomic coordinates and connectivity information. Carbohydrates can have various chemical modifications at different positions, making their chemical space much diverse. Unfortunately, current PDB files do not provide exact annotations for most carbohydrate derivatives and more than 50% of PDB glycan chains have at least one carbohydrate derivative that could not be correctly recognized by the original Glycan Reader. RESULTS: Glycan Reader has been improved and now identifies most sugar types and chemical modifications (including various glycolipids) in the PDB, and both PDB and PDBx/mmCIF formats are supported. CHARMM-GUI Glycan Reader is updated to generate the simulation system and input of various glycoconjugates with most sugar types and chemical modifications. It also offers a new functionality to edit the glycan structures through addition/deletion/modification of glycosylation types, sugar types, chemical modifications, glycosidic linkages, and anomeric states. The simulation system and input files can be used for CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Glycan Fragment Database in GlycanStructure.Org is also updated to provide an intuitive glycan sequence search tool for complex glycan structures with various chemical modifications in the PDB. AVAILABILITY AND IMPLEMENTATION: http://www.charmm-gui.org/input/glycan and http://www.glycanstructure.org. CONTACT: wonpil@lehigh.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Quantifying the Tunable Conjugated Area of Graphene Oxide by Using Pyrene as a Fluorescent Probe.

The determination of oxygenous groups, conjugated area ratio, and reduction efficiency of graphene oxide (GO) is a difficult task because of its heterogeneous structure. Herein, a novel approach is described for a detailed understanding of the surface chemistry of GO by using pyrene as a fluorescent probe through π-π stacking interactions.

MicroRNA-383 is a tumor suppressor in human lung cancer by targeting endothelial PAS domain-containing protein 1.

Lung cancer is the deadliest of all human cancers worldwide. The role of microRNA (miR)-383 has been controversial in the initiation and progression of different cancers. We aimed to investigate the function of miR-383 in human lung cancer both in vitro and in vivo. MicroRNA-383 levels were analyzed in noncancerous versus cancerous human lung tissues and in normal versus lung cancer cell lines. Effect of miR-383 on cell migration and invasion was examined in vitro and on tumor growth by using a xenograft mouse model in vivo. Potential mRNA target of miR-383 was predicted, and underlying mechanism was explored as well. MicroRNA-383 was downregulated in lung cancer tissue and cell lines. Expression of miR-383 inhibited migration and invasion of human lung cancer cell lines in vitro and tumorigenesis of lung cancer xenografts in vivo. MicroRNA-383 directly targeted 3' untranslated region of endothelial PAS domain-containing protein 1 (EPAS1) messenger RNA and inhibited both its mRNA and protein expressions. Reintroduction of EPAS1 could bypass the inhibition by miR-383 on tumorigenesis of human lung cancer cell lines. MicroRNA-383 is a tumor suppressor in human lung cancer by inhibiting EPAS1, both of which could serve as potential therapeutic targets in the treatment of lung cancer. SIGNIFICANCE OF THE STUDY: MicroRNA-383 is a tumor suppressor in human lung cancer, which functions to inhibit tumorigenesis of lung cancer cells both in vitro and in vivo. This inhibitory effect is mediated by direct targeting of EPAS1 mRNA and subsequent repressing of its expression. Both microRNA-383 and EPAS1 could serve as potential therapeutic targets in the treatment of lung cancer.

Characteristics of a novel heterotrophic nitrification and aerobic denitrification bacterium and its bioaugmentation performance in a membrane bioreactor.

A novel bacteria with heterotrophic nitrification and aerobic denitrification ability was obtained from a membrane bioreactor (MBR) and identified as Acinetobacter sp. TSH1. The nitrogen removal characteristics, nitrogen balance analysis, kinetic characteristics, and enhanced biological treatment in MBR of the novel isolated strain TSH1 were determined. Results showed that strain TSH1 could remove approximately 96.6% of NH4+-N, 82.9% of NO2--N and 98.7% of NO3--N in 24 h, and the corresponding maximum removal rates were 3.64 mg-N/(L·h), 1.77 mg-N/(L·h) and 3.94 mg-N/(L·h). The nitrogen balance analysis indicated that most of NH4+-N (62.6%) and NO3--N (71.9%) were transformed to gaseous nitrogen. The kinetic experiments showed that strain TSH1 had a high Km of 151.64 mg-NH4+-N/L and 203.25 mg-NO3--N/L. The enhanced biological treatment of synthetic wastewater in MBR showed that the strain TSH1 can significantly improve the nitrogen removal efficiency.

Characterization of a novel marine aerobic denitrifier Vibrio spp. AD2 for efficient nitrate reduction without nitrite accumulation.

Aerobic denitrifiers have the potential to reduce nitrate in polluted water under aerobic conditions. A salt-tolerant aerobic denitrifier was newly isolated and identified as Vibrio spp. AD2 from a marine recirculating aquaculture system, in which denitrification performance was investigated via single-factor experiment, Box-Behnken experiment, and nitrogen balance analysis. Nitrate reductase genes were identified by polymerase chain reaction. Results showed that strain AD2 removed 98.9% of nitrate-nitrogen (NO3--N) with an initial concentration about 100 mg·L-1 in 48 h without nitrite-nitrogen (NO2--N) accumulation. Nitrogen balance indicated that approximately 17.5% of the initial NO3--N was utilized for bacteria synthesis themselves, 4.02% was converted to organic nitrogen, 39.8% was converted to nitrous oxide (N2O), and 31.1% was converted to nitrogen (N2). Response surface methodology experiment showed that the maximum removal of total nitrogen (TN) occurred under the condition of C/N ratio 11.5, shaking speed 127.9 rpm, and temperature 30.8 °C. Sequence amplification indicated that the denitrification genes, napA and nirS, were present in strain AD2. These results indicated that the strain AD2 has potential applications for removing NO3--N from high-salinity (3%) wastewater.

The Nitrogen-Removal Efficiency of a Novel High-Efficiency Salt-Tolerant Aerobic Denitrifier, Halomonas Alkaliphile HRL-9, Isolated from a Seawater Biofilter.

Aerobic denitrification microbes have great potential to solve the problem of NO3--N accumulation in industrialized recirculating aquaculture systems (RASs). A novel salt-tolerant aerobic denitrifier was isolated from a marine recirculating aquaculture system (RAS) and identified as Halomonas alkaliphile HRL-9. Its aerobic denitrification performance in different dissolved oxygen concentrations, temperatures, and C/N ratios was studied. Investigations into nitrogen balance and nitrate reductase genes (napA and narG) were also carried out. The results showed that the optimal conditions for nitrate removal were temperature of 30 °C, a shaking speed of 150 rpm, and a C/N ratio of 10. For nitrate nitrogen (NO3--N) (initial concentration 101.8 mg·L-1), the sole nitrogen source of the growth of HRL-9, the maximum NO3--N removal efficiency reached 98.0% after 24 h and the maximum total nitrogen removal efficiency was 77.3% after 48 h. Nitrogen balance analysis showed that 21.7% of NO3--N was converted into intracellular nitrogen, 3.3% of NO3--N was converted into other nitrification products (i.e., nitrous nitrogen, ammonium nitrogen, and organic nitrogen), and 74.5% of NO3--N might be converted to gaseous products. The identification of functional genes confirmed the existence of the napA gene in strain HRL-9, but no narG gene was found. These results confirm that the aerobic denitrification strain, Halomonas alkaliphile HRL-9, which has excellent aerobic denitrification abilities, can also help us understand the microbiological mechanism and transformation pathway of aerobic denitrification in RASs.

[HLA class I and II polymorphism and haplotypes in Guangdong Han population].

OBJECTIVE: To analyze the polymorphism and haplotypes of HLA class I and II in Guangdong Han population and detect the HLA-A, B, Cw and DRB1 allele frequencies. METHODS: An auto semi-quantitative PCR-sequence speacific oligonucleotide probe(PCR-SSOP) method was adopted in exploring the HLA-A, B, Cw and DRB1 genotypes of the samples from 160 bone marrow donors. RESULTS: Twelve HLA-A, 23 B, 11 Cw and 13 DRB1 alleles were obtained. A total of 9 HLA-A-B, 20 Cw-B, 7 A-Cw, and 8 A-DRB1, 9 B-DRB1, 10 Cw-DRB1 haplotypes were found. CONCLUSION: HLA class I and II alleles in Guangdong Han population have plenty of polymorphisms. The haplotype distribution possesses territory characteristic.

[HLA-Cw alleles polymorphism and haplotypes in Guangdong Han population].

OBJECTIVE: To analyze the polymorphism and haplotypes of HLA-Cw and detect HLA-A, B, Cw and DRB1 allele frequencies in Guangdong Han population. METHOD: An auto semi-quantitative PCR with reverse sequence-specific oligonucleo- tide was adopted to explore the HLA-A, B, Cw and DRB1 genotypes of 185 bone marrow donors. RESULT: Eleven HLA-Cw alleles were obtained in which Cw*03 (0.2580), 07 (0.1887), 01 (0.1732), and 08 (0.1071) had much higher allele frequencies. A total of 7 HLA-Cw-A, 20 HLA-Cw-B and 10 HLA-Cw-DRB1 haplotypes were found. CONCLUSION: HLA-Cw alleles have richer polymorphisms and their linkage disequilibrium with HLA-A, B, DRB1 exhibits geographic genetic characteristics.

[Killer immunoglobulin-like receptor gene distribution in Guangdong Han population].

OBJECTIVE: To investigate the distribution of killer immunoglobulin-like receptor (KIR) gene in Guangdong Han population. METHODS: KIR phenotype was examined by PCR with sequence-specific primers in 96 subjects of Han nationality in Guangdong Province of China, and KIR frequency was calculated and compared with those in Caucasian, north Indian and Japanese populations. RESULT: The gene expression frequency of KIR in Guangdong Han people was 2DL1(0.85), 2DL2(0.12), 2DL3(0.58), 2DL4(1), 2DL5(0.24), 3DL1(0.96), 3DL2(1), 3DL3(1), 2DP1(0.97), 2DP2(0.98), 2DS1(0.10), 2DS2(0.30), 2DS3(0.02), 2DS4(0.28), 1D(0.65), 2DS5(0.19), and 3DS1(0.23) respectively. Comparison of the KIR recognizing the same HLA ligand suggested significantly higher expression frequency of inhibitory KIR than that of activating KIR. Compared with Caucasian and north Indian populations, Guangdong Han population had significantly lower expression frequency of activating KIR gene with the exception of KIR2DS4. CONCLUSION: Different KIR genes have different expression frequencies in Guangdong Han population, and KIR gene distribution varies between populations of different races.

[Hematoporphyrin derivative-mediated photodynamic therapy for human colon carcinoma: a comparative study with LoVo and CoLo205 cells in vitro].

OBJECTIVE: To investigate the killing effect of photodynamic therapy (PDT) mediated by hematoporphyrin derivative (HpD) on human colon carcinoma LoVo and CoLo205 cells in vitro. METHODS: LoVo and CoLo205 cells cultured in vitro were incubated in the presence of 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, and 4.0 microg/ml HpD for 4 h and exposed to different light doses delivered using a semiconductor laser at 630 nm with the energy density of 2, 5, 10, and 20 J/cm(2). After further culture for 24 h, the survival rate of LoVo and CoLo205 cells were analyzed by MTT assay, and the cellular fluorescence intensities of HpD were measured with a luminescence spectrometer. RESULTS: HpD-PDT resulted in effective cell killing to a comparable magnitude in LoVo and CoLo205 cells cultured in vitro (P>0.05). The killing effects were positively correlated with the concentration of HpD and the dosage of laser irradiation. Exposure to 20 J/cm(2) resulted in an IC(50) of LoVo and CoLo205 cells of 0.4 and 0.6 microg/ml respectively, which were not significantly different (P>0.05). The cellular HpD fluorescence intensities were also similar between the two cells. CONCLUSION: HpD-PDT may effectively kill LoVo and CoLo205 cells cultured in vitro.

[Hematoporphyrin derivative-mediated photodynamic therapy for human nasopharyngeal carcinoma: a comparative study with CNE2 and C666-1 cell lines in vitro].

OBJECTIVE: To investigate biological effect of hematoporphyrin derivative (HpD) photodynamic therapy (PDT) on in vitro cultured nasopharyngeal carcinoma (NPC) cell lines CNE2 and C666-1. METHODS: CNE2 and C666-1 cells cultured in vitro were incubated in a medium containing HpD at different concentrations (0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, and 4.0 microg/ml) for 4 h followed by exposure to different light doses (2, 5, 10, and 20 J/cm2) using a diode laser at 630 nm with power density of 20 mW/cm2. After 24 h of incubation with HpD-PDT, the survival rate of CNE2 and C666-1 cells were analyzed by MTT assay. RESULTS: HpD-PDT produced effective killing of CNE2 and C666-1 cells cultured in vitro, and the killing effects were positively correlated with HpD concentration and the irradiation dose. Exposure of CNE2 and C666-1 cells to irradiation dose of 20 J/cm2 resulted in the IC50 of 0.7 and 1.2 microg/ml, respectively (P<0.01). With the same HpD concentration and irradiation dose, the survival rate of C666-1 cells, however, was significantly higher than that of CNE2 cells (P<0.05). CONCLUSION: HpD-PDT may result in effective killing of CNE2 and C666-1 cells cultured in vitro, although C666-1 cells are less sensitive to HpD-PDT than CNE2 cells.

[Relationship between the genetic background of donor KIR recipient HLA and the outcomes in HLA-identical sibling HSCT].

OBJECTIVE: To explore the relationship between the genetic background of donor KIR/recipient HLA and the outcomes in HLA-identical sibling HSCT. METHODS: HLA genotype was determined by polymerase chain reaction-sequence-specific oligonucleotide probes (PCR-SSOP) and/or PCR-sequence-specific primer (PCR-SSP). Donor KIR genotype was determined by PCR-SSP. A retrospective study was carried out to analyze the outcomes of 59 patients with various hematologic malignancies received non T-cell-depleted transplant from HLA-identical sibling donors. RESULTS: Incidence of grade II-IV acute graft-versus-host disease (aGVHD) was significantly lower in patients of KIR/HLA matched group than in KIR/HLA mismatched group (32% vs 78%, P = 0.026). The incidence of grade II-IV aGVHD (24% vs 61%, P = 0.018) and fungus infection (14% vs 44%, P = 0.028) were significantly lower in Bw4 matched group than in Bw4 mismatched group. In myeloid diseases, Bw4 matched patients had much lower incidence of fungus infection (12% vs 80%, P = 0.002) compared with Bw4 mismatched patients, and C2 matched patients had higher overall survival (OS) compared with C2 mismatched patients (P = 0.01). CONCLUSIONS: Donor KIR/recipient HLA genetic background is correlated with the outcomes of HLA-identical sibling HSCT in incidences of grade II-IV aGVHD, fungus infection and OS. KIR/HLA matched patients may have lower incidence of aGVHD. Bw4 matched patients may have lower incidences of aGVHD and fungus infection. C2 matched patients may have longer OS.

[Progress on the study of HLA-Cw--review].

HLA-Cw belongs to classic HLA-I gene, HLA-Cw molecules have high polymorphism like HLA-A and B molecules. They distribute extensively on the surfaces of karyote, not only presenting endogenetic antigen to CD8+ T cells to induce specific killing effect, but also participating in immunologic reaction as the ligands of killer cell immunoglobulin-like receptor (KIR). Thus it has been valued for their relations to diseases and the functions in transplantation immunity, anti virus and anti-tumor immunity.