Characterization and classification of Turkish wines based on elemental composition

Commercial wines from 13 native and nonnative varieties in Turkey were analyzed for their elemental composition. Wines from four vintages (2006-2009) were analyzed by inductively coupled plasma with atomic emission spectrometry and mass spectroscopy (ICP-AES and ICP-MS) followed by multivariate statistics to study vintage, varietal, and regional differences. According to the partial least squares-discriminant analysis, wines from western regions could be discriminated with their higher Pb content. The red wines of two native grapes, Boǧazkere and Öküzgözü, were separated from the remaining varieties based on their high Ca and low B and Cu levels. Öküzgözü wines were different from Syrah and Cabernet Sauvignon wines. Similarly, native Emir wines showed differences from Muscat wines. The effective variables for discrimination analysis were natural minerals (Sr, Li, Al, Ba, and B) and minerals originating from agricultural activities, processing, or pollution (Ca, Cu, Mg, Co, Pb, and Ni). Characteristics of Turkish wines from native and nonnative grape varieties such as Cabernet Sauvignon, Merlot, Syrah, and Chardonnay were defined in terms of their mineral content for the first time.Scientific Research Project of Izmir Institute of Technology (IYTE-BAP-18-2008

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba <i>Dictyostelium discoideum</i>

Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.</p

Additional file 1: of Combinatorial identification of DNA methylation patterns over age in the human brain

The union of significant CpG sites (annotated) for all age cuts, showing 1 if a specific site is significant for a specific age. (XLSX 67 kb

Additional file 2: Figure S1. of Combinatorial identification of DNA methylation patterns over age in the human brain

Histogram of beta values after filtering for standard deviations across all samples. Figure S2. Histogram of the samples’ ages. Table S3. Top 5 rules classifying the ‘fetus’ class. Table S4. Top 5 rules classifying the ‘Age 0To4’ class. Table S5. Top 5 rules classifying the ‘Age 5To27’ class. Table S6. Top 5 rules classifying the ‘Age 28plus’ class. (DOCX 82 kb

Summarizing image showing the transformation from the motile trophozoite via encyzoite to the final cyst stage.

The trophozoite monitors the external environment and encystation is induced via intracellular pathways that remain largely unknown. The cell passes a “point of no return” during early encystation after which it is no longer possible to relapse to the proliferating stage. Transcription factors (e.g. Myb2) activates encystation-specific genes among them are cyst wall proteins (CWP1-3). An overall increase of translation could be observed early in encystation as the production of CWPs is dramatically increased and the transportation in encystation vesicles (ESVs) begins. The vesicles undergo maturation steps after leaving the ER. The other component of the cyst wall, the UDP-GalNAc sugar (giardin), is also synthesized and secreted via encystation positive carbohydrate vesicles (ECVs). The enzymes involved in giardin synthesis are induced during encystation. During late encystation, the cell changes shape as it enters dormancy and the ventral disc together with the flagella are disassembled as the construction of the cyst wall proceeds. But the mechanism behind the assembly is still unknown. Often pre-cyst stages with a “tail” can be observed in encystation. Two rounds of DNA replication occur without cytokinesis rendering a cyst with four nuclei each with the genome ploidy of 4N. Interconnections between the nuclei in the cysts are formed and genetic material can be exchanged through the process “diplomixis”. During excystation, each cell receives one pair of non-sister nuclei (indicated as red and blue).</p

Transcription of VSPs switch during differentiation.

<p>Non-clustering heatmap of the highest transcribed VSPs during differentiation reveal changes in VSP expression along the trajectory of encystation. Elevations in abundance of several VSP transcripts not expressed in the starting population are observed at the different time points. The VSP with the highest cumulative level of expression in the population throughout encystation was GL50803_113797 (bolded) also known as TSA 417.</p

Localizations of epitope tagged proteins of genes in consensus between transcriptional studies.

<p>Proteins tagged with HA or 3xHA (red) were visualized in conjunction with CWP1 (green) and DAPI stained DNA (blue) for trophozoites, 7 and 22 h post induction of encystation and cysts. (A) The hypothetical protein 10552-3xHA displayed an ER-like localization in a punctuate manner at both 7 and 22 h. (B) 12082-3xHA appears in vesicle like compartments in early encysting cells and ER like localization in late encysting cells. (C) 102813-3xHA is annotated as a Protein 21.1 and localizes to the nuclei in a proportion of the cells in the population, but not in cysts. (D) 103785-HA localizes to the ER and non-ESV, vesicle-like structures during encystation and in cysts. Scale bars represent 10 μm.</p