HPV16 E6 gene variations in invasive cervical squamous cell carcinoma and cancer in situ from Russian patients

HPV16 is frequently seen in invasive cervical cancer (ICC) and cervical intraepithelial neoplasia (CIN). Its E6 gene has frequent sequence variations. Although some E6 variants have been reported to have different biochemical or biological properties, they do not show geographical identity. Moreover, the definition of ‘variant’ has been a source of confusion because it has been based on all departures from the ‘prototype’ once isolated randomly from an ICC case. We amplified the HPV16 E6 gene by PCR from fresh-frozen tissue of 104 cases of ICC and CIN from Russian patients and sequenced it in positive cases. We found that 32 of 55 (58.2%) ICC cases and 18 of 49 (36.7%) CIN cases were HPV 16-positive and we could identify 3 groups of E6 variants: group A was characterized by G at nt 350 where group B had T, and group M was a heterogeneous mixture of unique E6 variants; no significant difference existed in the distribution of the different groups between ICC and CIN; the clinically malignant (as defined by FIGO stage) order between the groups was M > A > B in ICC; in the cases with a single HPV16 E6 sequence, coexisting ICC, CIN and normal epithelium in the same patient shared the E6 variant; and 4 cases of ICC had double/multiple E6 variants. The results did not show any importance of E6 variants for ICC progression in Russian women. The results also indicated that the original HPV16 variant persisted during ICC progression, and that at a low frequency, double infections and/or mutation of variants might occur. © 2001 Cancer Research Campaign http://www.bjcancer.co

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp

Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments

Antibody validation of immunohistochemistry for biomarker discovery: Recommendations of a consortium of academic and pharmaceutical based histopathology researchers

As biomarker discovery takes centre-stage, the role of immunohistochemistry within that process is increasing. At the same time, the number of antibodies being produced for ‘‘research use’’ continues to rise and it is important that antibodies to be used as biomarkers are validated for specificity and sensitivity before use. This guideline seeks to provide a stepwise approach for the validation of an antibody for immunohistochemical assays, reflecting the views of a consortium of academic and pharmaceutical based histopathology researchers. We propose that antibodies are placed into a tier system, level 1–3, based on evidence of their usage in immunohistochemistry, and that the degree of validation required is proportionate to their place on that tier

Crystal structure of Cu-Sn-In alloys around the {\eta} phase field studied by neutron diffraction

The study of the Cu-Sn-In ternary system has become of great importance in recent years, due to new environmental regulations forcing to eliminate the use of Pb in bonding technologies for electronic devices. A key relevant issue concerns the intermetallic phases which grow in the bonding zone and are determining in their quality and performance. In this work, we focus in the {\eta}-phase (Cu2In or Cu6Sn5) that exists in both end binaries and as a ternary phase. We present a neutron diffraction study of the constitution and crystallography of a series of alloys around the 60 at.% Cu composition, and with In contents ranging from 0 to 25 at.%, quenched from 300\degreeC. The alloys were characterized by scanning electron microscopy, probe microanalysis and high-resolution neutron diffraction. The Rietveld refinement of neutron diffraction data allowed to improve the currently available model for site occupancies in the hexagonal {\eta}-phase in the binary Cu-Sn as well as in ternary alloys. For the first time, structural data is reported in the ternary Cu-Sn-In {\eta}-phase as a function of composition, information that is of fundamental technological importance as well as valuable input data for ongoing modelisations of the ternary phase diagram.Comment: 8 pages, 10 figure