Cascade screening for familial hypercholesterolemia-identification of the C308Y mutation in multiple family members and relatives for the first time in mainland China.

BACKGROUND: Familial hypercholesterolemia (FH), an autosomal dominant genetic disorder, is underdiagnosed and undertreated. The majority of FH cases are caused by low density lipoprotein receptor (LDL-R) gene mutations. The C308Y mutation in LDL-R results in approximately 70% loss of LDL-R activity, leading to the elevation of low density lipoprotein-cholesterol (LDL-C) and an increased risk of premature coronary heart disease (CHD). The aim of this study was to identify FH cases by cascade screening in family members and relatives of a 37-year old male with premature CHD and hypercholesterolemia. METHODS: Clinical exam, blood lipid profiling and genomic DNA sequencing of all exons of LDL-R were performed for the proband and his 14 family members and relatives. FH diagnosis was carried out using the Dutch Lipid Clinic Network (DLCN) criteria. RESULTS: Lipid profiling showed that 9 individuals, including the proband, had hypercholesterolemia. All these 9 subjects had a G > A substitution at nucleotide 986 in exon 7 resulting in the C308Y mutation as determined by DNA sequencing, and all those carrying the mutation were diagnosed as having definite FH under the DLCN criteria. However, most (7/9) did not have suggestive clinical manifestations of CHD. CONCLUSIONS: The C308Y mutation was discovered in multiple family members and relatives for the first time in mainland China. Cascade screening is key for the confirmatory diagnosis of FH. Our hypothesis that the C308Y is a common variant in the population of Southern China origin warrants further validation by screening for the C308Y mutation in a large population.

Promoter engineering strategies for the overproduction of valuable metabolites in microbes.

Promoter engineering is an enabling technology in metabolic engineering and synthetic biology. As an indispensable part of synthetic biology, the promoter is a key factor in regulating genetic circuits and in coordinating multi-gene biosynthetic pathways. In this review, we summarized the recent progresses in promoter engineering in microbes. Specifically, the endogenous promoters are firstly discussed, followed by the statement of the influence of nucleotides exchange on the strength of promoters explored by site-selective mutagenesis. We then introduced the promoter libraries with a wide range of strength, which are constructed focusing on core promoter regions and upstream activating sequences by rational designs. Finally, the application of promoter libraries in the optimization of multi-gene metabolic pathways for high-yield production of metabolites was illustrated with a couple of recent examples.

Convergent alteration of lung tissue microbiota and tumor cells in lung cancer.

Microbiota-host interaction plays an important role in cancer predisposing, initiation, progression, and response to therapy. Here, we explored the composition of lung tissue microbiota in 143 Chinese patients through conducting 16S rRNA gene sequencing, while TP53 mutation in tumor cells was assessed simultaneously. We found PAH-degrading microbes were more abundant in lung tumor microbiota from smokers. Furthermore, TP53 mutation was more prevalent in smokers, and TP53-mutated tumor harbored more Massilia, as well as Acidovorax that was also capable of degrading PAH. Further analysis showed DNA recombination and repair pathway was enriched in microbiota of smokers, which was convergent to the alteration occurred in tumor cells. Meanwhile, the microbiota of TP53-mutated tumor also exhibited dysregulation of p53 signaling pathway. Our results provided insights into the association of lung commensal microbes with tobacco exposure and host gene mutation, suggesting microbiota and tumor cells might undergo convergent alteration and mutually benefit each other.

Artificial duplicate reads in sequencing data of 454 Genome Sequencer FLX System.

The 454 Genome Sequencer (GS) FLX System is one of the next-generation sequencing systems featured by long reads, high accuracy, and ultra-high throughput. Based on the mechanism of emulsion PCR, a unique DNA template would only generate a unique sequence read after being amplified and sequenced on GS FLX. However, biased amplification of DNA templates might occur in the process of emulsion PCR, which results in production of artificial duplicate reads. Under the condition that each DNA template is unique to another, 3.49%-18.14% of total reads in GS FLX-sequencing data were found to be artificial duplicate reads. These duplicate reads may lead to misunderstanding of sequencing data and special attention should be paid to the potential biases they introduced to the data.

[Characterization and secreted expression of dengue virus type I-IV envelope glycoprotein domain III in Pichia pastoris].

OBJECTIVE: To achieve secretory and extracellular production of recombinant dengue virus serotypes I-IV envelope glycoprotein domain III (DENV-1-4 EDIII) in Pichia pastoris. METHODS: EDIII genes of DENVI-IV were amplified and cloned into vector pPIC9K, respectively. These recombinant plasmids were then linearized and transferred into Pichia pastoris strain GS115. Clones highly produced in 4.0 mg/ml G418 were amplified and induced by methanol to achieve the secreted recombinant proteins. Ni-NTA agarose beads were used for purification, while SDS-PAGE and Western blotting were used for identification. RESULTS: The recombinant plasmids pPIC9K-DENV-1-4 EDIII were constructed and successfully transferred into Pichia pastoris strain GS115. The recombinant EDIII proteins were expressed in a secretory way with the molecular weight about 12 × 10(3) and specifically identified by anti-His monoclonal antibody and anti-DENVI-IV mice sera. CONCLUSION: DENVI-IV EDIII proteins are successfully achieved from Pichia pastoris expression system and could be used for development of dengue vaccines, diagnostic reagents and study of biological function of the E protein.

Integrated gene expression profile predicts prognosis of breast cancer patients.

Gene expression data has in recent years demonstrated the superior capacity to predict the prognosis of breast cancer patients unreceiving adjuvant chemotherapy comparing to the information available from traditional clinical and pathological sources. Meanwhile, adjuvant chemotherapy can significantly improve survival of breast cancer. It would be inappropriate to ignore its effect on prognosis. We hypothesized that an integrated gene expression profile can predict the prognosis of breast cancer patients receiving chemotherapy. Therefore, we screened the specific gene markers and constructed an integrated 24-gene signature by low-density microarray including the "poor signature" and genes related to resistance to chemotherapy. The gene signature stratified correctly patients into good prognosis group and poor prognosis group. In addition, the Kaplan-Meier analyses for disease-free survival as a function of the 24-gene signature showed highly significant differences between the two groups (Log Rank test P < 0.0001 = Univariate and multivariate Cox's proportional-hazards regression analyses indicated that the signature represents the strongest independent prognostic factor for breast cancer patients. When compared with single signature, such as Oncotype DX and 70 poor signature, the integrated signature showed more predominant power of predication in breast cancer patients receiving chemotherapy. Such integrated signature will critically aid clinical decision making at the level of individualization for most breast cancer patients receiving chemotherapy.

Use of serial analysis of gene expression to reveal the specific regulation of gene expression profile in asthmatic rats treated by acupuncture.

BACKGROUND: Asthma has become an important public health issue and approximately 300 million people have suffered from the disease worldwide. Nowadays, the use of acupuncture in asthma is increasing. This study intended to systematically analyze and compare the gene expression profiles between the asthmatic and acupuncture-treated asthmatic rat lung, and tried to gain insight into the molecular mechanism underlying the early airway response (EAR) phase of asthma treated by acupuncture. METHODS: Four tag libraries of serial analysis of gene expression (SAGE) were established from lung tissues of control rats (CK), asthmatic rats (AS), asthmatic rats treated by acupuncture (ASAC), and control rats treated by acupuncture (CKAC). Bioinformatic analyses were carried out by using the methods including unsupervised hierarchical clustering, functional annotation tool of the database for annotation, visualization, and integrated discovery (DAVID), gene ontology (GO) tree machine, and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. RESULTS: There were totally 186 differentially expressed tags (P < 0.05, P(CK/AS)) between the libraries of CK and AS, 130 differentially expressed tags between libraries of AS/ASAC (P < 0.05, P(AS/ASAC)), and 144 differentially expressed tags between libraries of CK/CKAC (P < 0.05, P(CK/CKAC)). The gene expression profiles of AS and ASAC were more similar than other libraries via unsupervised SAGE clustering. By comparison of P(CK/AS) and P(AS/ASAC), the DAVID genes functional classification was found to be changed from "immune response" to "response to steroid hormone stimulus", and the GO term "antigen processing and presentation of peptide antigen" disappeared in P(AS/ASAC). Totally 3 same KEGG pathways were found among the three groups. Moreover, 21 specific tags of the acupuncture in treating asthma were detected using Venn diagrams. CONCLUSION: Our SAGE research indicates that the gene expression profile of the EAR phase of asthma could be effectively and specifically regulated by acupuncture, which suggests that the gene expression of immune response and steroid hormone may play an important role in the treatment.

Modeling of protein refolding from inclusion bodies.

Overexpression of foreign proteins in Escherichia coli often leads to the formation of inclusion bodies (IBs), which becomes the major bottleneck in the preparation of recombinant proteins and their applications. In the present study, 36 proteins from IBs were refolded using a simple refolding method. Refolding yields of these proteins were defined as the percentage of soluble proteins following dilution refolding in the amount of denatured proteins in the samples before diluting into refolding buffer. Furthermore, a mathematical model was deduced to evaluate the role of biochemical properties in the protein refolding. Our results indicated that under the experimental conditions, isoelectric point of proteins might be mostly contributing to the high efficacy of protein refolding since the increment of one unit resulted in a decrease of 14.83% in the refolding yield. Other important mediators were components of protein secondary structure and the molecular weight (R(2) = 0.98, P = 0.000, F-test). Six proteins with low efficiency in the protein refolding possessed relatively low isoelectric points. Furthermore, refolding yields of six additional proteins from IBs were predicted and further validated by refolding the proteins under the same conditions. Therefore, the model of protein refolding developed here could be used to predict the refolding yields of proteins from IBs through a simple method. Our study will be suggestive to optimize the methods for protein refolding from IBs according to their intrinsic properties.

Serial analysis of gene expression in a rat lung model of asthma.

BACKGROUND AND OBJECTIVE: The pathogenesis and molecular mechanism underlying asthma remain undetermined. The purpose of this study was to identify genes and pathways involved in the early airway response (EAR) phase of asthma by using serial analysis of gene expression (SAGE). METHODS: Two SAGE tag libraries of lung tissues derived from a rat model of asthma and controls were generated. Bioinformatic analyses were carried out using the Database for Annotation, Visualization and IntegratedDiscovery Functional Annotation Tool, Gene Ontology (GO) TreeMachine and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. RESULTS: A total of 26 552 SAGE tags of asthmatic rat lung were obtained, of which 12 221 were unique tags. Of the unique tags, 55.5% were matched with known genes. By comparison of the two libraries, 186 differentially expressed tags (P < 0.05) were identified, of which 103 were upregulated and 83 were downregulated. Using the bioinformatic tools these genes were classified into 23 functional groups, 15 KEGG pathways and 37 enriched GO categories. CONCLUSIONS: The bioinformatic analyses of gene distribution, enriched categories and the involvement of specific pathways in the SAGE libraries have provided information on regulatory networks of the EAR phase of asthma. Analyses of the regulated genes of interest may inform new hypotheses, increase our understanding of the disease and provide a foundation for future research.

Small surface antigen variants of HBV associated with responses to telbivudine treatment in chronic hepatitis B patients.

BACKGROUND: Nucleoside/nucleotide analogues are widely used to treat chronic HBV infection, but drug resistance is common. The role of HBV surface gene variants in drug resistance to nucleoside/nucleotide analogues is unknown. We are trying to investigate the dynamics of S gene mutations and how they relate to a patient's virological response in this study. METHODS: Thirty patients with chronic hepatitis B were enrolled and serum samples were collected at multiple time points during treatment with telbivudine (LdT). The coding regions of the small surface antigen (S-HBsAg) were amplified and sequenced using the 454 GS FLX+ System. RESULTS: Sequencing results revealed different dynamics of non-synonymous mutations, such as sL9P, sN40S, sG44E, sW172*, sW182* and sS187F, between patients with a complete virological response and those with a partial virological response. The viral population heterogeneity decreased at week 12 of LdT treatment in patients with a complete virological response, with a concomitant decline in non-synonymous mutations (from an average of 14 to 9.9 per sample) and an increase in the frequencies of major variants (from 14.3% to 40.4%). CONCLUSIONS: Our findings suggest that the decrease in viral population heterogeneity at an early stage of LdT treatment was associated with the subsequent optimal virological response, and the early appearance of some specific mutations, such as sG44E, sW172* and sW182*, is a potential indicator of a partial virological response in continuing therapy.

Clinical Outcomes of Wulingsan Subtraction Decoction Treatment of Postoperative Brain Edema and Fever as a Complication of Glioma Neurosurgery.

Objective. To evaluate the efficacy of Wulingsan subtraction ( WLSS) decoction in the treatment of postoperative brain edema and fever as a complication of glioma neurosurgery. Methods. This retrospective study was conducted at the Department of Neurosurgery of Liaocheng People's Hospital. Patients hospitalized between March 2011 and December 2014 were divided into three groups: Group A received WLSS oral liquid (50 mL), twice a day; Group B received an intravenous infusion of mannitol; and Group C received WLSS combined with mannitol (n = 30 patients per group). All patients were treated for 10 days continuously. Therapeutic efficacy was evaluated by measuring body temperature and indicators of renal function before and 3, 5, and 10 days after treatment. Results. Compared to the other two groups, significantly greater clinical efficacy was observed in the patients treated with mannitol (Group B; P < 0.05), although marked clinical efficacy was also observed over time in patients treated with WLSS (Group A). After 5 days, the quantifiable effects of the WLSS and mannitol combination group (Group C) were substantial (P < 0.05). The renal damage in Group B was more obvious after 5 days and 10 days. Conclusion. Compared with mannitol treatment alone, WLSS combined with mannitol induced a more rapid reduction in body temperature. Our findings suggest that patients should be started on mannitol for 3 days and then switched to WLSS to achieve obvious antipyretic effects and protect renal function. This method of treatment should be considered for clinical applications.

Effect of total flavonoids from Scutellaria baicalensis on dopaminergic neurons in the substantia nigra.

The aim of the present study was to investigate the effect of Scutellaria baicalensis stem-leaf total flavonoid (SSTF) on the dopaminergic neurons in the substantia nigra in a mouse model of Parkinson's disease (PD). The mouse model was established by intravenous injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). SSTF (5 mg/kg) was administered to the mice before or after MPTP injection, and the effects of SSTF on the behavior of the mice and the dopaminergic neurons in the substantia nigra were assessed. In addition, the level of serum malondialdehyde (MDA) was measured. Following injection of MPTP, the number of dopaminergic neurons in the substantia nigra was decreased and the neurons appeared atrophic. In addition, the level of serum MDA in the MPTP mice increased. The mean behavioral scores and the number of dopaminergic neurons in the SSTF treatment groups were significantly higher than in the MPTP group (P<0.05), and the mean serum MDA levels were significantly lower (P<0.05). Thus, SSTF improves the behaviors and the numbers of dopaminergic neurons in the substantia nigra in MPTP-induced PD in mice. These beneficial effects appear to be associated with the reduction in serum MDA.

[Sequencing and analysis of Vibrio cholerae typing phage VP3 genome].

DNA sequence and the genome of phage VP3 (a typing phage of V. cholera) were analyzed. A random library of VP3 DNA was constructed by shot-gun library method. The VP3 genome sequence was assembled with contigs sequences, the gaps between different contigs were filled with sequencing data from primer walking. ORFs were predicted; Phylogeny of DNA polymerase sequences was analyzed to determine the class of VP3; The activity of putative promoter genes were analyzed using lacZ report system. VP3 genome is a 39504bp of circular double-stranded DNA. Twenty-seven out of forty-nine putative ORFs were annotated; twenty gene products were homologous with T7-like phages, including DNAP, DNA replicative protein, capsid, tail tubular, tail fiber protein, and DNA packaged protein. The activity of the putative promoter regions was confirmed through cloning those regions to LacZ-fuse plasmid pRS1274 and analysis of the expression of beta galactosidase. The complete genomic sequence of VP3 and phylogenetic tree analysis suggests VP3 is a member of T7 phage family.

[Pharmacognostic studies on Desmodium gyrans].

OBJECTIVE: To study the characteristic features of Desmodium gyrans in order to provide a basis for rational exploitation and utilization of the herb. METHOD: Samples of the title plant were collected, the microscopic features of cross sections and powders were studied. TLC profiles and UV absorption of the plant extract were examined. RESULT: Calcium oxalate crystals were found in cells of transverse sections. Nonglandular hairs were observed on leaf surfaces. Characteristic peaks in the UV spectrum were identified. CONCLUSION: The distinct characteristic features revealed in this studies can serve as evidence for the identification of D. gyrans.

Composition and Interactions of Hepatitis B Virus Quasispecies Defined the Virological Response During Telbivudine Therapy.

Reverse transcriptase (RT) mutations contribute to hepatitis B virus resistance during antiviral therapy with nucleos(t)ide analogs. However, the composition of the RT quasispecies and their interactions during antiviral treatment have not yet been thoroughly defined. In this report, 10 patients from each of 3 different virological response groups, i.e., complete virological response, partial virological response and virological breakthrough, were selected from a multicenter trial of Telbivudine treatment. Variations in the drug resistance-related critical RT regions in 107 serial serum samples from the 30 patients were examined by ultra-deep sequencing. A total of 496,577 sequence reads were obtained, with an average sequencing coverage of 4,641X per sample. The phylogenies of the quasispecies revealed the independent origins of two critical quasispecies, i.e., the rtA181T and rtM204I mutants. Data analyses and theoretical modeling showed a cooperative-competitive interplay among the quasispecies. In particular, rtM204I mutants compete against other quasispecies, which eventually leads to virological breakthrough. However, in the absence of rtM204I mutants, synergistic growth of the drug-resistant rtA181T mutants with the wild-type quasispecies could drive the composition of the viral population into a state of partial virological response. Furthermore, we demonstrated that the frequency of drug-resistant mutations in the early phase of treatment is important for predicting the virological response to antiviral therapy.

[Detecting rpoB gene mutation in rifampin-resistant Mycobacterium tuberculosis by using the reverse dot-blot hybridization method].

OBJECTIVE: To establish a simple, rapid and sensitive hybridization method for detecting drug-resistance relevant gene mutation in Mycobacterium tuberculosis. METHODS: Fourteen single-strand specific probes designed to detect mutated and/or wild rpoB gene in Mycobacterium tuberculosis were spotted and fixed on nylon membranes, and PCR products labeled with biotin were obtained by using down-stream primer labeled with biotin, then hybridized and analyzed with streptavidin-HRP and TMB. RESULTS: Twenty-three rifampin-resistant Mycobacterium tuberculosis isolates and 11 rifampin-sensitive isolates were analyzed. The gene mutations were consistent with the DNA sequencing and the in vitro susceptibility test in 30/34 and 28/34 of the isolates, respectively. Mutations of Ser-531 were present in 11 of the 23 rifampin-resistant isolates, followed by His-526, Leu-533, and no mutation was found in 13 isolates, including 2 rifampin-resistant isolates. Mutations in loci 516 and 513 were not detected. CONCLUSION: Reverse dot-blot hybridization may be of potential use for the rapid diagnosis of rifampin-resistant tuberculosis.

Protective Effect of Polysaccharides from Inonotus obliquus on Streptozotocin-Induced Diabetic Symptoms and Their Potential Mechanisms in Rats.

The present study aimed to evaluate the therapeutic effects of polysaccharides from Inonotus obliquus (PIO) on streptozotocin- (STZ-) induced diabetic symptoms and their potential mechanisms. The effect of PIO on body weight, blood glucose, damaged pancreatic ß-cells, oxidative stresses, proinflammatory cytokines, and glucose metabolizing enzymes in liver was studied. The results show that administration of PIO can restore abnormal oxidative indices near normal levels. The STZ-damaged pancreatic ß-cells of the rats were partly recovered gradually after the mice were administered with PIO 6 weeks later. Therefore, we may assume that PIO is effective in the protection of STZ-induced diabetic rats and PIO may be of use as antihyperglycemic agent.

[Screening molecular markers in early breast cancer of the same pathological types but with different prognoses using Agilent gene chip].

OBJECTIVE: To screen molecular markers in early breast cancer and establish gene subtyping-based diagnostic criteria for predicting the prognosis of early breast cancers. METHODS: Tumor tissue specimens were obtained from 8 patients with early breast cancer for analysis of the differentially expressed genes using Agilent custom 8×15 000 chips in combination with the prognostic data of the patients. Another 42 tumor tissue specimens were used to validate the differential genes by real-time fluorescent quantitative PCR. RESULTS: Gene microarray analysis identified 132 differentially expressed genes between the patients with favorable and poor prognosis, and 44 of these genes were significantly up-regulated (by over two folds) and 88 down-regulated in patients with poor prognoses. CONCLUSION: The gene expression profiles differ in early breast cancer tissues of the same pathological type but with different clinical stages and prognoses, and CD44, MKI67, NTRK2, Nek2, C16orf60, TOP2A, ANCCA, and RRM2 genes can be used as the prognostic markers for early breast cancer.

Effects of acupuncture on the gene expression profile of lung tissue from normal rats.

Acupuncture has been demonstrated to be an effective treatment for various diseases. However, little attention has been paid to its physiological influences, especially on the changes in protein and mRNA levels following acupuncture treatment under normal conditions. In this study, we investigated the gene expression profile of lung tissue from acupuncture-treated normal rats and attempted to characterize the underlying mechanisms of the changes in expression. Three common acupoints, Dazhui (GV14), fengmen (BL12) and feishu (BL13) were selected for analysis, and 2 serial analyses of gene expression (SAGE) tag libraries of the lung tissues that were derived from the normal and acupuncture-treated rats were established. Bioinformatic analyses were carried out using the functional annotation tools of the database for annotation, visualization and integrated discovery (DAVID), the gene ontology (GO) Tree Machine and the Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. In total, 144 tags were differentially expressed (P<0.05), and the DAVID functional classification of genes demonstrated that the genes were divided into 6 types. Furthermore, GO Tree Machine analysis of the gene categories indicated that 10 enriched GO categories had become enriched after acupuncture, and that 15 KEGG pathways matched the differentially expressed tags of the 2 SAGE libraries. Our results show that the essential effects of acupuncture on normal rats include the regulation of macromolecular biosynthesis, transportation and metabolism. Cellular biosynthesis and cellular lipid metabolism are the common biological processes that occur in response to acupuncture under normal and morbid conditions, which may be the general physiological effects of acupuncture.

Alternatively expressed genes identified in the CD4+ T cells of allograft rejection mice.

Allograft rejection is a leading cause for the failure of allotransplantation. CD4(+) T cells play critical roles in this process. The identification of genes that alternatively expressed in CD4(+) T cells during allograft rejection will provide critical information for studying the mechanism of allograft rejection, finding specific gene markers for monitoring, predicting allograft rejection, and opening new ways to regulate and prevent allograft rejection. Here, we established allograft and isograft transplantation models by adoptively transferring wild-type BALB/c mouse CD4(+) T cells into severe combined immunodeficient (SCID) mice with a C57BL/6 or BALB/c mouse skin graft. Using the whole transcriptome sequencing-based serial analysis of gene expression (SAGE) technology, we identified 97 increasingly and 88 decreasingly expressed genes that may play important roles in allograft rejection and tolerance. Functional classification of these genes shows that apoptosis, transcription regulation, cell growth and maintenance, and signal transduction are among the frequently changed functional groups. This study provides a genome-wide view for the candidate genes of CD4(+) T cells related to allotransplantation, and this report is a good resource for further microarray studies and for identifying the specific markers that are associated with clinical organ transplantations.