Identification, Characteristics and Mechanism of 1-Deoxy-N-acetylglucosamine from Deep-Sea Virgibacillus dokdonensis MCCC 1A00493.

Xanthomonas oryzae pv. oryzae, which causes rice bacterial blight, is one of the most destructive pathogenic bacteria. Biological control against plant pathogens has recently received increasing interest. 1-Deoxy-N-acetylglucosamine (1-DGlcNAc) was extracted from the supernatant of Virgibacillus dokdonensis MCCC 1A00493 fermentation through antibacterial bioassay-guided isolation. Its structure was elucidated by LC/MS, NMR, chemical synthesis and time-dependent density functional theory (TD-DFT) calculations. 1-DGlcNAc specifically suppressed X. oryzae pv. oryzae PXO99A (MIC was 23.90 µg/mL), but not other common pathogens including Xanthomonas campestris pv. campestris str.8004 and Xanthomonas oryzae pv. oryzicola RS105. However, its diastereomer (2-acetamido-1,5-anhydro-2-deoxy-d-mannitol) also has no activity to X. oryzae pv. oryzae. This result suggested that activity of 1-DGlcNAc was related to the difference in the spatial conformation of the 2-acetamido moiety, which might be attributed to their different interactions with a receptor. Eighty-four unique proteins were found in X. oryzae pv. oryzae PXO99A compared with the genome of strains8004 and RS105 by blastp. There may be unique interactions between 1-DGlcNAc and one or more of these unique proteins in X. oryzae pv. oryzae. Quantitative real-time PCR and the pharmMapper server indicated that proteins involved in cell division could be the targets in PXO99A. This research suggested that specificity of active substance was based on the active group and spatial conformation selection, and these unique proteins could help to reveal the specific mechanism of action of 1-DGlcNAc against PXO99A.

A S-Layer Protein of Bacillus anthracis as a Building Block for Functional Protein Arrays by In Vitro Self-Assembly.

S-layer proteins create a cell-surface layer architecture in both bacteria and archaea. Because S-layer proteins self-assemble into a native-like S-layer crystalline structure in vitro, they are attractive building blocks in nanotechnology. Here, the potential use of the S-layer protein EA1 from Bacillus anthracis in constructing a functional nanostructure is investigated, and apply this nanostructure in a proof-of-principle study for serological diagnosis of anthrax. EA1 is genetically fused with methyl parathion hydrolase (MPH), to degrade methyl parathion and provide a label for signal amplification. EA1 not only serves as a nanocarrier, but also as a specific antigen to capture anthrax-specific antibodies. As results, purified EA1-MPH forms a single layer of crystalline nanostructure through self-assembly. Our chimeric nanocatalyst greatly improves enzymatic stability of MPH. When applied to the detection of anthrax-specific antibodies in serum samples, the detection of our EA1-MPH nanostructure is nearly 300 times more sensitive than that of the unassembled complex. Together, it is shown that it is possible to build a functional and highly sensitive nanosensor based on S-layer protein. In conclusion, our present study should serve as a model for the development of other multifunctional nanomaterials using S-layer proteins.

A comprehensive microRNA expression profile of the backfat tissue from castrated and intact full-sib pair male pigs.

BACKGROUND: It is widely known that castration has a significant effect on the accumulation of adipose tissue. microRNAs (miRNAs) are known to be involved in fat deposition and to be regulated by the androgen-induced androgen receptor (AR). However, there is little understanding of the relationship between miRNAs and fat deposition after castration. In this study, the high-throughput SOLiD sequencing approach was used to identify and characterize miRNA expression in backfat from intact and castrated full-sib male 23-week-old pigs. The patterns of adipogenesis and fat deposition were compared between castrated and intact male pigs. RESULTS: A total of 366 unique miRNA genes were identified, comprising 174 known pre-miRNAs and 192 novel pre-miRNAs. One hundred and sixty-seven pre-miRNAs were common to both castrated (F3) and intact (F4) male pig small RNA libraries. The novel pre-miRNAs encoded 153 miRNAs/miRNA*s and 141 miRNAs/miRNA*s in the F3 and F4 libraries, respectively. One hundred and seventy-seven miRNAs, including 45 up- and 132 down-regulated, had more than 2-fold differential expression between the castrated and intact male pigs (p-value < 0.001). Thirty-five miRNAs were further selected, based on the expression abundance and differentiation between the two libraries, to predict their targets in KEGG pathways. KEGG pathway analyses suggested that miRNAs differentially expressed between the castrated and intact male pigs are involved in proliferation, apoptosis, differentiation, migration, adipose tissue development and other important biological processes. The expression patterns of eight arbitrarily selected miRNAs were validated by stem-loop reverse-transcription quantitative polymerase chain reaction. These data confirmed the expression tendency observed with SOLiD sequencing. miRNA isomiRs and mirtrons were also investigated in this study. Mirtrons are a recently described category of miRNA relying on splicing rather than processing by the microprocessor complex to generate the RNAi pathway. The functions of miRNAs important for regulating fat deposition were also investigated in this study. CONCLUSIONS: This study expands the number of fat-deposition-related miRNAs in pig. The results also indicate that castration can significantly affect the expression patterns of fat-related miRNAs. The differentially expressed miRNAs may play important roles in fat deposition after castration.

A tract-based spatial statistics study of white matter integrity in epilepsy.

OBJECTIVE: To explore the changes of cerebral white matter diffusion tensor in epilepsy. METHODS: This study was a retrospective study based on diffusion tensor imaging (DTI). Twenty-six epileptic patients and 42 normal controls matched for sex, age and handedness were enrolled in our research. Based on the method of tract-based spatial statistics (TBSS), we analyzed the changes of each relevant parameter index of DTI in white matter of the brain in all subjects, including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD). RESULTS: In comparison with the control group, epileptic patients had decreased FA and elevated MD, AD, and RD in the anterior thalamic radiation, corticospinal tract, forceps major, forceps minor, cingulum, inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, superior longitudinal fasciculus and uncinate fasciculus (P < 0.05). CONCLUSION: Widespread white matter integrity was observed in epileptic patients, which may be the structural basis for the development of affective disorders, impaired cognition, and motor abnormalities.

YTHDF2 is a potential target of AML1/ETO-HIF1α loop-mediated cell proliferation in t(8;21) AML.

The t(8;21) fusion product, AML1/ETO, and hypoxia-inducible factor 1α (HIF1α) form a feed-forward transcription loop that cooperatively transactivates the DNA methyltransferase 3a gene promoter that leads to DNA hypermethylation and drives leukemia cell growth. Suppression of the RNA N6-methyladenosine (m6A)-reader enzyme YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) specifically compromises cancer stem cells in acute myeloid leukemia (AML) but promotes hematopoietic stem cell expansion without derailing normal hematopoiesis. However, the relevance of expression between AML1/ETO-HIF1α loop and YTHDF2, and its functional relationship with t(8;21) AML have not been documented. Here, we show that YTHDF2 is highly expressed in t(8;21) AML patients and associated with a higher risk of relapse and inferior relapse-free survival. Knockdown of YTHDF2 in leukemia cells causes an impaired cell proliferation rate in vitro and in mice. Mechanistically, HIF1α is able to bind to the hypoxia-response elements of the 5'-untranslated region of the YTHDF2 gene and promotes the transactivity of the YTHDF2 promoter. Knockdown and overexpression of either AML1/ETO or HIF1α resulted in decreased and increased YTHDF2 protein and mRNA expression in t(8;21) AML cells. In particular, knockdown of YTHDF2 resulted in increased global mRNA m6A levels in t(8;21) AML cells, accompanied by increased TNF receptor superfamily member 1b (TNFRSF1b) mRNA and protein expression levels. Last, we demonstrated that the m6A methylation and expression levels of the TNFRSF1b gene were both negatively correlated with HIF1α expression levels. In conclusion, YTHDF2 is a downstream target of the AML1/ETO-HIF1α loop and promotes cell proliferation probably by modulating the global m6A methylation in t(8;21) AML.

Phage display mediated immuno-PCR.

Immuno-PCR (IPCR) is a powerful detection technology in immunological study and clinical diagnosis due to its ultrasensitivity. Here we introduce a new strategy termed phage display mediated immuno-PCR (PD-IPCR). Instead of utilization of monoclonal antibody (mAb) and chemically bond DNA that required in the conventional IPCR, a recombinant phage particle is applied as a ready reagent for IPCR experiment. The surface displayed single chain variable fragment (scFv) and phage DNA themselves can directly serve as detection antibody and PCR template, respectively. The aim of the design is to overcome shortcoming of low detection sensitivity of scFv so as to largely facilitate the real application of scFv in immunoassay. The idea has been demonstrated by applying hantaan virus nucleocapsid protein (NP) and prion protein (PrP) as detection targets in three experimental protocols (indirect, sandwich and real-time PD-IPCR assays). The detection sensitivity was increased 1000- to 10,000-folds compared with conventional enzyme-linked immunosorbent assays (ELISAs). This proof-of-concept study may serve as a new model to develop an easy to operate, low cost and ultrasensitive immunoassay method for broad applications.

A dosimetric phantom study of thoracic radiotherapy based on three-dimensional modeling of mediastinal lymph nodes.

The aim of the present study was to investigate the optimal strategy and dosimetric measurement of thoracic radiotherapy based on three-dimensional (3D) modeling of mediastinal lymph nodes (MLNs). A 3D model of MLNs was constructed from a Chinese Visible Human female dataset. Image registration and fusion between reconstructed MLNs and original chest computed tomography (CT) images was conducted in the Eclipse™ treatment planning system (TPS). There were three plans, including 3D conformal radiotherapy (3D-CRT), intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT), which were designed based on 10 cases of simulated lung lesions (SLLs) and MLNs. The quality of these plans was evaluated via examining indexes, including conformity index (CI), homogeneity index and clinical target volume (CTV) coverage. Dose-volume histogram analysis was performed on SLL, MLNs and organs at risk (OARs). A Chengdu Dosimetric Phantom (CDP) was then drilled at specific MLNs according to 20 patients with thoracic tumors and of a medium-build. These plans were repeated on fused MLNs and CDP CT images in the Eclipse™ TPS. Radiation doses at the SLLs and MLNs of the CDP were measured and compared with calculated doses. The established 3D MLN model demonstrated the spatial location of MLNs and adjacent structures. Precise image registration and fusion were conducted between reconstructed MLNs and the original chest CT or CDP CT images. IMRT demonstrated greater values in CI, CTV coverage and OAR (lungs and spinal cord) protection, compared with 3D-CRT and VMAT (P<0.05). The deviation between the measured and calculated doses was within ± 10% at SLL, and at the 2R and 7th MLN stations. In conclusion, the 3D MLN model can benefit plan optimization and dosimetric measurement of thoracic radiotherapy, and when combined with CDP, it may provide a tool for clinical dosimetric monitoring.

Zoledronic acid inhibits infiltration of tumor-associated macrophages and angiogenesis following transcatheter arterial chemoembolization in rat hepatocellular carcinoma models.

Hepatic transcatheter arterial chemoembolization (TACE), a minimally invasive procedure to block the blood supply of tumors and release of cytotoxic agents, is preferentially applied to patients with hepatocellular carcinoma (HCC) who are not able to receive radical treatments. However, the long-term effects of TACE are unsatisfactory, as the microenvironment following procedure stimulates tumor angiogenesis, which promotes recurrence and metastasis of residual tumors. Tumor associated macrophages (TAMs) have been revealed to stimulate tumor growth and angiogenesis associated with poor prognosis in HCC. The present study focused on the changes in TAMs following TACE, and explored the effects of TACE in combination with the TAM inhibitor zoledronic acid (ZA) in rat HCC models. Orthotropic HCC rats were divided into three groups: Sham TACE, TACE alone and TACE combined with ZA treatment. At 7 or 14 days following TACE, tumor growth was evaluated by magnetic resonance imaging (MRI). Infiltration of TAMs was assessed by histological analysis and flow cytometry. Tumor angiogenesis was measured as the mean vessel density, and initial slope was calculated from dynamic contrast enhancement MRI. Local and systemic levels of vascular endothelial growth factor (VEGF) were determined by western blotting or an ELISA, respectively. The results revealed that TACE inhibited tumor growth at 7 days following the procedure, but this inhibition was attenuated at 14 days following the procedure compared with the sham TACE control. If combined with ZA treatment, TACE exhibited a stable inhibition effect on tumor growth until the end of observation. Investigation of the underlying mechanisms demonstrated that TACE combined with ZA treatment inhibited infiltration of F4/80 positive TAMs and tumor angiogenesis compared with the TACE alone group at 14 days following the procedure. Additionally, the combination treatment significantly inhibited secretion of VEGF in the present models. In conclusion, ZA treatment enhanced the effects of TACE through inhibiting TAM infiltration and tumor angiogenesis in rat HCC models.

Identification and characterization of Bacillus anthracis by multiplex PCR on DNA chip.

Bacillus anthracis can be identified by detecting virulence factor genes located on two plasmids, pXO1 and pXO2. Combining multiplex PCR with arrayed anchored primer PCR and biotin-avidin alkaline phosphatase indicator system, we developed a qualitative DNA chip method for characterization of B. anthracis, and simultaneous confirmation of the species identity independent of plasmid contents. The assay amplifies pag gene (in pXO1), cap gene (in pXO2) and Ba813 gene (a B. anthracis specific chromosomal marker), and the results were indicated by an easy-to-read profile based on the color reaction of alkaline phosphatase. About 1 pg of specific DNA fragments on the chip wells could be detected after PCR. With the proposed method, the avirulent (pXO1+/2-, pXO1-/2+ and pXO1-/2-) strains of B. anthracis and distinguished 'anthrax-like' strains from other B. cereus group bacteria were unambiguously identified, while the genera other than Bacillus gave no positive signal.

Clinical significance of expression of tissue factor and tissue factor pathway inhibitor in ulcerative colitis.

AIM: To investigate the clinical significance of expression of tissue factor (TF) and tissue factor pathway inhibitor (TFPI) in ulcerative colitis (UC). METHODS: Thirty UC specimens taken by colonoscopy from patients with active UC treated at the Department of Pathology, Central Hospital Affiliated to Shenyang Medical College from February 2010 to January 2012 were included in an experimental group, and 30 normal colon tissue samples taken by colonoscopy from non-UC patients were included in a control group. Expression of TF and TFPI in UC and normal colon tissue samples was detected by immunohistochemistry. RESULTS: The positive rate of TF in UC was significantly higher than that in normal colon tissue (63% vs 33%, χ(2) = 5.41, P < 0.05). The positive rate of TFPI in UC was also significantly higher than that in normal colon tissue (43% vs 17%, χ(2) = 5.08, P < 0.05). CONCLUSION: Positive rates of TF and TFPI expression in UC are significantly higher than those in normal colon tissue. TF and TFPI may play an important role in the pathogenesis of UC.

Global identification of prokaryotic glycoproteins based on an Escherichia coli proteome microarray.

Glycosylation is one of the most abundant protein posttranslational modifications. Protein glycosylation plays important roles not only in eukaryotes but also in prokaryotes. To further understand the roles of protein glycosylation in prokaryotes, we developed a lectin binding assay to screen glycoproteins on an Escherichia coli proteome microarray containing 4,256 affinity-purified E.coli proteins. Twenty-three E.coli proteins that bound Wheat-Germ Agglutinin (WGA) were identified. PANTHER protein classification analysis showed that these glycoprotein candidates were highly enriched in metabolic process and catalytic activity classes. One sub-network centered on deoxyribonuclease I (sbcB) was identified. Bioinformatics analysis suggests that prokaryotic protein glycosylation may play roles in nucleotide and nucleic acid metabolism. Fifteen of the 23 glycoprotein candidates were validated by lectin (WGA) staining, thereby increasing the number of validated E. coli glycoproteins from 3 to 18. By cataloguing glycoproteins in E.coli, our study greatly extends our understanding of protein glycosylation in prokaryotes.

[Study on the relationship between smoking behavior and other unhealthy behaviors among middle school students in 4 cities of China].

OBJECTIVE: To explore the situation of smoking behavior among the students of middle school in Beijing, Hangzhou, Wuhan and Urumchi and to analyze the relationship between smoking behavior and several unhealthy behaviors together with psychological troubles to provide evidence in developing an early intervention plan. METHODS: The National Health Education Institute (NHEI) of Chinese Center for Disease Control and Prevention (CDC) provided relevant data on all middle schools in the 4 cities and then U.S. CDC randomly sampled 100 common middle schools from them with a special sampling process. The core questionnaire developed by the experts from WHO and other countries was used in the survey among 9015 sampled students. RESULTS: Among all the sampled students, 29.4% of them had ever attempted cigarettes smoking while 6.6% of them tried tobacco in the 30 days before survey, 27.0% of the students with smoking behavior began smoking at the age of 9 or younger, 31.8% had learned how to refuse smoking from school education. The students with smoking behavior were more likely to drink alcohol, use drugs, bully others, be injured, miss classes, and have some psychological troubles than those without smoking behavior. CONCLUSION: There were increasing trends noticed on the incidence of attempt and smoking cigarettes. Smoking was closely related to other unhealthy behaviors and psychological troubles. Comprehensive education activities on "no-smoking" should be implemented as early as possible among adolescents, as well as to promote training on life skills.

[Alcohol consumption and drug use among middle school students aged 13-15 in 4 cities of China].

OBJECTIVE: To provide data on alcohol consumption and drug use among middle-school students aged 13-15 in 4 cities of China, and to provide evidence for developing intervention strategies on adolescents alcohol and drug use. METHODS: Standardized sample selection process of two-stage cluster-sampling was used in middle-school students in Beijing, Hangzhou, Wuhan and Urumchi. A self-administered questionnaire survey was conducted in Sept. 2003 and data was analyzed by Epi Info software. RESULTS: Among 7344 students from grade 1 to 3, 36.5% had tasted while 14.4% had drunk alcohol in the past 30 days. 9.9% had experienced drunkness, 5.1% had been in trouble because of drinking, and 1.6% had ever used illegal drugs. Significant differences had been found in all the cities. Higher graders, older students and boys had higher rates of alcohol and addictive drug use than low graders, younger students and girls. 51.9% had been taught on take alcohol safety and another 27.6% on skills of rejecting alcohol, during the past school year. CONCLUSIONS: The current situation of alcohol and addictive drug use among Chinese middle-school students aged 13-15 seemed to be quite critical, suggesting that it is necessary to carry out relevant health education in accordance with different characteristics in area, gender and age of the students.

Reversible immobilization of proteins with streptavidin affinity tags on a surface plasmon resonance biosensor chip.

Dissociation of biotin from streptavidin is very difficult due to their high binding affinity. The re-use of streptavidin-modified surfaces is therefore almost impossible, making devices containing them (e.g. surface plasmon resonance (SPR) sensor chips) expensive. This paper describes a new protocol for reversible and site-directed immobilization of proteins with streptavidin affinity tags on the streptavidin-coated SPR biosensor chip (SA chip). Two streptavidin affinity tags, nano-tag and streptavidin-binding peptide (SBP tag), were applied. They both can specifically interact with streptavidin but have weaker binding force compared to the biotin-streptavidin system, thus allowing association and dissociation under controlled conditions. The SA chip surface could be regenerated repeatedly without loss of activity by injection of 50 mM NaOH solution. The fusion construct of a SBP tag and a single-chain antibody to mature bovine prion protein (scFv-Z186-SBP) interacts with the SA chip, resulting in a single-chain-antibody-modified surface. The chip showed kinetic response to the prion antigen with equilibrium dissociation constant K (D) approximately equal to 4.01 x 10(-7). All results indicated that the capture activity of the SA chip has no irreversible loss after repeated immobilization and regeneration cycles. The method should be of great benefit to various biosensors, biochips and immunoassay applications based on the streptavidin capture surface.

Construction of single chain variable fragment (ScFv) and BiscFv-alkaline phosphatase fusion protein for detection of Bacillus anthracis.

This paper describes an attempt for convenient and sensitive detection of Bacillus anthracis with single chain variable fragment (scFv)-based protein chip. Phage display technology was employed to generate scFv by using the protective antigen (PA) of B. anthracis for immunization. V(H) and V(L) genes of the scFv were amplified separately by reverse transcriptase-PCR from mRNA of immunized mice and then assembled into scFv gene with a linker DNA sequence. The scFv gene was inserted into a phagemid vector pCANTAB-5E and then transformed into Escherichia coli TG1 to yield recombinant phages after infection with helper phage M13KO7. After six rounds of panning with PA, the phage clones displaying scFv fragments of the antibody were selected by ELISA. One phage clone scFv-6w10 showing the strongest positive signal in ELISA was selected. To enhance the affinity of the scFv-6w10, a recombinant bivalent single-chain Fv antibody (biscFv-6w10) directed against PA was constructed and tested in functional assays. The affinity of the biscFv-6w10 was much higher than that of scFv-6w10 and reached 6.5 x 10(9) M(-1). An expression system was constructed for the production of E. coli alkaline phosphatase (EAP) labeled biscFv-6w10 (biscFv-6w10-EAP) in E. coli cells. The expressed fusion protein retained both antigen-specific binding and enzymatic activity and thus directly served as an enzyme-labeled antibody. Detections of PA and bacterial cells of B. anthracis using biscFv-6w10-EAP and Cy3-labeled biscFv-6w10 were performed on a protein chip. The fusion protein (biscFv-6w10-EAP) chip could detect 10 pg of PA and 500-1000 bacterial cells in approximately 2 h, while the sensitivity of Cy3-labeled protein chip reached 1 pg of PA and 50-100 cells within 2 h.

[Study on health related behaviors and its protective factors of junior middle school students in 4 cities of China].

OBJECTIVE: To provide accurate data on health related behaviors and protective factors among students in middle schools in China, for developing priorities, programs and policies on health education. METHODS: We used a standard scientific sample selection process developed by American Center for Disease Control and Prevention (CDC) to conduct the questionnaire survey among middle schools from four cities--Beijing, Hangzhou, Wuhan and Urumchi. RESULTS: Data were found as: 3.2% of students are overweight; 25.3% of students rarely washing hands before eating at school, 20.5% of the students had seriously injured in the past 12 months, 30.4% of male students having had physical fighting, 17.1% of the students having serious attempted suicide, 29.7% of the students ever tried or experimented cigarette smoking, 13.0% having drunk from alcohol and 14.5% having been offered or selling drugs during the past 30 days, 78.9% were in an insufficient amount of physical activity and only 14.3% often used seat belt when riding in a car. CONCLUSIONS: There were many problems on health related behaviors among middle school students in these four cities, especially on hygiene, physical activities, psychological situation, smoking and drinking etc. It is absolutely necessary to develop health education for children and adolescence to promote their healthy behaviors and lifestyle.