R-Spondin 2 Signalling Mediates Susceptibility to Fatal Infectious Diarrhoea
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Β-Catenin-Mediated Hair Growth Induction Effect of 3,4,5-Tri-O- Caffeoylquinic Acid
www.aging-us.com AGING 2019, Vol. 11, No. 12 Research Paper β-catenin-mediated hair growth induction effect of 3,4,5-tri-O- caffeoylquinic acid Meriem Bejaoui1, Myra O. Villareal1,2,3, Hiroko Isoda1,2,3 1School of Integrative and Global Majors (SIGMA), University of Tsukuba, Tsukuba City, 305-8572 Japan 2Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba City, 305-8572 Japan 3Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba City, 305- 8572 Japan Correspondence to: Hiroko Isoda; email: [email protected] Keywords: 3,4,5-tri-O-caffeoylquinic acid (TCQA), β-catenin, dermal papilla, anagen, Wnt/β-catenin pathway Received: April 23, 2018 Accepted: June 17, 2019 Published: June 29, 2019 Copyright: Bejaoui et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT The hair follicle is a complex structure that goes through a cyclic period of growth (anagen), regression (catagen), and rest (telogen) under the regulation of several signaling pathways, including Wnt/ β-catenin, FGF, Shh, and Notch. The Wnt/β-catenin signaling is specifically involved in hair follicle morphogenesis, regeneration, and growth. β-catenin is expressed in the dermal papilla and promotes anagen induction and duration, as well as keratinocyte regulation and differentiation. In this study, we demonstrated the activation of β-catenin by a polyphenolic compound 3,4,5-tri-O-caffeoylquinic acid (TCQA) in mice model and in human dermal papilla cells to promote hair growth cycle. -
A Chromosome Level Genome of Astyanax Mexicanus Surface Fish for Comparing Population
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.06.189654; this version posted July 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Title 2 A chromosome level genome of Astyanax mexicanus surface fish for comparing population- 3 specific genetic differences contributing to trait evolution. 4 5 Authors 6 Wesley C. Warren1, Tyler E. Boggs2, Richard Borowsky3, Brian M. Carlson4, Estephany 7 Ferrufino5, Joshua B. Gross2, LaDeana Hillier6, Zhilian Hu7, Alex C. Keene8, Alexander Kenzior9, 8 Johanna E. Kowalko5, Chad Tomlinson10, Milinn Kremitzki10, Madeleine E. Lemieux11, Tina 9 Graves-Lindsay10, Suzanne E. McGaugh12, Jeff T. Miller12, Mathilda Mommersteeg7, Rachel L. 10 Moran12, Robert Peuß9, Edward Rice1, Misty R. Riddle13, Itzel Sifuentes-Romero5, Bethany A. 11 Stanhope5,8, Clifford J. Tabin13, Sunishka Thakur5, Yamamoto Yoshiyuki14, Nicolas Rohner9,15 12 13 Authors for correspondence: Wesley C. Warren ([email protected]), Nicolas Rohner 14 ([email protected]) 15 16 Affiliation 17 1Department of Animal Sciences, Department of Surgery, Institute for Data Science and 18 Informatics, University of Missouri, Bond Life Sciences Center, Columbia, MO 19 2 Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 20 3 Department of Biology, New York University, New York, NY 21 4 Department of Biology, The College of Wooster, Wooster, OH 22 5 Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 23 6 Department of Genome Sciences, University of Washington, Seattle, WA 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.06.189654; this version posted July 6, 2020. -
Increased Sensitivity of Diagnostic Mutation Detection by Re-Analysis Incorporating Local Reassembly of Sequence Reads
This is a repository copy of Increased Sensitivity of Diagnostic Mutation Detection by Re-analysis Incorporating Local Reassembly of Sequence Reads. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/123432/ Version: Accepted Version Article: Watson, CM, Camm, N, Crinnion, LA et al. (7 more authors) (2017) Increased Sensitivity of Diagnostic Mutation Detection by Re-analysis Incorporating Local Reassembly of Sequence Reads. Molecular Diagnosis and Therapy, 21 (6). pp. 685-692. ISSN 1177-1062 https://doi.org/10.1007/s40291-017-0304-x © Springer International Publishing AG 2017. This is an author produced version of a paper published in Molecular Diagnosis and Therapy. Uploaded in accordance with the publisher's self-archiving policy. The final publication is available at Springer via https://doi.org/10.1007/s40291-017-0304-x. Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ TITLE Increased sensitivity of diagnostic mutation detection by re-analysis incorporating local reassembly of sequence reads RUNNING HEAD ABRA reassembly improves test sensitivity Christopher M. -
Latest Version of Intermine in Any Repository
InterMine Documentation InterMine Apr 26, 2021 Contents 1 Contents 3 1.1 System Requirements..........................................3 1.2 Get started................................................ 21 1.3 InterMine................................................. 52 1.4 Data Model................................................ 69 1.5 Database................................................. 78 1.6 Guide to Customising your Web Application.............................. 154 1.7 Web Services............................................... 250 1.8 Embedding InterMine components................................... 251 1.9 InterMine API Description........................................ 279 1.10 Support.................................................. 284 1.11 About Us................................................. 287 1.12 InterMine Video Tutorial Collection................................... 290 2 Indices 295 Index 297 i ii InterMine Documentation InterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data. Developed by the Micklem lab at the University of Cambridge, InterMine enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data. InterMine includes an attractive, user- friendly web interface that works ‘out of the box’ and can be easily customised for your specific needs, as well as a powerful, scriptable -
A Curated Ortholog Database for Yeasts and Fungi Spanning 600 Million Years of Evolution
bioRxiv preprint doi: https://doi.org/10.1101/237974; this version posted October 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution Kevin Correia1, Shi M. Yu1, and Radhakrishnan Mahadevan1,2,* 1Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada, ON 2Institute of Biomaterials and Biomedical Engineering, University of Toronto, Ontario, Canada Corresponding author: Radhakrishnan Mahadevan∗ Email address: [email protected] ABSTRACT Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution. OrthoMCL and OrthoDB were used to cluster protein sequence into ortholog and homolog groups, respectively; MAFFT and PhyML were used to reconstruct the phylogeny of all homolog groups. Ortholog assignments for enzymes and small metabolite transporters were compared to their phylogenetic reconstruction, and curated to resolve any discrepancies. Information on homolog and ortholog groups can be viewed in the AYbRAH web portal (https://kcorreia.github. io/aybrah/) to review ortholog groups, predictions for mitochondrial localization and transmembrane domains, literature references, and phylogenetic reconstructions. -
Meta-Analysis of 8Q24 for Seven Cancers Reveals a Locus Between
Brisbin et al. BMC Medical Genetics 2011, 12:156 http://www.biomedcentral.com/1471-2350/12/156 RESEARCHARTICLE Open Access Meta-analysis of 8q24 for seven cancers reveals a locus between NOV and ENPP2 associated with cancer development Abra G Brisbin1, Yan W Asmann1, Honglin Song2, Ya-Yu Tsai3, Jeremiah A Aakre1, Ping Yang1, Robert B Jenkins4, Paul Pharoah2, Fredrick Schumacher5, David V Conti5, David J Duggan6, Mark Jenkins7, John Hopper7, Steven Gallinger8, Polly Newcomb9, Graham Casey5, Thomas A Sellers3 and Brooke L Fridley1* Abstract Background: Human chromosomal region 8q24 contains several genes which could be functionally related to cancer, including the proto-oncogene c-MYC. However, the abundance of associations around 128 Mb on chromosome 8 could mask the appearance of a weaker, but important, association elsewhere on 8q24. Methods: In this study, we completed a meta-analysis of results from nine genome-wide association studies for seven types of solid-tumor cancers (breast, prostate, pancreatic, lung, ovarian, colon, and glioma) to identify additional associations that were not apparent in any individual study. Results: Fifteen SNPs in the 8q24 region had meta-analysis p-values < 1E-04. In particular, the region consisting of 120,576,000-120,627,000 bp contained 7 SNPs with p-values < 1.0E-4, including rs6993464 (p = 1.25E-07). This association lies in the region between two genes, NOV and ENPP2, which have been shown to play a role in tumor development and motility. An additional region consisting of 5 markers from 128,478,000 bp - 128,524,000 (around gene POU5F1B) had p-values < 1E-04, including rs6983267, which had the smallest p-value (p = 6.34E-08). -
Sudden Unexpected Death with Rare Compound Heterozygous Variants in PRICKLE1
neurogenetics (2019) 20:39–43 https://doi.org/10.1007/s10048-018-0562-8 SHORT COMMUNICATION Sudden unexpected death with rare compound heterozygous variants in PRICKLE1 Yukiko Hata1 & Koji Yoshida2,3 & Naoki Nishida1 Received: 29 October 2018 /Accepted: 8 December 2018 /Published online: 18 December 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Progressive myoclonus epilepsy-ataxia syndrome (EPM5) is an autosomal recessive form of progressive myoclonus epilepsy that has been associated with a homozygous missense mutation in PRICKLE1. We report a 23-year-old male who died shortly after refractory convulsion and respiratory failure. Autopsy showed unilateral hippocampal malformation without significant neuronal loss or gliosis. Genetic analysis that targeted both epilepsy and cardiac disease using next-generation sequencing revealed two variants of PRICKLE1. Additional investigation showed that the patient’s father (p.Asp760del) and mother (p.Asp201Asn) each had a mutation in this gene. The present case shows that EPM5 can also be caused by compound heterozygous mutations. Keywords Compound heterozygous mutation . Hippocampus . Neuropathology . PRICKLE1 . Progressive myoclonus epilepsy . Sudden death Introduction Here we report the autopsy of a young man with a complex heterozygous mutation in PRICKLE1 whodiedsuddenly Progressive myoclonus epilepsy (PME) is a complex of neu- without medical treatment antemortem. rodegenerative diseases that show action myoclonus, epileptic seizures and progressive neurologic -
Dsir2 and Dmp53 Interact to Mediate Aspects of CR-Dependent Life Span
β-catenin-mediated hair growth induction effect of 3,4,5-tri-O-caffeoylquinic acid 著者(英) Meriem Bejaoui, Myra Orlina VILLAREAL, Hiroko ISODA journal or Aging publication title volume 11 number 12 page range 4216-4237 year 2019-06 権利 Bejaoui et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. URL http://hdl.handle.net/2241/00157702 doi: 10.18632/aging.102048 Creative Commons : 表示 http://creativecommons.org/licenses/by/3.0/deed.ja www.aging-us.com AGING 2019, Vol. 11, No. 12 Research Paper β-catenin-mediated hair growth induction effect of 3,4,5-tri-O- caffeoylquinic acid Meriem Bejaoui1, Myra O. Villareal1,2,3, Hiroko Isoda1,2,3 1School of Integrative and Global Majors (SIGMA), University of Tsukuba, Tsukuba City, 305-8572 Japan 2Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba City, 305-8572 Japan 3Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba City, 305- 8572 Japan Correspondence to: Hiroko Isoda; email: [email protected] Keywords: 3,4,5-tri-O-caffeoylquinic acid (TCQA), β-catenin, dermal papilla, anagen, Wnt/β-catenin pathway Received: April 23, 2018 Accepted: June 17, 2019 Published: June 29, 2019 Copyright: Bejaoui et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. -
4 B Chromosome Conference
BMC Proceedings 2019, 13(Suppl 4):4 https://doi.org/10.1186/s12919-019-0165-x BMC Proceedings MEETING ABSTRACTS Open Access Abstract Book - 4th B Chromosome Conference Botucatu, Brazil. 20 - 23 July 2019 Published: 17 June 2019 I-01 last few years). Recent advances in next generation sequencing (NGS) Welcome to the 4th B Chromosome Conference technologies and high-throughput molecular biology protocols have led to Cesar Martins (Chair: 4th B Chromosome Conference) B chromosomes becoming the subject of massive data analysis, thus Institute of Biosciences at Botucatu, São Paulo State University (UNESP), enabling an investigation of structural and functional issues at a level that Botucatu, SP, Brazil was previously never considered possible. Therefore, the 4th BCC in Brazil is BMC Proceedings 2019, 13(Suppl 4):I-01 an excellent opportunity to bring exciting B-chromosome related topics and new technologies together for discussion under the view of the most Correspondence: Cesar Martins ([email protected]) outstanding chromosome biologists. Furthermore, this meeting will, for the Organization first time, promote an educational activity focused on science and biology Institute of Biosciences at Botucatu, São Paulo State University teachers in order to highlight methodologies and practical approaches that (UNESP) can be used in chromosome teaching/learning. Support The importance of B chromosomes is illustrated by the series of conferences International Chromosome and Genome Society on this issue that have been organized during the last three decades - 1st, Brazilian Genetics Society 2nd and 3rd B Chromosome Conferences - organized in 1993 (Spain), 2004 (Spain), and 2014 (Germany), respectively. The first B Chromosome Funding Support Conference (BCC) took place in Miraflores de la Sierra (Madrid, Spain) from The conference and this publication was funded by Fundação de Amparo à 21 to 25 of September 1993. -
Prognostic B-Cell Signatures Using Mrna-Seq in Patients with Subtype-Specific Breast and Ovarian Cancer
Published OnlineFirst June 10, 2014; DOI: 10.1158/1078-0432.CCR-13-3368 Clinical Cancer Biology of Human Tumors Research Prognostic B-cell Signatures Using mRNA-Seq in Patients with Subtype-Specific Breast and Ovarian Cancer Michael D. Iglesia1,2, Benjamin G. Vincent1,3, Joel S. Parker1,4, Katherine A. Hoadley1,4, Lisa A. Carey1,3, Charles M. Perou1,4,5, and Jonathan S. Serody1,3,6 Abstract Purpose: Lymphocytic infiltration of tumors predicts improved survival in patients with breast cancer. Previous studies have suggested that this survival benefit is confined predominantly to the basal-like subtype. Immune infiltration in ovarian tumors is also associated with improved prognosis. Currently, it is unclear what aspects of the immune response mediate this improved outcome. Experimental Design: Using The Cancer Genome Atlas mRNA-seq data and a large microarray dataset, we evaluated adaptive immune gene expression by genomic subtype in breast and ovarian cancer. To investigate B-cells observed to be prognostic within specific subtypes, we developed methods to analyze B- cell population diversity and degree of somatic hypermutation (SHM) from B-cell receptor (BCR) sequences in mRNA-seq data. Results: Improved metastasis-free/progression-free survival was correlated with B-cell gene expression signatures, which were restricted mainly to the basal-like and HER2-enriched breast cancer subtypes and the immunoreactive ovarian cancer subtype. Consistent with a restricted epitope-driven response, a subset of basal-like and HER2-enriched breast tumors and immunoreactive ovarian tumors showed high expression of a low-diversity population of BCR gene segments. More BCR segments showed improved prognosis with increased expression in basal-like breast tumors and immunoreactive ovarian tumors compared with other subtypes. -
Mouse Abra Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Abra Knockout Project (CRISPR/Cas9) Objective: To create a Abra knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Abra gene (NCBI Reference Sequence: NM_175456 ; Ensembl: ENSMUSG00000042895 ) is located on Mouse chromosome 15. 2 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 2 (Transcript: ENSMUST00000054742). Exon 1~2 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: Mice homozygous for a knock-out allele exhibit impaired arteriogenesis following occlusion. Exon 1 starts from about 0.09% of the coding region. Exon 1~2 covers 100.0% of the coding region. The size of effective KO region: ~3789 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 5' gRNA region gRNA region 3' 1 2 Legends Exon of mouse Abra Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of start 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. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of stop codon is aligned with itself to determine if there are tandem repeats. -
Agricultural University of Athens
ΓΕΩΠΟΝΙΚΟ ΠΑΝΕΠΙΣΤΗΜΙΟ ΑΘΗΝΩΝ ΣΧΟΛΗ ΕΠΙΣΤΗΜΩΝ ΤΩΝ ΖΩΩΝ ΤΜΗΜΑ ΕΠΙΣΤΗΜΗΣ ΖΩΙΚΗΣ ΠΑΡΑΓΩΓΗΣ ΕΡΓΑΣΤΗΡΙΟ ΓΕΝΙΚΗΣ ΚΑΙ ΕΙΔΙΚΗΣ ΖΩΟΤΕΧΝΙΑΣ ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ ΑΘΗΝΑ 2020 ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Genome-wide association analysis and gene network analysis for (re)production traits in commercial broilers ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ Τριμελής Επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Επταμελής εξεταστική επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Πηνελόπη Μπεμπέλη (Καθ. ΓΠΑ) Δημήτριος Βλαχάκης (Επ. Καθ. ΓΠΑ) Ευάγγελος Ζωίδης (Επ.Καθ. ΓΠΑ) Γεώργιος Θεοδώρου (Επ.Καθ. ΓΠΑ) 2 Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Περίληψη Σκοπός της παρούσας διδακτορικής διατριβής ήταν ο εντοπισμός γενετικών δεικτών και υποψηφίων γονιδίων που εμπλέκονται στο γενετικό έλεγχο δύο τυπικών πολυγονιδιακών ιδιοτήτων σε κρεοπαραγωγικά ορνίθια. Μία ιδιότητα σχετίζεται με την ανάπτυξη (σωματικό βάρος στις 35 ημέρες, ΣΒ) και η άλλη με την αναπαραγωγική