EBV and the Pathogenesis of NK/T Cell Lymphoma
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Effective Population Size and Genetic Conservation Criteria for Bull Trout
North American Journal of Fisheries Management 21:756±764, 2001 q Copyright by the American Fisheries Society 2001 Effective Population Size and Genetic Conservation Criteria for Bull Trout B. E. RIEMAN* U.S. Department of Agriculture Forest Service, Rocky Mountain Research Station, 316 East Myrtle, Boise, Idaho 83702, USA F. W. A LLENDORF Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA Abstract.ÐEffective population size (Ne) is an important concept in the management of threatened species like bull trout Salvelinus con¯uentus. General guidelines suggest that effective population sizes of 50 or 500 are essential to minimize inbreeding effects or maintain adaptive genetic variation, respectively. Although Ne strongly depends on census population size, it also depends on demographic and life history characteristics that complicate any estimates. This is an especially dif®cult problem for species like bull trout, which have overlapping generations; biologists may monitor annual population number but lack more detailed information on demographic population structure or life history. We used a generalized, age-structured simulation model to relate Ne to adult numbers under a range of life histories and other conditions characteristic of bull trout populations. Effective population size varied strongly with the effects of the demographic and environmental variation included in our simulations. Our most realistic estimates of Ne were between about 0.5 and 1.0 times the mean number of adults spawning annually. We conclude that cautious long-term management goals for bull trout populations should include an average of at least 1,000 adults spawning each year. Where local populations are too small, managers should seek to conserve a collection of interconnected populations that is at least large enough in total to meet this minimum. -
The Popeye Domain Containing Protein Family E a Novel Class of Camp Effectors with Important Functions in Multiple Tissues
Progress in Biophysics and Molecular Biology xxx (2016) 1e9 Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio The Popeye domain containing protein family e A novel class of cAMP effectors with important functions in multiple tissues * Roland F.R. Schindler, Thomas Brand Heart Science Centre, National Heart and Lung Institute (NHLI), Imperial College London, United Kingdom article info abstract Article history: Popeye domain containing (Popdc) proteins are a unique family, which combine several different Received 16 September 2015 properties and functions in a surprisingly complex fashion. They are expressed in multiple tissues and Received in revised form cell types, present in several subcellular compartments, interact with different classes of proteins, and 3 December 2015 are associated with a variety of physiological and pathophysiological processes. Moreover, Popdc proteins Accepted 4 January 2016 bind the second messenger cAMP with high affinity and it is thought that they act as a novel class of Available online xxx cAMP effector proteins. Here, we will review the most important findings about the Popdc family, which accumulated since its discovery about 15 years ago. We will be focussing on Popdc protein interaction Keywords: Popeye domain containing genes and function in striated muscle tissue. However, as a full picture only emerges if all aspects are taken into cAMP account, we will also describe what is currently known about the role of Popdc proteins in epithelial cells Proteineprotein interaction and in various types of cancer, and discuss these findings with regard to their relevance for cardiac and Ion channel skeletal muscle. -
Análise Integrativa De Perfis Transcricionais De Pacientes Com
UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. -
Probabilistic Models for Collecting, Analyzing, and Modeling Expression Data
Probabilistic Models for Collecting, Analyzing, and Modeling Expression Data Hai-Son Phuoc Le May 2013 CMU-ML-13-101 Probabilistic Models for Collecting, Analyzing, and Modeling Expression Data Hai-Son Phuoc Le May 2013 CMU-ML-13-101 Machine Learning Department School of Computer Science Carnegie Mellon University Thesis Committee Ziv Bar-Joseph, Chair Christopher Langmead Roni Rosenfeld Quaid Morris Submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy. Copyright @ 2013 Hai-Son Le This research was sponsored by the National Institutes of Health under grant numbers 5U01HL108642 and 1R01GM085022, the National Science Foundation under grant num- bers DBI0448453 and DBI0965316, and the Pittsburgh Life Sciences Greenhouse. The views and conclusions contained in this document are those of the author and should not be interpreted as representing the official policies, either expressed or implied, of any sponsoring institution, the U.S. government or any other entity. Keywords: genomics, gene expression, gene regulation, microarray, RNA-Seq, transcriptomics, error correction, comparative genomics, regulatory networks, cross-species, expression database, Gene Expression Omnibus, GEO, orthologs, microRNA, target prediction, Dirichlet Process, Indian Buffet Process, hidden Markov model, immune response, cancer. To Mom and Dad. i Abstract Advances in genomics allow researchers to measure the complete set of transcripts in cells. These transcripts include messenger RNAs (which encode for proteins) and microRNAs, short RNAs that play an important regulatory role in cellular networks. While this data is a great resource for reconstructing the activity of networks in cells, it also presents several computational challenges. These challenges include the data collection stage which often results in incomplete and noisy measurement, developing methods to integrate several experiments within and across species, and designing methods that can use this data to map the interactions and networks that are activated in specific conditions. -
The Tempus HRD Test a New Companion Test for Detecting Homologous Recombination Deficiency from Next-Generation Sequencing Data
TEMPUS TECH SPOTLIGHT The Tempus HRD Test A New Companion Test for Detecting Homologous Recombination Deficiency From Next-generation Sequencing Data INTRODUCTION As part of our mission to provide precision medicine to cancer patients, Tempus Labs has recently developed a laboratory test to detect homologous recombination deficiency (HRD) from next-generation sequencing (NGS) data. Tempus HRD is a DNA-based test available as an additional assessment for patients who receive the Tempus|xT Solid Tumor + Normal Test. We offer the HRD test to ensure physicians and patients have every tool available to make informed treatment decisions without requiring additional specimens. The HRD test is designed and analytically validated to provide insights regarding patients who may be sensitive to Poly (ADP-ribose) Polymerase inhibitors (PARPi). The Emergence of PARPi Therapy in Oncology In recent years, PARPi have been established as a viable therapy for the treatment and maintenance of BRCA-mutated cancers. Besides the FDA approval of various PARPi in BRCA-mutated ovarian, breast, pancreatic, and prostate cancers,1,2 emerging evidence also suggests therapeutic benefit in bladder, endometrial, gastric, colon, lung, and other solid tumors.3-7 Furthermore, treatment with PARPi has demonstrated clinical utility beyond the setting of BRCA-mutated cancers,8-10 including a recent FDA approval for the treatment of castration-resistant metastatic prostate cancers harboring mutations in any homologous recombination (HR)-related gene.11 Another notable example is the FDA approval of niraparib for the treatment of patients with HRD-positive ovarian cancer, regardless of germline BRCA mutation status. The approval was based on results from the PRIMA trial, wherein patients who progressed within ≥6 months of their last platinum-based treatment were selected for PARPi therapy solely based on HRD status. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
The Genetics of Bipolar Disorder
Molecular Psychiatry (2008) 13, 742–771 & 2008 Nature Publishing Group All rights reserved 1359-4184/08 $30.00 www.nature.com/mp FEATURE REVIEW The genetics of bipolar disorder: genome ‘hot regions,’ genes, new potential candidates and future directions A Serretti and L Mandelli Institute of Psychiatry, University of Bologna, Bologna, Italy Bipolar disorder (BP) is a complex disorder caused by a number of liability genes interacting with the environment. In recent years, a large number of linkage and association studies have been conducted producing an extremely large number of findings often not replicated or partially replicated. Further, results from linkage and association studies are not always easily comparable. Unfortunately, at present a comprehensive coverage of available evidence is still lacking. In the present paper, we summarized results obtained from both linkage and association studies in BP. Further, we indicated new potential interesting genes, located in genome ‘hot regions’ for BP and being expressed in the brain. We reviewed published studies on the subject till December 2007. We precisely localized regions where positive linkage has been found, by the NCBI Map viewer (http://www.ncbi.nlm.nih.gov/mapview/); further, we identified genes located in interesting areas and expressed in the brain, by the Entrez gene, Unigene databases (http://www.ncbi.nlm.nih.gov/entrez/) and Human Protein Reference Database (http://www.hprd.org); these genes could be of interest in future investigations. The review of association studies gave interesting results, as a number of genes seem to be definitively involved in BP, such as SLC6A4, TPH2, DRD4, SLC6A3, DAOA, DTNBP1, NRG1, DISC1 and BDNF. -
Supplemental Figure and Table Legends
Supplemental figure and table legends Supplementary Figure 1: KIAA1841 is well conserved among vertebrates. NCBI HomoloGene pairwise alignment scores of human KIAA1841 sequence compared to other vertebrate orthologs. Supplementary Figure 2: µ-germline transcripts (GLT) and AID mRNA expression are not affected by overexpression of KIAA1841. Splenic B cells were isolated from wild-type mice, and transduced with retroviral vector control (pMIG) or a vector expressing KIAA1841. Levels of µ-GLT and AID mRNA were determined at 72h post-infection by RT-qPCR, and normalized to -actin mRNA and the pMIG control. The mean of three independent experiments +/- SD is shown. NS, p = not significant, p 0.05, two-tailed paired student’s t-test. Supplementary Figure 3: Overexpression of untagged and Xpress-tagged KIAA1841 does not affect cell proliferation. Splenic B cells were isolated from wild-type mice, stimulated with LPS+IL4, and transduced with retroviral vector control (pMIG) or a vector expressing KIAA1841 or Xpress (Xp)-tagged KIAA1841. Cells are labeled with seminaphthorhodafluor (SNARF) cell tracking dye and SNARF intensity was measured at 0h, 24h, and 48h after retroviral infection. Histograms of transduced cells (GFP+) for pMIG control, KIAA1841 and Xp-KIAA1841 were superimposed at each time point. Three independent retroviral infection experiments are shown. Supplementary Figure 4: Sequence alignment of the putative SANT domain of KIAA1841 with the SANT domain of SWI3. Alignment was performed using ClustalOmega; *, conserved residue, :, strongly similar residues, ., weakly similar residues. Numbers indicate amino acid residues in each sequence. Helix 3, which has been reported to be important for the chromatin remodeling function of SWI3 (Boyer et. -
Loss of Heterozygosity at the BRCA2 Locus Detected by Multiplex
Human Cancer Biology Loss of Heterozygosity at the BRCA2 Locus Detected by Multiplex Ligation-Dependent Probe Amplification is Common in Prostate Cancers from Men with a Germline BRCA2 Mutation Amber J. Willems,1Sarah-Jane Dawson,2 Hema Samaratunga,4 Alessandro De Luca,5 Yoland C. Antill,2 John L. Hopper,3 Heather J. Thorne1 and kConFab Investigators Abstract Purpose: Prostate cancer risk is increased for men carrying a pathogenic germline mutation in BRCA2 , and perhaps BRCA1. Our primary aim was to test for loss of heterozygosity (LOH) at the locus of the mutation in prostate cancers from men who a carry pathogenic germline mutation in BRCA1 or BRCA2 , and to assess clinical and pathologic features of these tumors. Experimental Design: From 1,243 kConFab families: (a) 215 families carried a pathogenic BRCA1 mutation, whereas 188 families carried a pathogenic BRCA2 mutation; (b)ofthe158 men diagnosed with prostate cancer (from 137 families), 8 were confirmed to carry the family- specific BRCA1 mutation, whereas 20 were confirmed to carry the family-specific BRCA2 mutation; and (c) 10 cases were eliminated from analysis because no archival material was available. The final cohort comprised 4 and 14 men with a BRCA1 and BRCA2 mutation, respec- tively. We examined LOH at the BRCA1 and BRCA2 genes using multiplex ligation-dependent probe amplification of DNA from microdissected tumor. Results: LOH at BRCA2 was observed in 10 of 14 tumors from BRCA2 mutation carriers (71%), whereas no LOHat BRCA1 was observed in four tumors from BRCA1 mutation carriers (P =0.02). Under the assumption that LOH occurs only because the cancer was caused by the germline mutation, carriers of BRCA2 mutations are at 3.5-fold (95% confidence interval, 1.8-12) increased risk of prostate cancer. -
In Silico Prediction and Experimental Validation of Natural Antisense Transcripts in Two Cancer-Associated Regions of Human Chromosome 6
1099-1108 27/2/2009 01:48 ÌÌ ™ÂÏ›‰·1099 INTERNATIONAL JOURNAL OF ONCOLOGY 34: 1099-1108, 2009 In silico prediction and experimental validation of natural antisense transcripts in two cancer-associated regions of human chromosome 6 LAURA MONTI1*, RAFFAELLA CINQUETTI1*, ALESSANDRO GUFFANTI2*, FRANCESCO NICASSIO3, MATTIA CREMONA4, GIOVANNI LAVORGNA5, FABRIZIO BIANCHI3, FRANCESCA VIGNATI1, DAVIDE CITTARO6, ROBERTO TARAMELLI1 and FRANCESCO ACQUATI1 1Department of Biotechnology and Molecular Sciences, University of Insubria, Via JH Dunant 3, I-21100 Varese; 2Nanotechnologies Group, Institute of Biomedical Technologies, CNR, Via Fantoli 16/15, I-20138 Milano; 3IFOM - FIRC Institute of Molecular Oncology, Via Adamello 16, I-20139 Milano; 4Proteomic Unit, Department of Experimental Oncology, National Institute of Cancer, Via Venezian 21, I-20133 Milano; 5DIBIT, San Raffaele Hospital, Via Olgettina 58, I-20132 Milano; 6HPC and Bioinformatics Systems @ Informatics Core, FIRC Insitute of Molecular Oncology (IFOM), Via Adamello 16, I-20139 Milano, Italy Received August 28, 2008; Accepted October 27, 2008 DOI: 10.3892/ijo_00000237 Abstract. Antisense transcription has long been recognized human malignancies, such as non-Hodgkin's lymphomas, as a mechanism involved in the regulation of gene expression. melanoma and carcinomas of the mammary gland, ovary, Therefore, several human diseases associated with abnormal uterus, stomach, kidney and salivary gland (1-3). The involve- patterns of gene expression might display antisense RNA- ment of this chromosome in the pathogenesis of the above- mediated pathogenetic mechanisms. Such issue could be mentioned cancer types has been demonstrated by LOH particularly relevant for cancer pathogenesis, since deregulated studies and chromosome-transfer assays, which led to the gene expression has long been established as a hallmark of identification of several regions of minimal deletion spanning cancer cells. -
Prognostic Value of Loss of Heterozygosity at BRCA2 in Human Breast Carcinoma
British Joumal of Cancer (1997) 76(11), 1416-1418 © 1997 Cancer Research Campaign Prognostic value of loss of heterozygosity at BRCA2 in human breast carcinoma I Bieche', C Nogubs2, S Rivoilan', A Khodja1, A Latill and R Lidereau1 'Laboratoire d'Oncogenetique and 2D6partement de Statistiques M6dicales, Centre Rend Huguenin, 35 rue Daily, F-92211 St-Cloud, France Summary To confirm several recent studies pointing to loss of heterozygosity (LOH) at BRCA2 as a prognostic factor in sporadic breast cancer, we examined this genetic alteration in a large series of human primary breast tumours for which long-term patient outcomes were known. LOH at BRCA2 correlated only with low oestrogen and progesterone receptor content. Univariate analysis of metastasis-free survival and overall survival (log-rank test) showed no link with BRCA2 status (P = 0.34, P = 0.29 respectively). LOH at BRCA2 does not therefore appear to be a major prognostic marker in sporadic breast cancer. Keywords: BRCA2; loss of heterozygosity; prognostic value; breast cancer Breast cancer, one of the most common life-threatening diseases in this gene in the aggressiveness of breast tumours (Bignon et al, women, occurs in hereditary and sporadic forms. The two major 1995; Beckmann et al, 1996; Kelsell et al, 1996). Recently, in a breast cancer susceptibility genes, BRCAI and BRCA2, were pilot study, LOH at BRCA2 was found to be an independent prog- recently isolated (Miki et al, 1994; Wooster et al, 1995; Couch et nostic factor (van den Berg et al, 1996). However, this study al, 1996). Both are considered to be tumour-suppressor genes and involved a heterogeneous population of 84 primary tumours from are thought to be inactivated by a 'two-hit' mechanism originally both familial (n = 45) and sporadic (n = 39) cases of breast cancer. -
The Transition from Gastric Intestinal Metaplasia to Gastric Cancer Involves POPDC1 and POPDC3 Downregulation
International Journal of Molecular Sciences Article The Transition from Gastric Intestinal Metaplasia to Gastric Cancer Involves POPDC1 and POPDC3 Downregulation Rachel Gingold-Belfer 1,2,3,* , Gania Kessler-Icekson 1,3, Sara Morgenstern 4, Lea Rath-Wolfson 3,4, Romy Zemel 1,3, Doron Boltin 2,3, Zohar Levi 2,3 and Michal Herman-Edelstein 1,3,5 1 The Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva 4941492, Israel; [email protected] (G.K.-I.); [email protected] (R.Z.); [email protected] (M.H.-E.) 2 Rabin Medical Center, Gastroenterology Division, Petah Tikva 4941492, Israel; [email protected] (D.B.); [email protected] (Z.L.) 3 Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; [email protected] 4 Rabin Medical Center, Department of Pathology, Petah Tikva 4941492, Israel; [email protected] 5 Rabin Medical Center, Department of Nephrology, Petah Tikva 4937211, Israel * Correspondence: [email protected]; Tel.: +972-52-2405895 Abstract: Intestinal metaplasia (IM) is an intermediate step in the progression from premalignant to malignant stages of gastric cancer (GC). The Popeye domain containing (POPDC) gene family encodes three transmembrane proteins, POPDC1, POPDC2, and POPDC3, initially described in muscles and later in epithelial and other cells, where they function in cell–cell interaction, and cell migration. POPDC1 and POPDC3 downregulation was described in several tumors, including colon and gastric cancers. We questioned whether IM-to-GC transition involves POPDC gene Citation: Gingold-Belfer, R.; dysregulation. Gastric endoscopic biopsies of normal, IM, and GC patients were examined for Kessler-Icekson, G.; Morgenstern, S.; expression levels of POPDC1-3 and several suggested IM biomarkers, using immunohistochemistry Rath-Wolfson, L.; Zemel, R.; Boltin, and qPCR.