Unbalanced translocation in an adult patient with premature ovarian failure and mental retardation detected by spectral karyotyping and array-comparative genomic hybridization

BACKGROUND

There are only three cases of unbalanced translocation (X;1) reported in childhood in the literature, while no such phenotypic information is available in adults.

MATERIALS AND METHODS

To delineate the phenotype-genotype relationship of unbalanced translocation (X;1) in adulthood, we reported here a 20-year-old female with an unbalanced translocation (X;1) which was determined by spectral karyotyping, array-comparative genomic hybridization and subtelomeric fluorescence in situ hybridization (FISH).

RESULTS

The phenotype of partial trisomy 1 and partial monosomy X of the present case was much attenuated, including premature ovarian failure, mental retardation, class I obesity, mild dysmorphism and delayed secondary sexual characteristics. The breakpoints of the unbalanced translocation were accurately located at Xq28 and 1q32.1. The large amplification on Chromosome 1 q arm was found to involve 312 genes and the deletion on Chromosome X q arm also involved 141 genes. Overall, genes associated with physiological process (47 genes), cellular process (33), development (23), response to stimulus (1) and reproduction (1) were observed in the amplification on Chromosome 1 q arm. In addition, genes related to physiological process (23 genes), cellular process (13), development (6) and response to stimulus (2) were observed in the large deletion on chromosome X q arm. Late-replication studies revealed the existence of skewed X inactivation in the derivative X chromosome.

CONCLUSIONS

The phenotype of partial monosomy X and partial trisomy 1q is much attenuated in case of unbalanced translocation (X;1) in adulthood probably owing to skewed X inactivation in derivative X chromosome.

A coupled simulation-optimization approach for groundwater remediation design under uncertainty: an application to a petroleum-contaminated site

This study provides a coupled simulation-optimization approach for optimal design of petroleum-contaminated groundwater remediation under uncertainty. Compared to the previous approaches, it has the advantages of: (1) addressing the stochasticity of the modeling parameters in simulating the flow and transport of NAPLs in groundwater, (2) providing a direct and response-rapid bridge between remediation strategies (pumping rates) and remediation performance (contaminant concentrations) through the created proxy models, (3) alleviating the computational cost in searching for optimal solutions, and (4) giving confidence levels for the obtained optimal remediation strategies. The approach is applied to a practical site in Canada for demonstrating its performance. The results show that mitigating the effects of uncertainty on optimal remediation strategies (through enhancing the confidence level) would lead to the rise of remediation cost due to the increase in the total pumping rate.

Study of magnetic anisotropy and magnetization reversal using the quadratic magnetooptical effect in epitaxial Co(x)Mn(y)Ge(z)(111) films

Magnetic anisotropy, magnetization reversal and the magnetooptic Kerr effect in Co(x)Mn(y)Ge(z) have been studied over a range of compositions between 0 and 50 at.% of Ge and between 1 and 3 in the Co to Mn atomic ratio, including the Heusler alloy Co(2)MnGe. A strong quadratic magnetooptic Kerr effect has been observed within a narrow region of composition centered around the Co to Mn atomic ratio of 2, which has been used to probe and quantify the magnetic anisotropy and magnetization reversal of the system. The anisotropy is sixfold with a weak uniaxial component, and it exhibits sensitive dependence on composition, especially on the atomic ratio between Co and Mn. The magnetization reversal process is consistent with the single-domain Stoner-Wohlfarth model.

Prolonging microtubule dysruption enhances the immunogenicity of chronic lymphocytic leukaemia cells

Cytotoxic chemotherapies do not usually mediate the expression of an immunogenic gene programme in tumours, despite activating many of the signalling pathways employed by highly immunogenic cells. Concomitant use of agents that modulate and complement stress-signalling pathways activated by chemotherapeutic agents may then enhance the immunogenicity of cancer cells, increase their susceptibility to T cell-mediated controls and lead to higher clinical remission rates. Consistent with this hypothesis, the microtubule inhibitor, vincristine, caused chronic lymphocytic leukaemia (CLL) cells to die rapidly, without increasing their immunogenicity. Protein kinase C (PKC) agonists (such as bryostatin) delayed the death of vincristine-treated CLL cells and made them highly immunogenic, with increased stimulatory abilities in mixed lymphocyte responses, production of proinflammatory cytokines, expression of co-stimulatory molecules and activation of c-Jun N-terminal kinase (JNK), p38 and nuclear factor kappa B (NF-kappaB) signalling pathways. This phenotype was similar to the result of activating CLL cells through Toll-like receptors (TLRs), which communicate 'danger' signals from infectious pathogens. Use of PKC agonists and microtubule inhibitors to mimic TLR-signalling, and increase the immunogenicity of CLL cells, has implications for the design of chemo-immunotherapeutic strategies.

Variants in KCNQ1 are associated with susceptibility to type 2 diabetes in the population of mainland China

AIMS/HYPOTHESIS

Two recent genome-wide association studies have identified several novel type 2 diabetes susceptibility variants in intron 15 of the KCNQ1 gene. We aimed to evaluate the effects of the variants in KCNQ1 on type 2 diabetes and metabolic traits in the population of mainland China.

METHODS

Three candidate single nucleotide polymorphisms were genotyped in 1,912 individuals with type 2 diabetes and 2,041 normal controls using the ligase detection reaction method.

RESULTS

We confirmed the association of KCNQ1 with type 2 diabetes in the population of mainland China. Allele frequency ORs of the three single nucleotide polymorphisms (SNPs) were: rs2237892 (OR 1.19, 95% CI 1.08-1.31, p = 3.0 x 10(-4)); rs2237895 (OR 1.20, 95% CI 1.09-1.32, p = 1.9 x 10(-4)); and rs2237897 (OR 1.24, 95% CI 1.13-1.36, p = 3.9 x 10(-5)). We also found a significant difference in the distribution of the global haplotypes between the type 2 diabetes group and the normal control group (p = 2.6 x 10(-5)). In addition, in the control group SNP rs2237892 was marginally associated with increasing fasting plasma glucose and SNPs rs2237892 and rs2237897 were associated with HbA(1c). Furthermore, for all three variants, homozygous carriers of the diabetes-associated allele had significantly decreased BMI and waist circumferences.

CONCLUSIONS/INTERPRETATION

Our investigation confirmed the effects of KCNQ1 variants on type 2 diabetes risk in the Chinese population.

A two-method meta-analysis of Neuregulin 1(NRG1) association and heterogeneity in schizophrenia

NRG1 is one of the most researched genes associated with schizophrenia. Although three meta-analyses in this area have been published, the results have been inconclusive and even conflicting. Family based studies can be problematical due to the difficulty of synthesizing them with case-control studies. Heterogeneity is another persistently difficult problem which tends to be side-stepped in genetic studies. To deal with these points, we performed a meta-analysis of 26 published case-control and family-based association studies up to September 2008 covering 8049 cases, 8869 controls and 1515 families. The matrix of coancestry coefficient was also calculated using population genetics. Across these studies, the conclusions are as follows: Firstly, only SNP8NRG221132, 420M9-1395(0) and 478B14-848(0) showed significant association in the relatively small sample size. Secondly, we applied both Kazeem's and Lohmueller's methods for synthesizing family and case control studies and there was no statistically significant difference between the results from the two methods, suggesting that either method can be used. In addition, the association analysis of case-control studies was statistically consistent with that of family studies. Finally, the matrix of coancestry coefficient suggested obvious population stratification. The study reveals that one SNP of the NRG1 gene does not contribute significantly to schizophrenia and that population stratification is evident. In future genetic association analysis on complex psychic diseases, haplotype blocks and population structure should be given greater consideration.

Phase I clinical results of an APC-targeted hCGβ vaccine (CDX-1307) with TLR agonists

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Background: Effective immunization requires efficient antigen delivery to antigen presenting cells (APCs). Antigens attached to the human antibody B11, targeting mannose receptors on APCs, have been shown to be processed and presented efficiently, and generate robust immune responses when combined with toll-like receptor (TLR) agonists. The CDX-1307 vaccine is composed of B11 fused with hCGβ, a tumor antigen correlated with advanced stage of disease and poor prognosis in a number of common epithelial cancers, but reported at variable rates of expression. Methods: Two phase I studies investigate intradermal (id) vs. systemic (iv) administration of CDX-1307. Patients with advanced epithelial cancers known to frequently express hCGβ receive 4 biweekly vaccinations of CDX-1307, alone or in combination with immunostimulants including GM-CSF (GM), the TLR3 agonist Poly-ICLC, and the TLR7/8 agonist resiquimod. Results: Dose-escalation is complete. In the id study, 37 patients received CDX-1307 at doses of 0.3, 1.0, and 2.5 mg, then 2.5 mg + GM, 2.5 mg + GM + Poly-ICLC, and 2.5 mg + GM + resiquimod. 2.5 mg + GM + Poly-ICLC + resiquimod is planned. In the iv study, 24 patients were treated at 1, 3, 10, and 30 mg, as well as 10 mg + GM and 30 mg + GM. 30 mg + GM + Poly-ICLC is enrolling. Treatment-related toxicities were generally mild to moderate with no dose-limiting toxicities, most frequently injection site reactions and fatigue in the id study, and fatigue, myalgia, and flu-like illness in the iv study. Humoral responses to hCGβ were increased in 56% of the analyzed patients receiving adjuvants. Serum hCGβ was frequently elevated at study entry or during treatment (males = 88%, females = 53%, pancreatic = 89%, colorectal = 78%, breast = 47%). hCGβ decreases were seen in some patients with immune responses. To date, a significant mixed response was seen in one patient with pancreatic cancer (id), while stable disease has been seen in 4 patients (2 with breast cancer = 25, 27 weeks and 2 with colorectal cancer = 9+ weeks). Conclusions: CDX-1307 is well tolerated and results in immune responses that are enhanced by immunostimulants. Elevated hCGβ was detected at a higher than expected frequency in these tumors.

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Antibacterial activities of zinc oxide nanoparticles against Escherichia coli O157:H7

AIMS

To investigate antibacterial activities of zinc oxide nanoparticles (ZnO NP) and their mode of action against an important foodborne pathogen, Escherichia coli O157:H7.

METHODS AND RESULTS

ZnO NP with sizes of 70 nm and concentrations of 0, 3, 6 and 12 mmol l(-1) and NP-free solutions were used in antimicrobial tests against E. coli O157:H7. ZnO NP showed increasing inhibitory effects on the growth of E. coli O157:H7 as the concentrations of ZnO NP increased. A complete inhibition of microbial growth was achieved at the concentration level of 12 mmol l(-1) or higher. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Raman spectroscopy were used to characterize the changes of morphology and cellular compositions of bacterial cells treated with ZnO NP and study the mode of action of ZnO NP against E. coli O157:H7. The intensity of lipid and protein bands in the Raman spectra of bacterial cells increased after exposure to ZnO NP, while no significant changes in nucleic acid bands were observed.

CONCLUSIONS

ZnO NP were found to have antibacterial activity against E. coli O157:H7. The inhibitory effects increase as the concentration of ZnO NP increased. Results indicate that ZnO NP may distort and damage bacterial cell membrane, resulting in a leakage of intracellular contents and eventually the death of bacterial cells.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results suggest that ZnO NP could potentially be used as an effective antibacterial agent to protect agricultural and food safety.

Flexible interval mixed-integer bi-infinite programming for environmental systems management under uncertainty

A number of inexact programming methods have been developed for municipal solid waste management under uncertainty. However, most of them do not allow the parameters in the objective and constraints of a programming problem to be functional intervals (i.e., the lower and upper bounds of the intervals are functions of impact factors). In this study, a flexible interval mixed-integer bi-infinite programming (FIMIBIP) method is developed in response to the above concern. A case study is also conducted; the solutions are then compared with those obtained from interval mixed-integer bi-infinite programming (IMIBIP) and fuzzy interval mixed-integer programming (FIMIP) methods. It is indicated that the solutions through FIMIBIP can provide decision support for cost-effectively diverting municipal solid waste, and for sizing, timing and siting the facilities' expansion during the entire planning horizon. These schemes are more flexible than those identified through IMIBIP since the tolerance intervals are introduced to measure the level of constraints satisfaction. The FIMIBIP schemes may also be robust since the solutions are "globally-optimal" under all scenarios caused by the fluctuation of gas/energy prices, while the conventional ones are merely "locally-optimal" under a certain scenario.

Molecular characterization and expression of three heat shock protein70 genes from the carmine spider mite, Tetranychus cinnabarinus (Boisduval)

Three heat shock protein 70 (Hsp70) cDNAs were isolated from the carmine spider mite, Tetranychus cinnabarinus. They were tentatively named as TCHsp70-1, TCHsp70-2 and TCHsp70-3. Structural analyses showed that all of the three TCHsp70 cDNAs held the full open reading frame (ORF). Putative protein sequences and a phylogenetic tree suggested that TCHsp70-1 and TCHsp70-3 were cytoplasm HSP70 and TCHsp70-2 was endoplasmic reticulum HSP70. Comparison of deduced amino acid sequences of TCHsp70-1 and TCHsp70-3 showed 84.78% identity, TCHsp70-1 and TCHsp70-2 showed 57.33% identity, TCHsp70-2 and TCHsp70-3 showed 58.26% identity. Real-time comparative quantitative PCR revealed that the relative expression of TCHsp70-2 was lower than TCHsp70-1 and TCHsp70-3 at each temperature tested. TCHsp70-1 and TCHsp70-3 shared a similar expression pattern after cold and heat shock compared with their expression at normal temperature (26 degrees C), but the mRNA expression of TCHsp70-1 was significantly higher and lower than that of TCHsp70-3 at cold and heat shock temperatures (except for 34 degrees C), respectively. This result possibly indicated the expression patterns of TCHsp70 were affected by their location in different cellular compartments. The results also indicated that three TCHsp70s, especially TCHsp70-1 and TCHsp70-3, may play an important role in mediating tolerance to cold, thermal stress for Tetranychus cinnabarinus.

Two cases with progressive cystic leukoencephalopathy

Leukoencephalopathies with cystic changes in the white matter on magnetic resonance imaging are aetiologically heterogeneous neurological disorders seen in children. A group of leukoencephalopathies characterised by white matter lesions progressing to multifocal cystic degeneration has been reported in various disorders, including mitochondrial enzyme deficiencies, leukodystrophies, and infectious processes. We report two patients with leukoencephalopathy showing progressive cystic changes on serial MRI, and magnetic resonance spectroscopy resembling progressive cavitating leukoencephalopathy.

Detection of melamine in gluten, chicken feed, and processed foods using surface enhanced Raman spectroscopy and HPLC

Melamine, a nitrogen-rich chemical, was implicated in pet and human food recalls in 2007, which caused enormous economic losses to the food industry. In this study, melamine concentration in wheat gluten, chicken feed, and processed foods (that is, cake and noodle) was measured by surface enhanced Raman spectroscopy (SERS) in combination with SERS-active substrates. SERS was able to rapidly detect 0.1% melamine in wheat gluten, 0.05% in chicken feed, 0.05% in cakes, and 0.07% in noodle, respectively. A partial least squares (PLS) model was established for the quantification of melamine in foods by SERS: R= 0.90, RMSEP = 0.33. In addition, SERS results were verified by HPLC analysis based on a simplified FDA method. Compared with HPLC, the SERS method is much faster and simpler, requires minimum sample preparation, but still yields satisfactory qualitative and quantitative results. These results demonstrate that it is an applicable approach to use SERS to screen foods, eliminate presumptive negative samples of melamine contamination from the sample population, and then verify presumptive positive samples using HPLC protocols. Combining these 2 methods could provide a more rapid and cost-effective way for monitoring melamine contamination in increasingly large numbers of imported foods and feed products.

Simulation and optimization technologies for petroleum waste management and remediation process control

Leakage and spill of petroleum hydrocarbons from underground storage tanks and pipelines have posed significant threats to groundwater resources across many petroleum-contaminated sites. Remediation of these sites is essential for protecting the soil and groundwater resources and reducing risks to local communities. Although many efforts have been made, effective design and management of various remediation systems are still challenging to practitioners. In recent years, the subsurface simulation model has been combined with techniques of optimization to address important problems of contaminated site management. The combined simulation-optimization system accounts for the complex behavior of the subsurface system and identifies the best management strategy under consideration of the management objectives and constraints. During the past decades, a large number of studies were conducted to simulate contaminant flow and transport in the subsurface and seek cost-effective remediation designs. This paper gives a comprehensive review on recent developments, advancements, challenges, and barriers associated with simulation and optimization techniques in supporting process control of petroleum waste management and site remediation. A number of related methodologies and applications were examined. Perspectives of effective site management were investigated, demonstrating many demanding areas for enhanced research efforts, which include issues of data availability and reliability, concerns in uncertainty, necessity of post-modeling analysis, and usefulness of development of process control techniques.

Analysis of 10 independent samples provides evidence for association between schizophrenia and a SNP flanking fibroblast growth factor receptor 2

We and others have previously reported linkage to schizophrenia on chromosome 10q25-q26 but, to date, a susceptibility gene in the region has not been identified. We examined data from 3606 single-nucleotide polymorphisms (SNPs) mapping to 10q25-q26 that had been typed in a genome-wide association study (GWAS) of schizophrenia (479 UK cases/2937 controls). SNPs with P<0.01 (n=40) were genotyped in an additional 163 UK cases and those markers that remained nominally significant at P<0.01 (n=22) were genotyped in replication samples from Ireland, Germany and Bulgaria consisting of a total of 1664 cases with schizophrenia and 3541 controls. Only one SNP, rs17101921, was nominally significant after meta-analyses across the replication samples and this was genotyped in an additional six samples from the United States/Australia, Germany, China, Japan, Israel and Sweden (n=5142 cases/6561 controls). Across all replication samples, the allele at rs17101921 that was associated in the GWAS showed evidence for association independent of the original data (OR 1.17 (95% CI 1.06-1.29), P=0.0009). The SNP maps 85 kb from the nearest gene encoding fibroblast growth factor receptor 2 (FGFR2) making this a potential susceptibility gene for schizophrenia.

An inexact dynamic optimization model for municipal solid waste management in association with greenhouse gas emission control

Municipal solid waste (MSW) should be properly disposed in order to help protect environmental quality and human health, as well as to preserve natural resources. During MSW disposal processes, a large amount of greenhouse gas (GHG) is emitted, leading to a significant impact on climate change. In this study, an inexact dynamic optimization model (IDOM) is developed for MSW-management systems under uncertainty. It grounds upon conventional mixed-integer linear programming (MILP) approaches, and integrates GHG components into the modeling framework. Compared with the existing models, IDOM can not only deal with the complex tradeoff between system cost minimization and GHG-emission mitigation, but also provide optimal allocation strategies under various emission-control standards. A case study is then provided for demonstrating applicability of the developed model. The results indicate that desired waste-flow patterns with a minimized system cost and GHG-emission amount can be obtained. Of more importance, the IDOM solution is associated with over 5.5 million tonnes of TEC reduction, which is of significant economic implication for real implementations. Therefore, the proposed model could be regarded as a useful tool for realizing comprehensive MSW management with regard to mitigating climate-change impacts.

Health-risk-based groundwater remediation system optimization through clusterwise linear regression

This study develops a health-risk-based groundwater management (HRGM) model. The model incorporates the considerations of environmental quality and human health risks into a general framework. To solve the model, a proxy-based optimization approach is proposed, where a semiparametric statistical method (i.e., clusterwise linear regression) is used to create a set of rapid-response and easy-to-use proxy modules for capturing the relations between remediation policies and the resulting human health risks. Through replacing the simulation and health risk assessment modules with the proxy ones, many orders of magnitude of computational cost can be saved. The model solutions reveal that (i) a long remediation period corresponds to a low total pumping rate, (ii) a stringent risk standard implies a high total pumping rate, and (iii) the human health risk associated with benzene would be significantly reduced if it is regarded as constraints of the model. These implications would assist decision makers in understanding the effects of remediation duration and human-health risk level on optimal remediation policies and in designing a robust groundwater remediation system. Results from postoptimization simulation show that the carcinogenic risk would decrease to satisfy the regulated risk standard under the given remediation policies.

The --1019 C/G polymorphism of the 5-HT(1)A receptor gene is associated with negative symptom response to risperidone treatment in schizophrenia patients

The application of pharmacogenetics is currently one of the most promising developments in anti-psychotic treatment and is attracting more and more attention. Although risperidone belongs to the first-line atypical anti-psychotics, there have been relatively few risperidone pharmacogenetic studies, especially in Asian populations. We investigated the relationship between the C825T polymorphism of GBN3 (rs5443) and the -1019 C/G polymorphism of 5-HT(1)A (rs6295) and response to risperidone treatment. One-hundred and thirty schizophrenia patients were recruited. They were treated with risperidone monotherapy for eight weeks. Clinical response was assessed on the Positive and Negative Syndrome Scale (PANSS) on the day of admission and was subsequently assessed after eight weeks following the treatment. Patients were genotyped for two functional polymorphisms: C825T of GBN3 (rs5443) and -1019 C/G of HT(1)A (rs6295). Association tests between genotypes and percentage improvement in total PANSS scores, as well as positive symptom scores and negative symptom scores, were performed using analyses of variance (ANOVA). The -1019 C/G polymorphism of HT(1)A (rs6295) was associated with negative symptom response to treatment. Patients with the CC genotype showed substantial improvement as regards negative symptom response (F = 4.177, df = 2, P = 0.019), compared with the patients with the CG and GG genotypes. No association was observed between C825T of GBN3 (rs5443) and changes in PANSS scores. The results suggest that the -1019 C/G polymorphism (rs6295) in the 5-HT(1)A gene may be a useful predictor of reduction in negative symptoms in schizophrenic patients treated with risperidone.