bluuebunny/crossref_metadata_2025 huggingface dataset:
Small-Molecule Anticancer Compounds Selectively Target the Hemopexin Domain of Matrix Metalloproteinase-9
Authors: Dufour Antoine , Sampson Nicole S. , Li Jian , Kuscu Cem , Rizzo Robert C. , DeLeon Jennifer L. , Zhi Jizu , Jaber Nadia , Liu Eric , Zucker Stanley , Cao Jian
Published: June 2011

Lack of target specificity by existing matrix metalloproteinase (MMP) inhibitors has hindered antimetastatic cancer drug discovery. Inhibitors that bind to noncatalytic sites of MMPs and disrupt protease signaling function have the potential to be more specific and selective. In this work, compounds that target the hemopexin (PEX) domain of MMP-9 were identified using an in silico docking approach and evaluated using biochemical and biological approaches. Two of the selected compounds interfere with MMP-9–mediated cancer cell migration and proliferation in cells expressing exogenous or endogenous MMP-9. Furthermore, these inhibitors do not modulate MMP-9 catalytic activity. The lead compound, N-[4-(difluoromethoxy)phenyl]-2-[(4-oxo-6-propyl-1H-pyrimidin-2-yl)sulfanyl]-acetamide, specifically binds to the PEX domain of MMP-9, but not other MMPs. This interaction between the compound and the PEX domain results in the abrogation of MMP-9 homodimerization and leads to blockage of a downstream signaling pathway required for MMP-9–mediated cell migration. In a tumor xenograft model, this pyrimidinone retarded MDA-MB-435 tumor growth and inhibited lung metastasis. Thus, we have shown for the first time that a novel small-molecule interacts specifically with the PEX domain of MMP-9 and inhibits tumor growth and metastasis by reducing cell migration and proliferation. Cancer Res; 71(14); 4977–88. ©2011 AACR.
18F-Fluorodeoxy-glucose Positron Emission Tomography Marks MYC-Overexpressing Human Basal-Like Breast Cancers
Authors: Palaskas Nicolaos , Larson Steven M. , Schultz Nikolaus , Komisopoulou Evangelia , Wong Justin , Rohle Dan , Campos Carl , Yannuzzi Nicolas , Osborne Joseph R. , Linkov Irina , Kastenhuber Edward R. , Taschereau Richard , Plaisier Seema B. , Tran Chris , Heguy Adriana , Wu Hong , Sander Chris , Phelps Michael E. , Brennan Cameron , Port Elisa , Huse Jason T. , Graeber Thomas G. , Mellinghoff Ingo K.
Published: June 2011

In contrast to normal cells, cancer cells avidly take up glucose and metabolize it to lactate even when oxygen is abundant, a phenomenon referred to as the Warburg effect. This fundamental alteration in glucose metabolism in cancer cells enables their specific detection by positron emission tomography (PET) following i.v. injection of the glucose analogue 18F-fluorodeoxy-glucose (18FDG). However, this useful imaging technique is limited by the fact that not all cancers avidly take up FDG. To identify molecular determinants of 18FDG retention, we interrogated the transcriptomes of human-cancer cell lines and primary tumors for metabolic pathways associated with 18FDG radiotracer uptake. From ninety-five metabolic pathways that were interrogated, the glycolysis, and several glycolysis-related pathways (pentose phosphate, carbon fixation, aminoacyl-tRNA biosynthesis, one-carbon-pool by folate) showed the greatest transcriptional enrichment. This “FDG signature” predicted FDG uptake in breast cancer cell lines and overlapped with established gene expression signatures for the “basal-like” breast cancer subtype and MYC-induced tumorigenesis in mice. Human breast cancers with nuclear MYC staining and high RNA expression of MYC target genes showed high 18FDG-PET uptake (P < 0.005). Presence of the FDG signature was similarly associated with MYC gene copy gain, increased MYC transcript levels, and elevated expression of metabolic MYC target genes in a human breast cancer genomic dataset. Together, our findings link clinical observations of glucose uptake with a pathologic and molecular subtype of human breast cancer. Furthermore, they suggest related approaches to derive molecular determinants of radiotracer retention for other PET-imaging probes. Cancer Res; 71(15); 5164–74. ©2011 AACR.
Ex Vivo Graft Purging and Expansion of Autologous Blood Progenitor Cell Products from Patients with Multiple Myeloma
Authors: Yang Hong , Robinson Simon N. , Nieto Yago , Jones Richard J. , Gocke Christopher D. , Lu Junjun , Giralt Sergio A. , Jones Roy B. , Decker William K. , Xing Dongxia , Steiner David , Champlin Richard E. , McMannis John D. , Ng Jingjing , Thomas Michael W. , Shah Nina , Andersson Borje S. , Parmar Simrit , Shpall Elizabeth J.
Published: June 2011

Autologous peripheral blood progenitor cell (PBPC) transplantation is the treatment of choice for selected myeloma patients. However, tumor cells contaminating the apheresis product are a potential source of relapse. Here we report a sequential purging strategy targeting mature and immature clonogenic myeloma cell populations in the autograft. Thawed PBPC products of myeloma patients were treated with rituximab to kill CD138−20+ B cells (highly clonogenic immature cells), and bortezomib to target CD138+ cells (normal and differentiated myeloma plasma cells), followed by coculture with allogeneic mesenchymal stem cells (MSC) from normal donors. After 7 days of coculture, nonadherent cells were removed and cultured in the absence of MSC for an additional 7 days. Then, efficacy of purging (removal of CD138−20+ and CD138+ cells) was assessed by flow cytometry and PCR. We used our ex vivo purging strategy to treat frozen aphereses from 16 patients. CD138+ and CD138−20+(19+) cells present in the initial products were depleted more than 3 and 4 logs, respectively based on 106 flow-acquisition events, and to levels below the limit of detection by PCR. In contrast, total nucleated cell (TNC), CD34+ cell, and colony-forming cell numbers were increased by approximately 12 to 20, 8-, and 23-fold, respectively. Overall, ex vivo treatment of apheresis products with rituximab, bortezomib, and coculture with normal donor MSC depleted mature and immature myeloma cells from clinical aphereses while expanding the normal hematopoietic progenitor cell compartment. Cancer Res; 71(14); 5040–9. ©2011 AACR.
Decision Tree–Based Modeling of Androgen Pathway Genes and Prostate Cancer Risk
Authors: Barnholtz-Sloan Jill S. , Guan Xiaowei , Zeigler-Johnson Charnita , Meropol Neal J. , Rebbeck Timothy R.
Published: June 2011

Background: Inherited variability in genes that influence androgen metabolism has been associated with risk of prostate cancer. The objective of this analysis was to evaluate interactions for prostate cancer risk by using classification and regression tree (CART) models (i.e., decision trees), and to evaluate whether these interactive effects add information about prostate cancer risk prediction beyond that of “traditional” risk factors.

Methods: We compared CART models with traditional logistic regression (LR) models for associations of factors with prostate cancer risk using 1,084 prostate cancer cases and 941 controls. All analyses were stratified by race. We used unconditional LR to complement and compare with the race-stratified CART results using the area under curve (AUC) for the receiver operating characteristic curves.

Results: The CART modeling of prostate cancer risk showed different interaction profiles by race. For European Americans, interactions among CYP3A43 genotype, history of benign prostate hypertrophy, family history of prostate cancer, and age at consent revealed a distinct hierarchy of gene–environment and gene–gene interactions, whereas for African Americans, interactions among family history of prostate cancer, individual proportion of European ancestry, number of GGC androgen receptor repeats, and CYP3A4/CYP3A5 haplotype revealed distinct interaction effects from those found in European Americans. For European Americans, the CART model had the highest AUC whereas for African Americans, the LR model with the CART discovered factors had the largest AUC.

Conclusion and Impact: These results provide new insight into underlying prostate cancer biology for European Americans and African Americans. Cancer Epidemiol Biomarkers Prev; 20(6); 1146–55. ©2011 AACR.
Low Plasma Coenzyme Q10 Levels and Breast Cancer Risk in Chinese Women
Authors: Cooney Robert V. , Dai Qi , Gao Yu-Tang , Chow Wong-Ho , Franke Adrian A. , Shu Xiao-Ou , Li Honglan , Ji Butian , Cai Qiuyin , Chai Weiwen , Zheng Wei
Published: June 2011

Background: Low circulating levels of coenzyme Q10 (CoQ10) have been associated with increased cancer incidence and poor prognosis for a number of cancer types, while a recent prospective study observed a positive association for CoQ10 with breast cancer risk.

Methods: We prospectively examined the association of plasma CoQ10 with breast cancer risk in a nested case-control study of Chinese women within the Shanghai Women's Health Study (SWHS). Prediagnostic plasma samples were obtained from 340 cases and 653 age-matched controls and analyzed for total CoQ10.

Results: A borderline significant inverse association for breast cancer incidence with plasma CoQ10 level was observed by a conditional logistic regression model adjusted for age and age at first live birth, which became significant after elimination of cases diagnosed within 1 year of blood draw (Ptrend = 0.03). This association was independent of menopausal status. Plasma CoQ10 levels were also observed to be significantly associated with circulating γ-tocopherol (r = 0.50; P < 0.0001) and α-tocopherol (r = 0.38; P < 0.0001) levels.

Conclusions: Circulating levels of CoQ10 were generally low in this population and the observed association with breast cancer risk may be limited to those women with exceptionally low values.

Impact: This study reports an inverse relationship between circulating CoQ10 and breast cancer risk, while the only other prospective study of CoQ10 and breast cancer to date found a positive association. Lower levels of CoQ10 in the SWHS population suggest that the 2 studies may not be contradictory and indicate a possible nonlinear (U-shaped) association of CoQ10 with risk. Cancer Epidemiol Biomarkers Prev; 20(6); 1124–30. ©2011 AACR.
Lower Risk in Parous Women Suggests That Hormonal Factors Are Important in Bladder Cancer Etiology
Authors: Davis-Dao Carol A. , Henderson Katherine D. , Sullivan-Halley Jane , Ma Huiyan , West Dee , Xiang Yong-Bing , Gago-Dominguez Manuela , Stern Mariana C. , Castelao J. Esteban , Conti David V. , Pike Malcolm C. , Bernstein Leslie , Cortessis Victoria K.
Published: June 2011

Background: Urinary bladder cancer is two to four times more common among men than among women, a difference in risk not fully explained by established risk factors. Our objective was to determine whether hormonal and reproductive factors are involved in female bladder cancer.

Methods: We analyzed data from two population-based studies: the Los Angeles–Shanghai Bladder Cancer Study, with 349 female case–control pairs enrolled in Los Angeles and 131 female cases and 138 frequency-matched controls enrolled in Shanghai, and the California Teachers Study (CTS), a cohort of 120,857 women with 196 incident cases of bladder urothelial carcinoma diagnosed between 1995 and 2005. We also conducted a meta-analysis summarizing associations from our primary analyses together with published results.

Results: In primary data analyses, parous women experienced at least 30% reduced risk of developing bladder cancer compared with nulliparous women (Shanghai: OR = 0.38, 95% CI: 0.13–1.10; CTS: RR = 0.69, 95% CI: 0.50–0.95) consistent with results of a meta-analysis of nine studies (summary RR = 0.73, 95% CI: 0.63–0.85). The CTS, which queried formulation of menopausal hormone therapy (HT), revealed a protective effect for use of combined estrogen and progestin compared with no HT (RR = 0.60, 95% CI: 0.37–0.98). Meta-analysis of three studies provided a similar effect estimate (summary RR = 0.65, 95% CI: 0.48–0.88).

Conclusions: A consistent pattern of reduced bladder cancer risk was found among parous women and those who used estrogen and progestin for HT.

Impact: These results suggest that more research is warranted to investigate hormonal and reproductive factors as possible contributors to bladder cancer risk. Cancer Epidemiol Biomarkers Prev; 20(6); 1156–70. ©2011 AACR.
Age-Stratified Performance of the Cervista HPV 16/18 Genotyping Test in Women with ASC-US Cytology
Authors: Einstein Mark H. , Garcia Francisco A.R. , Mitchell Amy L. , Day Stephen P.
Published: June 2011

Background: The objective of this study was to evaluate the clinical performance of the Cervista HPV 16/18 genotyping test for detection of human papilloma virus (HPV) 16 and 18 in cervical cytology specimens in women stratified by age.

Methods: In a multicenter, prospective clinical study, ThinPrep specimens were tested for the presence of HPV 16 and 18 using the HPV 16/18 genotyping test. Genotyping results from women with atypical squamous cells of undetermined significance or greater cytology were compared with local colposcopy and/or histology results. Sensitivity, specificity, and negative and positive predictive values (NPV and PPV) were determined.

Results: The prevalence of cervical intraepithelial neoplasia (CIN) 2+ in subjects positive for HPV 16/18 was 6.6% and 4.1% for women <30 and ≥30 years of age, respectively. The sensitivity of the test was 70.0% (95% CI: 54.6–81.9) and 66.7% (95% CI: 46.7–82.0) in women <30 and ≥30 years, respectively. The NPV was 95.5% (95% CI: 93.4–97.6) in women <30 years and 96.6% (95% CI: 94.8–98.5) in women ≥30 years. Specificity was higher in women ≥30 years (79.9%; 95% CI: 74.9–84.2) than women <30 years (61.9%; 95% CI: 57.1–66.4). The PPV was 15.2% (95% CI: 12.7–19.1) in women <30 years and 21.9% (95% CI: 17.0–30.7) in women ≥30 years.

Conclusions: The performance of the Cervista HPV 16/18 genotyping test for predicting ≥CIN 2 is what would be expected across the key ≥CIN 2 age strata.

Impact: HPV 16/18 genotyping may help further stratify women with a greater potential to develop cervical cancer. Cancer Epidemiol Biomarkers Prev; 20(6); 1185–9. ©2011 AACR.
Trends in Extreme Apparent Temperatures over the United States, 1949–2010
Authors: Grundstein Andrew , Dowd John
Published: June 2011

Biometeorological indices, such as the apparent temperature, are widely used in studies of heat-related mortality to quantify the human sensation to the environmental conditions. Increases in the frequency of environmentally stressful days as indicated by biometeorological indices may augment the risk for heat-related morbidity and mortality. This study examines trends in the frequency of days with extreme maximum and minimum apparent temperatures across the United States for 1949–2010. An increase in occurrence of 1-day extreme minimum apparent temperatures is particularly notable, especially in the eastern and western United States, with 44% of stations exhibiting positive trends. About 20% of stations have positive trends in 1-day extreme maximum apparent temperature, mostly in the western United States. The median trend for both 1-day extreme maximum and minimum apparent temperature is approximately 2 days per 10 yr, indicating that by 2010 there were 12 more days with extreme apparent temperatures than there were in 1949. Few stations with trends in 4-day extreme minimum or maximum apparent temperatures were noted. An important finding is that there has been a 53% increase in stations with positive trends in 1-day extreme minimum apparent temperatures and a 63% increase in stations with positive trends in 1-day extreme maximum apparent temperatures since a similar study by Gaffen and Ross was conducted using the period 1949–95. Although there is a clear increase in the hazard for days with extreme apparent temperatures, changes in health outcomes are modulated by factors, such as the age of the population and access to air conditioning, that affect social vulnerability.
‘Multicultural Planning’ as a Contested Device in Urban Renewal and Housing
Authors: van der Horst Hilje , Ouwehand André
Published: June 2011

The academic literature on multicultural planning is rife with normative views which complicates any conceptualisation grounded in empirical realities. This paper offers a critical review of the dynamic and heterogeneous goals and challenges in multicultural urban planning in the Netherlands during a decade of waning support for multiculturalism. Multicultural planning has been used to justify various goals such as emancipating ethnic groups, matching supply and demand in the housing stock, enriching the urban landscape and ‘branding’ urban areas. The importance of each of these is strongly dependent on the socio-political context. From the review it is concluded that multicultural planning cannot be simply analysed according to normative positions as currently presented in the literature. It is argued that it is necessary to set aside normative definitions in order to analyse effectively the different and dynamic objectives and challenges associated with multicultural planning.
Assessment of the Relative Potency of Fentanyl Buccal Tablet to Intravenous Morphine in Healthy Volunteers Using a Thermally Induced Hyperalgesia Pain Model
Authors: Saunders David L. , Messina John , Darwish Mona , Xie Fang , Leary Kevin J. , Cantilena Louis R.
Published: June 2011

This exploratory randomized, double‐blind, placebo‐controlled, 5‐treatment, 5‐period crossover study was conducted using a thermally induced hyperalgesia pain model in 51 healthy volunteers (33 evaluable) to characterize the relative potency of fentanyl buccal tablet (FBT) versus intravenous morphine. Relative potency was assessed using the sum of pain intensity differences over 60 minutes after the application of a 43°C, 46°C, and 49°C painful stimulus following thermally induced hyperalgesia. Relative potency was also assessed by pupil diameter and responses to subjective questionnaires. The relative potency of FBT was 46.2 times that of intravenous morphine (95% confidence interval [CI], 17.6–575.3) based on the 49°C stimulus. The relative potency of FBT based on opiate‐induced miosis was 44.6 (95% CI, 29.7–77.0) at 60 minutes. These results are an initial relative potency assessment and should not be considered guidance for dose‐equivalent switching between agents in clinical practice.
A combustor-representative swirl simulator for a transonic turbine research facility
Authors: Qureshi I , Povey T
Published: June 2011

Tighter aircraft emissions regulations have let to considerable improvement in gas turbine combustion in the past few decades. Modern combustors employ aggressive swirlers to increase mixing and to improve flame stability during the combustion process. The flow at combustor exit can therefore have high residual swirl. The impact of this swirl on the aerodynamic and heat transfer characteristics of the HP turbine stage has not yet received much attention.

In order to investigate the effects of swirl on the HP turbine stage, an inlet swirl simulator has been designed and commissioned in an engine scale, short duration, rotating transonic turbine facility. The test facility simulates engine representative Mach number, Reynolds number, non-dimensional speed and gas-to-wall temperature ratio at the turbine inlet. The target swirl profile at turbine stage inlet was based upon extreme exit swirl conditions for a modern low-NO x combustor with peak yaw and pitch angles over ±40°. A number of candidate swirler designs were considered during a pilot study that was conducted in a subsonic wind tunnel to achieve suitable swirler design. The swirl simulator was developed based upon the pilot study results, which achieved a good match to the target profile after commissioning in the facility. This article mainly deals with the design and development of the swirl generator. It presents the experimental and computational results of the pilot study, followed by the description of the installation and commissioning of the swirl simulator on the test facility. Novel instrumentation was required to survey the swirl profile, which is also described. A comparison of the measured and computational aerodynamic results with and without swirl, at 10 per cent and 90 per cent span of HP nozzle guide vane is also presented. The comparison highlights significant impact of swirl on the vane incidence angle, and therefore a considerable affect on the loading distribution of the vane.
The art of becoming ‘Swedish’: Immigrant youth, school careers and life plans
Authors: Johansson Thomas , Olofsson Rita
Published: June 2011

When discussing barriers to integration, we often focus on language skills, cultural capital, supportive environments and other more obvious, distinct and material aspects that have an impact on educational achievement. In the present study, we have instead chosen to look at how young immigrants construct their life plans, and how this relates to their perceptions of ethnicity, neighbourhood and identity. The sample used here consists of a total of 10 individuals. The interviews were used to explore certain designated dimensions and processes. All interviews were conducted in the school environment, in classrooms and other locations within the school. The students attended two different vocationally oriented study programmes: one focused on health promotion, the other on pre-school children. A narrative—sociological approach is used in the analysis. The young people’s perceptions and narratives are analysed in relation to concepts such as: territorial stigmatization, identity, inclusion/exclusion and life plans. The key finding is that these young people try to adapt to certain normative expectations connected to the notion of Swedishness. Being ‘in sync’ with this normative conception leads to self-confidence, whereas being ‘out-of-sync’ leads to low self-esteem.
Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
Authors: Faivre Rampant Patricia , Lesur Isabelle , Boussardon Clément , Bitton Frédérique , Martin-Magniette Marie-Laure , Bodénès Catherine , Le Provost Grégoire , Bergès Hélène , Fluch Sylvia , Kremer Antoine , Plomion Christophe
Published: June 2011

Background

One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library forQuercus robur, its characterization and an analysis of BAC end sequences.

Results

TheEcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements whileab initiorepeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences ofArabidopsis thaliana,Vitis viniferaandPopulus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 ofV. vinifera.

Conclusions

This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.
Aberrant methylation of N-methyl-D-aspartate receptor type 2B (NMDAR2B) in non-small cell carcinoma
Authors: Tamura Hajime , Suzuki Makoto , Moriya Yasumitsu , Hoshino Hidehisa , Okamoto Tatsuro , Yoshida Shigetoshi , Yoshino Ichiro
Published: June 2011

Background

N-methyl-D-aspartate receptors (NMDAR) act as tumor suppressors of digestive malignancies. The expression and genetic methylation patterns ofNMDAR2Bin non-small cell lung cancer (NSCLC) are unknown.

Methods

The relationship between gene methylation and expression ofNMDAR2Bwas analyzed in NSCLC cell lines (N = 9) and clinical tissues (N = 216). The cell lines were studied using RT-PCR and 5-aza-2'-deoxycytidine treatment, while the clinical tissues were examined by methylation specific real-time quantitative PCR and immunohistochemistry. Retrospective investigation of patient records was used to determine the clinical significance ofNMDAR2Bmethylation.

Results

NMDAR2Bwas silenced in five of the nine cell lines; 5-aza-2'-deoxycytidine treatment restored expression, and was inversely correlated with methylation. Aberrant methylation ofNMDAR2B, detected in 61% (131/216) of clinical NSCLC tissues, was inversely correlated with the status of protein expression in 20 randomly examined tumors. Aberrant methylation was not associated with clinical factors such as gender, age, histological type, or TNM stage. However, aberrant methylation was an independent prognostic factor in squamous cell carcinoma cases.

Conclusions

Aberrant methylation of theNMDAR2Bgene is a common event in NSCLC. The prognosis was significantly better for cases of squamous cell carcinoma in whichNMDAR2Bwas methylated. It may have different roles in different histological types.
Rapid label-free identification of mixed bacterial infections by surface plasmon resonance
Authors: Wang Jue , Luo Yang , Zhang Bo , Chen Ming , Huang Junfu , Zhang Kejun , Gao Weiyin , Fu Weiling , Jiang Tianlun , Liao Pu
Published: June 2011

Background

Early detection of mixed aerobic-anaerobic infection has been a challenge in clinical practice due to the phenotypic changes in complex environments. Surface plasmon resonance (SPR) biosensor is widely used to detect DNA-DNA interaction and offers a sensitive and label-free approach in DNA research.

Methods

In this study, we developed a single-stranded DNA (ssDNA) amplification technique and modified the traditional SPR detection system for rapid and simultaneous detection of mixed infections of four pathogenic microorganisms (Pseudomonas aeruginosa, Staphylococcus aureus, Clostridium tetani and Clostridium perfringens).

Results

We constructed the circulation detection well to increase the sensitivity and the tandem probe arrays to reduce the non-specific hybridization. The use of 16S rDNA universal primers ensured the amplification of four target nucleic acid sequences simultaneously, and further electrophoresis and sequencing confirmed the high efficiency of this amplification method. No significant signals were detected during the single-base mismatch or non-specific probe hybridization (P < 0.05). The calibration curves of amplification products of four bacteria had good linearity from 0.1 nM to 100 nM, with all R2 values of >0.99. The lowest detection limits were 0.03 nM for P. aeruginosa, 0.02 nM for S. aureus, 0.01 nM for C. tetani and 0.02 nM for C. perfringens. The SPR biosensor had the same detection rate as the traditional culture method (P < 0.05). In addition, the quantification of PCR products can be completed within 15 min, and excellent regeneration greatly reduces the cost for detection.

Conclusions

Our method can rapidly and accurately identify the mixed aerobic-anaerobic infection, providing a reliable alternative to bacterial culture for rapid bacteria detection.
Reliable processing of graphene using metal etchmasks
Authors: Kumar Shishir , Peltekis Nikos , Lee Kangho , Kim Hye-Young , Duesberg Georg Stefan
Published: June 2011

Graphene exhibits exciting properties which make it an appealing candidate for use in electronic devices. Reliable processes for device fabrication are crucial prerequisites for this. We developed a large area of CVD synthesis and transfer of graphene films. With patterning of these graphene layers using standard photoresist masks, we are able to produce arrays of gated graphene devices with four point contacts. The etching and lift off process poses problems because of delamination and contamination due to polymer residues when using standard resists. We introduce a metal etch mask which minimises these problems. The high quality of graphene is shown by Raman and XPS spectroscopy as well as electrical measurements. The process is of high value for applications, as it improves the processability of graphene using high-throughput lithography and etching techniques.
Determination of the relative economic impact of different molecular-based laboratory algorithms for respiratory viral pathogen detection, including Pandemic (H1N1), using a secure web based platform
Authors: Lee Bonita E , Mukhi Shamir N , May-Hadford Jennifer , Plitt Sabrina , Louie Marie , Drews Steven J
Published: June 2011

Background

During period of crisis, laboratory planners may be faced with a need to make operational and clinical decisions in the face of limited information. To avoid this dilemma, our laboratory utilizes a secure web based platform, Data Integration for Alberta Laboratories (DIAL) to make near real-time decisions.

This manuscript utilizes the data collected by DIAL as well as laboratory test cost modeling to identify the relative economic impact of four proposed scenarios of testing for Pandemic H1N1 (2009) and other respiratory viral pathogens.

Methods

Historical data was collected from the two waves of the pandemic using DIAL. Four proposed molecular testing scenarios were generated: A) Luminex respiratory virus panel (RVP) first with/without US centers for Disease Control Influenza A Matrix gene assay (CDC-M), B) CDC-M first with/without RVP, C) RVP only, and D) CDC-M only. Relative cost estimates of different testing algorithm were generated from a review of historical costs in the lab and were based on 2009 Canadian dollars.

Results

Scenarios A and B had similar costs when the rate of influenza A was low (< 10%) with higher relative cost in Scenario A with increasing incidence. Scenario A provided more information about mixed respiratory virus infection as compared with Scenario B.

Conclusions

No one approach is applicable to all conditions. Testing costs will vary depending on the test volume, prevalence of influenza A strains, as well as other circulating viruses and a more costly algorithm involving a combination of different tests may be chosen to ensure that tests results are returned to the clinician in a quicker manner. Costing should not be the only consideration for determination of laboratory algorithms.
Rotavirus NSP4: Cell type-dependent transport kinetics to the exofacial plasma membrane and release from intact infected cells
Authors: Gibbons Thomas F , Storey Stephen M , Williams Cecelia V , McIntosh Avery , Mitchel DeAnne M , Parr Rebecca D , Schroeder Megan E , Schroeder Friedhelm , Ball Judith M
Published: June 2011

Background

Rotavirus NSP4 localizes to multiple intracellular sites and is multifunctional, contributing to RV morphogenesis, replication and pathogenesis. One function of NSP4 is the induction of early secretory diarrhea by binding surface receptors to initiate signaling events. The aims of this study were to determine the transport kinetics of NSP4 to the exofacial plasma membrane (PM), the subsequent release from intact infected cells, and rebinding to naïve and/or neighboring cells in two cell types.

Methods

Transport kinetics was evaluated using surface-specific biotinylation/streptavidin pull-downs and exofacial exposure of NSP4 was confirmed by antibody binding to intact cells, and fluorescent resonant energy transfer. Transfected cells similarly were monitored to discern NSP4 movement in the absence of infection or other viral proteins. Endoglycosidase H digestions, preparation of CY3- or CY5- labeled F(ab)2 fragments, confocal imaging, and determination of preferential polarized transport employed standard laboratory techniques. Mock-infected, mock-biotinylated and non-specific antibodies served as controls.

Results

Only full-length (FL), endoglycosidase-sensitive NSP4 was detected on the exofacial surface of two cell types, whereas the corresponding cell lysates showed multiple glycosylated forms. The C-terminus of FL NSP4 was detected on exofacial-membrane surfaces at different times in different cell types prior to its release into culture media. Transport to the PM was rapid and distinct yet FL NSP4 was secreted from both cell types at a time similar to the release of virus. NSP4-containing, clarified media from both cells bound surface molecules of naïve cells, and imaging showed secreted NSP4 from one or more infected cells bound neighboring cell membranes in culture. Preferential sorting to apical or basolateral membranes also was distinct in different polarized cells.

Conclusions

The intracellular transport of NSP4 to the PM, translocation across the PM, exposure of the C-terminus on the cell surface and subsequent secretion occurs via an unusual, complex and likely cell-dependent process. The exofacial exposure of the C-terminus poses several questions and suggests an atypical mechanism by which NSP4 traverses the PM and interacts with membrane lipids. Mechanistic details of the unconventional trafficking of NSP4, interactions with host-cell specific molecules and subsequent release require additional study.
Transcription Factors Sp1 and Sp4 Regulate TRPV1 Gene Expression in Rat Sensory Neurons
Authors: Chu Catherine , Zavala Kathryn , Fahimi Atefeh , Lee Jessica , Xue Qing , Eilers Helge , Schumacher Mark A
Published: June 2011

Background:

The capsaicin receptor, transient receptor potential vanilloid type −1 (TRPV1) directs complex roles in signal transduction including the detection of noxious stimuli arising from cellular injury and inflammation. Under pathophysiologic conditions, TRPV1 mRNA and receptor protein expression are elevated in dorsal root ganglion (DRG) neurons for weeks to months and is associated with hyperalgesia. Building on our previous isolation of a promoter system for the rat TRPV1 gene, we investigated the proximal TRPV1 P2-promoter by first identifying candidate Sp1-like transcription factors bound in vivo to the P2-promoter using chromatin immunoprecipitation (ChIP) assay. We then performed deletion analysis of GC-box binding sites, and quantified promoter activity under conditions of Sp1 / Sp4 over-expression versus inhibition/knockdown. mRNA encoding Sp1, Sp4 and TRPV1 were quantified by qRT-PCR under conditions of Sp1/Sp4 over-expression or siRNA mediated knockdown in cultured DRG neurons.

Results:

Using ChIP analysis of DRG tissue, we demonstrated that Sp1 and Sp4 are bound to the candidate GC-box site region within the endogenous TRPV1 P2-promoter. Deletion of GC-box “a“ or “a + b” within the P2-promoter resulted in a complete loss of transcriptional activity indicating that GC-box “a“ was the critical site for promoter activation. Co-transfection of Sp1 increased P2-promoter activity in cultured DRG neurons whereas mithramycin-a, an inhibitor of Sp1-like function, dose dependently blocked NGF and Sp1-dependent promoter activity in PC12 cells. Co-transfection of siRNA directed against Sp1 or Sp4 decreased promoter activity in DRG neurons and NGF treated PC12 cells. Finally, electroporation of Sp1 or Sp4 cDNA into cultures of DRG neurons directed an increase in Sp1/Sp4 mRNA and importantly an increase in TRPV1 mRNA. Conversely, combined si-RNA directed knockdown of Sp1/Sp4 resulted in a decrease in TRPV1 mRNA.

Conclusion:

Based on these studies, we now propose a model of TRPV1 expression that is dependent on Sp1-like transcription factors with Sp4 playing a predominant role in activating TRPV1 RNA transcription in DRG neurons. Given that increases of TRPV1 expression have been implicated in a wide range of pathophysiologic states including persistent painful conditions, blockade of Sp1-like transcription factors represents a novel direction in therapeutic strategies.
Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival
Authors: Serão Nicola VL , Delfino Kristin R , Southey Bruce R , Beever Jonathan E , Rodriguez-Zas Sandra L
Published: June 2011

Background

Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this study was to identify general and clinical-dependent biomarker genes and biological processes of three complementary events: lifetime, overall and progression-free glioblastoma survival.

Methods

A novel analytical strategy was developed to identify general associations between the biomarkers and glioblastoma, and associations that depend on cohort groups, such as race, gender, and therapy. Gene network inference, cross-validation and functional analyses further supported the identified biomarkers.

Results

A total of 61, 47 and 60 gene expression profiles were significantly associated with lifetime, overall, and progression-free survival, respectively. The vast majority of these genes have been previously reported to be associated with glioblastoma (35, 24, and 35 genes, respectively) or with other cancers (10, 19, and 15 genes, respectively) and the rest (16, 4, and 10 genes, respectively) are novel associations. Pik3r1, E2f3, Akr1c3, Csf1, Jag2, Plcg1, Rpl37a, Sod2, Topors, Hras, Mdm2, Camk2g, Fstl1, Il13ra1, Mtap and Tp53 were associated with multiple survival events.

Most genes (from 90 to 96%) were associated with survival in a general or cohort-independent manner and thus the same trend is observed across all clinical levels studied. The most extreme associations between profiles and survival were observed for Syne1, Pdcd4, Ighg1, Tgfa, Pla2g7, and Paics. Several genes were found to have a cohort-dependent association with survival and these associations are the basis for individualized prognostic and gene-based therapies. C2, Egfr, Prkcb, Igf2bp3, and Gdf10 had gender-dependent associations; Sox10, Rps20, Rab31, and Vav3 had race-dependent associations; Chi3l1, Prkcb, Polr2d, and Apool had therapy-dependent associations. Biological processes associated glioblastoma survival included morphogenesis, cell cycle, aging, response to stimuli, and programmed cell death.

Conclusions

Known biomarkers of glioblastoma survival were confirmed, and new general and clinical-dependent gene profiles were uncovered. The comparison of biomarkers across glioblastoma phases and functional analyses offered insights into the role of genes. These findings support the development of more accurate and personalized prognostic tools and gene-based therapies that improve the survival and quality of life of individuals afflicted by glioblastoma multiforme.
Molecular identification of Clonorchis sinensis and discrimination with other opisthorchid liver fluke species using multiple Ligation-depended Probe Amplification (MLPA)
Authors: Sun Jiufeng , Xu Jin , Liang Pei , Mao Qiang , Huang Yan , Lv Xiaoli , Deng Chuanhuan , Liang Chi , de Hoog G S , Yu Xinbing
Published: June 2011

Background

Infections with the opisthorchid liver flukes Clonorchis sinensis, Opisthorchis viverrini, and O. felineus cause severe health problems globally, particularly in Southeast Asia. Early identification of the infection is essential to provide timely and appropriate chemotherapy to patients.

Results

In this study we evaluate a PCR-based molecular identification method, Multiplex Ligation-dependent Probe Amplification (MLPA), which allows rapid and specific detection of single nucleotide acid differences between Clonorchis sinensis, Opisthorchis viverrini and O. felineus. Three probe pairs were derived from the Internally Transcribed Spacer 1 (ITS1) of three opisthorchid liver flukes using a systematic phylogenetic analysis. Specific loci were detected in all three species, yielding three amplicons with 198,172 and 152 bp, respectively, while no cross reactions were observed. A panel of 66 C. sinensis isolates was screened using MLPA. All species were positively identified, and no inhibition was observed. The detection limit was 103 copies of the ITS gene for the three liver flukes, or about 60 pg genomic DNA for Clonorchis sinensis. Amplification products can be detected by electrophoresis on agarose gel or in a capillary sequencer. In addition, genomic DNA of Clonorchis sinensis in fecal samples of infected rats was positively amplified by MLPA.

Conclusion

The flexibility and specificity make MLPA a potential tool for specific identification of infections by opisthorchid liver flukes in endemic areas.
Gene expression in bryozoan larvae suggest a fundamental importance of pre-patterned blastemic cells in the bryozoan life-cycle
Authors: Fuchs Judith , Martindale Mark Q , Hejnol Andreas
Published: June 2011

Background

Bryozoa is a clade of aquatic protostomes. The bryozoan life cycle typically comprises a larval stage, which metamorphoses into a sessile adult that proliferates by asexual budding to form colonies. The homology of bryozoan larvae with other protostome larvae is enigmatic. Bryozoan larvae exhibit blastemic tissues that contribute to build the adult during morphogenesis. However, it remains unclear if the cells of these tissues are pre-determined according to their future fate or if the cells are undifferentiated, pluripotent stem cells. Gene expression studies can help to identify molecular patterning of larval and adult tissues and enlighten the evolution of bryozoan life cycle stages.

Results

We investigated the spatial expression of 13 developmental genes in the larval stage of the gymnolaemate bryozoanBugula neritina. We found most genes expressed in discrete regions in larval blastemic tissues that form definitive components of the adult body plan. Only two of the 13 genes,BnTropomyosinandBnFoxAB, were exclusively expressed in larval tissues that are discarded during metamorphosis.

Conclusions

Our results suggest that the larval blastemas inBugulaare pre-patterned according to their future fate in the adult. The gene expression patterns indicate that some of the bryozoan blastemas can be interpreted to correspond to homologous adult tissues of other animals. This study challenges an earlier proposed view that metazoan larvae share homologous undifferentiated "set-aside cells", and instead points to an independent origin of the bryozoan larval stage with respect to other lophotrochozoans.
Imaging the effect of receptor for advanced glycation endproducts on angiogenic response to hindlimb ischemia in diabetes
Authors: Tekabe Yared , Shen Xiaoping , Luma Joane , Weisenberger Drew , Yan Shi Fang , Haubner Roland , Schmidt Ann Marie , Johnson Lynne
Published: June 2011

Background

Receptor for advanced glycation endproducts (RAGE) expression contributes to the impaired angiogenic response to limb ischemia in diabetes. The aim of this study was to detect the effect of increased expression of RAGE on the angiogenic response to limb ischemia in diabetes by targeting αvβ3 integrin with 99mTc-labeled Arg-Gly-Asp (RGD).

Methods

Male wild-type (WT) C57BL/6 mice were either made diabetic or left as control for 2 months when they underwent femoral artery ligation. Four groups were studied at days 3 to 7 after ligation: WT without diabetes (NDM) (n = 14), WT with diabetes (DM) (n = 14), RAGE-/- NDM (n = 16), and RAGE-/- DM (n = 14). Mice were injected with 99mTc-HYNIC-RGD and imaged. Count ratios for ischemic/non-ischemic limbs were measured. Muscle was stained for RAGE, αvβ3, and lectins.

Results

There was no difference in count ratio between RAGE-/- and WT NDM groups. Mean count ratio was lower for WT DM (1.38 ± 0.26) vs. WT NDM (1.91 ± 0.34) (P<0.001). Mean count ratio was lower for the RAGE-/- DM group than for RAGE-/- NDM group (1.75 ± 0.22 vs. 2.02 ± 0.29) (P<0.001) and higher than for the WT DM group (P<0.001). Immunohistopathology supported the scan findings.

Conclusions

In vivo imaging of αvβ3 integrin can detect the effect of RAGE on the angiogenic response to limb ischemia in diabetes.
Telomerase expression and telomere length in breast cancer and their associations with adjuvant treatment and disease outcome
Authors: Lu Lingeng , Zhang Chong , Zhu Gongjian , Irwin Melinda , Risch Harvey , Menato Guido , Mitidieri Marco , Katsaros Dionyssios , Yu Herbert
Published: June 2011

Introduction

Telomere length plays important roles in maintaining genome stability and regulating cell replication and death. Telomerase has functions not only to extend telomere length but also to repair DNA damage. Studies have shown that telomerase may increase cancer cell resistance to DNA-damaging anticancer agents; tamoxifen may suppress telomerase expression in breast cancer cells. This study aimed to investigate the role of telomere length and telomerase activity in breast cancer prognosis.

Methods

qPCR and qRT-PCR were used to analyze telomere length and telomerase expression, respectively, in tumor samples of 348 breast cancer patients. Cox regression analysis was performed to examine telomere length and telomerase expression in association with disease-free survival and cause-specific mortality.

Results

Telomere length had no relation to tumor features or disease outcomes. Telomerase expression was detected in 53% of tumors. Larger tumors or aggressive disease were more likely to have telomerase expression. Among patients treated with chemotherapy, high telomerase was found to be associated with increased risk of death (hazard ratio (HR) = 3.15; 95% CI: 1.34 to 7.40) and disease recurrence (HR = 2.04; 95% CI: 0.96 to 4.30) regardless of patient age, disease stage, tumor grade, histological type or hormone receptor status. Patients treated with endocrine therapy had different results regarding telomerase: high telomerase appeared to be associated with better survival outcomes. Telomerase expression made no survival difference in patients who received both chemotherapy and endocrine therapy.

Conclusions

Overall, telomerase expression was not associated with disease outcome, but this finding may be masked by adjuvant treatment. Patients with high telomerase expression responded poorly to chemotherapy in terms of disease-free and overall survival, but fared better if treated with endocrine therapy.