A major zebrafish polymorphism resource for genetic mapping

645,088 candidate polymorphisms in zebrafish were identified and positioned on genetic and physical maps as a resource for positional cloning

Quantification of Alternative Splicing Variants of Human Telomerase Reverse Transcriptase and Correlations with Telomerase Activity in Lung Cancer

Telomerase plays important roles in the development and progression of malignant tumors, and its activity is primarily determined by transcriptional regulation of human telomerase reverse transcriptase (hTERT). Several mRNA alternative splicing variants (ASVs) for hTERT have been identified, but it remains unclear whether telomerase activity is directly associated with hTERT splicing transcripts. In this study, we developed novel real-time PCR protocols using molecular beacons and applied to lung carcinoma cell lines and cancerous tissues for quantification of telomerase activity and three essential hTERT deletion transcripts respectively. The results showed that lung carcinoma cell lines consistently demonstrated telomerase activity (14.22–31.43 TPG units per 100 cells) and various hTERT alternative splicing transcripts. For 165 lung cancer cases, telomerase activity showed significant correlation with tumor differentiation (poorly->moderately->well-differentiated, P<0.01) and with histotypes (combined small cell and squamous cell carcinoma>squamous cell carcinoma>adenosquamous carcinoma>adenocarcinoma, P<0.05). Although the overall hTERT transcripts were detected in all the samples, they were not associated with telomerase activity (r = 0.092, P = 0.24). Telomerase activity was significantly correlated with the transcriptional constituent ratio of α-deletion (r = -0.267, P = 0.026), β-deletion (r = -0.693, P = 0.0001) and γ-deletion (r = –0.614, P = 0.001). The positive rate and average constituent ratio of β-deletion transcripts (92.12%, 0.23) were higher than those of α-deletion (41.82%, 0.12) or γ-deletion (16.36%, 0.18) transcripts. The combined small-cell and squamous cell carcinomas expressed less deletion transcripts, especially β-deletion, than other histotypes, which might explain their higher telomerase activity. In conclusion, the molecular beacon-based real-time PCR protocols are rapid, sensitive and specific methods to quantify telomerase activity and hTERT ASVs. Telomerase activity may serve as a reliable and effective molecular marker to assist the evaluation of histological subtype and differentiation of lung carcinomas. Further studies on hTERT deletion splicing transcripts, rather than the overall hTERT transcripts, may improve our understanding of telomerase regulation

Apoptosis versus oncotic necrosis in hepatic ischemia/reperfusion injury

AbstractWarm and cold hepatic ischemia followed by reperfusion leads to necrotic cell death (oncosis), which often occurs within minutes of reperfusion. Recent studies also suggest a large component of apoptosis after ischemia/reperfusion. Here, we review the mechanisms underlying adenosine triphosphate depletion—dependent oncotic necrosis and caspase-dependent apoptosis, with emphasis on shared features and pathways. Although apoptosis causes internucleosomal DNA degradation that can be detected by terminal deoxynucleotidyl transferase—mediated deoxyuridine triphosphate nick-end labeling and related assays, DNA degradation also occurs after oncotic necrosis and leads to pervasive terminal deoxynucleotidyl transferase—mediated deoxyuridine triphosphate nick-end labeling staining far in excess of that for apoptosis. Similarly, although apoptosis can occur in a physiological setting without inflammation, in pathophysiological settings apoptosis frequently induces inflammation because of the onset of secondary necrosis and stimulation of cytokine and chemokine formation. In liver, the mitochondrial permeability transition represents a shared pathway that leads to both oncotic necrosis and apoptosis. When the mitochondrial permeability transition causes severe adenosine triphosphate depletion, plasma membrane failure and necrosis ensue. If adenosine triphosphate is preserved, at least in part, cytochrome c release after the mitochondrial permeability transition activates caspase-dependent apoptosis. Mitochondrial permeability transition-dependent cell death illustrates the concept of necrapoptosis, whereby common pathways lead to both necrosis and apoptosis. In conclusion, oncotic necrosis and apoptosis can share features and mechanisms, which sometimes makes discrimination between the 2 forms of cell death difficult. However, elucidation of critical cell death pathways under clinically relevant conditions will show potentially important therapeutic intervention strategies in hepatic ischemia/reperfusion injury

Assessment of Flow Rate as a Quality Control Test for Ceramic Pot Filters

The ceramic pot filter (CPF) is a low-cost household drinking water treatment system designed to provide potable water to families in developing countries. Among the indirect tests used for quality control the most common is the flow rate test, normally conducted with a T-piece tool. The target flow rate of a production sized CPF is 1 to 2 L/h, but the strength and type of relationship between flow rate and microbiological efficacy is not clear. The objective of this preliminary research was to understand how accurately current indirect testing procedures represent microbiological removal capacity. Fifteen experimental sized CPFs with different clay-burnout material ratios were made using methods and materials which mimicked CPF production at a filter factory in Guatemala. The experimental CPFs were tested to determine porosity, flow rate, and efficacy as measured by the logarithmic reduction value of total coliforms. Testing for the three parameters was repeated in Guatemala using six production sized filters from the local CPF factory. Collected data were studied to find relationships between the three parameters. Flow rates measured by the factory workers using the T-piece tool were compared with those determined in the factory laboratory. The results show that a linear or inverse relationship between efficacy and flow rate should be considered. The percent difference between flow rate measurements recorded using the T-piece tool and those conducted in the laboratory ranged from 1 to 45 percent. Further studies should be conducted with a larger sample of production sized CPFs to confirm the type of relationship and the commonly used range of 1 to 2 L/h