Surface exposure dating of Holocene basalt flows and cinder cones in the Kula volcanic field (Western Turkey) using cosmogenic 3He and 10Be

The Kula volcanic field in Western Turkey comprises about 80 cinder cones and associated basaltic lava flows of Quaternary age. Based on geomorphological criteria and K-Ar dating, three eruption phases, beta 2-beta 4, were distinguished in previous studies. Human footprints in ash deposits document that the early inhabitants of Anatolia were affected by the volcanic eruptions, but the age of the footprints has been poorly constrained. Here we use He-3 and Be-10 exposure dating of olivine phenocrysts and quartz-bearing xenoliths to determine the age of the youngest lava flows and cinder cones. In the western part of the volcanic field, two basalt samples from a 15-km-long block lava flow yielded He-3 ages of 1.5 +/- 0.3 ka and 2.5 +/- 0.4 ka, respectively, with the latter being in good agreement with a Be-10 age of 2.4 +/- 0.3 ka for an augen gneiss xenolith from the same flow. A few kilometers farther north, a metasedimentary xenolith from the top of the cinder cone Cakallar Tepe gave a Be-10 age of 11.2 +/- 1.1 ka, which dates the last eruption of this cone and also the human footprints in the related ash deposits. In the center of the volcanic field, a basalt sample and a metasedimentary xenolith from another cinder cone gave consistent He-3 and Be-10 ages of 2.6 +/- 0.4 ka and 2.6 +/- 0.3 ka, respectively. Two beta 4 lava flows in the central and eastern part of the volcanic province yielded He-3 ages of 33 +/- 0.4 ka and 0.9 +/- 0.2 ka, respectively. Finally, a relatively well-preserved beta 3 flow gave a He-3 age of similar to 13 ka. Taken together, our results demonstrate that the penultimate eruption phase beta 3 in the Kula volcanic field continued until similar to 11 ka, whereas the youngest phase beta 4 started less than four thousand years ago and may continue in the future. (C) 2016 Elsevier B.V. All rights reserved

Identification of Candidate B-Lymphoma Genes by Cross-Species Gene Expression Profiling

<div><p>Comparative genome-wide expression profiling of malignant tumor counterparts across the human-mouse species barrier has a successful track record as a gene discovery tool in liver, breast, lung, prostate and other cancers, but has been largely neglected in studies on neoplasms of mature B-lymphocytes such as diffuse large B cell lymphoma (DLBCL) and Burkitt lymphoma (BL). We used global gene expression profiles of DLBCL-like tumors that arose spontaneously in <i>Myc</i>-transgenic C57BL/6 mice as a phylogenetically conserved filter for analyzing the human DLBCL transcriptome. The human and mouse lymphomas were found to have 60 concordantly deregulated genes in common, including 8 genes that Cox hazard regression analysis associated with overall survival in a published landmark dataset of DLBCL. Genetic network analysis of the 60 genes followed by biological validation studies indicate <i>FOXM1</i> as a candidate DLBCL and BL gene, supporting a number of studies contending that FOXM1 is a therapeutic target in mature B cell tumors. Our findings demonstrate the value of the “mouse filter” for genomic studies of human B-lineage neoplasms for which a vast knowledge base already exists.</p> </div

FOXM1 inhibitors impair growth and survival of DLBCL and BL cells <i>in vitro</i>.

<p>(A) Determination of the mean inhibitory concentration (IC₅₀) of thiostrepton in 13 cell lines. Nine DLBCL and 4 BL cell lines were treated for 24 hrs with increasing concentrations of drug. Dose response curves are representative of at least three independent experiments. Cell metabolic activity was measured using the MTS assay. IC₅₀ values and standard deviations are shown to the right. (B) Thiostrepton-dependent inhibition of cell proliferation and increased cell death. Tumor cell lines were exposed for 24 hrs to DMSO (vehicle control) or thiostrepton at IC₅₀ levels shown in panel A, followed by flow cytometric determination of cells in S phase (DNA content analysis, left panel), number of viable cells (Guava ViaCount® analysis, middle panel), and apoptotic cells (annexin V immunoreactivity, right panel). Results are grouped by molecular subtype and shown as the average percent difference of the mean ± SD of thiostrepton- versus DMSO-treated cells. (C) Thiostrepton-dependent loss of gene expression. Cells were treated as described in panel B. RNA was isolated and gene transcript levels were measured using qPCR. Data are presented as described in panel B. (D) ARF peptide-dependent loss of cell metabolic activity. Four DLBCL and 2 BL cell lines were treated for 24 hrs with the indicated concentration (µM) of wild-type (WT) ARF peptide (black bars) or mutant (MUT) peptide (white bars) used as control. Cell metabolic activity was measured using the MTS (SUDHL4, BJAB, HBL1, TMD8) or CellTiter-Glo® (Daudi, Ramos, Raji, DG75) assays and is normalized to the mean of the lowest concentration of MUT peptide treatment per cell type. Blue, red and black outline colors indicate GCB, ABC, and BL cell lines, respectively. Data are representative of at least two independent experiments.</p

Stringent cross-species comparison of gene expression changes in B-cell lymphoma discovers 60 concordantly deregulated genes, designated DMB (DLBCL/iMycBCL).

<p>(A) The Venn diagram on the left shows the degree of human-in-mouse overlap of gene probesets found to be significantly variable in both species. Results at FDR threshold values of 5% and 1% are indicated in blue and red, respectively. A heat map of unsupervised cluster analysis of matching human-mouse gene sets at FDR 0.05 is depicted on the right. (B) Degree of mouse-in-human overlap of significantly variable gene probesets in both species, using the same approach as in panel A. Panels A and B depict reciprocal results. (C) Venn diagram indicating that overlapping gene sets from panels A and B (FDR 0.01 in both cases) represent 130 concordantly deregulated genes in human DLBCL and mouse iMycBCL. (D) Diagrammatic representation of two filtering steps that narrowed the gene list from 130 genes to 60 genes. The genes eliminated in this process are indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076889#pone.0076889.s004" target="_blank">Table S1</a>. (E) Column diagram indicating the top five gene ontology (GO) categories for the 130 concordantly deregulated genes from panels C and D left. GO categories were determined using DAVID. Pathway names and numbers are shown to the right.</p

Validation of microarray data using quantitative PCR.

<p>Expression levels of DMB genes found to be up regulated (red; top and center rows) or down regulated (green; bottom row) on microarrays were determined with the assistance of qPCR (ΔΔCT method) in human (circle) and mouse (square) lymphoma (open) counterparts. Normal B cells (closed) were included for comparison. <i>HPRT1</i> and <i>Hprt</i> were used as internal reference genes for human and mouse samples, respectively. Median gene expression levels are indicated by horizontal lines. Statistical analysis relied on the Mann-Whitney test.</p

Global gene expression profiles of human and mouse B lymphoma contain an abundance of deregulated genes.

<p>(A) Representative tissue sections of human DLBCL (top) and mouse iMycBCL (bottom) stained with hematoxylin and eosin. The normal lymphoid tissue structure is effaced in both species by sheets of medium to large tumor cells that contain scant cytoplasm and round to polygonal nuclei with one to two nucleoli. Tingible body macrophages that harbor apoptotic bodies are abundant. Microscopic slides were read using an Olympus BX-51 light microscope equipped with UPLSAPO objectives (Olympus). The light temperature of the microscope bulb varied between 3000 and 3400 K. Imaging medium was air. Images were acquired with the help of a 40x objective (0.95 numerical aperture), DP2 digital camera (Olympus), and DP2-BSW imaging software (Olympus). Images were saved as TIF (tagged image file) data files and enhanced with respect to brightness, contrast and color balance using the Adobe Photoshop CS2 Version 9.0.2 software (Adobe Systems Inc). (B) Flow chart of global gene expression analysis of human and mouse lymphoma counterparts carried out in parallel and using the same statistical parameters (RMA, robust multi-averaging; ANOVA, analysis of variance; FDR, false discovery rate). Gene expression profiles of human DLBCL and normal B cells were compared on HG U133 microarrays. Gene expression profiles of mouse iMycBCL and normal B cells were compared on MG 430 microarrays.</p