Analytical validation of a prognostic prostate cancer gene expression assay using formalin fixed paraffin embedded tissue

Background

There is a clear need for assays that can predict the risk of metastatic prostate cancer following curative procedures. Importantly these assays must be analytically robust in order to provide quality data for important clinical decisions. DNA microarray based gene expression assays measure several analytes simultaneously and can present specific challenges to analytical validation. This study describes the analytical validation of one such assay designed to predict metastatic recurrence in prostate cancer using primary formalin fixed paraffin embedded tumour material.

Methods

Accuracy was evaluated with a method comparison study between the assay development platform (Prostate Disease Specific Array) and an alternative platform (Xcel? microarray) using 50 formalin-fixed, paraffin-embedded prostate cancer patient samples. An additional 70 samples were used to establish the assay reportable range. Determination of assay precision and sensitivity was performed on multiple technical replicates of three prostate cancer samples across multiple variables (operators, days, runs, reagent lots, and equipment) and RNA/cDNA inputs respectively using the appropriate linear mixed model.

Results

The overall agreement between the development and alternative platform was 94.7% (95% confidence interval, 86.9–98.5%). The reportable range was determined to be 0.150 to 1.107 for core needle biopsy samples and???0.214 to 0.844 for radical prostatectomy samples. From the precision study, the standard deviations for assay repeatability and reproducibility were 0.032 and 0.040 respectively. The sensitivity study demonstrated that a total RNA input and cDNA input of 50?ng and 3.5?μg respectively was conservative.

Conclusion

The Metastatic Assay was found to be highly reproducible and precise. In conclusion the studies demonstrated an acceptable analytical performance for the assay and support its potential use in the clinic.

     

Elicitation of <Emphasis Type="Italic">Streptomyces coelicolor</Emphasis> with dead cells of <Emphasis Type="Italic">Bacillus subtilis</Emphasis> and <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> in a bioreactor increases production of undecylprodigiosin

Since microorganisms normally co-exist with other species in nature, they have developed complex metabolic and physiological responses as a result of such interspecies interactions. We utilized some of these interactions by introducing heat-killed cells of Bacillus subtilis and Staphylococcus aureus to Streptomyces coelicolor cultures and, as a result, stimulated undecylprodigiosin production. Undecylprodigiosin is not only an antibiotic; it has also been attributed with antitumor activities, but, in a defined medium, pure cultures of S. coelicolor produced only low concentrations. Elicitation with B. subtilis increased the maximum undecylprodigiosin concentration by threefold and S. aureus by fivefold compared with the pure culture of S. coelicolor. Growth and glucose consumption of elicited S. coelicolor, however, remained similar to those observed in the pure culture. Furthermore, another positive outcome of the elicitation with both B. subtilis and S. aureus was the earlier onset of undecylprodigiosin production by 24 h compared with the pure culture of S. coelicolor. This is the first time that such a phenomenon has been seen in 2L bioreactors. Our work supports the use of biotic elicitation in order to enhance the production of secondary metabolites for industrial-scale applications.     

Red Blood Cell and Serum Magnesium Levels Among Children and Adolescents With Sickle Cell Anemia

This study investigated neurotoxicity of chronic fluorosis in the rat hippocampus. Newly weaning, male, Sprague-Dawley (SD) rats were administered 15, 30, and 60 mg/L sodium fluoride (NaF) solution (fluorine ion concentration 8.25, 16.50, and 33.00 mg/L, respectively), and tap water, for 18 months. The neurotoxicological mechanism was examined with a focus on intracellular calcium overload. Results showed that as the fluoride concentration increased, calcium ion concentration [Ca²⁺], the expression of calcium/calmodulin-dependent protein kinase II α (CaMKIIα), and the expression of catus proto-oncogene protein c-fos (c-fos) all tend to increase. Compared to the control group, Ca²⁺, CaMKIIα, and c-fos significantly increased (P < 0.05) in the moderate-fluoride and the high-fluoride groups. These results indicate that Ca²⁺/CaMKIIα/c-fos channel signal may be the molecular mechanism of central nervous system damage caused by chronic fluoride intoxication. Moreover, elevated Ca²⁺ concentration in the hippocampus may be the initiating factor of neuronal apoptosis induced by fluoride.     

Wide Bandpass and Narrow Bandstop Microstrip Filters Based on Hilbert Fractal Geometry: Design and Simulation Results

This paper presents new Wide Bandpass Filter (WBPF) and Narrow Bandstop Filter (NBSF) incorporating two microstrip resonators, each resonator is based on 2^nd iteration of Hilbert fractal geometry. The type of filter as pass or reject band has been adjusted by coupling gap parameter (d) between Hilbert resonators using a substrate with a dielectric constant of 10.8 and a thickness of 1.27 mm. Numerical simulation results as well as a parametric study of d parameter on filter type and frequency responses are presented and studied. WBPF has designed at resonant frequencies of 2 and 2.2 GHz with a bandwidth of 0.52 GHz, −28 dB return loss and −0.125 dB insertion loss while NBSF has designed for electrical specifications of 2.37 GHz center frequency, 20 MHz rejection bandwidth, −0.1873 dB return loss and 13.746 dB insertion loss. The proposed technique offers a new alternative to construct low-cost high-performance filter devices, suitable for a wide range of wireless communication systems.     

Serum Myeloperoxidase as a Biomarker of Asthma Severity Among Adults: A Case Control Study

Background:The contribution of neutrophils is still indistinct in the inflammatory response of bronchial asthma (BAs). Myeloperoxidase (MPO) is an enzyme released from the primary azurophilic granules of the neutrophils. The study aimed to evaluate the levels of serum MPO as a biomarker for the assessment of the level of asthma control. Methods:The study participants included 94 asthmatic patients and 86 healthy controls. The identification of asthma severity had assessed using the ''''Global Initiative for Asthma guidelines''''. Asthmatic adults had divided into three groups: Good (n= 22), partial (n= 30), and poor control (n= 44). Also, patients have been divided again into two groups (treated and untreated) for BAs.Results:The predicted FEV1% and the peak expiratory flow (PEF/L) of all participants had verified by spirometry. The mean patients’ age was 31.9±15.1 year, with a predominance of females. The mean asthma duration was 10.5±8.6 years. Mean spirometric parameters (FEV1 and PEF) were significantly lower among the patients (0.00). Significant higher MPO levels had observed among BAs patients (p-0.00). The MPO levels have not differed significantly with asthma levels and had significant differences with the history of treatment. There was a nonsignificant negative correlation between the mean MPO levels and the spirometry variables among the patients. ROC curves revealed a sensitivity, specificity, accuracy for MPO (80.9%, 72.1%, and 84.3%), respectively to predict asthmatic severity.Conclusion:There were significantly higher MPO levels compared to healthy controls. Levels of serum MPO had a non-significant positive correlation with levels of asthma control, but a negative non-significant correlation with spirometric results. Key Words: Asthma, And Neutrophils, FEV1, MPO, PEF     

Detection of secreted antimicrobial peptides isolated from cell-free culture supernatant of Paenibacillus alvei AN5

An antimicrobial substance produced by the Paenibacillus alvei strain AN5 was detected in fermentation broth. Subsequently, cell-free culture supernatant (CFCS) was obtained by medium centrifugation and filtration, and its antimicrobial activity was tested. This showed a broad inhibitory spectrum against both Gram-positive and -negative bacterial strains. The CFCS was then purified and subjected to SDS-PAGE and infrared spectroscopy, which indicated the proteinaceous nature of the antimicrobial compound. Some de novo sequencing using an automatic Q-TOF premier system determined the amino acid sequence of the purified antimicrobial peptide as Y-S-K-S-L-P-L-S-V-L-N-P (1,316 Da). The novel peptide was designated as peptide AN5-1. Its mode of action was bactericidal, inducing cell lysis in E. coli ATCC 29522 and S. aureus, and non-cell lysis in both S. marcescens and B. cereus ATCC 14579. Peptide AN5-1 displayed stability at a wide range of pH values (2–12) and remained active after exposure to high temperatures (100 °C). It also maintained its antimicrobial activity after incubation with chemicals such as SDS, urea and EDTA.     

Investigation of New Microstrip Bandpass Filter Based on Patch Resonator with Geometrical Fractal Slot

A compact dual-mode microstrip bandpass filter using geometrical slot is presented in this paper. The adopted geometrical slot is based on first iteration of Cantor square fractal curve. This filter has the benefits of possessing narrower and sharper frequency responses as compared to microstrip filters that use single mode resonators and traditional dual-mode square patch resonators. The filter has been modeled and demonstrated by Microwave Office EM simulator designed at a resonant frequency of 2 GHz using a substrate of ε_r = 10.8 and thickness of h = 1.27 mm. The output simulated results of the proposed filter exhibit 22 dB return loss, 0.1678 dB insertion loss and 12 MHz bandwidth in the passband region. In addition to the narrow band gained, miniaturization properties as well as weakened spurious frequency responses and blocked second harmonic frequency in out of band regions have been acquired. Filter parameters including insertion loss, return loss, bandwidth, coupling coefficient and external quality factor have been compared with different values of perturbation dimension (d). Also, a full comparative study of this filter as compared with traditional square patch filter has been considered.     

Gas chromatographic determination of eugenol in ethanol extract of cloves

An ethanolic extract of cloves was analyzed by gas chromatography directly to identify eugenol and other major phenolic compounds without previous separation of other components. Separation was performed on a fused-silica capillary column of 30 mx0.53 mm I.D., 0.53 μm film thickness. The detector was a flame ionization detector. Helium gas at a flow-rate of 3 ml/min was used as a carrier gas. The analysis were performed with linear temperature programming. Nine components were detected and special attention was given to the major phenolic compound, eugenol.     

Bacterial l-asparaginases for cancer therapy: Current knowledge and future perspectives

l -Asparaginases hydrolyzing plasma l -asparagine and l -glutamine has attracted tremendous attention in recent years owing to remarkable anticancer properties. This enzyme is efficiently used for acute lymphoblastic leukemia (ALL) and lymphosarcoma and emerged against ALL in children, neoplasia, and some other malignancies. Cancer cells reduce the expression of l -asparaginase leading to their elimination. The l -asparaginase anticancerous application approach has made incredible breakthrough in the field of modern oncology through depletion of plasma l -asparagine to inhibit the cancer cells growth; particularly among children. High level of l -asparaginase enzyme production by Escherichia coli, Erwinia species, Streptomyces, and Bacillus subtilis species is highly desirable as bacterial alternative enzyme sources for anticancer therapy. Thermal or harsh conditions stability of those from the two latter bacterial species is considerable. Some enzymes from marine bacteria have conferred stability in adverse conditions being more advantageous in cancer therapy. Several side effects exerted by l -asparaginases such as hypersensitivity should be hindered or decreased through alternative therapies or use of immune-suppressor drugs. The l -asparaginase from Erwinia species has displayed remarkable traits in children with this regard. Noticeably, Erwinia chrysanthemi l -asparaginase exhibited negligible glutaminase activity representing a promising efficiency mitigating related side effects. Application of software such as RSM would optimize conditions for higher levels of enzyme production. Additionally, genetic recombination of the encoding gene would indisputably help improving enzyme traits. Furthermore, the possibility of anticancer combination therapy using two or more l -asparaginases from various sources is plausible in future studies to achieve better therapeutic outcomes with lower side effects.