Electrical switch to the resonant magneto-phonon effect in graphene.

We report a comprehensive study of the tuning with electric fields of the resonant magneto-exciton optical phonon coupling in gated graphene. For magnetic fields around B ∼ 25 T that correspond to the range of the fundamental magneto-phonon resonance, the electron-phonon coupling can be switched on and off by tuning the position of the Fermi level in order to Pauli block the two fundamental inter-Landau level excitations. The effects of such a profound change in the electronic excitation spectrum are traced through investigations of the optical phonon response in polarization resolved magneto-Raman scattering experiments. We report on the observation of a splitting of the phonon feature with satellite peaks developing at particular values of the Landau level filling factor on the low or on the high energy side of the phonon, depending on the relative energy of the discrete electronic excitation and of the optical phonon. Shifts of the phonon energy as large as ±60 cm(-1) are observed close to the resonance. The intraband electronic excitation, the cyclotron resonance, is shown to play a relevant role in the observed spectral evolution of the phonon response.

Examination of internal metabolome and VOCs profile of brewery yeast and their mutants producing beer with improved aroma.

Volatile organic compounds (VOCs) are metabolites pivotal in determining the aroma of various products. A well-known VOC producer of industrial importance is Saccharomyces cerevisiae, partially responsible for flavor of beers and wines. We identified VOCs in beers produced by yeast strains characterized by improved aroma obtained in UV-induced mutagenesis. We observed significant increase in concentration of compounds in strains: 1214uv16 (2-phenylethyl acetate, 2- phenylethanol), 1214uv31 (2-ethyl henxan-1-ol), 1214uv33 (ethyl decanoate, caryophyllene). We observed decrease in production of 2-phenyethyl acetate in strain 1214uv33. Analysis of intracellular metabolites based on 1H NMR revealed that intracellular phenylalanine concentration was not changed in strains producing more phenylalanine related VOCs (1214uv16 and 1214uv33), so regulation of this pathway seems to be more sophisticated than is currently assumed. Metabolome analysis surprisingly showed the presence of 3-hydroxyisobutyrate, a product of valine degradation, which is considered to be absent in S. cerevisiae. Our results show that our knowledge of yeast metabolism including VOC production has gaps regarding synthesis pathways for individual metabolites and regulation mechanisms. Detailed analysis of 1214uv16 and 1214uv33 may enhance our knowledge of the regulatory mechanisms of VOC synthesis in yeast, and analysis of strain 1214uv31 may reveal the pathway of 2-ethyl henxan-1-ol biosynthesis.

Assessment of three epigenotypes in colorectal cancer by combined bisulfite restriction analysis.

Recent investigations have demonstrated the clear heterogeneity of sporadic colorectal cancer (CRC) with regard to CpG island methylation. Two unsupervised cluster analyses revealed that CRCs form three distinct DNA methylation subsets, which are referred to as the high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME, respectively). A recent study by Yagi et al. found a fairly sensitive and specific identification of HME, IME, and LME using two marker panels analyzed by MALDI-TOF mass spectrometry (MassARRAY). However, the expensive equipment required for this method substantially increases the cost and complexity of the assay. In this article, we demonstrate the assessment of HME, IME, and LME in a group of 233 sporadic CRCs using seven markers proposed by Yagi et al. The DNA methylation of each marker was quantified using combined bisulfite restriction analysis (COBRA) and analyzed along with various genetic factors associated with CRC [the BRAF and KRAS mutations, MLH1 methylation and microsatellite instability (MSI)]. The baseline methylation of each marker was generated from pooled DNA isolated from 50 normal colon tissues. We demonstrate that the correlation of HME, IME, and LME epigenotyped by COBRA using different molecular classifiers is similar to that achieved by MassARRAY. Therefore, epigenotyping CRCs using COBRA is a simple, specific, and cost-effective method that has the potential to be widely used in CRC research.

The C/A polymorphism in intron 11 of the XPC gene plays a crucial role in the modulation of an individual's susceptibility to sporadic colorectal cancer.

Epidemiological data show that colorectal cancer (CRC) is the second most frequent malignancy worldwide. The involvement of "minor impact genes" such as XME and DNA-repair genes in the etiology of sporadic cancer has been postulated by other authors. We focused on analyzing polymorphisms in DNA-repair genes in CRC. We considered the following genes involved in DNA-repair pathways: base excision repair (OGG1 Ser326Cys, XRCC1 Trp194Arg and Arg399Gln); nucleotide excision repair [XPA (-4)G/A, XPC C/A (i11) and A33512C (Lys939Gln), XPD Asp312Asn and A18911C (Lys751Gln), XPF Arg415Gln, XPG Asp1104His, ERCC1 C118T]; homologous recombination repair [NBS1 Glu185Gln, Rad51 135G/C, XRCC3 C18067 (Thr241Met)]. The study group consisted of 133 patients diagnosed with sporadic CRC, while the control group was composed of 100 age-matched non-cancer volunteers. Genotyping was performed by PCR and PCR-RFLP. Fisher's exact test with a Bonferroni correction for multiple testing was used. We found that: (i) XPC C/A (i11) heterozygous variant is associated with increased risk of CRC [OR is 2.07 (95% CI 1.1391, 3.7782) P=0.038], (ii) XPD A18911C (Lys751Gln) is associated with decreased risk of CRC [OR=0.4497, (95% CI 0.2215, 0.9131) P=0.031] for an individual with at least one A allele at this locus. (1) The XPC C/A (i11) genotype is associated with an increased risk of sporadic colorectal cancer. (2) The NER pathway has been highlighted in our study, as a most important in modulation of individual susceptibility to sCRC.

The Potential of Traditional Norwegian KVEIK Yeast for Brewing Novel Beer on the Example of Foreign Extra Stout.

The development of craft brewing has spurred huge interest in unusual and traditional technologies and ingredients allowing the production of beers that would fulfil consumers' growing demands. In this study, we evaluated the brewing performance of traditional Norwegian KVEIK yeast during the production of Foreign Extra Stout beer. The content of alcohol of the KVEIK-fermented beer was 5.11-5.58% v/v, the extract content was 5.05-6.66% w/w, and the pH value was 4.53-4.83. The KVEIK yeast was able to completely consume maltose and maltotriose. The mean concentration of glycerol in KVEIK-fermented beers was higher than in the control sample (1.51 g/L vs. 1.12 g/L, respectively). The use of KVEIK-type yeast can offer a viable method for increasing the concentration of phenolic compounds in beer and for boosting its antioxidative potential. The beers produced with KVEIK-type yeast had a total phenol content of 446.9-598.7 mg GAE/L, exhibited antioxidative potential of 0.63-1.08 mM TE/L in the DPPH• assay and 3.85-5.16 mM TE/L in the ABTS•+ assay, and showed a ferric ion reducing capacity (FRAP) of 3.54-4.14 mM TE/L. The KVEIK-fermented bears contained various levels of volatile compounds (lower or higher depending on the yeast strain) and especially of higher alcohols, such as 3-metylobutanol, 2-metylobutanol, and 1-propanol, or ethyl esters, such as ethyl acetate or decanoate, compared to the control beers. In addition, they featured a richer fruity aroma (apricot, dried fruit, apples) than the control beers fermented with a commercial US-05 strain.

The First Evidence of Cryptosporidium meleagridis Infection in a Colon Adenocarcinoma From an Immunocompetent Patient.

Objectives: The potential linkage between Cryptosporidium spp. infection and colorectal human cancer was suggested by limited reports showing higher prevalence of C. parvum and C. hominis in patients with colon cancer. Here we conducted research concerning presence of Cryptosporidium spp. in malignant tissue collected from patients with colorectal cancer. Methods: Cancerous colon tissue samples collected from 145 non-HIV infected patients with colorectal cancer were screened for Cryptosporidium spp. by immunofluorescence antibody test and genus-specific nested polymerase chain reaction followed by sequencing. Results: Screened pathogen was found in cancerous tissue originating from immunocompetent man with colon adenocarcinoma. Genotyping revealed presence of Cryptosporidium meleagridis. The presence of Cryptosporidium life cycle stages (oocysts and endogenous stages) in colon carcinoma tissue was confirmed by genus-specific FITC-labeling. Conclusions: Herein, we report on a C. meleagridis infection of a colon adenocarcinoma in an immunocompetent patient. This is the first report of C. meleagridis infection in the human colon and first evidence of active development of this species in cancer tissue.

Assessment of the FTO gene polymorphisms in male patients with metabolic syndrome.

BACKGROUND: Accumulating evidence indicates the potential involvement of the FTO gene polymorphisms in the etiology of metabolic syndrome (MetS) and related disorders. OBJECTIVES: In this study, we aimed to investigate whether the FTO gene polymorphisms are associated with the risk of MetS and its simple components in a homogeneous sample of males. MATERIAL AND METHODS: Anthropometric and biochemical parameters were assessed in 192 males. A total of 100 males met the National Cholesterol Education Program Adult Treatment Panel III (NCEP-ATPIII) criteria for a diagnosis of MetS. The following FTO gene polymorphisms were genotyped: rs1421085, rs17817449, rs1558902, and rs9939609. RESULTS: There were significant differences between participants with distinct rs9939609 genotypes with respect to waist-to-hip ratio (WHR) and the levels of total cholesterol. Individuals with the rs1421085 CC genotype had significantly higher levels of triglycerides compared to those with other corresponding genotypes. Participants with the rs1558902 AA genotype had significantly higher body mass index (BMI), WHR, as well as the levels of total cholesterol and triglycerides. There were no significant differences in genotype distribution allelic frequencies of all tested polymorphisms between individuals with MetS and control subjects. CONCLUSIONS: Our results indicate that the genetic variation in the FTO gene might be related to single metabolic disturbances. However, the FTO gene polymorphisms are not associated with the risk of MetS.

The Influence of Tumor Microenvironment on ATG4D Gene Expression in Colorectal Cancer Patients.

Despite great progress in research on the subject, the involvement of autophagy in colorectal cancer (CRC) pathogenesis (initiation, progression, metastasis) remains obscure and controversial. Autophagy is a catabolic process, fundamental to cell viability and connected with degradation/recycling of proteins and organelles. In this study, we aimed at investigating the relative expression level of mRNA via Real-Time PCR of 16 chosen genes belonging to Atg8 mammalian orthologs and their conjugation system, comprising GABARAP, GABARAPL1, GABARAPL2, MAP1LC3A, MAP1LC3B, MAP1LC3C, ATG3, ATG7, ATG10, ATG4A, ATG4B, ATG4C, ATG4D, and three genes encoding proteins building the multimeric ATG16L1 complex, namely ATG5, ATG12, and ATG16L1, in 73 colorectal tumors and paired adjacent normal colon mucosa. Our study demonstrated the relative downregulation of all examined genes in CRC tissues in comparison to adjacent noncancerous mucosa, with the highest rate of expression in both tumor and non-tumor tissues observed for GAPARBPL2 and the lowest for MAP1LC3C. Moreover, in patients with advanced-stage tumors and high values of regional lymph nodes, statistically significant downregulation of ATG4D expression in adjacent normal cells was observed. Our study confirms the role of autophagy genes as cancer suppressors in colorectal carcinogenesis. Furthermore, in regard to the ATG4D gene, we observed the influence of tumor microenvironments on gene expression in adjacent colon mucosa.

The BAX gene as a candidate for negative autophagy-related genes regulator on mRNA levels in colorectal cancer.

Autophagy is a catabolic process, which is involved in the maintenance of intracellular homeostasis by degrading redundant molecules and organelles. Autophagy begins with the formation of a double-membrane phagophore, followed by its enclosure, thus leading to the appearance of an autophagosome which fuses with lysosome. This process is highly conserved, precisely orchestrated and regulated by autophagy-related genes. Recently, autophagy has been widely studied in different types of cancers, including colorectal cancer. As it has been revealed, autophagy plays two opposite roles in tumorigenesis, as a tumor suppressor and a tumor enhancer/activator, and therefore is called a double-edge sword. Recently, interaction between autophagy and apoptosis has been found. Therefore, we aimed to study the mRNA levels of genes engaged in autophagy and apoptosis in colorectal cancer tissues. Colorectal cancer and adjacent healthy tissues were obtained from 73 patients diagnosed with primary colorectal cancer. Real-time PCR analysis employing Universal Probe Library was used to assess the expression of the seven following selected genes: BECN1, UVRAG, ULK1, ATG13, Bif-1, BCL2 and BAX. For all but one of the tested genes, a decrease in expression was observed. An increase in expression was observed for BAX. BAX expression decreases consistently from early to more advanced stages. High expression of BAX was strongly associated with negative UVRAG expression. The high expression of the BAX gene seems to be a negative regulator of autophagy in colorectal cancer cells. The relative downregulation of autophagy-related genes was observed in colorectal cancer samples.

Aberrant methylation of ERBB pathway genes in sporadic colorectal cancer.

The ErbB signalling network plays a crucial role in the growth and progression of several cancers, including colorectal cancer (CRC), and includes potentially drug-targetable genes. Oncogenic activation of the ErbB pathway by mutations and focal amplifications have emerged recently as an important predictive marker of the prognosis of CRC patients. However, in contrast to genetic events, little is known about epigenetic alternations of ErbB-associated genes and their impact on gene expression. Genome-wide methylation in sporadic CRCs (n = 12) paired with adjacent normal tissues have been previously analysed by Illumina Infinium HumanMethylation27 (HM27) at 27,578 CpG sites. For confirmation of our initial genome-wide analysis, we used a published HM27 dataset (GSE25062). Subsequently, CpG island methylation of selected ErbB pathway-associated genes was assessed on 233 CRC samples using methylation-sensitive polymerase chain reaction (MS-PCR) and analysed along with various genetic factors associated with CRC [epigenotype, BRAF and KRAS mutations, microsatellite instability (MSI)]. Methylation and expression integration was performed using published datasets including 25 pairs of CRC and normal colon tissues (GSE25062 and GSE25070), and confirmed with real-time PCR. Our previous microarray-based genome-wide DNA methylation analysis of 12 CRCs revealed that four ErbB-associated genes (PIK3CD, PKCΒ, ERBB4, ) were differentially methylated in CRCs. This was further confirmed by statistical re-analysis of an HM27 dataset (GSE25062). Frequent methylation at these loci in tumours was subsequently confirmed by MS-PCR (63%, 43%, 43% and 92%, respectively). Hypermethylation of PKCΒ associated with KRAS mutation (p = 0.04), whereas hypermethylation of ERBB4 associated with high-methylation epigenotypes (HME), BRAF mutation and MSI (p = 0.001, 0.002 and 0.0002, respectively). One of the four analysed genes (PKCΒ) was significantly downregulated in CRC tissue, as revealed by real-time PCR and re-analysis of the GSE25062 and GSE25070 datasets. After careful re-analysis of published methylation and expression data, we conclude that methylation of ERBB4, PAK7 and PIK3CD has no functional role in CRC carcinogenesis. In contrast, methylation seems to have a potential impact on the biology of colorectal tumours by negatively modulating the expression of PKCΒ. Importantly, the relationship between DNA methylation of PKCΒ and gene expression may warrant further attention in the context of colon cancer chemoprevention and anti-cancer therapy.

Global DNA methylation status in laryngeal cancer.

BACKGROUND: The purpose of our study was to evaluate if DNA methylation level in leukocytes may be used as a surrogate marker of genome methylation status in laryngeal cancer tissues. METHODS: We evaluated global DNA methylation using an ultra performance liquid chromatography (UPLC)-based method to assess the total content of 5-methylcytosine (5 mC). RESULTS: The study was performed on DNA isolated from cancer tissues, adjacent normal tissues, and peripheral blood leukocytes in a group of 72 patients with laryngeal cancer. DNA hypomethylation was found in tumor tissue (56%) and normal tissue (49%). There was a significant correlation between the levels of 5 mC in these 2 types of tissue. There was no significant DNA hypomethylation in blood. A negative correlation between tumor grade and blood levels of 5 mC was found. CONCLUSION: The level of leukocyte DNA methylation measured using total 5 mC content cannot be used as a surrogate marker for genome methylation status in laryngeal cancer tissues.

The Role of -786T/C Polymorphism in the Endothelial Nitric Oxide Synthase Gene in Males with Clinical and Biochemical Features of the Metabolic Syndrome.

Background. Extensive evidence, arising from models of endothelial nitric oxide synthase gene (NOS3)-knockout mice supports the role of endothelial malfunction in the pathogenesis of the metabolic syndrome (MS). Aims. The aim of this study was to evaluate the role of -786T/C polymorphism in the etiology of MS and assess previously reported interaction with cigarette smoking. Methods. Based on International Diabetes Federation 2005 criteria, we recruited randomly 152 subjects with MS and 75 subjects without MS. Results. Allelic and genotype frequencies did not differ significantly between both groups. Total cholesterol level (CHOLT) and intima-media thickness of carotid arteries were significantly higher in -786CC homozygotes, in comparison with -786TC and -786TT patients. Regarding current smoking status, -786C allele was associated with higher CHOLT than -786T allele. Conclusion. Our study indicates the putative role of -786T/C polymorphism in the development of hypercholesterolemia, in patients with MS, which might be enhanced by cigarette smoking.