The Regulation and Function of Histone Methylation

Histones are wrapped around by genomic DNA to form nucleosomes which are the basic units of chromatin. In eukaryotes histones undergo various covalent modifications such as methylation, phosphorylation, acetylation, ubiquitination and ribosylation. Histone modifications play a fundamental role in the epigenetic regulation of gene expression in multicellular eukaryotes. Histone methylation is one of the most important modifications occurring on Lysine (K) and Arginine (R) residues of histones, dynamically regulated by histone methyltransferases and demethylases. Identifications of such histone modification enzymes and to study how they work are the most fundamental questions needs to be answered. Uncovering the regulation and functions of the various histone methylation enzymes will help us to better understand the epigenetic code. This review summarizes the regulation of histone methyltransferases activity, the recruitment of methyltransferases and the distribution patterns and function of histone methylations.     

Transformation of Curvularia lunata IM 2901 with pAN7-1 influences selected physiological properties of the fungus

Genetic analysis of Curvularia lunata IM 2901 transformants, previously obtained by electroporation with plasmid pAN7-1, was carried out. Isolates displayed several differences in hygromycin B resistance and their physiology. It was shown that plasmid pAN7-1 was integrated in different copy numbers and at different positions in the genome of the strains studied. Both the wild type and pAN7-1 isolates, when growing in liquid media, produced an extracellular emulsifying agent. The transformants differed in their growth kinetics, intensity of surfactant production and in the efficiency of cortexolone 11beta-hydroxylation, in comparison with the wild type. The micro-organisms varied in susceptibility to the lytic enzyme complex (Novozyme 234), which indicated the presence of differences in their cell wall composition and/or in architecture caused by an integrated plasmid pAN7-1.     

Cellulolytic enzymes on lignocellulosic substrates in solid state fermentation by <Emphasis Type="Italic">Aspergillus niger</Emphasis>

The production of cellulolytic enzymes by Aspergillus niger on lignocellulosic substrates groundnut fodder, wheat bran, rice bran and sawdust in solid state fermentation in a laboratory scale was compared. Czapek Dox liquid broth amended with cellulose (0.5%) was used to moisten lignocellulosic solid supports for cultivation of Aspergillus niger. The production of filter paperase, carboxymethyl cellulase and -glucosidase were monitored at daily intervals for 5 days. The peak production of the enzymes occurred within 3 days of incubation. Among solid supports used in the study, wheat bran was the best solid matrix followed by groundnut fodder in production of cellulolytic enzymes in solid state fermentation. Groundnut fodder supported significant production of FPase (2.09 FPU/g), CMCase (1.36 U/g) and -glucosidase activity (0.0117 U/g) in solid state fermentation. Considerable secretion of protein (5.10 mg/g) on groundnut fodder at peak time interval 1st day of incubation was recorded.     

Molecular Characterization of Microbial Population Dynamics during Sildenafil Citrate Degradation

Little is known about pharmaceutical and personal care products pollutants (PPCPs), but there is a growing interest in how they might impact the environment and microbial communities. The widespread use of Viagra (sildenafil citrate) has attracted great attention because of the high usage rate, the unpredictable disposal and the unknown potential effects on wildlife and the environment. Until now information regarding the impact of Viagra on microbial community in water environment has not been reported. In this research, for the first time, the genetic profile of the microbial community, developing in a Viagra polluted water environment, was evaluated by means of the 16S and 18S rRNA genes, for bacteria and fungi, respectively, amplified by polymerase chain reaction (PCR) and separated using the denaturing gradient gel electrophoresis (DGGE) technique. The DGGE results revealed a complex microbial community structure with most of the population persisting throughout the experimental period. DNA sequences from bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria and fungi found previously mainly in polluted environmental and treating bioreactors. Biotransformation ability of sildenafil citrate by the microbial pool was studied and the capability of these microorganisms to detoxify a polluted water ecosystem was assessed. The bacterial and fungal population was able to degrade sildenafil citrate entirely. Additionally, assays conducted on Daphnia magna, algal growth inhibition assay and cell viability determination on HepG2 human cells showed that biotransformation products obtained from the bacterial growth was not toxic. The higher removal efficiency for sildenafil citrate and the lack of toxicity by the biotransformation products obtained showed that the microbial community identified here represented a composite population that might have biotechnological relevance to retrieve sildenafil citrate contaminated sites.     

Vertical distribution of bacterial community structure in the sediments of two eutrophic lakes revealed by denaturing gradient gel electrophoresis (DGGE) and multivariate analysis techniques

Vertical distribution of bacterial community structure was investigated in the sediments of two eutrophic lakes of China, Lake Taihu and Lake Xuanwu. Profiles of bacterial communities were generated using a molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis, and the results were interpreted with multivariate statistical analysis. To assess changes in the genetic diversity of bacterial communities with changing depth, DGGE banding patterns were analysed by cluster analysis. Distinct clusters were recognized in different sampling stations of Lake Taihu. Canonical correspondence analysis (CCA) was carried out to infer the relationship between environmental variables and bacterial community structure. DGGE samples collected at the same sampling site clustered together in both lakes. Total phosphorus, organic matter and pH were considered to be the key factors driving the changes in bacterial community composition.     

Expression of a novel <Emphasis Type="Italic">OSPGYRP</Emphasis> (rice proline-, glycine- and tyrosine-rich protein) gene,which is involved in vesicle trafficking,enhanced cold tolerance in <Emphasis Type="Italic">E. coli</Emphasis>

A novel OSPGYRP gene encoding a rice proline-, glycine- and tyrosine-rich protein was isolated from cold-stress treated rice seedlings using suppression subtractive hybridization. Both amino acid sequence analysis and subcellular localization confirm that OsPGYRP is a novel protein involved in vesicle trafficking. The expression of the OSPGYRP gene was induced by cold, salt, and osmotic stress. In addition, expression of the OSPGYRP gene in E. coli increased the resistance to cold stress. These results show that OsPGYRP is a novel protein involved in vesicle trafficking and plays an important role in plant adaptation to stress. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Independence of stem and leaf hydraulic traits in six Euphorbiaceae tree species with contrasting leaf phenology

Hydraulic traits and hydraulic-related structural properties were examined in three deciduous (Hevea brasiliensis, Macaranga denticulate, and Bischofia javanica) and three evergreen (Drypetes indica, Aleurites moluccana, and Codiaeum variegatum) Euphorbiaceae tree species from a seasonally tropical forest in south-western China. Xylem water potential at 50% loss of stem hydraulic conductivity (P50_stem) was more negative in the evergreen tree, but leaf water potential at 50% loss of leaf hydraulic conductivity (P50_leaf) did not function as P50_stem did. Furthermore, P50_stem was more negative than P50_leaf in the evergreen tree; contrarily, this pattern was not observed in the deciduous tree. Leaf hydraulic conductivity overlapped considerably, but stem hydraulic conductivity diverged between the evergreen and deciduous tree. Correspondingly, structural properties of leaves overlapped substantially; however, structural properties of stem diverged markedly. Consequently, leaf and stem hydraulic traits were closely correlated with leaf and stem structural properties, respectively. Additionally, stem hydraulic efficiency was significantly correlated with stem hydraulic resistance to embolism; nevertheless, such a hydraulic pattern was not found in leaf hydraulics. Thus, these results suggest: (1) that the evergreen and deciduous tree mainly diverge in stem hydraulics, but not in leaf hydraulics, (2) that regardless of leaf or stem, their hydraulic traits result primarily from structural properties, and not from leaf phenology, (3) that leaves are more vulnerable to drought-induced embolism than stem in the evergreen tree, but not always in the deciduous tree and (4) that there exists a trade-off between hydraulic efficiency and safety for stem hydraulics, but not for leaf hydraulics.     

Subcellular localization of EGFR in esophageal carcinoma cell lines

Background: The EGF receptor is a therapeutic target in cancer cells, whereby mutations of EGFR and/or signalling members act as predictive markers. EGFR however also exhibits dynamic changes of subcellular localization, leading to STAT5 complex formation, nuclear translocation and induction of Aurora-A expression in squamous cancer cells. We previously described high EGFR and Aurora-A expression in esophageal cancer cells. Here, we investigated subcellular localization of EGFR and STAT5 in esophageal cancer cells. Results: Quantitative immunofluorescence analyses of four esophageal cancer cell lines reflecting esophageal squamous cell carcinomas (ESCC) and esophageal adenocarcinomas (EAC) revealed that the subcellular localization of EGFR was shifted from a membranous to cytoplasmic localization upon EGF-stimulation in OE21 (ESCC) cells. Thereby, EGFR in part co-localized with E-Cadherin. In parallel, phosphorylated STAT5-Tyr694 appeared to increase in the nucleus and to decrease at the cell membrane. In three additional cell lines, EGFR was only marginally (Kyse-410/ESCC; OE19/EAC) and weakly (OE33, EAC) detectable at the cell membrane. Partial co-localization of EGFR and E-Cadherin occurred in OE33 cells. Post EGF-stimulation, EGFR was detected in the cytoplasm, resembling endosomal compartments. Furthermore, OE19 and OE33 exhibited nuclear STAT5-Tyr694 phosphorylation upon EGF-stimulation. None of the four cell lines showed nuclear EGFR expression and localization. Conclusion: In contrast to other (squamous) cancer cells, activation of EGFR in esophageal squamous cancer cells does not result in nuclear translocation of EGFR. Still, the subcellular localization of EGFR may influence STAT5-associated signaling pathways in esophageal cancer cells and hence possibly also the responses to ErbB, respective EGFR-targeted therapies.     

Association of five SNPs with human hair colour in the Polish population

Twenty-two variants (single nucleotide polymorphisms – SNPs) of the genes involved in hair pigmentation (OCA2, HERC2, MC1R, SLC24A5, SLC45A2, TPCN2, TYR, TYRP1) were genotyped in a group of 186 Polish participants, representing a range of hair colours (45 red, 64 blond, 77 dark). A genotype-phenotype association analysis was performed.Using z-statistics we identified three variants highly associated with different hair colour categories (rs12913832:A>G in HERC2, rs1805007:T>C and rs1805008:C>T in MC1R). Two variants: rs1800401:C>T in OCA2 and rs16891982:C>G in SLC45A2 showed a high probability of a relation with hair colour, although that probability did not exceed the threshold of statistical significance after applying the Bonferroni correction. We created and validated mathematical logistic regression models in order to test the usefulness of the sets of polymorphisms for hair colour prediction in the Polish population. We subjected four models to stratified cross-validation. The first model consisted of three polymorphisms that proved to be important in the associative analysis. The second model included, apart from the mentioned polymorphisms, additionally rs16891982:C>G in SLC45A. The third model included, apart from the variants relevant in the associating analysis, rs1800401:C>T in OCA. The fourth model consisted of the set of polymorphisms from the first model supplemented with rs16891982:C>G in SLC45A and rs1800401:C>T in OCA. The validation of our models has shown that the inclusion of rs16891982:C>G in SLC45A and rs1800401:C>T in OCA increases the prediction of red hair in comparison with the algorithm including only rs12913832:A>G in HERC2, rs1805007:T>C and rs1805008:C>T in MC1R. The model consisting of all the five above-mentioned genetic variants has shown good prediction accuracies, expressed by the area under the curve (AUC) of the receiver operating characteristics: 0.84 for the red-haired, 0.82 for the dark-haired and 0.71 for the blond-haired.A genotype-phenotype association analysis brought results similar to those in other studies and confirmed the role of rs16891982:C>G, rs12913832:A>G, rs1805007:T>C and rs1805008:C>T in hair colour determination in the Polish population. Our study demonstrated for the first time the possibility of a share of the rs1800401:C>T SNP in the OCA2 gene in hair colour determination. Including this single nucleotide polymorphism in the actual hair colour predicting models would improve their predictive accuracy.