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Evans M, Ellis DA, Vesco AT, Feldman MA, Weissberg-Benchell J, Carcone AI, Miller J, Boucher-Berry C, Buggs-Saxton C, Degnan B, Dekelbab B, Drossos T. Diabetes distress in urban Black youth with type 1 diabetes and their caregivers: associations with glycemic control, depression, and health behaviors. J Pediatr Psychol 2024:jsad096. [PMID: 38216126 DOI: 10.1093/jpepsy/jsad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024] Open
Abstract
OBJECTIVES Adolescents with type 1 diabetes (T1D) and their caregivers endorse high diabetes distress (DD). Limited studies have documented the impact of DD on Black youth. The aims of the present study were to (1) describe DD among a sample of Black adolescents with T1D and their caregivers, (2) compare their DD levels with published normative samples, and (3) determine how DD relates to glycemic outcomes, diabetes self-management, parental monitoring of diabetes, and youth depressive symptoms. METHODS Baseline data from a multicenter clinical trial were used. Participants (N = 155) were recruited from 7 Midwestern pediatric diabetes clinics. Hemoglobin A1c (HbA1c) and measures of DD, parental monitoring of diabetes care, youth depression and diabetes management behaviors were obtained. The sample was split into (1) adolescents (ages 13-14; N = 95) and (2) preadolescents (ages 10-12; N = 60). Analyses utilized Cohen's d effect sizes, Pearson correlations, t-tests, and multiple regression. RESULTS DD levels in youth and caregivers were high, with 45%-58% exceeding either clinical cutoff scores or validation study sample means. Higher DD in youth and caregivers was associated with higher HbA1c, lower diabetes self-management, and elevated depressive symptoms, but not with parental monitoring of diabetes management. CONCLUSIONS Screening for DD in Black youth with T1D and caregivers is recommended, as are culturally informed interventions that can reduce distress levels and lead to improved health outcomes. More research is needed on how systemic inequities contribute to higher DD in Black youth and the strategies/policy changes needed to reduce these inequities.
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Affiliation(s)
- Meredyth Evans
- Pritzker Department of Psychiatry and Behavioral Health, Ann and Robert H. Lurie Children's Hospital and Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL, United States
| | - Deborah A Ellis
- School of Medicine, Wayne State University, Detroit, MI, United States
| | - Anthony T Vesco
- Pritzker Department of Psychiatry and Behavioral Health, Ann and Robert H. Lurie Children's Hospital and Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL, United States
| | - Marissa A Feldman
- Division of Psychology, Johns Hopkins, All Children's Hospital, St Petersburg, FL, United States
| | - Jill Weissberg-Benchell
- Pritzker Department of Psychiatry and Behavioral Health, Ann and Robert H. Lurie Children's Hospital and Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL, United States
| | | | - Jennifer Miller
- Pritzker Department of Psychiatry and Behavioral Health, Ann and Robert H. Lurie Children's Hospital and Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL, United States
| | - Claudia Boucher-Berry
- Division of Pediatric Endocrinology, University of Illinois at Chicago, Chicago, IL, United States
| | | | - Bernard Degnan
- Pediatric Endocrinology, Ascension St John Children's Hospital, Detroit, MI, United States
| | - Bassem Dekelbab
- Pediatric Endocrinology, Beaumont Health Care, Royal Oak, MI, United States
| | - Tina Drossos
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, United States
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Da Fonseca Ferreira A, Wei J, Zhang L, Macon CJ, Degnan B, Jayaweera D, Hare JM, Kolber MA, Bellio M, Khan A, Pan Y, Dykxhoorn DM, Wang L, Dong C. HIV Promotes Atherosclerosis via Circulating Extracellular Vesicle MicroRNAs. Int J Mol Sci 2023; 24:7567. [PMID: 37108729 PMCID: PMC10146407 DOI: 10.3390/ijms24087567] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
People living with HIV (PLHIV) are at a higher risk of having cerebrocardiovascular diseases (CVD) compared to HIV negative (HIVneg) individuals. The mechanisms underlying this elevated risk remains elusive. We hypothesize that HIV infection results in modified microRNA (miR) content in plasma extracellular vesicles (EVs), which modulates the functionality of vascular repairing cells, i.e., endothelial colony-forming cells (ECFCs) in humans or lineage negative bone marrow cells (lin- BMCs) in mice, and vascular wall cells. PLHIV (N = 74) have increased atherosclerosis and fewer ECFCs than HIVneg individuals (N = 23). Plasma from PLHIV was fractionated into EVs (HIVposEVs) and plasma depleted of EVs (HIV PLdepEVs). HIVposEVs, but not HIV PLdepEVs or HIVnegEVs (EVs from HIVneg individuals), increased atherosclerosis in apoE-/- mice, which was accompanied by elevated senescence and impaired functionality of arterial cells and lin- BMCs. Small RNA-seq identified EV-miRs overrepresented in HIVposEVs, including let-7b-5p. MSC (mesenchymal stromal cell)-derived tailored EVs (TEVs) loaded with the antagomir for let-7b-5p (miRZip-let-7b) counteracted, while TEVs loaded with let-7b-5p recapitulated the effects of HIVposEVs in vivo. Lin- BMCs overexpressing Hmga2 (a let-7b-5p target gene) lacking the 3'UTR and as such is resistant to miR-mediated regulation showed protection against HIVposEVs-induced changes in lin- BMCs in vitro. Our data provide a mechanism to explain, at least in part, the increased CVD risk seen in PLHIV.
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Affiliation(s)
- Andrea Da Fonseca Ferreira
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jianqin Wei
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lukun Zhang
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Conrad J. Macon
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Bernard Degnan
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Dushyantha Jayaweera
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Joshua M. Hare
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Kolber
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael Bellio
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Aisha Khan
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yue Pan
- Biostatistics Division, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Derek M. Dykxhoorn
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Liyong Wang
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Chunming Dong
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Section of Cardiology, Department of Medicine, Miami VA Health System, University of Miami, Miami, FL 33146, USA
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3
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Cornejo-Paramo P, Roper K, Degnan S, Degnan B, Wong ES. Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis. Genome Res 2022; 32:474-487. [PMID: 35045977 PMCID: PMC8896464 DOI: 10.1101/gr.275864.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
The chromatin environment plays a central role in regulating developmental gene expression in metazoans. Yet, the ancestral regulatory landscape of metazoan embryogenesis is unknown. Here, we generate chromatin accessibility profiles for six embryonic, plus larval and adult stages in the sponge Amphimedon queenslandica. These profiles are reproducible within stages, reflect histone modifications, and identify transcription factor (TF) binding sequence motifs predictive of cis-regulatory elements operating during embryogenesis in other metazoans, but not the unicellular relative Capsaspora. Motif analysis of chromatin accessibility profiles across Amphimedon embryogenesis identifies three major developmental periods. As in bilaterian embryogenesis, early development in Amphimedon involves activating and repressive chromatin in regions both proximal and distal to transcription start sites. Transcriptionally repressive elements (“silencers”) are prominent during late embryogenesis. They coincide with an increase in cis-regulatory regions harboring metazoan TF binding motifs, as well as an increase in the expression of metazoan-specific genes. Changes in chromatin state and gene expression in Amphimedon suggest the conservation of distal enhancers, dynamically silenced chromatin, and TF-DNA binding specificity in animal embryogenesis.
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4
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Gurung RD, Iwata M, Hiyama A, Taira W, Degnan B, Degnan S, Otaki JM. Comparative Morphological Analysis of the Immature Stages of the Grass Blue Butterflies Zizeeria and Zizina (Lepidoptera: Lycaenidae). Zoolog Sci 2016; 33:384-400. [PMID: 27498798 DOI: 10.2108/zs150171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The pale grass blue butterfly has been used to assess the biological effects of the Fukushima nuclear accident. Zizeeria and Zizina are two closely related genera of grass blue butterflies that are widely distributed in tropical to temperate Asia, Australia, and Africa, making them suitable environmental indicators for these areas. However, the morphological features of the immature stages have been examined only in fragmentary fashion. Here, we reared Zizeeria maha argia, Zizeeria maha okinawana, Zizeeria karsandra karsandra, Zizina emelina emelina, Zizina otis labradus, and Zizina otis riukuensis using a standard rearing method that was developed for Zizeeria maha, and comparatively identified morphological traits to effectively classify the immature stages of species or subspecies. Morphological information on these and other subspecies including Zizeeria knysna knysna and Zizina otis antanossa from Africa was also collected from literature. The subspecies were all reared successfully. The subspecies all had dorsal nectary and tentacle organs with similar morphology. For the subspecies of Zizeeria maha, only minor morphological differences were noted. Similarly, the subspecies of Zizina otis shared many traits. Most importantly, Zizeeria and Zizina differed in the shape of the sensory hairs that accompany the dorsal nectary organ; Zizeeriahad pointed hairs, and Zizina had blunt or rounded hairs. However, Zizina emelina exhibited several intermediate features between these two genera. Overall, the morphological traits did not completely reflect the conventional systematic relationships. This comparative study describes the efficient rearing of the grass blue butterflies and provides a morphological basis for the use of these species as environmental indicators.
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Affiliation(s)
- Raj D Gurung
- 1 The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science,Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Masaki Iwata
- 1 The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science,Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Atsuki Hiyama
- 1 The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science,Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Wataru Taira
- 1 The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science,Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Bernard Degnan
- 2 Faculty of Science, School of Biological Sciences, University of Queensland,St. Lucia, Brisbane, QLD 4072, Australia
| | - Sandie Degnan
- 2 Faculty of Science, School of Biological Sciences, University of Queensland,St. Lucia, Brisbane, QLD 4072, Australia
| | - Joji M Otaki
- 1 The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science,Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
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5
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Abstract
The first step on the path of flux analysis of a new organism with little available literature is the determination of the biomass composition. Once the content of the macromolecular components (protein, RNA, DNA, carbohydrates, lipids) and their composition is known, this composition can be converted into a biomass equation. The biomass equation is an important part of metabolic flux analysis. This equation provides the information about the precursor and energy needs for growth. In many experiments the determination of the growth rate is the simplest flux to be determined, yet this rate determines the net fluxes of a whole range of anabolic pathways in the system and often is used as the objective function in FBA analysis. The challenge for the scientist is to create a biomass equation that represents the organisms of choice under the conditions studied. This chapter outlines basic protocols that can be applied to the quantification of the macromolecular components, using the marine demosponge Amphimedon queenslandica as a case study. As is true for all other sponges and indeed marine animals, A. queenslandica is a holobiont, comprising an animal host plus symbiotic and other associated microbial cells. We show how this complexity can be overcome by developing a fast, yet robust, method for biomass quantification of sponges using the displacement volume. The analytical protocols we describe herein are widely applicable not only to other organisms sampled from complex environments but also to cell cultures. The second part of the chapter highlights the procedures needed to convert a macromolecular composition into a biomass equation.
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Affiliation(s)
- Jabin Watson
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
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6
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Brink S, Nease S, Hasler P, Ramakrishnan S, Wunderlich R, Basu A, Degnan B. A learning-enabled neuron array IC based upon transistor channel models of biological phenomena. IEEE Trans Biomed Circuits Syst 2013; 7:71-81. [PMID: 23853281 DOI: 10.1109/tbcas.2012.2197858] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We present a single-chip array of 100 biologically-based electronic neuron models interconnected to each other and the outside environment through 30,000 synapses. The chip was fabricated in a standard 350 nm CMOS IC process. Our approach used dense circuit models of synaptic behavior, including biological computation and learning, as well as transistor channel models. We use Address-Event Representation (AER) spike communication for inputs and outputs to this IC. We present the IC architecture and infrastructure, including IC chip, configuration tools, and testing platform. We present measurement of small network of neurons, measurement of STDP neuron dynamics, and measurement from a compiled spiking neuron WTA topology, all compiled into this IC.
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Affiliation(s)
- S Brink
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332-250, USA
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7
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Marie B, Le Roy N, Marie A, Dubost L, Milet C, Bedouet L, Becchi M, Zanella-Cléon I, Jackson D, Degnan B, Luquet G, Marin F. Nacre Evolution : A Proteomic Approach. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-1187-kk01-03] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractFrom an evolutionary viewpoint, the molluscan nacre constitutes a fascinating object. This microstructure appeared early, in the Lower Cambrian period, about 530 million years ago, and since then, has been kept unchanged until today. Nacre is restricted to the conchiferan mollusks, where it occurs in t least three main classes, bivalves, gastropods and cephalopods. The aim of the present study is to investigate whether all nacres are built from the same “macromolecular tools”, proteins of the nacre matrix. To this end, we studied three new nacre models, the freshwater bivalve Unio pictorum, the cephalopod Nautilus macromphalus, and the gastropod Haliotis asinina, to which we applied a combined biochemical and proteomic characterization of their respective nacre matrices. The results of our approach, that can be defined as “shellomics” (proteomics applied to shell proteins) shed a new light on the macroevolution of nacre matrix proteins and on the in vitro design of nacre-like biomaterials.
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Shimeld SM, Degnan B, Luke GN. Evolutionary genomics of the Fox genes: origin of gene families and the ancestry of gene clusters. Genomics 2009; 95:256-60. [PMID: 19679177 DOI: 10.1016/j.ygeno.2009.08.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 08/03/2009] [Indexed: 11/16/2022]
Abstract
Over the past decade genomic approaches have begun to revolutionise the study of animal diversity. In particular, genome sequencing programmes have spread beyond the traditional model species to encompass an increasing diversity of animals from many different phyla, as well as unicellular eukaryotes that are closely related to the animals. Whole genome sequences allow researchers to establish, with reasonable confidence, the full complement of any particular family of genes in a genome. Comparison of gene complements from appropriate genomes can reveal the evolutionary history of gene families, indicating when both gene diversification and gene loss have occurred. More than that, however, assembled genomes allow the genomic environment in which individual genes are found to be analysed and compared between species. This can reveal how gene diversification occurred. Here, we focus on the Fox genes, drawing from multiple animal genomes to develop an evolutionary framework explaining the timing and mechanism of origin of the diversity of animal Fox genes. Ancient linkages between genes are a prominent feature of the Fox genes, depicting a history of gene clusters, some of which may be relevant to understanding Fox gene function.
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9
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Tompkins-Macdonald GJ, Gallin WJ, Sakarya O, Degnan B, Leys SP, Boland LM. Expression of a poriferan potassium channel: insights into the evolution of ion channels in metazoans. ACTA ACUST UNITED AC 2009; 212:761-7. [PMID: 19251990 DOI: 10.1242/jeb.026971] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Ion channels establish and regulate membrane potentials in excitable and non-excitable cells. How functional diversification of ion channels contributed to the evolution of nervous systems may be understood by studying organisms at key positions in the evolution of animal multicellularity. We have carried out the first analysis of ion channels cloned from a marine sponge, Amphimedon queenslandica. Phylogenetic comparison of sequences encoding for poriferan inward-rectifier K(+) (Kir) channels suggests that Kir channels from sponges, cnidarians and triploblastic metazoans each arose from a single channel and that duplications arose independently in the different groups. In Xenopus oocytes, AmqKirA and AmqKirB produced K(+) currents with strong inward rectification, as seen in the mammalian Kir2 channels, which are found in excitable cells. The pore properties of AmqKir channels demonstrated strong K(+) selectivity and block by Cs(+) and Ba(2+). We present an original analysis of sponge ion channel physiology and an examination of the phylogenetic relationships of this channel with other cloned Kir channels.
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Goldenberg N, Racine MS, Thomas P, Degnan B, Chandler W, Barkan A. Treatment of pituitary gigantism with the growth hormone receptor antagonist pegvisomant. J Clin Endocrinol Metab 2008; 93:2953-6. [PMID: 18492755 PMCID: PMC2515082 DOI: 10.1210/jc.2007-2283] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Treatment of pituitary gigantism is complex and the results are usually unsatisfactory. OBJECTIVE The objective of the study was to describe the results of therapy of three children with pituitary gigantism by a GH receptor antagonist, pegvisomant. DESIGN This was a descriptive case series of up to 3.5 yr duration. SETTING The study was conducted at a university hospital. PATIENTS Patients included three children (one female, two males) with pituitary gigantism whose GH hypersecretion was incompletely controlled by surgery, somatostatin analog, and dopamine agonist. INTERVENTION The intervention was administration of pegvisomant. MAIN OUTCOME MEASURES Plasma IGF-I and growth velocity were measured. RESULTS In all three children, pegvisomant rapidly decreased plasma IGF-I concentrations. Growth velocity declined to subnormal or normal values. Statural growth fell into lower growth percentiles and acromegalic features resolved. Pituitary tumor size did not change in two children but increased in one boy despite concomitant therapy with a somatostatin analog. CONCLUSIONS Pegvisomant may be an effective modality for the therapy of pituitary gigantism in children. Titration of the dose is necessary for optimal efficacy, and regular surveillance of tumor size is mandatory.
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Affiliation(s)
- Naila Goldenberg
- University of Michigan Medical Center, Division of MEND, Department of Internal Medicine, Ann Arbor, Michigan 48109, USA
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Satou Y, Sasakura Y, Yamada L, Imai KS, Satoh N, Degnan B. A genomewide survey of developmentally relevant genes in Ciona intestinalis. V. Genes for receptor tyrosine kinase pathway and Notch signaling pathway. Dev Genes Evol 2003; 213:254-63. [PMID: 12739141 DOI: 10.1007/s00427-003-0317-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2002] [Accepted: 03/11/2003] [Indexed: 10/26/2022]
Abstract
In the present survey, we identified most of the genes involved in the receptor tyrosine kinase (RTK), mitogen activated protein kinase (MAPK) and Notch signaling pathways in the draft genome sequence of Ciona intestinalis, a basal chordate. Compared to vertebrates, most of the genes found in the Ciona genome had fewer paralogues, although several genes including ephrin, Eph and fringe appeared to have multiplied or duplicated independently in the ascidian genome. In contrast, some genes including kit/flt, PDGF and Trk receptor tyrosine kinases were not found in the present survey, suggesting that these genes are innovations in the vertebrate lineage or lost in the ascidian lineage. The gene set identified in the present analysis provides an insight into genes for the RTK, MAPK and Notch signaling pathways in the ancient chordate genome and thereby how chordates evolved these signaling pathway.
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Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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12
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Yagi K, Satou Y, Mazet F, Shimeld SM, Degnan B, Rokhsar D, Levine M, Kohara Y, Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis. III. Genes for Fox, ETS, nuclear receptors and NFkappaB. Dev Genes Evol 2003; 213:235-44. [PMID: 12743820 DOI: 10.1007/s00427-003-0322-z] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2002] [Accepted: 03/11/2003] [Indexed: 10/26/2022]
Abstract
A survey against the draft genome sequence and the cDNA/EST database of Ciona intestinalis identified a number of genes encoding transcription factors regulating a variety of processes including development. In the present study, we describe almost complete sets of genes for Fox, ETS-domain transcription factors, nuclear receptors, and NFkappaB as well as other factors regulating NFkappaB activity, with their phylogenetic nature. Vertebrate Fox transcription factors are currently delineated into 17 subfamilies: FoxA to FoxQ. The present survey yielded 29 genes of this family in the Ciona genome, 24 of which were Ciona orthologues of known Fox genes. In addition, we found 15 ETS genes, 17 nuclear receptor genes, and several NFkappaB signaling pathway genes in the Ciona genome. The number of Ciona genes in each family is much smaller than that of vertebrates, which represents a simplified feature of the ascidian genome. For example, humans have two NFkappaB genes, three Rel genes, and five NFAT genes, while Ciona has one gene for each family. The Ciona genome also contains smaller numbers of genes for the NFkappaB regulatory system, i.e. after the split of ascidians/vertebrates, vertebrates evolved a more complex NFkappaB system. The present results therefore provide molecular information for the investigation of complex developmental processes, and an insight into chordate evolution.
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Affiliation(s)
- Kasumi Yagi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Yamada L, Kobayashi K, Degnan B, Satoh N, Satou Y. A genomewide survey of developmentally relevant genes in Ciona intestinalis. IV. Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail. Dev Genes Evol 2003; 213:245-53. [PMID: 12743819 DOI: 10.1007/s00427-003-0316-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2002] [Accepted: 03/11/2003] [Indexed: 10/26/2022]
Abstract
Many kinds of transcription factors and regulators play key roles in a variety of developmental processes. In the present survey, genes encoding proteins with conserved HMG-box, bZip domains, and some types of zinc finger motifs were surveyed in the completely sequenced genome of Ciona intestinalis. In the present analysis, 21 HMG-box-containing genes and 26 bZip genes were identified as well as four small groups of zinc finger genes in the Ciona genome. The results also showed that a less redundant set of genes is present in the Ciona genome compared with vertebrate genomes. In addition, cDNA clones for almost all genes identified have been cloned and distributed as a " Ciona intestinalis Gene Collection Release I". The present comprehensive analysis therefore provides a means to study the role of these transcription factors in developmental processes of basal chordates.
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Affiliation(s)
- Lixy Yamada
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KEM, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 2002; 298:2157-67. [PMID: 12481130 DOI: 10.1126/science.1080049] [Citation(s) in RCA: 1185] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.
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Affiliation(s)
- Paramvir Dehal
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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Abdel-Rehim M, Degnan B, El-Ghobary A, Hart A, El-Sayed H, El-Sheikh N, Goodacre J. Serum antibodies to group A streptococcal extracellular and cell-associated antigens in Egyptians with post-streptococcal diseases. FEMS Immunol Med Microbiol 2001; 31:21-7. [PMID: 11476977 DOI: 10.1111/j.1574-695x.2001.tb01581.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated serum antibodies to a comprehensive array of group A streptococcal antigens and superantigens in Egyptian subjects. Antibodies to Streptococcus pyogenes cell-associated proteins and to proteins released by rapidly dividing S. pyogenes were compared in four patient groups with different post-streptococcal diseases and in healthy controls. Enzyme-linked immunosorbent assays showed that total Ig and IgG to extracellular antigens were significantly higher in patients with acute rheumatic fever (ARF) compared to healthy controls, but no differences were found in either total Ig or IgG titres to cell-associated proteins between any of the groups. Western blotting showed that multiple extracellular and cell-associated antigens, covering a wide range of molecular masses, were recognised by all sera, including healthy controls. No evidence was obtained for putative dominant antigens associated with any disease group, although a low molecular mass cell-associated protein (approximately 4 kDa) was clearly recognised by two-thirds of subjects irrespective of disease status. These findings demonstrate that raised serum Ig and IgG titres to extracellular, but not cell-associated, S. pyogenes antigens are a feature of ARF in this population, and suggest that multiple S. pyogenes antigens contribute to this response.
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Affiliation(s)
- M Abdel-Rehim
- Lancashire Postgraduate School of Medicine and Health, Unversity of Central Lancashire, Preston, UK
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Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000; 408:86-9. [PMID: 11081512 DOI: 10.1038/35040556] [Citation(s) in RCA: 1642] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two small RNAs regulate the timing of Caenorhabditis elegans development. Transition from the first to the second larval stage fates requires the 22-nucleotide lin-4 RNA, and transition from late larval to adult cell fates requires the 21-nucleotide let-7 RNA. The lin-4 and let-7 RNA genes are not homologous to each other, but are each complementary to sequences in the 3' untranslated regions of a set of protein-coding target genes that are normally negatively regulated by the RNAs. Here we have detected let-7 RNAs of approximately 21 nucleotides in samples from a wide range of animal species, including vertebrate, ascidian, hemichordate, mollusc, annelid and arthropod, but not in RNAs from several cnidarian and poriferan species, Saccharomyces cerevisiae, Escherichia coli or Arabidopsis. We did not detect lin-4 RNA in these species. We found that let-7 temporal regulation is also conserved: let-7 RNA expression is first detected at late larval stages in C. elegans and Drosophila, at 48 hours after fertilization in zebrafish, and in adult stages of annelids and molluscs. The let-7 regulatory RNA may control late temporal transitions during development across animal phylogeny.
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Affiliation(s)
- A E Pasquinelli
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
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Degnan B, Taylor J, Hawkes C, O'Shea U, Smith J, Robinson JH, Kehoe MA, Boylston A, Goodacre JA. Streptococcus pyogenes type 5 M protein is an antigen, not a superantigen, for human T cells. Hum Immunol 1997; 53:206-15. [PMID: 9129980 DOI: 10.1016/s0198-8859(97)00028-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
M proteins are coiled-coil dimers expressed on group A streptococcal cell surfaces. They have an important role in host antistreptococcal immunity and in poststreptococcal autoimmune sequelae. Controversy has arisen regarding whether type 5 M proteins are superantigenic for human T cells. To investigate this, we have produced and tested M5 in the form of two novel recombinant proteins. We found no evidence of superantigenicity using either recombinant whole M5 protein (rM5) or recombinant pep M5 protein (rpepM5) to activate peripheral blood mononuclear cells (PBMC) from healthy adult volunteers. Short-term, rM5-specific T-cell lines from different subjects were uniformly self-APC restricted and showed no consistent pattern of TCR V beta usage. A synthetic peptide of M5 residues 217-237 was found to contain epitope(s) recognized by some rM5-specific human T cells. PBMC responses to rM5 and rpepM5 in 3- and 7-day proliferation assays were characteristic of antigenic rather than superantigenic stimulation. We conclude that type 5 M protein activates human T cells as a conventional antigen.
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Affiliation(s)
- B Degnan
- School of Clinical Medical Sciences (Rheumatology), University of Newcastle upon Tyne, United Kingdom
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