DOCSLIB.ORG

NLRP2 and FAF1 Deficiency Blocks Early Embryogenesis in the Mouse

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
NLRP2 and FAF1 Deficiency Blocks Early Embryogenesis in the Mouse REPRODUCTIONRESEARCH NLRP2 and FAF1 deficiency blocks early embryogenesis in the mouse Hui Peng1,*, Haijun Liu2,*, Fang Liu1, Yuyun Gao1, Jing Chen1, Jianchao Huo1, Jinglin Han1, Tianfang Xiao1 and Wenchang Zhang1 1College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, People’s Republic of China and 2Tianjin Institute of Animal Science and Veterinary Medicine, Tianjin, People’s Republic of China Correspondence should be addressed to W Zhang; Email: [email protected] *(H Peng and H Liu contributed equally to this work) Abstract Nlrp2 is a maternal effect gene specifically expressed by mouse ovaries; deletion of this gene from zygotes is known to result in early embryonic arrest. In the present study, we identified FAF1 protein as a specific binding partner of the NLRP2 protein in both mouse oocytes and preimplantation embryos. In addition to early embryos, both Faf1 mRNA and protein were detected in multiple tissues. NLRP2 and FAF1 proteins were co-localized to both the cytoplasm and nucleus during the development of oocytes and preimplantation embryos. Co-immunoprecipitation assays were used to confirm the specific interaction between NLRP2 and FAF1 proteins. Knockdown of the Nlrp2 or Faf1 gene in zygotes interfered with the formation of a NLRP2–FAF1 complex and led to developmental arrest during early embryogenesis. We therefore conclude that NLRP2 interacts with FAF1 under normal physiological conditions and that this interaction is probably essential for the successful development of cleavage-stage mouse embryos. Our data therefore indicated a potential role for NLRP2 in regulating early embryo development in the mouse. Reproduction (2017) 154 245–251 Introduction (Peng et al. 2012), the precise molecular mechanism underlying the role of NLRP2 in regulating early embryo During oogenesis, mammalian oocytes accumulate development still remains unclear. extensive amounts of mRNAs and proteins encoded NLRP proteins contain three conservative domains: by maternal effect genes. The selective knockout or an N-terminal pyrin domain (PYD), a central NACHT knockdown of certain maternal effect genes is known domain and a series of C-terminal leucine-rich repeats to block preimplantation embryogenesis, suggesting that (LRRs); the PYD and LRR domains are known to play these maternal proteins play crucial roles in early embryo critical roles in protein–protein interactions (Kobe & development (Christians et al. 2000, Leader et al. 2002, Kajava 2001, Eibl et al. 2012). Furthermore, within Burns et al. 2003, Payer et al. 2003, Wu et al. 2003, the NLRP family of proteins, the immunization-related Ma et al. 2006). NLRP proteins, including NLRP1, NLRP3 and NLRP Nlrp5/Mater is a member of the Nlrp family of 12, have been shown to interact with certain proteins genes, which is divided into immunization and to form specific complexes, which play central roles reproduction clades (Tian et al. 2009) and represents in the mammalian immune response (Lukens et al. one of the first maternal effect genes to be identified in 2015, Arbore et al. 2016, Zhong et al. 2016). Moreover, mammals (Tong et al. 2000). Knockout of Nlrp5 results NLRP5, a reproduction-related protein, interacts with in developmental arrest in preimplantation embryos, FLOPED, FILIA and TLE6 and assembles a subcortical and female Nlrp5-null mice are known to be infertile maternal complex (SCMC) located in the subcortex despite normal patterns of oogenesis, oocyte maturation of mouse oocytes and early embryos (Li et al. 2008, and fertilization (Tong et al. 2000). Furthermore, the Ohsugi et al. 2008). Genetic ablation of NLRP5, knockdown of Nlrp14, a gene associated with the FLOPED or TLE6 leads to the developmental failure Nlrp reproduction-clade, in mouse zygotes leads to of preimplantation embryos (Tong et al. 2000, Li et al. early embryonic arrest between the 1-cell and 8-cell 2008, Yu et al. 2014). stages (Hamatani et al. 2004). While our previous study Yeast two-hybrid assays have also shown that successfully verified that Nlrp2 is a maternal effect gene human NLRP2/PYPAF2 protein exhibits moderate required for early embryonic development in the mouse levels of interaction with FAF1 (Fas-associated protein © 2017 Society for Reproduction and Fertility DOI: 10.1530/REP-16-0629 ISSN 1470–1626 (paper) 1741–7899 (online) Online version via www.reproduction-online.org Downloaded from Bioscientifica.com at 09/24/2021 08:57:36PM via free access 10.1530/REP-16-0629 246 H Peng, H Liu and others factor) (Kinoshita et al. 2006). Another study, using a First-strand cDNA was synthesized using a PrimeScript II 1st combination of immunohistochemistry and reverse Strand cDNA Synthesis Kit (TaKaRa). Ten oocytes and embryos transcriptase polymerase chain reaction (RT-PCR), lysis, reverse transcription and qRT-PCR were performed indicated that Faf1 products can be detected in both using the Power SYBR Green Cells-to-Ct Kit (Thermo Fisher mouse oocytes and early embryos and that mutation of Scientific). The primer pairs used for qRT-PCR analysis were the Faf1 gene results in the death of Faf1GT/GT embryos as follows: Faf1, 5′-AACCTGGGCTTGGGATCTGAC-3′ (Adham et al. 2008). Taking our previous study of NLRP2 (forward), 5′-GTGCAATAACGCTGCCAAAGTG-3′ (reverse); into account, we therefore hypothesized that the NLRP2 β-actin, 5′-GAAGTGTGACGTTGACATCCG-3′ (forward), protein interacts with FAF1 to form a maternal complex 5′-ACTTGCGGTGCACGATGGAGG-3′ (reverse). Relative expression levels were normalized using the levels of that plays an essential role in the preimplantation -actin mRNA. Changes in Faf1 gene expression were development of mouse embryos. β calculated using established 2−ΔΔCT methodology (Livak & In the present study, we used the mouse model to Schmittgen 2001). investigate the expression of FAF1 and demonstrated that NLRP2 protein interacts with FAF1 in both oocytes and cleavage-stage embryos. This novel step in the Western blotting characterization of NLRP2-binding proteins indicates Western blotting was carried out as described previously a potential mechanism for NLRP2 in regulating early (Peng et al. 2014). In brief, protein samples from a range of embryo development in the mouse. mouse tissues, fifty oocytes and preimplantation embryos were homogenized and solubilized in RIPA lysis buffer (Beyotime; Jiangsu, PR China), separated by sodium dodecyl Materials and methods sulfate polyacrylamide electrophoresis (SDS-PAGE) and then Animals transferred to polyvinylidene difluoride (PVDF) membranes (Millipore). Membranes were blocked with Tris-buffered saline All experimental procedures were approved by the Animal (TBS pH 7.4)/0.1% Tween 20 (TBS/T) containing 5% non-fat Care Commission of the College of Animal Science, Fujian milk and then incubated at 4°C overnight in TBS/T with 5% Agriculture and Forestry University. All mice were of the ICR non-fat milk containing anti-FAF1 antibody (1:200, Santa strain and were purchased from the Experimental Animal Cruz). After several washes, membranes were incubated with Center of Fujian Medical University (Fuzhou, China). Mice horseradish peroxidase-linked secondary antibody (1:2000, were provided with water and mouse-chow ad libitum and Pierce) and washed. Finally, the enhanced chemiluminescence were maintained on a 14/10 h light/darkness cycle in the (ECL) Advanced Western Blotting Detection System (Pierce) Laboratory Animal Facility of the College of Animal Science, was used to detect FAF1 protein on membranes. β-actin was Fujian Agriculture and Forestry University. used during Western blotting as a loading control (1:1000, Santa Cruz). Chemicals All chemicals and reagents were purchased from Sigma- Co-immunoprecipitation Aldrich unless stated otherwise. Co-immunoprecipitation of target proteins within ovarian lysates was performed with a Pierce Co-Immunoprecipitation Collection of oocytes and embryos Kit (26149, Pierce) in accordance with the manufacturer’s instructions. In brief, 1 mg of protein lysate was first pre- To induce super-ovulation, female mice (8–10 weeks of age) cleared by incubation with control agarose resin to minimize ICR were injected with 10 international units (IU) of pregnant non-specific binding. Protein lysates were then loaded onto mare serum gonadotrophin (PMSG) followed 48 h later by columns containing 1 µg of immobilized antibodies covalently 10 IU of human chorionic gonadotrophin (hCG). Metaphase coupled onto an amine-reactive resin and then incubated II oocytes and zygotes were then collected from the oviduct at 4°C overnight. Negative controls consisted of identical ampullae 16 h after the injection of hCG. Cumulus masses reactions with anti-IgG antibody. Resultant immunoprecipitates were removed from oocytes with hyaluronidase (1 mg/mL). were subsequently recovered by centrifugation, washed Preimplantation embryos were recovered from the oviducts or and used for Western blot analysis. Western blotting with uteri of super-ovulated female by flushing with HEPES-KSOM anti-FAF1 antibodies (1:200, Santa Cruz) or anti-NLRP2 medium (Wang et al. 2008). antibodies (1:500, Abnova, Taipei) was performed when co-immunoprecipitating with anti-NLRP2 antibodies or anti- FAF1 antibodies respectively. Ovarian lysates were loaded as Synthesis of complementary DNA (cDNA) and a positive control. quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) Immunofluorescence Total RNA was extracted from a range of tissues from 4-week-old mice (ovary, testis, uterus, kidney, lung, stomach Immunofluorescence
Load more

Recommended publications
  • Genetic Diagnosis in First Or Second Trimester Pregnancy Loss Using Exome Sequencing: a Systematic Review of Human Essential Genes
    Journal of Assisted Reproduction and Genetics (2019) 36:1539–1548 https://doi.org/10.1007/s10815-019-01499-6 REVIEW Genetic diagnosis in first or second trimester pregnancy loss using exome sequencing: a systematic review of human essential genes Sarah M. Robbins1,2 & Matthew A. Thimm3 & David Valle1 & Angie C. Jelin4 Received: 18 December 2018 /Accepted: 29 May 2019 /Published online: 4 July 2019 # Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Purpose Non-aneuploid recurrent pregnancy loss (RPL) affects approximately 100,000 pregnancies worldwide annually. Exome sequencing (ES) may help uncover the genetic etiology of RPL and, more generally, pregnancy loss as a whole. Previous studies have attempted to predict the genes that, when disrupted, may cause human embryonic lethality. However, predictions by these early studies rarely point to the same genes. Case reports of pathogenic variants identified in RPL cases offer another clue. We evaluated known genetic etiologies of RPL identified by ES. Methods We gathered primary research articles from PubMed and Embase involving case reports of RPL reporting variants identified by ES. Two authors independently reviewed all articles for eligibility and extracted data based on predetermined criteria. Preliminary and amended analysis isolated 380 articles; 15 met all inclusion criteria. Results These 15 articles described 74 families with 279 reported RPLs with 34 candidate pathogenic variants in 19 genes (NOP14, FOXP3, APAF1, CASP9, CHRNA1, NLRP5, MMP10, FGA, FLT1, EPAS1, IDO2, STIL, DYNC2H1, IFT122, PA DI6, CAPS, MUSK, NLRP2, NLRP7) and 26 variants of unknown significance in 25 genes. These genes cluster in four essential pathways: (1) gene expression, (2) embryonic development, (3) mitosis and cell cycle progression, and (4) inflammation and immunity.
    [Show full text]
  • Kids First Pediatric Research Program (Kids First) Poster Session at ASHG Accelerating Pediatric Genomics Research Through Collaboration October 15Th, 2019
    The Gabriella Miller Kids First Pediatric Research Program (Kids First) Poster Session at ASHG Accelerating Pediatric Genomics Research through Collaboration October 15th, 2019 Background The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans- NIH Common Fund program initiated in response to the 2014 Gabriella Miller Kids First Research Act. The program’s vision is to alleviate suffering from childhood cancer and structural birth defects by fostering collaborative research to uncover the etiology of these diseases and support data sharing within the pediatric research community. This is implemented through developing the Gabriella Miller Kids First Data Resource (Kids First Data Resource) and populating this resource with whole genome sequence datasets and associated clinical and phenotypic information. Both childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions. Purpose During this evening poster session, attendees will gain a broad understanding of the utility of the genomic data generated by Kids First, learn about the progress of Kids First X01 cohort projects, and observe demonstrations of the tools and functionalities of the recently launched Kids First Data Resource Portal. The session is an opportunity for the scientific community and public to engage with Kids First investigators, collaborators, and a growing community of researchers, patient foundations, and families. Several other NIH and external data efforts will present posters and be available to discuss collaboration opportunities as we work together to accelerate pediatric research.
    [Show full text]
  • Post-Transcriptional Inhibition of Luciferase Reporter Assays
    THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 34, pp. 28705–28716, August 17, 2012 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Post-transcriptional Inhibition of Luciferase Reporter Assays by the Nod-like Receptor Proteins NLRX1 and NLRC3* Received for publication, December 12, 2011, and in revised form, June 18, 2012 Published, JBC Papers in Press, June 20, 2012, DOI 10.1074/jbc.M111.333146 Arthur Ling‡1,2, Fraser Soares‡1,2, David O. Croitoru‡1,3, Ivan Tattoli‡§, Leticia A. M. Carneiro‡4, Michele Boniotto¶, Szilvia Benko‡5, Dana J. Philpott§, and Stephen E. Girardin‡6 From the Departments of ‡Laboratory Medicine and Pathobiology and §Immunology, University of Toronto, Toronto M6G 2T6, Canada, and the ¶Modulation of Innate Immune Response, INSERM U1012, Paris South University School of Medicine, 63, rue Gabriel Peri, 94276 Le Kremlin-Bicêtre, France Background: A number of Nod-like receptors (NLRs) have been shown to inhibit signal transduction pathways using luciferase reporter assays (LRAs). Results: Overexpression of NLRX1 and NLRC3 results in nonspecific post-transcriptional inhibition of LRAs. Conclusion: LRAs are not a reliable technique to assess the inhibitory function of NLRs. Downloaded from Significance: The inhibitory role of NLRs on specific signal transduction pathways needs to be reevaluated. Luciferase reporter assays (LRAs) are widely used to assess the Nod-like receptors (NLRs)7 represent an important class of activity of specific signal transduction pathways. Although pow- intracellular pattern recognition molecules (PRMs), which are erful, rapid and convenient, this technique can also generate implicated in the detection and response to microbe- and dan- www.jbc.org artifactual results, as revealed for instance in the case of high ger-associated molecular patterns (MAMPs and DAMPs), throughput screens of inhibitory molecules.
    [Show full text]
  • NOD-Like Receptors in the Eye: Uncovering Its Role in Diabetic Retinopathy
    International Journal of Molecular Sciences Review NOD-like Receptors in the Eye: Uncovering Its Role in Diabetic Retinopathy Rayne R. Lim 1,2,3, Margaret E. Wieser 1, Rama R. Ganga 4, Veluchamy A. Barathi 5, Rajamani Lakshminarayanan 5 , Rajiv R. Mohan 1,2,3,6, Dean P. Hainsworth 6 and Shyam S. Chaurasia 1,2,3,* 1 Ocular Immunology and Angiogenesis Lab, University of Missouri, Columbia, MO 652011, USA; [email protected] (R.R.L.); [email protected] (M.E.W.); [email protected] (R.R.M.) 2 Department of Biomedical Sciences, University of Missouri, Columbia, MO 652011, USA 3 Ophthalmology, Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 652011, USA 4 Surgery, University of Missouri, Columbia, MO 652011, USA; [email protected] 5 Singapore Eye Research Institute, Singapore 169856, Singapore; [email protected] (V.A.B.); [email protected] (R.L.) 6 Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO 652011, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-573-882-3207 Received: 9 December 2019; Accepted: 27 January 2020; Published: 30 January 2020 Abstract: Diabetic retinopathy (DR) is an ocular complication of diabetes mellitus (DM). International Diabetic Federations (IDF) estimates up to 629 million people with DM by the year 2045 worldwide. Nearly 50% of DM patients will show evidence of diabetic-related eye problems. Therapeutic interventions for DR are limited and mostly involve surgical intervention at the late-stages of the disease. The lack of early-stage diagnostic tools and therapies, especially in DR, demands a better understanding of the biological processes involved in the etiology of disease progression.
    [Show full text]
  • ATP-Binding and Hydrolysis in Inflammasome Activation
    molecules Review ATP-Binding and Hydrolysis in Inflammasome Activation Christina F. Sandall, Bjoern K. Ziehr and Justin A. MacDonald * Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada; [email protected] (C.F.S.); [email protected] (B.K.Z.) * Correspondence: [email protected]; Tel.: +1-403-210-8433 Academic Editor: Massimo Bertinaria Received: 15 September 2020; Accepted: 3 October 2020; Published: 7 October 2020 Abstract: The prototypical model for NOD-like receptor (NLR) inflammasome assembly includes nucleotide-dependent activation of the NLR downstream of pathogen- or danger-associated molecular pattern (PAMP or DAMP) recognition, followed by nucleation of hetero-oligomeric platforms that lie upstream of inflammatory responses associated with innate immunity. As members of the STAND ATPases, the NLRs are generally thought to share a similar model of ATP-dependent activation and effect. However, recent observations have challenged this paradigm to reveal novel and complex biochemical processes to discern NLRs from other STAND proteins. In this review, we highlight past findings that identify the regulatory importance of conserved ATP-binding and hydrolysis motifs within the nucleotide-binding NACHT domain of NLRs and explore recent breakthroughs that generate connections between NLR protein structure and function. Indeed, newly deposited NLR structures for NLRC4 and NLRP3 have provided unique perspectives on the ATP-dependency of inflammasome activation. Novel molecular dynamic simulations of NLRP3 examined the active site of ADP- and ATP-bound models. The findings support distinctions in nucleotide-binding domain topology with occupancy of ATP or ADP that are in turn disseminated on to the global protein structure.
    [Show full text]
  • Chromatin-Associated Degradation Is Defined by UBXN-3/FAF1 To
    ARTICLE Received 27 Jul 2015 | Accepted 5 Jan 2016 | Published 4 Feb 2016 DOI: 10.1038/ncomms10612 OPEN Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression Andre´ Franz1, Paul A. Pirson1, Domenic Pilger1,2, Swagata Halder2, Divya Achuthankutty2, Hamid Kashkar3, Kristijan Ramadan2 & Thorsten Hoppe1 The coordinated activity of DNA replication factors is a highly dynamic process that involves ubiquitin-dependent regulation. In this context, the ubiquitin-directed ATPase CDC-48/p97 recently emerged as a key regulator of chromatin-associated degradation in several of the DNA metabolic pathways that assure genome integrity. However, the spatiotemporal control of distinct CDC-48/p97 substrates in the chromatin environment remained unclear. Here, we report that progression of the DNA replication fork is coordinated by UBXN-3/FAF1. UBXN-3/FAF1 binds to the licensing factor CDT-1 and additional ubiquitylated proteins, thus promoting CDC-48/p97-dependent turnover and disassembly of DNA replication factor complexes. Consequently, inactivation of UBXN-3/FAF1 stabilizes CDT-1 and CDC-45/GINS on chromatin, causing severe defects in replication fork dynamics accompanied by pronounced replication stress and eventually resulting in genome instability. Our work identifies a critical substrate selection module of CDC-48/p97 required for chromatin- associated protein degradation in both Caenorhabditis elegans and humans, which is relevant to oncogenesis and aging. 1 Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany. 2 Department of Oncology, University of Oxford, Cancer Research UK/Medical Research Council Oxford, Institute for Radiation Oncology, Old Road Campus Research Building, OX3 7DQ Oxford, UK.
    [Show full text]
  • The Landscape of Genomic Imprinting Across Diverse Adult Human Tissues
    Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Research The landscape of genomic imprinting across diverse adult human tissues Yael Baran,1 Meena Subramaniam,2 Anne Biton,2 Taru Tukiainen,3,4 Emily K. Tsang,5,6 Manuel A. Rivas,7 Matti Pirinen,8 Maria Gutierrez-Arcelus,9 Kevin S. Smith,5,10 Kim R. Kukurba,5,10 Rui Zhang,10 Celeste Eng,2 Dara G. Torgerson,2 Cydney Urbanek,11 the GTEx Consortium, Jin Billy Li,10 Jose R. Rodriguez-Santana,12 Esteban G. Burchard,2,13 Max A. Seibold,11,14,15 Daniel G. MacArthur,3,4,16 Stephen B. Montgomery,5,10 Noah A. Zaitlen,2,19 and Tuuli Lappalainen17,18,19 1The Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel; 2Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA; 3Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA; 5Department of Pathology, Stanford University, Stanford, California 94305, USA; 6Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA; 7Wellcome Trust Center for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, United Kingdom; 8Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland; 9Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland;
    [Show full text]
  • NOD2 and Inflammation: Current Insights
    Journal name: Journal of Inflammation Research Article Designation: REVIEW Year: 2018 Volume: 11 Journal of Inflammation Research Dovepress Running head verso: Negroni et al Running head recto: NOD2 and inflammation open access to scientific and medical research DOI: http://dx.doi.org/10.2147/JIR.S137606 Open Access Full Text Article REVIEW NOD2 and inflammation: current insights Anna Negroni1 Abstract: The nucleotide-binding oligomerization domain (NOD) protein, NOD2, belonging to Maria Pierdomenico2 the intracellular NOD-like receptor family, detects conserved motifs in bacterial peptidoglycan Salvatore Cucchiara2 and promotes their clearance through activation of a proinflammatory transcriptional program Laura Stronati3 and other innate immune pathways, including autophagy and endoplasmic reticulum stress. An inactive form due to mutations or a constitutive high expression of NOD2 is associated 1Division of Health Protection Technologies, Territorial and with several inflammatory diseases, suggesting that balanced NOD2 signaling is critical for Production Systems Sustainability the maintenance of immune homeostasis. In this review, we discuss recent developments about Department, ENEA, Rome, Italy; the pathway and mechanisms of regulation of NOD2 and illustrate the principal functions of 2Department of Pediatrics and Infantile Neuropsychiatry, Pediatric the gene, with particular emphasis on its central role in maintaining the equilibrium between Gastroenterology and Liver Unit, intestinal microbiota and host immune responses to control
    [Show full text]
  • Genome Sequences of Tropheus Moorii and Petrochromis Trewavasae, Two Eco‑Morphologically Divergent Cichlid Fshes Endemic to Lake Tanganyika C
    www.nature.com/scientificreports OPEN Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco‑morphologically divergent cichlid fshes endemic to Lake Tanganyika C. Fischer1,2, S. Koblmüller1, C. Börger1, G. Michelitsch3, S. Trajanoski3, C. Schlötterer4, C. Guelly3, G. G. Thallinger2,5* & C. Sturmbauer1,5* With more than 1000 species, East African cichlid fshes represent the fastest and most species‑rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversifcation. We add high‑quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3–9 million years ago (mya), representing the earliest split of the so‑called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecifc), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecifc). GO enrichment analysis of gene regions afected by variants revealed several candidates which may infuence phenotype modifcations related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.
    [Show full text]
  • Greg's Awesome Thesis
    Analysis of alignment error and sitewise constraint in mammalian comparative genomics Gregory Jordan European Bioinformatics Institute University of Cambridge A dissertation submitted for the degree of Doctor of Philosophy November 30, 2011 To my parents, who kept us thinking and playing This dissertation is the result of my own work and includes nothing which is the out- come of work done in collaboration except where specifically indicated in the text and acknowledgements. This dissertation is not substantially the same as any I have submitted for a degree, diploma or other qualification at any other university, and no part has already been, or is currently being submitted for any degree, diploma or other qualification. This dissertation does not exceed the specified length limit of 60,000 words as defined by the Biology Degree Committee. November 30, 2011 Gregory Jordan ii Analysis of alignment error and sitewise constraint in mammalian comparative genomics Summary Gregory Jordan November 30, 2011 Darwin College Insight into the evolution of protein-coding genes can be gained from the use of phylogenetic codon models. Recently sequenced mammalian genomes and powerful analysis methods developed over the past decade provide the potential to globally measure the impact of natural selection on pro- tein sequences at a fine scale. The detection of positive selection in particular is of great interest, with relevance to the study of host-parasite conflicts, immune system evolution and adaptive dif- ferences between species. This thesis examines the performance of methods for detecting positive selection first with a series of simulation experiments, and then with two empirical studies in mammals and primates.
    [Show full text]
  • Mechanisms and Functions of Inflammasomes
    Leading Edge Review Mechanisms and Functions of Inflammasomes Mohamed Lamkanfi1,2,* and Vishva M. Dixit3,* 1Department of Medical Protein Research, VIB, Ghent 9000, Belgium 2Department of Biochemistry, Ghent University, Ghent 9000, Belgium 3Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA *Correspondence: mohamed.lamkanfi@vib-ugent.be (M.L.), [email protected] (V.M.D.) http://dx.doi.org/10.1016/j.cell.2014.04.007 Recent studies have offered a glimpse into the sophisticated mechanisms by which inflamma- somes respond to danger and promote secretion of interleukin (IL)-1b and IL-18. Activation of cas- pases 1 and 11 in canonical and noncanonical inflammasomes, respectively, also protects against infection by triggering pyroptosis, a proinflammatory and lytic mode of cell death. The therapeutic potential of inhibiting these proinflammatory caspases in infectious and autoimmune diseases is raised by the successful deployment of anti-IL-1 therapies to control autoinflammatory diseases associated with aberrant inflammasome signaling. This Review summarizes recent insights into inflammasome biology and discusses the questions that remain in the field. Introduction DNA and trigger the production of type I interferon (Paludan From the primitive lamprey to humans, vertebrates use innate and Bowie, 2013). and adaptive immune systems to defend against pathogens Many PRRs encountering PAMPs and DAMPs trigger (Boehm et al., 2012). In mammals, the innate immune system signaling cascades that promote gene transcription by nuclear mounts the initial response to threats. Concomitantly, den- factor-kB (NF-kB), activator protein 1 (AP1), and interferon regu- dritic cells and other antigen-presenting cells (APCs) relay in- latory factors (IRFs).
    [Show full text]
  • Toll-Like Receptors 1/2/4/6 and Nucleotide-Binding Oligomerization
    applied sciences Article Toll-Like Receptors 1/2/4/6 and Nucleotide-Binding Oligomerization Domain-Like Receptor 2 Are Key Damage-Associated Molecular Patterns Sensors on Periodontal Resident Cells Yu Chen 1, Xiao Xiao Wang 1, Corrie H. C. Ng 1, Sai Wah Tsao 2 and Wai Keung Leung 1,* 1 Faculty of Dentistry, The University of Hong Kong, Hong Kong, China; [email protected] (Y.C.); [email protected] (X.X.W.); [email protected] (C.H.C.N.) 2 School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; [email protected] * Correspondence: [email protected]; Tel.: +852-2859-0417 Featured Application: Damage-associated molecular patterns (DAMP) sensors on periodontal tissue and resident cells were characterized, indicating that nucleotide-binding oligomerization domain-like receptor 2 and toll-like receptors 1/2/4/6 could be significantly elevated in the disease state or upon stimulation. Further investigations are warranted to confirm the relevance of such DAMPs sensors in the innate defense of the cells/tissue concerned. Abstract: Background: Toll-like receptors (TLRs) and nucleotide-binding oligomerization domain Citation: Chen, Y.; Wang, X.X.; Ng, (NOD)-like receptors (NLRs) are innate, damage-associated molecular patterns (DAMP) sensors. C.H.C.; Tsao, S.W.; Leung, W.K. Their expressions in human periodontal resident cells and reactions toward irritations, such as Toll-Like Receptors 1/2/4/6 and hypoxia and lipopolysaccharide (LPS), remain not well characterized. This cross-sectional study Nucleotide-Binding Oligomerization aimed to investigate and characterize TLRs, NOD1/2 and NLRP1/2 expressions at the dento- Domain-Like Receptor 2 Are Key gingival junction.
    [Show full text]