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Sansone S, Ramos Y, Segal S, Asfaw TS, Morales DK. Uncovering Surface Penetration by Enterococci From Urinary Tract Infection Patients. Urogynecology (Phila) 2024; 30:320-329. [PMID: 38484249 DOI: 10.1097/spv.0000000000001476] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
IMPORTANCE The relationship between Enterococcus faecalis vaginal colonization and urinary tract infections (UTIs) remains uncertain. OBJECTIVE We aimed to evaluate the surface invasion capability of E faecalis isolates from patients with and without UTIs as a potential readout of pathogenicity. STUDY DESIGN Participants were females from urogynecology clinics, comprising symptomatic UTI and asymptomatic non-UTI patients, categorized by the presence or absence of E faecalis-positive cultures identified via standard urine culture techniques. Vaginal and urine samples from patients were plated on enterococci selective medium, and E faecalis isolates detected in both cohorts were species specific identified using 16S rRNA sequencing. Clinical isolates were inoculated on semisolid media, and both external colonies and underneath colony prints formed by agar-penetrating enterococci were imaged. External growth and invasiveness were quantified by determining colony-forming units of the noninvading and agar-penetrating cells and compared with the E faecalis OG1RF. RESULTS We selected E faecalis isolates from urine and vaginal samples of 4 patients with and 4 patients without UTIs. Assays demonstrated that most isolates formed similarly sized external colonies with comparable colony-forming unit. Surface invasion differed across patients and isolation sites compared with OG1RF. The vaginal isolate from UTI patient 1, who had the most recurrences, exhibited significantly greater agar-invading capacity compared with OG1RF. CONCLUSIONS Our pilot study indicates that ex vivo invasion assays may unveil virulence traits in E faecalis from UTI patients. Enhanced enterococcal surface penetration could increase urogenital invasion risk. Further research is needed to correlate penetration with disease severity in a larger patient group.
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Affiliation(s)
- Stephanie Sansone
- From the Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
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Hwang SM, Awasthi D, Jeong J, Sandoval TA, Chae CS, Ramos Y, Tan C, Falco MM, McBain IT, Mishra B, Ivashkiv LB, Zamarin D, Cantillo E, Chapman-Davis E, Holcomb K, Morales DK, Rodriguez PC, Conejo-Garcia JR, Kaczocha M, Vähärautio A, Song M, Cubillos-Ruiz JR. Transgelin 2 guards T cell lipid metabolic programming and anti-tumor function. Res Sq 2023:rs.3.rs-3683989. [PMID: 38168227 PMCID: PMC10760247 DOI: 10.21203/rs.3.rs-3683989/v1] [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] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mounting effective immunity against pathogens and tumors relies on the successful metabolic programming of T cells by extracellular fatty acids1-3. During this process, fatty-acid-binding protein 5 (FABP5) imports lipids that fuel mitochondrial respiration and sustain the bioenergetic requirements of protective CD8+ T cells4,5. Importantly, however, the mechanisms governing this crucial immunometabolic axis remain unexplored. Here we report that the cytoskeletal organizer Transgelin 2 (TAGLN2) is necessary for optimal CD8+ T cell fatty acid uptake, mitochondrial respiration, and anti-cancer function. We found that TAGLN2 interacts with FABP5, enabling the surface localization of this lipid importer on activated CD8+ T cells. Analysis of ovarian cancer specimens revealed that endoplasmic reticulum (ER) stress responses elicited by the tumor microenvironment repress TAGLN2 in infiltrating CD8+ T cells, enforcing their dysfunctional state. Restoring TAGLN2 expression in ER-stressed CD8+ T cells bolstered their lipid uptake, mitochondrial respiration, and cytotoxic capacity. Accordingly, chimeric antigen receptor T cells overexpressing TAGLN2 bypassed the detrimental effects of tumor-induced ER stress and demonstrated superior therapeutic efficacy in mice with metastatic ovarian cancer. Our study unveils the role of cytoskeletal TAGLN2 in T cell lipid metabolism and highlights the potential to enhance cellular immunotherapy in solid malignancies by preserving the TAGLN2-FABP5 axis.
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Affiliation(s)
- Sung-Min Hwang
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Deepika Awasthi
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Jieun Jeong
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Tito A. Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Chang-Suk Chae
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Chen Tan
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Matías Marin Falco
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ian T. McBain
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
| | - Bikash Mishra
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Lionel B. Ivashkiv
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Dmitriy Zamarin
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Evelyn Cantillo
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Eloise Chapman-Davis
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Kevin Holcomb
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Diana K. Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Paulo C. Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute. Tampa, FL, USA
| | - Jose R. Conejo-Garcia
- Department of Integrated Immunobiology, Duke School of Medicine, Durham, NC 27710, USA
- Duke Cancer Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Martin Kaczocha
- Department of Anesthesiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook University Pain and Analgesia Research Center (SPARC), Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anna Vähärautio
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Minkyung Song
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Juan R. Cubillos-Ruiz
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
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Affiliation(s)
- Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States of America
| | - Stephanie Sansone
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States of America
- Department of Urology, Weill Cornell Medicine, New York, New York, United States of America
| | - Diana K. Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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Besada V, Ramos Y, Espinosa LA, Fu W, Perera Y, González LJ. FAIMS-MS might contribute to phosphopeptides identification in plasma. J Proteomics 2021; 234:104102. [PMID: 33412312 DOI: 10.1016/j.jprot.2021.104102] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 01/03/2021] [Indexed: 01/24/2023]
Abstract
FAIMS interface is gaining popularity because of the impressive 100-fold signal to noise enhancement in addition to the recent coupling to the Orbitrap technology, the most important analyzer developed in the last 20 years. The selection of group of ions and effective removal of single-charged ones at particular compensation voltages increases around 50% the proteome coverage at expenses of lower peptides coverage. However, specific setting for phosphoproteome analysis is yet poorly described. Here we have found the maximum transmission for several tryptic phosphopeptides isolated from a single complex mixture and we have set an experimental method based on five compensation voltages partially different to the ones described previously, demonstrating the relevance of voltages higher than 47 V, with an increase of around 20% of unique phosphopeptides. Using this experimental setup two complex phosphoproteomes isolates (SH-SY5Y cell line and plasma) were analyzed and found increments of 50% on phosphopeptides identification with the proposed method with respect to a previous one, for the cell line extract. Meanwhile for plasma 109 of the detected phosphopeptides are found for first time in this body fluid, presumably due to the release of intracellular proteins. With this FAIMS setup, 60% of the proteins identified are classified as very low abundant proteins.
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Affiliation(s)
- V Besada
- Mass Spectrometry Laboratory, Department of Proteomics, Center for Genetic Engineering and Biotechnology (CIGB), Havana CP: 10600, Cuba; Proteomics Laboratory, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Yongzhou Zhong Gu Biotechnology Co., Ltd, Yangjiaqiao Street, Lengshuitan District, Yongzhou City, Hunan Province CP: 425000, China.
| | - Y Ramos
- Mass Spectrometry Laboratory, Department of Proteomics, Center for Genetic Engineering and Biotechnology (CIGB), Havana CP: 10600, Cuba.
| | - L A Espinosa
- Mass Spectrometry Laboratory, Department of Proteomics, Center for Genetic Engineering and Biotechnology (CIGB), Havana CP: 10600, Cuba.
| | - W Fu
- Proteomics Laboratory, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Yongzhou Zhong Gu Biotechnology Co., Ltd, Yangjiaqiao Street, Lengshuitan District, Yongzhou City, Hunan Province CP: 425000, China.
| | - Y Perera
- Mass Spectrometry Laboratory, Department of Proteomics, Center for Genetic Engineering and Biotechnology (CIGB), Havana CP: 10600, Cuba; Proteomics Laboratory, China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Yongzhou Zhong Gu Biotechnology Co., Ltd, Yangjiaqiao Street, Lengshuitan District, Yongzhou City, Hunan Province CP: 425000, China.
| | - L J González
- Mass Spectrometry Laboratory, Department of Proteomics, Center for Genetic Engineering and Biotechnology (CIGB), Havana CP: 10600, Cuba.
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Picón-Jaimes YA, Orozco-Chinome JE, Gómez-Herazo D, Quintana-Pájaro L, Ramos Y, Moscote-Salazar LR. [Gossypibomas in neurosurgery]. Rev Neurol 2019; 69:377-382. [PMID: 31657450 DOI: 10.33588/rn.6909.2019282] [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: 11/24/2022]
Abstract
INTRODUCTION The term «gossypiboma» comes from the Latin gossypium, which refers to a genus of cotton plants, and from the Swahili word boma, which translates as «place of concealment». It may be mistaken for tumorous lesions or abscesses due to the way it is encapsulated, as evidenced in imaging examinations, and its variable and non-specific clinical features, which give rise to difficulty in its diagnosis and significant morbidity. AIM To synthesise the available evidence on the presence of gossypibomas during neurosurgical procedures. DEVELOPMENT A review was performed that included a search for articles in English and Spanish published in the last 15 years in PubMed, Ebsco Host, Embase, Mediclatina, Cochrane, Lilacs and Scopus, between January and June 2019, using the keywords «gossypiboma», «textiloma», «neurosurgery» and «neurosurgical procedures». In all, a total of 630 articles were found in the search, although, after selecting them by title and abstract, 22 case report articles were included for this review process. Altogether 36 individuals were identified, of whom 21 (58.3%) were women, and whose mean age was 56.1 years. Surgical sponges were observed as gossypibomas in 20 cases (55.6%). CONCLUSIONS Gossypiboma is a complication secondary to surgical procedures that presents fairly unspecific signs and symptoms. The time that elapses before it appears usually ranges from a few days to several years after surgery and is correlated with multiple medical and legal implications.
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Affiliation(s)
| | | | | | | | - Y Ramos
- Universidad de Cartagena, Cartagena de Indias, Colombia
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Ramos Y, Morales DK. Exopolysaccharide-mediated surface penetration as new virulence trait in Enterococcus faecalis. Commun Integr Biol 2019; 12:144-147. [PMID: 31666914 PMCID: PMC6802913 DOI: 10.1080/19420889.2019.1657373] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/15/2019] [Indexed: 11/07/2022] Open
Abstract
Enterococcus faecalis is a commensal bacterium that normally inhabits the gastrointestinal tract of humans. This non-motile microorganism can also cause lethal infections in other organs by penetrating and breaching the intestinal barrier. However, the precise molecular mechanisms enabling E. faecalis movement and translocation across epithelial barriers remain incompletely characterized. We recently reported that E. faecalis utilizes the RpiA-GlnA-EpaX metabolic axis to generate β-1,6-linked poly-N-acetylglucosamine (polyGlcNAc)-containing exopolymers that are necessary for its optimal migration into semisolid surfaces and efficient translocation through human epithelial cell monolayers. These findings provide new evidence indicating that non-motile bacterial pathogens can exploit carbohydrate metabolism to penetrate surfaces. Hence, targeting this process might represent a new strategy to more effectively control systemic infections by E. faecalis.
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Affiliation(s)
- Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
| | - Diana K Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
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Ramos Y, Rocha J, Hael AL, van Gestel J, Vlamakis H, Cywes-Bentley C, Cubillos-Ruiz JR, Pier GB, Gilmore MS, Kolter R, Morales DK. PolyGlcNAc-containing exopolymers enable surface penetration by non-motile Enterococcus faecalis. PLoS Pathog 2019; 15:e1007571. [PMID: 30742693 PMCID: PMC6386517 DOI: 10.1371/journal.ppat.1007571] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/22/2019] [Accepted: 01/08/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial pathogens have evolved strategies that enable them to invade tissues and spread within the host. Enterococcus faecalis is a leading cause of local and disseminated multidrug-resistant hospital infections, but the molecular mechanisms used by this non-motile bacterium to penetrate surfaces and translocate through tissues remain largely unexplored. Here we present experimental evidence indicating that E. faecalis generates exopolysaccharides containing β-1,6-linked poly-N-acetylglucosamine (polyGlcNAc) as a mechanism to successfully penetrate semisolid surfaces and translocate through human epithelial cell monolayers. Genetic screening and molecular analyses of mutant strains identified glnA, rpiA and epaX as genes critically required for optimal E. faecalis penetration and translocation. Mechanistically, GlnA and RpiA cooperated to generate uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) that was utilized by EpaX to synthesize polyGlcNAc-containing polymers. Notably, exogenous supplementation with polymeric N-acetylglucosamine (PNAG) restored surface penetration by E. faecalis mutants devoid of EpaX. Our study uncovers an unexpected mechanism whereby the RpiA-GlnA-EpaX metabolic axis enables production of polyGlcNAc-containing polysaccharides that endow E. faecalis with the ability to penetrate surfaces. Hence, targeting carbohydrate metabolism or inhibiting biosynthesis of polyGlcNAc-containing exopolymers may represent a new strategy to more effectively confront enterococcal infections in the clinic. Enterococcus faecalis is a microbial inhabitant of the human gastrointestinal tract that can cause lethal infections. Typically classified as a non-motile bacterium, E. faecalis can readily migrate and translocate across epithelial barriers to invade distant organs. Nevertheless, the molecular pathways driving enterococcal invasive attributes remain poorly understood. In this study, we uncover that E. faecalis produces a polyGlcNAc-containing extracellular glycopolymer to efficiently migrate into semisolid surfaces and translocate through human epithelial cell monolayers. Our work provides evidence that non-motile bacterial pathogens can exploit endogenous carbohydrate metabolic pathways to penetrate surfaces. Thus, targeting glycopolymer biosynthetic programs might be useful to control infections by Gram-positive cocci in the clinic.
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Affiliation(s)
- Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
| | - Jorge Rocha
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Ana L. Hael
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Hera Vlamakis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Colette Cywes-Bentley
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Juan R. Cubillos-Ruiz
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
| | - Gerald B. Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Michael S. Gilmore
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
- Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America
| | - Roberto Kolter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Diana K. Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
- * E-mail:
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Birkhaeuser M, Bitzer J, Braat S, Ramos Y. Esmirtazapine treatment of postmenopausal vasomotor symptoms: two randomized controlled trials. Climacteric 2019; 22:312-322. [DOI: 10.1080/13697137.2018.1561664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- M. Birkhaeuser
- Division of Gynaecological Endocrinology and Reproductive Medicine, Department of Obstetrics & Gynaecology, University of Bern, Bern, Switzerland
| | - J. Bitzer
- Department of Obstetrics and Gynecology, University Hospital, Basel, Switzerland
| | - S. Braat
- MSD, Oss, The Netherlands
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Y. Ramos
- MSD, Munich, Germany
- Ramos Pharma Consulting, Munich, Germany
- Formerly Organon GmbH, Oberschleissheim, Germany
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Martínez-Santiago O, Marrero-Ponce Y, Vivas-Reyes R, Rivera-Borroto OM, Hurtado E, Treto-Suarez MA, Ramos Y, Vergara-Murillo F, Orozco-Ugarriza ME, Martínez-López Y. Exploring the QSAR's predictive truthfulness of the novel N-tuple discrete derivative indices on benchmark datasets. SAR QSAR Environ Res 2017; 28:367-389. [PMID: 28590848 DOI: 10.1080/1062936x.2017.1326403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Graph derivative indices (GDIs) have recently been defined over N-atoms (N = 2, 3 and 4) simultaneously, which are based on the concept of derivatives in discrete mathematics (finite difference), metaphorical to the derivative concept in classical mathematical analysis. These molecular descriptors (MDs) codify topo-chemical and topo-structural information based on the concept of the derivative of a molecular graph with respect to a given event (S) over duplex, triplex and quadruplex relations of atoms (vertices). These GDIs have been successfully applied in the description of physicochemical properties like reactivity, solubility and chemical shift, among others, and in several comparative quantitative structure activity/property relationship (QSAR/QSPR) studies. Although satisfactory results have been obtained in previous modelling studies with the aforementioned indices, it is necessary to develop new, more rigorous analysis to assess the true predictive performance of the novel structure codification. So, in the present paper, an assessment and statistical validation of the performance of these novel approaches in QSAR studies are executed, as well as a comparison with those of other QSAR procedures reported in the literature. To achieve the main aim of this research, QSARs were developed on eight chemical datasets widely used as benchmarks in the evaluation/validation of several QSAR methods and/or many different MDs (fundamentally 3D MDs). Three to seven variable QSAR models were built for each chemical dataset, according to the original dissection into training/test sets. The models were developed by using multiple linear regression (MLR) coupled with a genetic algorithm as the feature wrapper selection technique in the MobyDigs software. Each family of GDIs (for duplex, triplex and quadruplex) behaves similarly in all modelling, although there were some exceptions. However, when all families were used in combination, the results achieved were quantitatively higher than those reported by other authors in similar experiments. Comparisons with respect to external correlation coefficients (q2ext) revealed that the models based on GDIs possess superior predictive ability in seven of the eight datasets analysed, outperforming methodologies based on similar or more complex techniques and confirming the good predictive power of the obtained models. For the q2ext values, the non-parametric comparison revealed significantly different results to those reported so far, which demonstrated that the models based on DIVATI's indices presented the best global performance and yielded significantly better predictions than the 12 0-3D QSAR procedures used in the comparison. Therefore, GDIs are suitable for structure codification of the molecules and constitute a good alternative to build QSARs for the prediction of physicochemical, biological and environmental endpoints.
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Affiliation(s)
- O Martínez-Santiago
- a Department of Chemical Sciences , Central University 'Martha Abreu' of Las Villas , Santa Clara , Cuba
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
- c Group of Quantum and Theoretical Chemistry , University of Cartagena , Cartagena de Indias , Colombia
- d Facultad de Ingeniería , Grupo CipTec, Fundación Universitaria Tecnológico Comfenalco , Cartagena de Indias , Colombia
| | - Y Marrero-Ponce
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
- e Escuela de Medicina, Edificio de Especialidades Médicas , Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA) , Av. Interoceánica Km 12 ½, Cumbayá , Ecuador
- f Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica , Quito , Ecuador
- g Grupo de Investigación Ambiental (GIA) , Fundación Universitaria Tecnológico de Comfenalco , Cartagena de Indias , Colombia
| | - R Vivas-Reyes
- c Group of Quantum and Theoretical Chemistry , University of Cartagena , Cartagena de Indias , Colombia
- d Facultad de Ingeniería , Grupo CipTec, Fundación Universitaria Tecnológico Comfenalco , Cartagena de Indias , Colombia
| | - O M Rivera-Borroto
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
- h Departamento de Química Física Aplicada , Universidad Autónoma de Madrid (UAM) , Madrid , España
| | - E Hurtado
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
| | - M A Treto-Suarez
- i Center of Applied Nanosciences (CENAP), Andres Bello University , Chile
| | - Y Ramos
- j Department of Economic Sciences , University of Camagüey , Camagüey , Cuba
| | - F Vergara-Murillo
- c Group of Quantum and Theoretical Chemistry , University of Cartagena , Cartagena de Indias , Colombia
- d Facultad de Ingeniería , Grupo CipTec, Fundación Universitaria Tecnológico Comfenalco , Cartagena de Indias , Colombia
| | - M E Orozco-Ugarriza
- k Seccional Cartagena y Grupo de Investigación Traslacional en Biomedicina & Biotecnología - GITB&B , Universidad del Sinú - Elías Bechara Zainúm , Cartagena de Indias , Colombia
| | - Y Martínez-López
- b Unit of Computer-Aided Molecular 'Biosilico' Discovery and Bioinformatics Research International Network (CAMD-BIR IN) , Quito , Ecuador
- l Grupo de Investigación de Inteligencia Artificial (AIRES) , Universidad de Camagüey , Camagüey , Cuba
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Falco A, Ramos Y, Franco E, Guzmán A, Takiff H. A cluster of KPC-2 and VIM-2-producing Klebsiella pneumoniae ST833 isolates from the pediatric service of a Venezuelan Hospital. BMC Infect Dis 2016; 16:595. [PMID: 27770796 PMCID: PMC5075218 DOI: 10.1186/s12879-016-1927-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 09/26/2015] [Accepted: 10/12/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a bacterial pathogen that has developed resistance to multiple antibiotics and is a major cause of nosocomial infections worldwide. Carbapenemase-producing Klebsiella pneumoniae have been isolated in many hospitals in Venezuela, but they have not been well-studied. The aim of this study was to characterize carbapenem-resistant Klebsiella pneumoniae isolates from the pediatric service of a hospital located in Anzoategui State, in the eastern part of Venezuela. METHODS Nineteen Klebsiella pneumoniae strains isolated in the hospital from April to July 2014 were evaluated phenotypically and molecularly for the presence of carbapenemases blaKPC, blaIMP and blaVIM. Molecular epidemiology was performed with Repetitive Extragenic Palindromic-PCR (REP-PCR) and Multilocus Sequence Typing (MLST). They were also studied for phenotypic and molecular resistance to a quaternary ammonium compound (QAC) disinfectant. RESULTS All 19 isolates contained both bla VIM-2 and bla KPC-2 genes, and the bla KPC-2 gene was associated with Tn4401b. All isolates were phenotypically sensitive to QACs and contained qacΔE and addA2 genes typical of class 1 integrons. Analysis by REP-PCR and MLST showed that all isolates had identical profiles characteristic of sequence type ST833. CONCLUSION All 19 strains are bla VIM-2 and bla KPC-2-producing ST833 K. pneumoniae sensitive to QACs. This analysis may help to understand the routes of dissemination and confirms that QAC disinfectants can be used to help control their spread.
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Affiliation(s)
- Aura Falco
- Laboratorio de Genética Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Yusibeska Ramos
- Laboratorio B, Dirección de Energía y Ambiente, Instituto de Estudios Avanzados, Caracas, Venezuela
| | - Esther Franco
- Servicio de Laboratorio Clínico del anexo pediátrico "Dr. Rafael Tobías Guevara" del Complejo Hospitalario Universitario "Dr. Luis Razetti", Barcelona, Venezuela
| | - Alegría Guzmán
- Servicio de Laboratorio Clínico del anexo pediátrico "Dr. Rafael Tobías Guevara" del Complejo Hospitalario Universitario "Dr. Luis Razetti", Barcelona, Venezuela
| | - Howard Takiff
- Laboratorio de Genética Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela.
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Ardalan B, Subbarayan PR, Ramos Y, Gonzalez M, Mezentsev D, Reis IM, Duncan R, Ganjei-Azar P, Lee K. Phase I study of 5-FU and arsenic trioxide (ATO) in patients with refractory metastatic colorectal carcinoma. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.e14081] [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: 11/20/2022] Open
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12
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Quispe E, Alfonso L, Flores A, Guillén H, Ramos Y. Bases para un programa de mejora de alpacas en la region altoandina de Huancavelica-Perú. Arch zootec 2009. [DOI: 10.4321/s0004-05922009000400008] [Citation(s) in RCA: 2] [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: 11/11/2022] Open
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Quispe EC, Alfonso L, Flores A, Guillén H, Ramos Y. Bases para un programa de mejora de alpacas en la region altoandina de Huancavelica-Perú. ARCH ZOOTEC 2008. [DOI: 10.21071/az.v58i224.5060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
El estudio se desarrolló en 544 alpacas Huacaya de color blanco localizadas en 19 centros de producción de la Región de Huancavelica, ubicadas un rango de altitud entre 4000 y 4800 msnm. Antes de la esquila se tomaron muestras del vellón de aproximadamente 20 g de la zona del costillar y posterior a ella se registró el peso de vellón grasiento (PVG), sexo, edad y unidad productiva de cada animal. El diámetro de fibra (DF), coeficiente de variación del diámetro de fibra (CVDF) y el factor de picazón (FP) fue determinado utilizando el Sirolan-Laserscan. En función a los datos obtenidos se realizó el planteamiento de un esquema de mejora y sobre ello se estimó la respuesta a la selección bajo distintos escenarios. Los promedios ±E.E. del PVG, DF, CVDF y FP fueron de 2300±39 g, 21,56±0,12 mm, 22,82±0,12% y 6,33 ± 0,30% respectivamente. El PVG y el DF muestran variaciones significativas (p
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Devera R, Pérez C, Ramos Y. [Enterobiasis in students from Ciudad Bolivar, Venezuela]. Bol Chil Parasitol 1998; 53:14-8. [PMID: 9830718] [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: 02/09/2023]
Abstract
Enterobius vermicularis is a nematode with a peculiar biological cycle, thus requiring a special diagnostic technique. In order to determine the prevalence of E. vermicularis infection among schoolchildren in Ciudad Bolívar, Venezuela, 282 children aged 5-14 years old were evaluated between november 1995 and august 1996 by the Graham technique (three perianal swabs with adhesive cellulose tape). The prevalence of enterobiasis in the studied children was estimated 19.1% (54/282). There was no difference between sexes (P > 0.05), but there was a difference between ages (x2 = 13.8; 1.g. = 4), being the infection more frequent between 5 and 8 years. Symptoms were observed in 90.7% of the schoolchildren. Anal pruritus was the most common clinical finding (81.6%). Other less frequent manifestations were enuresis (28.6%) and vulvitis in girls (26.1%). This intestinal parasitosis occurs with high frequency among schoolchildren in Ciudad Bolívar with characteristic and identifiable symptoms in most cases. The Graham method must be used for its diagnosis. This test is not routinely performed in our laboratories unless specifically requested by the attending physician.
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Affiliation(s)
- R Devera
- Departamento de Parasitología y Microbiología, Escuela de Medicina, Universidad de Oriente, Ciudad Bolívar, Venezuela
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