Next-Generation Sequencing-Based HPV Genotyping Assay Validated in Formalin-Fixed,Paraffin-Embedded Oropharyngeal and Cervical Cancer Specimens

Available clinical human papilloma virus (HPV) diagnostics for head and neck cancer have limited sensitivity and/or fail to define the HPV genotype. Common HPV genotyping assays are costly and labor intensive. We sought to develop a next-generation sequencing (NGS)-based HPV genotyping assay that was sensitive enough to work on formalin-fixed paraffin-embedded (FFPE) samples. We developed an ion torrent NGS HPV genotyping assay using barcoded HPV PCR broad-spectrum general primers 5⁺/6⁺ (BSGP)5⁺/6⁺. To validate genotype specificity and use in archived clinical FFPE tumor samples, we compared NGS HPV genotyping at 2 sequencing centers with typing by Roche Linear Array assay in 42 oropharyngeal and cervical cancer specimens representing 10 HPV genotypes, as well as HPV-negative cases. To demonstrate the detection of a broad range of HPV genotypes, we genotyped a cohort of 266 cervical cancers. A comparison of NGS genotyping of FFPE cancer specimens with genotyping by Linear Array showed concordant results in 34/37 samples (92%) at sequencing site 1 and 39/42 samples (93%) at sequencing site 2. Concordance between sites was 92%. Designed for use with 10 ng genomic DNA, the assay detected HPV using as little as 1.25 ng FFPE-derived genomic DNA. In 266 cervical cancer specimens, the NGS assay identified 20 different HPV genotypes, including all 13 carcinogenic genotypes. This novel NGS assay provides a sensitive and specific high-throughput method to detect and genotype HPV in a range of clinical specimens derived from FFPE with low per-sample cost.     

Alkylpyrazines: alarm pheromone components of the little fire ant, Wasmannia auropunctata (Roger) (Hymenoptera, Formicidae)

The previous identification of 2,5-dimethyl-3-(3-methylbutyl)pyrazine as the mandibular alarm pheromone of the little fire ant Wasmannia auropunctata (Roger), has been found to be incorrect. Gas chromatography–mass spectrometry (GC/MS) of ant extracts suggested the correct structure to be the regioisomer 2,5-dimethyl-3-(2-methylbutyl)pyrazine, which was confirmed by comparison with the synthetic pyrazine. GC/MS analysis also revealed the presence of an additional disubstituted alkylpyrazine which was identified as 3-methyl-2-(2-methylbutyl)pyrazine. Headspace sampling of confined ants with SPME and Porapak Q followed by GC/MS analysis showed 2,5-dimethyl-3-(2-methylbutyl)pyrazine as the major volatile released by W. auropunctata workers while 3-methyl-2-(2-methylbutyl)pyrazine was only detected in trace amounts. In laboratory bioassays, W. auropunctata workers were attracted and arrested by both pyrazines, although the results were not always consistent. Synthetic pyrazines generally attracted as many W. auropunctata workers as were attracted to a single crushed ant. However, higher numbers of W. auropunctata were arrested by crushed ant treatments than by synthetic pyrazines in all bioassays but one.     

Interaction between left and right intercostal muscles in airway pressure generation.

The interactions between the different rib cage inspiratory muscles in the generation of pleural pressure remain largely unknown. In the present study, we have assessed in dogs the interactions between the parasternal intercostals and the interosseous intercostals situated on the right and left sides of the sternum. For each set of muscles, the changes in airway opening pressure (DeltaPao) obtained during separate right and left activation were added, and the calculated values (predicted DeltaPao) were then compared with the DeltaPao values obtained during symmetric, bilateral activation (measured DeltaPao). When the parasternal intercostals in one or two interspaces were activated, the measured DeltaPao was commonly greater than the predicted value. The difference, however, was only 10%. When the interosseous intercostals were activated, the measured DeltaPao was nearly equal to the predicted value. These observations strengthen our previous conclusion that the pressure changes produced by the rib cage inspiratory muscles are essentially additive. As a corollary, the rib cage can be considered as a linear elastic structure over a wide range of distortion.     

Mechanical arrangement of the parasternal intercostals in the different interspaces

When the parasternal intercostal in a single interspace is selectively denervated in dogs with diaphragmatic paralysis, it continues to shorten during both quiet and occluded inspiration. In the present studies, we have tested the hypothesis that this passive parasternal inspiratory shortening is due to the action of the other parasternal intercostals. Changes in length of the denervated third right parasternal were measured in eight supine phrenicotomized animals. We found that 1) the inspiratory muscle shortening increased after denervation of the third left parasternal but gradually decreased with denervation of the parasternals situated in the second, fourth, and fifth interspaces; 2) the muscle, however, always continued to shorten during inspiration, even after denervation of all the parasternals; 3) stimulating selectively the third left parasternal caused a muscle lengthening; and 4) bilateral stimulation of the parasternals in the second or the fourth interspace produced a muscle shortening. We conclude that 1) the two parasternals situated in the same interspace on both sides of the sternum are mechanically arranged in series, whereas the parasternals located in adjacent interspaces are mechanically arranged in parallel; and 2) if a denervated parasternal continues to shorten during inspiration, this is in part because of the action of the parasternals in the adjacent interspaces and in part because of other inspiratory muscles of the rib cage, possibly the external intercostals and the levator costae.     

Respiratory and postural changes in intercostal muscle length in supine dogs

In an attempt to assess the physiological function(s) of the external (E) and internal interosseous (I) intercostal muscles, we measured the changes in intercostal muscle length during spontaneous breathing, during passive inflation, and during passive rotation of the trunk. Studies were performed on 46 muscles from 16 supine anesthetized dogs, and changes in muscle length were assessed by sonomicrometry. The changes were small during spontaneous breathing, whether before or after bilateral phrenicotomy, and the pattern was variable among animals and among interspaces. The E, however, particularly in the lower interspaces, often lengthened with inspiration, and the I, in particular in the upper interspaces, often shortened with inspiration. Only occasionally did the E and I in one interspace change in length in opposing directions. This was also true during passive inflation, where both E and I usually shortened in the upper interspaces and lengthened in the lower interspaces. By contrast, during passive rotation of the trunk, the E and I systematically changed in length in opposing directions, and either muscle could successively lengthen and shorten a substantial amount depending on the side of rotation. These results suggest that 1) the E and I in supine dogs do not behave as antagonistic muscles during moderate respiratory efforts; and 2) they do behave as antagonistic muscles during rotation of the trunk. A primary function of these muscles as rotators of the trunk, unlike breathing, may explain why two layers of intercostal muscles with different fiber orientation exist between the ribs.     

Cytotherapy with naive rat umbilical cord matrix stem cells significantly attenuates growth of murine pancreatic cancer cells and increases survival in syngeneic mice

Background aimsPancreatic cancer, sometimes called a ‘silent killer’, is one of the most aggressive human malignancies, with a very poor prognosis. It is the fourth leading cause of cancer-related morbidity and mortality in the USA.MethodsA mouse peritoneal model was used to test the ability of unengineered rat umbilical cord matrix-derived stem cells (UCMSC) to control growth of pancreatic cancer. In vivo results were supported by various in vitro assays, such as 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), direct cell count, [³H]thymidine uptake and soft agar colony assays.ResultsCo-culture of rat UCMSC with PAN02 murine pancreatic carcinoma cells (UCMSC:PAN02, 1:6 and 1:3) caused G0/G1 arrest and significantly attenuated the proliferation of PAN02 tumor cells, as monitored by MTT assay, direct cell counts and [³H]thymidine uptake assay. Rat UCMSC also significantly reduced PAN02 colony size and number, as measured by soft agar colony assay. The in vivo mouse studies showed that rat UCMSC treatment significantly decreased the peritoneal PAN02 tumor burden 3 weeks after tumor transplantation and increased mouse survival time. Histologic study revealed that intraperitoneally administered rat UCMSC survived for at least 3 weeks, and the majority were found near or inside the tumor.ConclusionsThese results indicate that naive rat UCMSC alone remarkably attenuate the growth of pancreatic carcinoma cells in vitro and in a mouse peritoneal model. This implies that UCMSC could be a potential tool for targeted cytotherapy for pancreatic cancer.     

Long-term exposure to elevated zinc concentrations induced structural changes and zinc tolerance of the nitrifying community in soil

A series of long-term Zn-contaminated soils was sampled around a galvanized pylon. The potential nitrification rate (PNR) was unaffected by the soil total Zn concentrations up to 25 mmol Zn kg(-1) whereas spiking the uncontaminated control soil with ZnCl(2) to identical total concentrations completely eliminated nitrification. The larger sensitivity of the PNR to spiked ZnCl(2) than to the Zn added in the field was equally found when relating the PNR to the Zn concentrations in the pore water of these soils, suggesting differences in Zn tolerance of the nitrifying communities. Zinc tolerance in the long-term Zn-contaminated soil was demonstrated by showing that (i) the nitrifying community of long-term Zn-contaminated soil samples was less sensitive to Zn than that of the uncontaminated control soil when both communities were inoculated in sterile ZnCl(2)-contaminated soil samples, and, that (ii) addition of ZnCl(2) to the long-term Zn-contaminated soil samples affected nitrification less than equal additions of ZnCl(2) to uncontaminated control samples. Denaturing gradient gel electrophoresis fingerprinting of polymerase chain reaction amplified 16SrRNA gene fragments of ammonia-oxidizing bacteria showed that the community structure in uncontaminated and long-term contaminated soil samples was different and could be related to soil Zn concentrations.     

The effect of lung inflation on the inspiratory action of the canine parasternal intercostals.

Inflation induces a marked decrease in the lung-expanding ability of the diaphragm, but its effect on the parasternal intercostal muscles is uncertain. To assess this effect, the phrenic nerves and the external intercostals were severed in anesthetized, vagotomized dogs, such that the parasternal intercostals were the only muscles active during inspiration, and the endotracheal tube was occluded at different lung volumes. Although the inspiratory electromyographic activity recorded from the muscles was constant, the change in airway opening pressure decreased with inflation from -7.2+/-0.6 cmH2O at functional residual capacity to -2.2+/-0.2 cmH2O at 20-cmH2O transrespiratory pressure (P<0.001). The inspiratory cranial displacement of the ribs remained virtually unchanged, and the inspiratory caudal displacement of the sternum decreased moderately. However, the inspiratory outward rib displacement decreased markedly and continuously; at 20 cmH2O, this displacement was only 23+/-2% of the value at functional residual capacity. Calculations based on this alteration yielded substantial decreases in the change in airway opening pressure. It is concluded that, in the dog, 1) inflation affects adversely the lung-expanding actions of both the parasternal intercostals and the diaphragm; and 2) the adverse effect of inflation on the parasternal intercostals is primarily related to the alteration in the kinematics of the ribs. As a corollary, it is likely that hyperinflation also has a negative impact on the parasternal intercostals in patients with chronic obstructive pulmonary disease.     

Genetic Variants in Nuclear-Encoded Mitochondrial Genes Influence AIDS Progression

Background

The human mitochondrial genome includes only 13 coding genes while nuclear-encoded genes account for 99% of proteins responsible for mitochondrial morphology, redox regulation, and energetics. Mitochondrial pathogenesis occurs in HIV patients and genetically, mitochondrial DNA haplogroups with presumed functional differences have been associated with differential AIDS progression.

Methodology/Principal Findings

Here we explore whether single nucleotide polymorphisms (SNPs) within 904 of the estimated 1,500 genes that specify nuclear-encoded mitochondrial proteins (NEMPs) influence AIDS progression among HIV-1 infected patients. We examined NEMPs for association with the rate of AIDS progression using genotypes generated by an Affymetrix 6.0 genotyping array of 1,455 European American patients from five US AIDS cohorts. Successfully genotyped SNPs gave 50% or better haplotype coverage for 679 of known NEMP genes. With a Bonferroni adjustment for the number of genes and tests examined, multiple SNPs within two NEMP genes showed significant association with AIDS progression: acyl-CoA synthetase medium-chain family member 4 (ACSM4) on chromosome 12 and peroxisomal D3,D2-enoyl-CoA isomerase (PECI) on chromosome 6.

Conclusions

Our previous studies on mitochondrial DNA showed that European haplogroups with presumed functional differences were associated with AIDS progression and HAART mediated adverse events. The modest influences of nuclear-encoded mitochondrial genes found in the current study add support to the idea that mitochondrial function plays a role in AIDS pathogenesis.