DOCSLIB.ORG

Mouse Rabac1 Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

https://www.alphaknockout.com

Mouse Rabac1 Knockout Project (CRISPR/Cas9)

Objective:

To create a Rabac1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.

Strategy summary:

The Rabac1 gene (NCBI Reference Sequence: NM_010261 ; Ensembl: ENSMUSG00000003380 ) is located on Mouse chromosome 7. 5 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 5 (Transcript: ENSMUST00000076961). Exon 1~5 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis.

Note:

Exon 1 starts from about 0.18% of the coding region. Exon 1~5 covers 100.0% of the coding region. The size of effective KO region: ~2657 bp. The KO region does not have any other known gene.

Page 1 of 8

https://www.alphaknockout.com

Overview of the Targeting Strategy

Wildtype allele

  • gRNA region
  • gRNA region

  • 5'
  • 3'

  • 1
  • 2
  • 3
  • 4
  • 5

Legends

  • Exon of mouse Rabac1
  • Knockout region

Page 2 of 8

https://www.alphaknockout.com

Overview of the Dot Plot (up)

Window size: 15 bp

  • Forward
  • Reverse Complement

Note: The 2000 bp section upstream of start codon is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis.

Overview of the Dot Plot (down)

Window size: 15 bp

  • Forward
  • Reverse Complement

Note: The 2000 bp section downstream of stop codon is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats.

Page 3 of 8

https://www.alphaknockout.com

Overview of the GC Content Distribution (up)

Window size: 300 bp

Summary: Full Length(2000bp) | A(25.65% 513) | C(27.7% 554) | T(25.3% 506) | G(21.35% 427)

Note: The 2000 bp section upstream of start codon is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis.

Overview of the GC Content Distribution (down)

Window size: 300 bp

Summary: Full Length(2000bp) | A(24.65% 493) | C(26.35% 527) | T(22.45% 449) | G(26.55% 531)

Note: The 2000 bp section downstream of stop codon is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis.

Page 4 of 8

https://www.alphaknockout.com

BLAT Search Results (up)

QUERY SCORE START END QSIZE IDENTITY CHROM
-------------------------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr7 24972583 24974582 2000
+ 126146270 126146408
83003775 83003907

  • STRAND START
  • END SPAN

-

browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq

98 95 89 88 88 88 88 87 86 85 85 84 84 84 83 83 83 82 82
3 147 2000 3 136 2000 2 134 2000 7 144 2000 1 134 2000 2 121 2000 2 131 2000 2 132 2000
14 129 2000
2 134 2000
14 143 2000
2 134 2000 7 143 2000 8 131 2000 1 121 2000 5 134 2000 2 126 2000
21 125 2000
8 121 2000
80.6% chr10 84.7% chr3 83.5% chr4 82.6% chr8 82.9% chr4 89.4% chr11 87.1% chr1 84.3% chr14 85.3% chr2 85.4% chr12 83.1% chrX 88.5% chr7 82.9% chr11 83.9% chr4 84.9% chr18 82.2% chr5 83.8% chr11 89.6% chr12 86.0% chr11
139 133 133 136 134 123 193 133 115 132 132 132 141 124 122 132 126
-- 103181280 103181412 - 128708275 128708410 - 118327394 118327527

  • -
  • 62109451 62109573

- 157422345 157422537
20983029 20983161
- 132207057 132207171 --+
25151378 25151509
7636566 7636697
- 126222317 126222448
6197536 6197676
+ 118966270 118966393
32076461 32076582
--+ 128062550 128062681 + 120637935 120638060

  • -
  • 54809763 54814142 4380

- 102966181 102966294 114

Note: The 2000 bp section upstream of start codon is BLAT searched against the genome. No significant similarity is found.

BLAT Search Results (down)

  • QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START
  • END SPAN

-----------------------------------------------------------------------------------------------

browser details YourSeq 2000

  • 1 2000 2000 100.0% chr7 -
  • 24967924 24969923 2000

63000526 63327033 326508 44023490 44287514 264025 browser details YourSeq 272 237 1652 2000 browser details YourSeq 138 265 871 2000 browser details YourSeq 115 237 491 2000 browser details YourSeq 108 239 900 2000 browser details YourSeq 102 240 481 2000 browser details YourSeq 101 236 478 2000
92.0% chr10 - 84.5% chr10 -

  • 86.2% chr10 + 128403396 128403794
  • 399

87.5% chr11 + 84.9% chr11 - 85.9% chr8 - 84.1% chr7 -
96564165 96898566 334402 85175090 85175332 25502961 25503526 34318815 34319190
243 566 376 214 567 288 372 301 318 487

browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq browser details YourSeq

Recommended publications
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • Genome-Wide Rnai Screening Identifies Human Proteins with A

    Genome-Wide Rnai Screening Identifies Human Proteins with A

    RESOURCES Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway Jeremy C. Simpson1,7, Brigitte Joggerst2, Vibor Laketa2, Fatima Verissimo2, Cihan Cetin2, Holger Erfle2,6, Mariana G. Bexiga1, Vasanth R. Singan1, Jean-Karim Hériché3, Beate Neumann3, Alvaro Mateos2, Jonathon Blake4, Stephanie Bechtel5, Vladimir Benes4, Stefan Wiemann5, Jan Ellenberg2,3 and Rainer Pepperkok2,7 The secretory pathway in mammalian cells has evolved to facilitate the transfer of cargo molecules to internal and cell surface membranes. Use of automated microscopy-based genome-wide RNA interference screens in cultured human cells allowed us to identify 554 proteins influencing secretion. Cloning, fluorescent-tagging and subcellular localization analysis of 179 of these proteins revealed that more than two-thirds localize to either the cytoplasm or membranes of the secretory and endocytic pathways. The depletion of 143 of them resulted in perturbations in the organization of the COPII and/or COPI vesicular coat complexes of the early secretory pathway, or the morphology of the Golgi complex. Network analyses revealed a so far unappreciated link between early secretory pathway function, small GTP-binding protein regulation, actin cytoskeleton organization and EGF-receptor-mediated signalling. This work provides an important resource for an integrative understanding of global cellular organization and regulation of the secretory pathway in mammalian cells. Within higher eukaryotic cells membrane traffic pathways connect the Extensive efforts over many years have revealed a significant number various membrane-bounded organelles, thereby ensuring that they of regulators associated with the secretory pathway. Early biochemical retain the correct complement of proteins and lipids to maintain approaches to identify individual machinery components have started cellular homeostasis.
  • PRA1 (RABAC1) Rabbit Monoclonal Antibody [Clone ID: EPR1747Y] Product Data

    PRA1 (RABAC1) Rabbit Monoclonal Antibody [Clone ID: EPR1747Y] Product Data

    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TA301019 PRA1 (RABAC1) Rabbit Monoclonal Antibody [Clone ID: EPR1747Y] Product data: Product Type: Primary Antibodies Clone Name: EPR1747Y Applications: WB Recommended Dilution: WB: 1:1000 - 1:20000; IP: 1:30; FC: 1:100 Reactivity: Human, Mouse, Rat Host: Rabbit Isotype: IgG Clonality: Monoclonal Immunogen: A synthetic peptide corresponding to residues near the C-terminus of human PRA1 was used as an immunogen. Formulation: PBS 49%,Sodium azide 0.01%,Glycerol 50%,BSA 0.05% Purification: Tissue culture supernatant Conjugation: Unconjugated Storage: Store at -20°C as received. Stability: Stable for 12 months from date of receipt. Predicted Protein Size: 21 kDa Gene Name: Rab acceptor 1 Database Link: NP_006414 Entrez Gene 14470 MouseEntrez Gene 83583 RatEntrez Gene 10567 Human Q9UI14 Background: PRA1 (prenylated Rab acceptor) is a general regulator of Rab proteins. It has been shown that PRA1 interacts with Rab proteins and with VAMP2. Therefore PRA1 is probably an important factor for membrane traffic, linking together the function of Rab proteins and SNAREs (1). Human cells contain more than 60 small G proteins of the Rab family, which are localized to the surfaces of distinct membrane compartments and regulate transport vesicle formation, motility, docking and fusion. Prenylated Rabs also occur in the cytosol bound to GDI (guanine nucleotide dissociation inhibitor), which binds to Rabs in their inactive state (2). Synonyms: PRA1; PRAF1; YIP3 This product is to be used for laboratory only.
  • Setd1 Histone 3 Lysine 4 Methyltransferase Complex Components in Epigenetic Regulation

    Setd1 Histone 3 Lysine 4 Methyltransferase Complex Components in Epigenetic Regulation

    SETD1 HISTONE 3 LYSINE 4 METHYLTRANSFERASE COMPLEX COMPONENTS IN EPIGENETIC REGULATION Patricia A. Pick-Franke Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Master of Science in the Department of Biochemistry and Molecular Biology Indiana University December 2010 Accepted by the Faculty of Indiana University, in partial fulfillment of the requirements for the degree of Master of Science. _____________________________________ David Skalnik, Ph.D., Chair _____________________________________ Kristin Chun, Ph.D. Master’s Thesis Committee _____________________________________ Simon Rhodes, Ph.D. ii DEDICATION This thesis is dedicated to my sons, Zachary and Zephaniah who give me great joy, hope and continuous inspiration. I can only hope that I successfully set a good example demonstrating that one can truly accomplish anything, if you never give up and reach for your dreams. iii ACKNOWLEDGEMENTS I would like to thank my committee members Dr. Skalnik, Dr. Chun and Dr. Rhodes for allowing me to complete this dissertation. They have been incredibly generous with their flexibility. I must make a special thank you to Jeanette McClintock, who willingly gave her expertise in statistical analysis with the Cfp1 microarray data along with encouragement, support and guidance to complete this work. I would like to thank Courtney Tate for her ceaseless willingness to share ideas, and her methods and materials, and Erika Dolbrota for her generous instruction as well as the name of a good doctor. I would also like to acknowledge the superb mentorship of Dr. Jeon Heong Lee, PhD and the contagious passion and excitement for the life of science of Dr.
  • A High-Throughput Study in Melanoma Identifies Epithelial- Mesenchymal Transition As a Major Determinant of Metastasis

    A High-Throughput Study in Melanoma Identifies Epithelial- Mesenchymal Transition As a Major Determinant of Metastasis

    Research Article A High-Throughput Study in Melanoma Identifies Epithelial- Mesenchymal Transition as a Major Determinant of Metastasis Soledad R. Alonso,1 Lorraine Tracey,1 Pablo Ortiz,4 Beatriz Pe´rez-Go´mez,5 Jose´ Palacios,1 Marina Polla´n,5 Juan Linares,6 Salvio Serrano,7 Ana I. Sa´ez-Castillo,6 Lydia Sa´nchez,2 Raquel Pajares,2 Abel Sa´nchez-Aguilera,1 Maria J. Artiga,1 Miguel A. Piris,1 and Jose´ L. Rodrı´guez-Peralto3 1Molecular Pathology Programme and 2Histology and Immunohistochemistry Unit, Centro Nacional de Investigaciones Oncolo´gicas; Departments of 3Pathology and 4Dermatology, Hospital Universitario 12 de Octubre; 5Centro Nacional de Epidemiologı´a, Instituto de Salud Carlos III, Madrid, Spain; and Departments of 6Pathology and 7Dermatology, Hospital Universitario San Cecilio, Granada, Spain Abstract with a less favorable prognosis as potential candidates for adjuvant Metastatic disease is the primary cause of death in cutaneous or novel therapies. malignant melanoma (CMM) patients. To understand the Currently, the prognosis of primary CMM is mainly based mechanisms of CMM metastasis and identify potential on histopathologic criteria. The most important of these is the predictive markers, we analyzed gene-expression profiles of Breslow index, although it is merely a measure of tumor depth. 34 vertical growth phase melanoma cases using cDNA micro- New molecular markers that correlate with melanoma genesis and/or progression are continuously being identified but, to date, arrays. All patients had a minimum follow-up of 36 months. Twenty-one cases developed nodal metastatic disease and 13 most of them have been obtained in experimental models and did not.
  • The Role of Lamin Associated Domains in Global Chromatin Organization and Nuclear Architecture

    The Role of Lamin Associated Domains in Global Chromatin Organization and Nuclear Architecture

    THE ROLE OF LAMIN ASSOCIATED DOMAINS IN GLOBAL CHROMATIN ORGANIZATION AND NUCLEAR ARCHITECTURE By Teresa Romeo Luperchio A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland March 2016 © 2016 Teresa Romeo Luperchio All Rights Reserved ABSTRACT Nuclear structure and scaffolding have been implicated in expression and regulation of the genome (Elcock and Bridger 2010; Fedorova and Zink 2008; Ferrai et al. 2010; Li and Reinberg 2011; Austin and Bellini 2010). Discrete domains of chromatin exist within the nuclear volume, and are suggested to be organized by patterns of gene activity (Zhao, Bodnar, and Spector 2009). The nuclear periphery, which consists of the inner nuclear membrane and associated proteins, forms a sub- nuclear compartment that is mostly associated with transcriptionally repressed chromatin and low gene expression (Guelen et al. 2008). Previous studies from our lab and others have shown that repositioning genes to the nuclear periphery is sufficient to induce transcriptional repression (K L Reddy et al. 2008; Finlan et al. 2008). In addition, a number of studies have provided evidence that many tissue types, including muscle, brain and blood, use the nuclear periphery as a compartment during development to regulate expression of lineage specific genes (Meister et al. 2010; Szczerbal, Foster, and Bridger 2009; Yao et al. 2011; Kosak et al. 2002; Peric-Hupkes et al. 2010). These large regions of chromatin that come in molecular contact with the nuclear periphery are called Lamin Associated Domains (LADs). The studies described in this dissertation have furthered our understanding of maintenance and establishment of LADs as well as the relationship of LADs with the epigenome and other factors that influence three-dimensional chromatin structure.
  • Praf2 Is a Novel Bcl-Xl/Bcl-2 Interacting Protein with the Ability to Modulate Survival of Cancer Cells

    Praf2 Is a Novel Bcl-Xl/Bcl-2 Interacting Protein with the Ability to Modulate Survival of Cancer Cells

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Praf2 Is a Novel Bcl-xL/Bcl-2 Interacting Protein with the Ability to Modulate Survival of Cancer Cells Maria Teresa Vento1., Valeria Zazzu1.¤a, Alessia Loffreda1, Justin R. Cross2¤b, Julian Downward2, Maria Patrizia Stoppelli1, Ingram Iaccarino1* 1 Institute of Genetics and Biophysics ‘‘Adriano Buzzati-Traverso,’’ Consiglio Nazionale delle Ricerche (CNR), Naples, Italy, 2 Signal Transduction Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom Abstract Increased expression of Bcl-xL in cancer has been shown to confer resistance to a broad range of apoptotic stimuli and to modulate a number of other aspects of cellular physiology, including energy metabolism, cell cycle, autophagy, mitochondrial fission/fusion and cellular adhesion. However, only few of these activities have a mechanistic explanation. Here we used Tandem Affinity purification to identify novel Bcl-xL interacting proteins that could explain the pleiotropic effects of Bcl-xL overexpression. Among the several proteins co-purifying with Bcl-xL, we focused on Praf2, a protein with a predicted role in trafficking. The interaction of Praf2 with Bcl-xL was found to be dependent on the transmembrane domain of Bcl-xL. We found that Bcl-2 also interacts with Praf2 and that Bcl-xL and Bcl-2 can interact also with Arl6IP5, an homologue of Praf2. Interestingly, overexpression of Praf2 results in the translocation of Bax to mitochondria and the induction of apoptotic cell death. Praf2 dependent cell death is prevented by the co-transfection of Bcl-xL but not by its transmembrane domain deleted mutant.
  • Association of Chromosome 19 to Lung Cancer Genotypes and Phenotypes

    Association of Chromosome 19 to Lung Cancer Genotypes and Phenotypes

    Cancer Metastasis Rev DOI 10.1007/s10555-015-9556-2 Association of chromosome 19 to lung cancer genotypes and phenotypes Xiangdong Wang1 & Yong Zhang 1 & Carol L. Nilsson2 & Frode S. Berven3 & Per E. Andrén4 & Elisabet Carlsohn5 & Johan Malm7 & Manuel Fuentes7 & Ákos Végvári6,8 & Charlotte Welinder6,9 & Thomas E. Fehniger6,10 & Melinda Rezeli8 & Goutham Edula11 & Sophia Hober12 & Toshihide Nishimura13 & György Marko-Varga6,8,13 # Springer Science+Business Media New York 2015 Abstract The Chromosome 19 Consortium, a part of the aberrations include translocation t(15, 19) (q13, p13.1) fusion Chromosome-Centric Human Proteome Project (C-HPP, oncogene BRD4-NUT, DNA repair genes (ERCC1, ERCC2, http://www.C-HPP.org), is tasked with the understanding XRCC1), TGFβ1 pathway activation genes (TGFB1, LTBP4) chromosome 19 functions at the gene and protein levels, as , Dyrk1B, and potential oncogenesis protector genes such as well as their roles in lung oncogenesis. Comparative genomic NFkB pathway inhibition genes (NFKBIB, PPP1R13L) and hybridization (CGH) studies revealed chromosome aberration EGLN2. In conclusion, neXtProt is an effective resource for in lung cancer subtypes, including ADC, SCC, LCC, and the validation of gene aberrations identified in genomic SCLC. The most common abnormality is 19p loss and 19q studies. It promises to enhance our understanding of lung gain. Sixty-four aberrant genes identified in previous genomic cancer oncogenesis. studies and their encoded protein functions were further vali- dated in the neXtProt database (http://www.nextprot.org/). Among those, the loss of tumor suppressor genes STK11, Keywords Proteins . Genes . Antibodies . mRNA . Mass MUM1, KISS1R (19p13.3), and BRG1 (19p13.13) is spectrometry .
  • Autocrine IFN Signaling Inducing Profibrotic Fibroblast Responses By

    Autocrine IFN Signaling Inducing Profibrotic Fibroblast Responses By

    Downloaded from http://www.jimmunol.org/ by guest on September 23, 2021 Inducing is online at: average * The Journal of Immunology , 11 of which you can access for free at: 2013; 191:2956-2966; Prepublished online 16 from submission to initial decision 4 weeks from acceptance to publication August 2013; doi: 10.4049/jimmunol.1300376 http://www.jimmunol.org/content/191/6/2956 A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Autocrine IFN Signaling Feng Fang, Kohtaro Ooka, Xiaoyong Sun, Ruchi Shah, Swati Bhattacharyya, Jun Wei and John Varga J Immunol cites 49 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130037 6.DC1 This article http://www.jimmunol.org/content/191/6/2956.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 23, 2021. The Journal of Immunology A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Inducing Autocrine IFN Signaling Feng Fang,* Kohtaro Ooka,* Xiaoyong Sun,† Ruchi Shah,* Swati Bhattacharyya,* Jun Wei,* and John Varga* Activation of TLR3 by exogenous microbial ligands or endogenous injury-associated ligands leads to production of type I IFN.
  • High-Density Array Comparative Genomic Hybridization Detects Novel Copy Number Alterations in Gastric Adenocarcinoma

    High-Density Array Comparative Genomic Hybridization Detects Novel Copy Number Alterations in Gastric Adenocarcinoma

    ANTICANCER RESEARCH 34: 6405-6416 (2014) High-density Array Comparative Genomic Hybridization Detects Novel Copy Number Alterations in Gastric Adenocarcinoma ALINE DAMASCENO SEABRA1,2*, TAÍSSA MAÍRA THOMAZ ARAÚJO1,2*, FERNANDO AUGUSTO RODRIGUES MELLO JUNIOR1,2, DIEGO DI FELIPE ÁVILA ALCÂNTARA1,2, AMANDA PAIVA DE BARROS1,2, PAULO PIMENTEL DE ASSUMPÇÃO2, RAQUEL CARVALHO MONTENEGRO1,2, ADRIANA COSTA GUIMARÃES1,2, SAMIA DEMACHKI2, ROMMEL MARIO RODRÍGUEZ BURBANO1,2 and ANDRÉ SALIM KHAYAT1,2 1Human Cytogenetics Laboratory and 2Oncology Research Center, Federal University of Pará, Belém Pará, Brazil Abstract. Aim: To investigate frequent quantitative alterations gastric cancer is the second most frequent cancer in men and of intestinal-type gastric adenocarcinoma. Materials and the third in women (4). The state of Pará has a high Methods: We analyzed genome-wide DNA copy numbers of 22 incidence of gastric adenocarcinoma and this disease is a samples and using CytoScan® HD Array. Results: We identified public health problem, since mortality rates are above the 22 gene alterations that to the best of our knowledge have not Brazilian average (5). been described for gastric cancer, including of v-erb-b2 avian This tumor can be classified into two histological types, erythroblastic leukemia viral oncogene homolog 4 (ERBB4), intestinal and diffuse, according to Laurén (4, 6, 7). The SRY (sex determining region Y)-box 6 (SOX6), regulator of intestinal type predominates in high-risk areas, such as telomere elongation helicase 1 (RTEL1) and UDP- Brazil, and arises from precursor lesions, whereas the diffuse Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 type has a similar distribution in high- and low-risk areas and (B4GALT5).
  • Patterns of Sequence Conservation in Presynaptic Neural Genes

    Patterns of Sequence Conservation in Presynaptic Neural Genes

    University of Pennsylvania ScholarlyCommons Departmental Papers (CIS) Department of Computer & Information Science November 2006 Patterns of Sequence Conservation in Presynaptic Neural Genes Dexter Hadley University of Pennsylvania Tara Murphy University of Pennsylvania Otto Valladares University of Pennsylvania Sridhar Hannenhalli University of Pennsylvania Lyle H. Ungar University of Pennsylvania, [email protected] See next page for additional authors Follow this and additional works at: https://repository.upenn.edu/cis_papers Recommended Citation Dexter Hadley, Tara Murphy, Otto Valladares, Sridhar Hannenhalli, Lyle H. Ungar, Junhyong Kim, and Maja Bucan, "Patterns of Sequence Conservation in Presynaptic Neural Genes", . November 2006. Reprinted from Genome Biology, Volume 7, Issue 11, November 2006, pages R105.1-R105.19. Publisher URL: http://genomebiology.com/2006/7/11/R105 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/cis_papers/282 For more information, please contact [email protected]. Patterns of Sequence Conservation in Presynaptic Neural Genes Abstract Background: The neuronal synapse is a fundamental functional unit in the central nervous system of animals. Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved. Results: Evolutionary rate analysis revealed that presynaptic proteins evolve slowly, although some members of large gene families exhibit accelerated evolutionary rates relative to other family members. Comparative sequence analysis of 46 megabases spanning 150 presynaptic genes identified more than 26,000 elements that are highly conserved in eight vertebrate species, as well as a small subset of sequences (6%) that are shared among unrelated presynaptic genes.
  • STAT3 Targets Suggest Mechanisms of Aggressive Tumorigenesis in Diffuse Large B Cell Lymphoma

    STAT3 Targets Suggest Mechanisms of Aggressive Tumorigenesis in Diffuse Large B Cell Lymphoma

    STAT3 Targets Suggest Mechanisms of Aggressive Tumorigenesis in Diffuse Large B Cell Lymphoma Jennifer Hardee*,§, Zhengqing Ouyang*,1,2,3, Yuping Zhang*,4 , Anshul Kundaje*,†, Philippe Lacroute*, Michael Snyder*,5 *Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305; §Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520; and †Department of Computer Science, Stanford University School of Engineering, Stanford, CA 94305 1The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030 2Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269 3Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030 4Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT 06520 5Corresponding author: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305. Email: [email protected] DOI: 10.1534/g3.113.007674 Figure S1 STAT3 immunoblotting and immunoprecipitation with sc-482. Western blot and IPs show a band consistent with expected size (88 kDa) of STAT3. (A) Western blot using antibody sc-482 versus nuclear lysates. Lanes contain (from left to right) lysate from K562 cells, GM12878 cells, HeLa S3 cells, and HepG2 cells. (B) IP of STAT3 using sc-482 in HeLa S3 cells. Lane 1: input nuclear lysate; lane 2: unbound material from IP with sc-482; lane 3: material IP’d with sc-482; lane 4: material IP’d using control rabbit IgG. Arrow indicates the band of interest. (C) IP of STAT3 using sc-482 in K562 cells. Lane 1: input nuclear lysate; lane 2: material IP’d using control rabbit IgG; lane 3: material IP’d with sc-482.