Bioinformatics Analysis of RNA-seq Data Reveals Genes Related to Cancer Stem Cells in Colorectal Cancerogenesis

Cancer stem cells (CSC) play one of the crucial roles in the pathogenesis of various cancers, including colorectal cancer (CRC). Although great efforts have been made regarding our understanding of the cancerogenesis of CRC, CSC involvement in CRC development is still poorly understood. Using bioinformatics and RNA-seq data of normal mucosa, colorectal adenoma, and carcinoma (n = 106) from GEO and TCGA, we identified candidate CSC genes and analyzed pathway enrichment analysis (PEI) and protein–protein interaction analysis (PPI). Identified CSC-related genes were validated using qPCR and tissue samples from 47 patients with adenoma, adenoma with early carcinoma, and carcinoma without and with lymph node metastasis and were compared to normal mucosa. Six CSC-related genes were identified: ANLN, CDK1, ECT2, PDGFD, TNC, and TNXB. ANLN, CDK1, ECT2, and TNC were differentially expressed between adenoma and adenoma with early carcinoma. TNC was differentially expressed in CRC without lymph node metastases whereas ANLN, CDK1, and PDGFD were differentially expressed in CRC with lymph node metastases compared to normal mucosa. ANLN and PDGFD were differentially expressed between carcinoma without and with lymph node metastasis. Our study identified and validated CSC-related genes that might be involved in early stages of CRC development (ANLN, CDK1, ECT2, TNC) and in development of metastasis (ANLN, PDGFD).     

Establishing a high-accuracy spectral response scale in the near infrared with digital filters

Spectrally invariant detectors are commonly used to interpolate or extrapolate the responsivity of InGaAs detectors in the infrared from absolute calibrations at a few wavelengths. The random noise in such detectors limits the accuracy that can be achieved in a narrowband, double-monochromator setup. We propose the application of a dedicated digital filter, which reduces the uncertainty by 30%, and combine it by calibrating a group of three detectors. The uncertainties are propagated from the observed variance in the relative measurement to the combined uncertainty of 0.4% (2sigma) in the responsivity values of the InGaAs detectors in the range of 1010-1640 nm.     

Investigation of bulk and solar cell properties of ingots cast from compensated solar grade silicon

In this work, the effect of the concurrent presence of B and P on bulk and solar cell properties of directionally solidified multicrystalline ingots from commercially compensated solar grade silicon (SoG‐Si) feedstock produced by Elkem Solar was investigated. The initial B and P content prior to the directional solidification experiment was 1260 and 762 ppba, respectively. Two reference ingots have been solidified in a silica crucible from 100% electronic grade silicon (EG‐Si) feedstock, with 332 ppba of boron added. All ingots have been cast under similar process parameters. The resistivity measurements by Four Point Probe (FPP) are in good agreement with the net dopant content, i.e., N_A − N_D for p‐type material, measured by Glow Discharge Mass Spectrometer (GDMS). Bulk lifetime measurements show a decrease in the values compared to the EG reference. Lifetime distributions show the highest values of 13 and 19 µs at approximately half ingot height, compared to 30 and 44 µs in the reference ingots. This decrease can be due to the concurrent effect of compensation and of other impurities present in the ingot. However, the content of several transition metals measured by GDMS at half ingot height was not significantly higher than that of the reference ingots. Oxygen content as measured by Fourier Transform Infra‐Red (FTIR) spectroscopy shows no significant difference compared to the references. Solar cells made from the compensated ingots and processed under standard process conditions show efficiency values up to 15.5% and fill factor values up to 78%, comparable to conventional multicrystalline silicon cells. Copyright © 2010 John Wiley & Sons, Ltd.     

A self‐calibrating led‐based solar test platform

A compact platform for testing solar cells is presented. The light source comprises a multi‐wavelength high‐power LED (light emitting diode) array allowing the homogenous illumination of small laboratory solar cell devices (substrate size 50 × 25 mm) within the 390–940 nm wavelength range. The spectrum can be synthesized by independent tuning of the 18 different wavelengths to mimic AM1.5G as well as various indoor lamp spectra. The intensity can be controlled with a 2¹⁴‐bit accuracy and intensities up to 3 suns are possible with an approximate AM1.5G spectral distribution. For several wavelengths intensities up to 10 suns is possible, and for a few wavelengths up to 30 suns can be reached. The setup is equipped with reference diodes and an optical fibre coupling enabling calibration, monitoring and control of the light impinging on the sample. Through a computer controlled interface, it is possible to perform all the commonly employed measurements on the solar cell at very high speed without moving the sample. In particular, the LED‐based illumination system provides an alternative to light‐biased incident photon‐to‐current efficiency measurement to be performed which we demonstrate. Both top and bottom contact is possible and the atmosphere can be controlled around the sample during measurements. The setup was developed for the field of polymer and organic solar cells with particular emphasis on enabling different laboratories to perform measurements in the same manner and obtain a common basis for comparing data. The use of the platform is demonstrated using a standard P3HT:PCBM polymer solar cell but is generally applicable to any solar cell technology with a spectral response in the 390–950 nm region. Copyright © 2010 John Wiley & Sons, Ltd.     

Formation of biogenic amines in herring and mackerel

The formation of biogenic amines (histamine, cadaverine, putrescine and spermidine) was followed during vacuum packed storage at 2 °C or 10 °C in the scombroid fish mackerel and in the non-scombroid fish herring. Also the changes in the content of free amino acids and in the organoleptic and microbiological qualities were followed.At 10 °C the amine contents were 2–20 times higher at the time of rejection as compared with samples stored at 2 °C. In herring and mackerel similar amounts of histamine were accumulated, whilst cadaverine was formed at much higher levels in mackerel compared with herring. The high contents of cadaverine in mackerel can possibly explain why mackerel and not herring are often implicated in incidents of scombortoxic poisoning.

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Bildung von biogenen Aminen im Hering

Zusammenfassung Die Bildung von biogenen Aminen (Histamin, Cadaverin, Putrescin und Spermidin) wurde während der Lagerung bei 2 °C oder 10 °C, vacuumverpackt, in Makrelen und Hering verfolgt, ebenso die Veränderungen im Gehalt an freien Aminosäuren und der sensorischen bzw. mikrobiologischen Eigenschaften.Bei 10 °C war der Amingehalt 2- bis 20mal höher als bei den Proben bei 2 °C. Beim Hering und der Makrele haben sich die Histaminmengen gleichermaßen angehäuft, wahrend sich Cadaverin in der Makrele viel starker gebildet hatte als im Hering. Der hohe Gehalt an Cadaverin in der Makrele kann möglicherwerise erklären, warum Makrelen und nicht die Heringe an Vergiftungen beitragen.

     

Projecting demand and supply of forest biomass for heating in Norway

This paper assesses the increase in demand and supply for forest biomass for heating in Norway in 2020. By then there is a political aim to double the national production of bioenergy from the level in 2008. The competitiveness of woody biomass in central and district heating is analyzed in a model selecting the least-cost heating technology and scale in municipalities given a set of constraints and under different fuels price scenarios. The supply of forest biomass from roundwood is estimated based on data of forest inventories combined with elasticities regarding price and standing volumes. The supply of biomass from harvesting residues is estimated in an engineering approach based on data from the national forest inventories and roundwood harvest. The results show how the production of bioenergy is affected by changes in energy prices and support schemes for bioenergy. One conclusion from the analyses is that the government target of 14 TWh more bioenergy by 2020 is not likely to be met by current technologies and policy incentives. The contribution of the analysis is the detailed presentation of the heat market potentials and technology choices combined with supply functions for both roundwood and harvesting residues.     

Cu exposure under field conditions coselects for antibiotic resistance as determined by a novel cultivation-independent bacterial community tolerance assay

Environmental reservoirs of antibiotic resistance are important to human health, and recent evidence indicates that terrestrial resistance reservoirs have expanded during the antibiotic era. Our aim was to study the impact of Cu pollution as a selective driver for the spread of antibiotic resistance in soil. Bacteria were extracted from a well-characterized soil site solely contaminated with CuSO? more than 80 years ago and from a corresponding control soil. Pollution-induced bacterial community tolerance (PICT) to Cu and a panel of antibiotics was determined by a novel cultivation-independent approach based on [3H]bromodeoxyuridine (BrdU) incorporation into DNA and by resistance profiling of soil bacterial isolates on solid media. High Cu exposure selected for Cu-tolerant bacterial communities but also coselected for increased community-level tolerance to tetracycline and vancomycin. Cu-resistant isolates showed significantly higher incidence of resistance to five out of seven tested antibiotics (tetracycline, olaquindox, nalidixic acid, chloramphenicol, and ampicillin) than Cu-sensitive isolates. Our BrdU-PICT data demonstrate for the first time that soil Cu exposure coselects for resistance to clinically important antibiotics (e.g., vancomycin) at the bacterial community-level. Our study further indicates that Cu exposure provides a strong selection pressure for the expansion of the soil bacterial resistome.