Combination Of Polymerase Chain Reaction Research Articles

Analysis of ammonia-oxidizing bacteria dominating in lab-scale bioreactors with high ammonium bicarbonate loading

The ammonia-oxidizing bacterial community (AOB) was investigated in two types of laboratory-scale bioreactors performing partial oxidation of ammonia to nitrite or nitrate at high (80 mM) to extremely high (428 mM) concentrations of ammonium bicarbonate. At all conditions, the dominant AOB was affiliated to the Nitrosomonas europaea lineage as was determined by fluorescence in situ hybridization and polymerase chain reaction in combination with denaturing gradient gel electrophoresis. Molecular analysis of the mixed populations, based on the 16S rRNA and cbbL genes, demonstrated the presence of two different phylotypes of Nitrosomonas, while microbiological analysis produced a single phylotype, represented by three different morphotypes. One of the most striking features of the AOB populations encountered in the bioreactors was the domination of highly aggregated obligate microaerophilic Nitrosomonas, with unusual cellular and colony morphology, commonly observed in nitrifying bioreactors but rarely investigated by cultural methods. The latter is probably not an adaptation to stressful conditions created by high ammonia or nitrite concentrations, but oxygen seems to be a stressful factor in these bioreactors.

Human papillomavirus infection in lung and esophageal cancers: Analysis of 485 Asian cases

The role of human papillomavirus (HPV) in the development of lung and esophageal cancer remains inconclusive, which is in contrast to the established role HPV plays in the development of uterine cervical cancer. One of the reasons for this is the difference among reported HPV infection rates in these cancers. An analysis of 485 lung and esophageal cancers (176 lung squamous cell carcinoma, 128 lung adenocarcinoma, 181 esophageal carcinoma) in eight institutions in Asia (Tokyo, Kochi, Kagoshima, and Okinawa, Japan; Seoul and Daegu, Korea; Changhua, Republic of China (Taiwan); Singapore, Singapore) was carried out in order to clarify infection rates with HPV. Samples were examined in one laboratory of the Department of Pathology, the University of Tokyo, Japan in order to avoid inter-laboratory variation using a combination of polymerase chain reaction and in situ hybridization (ISH). HPV was found in 6.3%, 7%, and 9.4% of patients with lung squamous cell carcinoma, lung adenocarcinoma, and esophageal cancer, respectively. Among the geographic areas surveyed, Kagoshima exhibited a significantly higher prevalence of HPV infection in cases of esophageal carcinoma (24.1%). There was no geographical difference in the infection rates of HPV in lung carcinomas. Subtype-specific ISH was also performed, which identified the high-risk HPV types 16/18 in the majority (75.7%) of the patients with lung and esophageal cancer positive for HPV.

Complex cytogenetic analysis of early lethality mouse embryos

An increasing interest in the molecular mechanisms governing cell division has resulted in the discovery of several groups of genes that participate in the regulation of mitosis and meiosis in eukaryotes. Inactivation of these genes in mice often leads to early embryonic lethality. To show direct causality between mutations of these genes, chromosomal instability and embryonic death, a technique enabling detailed cytogenetic analysis of embryonic cells is required. Here, we develop and test a comprehensive approach that allows complex analysis of individual early postimplantation embryos and combines polymerase chain reaction genotyping with the preparation and detailed karyotypic inspection of cells at the metaphase and anaphase stages. The method enables good chromosomal spreading and scattering of nuclei to perform routine cytogenetics (i.e., standard stain and G-banding). It also permits the application of specialized techniques such as fluorescence in situ hybridization to detect particular chromosomes and to verify the integrity of individual chromosomes. Utility of the new method is demonstrated by an analysis of embryonic dayE7.5-E9.5 tissue from mice deficient in the spindle checkpoint gene Bub1b.

An immunoassay based on bio-barcode method for quantitative detection of semicarbazide

A functionalized gold nanoparticles bio-barcode technology was developed to detect semicarbazide. In the assay, the hapten CPSEM (4-[[2-(aminocarbonyl) hydrazinylidene] methyl]-benzoic acid) was first prepared and conjugated to bovine serum albumin as the coating antigen. Subsequently, gold nanoparticles dual-labeled with anti-CPSEM monoclonal antibodies and DNA oligonucleotide were synthesized via a one-step preparation method. Enzymatic signal was converted to DNA signal by combining polymerase chain reaction with indirect competitive ELISA (icELISA). The limit of detection of this method could reach 8 pg mL−1 for detecting SEM, about 25 times more sensitive than conventional ELISA. The immunosorbent bio-barcode assay is a rapid high-throughput screening tool adapted for ultra-high sensitive detection.

Epidemiology of recent outbreaks of infectious laryngotracheitis in poultry in Australia

Over the past 3 years, numerous outbreaks of infectious laryngotracheitis (ILT) have occurred in poultry in Australia. The objectives of this study were to identify the viral strains involved in the recent outbreaks and to determine possible epidemiological links between these outbreaks. A combination of polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analyses of several genes of the ILT virus was used to identify genetic differences in field/vaccine ILT virus isolates. In a previous study, these procedures had demonstrated five classes (1-5) in Australia. Analysis of 92 field ILT viruses demonstrated four new classes: 6, 7, 8 and 9. Class 6 was responsible for four outbreaks in one Victorian broiler company and demonstrated to be distinct from other Australian strains of ILT. Class 7 was the Nobilis ILT vaccine (Intervet Pty Ltd). Class 8 was responsible for the majority of the outbreaks in New South Wales and was phylogenetically close to class 7. On one occasion, classes 7 and 8 were identified in an outbreak on a Victorian farm that had used the Nobilis ILT vaccine. Class 9, also phylogenetically close to classes 7 and 8, was found only in New South Wales. The previously identified class 2 was also found to be responsible for a large number of outbreaks, mainly in Victoria. The results demonstrate that, epidemiologically, most outbreaks of ILT in New South Wales are unrelated to those in Victoria and suggest a link between classes 8 and 9 and the Nobilis ILT vaccine (class 7).

Association of N-Acetyltransferase-2 Genotypes and Anti-Tuberculosis Induced Liver Injury: First Case-Controlled Study from Iran

The goals of this study were to identify the frequency of N-acetyltransferase-2 genotypes and phenotypes in Iranian tuberculosis and healthy subjects and to evaluate correlation of acetylator phenotype and antituberculosis-induced hepatotoxicity in pulmonary tuberculosis patients. A total of 50 newly diagnosed pulmonary tuberculosis patients and 50 healthy Iranian subjects were enrolled in the study. A combination of polymerase chain reaction and restriction fragment length polymorphism were used to investigate N-acetyltransferase-2 alleles. The tuberculosis patients were followed for occurrence of antituberculosis induced hepatotoxicity during the treatment course. Correlation between N-acetyltransferase-2 phenotypes and antituberculosis induced hepatotoxicity was evaluated. Frequency of slow, intermediate and fast acetylator genotypes in the healthy group were 32%, 54% and 14% and in the tuberculosis patients were 28%, 64% and 8%, respectively. Hepatotoxicity was detected in 64.3% of slow acetylators, 15.6% of intermediate acetylators and interestingly in none of the fast acetylators. There were no significant difference in distribution of various N-acetyltransferase-2 alleles, genotypes and phenotypes between pulmonary TB patients and healthy individuals. Among patients, anti-tuberculosis induced hepatotoxicity was more frequent in slow acetylators in comparison with fast acetylators in Iranian tuberculosis patients.

Interleukin-6 G-174C gene polymorphism and serum resistin levels in North Indian women: Potential risk of metabolic syndrome

The present investigations were aimed to identify the possible association between genetic polymorphism in interleukin-6 (IL-6) G-174C gene, which confers susceptibility to metabolic syndrome, and serum level of resistin in North Indian women. The study population comprised 370 unrelated Indian women (192 having abdominal obesity and 178 controls). Polymorphism in genotype (CC+GC) of IL-6 G-174C gene was determined using a combination of polymerase chain reaction (PCR) and sequence-specific primer with restriction fragment length polymorphism (RFLP) technology. Insulin resistance (IR) and serum resistin level were also analyzed along with metabolic risk factors. Of 192 abdominal obese women, 147 (76.56%) were found to have mutant CC+GC (p = 0.001) genotype and allele frequency (p = 0.001), which was significantly higher 45 (23.44%) than non-obese and their respective wild type. The mutant genotype (CC+GC) of IL-6 gene was found to be associated significantly with high triglyceride (p = 0.025) and resistin level (p < 0.001), when compared with respective wild genotype (GG) in obese women. Non-obese women with no signs of metabolic risk factors were found to have significantly low level of serum resistin and IR in comparison to obese women having genetic polymorphism for IL-6 G-174C gene. Study suggests that IL-6 G-174C gene is one among the susceptibility loci for metabolic syndrome in North Indian women. Genotype for this polymorphism may prove informative for prediction of genetic risk for metabolic syndrome. Further, high level of serum resistin molecules may be targeted to correlate with metabolic syndrome risk factors and could be used as early prediction marker.

Bottlenecks and the Maintenance of Minor Genotypes during the Life Cycle of Trypanosoma brucei

African trypanosomes are digenetic parasites that undergo part of their developmental cycle in mammals and part in tsetse flies. We established a novel technique to monitor the population dynamics of Trypanosoma brucei throughout its life cycle while minimising the confounding factors of strain differences or variation in fitness. Clones derived from a single trypanosome were tagged with short synthetic DNA sequences in a non-transcribed region of the genome. Infections were initiated with mixtures of tagged parasites and a combination of polymerase chain reaction and deep sequencing were used to monitor the composition of populations throughout the life cycle. This revealed that a minimum of several hundred parasites survived transmission from a tsetse fly to a mouse, or vice versa, and contributed to the infection in the new host. In contrast, the parasites experienced a pronounced bottleneck during differentiation and migration from the midgut to the salivary glands of tsetse. In two cases a single tag accounted for ≥99% of the population in the glands, although minor tags could be also detected. Minor tags were transmitted to mice together with the dominant tag(s), persisted during a chronic infection, and survived transmission to a new insect host. An important outcome of the bottleneck within the tsetse is that rare variants can be amplified in individual flies and disseminated by them. This is compatible with the epidemic population structure of T. brucei, in which clonal expansion of a few genotypes in a region occurs against a background of frequent recombination between strains.

Application of PCR‐LDR‐nucleic acid detection strip in detection of YMDD mutation in hepatitis B patients treated with lamivudine

Chronic hepatitis B virus (CHBV) infection causes cirrhosis and hepatocellular carcinoma. Lamivudine (LAM) has been successfully used to treat CHBV infections but prolonged use leads to the emergence of drug-resistant variants. This is primarily linked to a mutation in the tyrosine-methionine-aspartate-aspartate (YMDD) motif of the HBV polymerase gene at position 204. Rapid diagnosis of drug-resistant HBV is necessary for a prompt treatment response. Common diagnostic methods such as sequencing and restriction fragment length polymorphism (RFLP) analysis lack sensitivity and require significant processing. The aim of this study was to demonstrate the usefulness of a novel diagnostic method that combines polymerase chain reaction (PCR), ligase detection reaction (LDR) and a nucleic acid detection strip (NADS) in detecting site-specific mutations related to HBV LAM resistance. We compared this method (PLNA) to direct sequencing and RFLP analysis in 50 clinical samples from HBV infected patients. There was 90% concordance between all three results. PLNA detected more samples containing mutant variants than both sequencing and RFLP analysis and was more sensitive in detecting mixed variant populations. Plasmid standards indicated that the sensitivity of PLNA is at or below 3,000 copies per ml and that it can detect a minor variant at 5% of the total viral population. This warrants its further development and suggests that the PLNA method could be a useful tool in detecting LAM resistance.

Novel SCN1A mutations in Indonesian patients with severe myoclonic epilepsy in infancy

Severe myoclonic epilepsy in infancy (SMEI) and borderline SMEI (SMEB) are caused by a mutation in SCN1A, which encodes a voltage-gated sodium channel alpha1-subunit protein. Although many mutations in SCN1A have been associated with clinical features of SMEI or SMEB from different ethnic groups, there have been no such reports from the South-East Asian populations so far. Patients 1 and 2 were Indonesian children diagnosed as having SMEI and SMEB based on their clinical features. SCN1A was screened for mutations using a combination of polymerase chain reaction and denaturing high-performance liquid chromatography. Nucleotide substitutions were confirmed on direct sequencing. In patient 1, a G-to-A heterozygous transition was detected at nucleotide 4834 (c.4834G>A) in exon 25, leading to substitution of valine with isoleucine at amino acid position 1612 (p.V1612I) in the SCN1A protein. In patient 2 a T-to-G heterozygous transversion was identified at nucleotide 5266 (c.5266T>G) in exon 26, leading to substitution of cysteine with glycine at amino acid 1756 (p.C1756G) in the SCN1A protein. Both amino acid substitutions might disrupt these highly conserved regions in species from drosophila to human, leading to dysfunction of the protein. p.V1612I and p.C1756G were determined as disease-causing mutations due to their absence in the control population. The first cases of SMEI and SMEB are reported in South-East Asian populations. Two novel SCN1A mutations are also identified in these patients, p.V1612I and p.C1756G, which may lead to neuronal excitability or convulsions.

Qualitative assessment of FMR1 (CGG)n triplet repeat status in normal, intermediate, premutation, full mutation, and mosaic carriers in both sexes: Implications for fragile X syndrome carrier and newborn screening

PurposeFragile X syndrome is caused by expansion and subsequent methylation of a CGG trinucleotide repeat in the FMR1 5′-untranslated region. Southern blot analysis is typically required to determine expansion size for triplet repeat lengths >200. We describe a triplet-primed polymerase chain reaction-based method using automated capillary electrophoresis detection for qualitative assessment of expanded CGG repeats. MethodsThe assay uses triplet-primed polymerase chain reaction in combination with GC-melting reagents and substitution of 7-deaza-2-deoxyGTP for dGTP. Amplicons are resolved by capillary electrophoresis. ResultsA distinctive pattern of tapering or “stutter” polymerase chain reaction amplification was evident on capillary electrophoresis in male and female patients harboring all expanded allele lengths examined (up to 2000 CGG repeats) and could be used to differentiate normal, intermediate, premutation, and full mutation alleles. Full mutation alleles exhibited an additional late-migrating amplicon on capillary electrophoresis. Mixing experiments demonstrated sensitivity as low as 1% for detection of the full mutation allele. In a 1275-sample concordance study against our existing polymerase chain reaction platform (with Southern blot analysis for repeat lengths ≥55), the triplet-primed polymerase chain reaction method exhibited 100% concordance for normal, intermediate, expanded, and full mutation alleles. This method also detected the full mutation alleles in DNA isolated from blood spots. ConclusionThis assay provides an accurate assessment of FMR1 repeat status and holds promise for use in carrier and newborn screening. The method distinguishes normal homozygous females from full mutation carrying females. Although the method is not useful for accurate sizing, it supplements the classic polymerase chain reaction method and results in significant reduction in the number of Southern blot analyses required to be performed in the laboratory to accurately assess the FMR1 genotype in all individuals.

Re: A Lifestyle Intervention Study in Patients with Diabetes or Impaired Glucose Tolerance: Translation of a Research Intervention into Practice

AIMS: Differentiation between actinic reticuloid and cutaneous T cell lymphoma can be extremely difficult. Demonstration of clonal T cell receptor (TCR) gene rearrangements has been suggested as a potential diagnostic criterion, but the results obtained thus far have been conflicting. This study investigated whether TCR gamma gene rearrangement analysis, using polymerase chain reaction (PCR) in combination with denaturing gradient gel electrophoresis (DGGE) and immunohistochemistry, can serve as a diagnostic criterion. METHODS: PCR/DGGE was performed on skin, peripheral blood mononuclear cells, and/or lymph nodes of seven patients with actinic reticuloid, 11 patients with Sézary syndrome, and 15 patients with a benign form of erythroderma. The results of PCR/DGGE and Southern blot analysis of TCR beta gene rearrangements were compared. In addition, CD4:CD8 ratios in skin and peripheral blood samples were investigated. RESULTS: Clonal T cell populations were detected in 19 of 21 samples obtained from patients with Sézary syndrome but were not detected in any of the 12 samples from patients with actinic reticuloid. Clonal T cells were detected in the peripheral blood of only one of 15 patients with a benign form of erythroderma. PCR/DGGE and Southern blot analysis gave concordant results in 28 of 29 samples. Immunophenotypic analysis demonstrated increased proportions of CD8+ T cells in skin (seven of seven cases) and peripheral blood (four of seven cases) of patients with actinic reticuloid. CONCLUSION: The results of this study demonstrate that gene rearrangement analysis, in combination with immunohistochemistry, may be an important adjunct in differentiating between actinic reticuloid and cutaneous T cell lymphoma. In patients suspected of having actinic reticuloid, application of both techniques is recommended.

Sequence and Phylogenetic Analysis of the Thrombospondin-Related Adhesive Protein (TRAP) Gene of Babesia gibsoni Isolates from Dogs in Taiwan

The genetic diversity of Babesia gibsoni strains worldwide is currently poorly defined. The aim of the present study was to characterize B. gibsoni strains in naturally infected dogs in Taiwan using a combination of polymerase chain reaction (PCR) and sequence analysis of both 18S rDNA and the gene encoding thrombospondin-related adhesive protein (TRAP). Genomic DNA was extracted from 29 parasitemic dogs, and the target genes were separately amplified, sequenced and aligned with corresponding sequences available in GenBank. All 18S rDNA sequences (1,262 bp) amplified from the Taiwanese isolates were identical to each other and had very high similarity (99.9-100%) with previously reported B. gibsoni sequences. These results provide the first molecular evidence showing infection of dogs with B. gibsoni from Taiwan. On the other hand, a phylogenetic analysis based on the deduced amino acid sequence of the TRAP gene demonstrated that the Taiwanese isolates were closely related to strains previously identified from Okinawa Island, Japan, but genetically distinct from strains found on Honshu in Japan and Jeju Island in South Korea. The divergence of TRAP among the geographically dispersed strains examined in this study and others supports the conclusion that this gene is useful for molecular genotyping of B. gibsoni strains.

Association of genetic variants with chronic kidney disease in Japanese individuals with or without hypertension or diabetes mellitus

Hypertension and diabetes mellitus are important risk factors for chronic kidney disease (CKD). The purpose of the present study was to identify genetic variants that confer susceptibility to CKD in individuals with or without hypertension or diabetes mellitus, thereby contributing to the personalized prevention of CKD in such individuals separately. The study population comprised 5835 unrelated Japanese individuals, including 1763 subjects with CKD and 4072 controls. The 150 polymorphisms were selected by genome-wide association studies of ischemic stroke and myocardial infarction with the use of the GeneChip Human Mapping 500K Array Set (Affymetrix). The genotypes for these polymorphisms were determined by a method that combines polymerase chain reaction and sequence-specific oligonucleotide probes with suspension array technology. The χ(2) test, multivariable logistic regression analysis with adjustment for covariates, as well as a stepwise forward selection procedure revealed that two different polymorphisms were significantly (P<0.005) associated with the prevalence of CKD in individuals with or without hypertension or diabetes mellitus: the A→G (Lys625Arg) polymorphism of CDH4 (rs6142884) in individuals without diabetes mellitus, and the C→T polymorphism of PTPRN2 (rs1638021) in individuals with hypertension and diabetes mellitus. No polymorphism was significantly associated with CKD in individuals with or without hypertension, in those with diabetes mellitus, or in those without hypertension or diabetes mellitus. Stratification of subjects based on hypertension or diabetes mellitus may thus be fundamental to achieving the personalized prevention of CKD with the use of genetic information.

Detection and Differentiation of Four Poultry Diseases Using Asymmetric Reverse Transcription Polymerase Chain Reaction in Combination with Oligonucleotide Microarrays

Asymmetric reverse transcription polymerase chain reaction (RT-PCR) and microarrays were combined to distinguish 4 viruses, including Avian influenza virus (AIV), Newcastle disease virus (NDV), Infectious bronchitis virus (IBV), and Infectious bursal disease virus (IBDV), and hemagglutinin (HA) subtypes H5, H7, and H9, and neuraminidase (NA) subtypes N1 and N2 of AIV. The AIV matrix protein (M), and HA and NA genes, IBV nucleoprotein (NP) gene, NDV NP gene, and IBDV A fragment gene were cloned into plasmids. These genes were amplified from these positive recombinant plasmids, which included the inserted target genes by PCR. The PCR products were purified and printed on the amino-modified slides as the probes. RNA was extracted from samples and labeled by asymmetric RT-PCR using a cyanine (Cy)3-labeled primers. The labeled complementary (c)DNA was hybridized to the probes immobilized on the glass slides. After hybridization, the microarrays were scanned, and the hybridization pattern agreed perfectly with the known location of each probe. No cross-hybridization could be detected. Results demonstrated that microarray based on asymmetric RT-PCR is an effective way to distinguish AIV, IBV, NDV, and IBDV simultaneously.

Association of a polymorphism of BCHE with ischemic stroke in Japanese individuals with chronic kidney disease

Although chronic kidney disease (CKD) is an important risk factor for ischemic stroke, the genetic variants that confer susceptibility to ischemic stroke in individuals with CKD remain largely unknown. We performed an association study for candidate gene polymorphisms and ischemic stroke in individuals with CKD. The study population comprised 1041 Japanese individuals with CKD, including 228 subjects with ischemic stroke and 813 controls. The genotypes of 150 polymorphisms of 127 candidate genes were determined by a method that combines polymerase chain reaction and sequence-specific oligonucleotide probes with suspension array technology. An initial χ2 test (false discovery rate <0.05) and subsequent multivariate logistic regression analysis with adjustment for covariates (P<0.05) revealed that the 1615G↷A (Ala539Thr) polymorphism (rs1803274) of BCHE (OR=3.33; 95% CI 1.32-8.28) and the 2445G↷A (Ala54Thr) polymorphism (rs1799883) of FABP2 (OR=1.66; 95% CI 1.01-2.70) were significantly associated with ischemic stroke. The variant alleles of BCHE and FABP2 were risk factors for ischemic stroke. A stepwise forward selection procedure demonstrated that the BCHE genotype was a significant (P<0.05) and independent determinant of ischemic stroke. Genotyping for BCHE may prove informative for the assessment of the genetic risk of ischemic stroke in Japanese individuals with CKD.

Bioaugmentation with the nicotine-degrading bacterium Pseudomonas sp. HF-1 in a sequencing batch reactor treating tobacco wastewater: Degradation study and analysis of its mechanisms

The highly effective nicotine-degrading bacterium Pseudomonas sp. HF-1 was augmented in an SBR system that is used to treat tobacco wastewater. Compared to the non-bioaugmented (non-BA) system, the bioaugmented (BA) system exhibited considerably stronger pollution disposal abilities, with 100% nicotine degradation and more than 84% chemical oxygen demand (COD) removal within 12 h. Nicotine degradation had a significant effect on COD removal in SBRs ( r = 0.928, p < 0.01). The mechanisms of bioaugmentation were systematically investigated using a combination of polymerase chain reaction and denaturing gradient gel electrophoresis (PCR–DGGE) and a toxicity assay (protein carbonyl (PC) and DNA–protein crosslinking (DPC)). DGGE fingerprint profiles showed that the number of bands and the Shannon–Wiener index decreased at a nicotine load of 250 mg/L compared to a 40–130 mg/L nicotine load in the non-BA system. However, a stepwise increase in the Shannon–Wiener index was found during all periods in the BA system. A comparison of sequences excised from DGGE gels demonstrated significant differences in the dominant microbial species between the two SBRs. This result suggested that bioaugmentation of strain HF-1 could select cooperators for treating complicated tobacco wastewater. The PC content and the DPC coefficient increased significantly at levels higher than 80 mg/L in the non-BA system; nevertheless, no increase was observed in the BA system during the stepwise nicotine load. This indicated that bioaugmentation of strain HF-1 resulted in the maintenance of high treatment activity by minimizing the nicotine toxicity for other microbes in the BA system. In conclusion, the rapid nicotine degradation of strain HF-1 performed a vital function in SBR by influencing the microbial community structure, dynamics and activity of the activated sludge system.

Diagnosis of intraocular lymphoma by polymerase chain reaction analysis and cytokine profiling of the vitreous fluid

To determine whether a diagnosis of intraocular lymphoma (IOL) can be made using a combination of polymerase chain reaction (PCR) analysis to detect gene rearrangement of immunoglobulin and cytokine concentrations in the vitreous fluid. Vitreous samples from 22 patients with clinically suspected IOL and ten control patients with acute retinal necrosis or cytomegalovirus retinitis were examined by PCR analysis and cytokine measurements. Genomic DNA was extracted from the cells in the vitreous, and the immunoglobulin heavy chain (IgH) gene was amplified by two PCR procedures: (1) microdissection and PCR to detect IgH gene rearrangement and (2) qualitative PCR to detect IgH VDJ gene rearrangement. The supernatants of the vitreous samples were used for enzyme-linked immunosorbent assay to determine interleukin (IL)-10 and IL-6 levels. PCR examinations detected IgH rearrangement in the vitreous in 21 of the 22 IOL patients (95.5%) and in none of the ten control patients. Elevated IL-10 concentrations (>100 pg/ml) and the IL-10/IL-6 ratio (>1.0) were positive in 18 of the 22 IOL patients (81.8%), but negative in all of the control patients. Sensitivity, specificity, positive predictive value, and negative predictive value of PCR for the diagnosis of IOL were calculated to be 0.955, 1.000, 1.000, and 0.909, respectively, and those of the cytokine concentration assay to be 0.818, 1.000, 1.000, and 0.714, respectively. When both the intravitreal cytokine assay and PCR analysis of the vitreous samples are used, as well as diagnostic criteria of IOL defined as a positive outcome from one of the two assays together with clinical signs, the sensitivity and specificity of the criteria were 1.000. A combination of PCR assay to detect gene rearrangement of IgH and cytokine profiling (IL-10 and IL-6) is extremely useful for the diagnosis of intraocular lymphoma.

Heap bioleaching of a complex sulfide ore: Part I: Effect of pH on metal extraction and microbial composition in pH controlled columns

The effect of pH on the bioleaching of a low-grade, black schist ore from Finland containing pyrrhotite, pyrite, pentlandite, chalcopyrite and other mineral sulfides was studied using columns containing 9.0 kg of agglomerated ore that was irrigated with nutrient supplemented surface water from the deposit at ambient temperature. Iron and sulfur-oxidizing enriched culture was used to inoculate the columns. Iron oxidation and metal leaching increased with decreasing pH. At pH 1.5, 59% Ni was bioleached after 140 days together with 59% Zn, 13% Cu and 16% Co. In comparison, at pH 3.0 only 15% Ni, 10% Zn, 5% Cu and 0.5% Co were leached; while at pH 2, 53% Ni was bioleached after 230 days. Based on an optimization between the leaching of metals, the acid consumption, the concentration of soluble iron and the dissolution of other gangue minerals, leaching at pH of 2.0 were recommended for this heap bioleaching application. The microbial composition as determined by a combination of Polymerase Chain Reaction (PCR)–Denaturing Gradient Gel Electrophoresis (DGGE)-sequencing approach was not significantly affected by pH. Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans were the dominant species in all the leach liquors. In addition, L. ferriphilum was detected for the first time in extracted leach residue liquor after 300 days of bioleaching. Sulfobacillus thermotolerans, A. caldus, A. thiooxidans and some unknown species were found to lesser extent. Archaeal species were also present in all leach liquors.

Risk Factors for and Outcomes Associated with Clinical Isolates of Escherichia coli and Klebsiella Species Resistant to Extended‐Spectrum Cephalosporins among Patients Admitted to Canadian Hospitals

Clinical features associated with Gram-negative bacterial isolates with extended-spectrum beta-lactamase (ESBL)- and AmpC-mediated resistance identified in Canadian hospitals is largely unknown. The objective of the present study was to determine the demographics, risk factors and outcomes of patients with ESBL- or AmpC-mediated resistant organisms in Canadian hospitals. Patients with clinical cultures of Escherichia coli or Klebsiella species were matched with patients with a similar organism but susceptible to third-generation cephalosporins. Molecular identification of the AmpC or ESBL was determined using a combination of polymerase chain reaction and sequence analysis. Univariate and multivariate logistic regression analysis was performed to identify variables associated with becoming a case. Eight Canadian hospitals identified 106 cases (ESBL/AmpC) and 106 controls. All risk factors identified in the univariate analysis as a predictor of being an ESBL/AmpC cases at the 0.20 P-value were included in the multivariate analysis. No significant differences in outcomes were observed (unfavourable responses 17% versus 15% and mortality rates 13% versus 7%, P not significant). Multivariate logistic regression found an association of becoming an ESBL/AmpC case with: previous admission to a nursing home (OR 8.28, P=0.01) or acute care facility (OR 1.96, P=0.03), length of stay before infection (OR 3.05, P=0.004), and previous use of first-generation cephalosporins (OR 2.38, P=0.02) or third-generation cephalosporins (OR 4.52, P=0.01). Appropriate antibiotics were more likely to be given to controls (27.0% versus 13.3%, P=0.05) and number of days to appropriate antibiotics was longer for cases (median 2.8 days versus 1.2 days, P=0.05). The importance of patient medical history, present admission and antibiotic use should be considered for all E coli or Klebsiella species patients pending susceptibility testing results.