1
|
Jacob P, Lindelöf H, Rustad CF, Sutton VR, Moosa S, Udupa P, Hammarsjö A, Bhavani GS, Batkovskyte D, Tveten K, Dalal A, Horemuzova E, Nordgren A, Tham E, Shah H, Merckoll E, Orellana L, Nishimura G, Girisha KM, Grigelioniene G. Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13. NPJ Genom Med 2023; 8:39. [PMID: 37993442 PMCID: PMC10665555 DOI: 10.1038/s41525-023-00380-x] [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: 04/06/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023] Open
Abstract
Spondyloepimetaphyseal dysplasia with severe short stature, RPL13-related (SEMD-RPL13), MIM#618728), is a rare autosomal dominant disorder characterized by short stature and skeletal changes such as mild spondylar and epimetaphyseal dysplasia affecting primarily the lower limbs. The genetic cause was first reported in 2019 by Le Caignec et al., and six disease-causing variants in the gene coding for a ribosomal protein, RPL13 (NM_000977.3) have been identified to date. This study presents clinical and radiographic data from 12 affected individuals aged 2-64 years from seven unrelated families, showing highly variable manifestations. The affected individuals showed a range from mild to severe short stature, retaining the same radiographic pattern of spondylar- and epi-metaphyseal dysplasia, but with varying severity of the hip and knee deformities. Two new missense variants, c.548 G>A, p.(Arg183His) and c.569 G>T, p.(Arg190Leu), and a previously known splice variant c.477+1G>A were identified, confirming mutational clustering in a highly specific RNA binding motif. Structural analysis and interpretation of the variants' impact on the protein suggests that disruption of extra-ribosomal functions of the protein through binding of mRNA may play a role in the skeletal phenotype of SEMD-RPL13. In addition, we present gonadal and somatic mosaicism for the condition.
Collapse
Affiliation(s)
- Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hillevi Lindelöf
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilie F Rustad
- Department of Medial Genetics, Oslo University Hospital, Oslo, Norway
| | - Vernon Reid Sutton
- Department of Molecular & Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Cape Town, South Africa
| | - Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Eva Horemuzova
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Else Merckoll
- Department of Radiology, Oslo University Hospital, Oslo, Norway
| | - Laura Orellana
- Protein Dynamics and Mutation lab, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gen Nishimura
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Radiology, Musashino-Yowakai Hospital, Tokyo, Japan
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
2
|
Matsuoka R, Fudim R, Jung S, Zhang C, Bazzone A, Chatzikyriakidou Y, Robinson CV, Nomura N, Iwata S, Landreh M, Orellana L, Beckstein O, Drew D. Author Correction: Structure, mechanism and lipid-mediated remodeling of the mammalian Na +/H + exchanger NHA2. Nat Struct Mol Biol 2023; 30:565. [PMID: 37029209 PMCID: PMC10113147 DOI: 10.1038/s41594-023-00970-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Affiliation(s)
- Rei Matsuoka
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Roman Fudim
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Sukkyeong Jung
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Chenou Zhang
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA
| | | | | | | | - Norimichi Nomura
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - So Iwata
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Orellana
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Beckstein
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA.
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| |
Collapse
|
3
|
Mhashal AR, Yoluk O, Orellana L. Exploring the Conformational Impact of Glycine Receptor TM1-2 Mutations Through Coarse-Grained Analysis and Atomistic Simulations. Front Mol Biosci 2022; 9:890851. [PMID: 35836931 PMCID: PMC9275627 DOI: 10.3389/fmolb.2022.890851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Pentameric ligand-gated ion channels (PLGICs) are a family of proteins that convert chemical signals into ion fluxes through cellular membranes. Their structures are highly conserved across all kingdoms from bacteria to eukaryotes. Beyond their classical roles in neurotransmission and neurological disorders, PLGICs have been recently related to cell proliferation and cancer. Here, we focus on the best characterized eukaryotic channel, the glycine receptor (GlyR), to investigate its mutational patterns in genomic-wide tumor screens and compare them with mutations linked to hyperekplexia (HPX), a Mendelian neuromotor disease that disrupts glycinergic currents. Our analysis highlights that cancer mutations significantly accumulate across TM1 and TM2, partially overlapping with HPX changes. Based on 3D-clustering, conservation, and phenotypic data, we select three mutations near the pore, expected to impact GlyR conformation, for further study by molecular dynamics (MD). Using principal components from experimental GlyR ensembles as framework, we explore the motions involved in transitions from the human closed and desensitized structures and how they are perturbed by mutations. Our MD simulations show that WT GlyR spontaneously explores opening and re-sensitization transitions that are significantly impaired by mutations, resulting in receptors with altered permeability and desensitization properties in agreement with HPX functional data.
Collapse
|
4
|
Matsuoka R, Fudim R, Jung S, Zhang C, Bazzone A, Chatzikyriakidou Y, Robinson CV, Nomura N, Iwata S, Landreh M, Orellana L, Beckstein O, Drew D. Structure, mechanism and lipid-mediated remodeling of the mammalian Na +/H + exchanger NHA2. Nat Struct Mol Biol 2022; 29:108-120. [PMID: 35173351 PMCID: PMC8850199 DOI: 10.1038/s41594-022-00738-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
The Na+/H+ exchanger SLC9B2, also known as NHA2, correlates with the long-sought-after Na+/Li+ exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite the functional importance of NHA2, structural information and the molecular basis for its ion-exchange mechanism have been lacking. Here we report the cryo-EM structures of bison NHA2 in detergent and in nanodiscs, at 3.0 and 3.5 Å resolution, respectively. The bison NHA2 structure, together with solid-state membrane-based electrophysiology, establishes the molecular basis for electroneutral ion exchange. NHA2 consists of 14 transmembrane (TM) segments, rather than the 13 TMs previously observed in mammalian Na+/H+ exchangers (NHEs) and related bacterial antiporters. The additional N-terminal helix in NHA2 forms a unique homodimer interface with a large intracellular gap between the protomers, which closes in the presence of phosphoinositol lipids. We propose that the additional N-terminal helix has evolved as a lipid-mediated remodeling switch for the regulation of NHA2 activity.
Collapse
Affiliation(s)
- Rei Matsuoka
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Roman Fudim
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Sukkyeong Jung
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Chenou Zhang
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA
| | | | | | | | - Norimichi Nomura
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - So Iwata
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Orellana
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Beckstein
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA.
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| |
Collapse
|
5
|
Driscoll A, Romaniuk H, Dinh D, Amerena J, Brennan A, Hare DL, Kaye D, Lefkovits J, Lockwood S, Neil C, Prior D, Reid CM, Orellana L. Clinical risk prediction model for 30-day all-cause re-hospitalisation or mortality in patients hospitalised with heart failure. Int J Cardiol 2021; 350:69-76. [PMID: 34979149 DOI: 10.1016/j.ijcard.2021.12.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/18/2021] [Accepted: 12/28/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND This study aimed to develop a risk prediction model (AUS-HF model) for 30-day all-cause re-hospitalisation or death among patients admitted with acute heart failure (HF) to inform follow-up after hospitalisation. The model uses routinely collected measures at point of care. METHODS We analyzed pooled individual-level data from two cohort studies on acute HF patients followed for 30-days after discharge in 17 hospitals in Victoria, Australia (2014-2017). A set of 58 candidate predictors, commonly recorded in electronic medical records (EMR) including demographic, medical and social measures were considered. We used backward stepwise selection and LASSO for model development, bootstrap for internal validation, C-statistic for discrimination, and calibration slopes and plots for model calibration. RESULTS The analysis included 1380 patients, 42.1% female, median age 78.7 years (interquartile range = 16.2), 60.0% experienced previous hospitalisation for HF and 333 (24.1%) were re-hospitalised or died within 30 days post-discharge. The final risk model included 10 variables (admission: eGFR, and prescription of anticoagulants and thiazide diuretics; discharge: length of stay>3 days, systolic BP, heart rate, sodium level (<135 mmol/L), >10 prescribed medications, prescription of angiotensin converting enzyme inhibitors or angiotensin receptor blockers, and anticoagulants prescription. The discrimination of the model was moderate (C-statistic = 0.684, 95%CI 0.653, 0.716; optimism estimate = 0.062) with good calibration. CONCLUSIONS The AUS-HF model incorporating routinely collected point-of-care data from EMRs enables real-time risk estimation and can be easily implemented by clinicians. It can predict with moderate accuracy risk of 30-day hospitalisation or mortality and inform decisions around the intensity of follow-up after hospital discharge.
Collapse
Affiliation(s)
- A Driscoll
- Deakin University, School of Nursing and Midwifery, 1 Gheringhap Street, Geelong, VIC 3220, Australia; Austin Health, Dept of Cardiology, Studley Rd, Heidelberg, VIC 3081, Australia.
| | - H Romaniuk
- Deakin University, Biostatistics Unit, Faculty of Health, 1 Gheringhap Street, Geelong, VIC 3220, Australia.
| | - D Dinh
- Monash University, School of Medicine and Preventive Health, Commercial Rd, Prahran, VIC 3121, Australia.
| | - J Amerena
- University Hospital Geelong, Cardiology Research Department, PO Box 281, Geelong 3220, Australia.
| | - A Brennan
- Monash University, School of Medicine and Preventive Health, Commercial Rd, Prahran, VIC 3121, Australia
| | - D L Hare
- Austin Health, Dept of Cardiology, Studley Rd, Heidelberg, VIC 3081, Australia; University of Melbourne, School of Medicine, Swanson St, Melbourne, VIC 3001, Australia.
| | - D Kaye
- Baker Heart and Diabetes Institute, Commercial Rd, Prahran, VIC 3121, Australia; Alfred Health, Department of Cardiology, Commercial Rd, Prahran, VIC 3121, Australia.
| | - J Lefkovits
- Monash University, School of Medicine and Preventive Health, Commercial Rd, Prahran, VIC 3121, Australia
| | - S Lockwood
- University Hospital Geelong, Cardiology Research Department, PO Box 281, Geelong 3220, Australia; Monash Health, Department of Cardiology, 246 Clayton Rd, Clayton, VIC 3168, Australia.
| | - C Neil
- University Hospital Geelong, Cardiology Research Department, PO Box 281, Geelong 3220, Australia; Western Health, Department of Cardiology, 160 Gordon St, Footscray, VIC 3011, Australia.
| | - D Prior
- St Vincents Hospital, Department of Cardiology, 41 Fitzroy Parade, Fitzroy, VIC 3065, Australia.
| | - C M Reid
- Curtin University, School of Public Health, NHMRC Centre for Research Excellence in Cardiovascular Outcomes Improvement, Kent St, Bentley, WA 6102, Australia.
| | - L Orellana
- Deakin University, Biostatistics Unit, Faculty of Health, 1 Gheringhap Street, Geelong, VIC 3220, Australia
| |
Collapse
|
6
|
Thulasingam M, Orellana L, Nji E, Ahmad S, Rinaldo-Matthis A, Haeggström JZ. Crystal structures of human MGST2 reveal synchronized conformational changes regulating catalysis. Nat Commun 2021; 12:1728. [PMID: 33741927 PMCID: PMC7979937 DOI: 10.1038/s41467-021-21924-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/16/2021] [Indexed: 11/23/2022] Open
Abstract
Microsomal glutathione S-transferase 2 (MGST2) produces leukotriene C4, key for intracrine signaling of endoplasmic reticulum (ER) stress, oxidative DNA damage and cell death. MGST2 trimer restricts catalysis to only one out of three active sites at a time, but the molecular basis is unknown. Here, we present crystal structures of human MGST2 combined with biochemical and computational evidence for a concerted mechanism, involving local unfolding coupled to global conformational changes that regulate catalysis. Furthermore, synchronized changes in the biconical central pore modulate the hydrophobicity and control solvent influx to optimize reaction conditions at the active site. These unique mechanistic insights pertain to other, structurally related, drug targets. Microsomal glutathione S-transferase 2 (MGST2) produces leukotriene C4, an intracrine mediator of cell death. Structural, biochemical and computational analyses of human MGST2 suggest a mechanism employed by the enzyme to restrict catalysis to only one active site within the MGST2 trimer.
Collapse
Affiliation(s)
- Madhuranayaki Thulasingam
- Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden.
| | - Laura Orellana
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16, 106 91 Stockholm, Sweden.,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Emmanuel Nji
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16, 106 91 Stockholm, Sweden.,BioStruct-Africa, Stockholm, Sweden
| | - Shabbir Ahmad
- Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Agnes Rinaldo-Matthis
- Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden
| | - Jesper Z Haeggström
- Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden.
| |
Collapse
|
7
|
Winklemann I, Matsuoka R, Meier PF, Shutin D, Zhang C, Orellana L, Sexton R, Landreh M, Robinson CV, Beckstein O, Drew D. Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9. EMBO J 2020; 39:e105908. [PMID: 33118634 PMCID: PMC7737618 DOI: 10.15252/embj.2020105908] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/21/2022] Open
Abstract
Na+ /H+ exchangers (NHEs) are ancient membrane-bound nanomachines that work to regulate intracellular pH, sodium levels and cell volume. NHE activities contribute to the control of the cell cycle, cell proliferation, cell migration and vesicle trafficking. NHE dysfunction has been linked to many diseases, and they are targets of pharmaceutical drugs. Despite their fundamental importance to cell homeostasis and human physiology, structural information for the mammalian NHE was lacking. Here, we report the cryogenic electron microscopy structure of NHE isoform 9 (SLC9A9) from Equus caballus at 3.2 Å resolution, an endosomal isoform highly expressed in the brain and associated with autism spectrum (ASD) and attention deficit hyperactivity (ADHD) disorders. Despite low sequence identity, the NHE9 architecture and ion-binding site are remarkably similar to distantly related bacterial Na+ /H+ antiporters with 13 transmembrane segments. Collectively, we reveal the conserved architecture of the NHE ion-binding site, their elevator-like structural transitions, the functional implications of autism disease mutations and the role of phosphoinositide lipids to promote homodimerization that, together, have important physiological ramifications.
Collapse
Affiliation(s)
- Iven Winklemann
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Rei Matsuoka
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Pascal F Meier
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Denis Shutin
- Department of ChemistryUniversity of OxfordOxfordUK
| | - Chenou Zhang
- Department of PhysicsCenter for Biological PhysicsArizona State UniversityTempeAZUSA
| | - Laura Orellana
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Ricky Sexton
- Department of PhysicsCenter for Biological PhysicsArizona State UniversityTempeAZUSA
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstituteStockholmSweden
| | | | - Oliver Beckstein
- Department of PhysicsCenter for Biological PhysicsArizona State UniversityTempeAZUSA
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| |
Collapse
|
8
|
Valentino G, Galgani JE, Álamos M, Orellana L, Adasme M, Berríos A, Acevedo M. Anthropometric and blood pressure changes in patients with or without nutritional counselling during cardiac rehabilitation: a retrospective study. J Hum Nutr Diet 2020; 34:402-412. [DOI: 10.1111/jhn.12823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 11/29/2022]
Affiliation(s)
- G. Valentino
- División de Enfermedades Cardiovasculares, Escuela de Medicina Facultad de Medicina Pontificia Universidad Católica de Chile Santiago Chile
- Carrera de Nutrición y Dietética Departamento de Ciencias de la Salud Facultad de Medicina Pontificia Universidad Católica de Chile Santiago Chile
| | - J. E. Galgani
- Carrera de Nutrición y Dietética Departamento de Ciencias de la Salud Facultad de Medicina Pontificia Universidad Católica de Chile Santiago Chile
- Departamento de Nutrición, Diabetes y Metabolismo Facultad de Medicina Pontificia Universidad Católica de Chile Santiago Chile
| | - M. Álamos
- Carrera de Nutrición y Dietética Departamento de Ciencias de la Salud Facultad de Medicina Pontificia Universidad Católica de Chile Santiago Chile
| | - L. Orellana
- División de Enfermedades Cardiovasculares, Escuela de Medicina Facultad de Medicina Pontificia Universidad Católica de Chile Santiago Chile
| | - M. Adasme
- División de Enfermedades Cardiovasculares, Escuela de Medicina Facultad de Medicina Pontificia Universidad Católica de Chile Santiago Chile
| | - A. Berríos
- División de Enfermedades Cardiovasculares, Escuela de Medicina Facultad de Medicina Pontificia Universidad Católica de Chile Santiago Chile
| | - M. Acevedo
- División de Enfermedades Cardiovasculares, Escuela de Medicina Facultad de Medicina Pontificia Universidad Católica de Chile Santiago Chile
| |
Collapse
|
9
|
Orellana L, Gustavsson J, Bergh C, Yoluk O, Lindahl E. eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces. Bioinformatics 2020; 35:3505-3507. [PMID: 30838394 PMCID: PMC6748756 DOI: 10.1093/bioinformatics/btz104] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 12/30/2018] [Accepted: 02/15/2019] [Indexed: 11/15/2022] Open
Abstract
SUMMARY Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Brownian Dynamics Importance Sampling, a coarse-grained simulation algorithm, which spontaneously predicts transition intermediates trapped experimentally. In addition to path-generation, the server provides an interactive 2D-motion landscape graphical representation of the transitions or any additional conformers to explore their structural relationships. AVAILABILITY AND IMPLEMENTATION eBDIMS is available online: http://ebdims.biophysics.se/ or as standalone software: https://github.com/laura-orellana/eBDIMS, https://github.com/cabergh/eBDIMS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Laura Orellana
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Johan Gustavsson
- Department of Computational Science and Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cathrine Bergh
- Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, Sweden
| | - Ozge Yoluk
- Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, Sweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, Sweden
| |
Collapse
|
10
|
Howard RJ, Zhuang Y, Heusser SA, Bergh CC, Rovsnik U, Orellana L, Lindahl E. Allosteric Gating Determinants in the Transmembrane Domain of Pentameric Ligand-Gated Ion Channels. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
11
|
Bergh C, Orellana L, Heusser SA, Howard RJ, Lindahl E. Mapping pH-Dependent State Transitions of a Pentameric Ligand-gated Ion Channel through Markov State Modeling. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
12
|
Qureshi AA, Suades A, Matsuoka R, Brock J, McComas SE, Nji E, Orellana L, Claesson M, Delemotte L, Drew D. The molecular basis for sugar import in malaria parasites. Nature 2020; 578:321-325. [PMID: 31996846 DOI: 10.1038/s41586-020-1963-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 01/03/2020] [Indexed: 12/11/2022]
Abstract
Elucidating the mechanism of sugar import requires a molecular understanding of how transporters couple sugar binding and gating events. Whereas mammalian glucose transporters (GLUTs) are specialists1, the hexose transporter from the malaria parasite Plasmodium falciparum PfHT12,3 has acquired the ability to transport both glucose and fructose sugars as efficiently as the dedicated glucose (GLUT3) and fructose (GLUT5) transporters. Here, to establish the molecular basis of sugar promiscuity in malaria parasites, we determined the crystal structure of PfHT1 in complex with D-glucose at a resolution of 3.6 Å. We found that the sugar-binding site in PfHT1 is very similar to those of the distantly related GLUT3 and GLUT5 structures4,5. Nevertheless, engineered PfHT1 mutations made to match GLUT sugar-binding sites did not shift sugar preferences. The extracellular substrate-gating helix TM7b in PfHT1 was positioned in a fully occluded conformation, providing a unique glimpse into how sugar binding and gating are coupled. We determined that polar contacts between TM7b and TM1 (located about 15 Å from D-glucose) are just as critical for transport as the residues that directly coordinate D-glucose, which demonstrates a strong allosteric coupling between sugar binding and gating. We conclude that PfHT1 has achieved substrate promiscuity not by modifying its sugar-binding site, but instead by evolving substrate-gating dynamics.
Collapse
Affiliation(s)
- Abdul Aziz Qureshi
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Albert Suades
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rei Matsuoka
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Joseph Brock
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sarah E McComas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Emmanuel Nji
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Laura Orellana
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Magnus Claesson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| |
Collapse
|
13
|
Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, Gahman TC, Shiau AK, Zhou H, DeGroot J, Sulman EP, Cavenee WK, Kolodner RD, Chen CC, Furnari FB. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell 2019; 36:690-691. [PMID: 31821785 PMCID: PMC6946119 DOI: 10.1016/j.ccell.2019.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
14
|
Abstract
Large-scale conformational changes are essential to link protein structures with their function at the cell and organism scale, but have been elusive both experimentally and computationally. Over the past few years developments in cryo-electron microscopy and crystallography techniques have started to reveal multiple snapshots of increasingly large and flexible systems, deemed impossible only short time ago. As structural information accumulates, theoretical methods become central to understand how different conformers interconvert to mediate biological function. Here we briefly survey current in silico methods to tackle large conformational changes, reviewing recent examples of cross-validation of experiments and computational predictions, which show how the integration of different scale simulations with biological information is already starting to break the barriers between the in silico, in vitro, and in vivo worlds, shedding new light onto complex biological problems inaccessible so far.
Collapse
Affiliation(s)
- Laura Orellana
- Institutionen för Biokemi och Biofysik, Stockholms Universitet, Stockholm, Sweden.,Science for Life Laboratory, Solna, Sweden
| |
Collapse
|
15
|
silva M, Wolff M, Orellana L, Carrasco C, Canals A, Lizama D. 1262. Comparative Evaluation of Native and Migrant HIV+ Pregnant Women in Chile. Open Forum Infect Dis 2019. [PMCID: PMC6808698 DOI: 10.1093/ofid/ofz360.1125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
The reported data of HIV + pregnant women in Latin America (LA) is scarce. Given the political and social changes that have occurred in recent years, Chile has had to face immigration as a recent phenomenon. Based on this, the objective of this analysis was to determine the baseline characteristics, virological during pregnancy and postpartum, and the impact of immigration on adult women infected with HIV
Methods
The registry of HIV + pregnant women of Fundación Arriarán was analyzed since 2006. The baseline characteristics,undetectability at delivery, vertical transmission and retention were determined.Estimators as mean and median,standard deviation and interquartile range; absolute and relative frequencies were used and for the bivariate analysis the t-test and chi2,Mann–Whitney and Fisher’s exact. For follow-up, the Kaplan–Meier method was used.
Results
A total of 214 pregnancies in 198 HIV + women were included. A 54% of foreigners (of Haitian predominance) was found, 2/3 of the foreigners were enrolled after 2016. A 73% was diagnosed with HIV at the time of pregnancy. Average age was 28.6 years. Baseline CD4 cell count was 396 cel/mm3. A 7.7% were admitted with advanced pregnancy and 4.6% had a history of drug addiction. None of these variables had significant differences between both groups. The variables of gestational age at admission (15 vs. 21; P < 0.001), gestational age at the beginning of therapy (18 vs. 21; P < 0.001), CDC stage and baseline viral load (9750 vs. 644 copies/mL;P < 0.001) were statistically significant between Chileans and foreigners. 58% of the patients achieved undetectability at the time of delivery without differences between both groups. (55% vs. 63%; p0.42) Almost 90% of women with detectable viral load at delivery was less than 1000 copies/mL (88,9%). 93% received full vertical transmission protocol and the prematurity rate was 16.6%. The vertical transmission was 2.6% without differences between nationals and foreigners. In the postpartum follow-up,70% were retained, 73% of them undetectable on the latest follow-up visit.
Conclusion
Despite the cultural and language limitations, foreign patients maintained a compliance similar to those of Chile, achieving a low transmission rate vertical and good adherence to postpartum controls.
Disclosures
All authors: No reported disclosures.
Collapse
Affiliation(s)
- macarena silva
- Fundacion Arriaran, Santiago, Region Metropolitana, Chile
| | - Marcelo Wolff
- Fundacion Arriaran, Santiago, Region Metropolitana, Chile
| | - Laura Orellana
- Fundacion Arriaran, Santiago, Region Metropolitana, Chile
| | | | - Andrea Canals
- University of Chile, Santiago, Region Metropolitana, Chile
| | - Danae Lizama
- Fundacion Arriaran, Santiago, Region Metropolitana, Chile
| |
Collapse
|
16
|
Orellana L. Convergence of EGFR glioblastoma mutations: evolution and allostery rationalizing targeted therapy. Mol Cell Oncol 2019; 6:e1630798. [PMID: 31528699 PMCID: PMC6736128 DOI: 10.1080/23723556.2019.1630798] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 12/31/2022]
Abstract
EGFR mutations display striking organ-site asymmetry and heterogeneity. We have shown that structurally diverse extracellular mutations, typical of glioblastomas, converge to a similar intermediate conformation, which can be synergistically targeted extra- and intracelullarly by antibody mAb806 and type-II kinase inhibitors. Our findings reveal convergence behind heterogeneity, paving the way for allostery-based co-targeting.
Collapse
Affiliation(s)
- Laura Orellana
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Solna, Sweden
| |
Collapse
|
17
|
Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, Gahman TC, Shiau AK, Zhou H, DeGroot J, Sulman EP, Cavenee WK, Kolodner RD, Chen CC, Furnari FB. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell 2019; 35:816. [PMID: 31085179 PMCID: PMC8717880 DOI: 10.1016/j.ccell.2019.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
18
|
Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, Gahman TC, Shiau AK, Zhou H, DeGroot J, Sulman EP, Cavenee WK, Kolodner RD, Chen CC, Furnari FB. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell 2019; 35:504-518.e7. [PMID: 30827889 PMCID: PMC6424615 DOI: 10.1016/j.ccell.2019.01.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 11/10/2018] [Accepted: 01/28/2019] [Indexed: 11/21/2022]
Abstract
Ionizing radiation (IR) and chemotherapy are standard-of-care treatments for glioblastoma (GBM) patients and both result in DNA damage, however, the clinical efficacy is limited due to therapeutic resistance. We identified a mechanism of such resistance mediated by phosphorylation of PTEN on tyrosine 240 (pY240-PTEN) by FGFR2. pY240-PTEN is rapidly elevated and bound to chromatin through interaction with Ki-67 in response to IR treatment and facilitates the recruitment of RAD51 to promote DNA repair. Blocking Y240 phosphorylation confers radiation sensitivity to tumors and extends survival in GBM preclinical models. Y240F-Pten knockin mice showed radiation sensitivity. These results suggest that FGFR-mediated pY240-PTEN is a key mechanism of radiation resistance and is an actionable target for improving radiotherapy efficacy.
Collapse
Affiliation(s)
- Jianhui Ma
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Jorge A Benitez
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Jie Li
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Shunichiro Miki
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Claudio Ponte de Albuquerque
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Thais Galatro
- Department of Neurology, Laboratory of Molecular and Cellular Biology, LIM15, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Laura Orellana
- Science for Life Laboratory, 17121 Stockholm, Sweden; Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 114 18 Stockholm, Sweden
| | - Ciro Zanca
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Rachel Reed
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Antonia Boyer
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Tomoyuki Koga
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Nissi M Varki
- Department of Pathology, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Suely Kazue Nagahashi Marie
- Department of Neurology, Laboratory of Molecular and Cellular Biology, LIM15, School of Medicine, University of São Paulo, São Paulo, Brazil; Center for Studies of Cellular and Molecular Therapy (NAP-NETCEM-NUCEL), University of São Paulo, São Paulo, Brazil
| | - Erik Lindahl
- Science for Life Laboratory, 17121 Stockholm, Sweden; Theoretical and Computational Biophysics, Department of Theoretical Physics, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 114 18 Stockholm, Sweden
| | - Timothy C Gahman
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Andrew K Shiau
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - Huilin Zhou
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA
| | - John DeGroot
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik P Sulman
- Departments of Radiation Oncology, Translational Molecular Pathology, and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, San Diego Branch, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660, USA; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pathology, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
19
|
Ugalde A, Aranda S, Paul C, Orellana L, Plueckhahn I, Segan C, Baird D, Otmar R, Brown S, Armstrong P, Wolff A, Shee AW, Livingston P. Improving Health Outcomes for People With Cancer in Rural and Regional Areas by Embedding Evidence-Based Smoking-Cessation Strategies Into Usual Care: A Study Protocol. J Glob Oncol 2018. [DOI: 10.1200/jgo.18.10100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] Open
Abstract
Background: Smoking following a diagnosis of cancer is a powerful clinical risk indicator, with known poorer health outcomes and associated health care costs. In Australia, smoking rates are higher in rural and regional areas. There are established and effective interventions to promote smoking cessation after a diagnosis of cancer yet these are not in routine practice. Aim: This protocol paper reports on a study that aims to embed evidence-based smoking cessation strategies for people with cancer who are current smokers into routine care, resulting in in system wide improvements, an implemented program and model for further dissemination. Methods: Across three rural/regional sites, and with partners Quit Victoria and Western Alliance, this study employs a variety of methodologies to embed smoking cessation support to improve outcomes for people with cancer who currently smoke. Specifically, the project will embed a system of responsibilities and training in rural and regional health services to routinely engage people with cancer who smoke in support services. The program will: · Promote routine delivery of smoking cessation care by trained oncology staff (oncologists/nurses/ allied health) · Establish referral pathways to Quitline · Correspond with general practitioners, to: i) outline the benefits of quitting in this context, ii) promote access to nicotine replacement therapy and iii) support quitting in the community. · Improve routine recording of smoking status and documentation of provision of brief intervention (personalised advice given, resources provided) and outcomes. Participants: are oncology staff and general practitioners across three health services: Ballarat Health Service, East Grampians Health Service (Ararat), Wimmera Health Care Group (Horsham), all located in Victoria, Australia. Data collection will occur across four sources: 1) Oncology staff: qualitative and quantitative data collection understanding confidence and views on provision on cessation advice; 2) Monitoring Quitline calls, 3) Interview with local general practitioners and 4) Medical record reviews to explore frequency of recording of smoking status. Data will be collected pre/postintervention. Results: The project is underway with the intervention manuals in development. The project is due for completion in 2020. Conclusion: This project takes a health services approach to integration of smoking cessation support in routine care for people with cancer in rural and regional areas. This program of work has capacity to determine best approaches to integrate smoking cessation into routine care, resulting in reduced mortality and morbidity, improved effectiveness of anticancer treatments, and reduced health care costs; by establishing internationally relevant, embedded health care interventions.
Collapse
Affiliation(s)
- A. Ugalde
- Deakin University, Melbourne, Australia
| | - S. Aranda
- Deakin University, Melbourne, Australia
| | - C. Paul
- Deakin University, Melbourne, Australia
| | | | | | - C. Segan
- Deakin University, Melbourne, Australia
| | - D. Baird
- Deakin University, Melbourne, Australia
| | - R. Otmar
- Deakin University, Melbourne, Australia
| | - S. Brown
- Deakin University, Melbourne, Australia
| | | | - A. Wolff
- Deakin University, Melbourne, Australia
| | | | | |
Collapse
|
20
|
Hoang N, Orellana L, Le T, Gibson R, Worsley A, Sinclair A, Szymlek-Gay E. Multiple micronutrient supplementation improves short-term cognitive function in children in Hai Phong city, Vietnam. Clin Nutr 2018. [DOI: 10.1016/j.clnu.2018.06.1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
21
|
Hoang N, Orellana L, Le T, Gibson R, Worsley A, Sinclair A, Szymlek-Gay E. Anaemia among primary school children in hai phong city, Vietnam: A cross-sectional study. Clin Nutr 2018. [DOI: 10.1016/j.clnu.2018.06.1886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
22
|
Binder ZA, Thorne AH, Bakas S, Wileyto EP, Bilello M, Akbari H, Rathore S, Ha SM, Zhang L, Ferguson CJ, Dahiya S, Bi WL, Reardon DA, Idbaih A, Felsberg J, Hentschel B, Weller M, Bagley SJ, Morrissette JJD, Nasrallah MP, Ma J, Zanca C, Scott AM, Orellana L, Davatzikos C, Furnari FB, O'Rourke DM. Epidermal Growth Factor Receptor Extracellular Domain Mutations in Glioblastoma Present Opportunities for Clinical Imaging and Therapeutic Development. Cancer Cell 2018; 34:163-177.e7. [PMID: 29990498 PMCID: PMC6424337 DOI: 10.1016/j.ccell.2018.06.006] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 02/27/2018] [Accepted: 06/11/2018] [Indexed: 12/19/2022]
Abstract
We explored the clinical and pathological impact of epidermal growth factor receptor (EGFR) extracellular domain missense mutations. Retrospective assessment of 260 de novo glioblastoma patients revealed a significant reduction in overall survival of patients having tumors with EGFR mutations at alanine 289 (EGFRA289D/T/V). Quantitative multi-parametric magnetic resonance imaging analyses indicated increased tumor invasion for EGFRA289D/T/V mutants, corroborated in mice bearing intracranial tumors expressing EGFRA289V and dependent on ERK-mediated expression of matrix metalloproteinase-1. EGFRA289V tumor growth was attenuated with an antibody against a cryptic epitope, based on in silico simulation. The findings of this study indicate a highly invasive phenotype associated with the EGFRA289V mutation in glioblastoma, postulating EGFRA289V as a molecular marker for responsiveness to therapy with EGFR-targeting antibodies.
Collapse
Affiliation(s)
- Zev A Binder
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Spyridon Bakas
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E Paul Wileyto
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michel Bilello
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hamed Akbari
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Saima Rathore
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sung Min Ha
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Logan Zhang
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cole J Ferguson
- Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Sonika Dahiya
- Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Wenya Linda Bi
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Brigham and Woman's Hospital, Harvard Medical Center, Boston, MA 02115, USA
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ahmed Idbaih
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris 75013, France
| | - Joerg Felsberg
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, Moorenstrasse 5, Duesseldorf 40225, Germany
| | - Bettina Hentschel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Medical Faculty, Härtelstrasse 16, Leipzig 04107, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich 8091, Switzerland
| | - Stephen J Bagley
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - MacLean P Nasrallah
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jianhui Ma
- Ludwig Institute for Cancer Research, La Jolla, San Diego 92093, USA
| | - Ciro Zanca
- Ludwig Institute for Cancer Research, La Jolla, San Diego 92093, USA
| | - Andrew M Scott
- Olivia Newton-John Cancer Research Institute, La Trobe University, Melbourne, Australia
| | - Laura Orellana
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, La Jolla, San Diego 92093, USA.
| | - Donald M O'Rourke
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
23
|
Gaskin C, Keesman K, Rogerson M, Salmon J, Orellana L. Physical activity and sedentary behavior among older adults with non-communicable diseases. Eur J Public Health 2017. [DOI: 10.1093/eurpub/ckx187.244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- C Gaskin
- Deakin University, Geelong, Australia
| | - K Keesman
- Deakin University, Geelong, Australia
| | | | - J Salmon
- Deakin University, Geelong, Australia
| | | |
Collapse
|
24
|
Orellana L, Yoluk Ö, Carrillo O, Orozco M, Lindahl E. Trapping On-Pathway Intermediates for Large Scale Conformational Changes with Coarse-Grained Simulations. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
25
|
Thorne AH, Orellana L, Parisian A, Cavenee W, Furnari F. CSIG-22. MUTATIONAL HETEROGENEITY OF THE EGFR EXTRACELLULAR DOMAIN PROMOTES AN ONCOGENIC UNTETHERED TRANSITIONAL CONFORMATION AND THE POTENTIAL FOR GREATER THERAPEUTIC TARGETING IN GBM PATIENTS. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now212.183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
26
|
Orellana L, Yoluk O, Orozco M, Lindahl E. Revealing the Mechanism for Conformational Changes from Structurally Rich Ensembles. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
27
|
Yoluk O, Orellana L, Bertaccini EJ, Trudell JR, Lindahl E. Principal Components from Ligand-Gated Ion Channel Structures Enable Ensemble Studies of Microsecond-Scale Transitions. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
28
|
Orellana L, Rueda M, Ferrer-Costa C, Lopez-Blanco JR, Chacón P, Orozco M. Approaching Elastic Network Models to Molecular Dynamics Flexibility. J Chem Theory Comput 2015; 6:2910-23. [PMID: 26616090 DOI: 10.1021/ct100208e] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Elastic network models (ENMs) are coarse-grained descriptions of proteins as networks of coupled harmonic oscillators. However, despite their widespread application to study collective movements, there is still no consensus parametrization for the ENMs. When compared to molecular dynamics (MD) flexibility in solution, the ENMs tend to disperse the important motions into multiple modes. We present here a new ENM, trained against a database of atomistic MD trajectories. The role of residue connectivity, the analytical form of the force constants, and the threshold for interactions were systematically explored. We found that contacts between the three nearest sequence neighbors are crucial determinants of the fundamental motions. We developed a new general potential function including both the sequential and spatial relationships between interacting residue pairs which is robust against size and fold variations. The proposed model provides a systematic improvement compared to standard ENMs: Not only do its results match the MD results-even for long time scales-but also the model is able to capture large X-ray conformational transitions as well as NMR ensemble diversity.
Collapse
Affiliation(s)
- Laura Orellana
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - Manuel Rueda
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - Carles Ferrer-Costa
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - José Ramón Lopez-Blanco
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - Pablo Chacón
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - Modesto Orozco
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| |
Collapse
|
29
|
Thorne AH, Orellana L, Parisian A, Cavenee W, Furnari F. ATPS-86MUTATIONS IN THE EGF RECEPTOR EXTRACELLULAR DOMAIN REVEAL AN UNTETHERED TRANSITIONAL STATE WHICH MEDIATES mAb806 BINDING. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov204.86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
30
|
Fenwick RB, Orellana L, Esteban-Martín S, Orozco M, Salvatella X. Correlated motions are a fundamental property of β-sheets. Nat Commun 2014; 5:4070. [PMID: 24915882 DOI: 10.1038/ncomms5070] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/08/2014] [Indexed: 01/19/2023] Open
Abstract
Correlated motions in proteins can mediate fundamental biochemical processes such as signal transduction and allostery. The mechanisms that underlie these processes remain largely unknown due mainly to limitations in their direct detection. Here, based on a detailed analysis of protein structures deposited in the protein data bank, as well as on state-of-the art molecular simulations, we provide general evidence for the transfer of structural information by correlated backbone motions, mediated by hydrogen bonds, across β-sheets. We also show that the observed local and long-range correlated motions are mediated by the collective motions of β-sheets and investigate their role in large-scale conformational changes. Correlated motions represent a fundamental property of β-sheets that contributes to protein function.
Collapse
Affiliation(s)
- R Bryn Fenwick
- 1] Joint BSC-CRG-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain [2]
| | - Laura Orellana
- 1] Joint BSC-CRG-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain [2]
| | - Santi Esteban-Martín
- Joint BSC-CRG-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Modesto Orozco
- 1] Joint BSC-CRG-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain [2] Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain
| | - Xavier Salvatella
- 1] Joint BSC-CRG-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| |
Collapse
|
31
|
Sfriso P, Emperador A, Orellana L, Hospital A, Gelpí JL, Orozco M. Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations. J Chem Theory Comput 2012; 8:4707-18. [DOI: 10.1021/ct300494q] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Pedro Sfriso
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
| | - Agusti Emperador
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
| | - Laura Orellana
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
| | - Adam Hospital
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
- Structural Bioinformatics Node,
Instituto Nacional De Bioinformática, Institute of Research
in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain
| | - Josep Lluis Gelpí
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
- Computational Bioinformatics Node,
Instituto Nacional De Bioinformática, Barcelona Supercomputing
Center, Jordi Girona 29, Barcelona, 08034, Spain
- Departament de Bioquímica,
Facultat de Biologia, Universtitat de Barcelona, Avgda Diagonal 647,
Barcelona, 08028, Spain
| | - Modesto Orozco
- Joint IRB-BSC Program in Computational
Biology, Institute of Research in Biomedicine, Josep Samitier 1-5,
Barcelona, 08028, Spain
- Structural Bioinformatics Node,
Instituto Nacional De Bioinformática, Institute of Research
in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain
- Departament de Bioquímica,
Facultat de Biologia, Universtitat de Barcelona, Avgda Diagonal 647,
Barcelona, 08028, Spain
| |
Collapse
|
32
|
Orozco M, Orellana L, Hospital A, Naganathan AN, Emperador A, Carrillo O, Gelpí JL. Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings. Adv Protein Chem Struct Biol 2011; 85:183-215. [PMID: 21920324 DOI: 10.1016/b978-0-12-386485-7.00005-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Flexibility is the key magnitude to understand the variety of functions of proteins. Unfortunately, its experimental study is quite difficult, and in fact, most experimental procedures are designed to reduce flexibility and allow a better definition of the structure. Theoretical approaches have become then the alternative but face serious timescale problems, since many biologically relevant deformation movements happen in a timescale that is far beyond the possibility of current atomistic models. In this complex scenario, coarse-grained simulation methods have emerged as a powerful and inexpensive alternative. Along this chapter, we will review these coarse-grained methods, and explain their physical foundations and their range of applicability.
Collapse
Affiliation(s)
- Modesto Orozco
- Joint IRB-BSC Program on Computational Biology, Barcelona Supercomputing Center and Institute of Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
33
|
Orellana L, Castaneda C, Lovo J, Henríquez A, Bixiones C, Blumenthal P. Method satisfaction among users of post partum IUD in El Salvador. Contraception 2010. [DOI: 10.1016/j.contraception.2010.04.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
34
|
Camps J, Carrillo O, Emperador A, Orellana L, Hospital A, Rueda M, Cicin-Sain D, D'Abramo M, Gelpi JL, Orozco M. FlexServ: an integrated tool for the analysis of protein flexibility. Bioinformatics 2009; 25:1709-10. [DOI: 10.1093/bioinformatics/btp304] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
35
|
Raviyan P, Tang J, Orellana L, Rasco B. Physicochemical Properties of a Time-Temperature Indicator Based on Immobilization of Aspergillus oryzae α-Amylase in Polyacrylamide Gel as Affected by Degree of Cross-linking Agent and Salt Content. J Food Sci 2003. [DOI: 10.1111/j.1365-2621.2003.tb05763.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
36
|
González CM, Pignata ML, Orellana L. Applications of redundancy analysis for the detection of chemical response patterns to air pollution in lichen. Sci Total Environ 2003; 312:245-253. [PMID: 12873413 DOI: 10.1016/s0048-9697(03)00253-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The lichens Ramalina celastri (Spreng.) Krog & Swinsc., Punctelia microsticta (Müll. Arg.) Krog and Canomaculina pilosa (Stizenb.) Elix & Hale were transplanted simultaneously to 17 urban-industrial sites in a northwestern area of Córdoba city, Argentina. The transplantation sites were set according to different environmental conditions: traffic, industries, tree cover, building height, topographic level, position in the block and distances from the river and from the power plant. Three months later, chlorophyll a, chlorophyll b, phaeophytin a, soluble proteins, hydroperoxy conjugated dienes, malondialdehyde concentration and sulfur accumulation were determined, and a pollution index was calculated for each sampling site. Redundancy analysis was applied to detect the variation pattern of the lichen variables that can be 'best' explained by the environmental variables considered. The present study provides information about both the specific pattern response of each species to atmospheric pollution, and environmental conditions that determine it. As regards pollutants emission sources R. celastri showed a chemical response associated mainly with pollutant released by the power plant and traffic. P. microsticta and C. pilosa responded mainly to industrial sources. Regarding environmental conditions that affect the spreading of air pollutants and their incidence on the bioindicator, the topographic level and tree cover surrounding the sampling site were found to be important for R. celastri, tree cover surrounding the sampling site and the building height affected P. microsticta, while building height did so for C. pilosa.
Collapse
Affiliation(s)
- C M González
- Cátedra de Química General, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Avda. Vélez Sársfield 299, 5000 Cordoba, Argentina.
| | | | | |
Collapse
|
37
|
Pignata ML, Gudiño GL, Wannaz ED, Plá RR, González CM, Carreras HA, Orellana L. Atmospheric quality and distribution of heavy metals in Argentina employing Tillandsia capillaris as a biomonitor. Environ Pollut 2002; 120:59-68. [PMID: 12199468 DOI: 10.1016/s0269-7491(02)00128-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The atmospheric quality and distribution of heavy metals were evaluated throughout a wide region of Argentina. In addition, the biomonitor performance of Tillandsia capillaris Ruiz & Pav. f. capillaris was studied in relation to the accumulation of heavy metals and to its physiologic response to air pollutants. A sampling area of 50,000 km2 was selected in the central region of the Argentine Republic. This area was subdivided into grids of 25 x 25 km. Pools of T. capillaris, where present, were collected at each intersection point. From each pool three sub-samples were analyzed independently. Furthermore, five replicates were collected at 20% of the points in order to analyze the variability within the site. The content of Co, Cu, Fe, Ni, Mn, Pb and Zn was determined by Atomic Absorption Spectrometry. Chemical-physiological parameters were also determined to detect symptoms of foliar damage. Chlorophylls, phaeophytins, hydroperoxy conjugated dienes, malondialdehyde and sulfur were quantified in T. capillaris. Some of these parameters were used to calculate a foliar damage index. Data sets were evaluated by one-way ANOVA, correlation analysis, principal component analysis and mapping. Geographical distribution patterns were obtained for the different metals reflecting the contribution of natural and anthropogenic emission sources. According to our results it can be inferred that Fe, Mn and Co probably originated in the soil. For Pb, the highest values were found in the mountainous area, which can be attributed to the presence of Pb in the granitic rocks. Ni showed mainly an anthropogenic origin, with higher values found in places next to industrial centers. For Zn the highest values were in areas of agricultural development. The same was observed for Cu, whose presence could be related to the employment of pesticides. The foliar damage index distribution map showed that the central and southeastern zones were the ones where the major damage in the bioindicator was found. The central zone coincides with the city of Córdoba whereas the southeastern area is strictly agricultural, so the high values found there could be related to the use of pesticides.
Collapse
Affiliation(s)
- M L Pignata
- Cátedra de Química General, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Argentina.
| | | | | | | | | | | | | |
Collapse
|
38
|
Pignata ML, Gudiño GL, Cañas MS, Orellana L. Relationship between foliar chemical parameters measured in Melia azedarach L. and environmental conditions in urban areas. Sci Total Environ 1999; 243-244:85-96. [PMID: 10635592 DOI: 10.1016/s0048-9697(99)00362-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A diagnostic study was done on Melia azedarach L. in relation to atmospheric pollutants in Córdoba city, Argentina. The study area receives regional pollutants, and it was categorized taking into account traffic level, industrial level, location of the sample point in relation to the corner, treeless condition, building type, topographic level and distance to the river. Water content and Specific Leaf Area (SLA) were calculated; and concentrations of soluble proteins, sulphur, hydroperoxy conjugated dienes (HPCD), chlorophylls (Total Chl) and pheophytins (Total Paeoph) were determined in leaf samples. HPCD correlated positively with industry, topographic level and distance to the river, and with a combination of the environmental variables (ECI); pigments correlated negatively with traffic level and with ECI; Total Phaeoph/Total Chl ratio correlated positively with traffic, building and ECI. On the basis of our results, traffic level, industrial level, building type, topographic level and distance to the river are the environmental variables to bear in mind when selecting analogous sampling points in a passive monitoring program. An approximation to predict tree injury may be obtained by measuring water content, soluble proteins, sulphur, HPCD and pigments as they are responsible for the major variability of data. This study revealed that M. azedarach was sensitive to air pollutants from traffic and industry. Thus, in those sampling sites with the maximum score for traffic level, industrial level and ECI, the highest values of the parameters that indicate foliar damage together with the least pigment concentration were observed.
Collapse
Affiliation(s)
- M L Pignata
- Cátedra de Química General, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Argentina.
| | | | | | | |
Collapse
|
39
|
Raddatz V, Alvo M, Durruty P, Orellana L, García de los Ríos M. [Decompensated diabetes mellitus and hyperchloremic metabolic acidosis: a case with both pathologies]. Rev Med Chil 1998; 126:1224-8. [PMID: 10030094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Diabetic ketoacidosis is manifested by elevated blood glucose levels, ketosis and metabolic acidosis with increased anion gap. A transitory hyperchloremic acidosis, with normal anion gap, can appear. We report a 21 years old female with a type 2 diabetes mellitus, admitted to the emergency room of a general hospital with hyperglycemia, absence of ketonemia, severe hypokalemia and hyperchloremic metabolic acidosis. Initially, she was diagnosed and treated as a severe diabetic ketoacidosis. Normal blood glucose levels were rapidly achieved but electrolyte and acid base alterations persisted, leading to the suspicion that another associated condition was causing the acidosis and hypokalemia. Urinary pH and anion gap measurement, the study of renal acidification and a bicarbonate overload test lead to the diagnosis of a distal renal tubular acidosis, secondary to a Sjögren syndrome, that was confirmed with a Schirmer test and positive anti Ro antibodies. In this diabetic patient, the acute hyperglycemia intensified the hypokalemia of her distal renal tubular acidosis and unchained the acute metabolic condition.
Collapse
Affiliation(s)
- V Raddatz
- Unidad de Diabetes y Nutrición, Universidad de Chile, Hospital San Juan de Dios, Santiago de Chile
| | | | | | | | | |
Collapse
|
40
|
Pignata ML, Canas MS, Carreras HA, Orellana L. Exploring Chemical Variables in Ligustrum lucidum Ait. F. Tricolor (Rehd.) Rehd. in Relation to Air Pollutants and Environmental Conditions. Environ Manage 1997; 21:793-801. [PMID: 9236292 DOI: 10.1007/s002679900068] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
/ A diagnostic study was done on Ligustrum lucidum Ait. f. tricolor (Rehd.) Rehd. in relation to atmospheric pollutants in Cordoba city, Argentina. The study area receives regional pollutants and was categorized taking into account traffic level, industrial density, type of industry, location of the sample point in relation to the street corner, treeless condition, and topographic level. Dried weight/fresh weight ratio (DW/FW) and specific leaf area (SLA) were calculated, and concentrations of chlorophylls, carotenoids, total sulfur, soluble proteins, malondialdehyde (MDA), and hydroperoxy conjugated dienes (HPCD) were determined in leaf samples. Sulfur content correlates positively with traffic density and SLA correlates negatively with some combinations of the categorical variables; MDA correlates positively with topographic level and total protein concentration correlates negatively with treeless condition. On the basis of our results, traffic, location of trees, type of industry, situation of a tree with respect to others, and topographic level are the environmental variables to bear in mind when selecting analogous sampling points in a passive monitoring program. An approximation to predict tree injury may be obtained by measuring DW/FW ratio, proteins, pigments, HPCD, and MDA as they are responsible for the major variability of data.KEY WORDS: L. lucidum Ait. f. tricolor (Rehd.) Rehd.; Air pollution; Sulfur accumulation; Pigments; Urban environment; Argentina
Collapse
Affiliation(s)
- ML Pignata
- Catedra de Quimica General Facultad de Ciencias Exactas, Fisicas y Naturales Universidad Nacional de Cordoba Avda. Velez Sarsfield 299 5000 Cordoba, Argentina
| | | | | | | |
Collapse
|
41
|
Madrid AH, Mestre JL, Moro C, Vivas E, Tejero I, Novo L, Marín E, Orellana L. Heart rate variability and inappropriate sinus tachycardia after catheter ablation of supraventricular tachycardia. Eur Heart J 1995; 16:1637-40. [PMID: 8881859 DOI: 10.1093/oxfordjournals.eurheartj.a060789] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Sinus tachycardia has been reported after radiofrequency catheter ablation of supraventricular tachycardia. Frequently, these patients require beta-blocking agents for symptomatic control. The purpose of this study was to evaluate prospectively the incidence of inappropriate sinus tachycardia and heart rate variability after ablation of atrioventricular nodal reentrant tachycardia and accessory pathways. Patients undergoing ablation had 24-h ambulatory monitoring ECG (Holter) performed before the procedure, on the day of the ablation, and 3 months afterwards. There were 170 patients, mean age 48 +/- 23 years; 93 were female. A complete study of the 24-h Holter with analysis of heart rate variability: SD, rMSSD, pNN50, high and low frequency was obtained. There was a low prevalence of inappropriate sinus tachycardia after the ablation procedure (10 of 170 patients: five with four atrioventricular nodal reentry, with posteroseptal accessory pathways and one of the latter following ablation of the left accessory pathway). There was no modification of time and frequency domain parameters of heart rate variability in the remaining patients who underwent radiofrequency ablation. Holter monitoring 3 months after ablation showed that parameters of heart rate and heart rate variability had normalized in patients who had developed inappropriate sinus tachycardia. Inappropriate sinus tachycardia may be initiated by both radiofrequency ablation of atrioventricular nodal reentrant tachycardia and radiofrequency ablation of posteroseptal accessory pathways. Specific damage to the posteroseptal region is responsible for these changes, which usually recover spontaneously after 3 months.
Collapse
Affiliation(s)
- A H Madrid
- Arrhythmia Unit, Ramón y Cajal Hospital, Madrid, Spain
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Agrelo F, Lobo B, Bazán M, Mas LB, Lozada C, Jazán G, Orellana L. [Prevalence of thinness and excessive fatness in a group of school children of the city of Cordoba, Argentina]. Arch Latinoam Nutr 1988; 38:69-80. [PMID: 3256287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Findings of a nutritional evaluation study, using triceps skinfold, are reported. The study was carried out in 1,615 school-children from 5 to 12 years, pertaining to the low socioeconomic status of the city of Córdoba, Argentina. Measurements were done during the years 1983 and 1984 by Center's examiners with a Lange caliper, according to international anthropometric methodology. Interintra observer technical error was found to be within tolerance limits reported by other authors. Local standards were used to determine the prevalence of thinness and excessive fatness, by comparing them to tricep skinfold of each child, and selecting those children where this parameter presented values less than or equal to 10th percentile and fatness greater than or equal to 90th percentile. Furthermore, comparison between median triceps skinfold of the examined group, the local standards and Frisancho's norms for US population was also made. Results revealed that: a) the prevalence of thinness (19.9%) was almost twice the percentage expected for a normal population; in contrast, occurrence of excessive fatness (6.4%) was found to be below the expected value; b) prevalence of thinness was not statistically associated to age nor sex; c) frequency of excessive fatness was significantly higher in the 8-11 year-old male group (8, 9%, p much less than 0.0005) and in the girls group (10.8%), P much less than 0.005) the prevalence of fatness in girls increased with age, and figures revealed that from eight years onwards this exceeded the expected percentage, and d) median triceps skinfold of the group under study was generally below local and foreign norms. It is concluded that potential or real nutrition problems as those mentioned above, may be grossly identified using the triceps skinfold as the single anthropometric indicator.
Collapse
Affiliation(s)
- F Agrelo
- Centro de Estudios del crecimiento y Desarrollo del Niño Hospital Pediátrico del Niño Jesús Córdoba, Argentina
| | | | | | | | | | | | | |
Collapse
|