A Polymerase-chain-reaction Assay for the Specific Identification of Transcripts Encoded by Individual Carcinoembryonic Antigen (CEA)-gene-family Members

Carcinoembryonic antigen (CEA) is a tumor marker that belongs to a family of closely related molecules with variable expression patterns. We have developed sets of oligonucleotide primers for the specific amplification of transcripts from individual CEA-family members using the reverse transcriptase/ polymerase chain reaction (RT/PCR). Specific primer sets were designed for CEA, non-specific cross-reacting antigen (NCA), biliary glycoprotein (BGP), carcinoembryonic antigen gene-family members 1, 6 and 7 (CGMI, CGM6 and CGM7), and one set for all pregnancy-specific glycoprotein (PSG) transcripts. Primers were first tested for their specificity against individual cDNA clones and product-hybridization with internal, transcript-specific oligonucleotides. Total RNA from 12 brain and 63 gynecological tumors were then tested for expression of CEA-related transcripts. None were found in tumors located in the brain, including various mesenchymal and neuro-epithelial tumors. CEA and NCA transcripts were, however, present in an adenocarcinoma located in the nasal sinuses. In ovarian mucinous adenocarcinomas, we always found co-expression of CEA and NCA transcripts, and occasionally BGP mRNA. CEA-related transcripts were also found in some serous, endometrioid and clear-cell ovarian carcinomas. CEA, NCA and BGP transcripts were present in endometrial carcinomas of the uterus and cervical carcinomas, whereas uterine leiomyomas were completely negative. No transcripts were found from CGM 1, CGM6, CGM7 or from PSG genes in any of the tumors tested. The PCR data were compared with immunohistochemical investigations of ovarian tumors at the protein level using CEA (26/3/13)-, NCA-50/90 (9A6FR) and NCA-95 (80H3)-specific monoclonal antibodies

HIV-1 Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection

Nucleoside analogs (NAs) are used to treat numerous viral infections and cancer. They compete with endogenous nucleotides (dNTP/NTP) for incorporation into nascent DNA/RNA and inhibit replication by preventing subsequent primer extension. To date, an integrated mathematical model that could allow the analysis of their mechanism of action, of the various resistance mechanisms, and their effect on viral fitness is still lacking. We present the first mechanistic mathematical model of polymerase inhibition by NAs that takes into account the reversibility of polymerase inhibition. Analytical solutions for the model point out the cellular- and kinetic aspects of inhibition. Our model correctly predicts for HIV-1 that resistance against nucleoside analog reverse transcriptase inhibitors (NRTIs) can be conferred by decreasing their incorporation rate, increasing their excision rate, or decreasing their affinity for the polymerase enzyme. For all analyzed NRTIs and their combinations, model-predicted macroscopic parameters (efficacy, fitness and toxicity) were consistent with observations. NRTI efficacy was found to greatly vary between distinct target cells. Surprisingly, target cells with low dNTP/NTP levels may not confer hyper-susceptibility to inhibition, whereas cells with high dNTP/NTP contents are likely to confer natural resistance. Our model also allows quantification of the selective advantage of mutations by integrating their effects on viral fitness and drug susceptibility. For zidovudine triphosphate (AZT-TP), we predict that this selective advantage, as well as the minimal concentration required to select thymidine-associated mutations (TAMs) are highly cell-dependent. The developed model allows studying various resistance mechanisms, inherent fitness effects, selection forces and epistasis based on microscopic kinetic data. It can readily be embedded in extended models of the complete HIV-1 reverse transcription process, or analogous processes in other viruses and help to guide drug development and improve our understanding of the mechanisms of resistance development during treatment

Modelling the contribution of biogenic volatile organic compounds to new particle formation in the Julich plant atmosphere chamber

We used the Aerosol Dynamics gas- and particle-phase chemistry model for laboratory CHAMber studies (ADCHAM) to simulate the contribution of BVOC plant emissions to the observed new particle formation during photooxidation experiments performed in the Julich Plant-Atmosphere Chamber and to evaluate how well smog chamber experiments can mimic the atmospheric conditions during new particle formation events. ADCHAM couples the detailed gas-phase chemistry from Master Chemical Mechanism with a novel aerosol dynamics and particle phase chemistry module. Our model simulations reveal that the observed particle growth may have either been controlled by the formation rate of semi- and low-volatility organic compounds in the gas phase or by acid catalysed heterogeneous reactions between semi-volatility organic compounds in the particle surface layer (e.g. peroxyhemiacetal dimer formation). The contribution of extremely low-volatility organic gas-phase compounds to the particle formation and growth was suppressed because of their rapid and irreversible wall losses, which decreased their contribution to the nano-CN formation and growth compared to the atmospheric situation. The best agreement between the modelled and measured total particle number concentration (R-2 > 0.95) was achieved if the nano-CN was formed by kinetic nucleation involving both sulphuric acid and organic compounds formed from OH oxidation of BVOCs.Peer reviewe

Prototype ATLAS IBL Modules using the FE-I4A Front-End Readout Chip

The ATLAS Collaboration will upgrade its semiconductor pixel tracking detector with a new Insertable B-layer (IBL) between the existing pixel detector and the vacuum pipe of the Large Hadron Collider. The extreme operating conditions at this location have necessitated the development of new radiation hard pixel sensor technologies and a new front-end readout chip, called the FE-I4. Planar pixel sensors and 3D pixel sensors have been investigated to equip this new pixel layer, and prototype modules using the FE-I4A have been fabricated and characterized using 120 GeV pions at the CERN SPS and 4 GeV positrons at DESY, before and after module irradiation. Beam test results are presented, including charge collection efficiency, tracking efficiency and charge sharing.Comment: 45 pages, 30 figures, submitted to JINS

Clear cell chondrosarcoma of the head and neck

Clear cell chondrosarcoma is a rare variant of chondrosarcoma that mostly involves the end of long bones. However, nine cases have been reported in the head and neck: four in larynx, two in nasal septum, two in maxilla and one in the skull. These cases form the basis of this review. Head and neck cases accounts for less than 5% of Clear cell chondrosarcomas in the whole body and the larynx is the most common place. The histological findings of head and neck cases are consistent with general features of this entity in the whole body and nearly all tumors in this case series had a component of conventional chondrosarcoma. Clear cell chondrosarcoma is an intracompartmental tumor and retains "Grenz zone" just beneath the epithelium. Therefore, the overlying mucosa remained intact in all laryngeal cases. Nasal tumor caused ballooning of the septum and the maxillary lesion did not involve the oral mucosa. This tumor presents various radiographic features in the head and neck area. Chondroblastoma, chondroma, osteoblastoma, osteosarcoma and metastatic renal cell carcinoma are included in the histologic differential diagnoses. Differentiation from chondroblastic osteosarcoma is important in the maxilla. A wide resection is adequate in most cases. However, some laryngeal cases show tendency to recur. Clear cell chondrosarcoma is a slow growing tumor and this necessitates a long time follow-up of patients. Due to the extreme rarity in the head and neck, diagnosis of Clear cell chondrosarcoma in this area, must be confirmed by histochemical and immunohistochemical studies

The IceCube Neutrino Observatory: Instrumentation and Online Systems

The IceCube Neutrino Observatory is a cubic-kilometer-scale high-energy neutrino detector built into the ice at the South Pole. Construction of IceCube, the largest neutrino detector built to date, was completed in 2011 and enabled the discovery of high-energy astrophysical neutrinos. We describe here the design, production, and calibration of the IceCube digital optical module (DOM), the cable systems, computing hardware, and our methodology for drilling and deployment. We also describe the online triggering and data filtering systems that select candidate neutrino and cosmic ray events for analysis. Due to a rigorous pre-deployment protocol, 98.4% of the DOMs in the deep ice are operating and collecting data. IceCube routinely achieves a detector uptime of 99% by emphasizing software stability and monitoring. Detector operations have been stable since construction was completed, and the detector is expected to operate at least until the end of the next decade.Comment: 83 pages, 50 figures; updated with minor changes from journal review and proofin

Decreased expression of 17β-hydroxysteroid dehydrogenase type 1 is associated with DNA hypermethylation in colorectal cancer located in the proximal colon

<p>Abstract</p> <p>Background</p> <p>The importance of 17β-estradiol (E2) in the prevention of large bowel tumorigenesis has been shown in many epidemiological studies. Extragonadal E2 may form by the aromatase pathway from androstenedione or the sulfatase pathway from estrone (E1) sulfate followed by E1 reduction to E2 by 17-β-hydroxysteroid dehydrogenase (HSD17B1), so <it>HSD17B1 </it>gene expression may play an important role in the production of E2 in peripheral tissue, including the colon.</p> <p>Methods</p> <p><it>HSD17B1 </it>expression was analyzed in colorectal cancer cell lines (HT29, SW707) and primary colonic adenocarcinoma tissues collected from fifty two patients who underwent radical colon surgical resection. Histopathologically unchanged colonic mucosa located at least 10-20 cm away from the cancerous lesions was obtained from the same patients. Expression level of <it>HSD17B1 </it>using quantitative PCR and western blot were evaluated. DNA methylation level in the 5' flanking region of <it>HSD17B1 </it>CpG rich region was assessed using bisulfite DNA sequencing and HRM analysis. The influence of DNA methylation on HSD17B1 expression was further evaluated by ChIP analysis in HT29 and SW707 cell lines. The conversion of estrone (E1) in to E2 was determined by electrochemiluminescence method.</p> <p>Results</p> <p>We found a significant decrease in HSD17B1 transcript (<it>p </it>= 0.0016) and protein (<it>p </it>= 0.0028) levels in colorectal cancer (CRC) from the proximal but not distal colon and rectum. This reduced <it>HSD17B1 </it>expression was associated with significantly increased DNA methylation (<it>p </it>= 0.003) in the CpG rich region located in the 5' flanking sequence of the <it>HSD17B1 </it>gene in CRC in the proximal but not distal colon and rectum. We also showed that 5-dAzaC induced demethylation of the 5' flanking region of <it>HSD17B1</it>, leading to increased occupation of the promoter by Polymerase II, and increased transcript and protein levels in HT29 and SW707 CRC cells, which contributed to the increase in E2 formation.</p> <p>Conclusions</p> <p>Our results showed that reduced <it>HSD17B1 </it>expression can be associated with DNA methylation in the 5' flanking region of <it>HSD17B1 </it>in CRC from the proximal colon.</p

Prognostic value of p27(Kip1 )expression in Basaloid Squamous Cell Carcinoma of the larynx

BACKGROUND: Very few reports have investigated the role of cell cycle regulators as biomarkers in Basaloid Squamous Cell Carcinoma (BSCC) of the larynx, a definite morphologic, uncommon, very aggressive variant of squamous cell carcinoma. Lower expression of Ki67/Mib-1, a proliferation marker highly expressed in the majority of tumours, and p53, a tumour suppressor protein that can induce an arrest of the G1-S transition, was related to a better prognosis in laryngeal BSCC. In the head and neck, p27(kip1), a member of the Cip1/Kip1 family of cyclin-dependent kinase inhibitors, has emerged as an independent prognostic factor, able to identify low-expressing tumours with unfavourable course. Up to date the role of this protein was never studied in BSCC. Aim of our study was to investigate the potential prognostic value of p27(kip1 )levels and their correlation with Ki67/Mib-1 and p53 expression in BSCC of the larynx. METHODS: The retrospective study group consisted of 15 male and 1 female patients, affected by laryngeal BSCC, ranging in age from 44 to 69 years (mean 58). The tumour originated from the supraglottis in thirtheen cases and from the glottis in the remaining three. Ten patients had metastatic cervical lymph nodes at presentation and were classified as N+. Post surgical stage was IV in four patients, III in nine, II in two cases and I in the remaining one. Follow-up ranged from a minimum of 5 months up to 9 years. Paraffin-embedded tissue sections of each laryngeal tumour were analyzed for p27(kip), Ki67/Mib-1 and p53 expression by immunohistochemistry. RESULTS: The immunohistochemical study showed p27(kip1 )expression in 40% of the patients with no evidence of disease (NED) and in none (0%) of the patients dead of disease (DOD), whilst p53 was expressed in 60% of patients in NED status and in 90% of patients in DOD status. Ki67/Mib-1 was positive in 80% of NED patients and in 100% of DOD patients. At multivariate analysis, performed by means of Discriminant analysis, low levels of p27(kip1 )expression significantly correlated with poor prognosis (P < 0.05). CONCLUSION: p27(kip1 )protein has been shown to be a significant independent prognostic factor in laryngeal SCC. In our series of laryngeal BSCC the resulting data seem to confirm the clinical prognostic relevance of p27(kip1 )low expression, which directly correlated with biological aggressiveness and consequent shortened survival

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

Atmospheric benzenoid emissions from plants rival those from fossil fuels

Despite the known biochemical production of a range of aromatic compounds by plants and the presence of benzenoids in floral scents, the emissions of only a few benzenoid compounds have been reported from the biosphere to the atmosphere. Here, using evidence from measurements at aircraft, ecosystem, tree, branch and leaf scales, with complementary isotopic labeling experiments, we show that vegetation (leaves, flowers, and phytoplankton) emits a wide variety of benzenoid compounds to the atmosphere at substantial rates. Controlled environment experiments show that plants are able to alter their metabolism to produce and release many benzenoids under stress conditions. The functions of these compounds remain unclear but may be related to chemical communication and protection against stress. We estimate the total global secondary organic aerosol potential from biogenic benzenoids to be similar to that from anthropogenic benzenoids (~10 Tg y-1), pointing to the importance of these natural emissions in atmospheric physics and chemistry