Search

Background Hypoxia inducible factor 1α (HIF-1α) is a stress-responsive transcription factor to hypoxia and its expression is correlated to tumor progression and angiogenesis. Several single nucleotide polymorphisms (SNPs) of HIF-1α gene in the oxygen-dependent degradation (ODD) domain was reportedly associated with increased HIF-1α activity. Results In this study, we focused on the relationship between SNP 1772 C > T (rs11549465) of HIF-1α gene and its breast cancer risk, as well as its correlation with HIF-1α expression and tumor angiogenesis. Ninety six breast cancer patients and 120 age-matched controls were enrolled. We found that 1772 T allele of HIF-1α gene was associated with increased breast cancer risk (adjusted OR = 14.51; 95% CI: 6.74-31.24). This SNP was not associated with clinicopathologic features of angiogenesis such as VEGF activity and the micro-vessel density and survival of breast cancer patients. Conclusion Taken together, the 1772 C > T of HIF-1α gene is a potential biomarker for breast cancer susceptibility. [ABSTRACT FROM AUTHOR]

Background: As a strong fermentator, Saccharomyces cerevisiae has the potential to be an excellent host forethanol production by consolidated bioprocessing. For this purpose, it is necessary to transform cellulose genesinto the yeast genome because it contains no cellulose genes. However, heterologous protein expression in S.cerevisiae often suffers from hyper-glycosylation and/or poor secretion. Thus, there is a need to genetically engineerthe yeast to reduce its glycosylation strength and to increase its secretion ability. Results: Saccharomyces cerevisiae gene-knockout strains were screened for improved extracellular activity of arecombinant exocellulase (PCX) from the cellulose digesting fungus Phanerochaete chrysosporium. Knockoutmutants of 47 glycosylation-related genes and 10 protein-trafficking-related genes were transformed with a PCX expression construct and screened for extracellular cellulase activity. Twelve of the screened mutants were found tohave a more than 2-fold increase in extracellular PCX activity in comparison with the wild type. The extracellular PCX activities in the glycosylation-related mnn10 and pmt5 null mutants were, respectively, 6 and 4 times higherthan that of the wild type; and the extracellular PCX activities in 9 protein-trafficking-related mutants, especially inthe chc1, clc1 and vps21 null mutants, were at least 1.5 times higher than the parental strains. Site-directed mutagenesis studies further revealed that the degree of N-glycosylation also plays an important role inheterologous cellulase activity in S. cerevisiae. Conclusions: Systematic screening of knockout mutants of glycosylation- and protein trafficking-associated genesin S. cerevisiae revealed that: (1) blocking Golgi-to-endosome transport may force S. cerevisiae to export cellulases; and (2) both over- and under-glycosylation may alter the enzyme activity of cellulases. This systematic gene-knockout screening approach may serve as a convenient means for increasing the extracellular activities of recombinant proteins expressed in S. cerevisiae. [ABSTRACT FROM AUTHOR]

Data retention is a major issue that significantly affects the reliability of nonvolatile memory. In this paper, data retention behaviors due to mobile ions are extensively characterized by using several test methods. The source of mobile ions during the sputtering of Ti/TiN layers for forming salicide inside array was identified by secondary ion mass spectroscopy (SIMS) analysis. Different test sequences clearly reveal the data retention caused by mobile ions. Salicide block material that includes silicon nitride effectively blocks the impact of mobile ions. Bitmapping patterns on an array indicate that the amount of charge loss spatially depends on its neighbor's high-V[sub th] cells via the Coulomb's r-square field. The spatial effects of neighboring cells on the charge loss are then estimated. Beyond 1.98 µm, the charge loss caused by mobile ions of a individual cell becomes unaffected by the V[sub th] state of its neighboring cells. Plasma charging cells also attract mobile ions. A considerable charge gain, by as much as 0.8 V with a radial distribution on fresh wafer, was observed after a UV-bake test. The interaction between plasma charging effect and mobile ions movement during wafer processing explains this interesting feature. [ABSTRACT FROM AUTHOR]

Describes the structure, operation and fabrication of a novel electrically erasable programmable read only memory and flash cell and array architecture. Description of cell, its operation and fabrication; Circuit schematic drawing of the cell imbedded in an array; Process parameters for cell implementation.

Background: The optimal radiotherapy dose for locally advanced cervical esophageal squamous cell carcinoma (C-ESqCC) treated with definitive concurrent chemoradiotherapy (dCCRT) is unclear. Here, we aimed to compare the survival of those treated with high dose versus standard dose via a population based approach. Methods: Eligible C-ESqCC patients diagnosed between 2011 and 2017 were identified via the Taiwan Cancer Registry. We used propensity score (PS) weighting to balance observable potential confounders between groups. The hazard ratio (HR) of death and incidence of esophageal cancer mortality (IECM) were compared between high (60-70 Gy) and standard dose (50-50.4 Gy). We also evaluated the outcome in supplementary analyses via alternative approaches. Results: Our primary analysis consisted of 141 patients in whom covariates were well balanced after PS weighting. The HR of death when high dose was compared with standard dose was 0.65 (95% confidence interval [CI]: 0.4-1.03, p = 0.07). The HR of IECM was 0.74 (p = 0.45). The HR of OS remained similarly insignificant in supplementary analyses. Conclusions: We observed a trend in favor of high radiotherapy dose versus standard dose for C-ESqCC treated with dCCRT in this population-based nonrandomized study. Further studies are needed to confirm the findings of the study. [ABSTRACT FROM AUTHOR]

Chronic hepatitis B (CHB) infection is rarely eradicated by current antiviral nucleos(t)ide analogues. We found that α2,6-biantennary sialoglycans of HBV surface antigen (HBsAg) bound human SIGLEC-3 (CD33) by IP and ELISA, and the binding affinity between SIGLEC-3 and α2,6-biantennary sialoglycans was determined by biolayer interferometry (equilibrium dissociation constant [KD]: 1.95 × 10-10 ± 0.21 × 10-10 M). Moreover, HBV activated SIGLEC-3 on myeloid cells and induced immunosuppression by stimulating immunoreceptor tyrosine-based inhibitory motif phosphorylation and SHP-1/-2 recruitment via α2,6-biantennary sialoglycans on HBsAg. An antagonistic anti-SIGLEC-3 mAb reversed this effect and enhanced cytokine production in response to TLR-7 agonist GS-9620 in PBMCs from CHB patients. Moreover, anti-SIGLEC-3 mAb alone was able to upregulate the expression of molecules involved in antigen presentation, such as CD80, CD86, CD40, MHC-I, MHC-II, and PD-L1 in CD14+ cells. Furthermore, SIGLEC-3 SNP rs12459419 C, which expressed a higher amount of SIGLEC-3, was associated with increased risk of hepatocellular carcinoma (HCC) in CHB patients (HR: 1.256, 95% CI: 1.027-1.535, P = 0.0266). Thus, blockade of SIGLEC-3 is a promising strategy to reactivate host immunity to HBV and lower the incidence of HCC in the CHB patient population. [ABSTRACT FROM AUTHOR]

Background: Patients with locally advanced colon cancer (LACC) have a relatively poor prognosis despite radical resection and adjuvant chemotherapy. This study investigated the treatment efficacy and toxicity of neoadjuvant chemoradiotherapy in patients with LACC.Methods: We retrospectively reviewed 36 patients with LACC preoperatively treated with chemotherapy and radiotherapy. Patients were administered chemoradiotherapy, which comprised radiotherapy and neoadjuvant chemotherapy involving a 5-fluorouracil, leucovorin, and oxaliplatin regimen every 2 weeks.Results: Median age was 64 years (45-86 years) and median follow-up period was 23.5 months (5.0-49.1 months). Seven (19.4%) patients developed grade 3 or 4 adverse events during neoadjuvant concurrent chemoradiotherapy. Pathologic responses were not evaluated in two patients who did not undergo radical resection. Of the 34 patients who underwent surgery, nine (26.4%) achieved a pathologic complete response (pCR). The 2-year estimated overall survival and disease-free survival rates were 88.7% and 73.6%, respectively.Conclusions: Our results demonstrated that neoadjuvant chemoradiotherapy is feasible and safe. A prominent pCR rate with an acceptable toxicity profile suggests that the multimodality therapy might be a treatment option for patients with LACC. [ABSTRACT FROM AUTHOR]

Background: This study is to evaluate the toxicity and outcomes of helical tomotherapy (HT) in patients treated for unresectable hepatocellular carcinoma (HCC). Methods: From March 2008 to September 2010, 38 patients with unresectable HCC were treated with HT. The median patient age was 67 years (range, 45-85). The median follow-up period was 17.2 months (range, 7-46). All patients had liver cirrhosis. Median radiation dose was 54 Gy (range, 46-71.8) delivered in 1.8 to 2.4-Gy fractions. The planning target volumes were 241.2 ± 153.1 cm3 (range, 45.8-722.4). Treatment responses were assessed in 3-6 months after HT. Results: There was a complete response in 2 patients (5.2 %), partial response in 18 patients (47.4 %), stable disease in 13 patients (34.2 %), and progressive disease in 5 patients (13.2 %). The median overall survival was 12.6 months, and 1- and 2-year overall survival rates were 56.2 and 31.7 %, respectively. Eastern Cooperative Oncology Group (ECOG score, p = 0.008), Child-Pugh classification (p = 0.012), albumin (p = 0.046), and hemoglobin (p = 0.028) were significant parameters that predicted primary tumor response to radiotherapy in multivariate analysis. ECOG score (p = 0.012), Child-Pugh class (p = 0.026), and response to radiotherapy (p = 0.016) were independent prognostic factors for overall survival in multivariate analysis. Responders had better overall survival than non-responders (23.6 vs. 5.8 months, p < 0.001). The 1- and 2-year overall survival rates for responders were 68.3 and 57 %, respectively, while for non-responders, they were 0 %. The 1- and 2-year local control rates were 88.2 and 82.3 %, respectively. Five patients (13.2 %) had grade 3 or greater liver toxicity, and one patient (2.6 %) had a grade 3 gastric ulcer. No treatment-related liver failure or death was documented in this study. Conclusions: Radiotherapy using HT seems to be a safe and effective treatment option for unresectable HCC patients. This study indicates that HT is a feasible treatment even in patients without good performance status and hepatic function reservation. [ABSTRACT FROM AUTHOR]

Cancer stem cells (CSCs) are a subset of cancer cells in tumors or established cancer cell lines that can initiate and sustain the growth of tumors in vivo. Cancer stem cells can be enriched in serum-free, suspended cultures that allow the formation of tumorspheres over several days to weeks. Brefeldin A (BFA) is a mycotoxin that induces endoplasmic reticulum (ER) stress in eukaryotic cells. We found that BFA, at sub-microgram per milliliter concentrations, preferentially induced cell death in MDA-MB-231 suspension cultures (EC50: 0.016 µg/mL) compared to adhesion cultures. BFA also effectively inhibited clonogenic activity and the migration and matrix metalloproteinases-9 (MMP-9) activity of MDA-MB-231 cells. Western blotting analysis indicated that the effects of BFA may be mediated by the down-regulation of breast CSC marker CD44 and anti-apoptotic proteins Bcl-2 and Mcl-1, as well as the reversal of epithelial-mesenchymal transition. Furthermore, BFA also displayed selective cytotoxicity toward suspended MDA-MB-468 cells, and suppressed tumorsphere formation in T47D and MDA-MB-453 cells, suggesting that BFA may be effective against breast cancer cells of various phenotypes. [ABSTRACT FROM AUTHOR]

Cancer stem cells are a subset of cancer cells that initiate the growth of tumors. Low levels of cancer stem cells also exist in established cancer cell lines, and can be enriched in serum-free tumorsphere cultures. Since cancer stem cells have been reported to be resilient to common chemotherapeutic drugs in comparison to regular cancer cells, screening for compounds selectively targeting cancer stem cells may provide an effective therapeutic strategy. We found that 5-azacytidine (5-AzaC) selectively induced anoikis of MCF-7 in suspension cultures with an EC50 of 8.014 μM, and effectively inhibited tumorsphere formation, as well as the migration and matrix metalloproteinases-9 (MMP-9) activity of MCF-7 cells. Furthermore, 5-AzaC and radiation collaboratively inhibited MCF-7 tumorsphere formation at clinically relevant radiation doses. Investigating the underlying mechanism may provide insight into signaling pathways crucial for cancer stem cell survival and pave the way to novel potential therapeutic targets. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the efficacy of helical tomotherapy plus capecitabine as a preoperative chemoradiotherapy (CRT) in patients with locally advanced rectal cancer (LARC). Thirty-six LARC patients receiving preoperative CRT were analyzed. Radiotherapy (RT) consisted of 45Gy to the regional lymph nodes and simultaneous-integrated boost (SIB) 50.4Gy to the tumor, 5 days/week for 5 weeks. Chemotherapy consisted of capecitabine 850mg/m2, twice daily, during the RT days. Patients underwent surgery 6-8 weeks after completion of CRT. Information was collected for patient characteristics, treatment response, and acute and late toxicities. Grade 3/4 (G3+) toxicities occurred in 11.1% of patients (4/36). Sphincter preservation rate was 85.2% (23/27). Five patients (14.3%) achieved pathological complete response. Tumor, nodal, and ypT0-2N0 downstaging were noted in 60% (21/35), 69.6% (16/23), and 57.1% (20/35). Tumor regression grade 2~4 was achieved in 28 patients (80%). After a median follow-up time of 35 months, the most common G3+ late morbidity was ileus and fistula (5.7%, 2/35).The study showed that capecitabine plus helical tomotherapy with an SIB is feasible in treatment of LARC.The treatment modality can achieve a very encouraging sphincter preservation rate and a favorable ypT0-2N0 downstaging rate without excessive toxicity. [ABSTRACT FROM AUTHOR]

Feathers have complex forms and are an excellent model to study the development and evolution of morphologies. Existing chicken feather mutants are especially useful for identifying genetic determinants of feather formation. This study focused on the gene F, underlying the frizzle feather trait that has a characteristic curled feather rachis and barbs in domestic chickens. Our developmental biology studies identified defects in feather medulla formation, and physical studies revealed that the frizzle feather curls in a stepwise manner. The frizzle gene is transmitted in an autosomal incomplete dominant mode. A whole-genome linkage scan of five pedigrees with 2678 SNPs revealed association of the frizzle locus with a keratin gene-enriched region within the linkage group E22C19W28&lowbar;E50C23. Sequence analyses of the keratin gene cluster identified a 69 bp in-frame deletion in a conserved region of KRT75,a n α-keratin gene. Retroviral-mediated expression of the mutated F cDNA in the wild-type rectrix qualitatively changed the bending of the rachis with some features of frizzle feathers including irregular kinks, severe bending near their distal ends, and substantially higher variations among samples in comparison to normal feathers. These results confirmed KRT75 as the F gene. This study demonstrates the potential of our approach for identifying genetic determinants of feather forms. [ABSTRACT FROM AUTHOR]

A CKD Care Program is found to help pre-ESRD patients prepare for dialysis initiation and is associated with a reduced probability of emergency dialysis and hospitalization and lowered medical costs. Aim: Multidisciplinary care of patients with chronic kidney disease (CKD) provides better care outcomes. This study is to evaluate the effectiveness of a CKD care program on pre-end-stage renal disease (ESRD) care. Methods: One hundred and forty incident haemodialysis patients were classified into the CKD Care Group ( n = 71) and the Nephrologist Care Group ( n = 69) according to participation in the CKD care program before dialysis initiation. The ‘total observation period’ was divided into ‘6 months before dialysis’ and ‘at dialysis initiation’. Quality of pre-ESRD care, service utilization and medical costs were evaluated and compared between groups. Results: The mean estimated glomerular filtration rates at dialysis initiation were low in both groups; but the levels of haematocrit and serum albumin of the CKD Care Group were significantly higher. The percentages of patients initiating dialysis with created vascular access, without insertion of double-lumen catheter and without hospitalization were 57.7%, 50.7% and 40.8%, respectively, in the CKD Care Group, and 37.7%, 29.0% and 18.8% in the Nephrologist Care Group ( P < 0.001). Participation in the CKD care program, though with higher costs during the 6 months before dialysis ($US1428 ± 2049 vs US$675 ± 962/patient, P < 0.001), was significantly associated with lower medical costs at dialysis initiation ($US942 ± 1941 vs $US2410 ± 2481/patient, P < 0.001) and for the total period of observation ($US2674 ± 2780 vs $US3872 ± 3270/patient, P = 0.009). The cost-saving effect came through the early preparation of vascular access and the lack of hospitalization at dialysis initiation. Conclusion: CKD care programs significantly improve quality of pre-ESRD care, decrease service utilization and save medical costs. [ABSTRACT FROM AUTHOR]

AbstractMany single nucleotide polymorphisms (SNPs) have been found to be associated with breast cancer, but their SNP interactions are seldom addressed. In this study, we focused on the joint effect for SNP combinations of seven CXCL12-related genes involved in major cancer-related pathways. SNP genotyping was determined by PCR-restriction fragment length polymorphism (RFLP) in this study (case 220, control 334). Different numbers of combinational SNPs with genotypes called the SNP barcodes from different chromosomes were used to evaluate their joint effect on breast cancer risk. Except for vascular endothelial growth factor (VEGF) rs3025039-CT, none of these SNPs were found to individually contribute to breast cancer risk. However, for two combined SNPs, the proportion of subjects with breast cancer was significantly low in the SNP barcode with CC–GG genotypes in rs2228014–1801157 (CXCR4–CXCL12) compared to those with non-CC–GG genotypes. Similarly, the SNP barcode of rs12812942–rs2228014–rs3025039 (CD4–CXCR4–VEGF) and rs12812942–rs3136685–rs2228014–rs1801157 (CD4– CCR7–CXCR4–CXCL12) with specific genotype patterns (AT-CC-CC and AT-AG-CC-GG) among three and four combinational SNPs were significantly low in breast cancer occurrence. More SNP combinations larger than five SNPs were also addressed, and these showed similar effects. After controlling for age, and comparing their corresponding non-SNP barcodes, the estimated odds ratios for breast cancer ranged between 0.20 and 0.71 for specific SNP barcodes with two to seven SNPs. In conclusion, we have associated the potential combined CXCL12-related SNPs with genotypes that were protective against breast cancer, and that may contribute to identification of a low-risk population for the development of breast cancer. [ABSTRACT FROM AUTHOR]

Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for understanding phenotypic and genome evolution. Here, we measure genome-wide allele-specific expression by deep sequencing to investigate the patterns of cis and trans expression variation between two strains of Saccharomyces cerevisiae. We propose a statistical modeling framework based on the binomial distribution that simultaneously addresses normalization of read counts derived from different parents and estimating the cis and trans expression variation parameters. We find that expression polymorphism in yeast is common for both cis and trans, though trans variation is more common. Constraint in expression evolution is correlated with other hallmarks of constraint, including gene essentiality, number of protein interaction partners, and constraint in amino acid substitution, indicating that both cis and trans polymorphism are clearly under purifying selection, though trans variation appears to be more sensitive to selective constraint. Comparing interspecific expression divergence between S. cerevisiae and S. paradoxus to our intraspecific variation suggests a significant departure from a neutral model of molecular evolution. A further examination of correlation between polymorphism and divergence within each category suggests that cis divergence is more frequently mediated by positive Darwinian selection than is trans divergence. [ABSTRACT FROM AUTHOR]

Both cis- and trans-regulatory mutations contribute to gene expression divergence within and between species. To estimate their relative contributions, we examined two yeast strains, BY (a laboratory strain) and RM (a wild strain), for their gene-expression divergence by microarray. Using these data and published ChIP-chip data, we obtained a set of single-regulator-regulated genes that showed expression divergence between BY and RM. We randomly selected 50 of these genes for further study. We developed a step-by-step approach to assess the relative contributions of cis- and trans-variations to expression divergence by using pyrosequencing to quantify the mRNA levels of the BY and RM alleles in the same culture (co-culture) and in hybrid diploids. Forty genes showed expression divergence between the two strains in co-culture, and pyrosequencing of the BY/RM hybrid diploids showed that 45% (18/40) can be attributed to differences in trans-acting factors alone, 17.5% (7/40) mainly to trans-variations, 20% (8/40) to both cis- and trans-acting factors, 7.5% (3/40) mainly to cis-variations, and 10% (4/40) to cis-acting factors alone. In addition, we replaced the BY promoter by the RM promoter in each of 10 BY genes that were found from our microarray data to have expression divergence between BY and RM, and in each case our quantitative PCR analysis revealed a cis effect of the promoter replacement on gene expression. In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important. [ABSTRACT FROM AUTHOR]