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Ortega A, Amorós D, García de la Torre J. Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models. Biophys J 2011; 101:892-8. [PMID: 21843480 DOI: 10.1016/j.bpj.2011.06.046] [Citation(s) in RCA: 515] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 06/23/2011] [Accepted: 06/24/2011] [Indexed: 11/19/2022] Open
Abstract
Here we extend the ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, to models with lower, residue-level resolution. Whereas in the former case there is one bead per nonhydrogen atom, the latter contains one bead per amino acid (or nucleotide) residue, thus allowing calculations when atomic resolution is not available or coarse-grained models are preferred. We parameterized the effective hydrodynamic radius of the elements in the atomic- and residue-level models using a very large set of experimental data for translational and rotational coefficients (intrinsic viscosity and radius of gyration) for >50 proteins. We also extended the calculations to very large proteins and macromolecular complexes, such as the whole 70S ribosome. We show that with proper parameterization, the two levels of resolution yield similar and rather good agreement with experimental data. The new version of HYDROPRO, in addition to considering various computational and modeling schemes, is far more efficient computationally and can be handled with the use of a graphical interface.
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Research Support, Non-U.S. Gov't |
14 |
515 |
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Ortega A, Garcı́a de la Torre J. Hydrodynamic properties of rodlike and disklike particles in dilute solution. J Chem Phys 2003. [DOI: 10.1063/1.1615967] [Citation(s) in RCA: 243] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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243 |
3
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Berenguer J, Moreno S, Laguna F, Vicente T, Adrados M, Ortega A, González-LaHoz J, Bouza E. Tuberculous meningitis in patients infected with the human immunodeficiency virus. N Engl J Med 1992; 326:668-72. [PMID: 1346547 DOI: 10.1056/nejm199203053261004] [Citation(s) in RCA: 242] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND AND METHODS Tuberculosis is a frequent complication of human immunodeficiency virus (HIV) infection. We describe the clinical manifestations and outcomes of tuberculous meningitis in patients with HIV infection, and compare them with those in non-HIV-infected patients. We reviewed the records from 1985 through 1990 at two large referral hospitals in Madrid for patients who had Mycobacterium tuberculosis isolated from cerebrospinal fluid. RESULTS Of 2205 patients with tuberculosis, 455 (21 percent) also had HIV infection, of whom 45 had M. tuberculosis isolated from the cerebrospinal fluid. Of the 37 HIV-infected patients with tuberculous meningitis for whom records were available, 24 (65 percent) had clinical or radiologic evidence of extrameningeal tuberculosis at the time of admission. In 18 of 26 patients (69 percent), a CT scan of the head was abnormal. In most patients, analysis of cerebrospinal fluid showed pleocytosis (median white-cell count, 0.234 x 10(9) per liter) and hypoglycorrhachia (median glucose level, 1.3 mmol per liter), but in 43 percent (15 of 35), the level of protein in cerebrospinal fluid was normal. In four patients with HIV infection, tuberculosis was only discovered after their deaths. Of the 33 patients who received antituberculous treatment, 7 died (in-hospital mortality, 21 percent). Illness lasting more than 14 days before admission and a CD4+ cell count of less than 0.2 x 10(9) per liter (200 per cubic millimeter) were associated with a poor prognosis. Comparison with tuberculous meningitis in patients without HIV infection showed that the presentation, clinical manifestations, cerebrospinal fluid findings, and mortality were generally similar in the two groups. However, of the 1750 patients without HIV infection, only 2 percent (38 patients) had tuberculous meningitis, as compared with 10 percent of the HIV-infected patients (P less than 0.001). CONCLUSIONS HIV-infected patients with tuberculosis are at increased risk for meningitis, but infection with HIV does not appear to change the clinical manifestations or the outcome of tuberculous meningitis.
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Comparative Study |
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Telenti A, Honoré N, Bernasconi C, March J, Ortega A, Heym B, Takiff HE, Cole ST. Genotypic assessment of isoniazid and rifampin resistance in Mycobacterium tuberculosis: a blind study at reference laboratory level. J Clin Microbiol 1997; 35:719-23. [PMID: 9041419 PMCID: PMC229657 DOI: 10.1128/jcm.35.3.719-723.1997] [Citation(s) in RCA: 225] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Progress in understanding the basis of resistance to isoniazid (INH) and rifampin (RMP) has allowed molecular tests for the detection of drug-resistant tuberculosis to be developed. Consecutive isolates (n = 95) of Mycobacterium tuberculosis, from a Spanish reference laboratory investigating outbreaks of multidrug-resistant tuberculosis, were coded and sent to two external laboratories for genotypic analysis of INH and RMP resistance by PCR-single-strand conformation polymorphism (SSCP) analysis of specific regions of four genes: part of the coding sequence of katG and the promoter regions of inhA and ahpC for INH and the RMP resistance region of rpoB. After correction for the presence of outbreak strains and multiple isolates from single patients, RMP resistance was detected successfully by PCR-SSCP in > 96% of the RMP-resistant strains. PCR-SSCP had a sensitivity of 87% for INH resistance detection, and mutations in katG, inhA, katG-inhA, ahpC, and katG-ahpC were identified in 36.8, 31.6, 2.6, 13.2, and 2.6%, respectively, of the unique strains. Specificity was 100%. Molecular detection of resistance to the two main antituberculous drugs, INH and RMP, can be accomplished accurately by using a strategy which limits analysis to four genetic regions. This may allow the expedient analysis of drug resistance by reference laboratories.
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research-article |
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de la Torre JG, Echenique GDR, Ortega A. Improved calculation of rotational diffusion and intrinsic viscosity of bead models for macromolecules and nanoparticles. J Phys Chem B 2007; 111:955-61. [PMID: 17266248 DOI: 10.1021/jp0647941] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conventional Kirkwood-Riseman calculation of the hydrodynamic properties of bead models gives abnormal results for rotational quantities and the intrinsic viscosities for models with a few beads or when one bead is dominant. The reason is that beads are treated as point sources of friction. This can be remedied by introducing terms that are neglected in the conventional treatment of orders 0 and -3 in interbead distances. An alternative strategy is the cubic substitution in which each bead is replaced by a cubic array of minibeads. These procedures require a computational overload that, in the case of the intrinsic viscosity, can be avoided using an estimate of the correction due to the nonzero volume of the beads. We have found how such a correction can be estimated from the geometry of the model, and its application yields results that are within the range of typical experimental errors.
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Journal Article |
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124 |
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Moreno S, García Altozano J, Pinilla B, López JC, de Quirós B, Ortega A, Bouza E. Lemierre's disease: postanginal bacteremia and pulmonary involvement caused by Fusobacterium necrophorum. REVIEWS OF INFECTIOUS DISEASES 1989; 11:319-24. [PMID: 2649965 DOI: 10.1093/clinids/11.2.319] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The combination of acute pharyngotonsillitis, neck pain, fever, and pulmonary septic emboli caused by Fusobacterium necrophorum in a healthy young person is extremely rare. The entity was described by Lemierre in 1936 as a typical syndrome easy to recognize and diagnose exclusively on clinical grounds. A case of Lemierre's disease is reported, and 10 other cases found in the medical literature are reviewed.
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Case Reports |
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108 |
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Aranaz A, Liébana E, Gómez-Mampaso E, Galán JC, Cousins D, Ortega A, Blázquez J, Baquero F, Mateos A, Súarez G, Domínguez L. Mycobacterium tuberculosis subsp. caprae subsp. nov.: a taxonomic study of a new member of the Mycobacterium tuberculosis complex isolated from goats in Spain. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY 1999; 49 Pt 3:1263-73. [PMID: 10425790 DOI: 10.1099/00207713-49-3-1263] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Isolates from the Mycobacterium tuberculosis complex cultured from caprine pathological tissue samples were biochemically and genetically characterized. The isolates were negative for nitrate reduction and niacin accumulation, they weakly hydrolysed Tween 80, were sensitive to pyrazinamide (50 micrograms ml-1) and were resistant to 1 and 2 micrograms tiophene-2-carboxylic acid hydrazide ml-1 but not to 5 or 10 micrograms tiophene-2-carboxylic acid hydrazide ml-1. Sequencing of the pncA gene revealed a polymorphism characteristic of M. tuberculosis, whereas oxyR, katG and gyrA sequences were characteristic of Mycobacterium bovis. The fingerprinting patterns obtained with IS6110, direct repeats and polymorphic G+C-rich sequence-associated RFLP and direct variable repeat-spacer oligonucelotide typing (spoligotyping) segregated these isolates from the other members of the complex. The results of this testing, together with the repeated association of this micro-organism with goats, suggest that a new member of this taxonomic complex not matching any of the classical species had been identified. This unusual mycobacterium may play a role in the epidemiology of animal and human tuberculosis in Spain. The name Mycobacterium tuberculosis subsp. caprae subsp. nov. is proposed for these isolates. The type strain of Mycobacterium tuberculosis subsp. caprae subsp. nov. is gM-1T (= CIP 105776T).
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Toledo H, Baly A, Castro O, Resik S, Laferté J, Rolo F, Navea L, Lobaina L, Cruz O, Míguez J, Serrano T, Sierra B, Pérez L, Ricardo ME, Dubed M, Lubián AL, Blanco M, Millán JC, Ortega A, Iglesias E, Pentón E, Martín Z, Pérez J, Díaz M, Duarte CA. A phase I clinical trial of a multi-epitope polypeptide TAB9 combined with Montanide ISA 720 adjuvant in non-HIV-1 infected human volunteers. Vaccine 2001; 19:4328-36. [PMID: 11457560 DOI: 10.1016/s0264-410x(01)00111-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A phase I clinical trial was performed to examine the safety and immunogenicity of a multi-epitope polypeptide comprising the central 15 amino acids of the V3 loop from six HIV-1 isolates. This protein called TAB9 was emulsified in Montanide ISA720 (Seppic, Paris) and administered intramuscularly at doses of 0, 0.2 and 1 mg to 24 healthy, HIV-1 seronegative adult males. Three immunisations were given at months 0, 1 and 6 in a randomised, double blind, placebo controlled clinical trial. The placebo was generally well tolerated. However, severe local reactions were observed in TAB9 vaccinated subjects after the second and third inoculations. Seven out of eight volunteers from the lower dose group showed moderate or severe local inflammation, while four out of eight subjects from the higher dose group developed granulomas and sterile abscesses. In general, the reactogenicity depended on the number of inoculations given and the dose of TAB9. Both doses were immunogenic, all immunised volunteers seroconverted and antibodies were broadly reactive against the V3 peptides included in the protein. All vaccine's sera reacted against gp120 in Western blot and 50% of them also neutralised at least one out of five laboratory isolates tested. No differences between doses were found. Anti TAB9 lymphoproliferative responses were observed, being more intense in the high dose group. Due to the strong local reactions that were found in this study, a change in the formulation will be required for further trials with this vaccine candidate in humans.
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Clinical Trial |
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Amole C, Ardid M, Arnquist I, Asner D, Baxter D, Behnke E, Bressler M, Broerman B, Cao G, Chen C, Chowdhury U, Clark K, Collar J, Cooper P, Coutu C, Cowles C, Crisler M, Crowder G, Cruz-Venegas N, Dahl C, Das M, Fallows S, Farine J, Felis I, Filgas R, Girard F, Giroux G, Hall J, Hardy C, Harris O, Hillier T, Hoppe E, Jackson C, Jin M, Klopfenstein L, Kozynets T, Krauss C, Laurin M, Lawson I, Leblanc A, Levine I, Licciardi C, Lippincott W, Loer B, Mamedov F, Mitra P, Moore C, Nania T, Neilson R, Noble A, Oedekerk P, Ortega A, Piro MC, Plante A, Podviyanuk R, Priya S, Robinson A, Sahoo S, Scallon O, Seth S, Sonnenschein A, Starinski N, Štekl I, Sullivan T, Tardif F, Vázquez-Jáuregui E, Walkowski N, Weima E, Wichoski U, Wierman K, Yan Y, Zacek V, Zhang J. Dark matter search results from the complete exposure of the PICO-60
C3F8
bubble chamber. Int J Clin Exp Med 2019. [DOI: 10.1103/physrevd.100.022001] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Pape S, Snijders RJALM, Gevers TJG, Chazouilleres O, Dalekos GN, Hirschfield GM, Lenzi M, Trauner M, Manns MP, Vierling JM, Montano-Loza AJ, Lohse AW, Schramm C, Drenth JPH, Heneghan MA, Alvarez F, Andrade R, Arikan C, Assis D, Bardou-Jacquet E, Biewenga M, Cancado E, Cazzagon N, Chazouillères O, Colloredo G, Cuarterolo M, Dalekos G, Debray D, Robles-Díaz M, Drenth J, Dyson J, Efe C, Engel B, Ferri S, Fontana R, Gatselis N, Gerussi A, Halilbasic E, Halliday N, Heneghan M, Hirschfield G, van Hoek B, Hørby Jørgensen M, Indolfini G, Iorio R, Jeong S, Jones D, Kelly D, Kerkar N, Lacaille F, Lammert C, Leggett B, Lenzi M, Levy C, Liberal R, Lleo A, Lohse A, Ines Lopez S, de Martin E, McLin V, Mieli-Vergani G, Milkiewicz P, Mohan N, Muratori L, Nebbia G, van Nieuwkerk C, Oo Y, Ortega A, Páres A, Pop T, Pratt D, Purnak T, Ranucci G, Rushbrook S, Schramm C, Stättermayer A, Swain M, Tanaka A, Taubert R, Terrabuio D, Terziroli B, Trauner M, Valentino P, van den Brand F, Villamil A, Wahlin S, Ytting H, Zachou K, Zeniya M. Systematic review of response criteria and endpoints in autoimmune hepatitis by the International Autoimmune Hepatitis Group. J Hepatol 2022; 76:841-849. [PMID: 35066089 DOI: 10.1016/j.jhep.2021.12.041] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 11/18/2021] [Accepted: 12/11/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Autoimmune hepatitis (AIH) has been well characterised and codified through the development of diagnostic criteria. These criteria have been adapted and simplified and are widely used in clinical practice. However, there is a need to update and precisely define the criteria for both treatment response and treatment. METHODS A systematic review was performed and a modified Delphi consensus process was used to identify and redefine the response criteria in autoimmune hepatitis. RESULTS The consensus process initiated by the International Autoimmune Hepatitis Group proposes that the term 'complete biochemical response' defined as 'normalization of serum transaminases and IgG below the upper limit of normal' be adopted to include a time point at 6 months after initiation of treatment. An insufficient response by 6 months was a failure to meet the above definition. Non-response was defined as '<50% decrease of serum transaminases within 4 weeks after initiation of treatment'. Remission is defined as liver histology with a Hepatitis Activity Index <4/18. Intolerance to treatment was agreed to stand for 'any adverse event possibly related to treatment leading to potential drug discontinuation'. CONCLUSIONS These definitions provide a simple and reproducible framework to define treatment response and non-response, irrespective of the therapeutic intervention. A consensus on endpoints is urgently required to set a global standard for the reporting of study results and to enable inter-study comparisons. Future prospective database studies are needed to validate these endpoints. LAY SUMMARY Consensus among international experts on response criteria and endpoints in autoimmune hepatitis is lacking. A consensus on endpoints is urgently required to set a global standard for the reporting of study results and to enable the comparison of results between clinical trials. Therefore, the International Autoimmune Hepatitis Group (IAIHG) herein presents a statement on 5 agreed response criteria and endpoints: complete biochemical response, insufficient response, non-response, remission, and intolerance to treatment, which can be used to guide future reporting.
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Systematic Review |
3 |
81 |
11
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Abstract
PURPOSE Transanal endorectal resection and pull-through technique (TERPT) for Hirschsprung's disease (HD) was described in 1998. It offers the advantages of avoiding laparotomy, laparoscopy, scars, abdominal contamination, and adhesions. The authors compared TERPT with 2 open standard endorectal pull-through approaches. METHODS Twenty-eight HD patients operated on by endorectal pull-through were compared in 3 groups. Group I had 10 patients with preliminary colostomy approached by laparotomy; group II, 8 by laparotomy; and group III, 10 patients treated by TERPT. Age, operating time and bleeding, complications, follow-up, and functional results were analyzed. Mean, standard deviation, and median were calculated. Groups were compared by 1-way analysis of variance (ANOVA) using the Kruskal-Wallis test. RESULTS Age and length of follow-up were not statistically different (P = .12 and .07, respectively). Operating time and bleeding were less in group III (P = .03 for both). An intestinal obstruction secondary to adhesions and a subhepatic abscess occurred in group I and II, respectively. Minimal complications occurred in group III. Good functional results were obtained in 80% to 90% of the patients in all groups. CONCLUSION TERPT minimizes blood loss in this study, was expeditious, uncomplicated, and as effective as the open standard techniques.
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Comparative Study |
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76 |
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Asensio JA, Stewart BM, Murray J, Fox AH, Falabella A, Gomez H, Ortega A, Fuller CB, Kerstein MD. Penetrating cardiac injuries. Surg Clin North Am 1996; 76:685-724. [PMID: 8782469 DOI: 10.1016/s0039-6109(05)70476-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Penetrating cardiac injuries pose a tremendous challenge to any trauma surgeon. Time, sound judgment, aggressive intervention, and surgical technique are the most important factors contributing to positive outcomes. This article extensively reviews the history, surgical management, and techniques needed to deal with these critical injuries. This year commemorates the one hundredth anniversary of the first successful repair of a cardiac injury.
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Review |
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75 |
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Ortega A, Eshhar N, Teichberg VI. Properties of kainate receptor/channels on cultured Bergmann glia. Neuroscience 1991; 41:335-49. [PMID: 1714547 DOI: 10.1016/0306-4522(91)90331-h] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Following the localization, at the electron microscope level, of the immunoreactivity towards a putative kainate receptor on Bergmann glial cells in the chick cerebellar cortex, cultures of Bergmann glia were used to establish the presence of functional kainate receptor/channels and study their properties. Bergmann glia were identified by their fusiform morphology and their ability to bind an anti-kainate binding protein monoclonal antibody, a kainate receptor high affinity ligand--kainyl-bovine serum albumin--and a glial marker--anti-vimentin monoclonal antibody. Membranes prepared from the culture cells displayed, using 25 nM [3H]kainate, the binding of 4.1 pmol of [3H]kainate/mg protein and showed the presence in Western blots of the two polypeptides of 49 and 93 kDa attributed to the kainate binding protein. Kainate, at concentrations above 0.1 mM, was found to increase the influx into cultured Bergmann glia of 22Na+, 86Rb+, 45Ca2+ and 36Cl- ions. The traffic of 22Na+, induced by kainate and glutamate, observed only in the presence of 1 mM ouabain, was blocked by kainate receptor antagonists and by 0.01 mM quisqualate. Analysis of the kinetics of incorporation of 22Na+ and 45Ca2+ ions showed an initial accumulation of 22Na+ and 45Ca2+ ions followed by their total dissipation. The results indicate that the kainate-induced influx of Na+ ions through the kainate receptor/channel causes the reverse transport of Na+ ions, by activation of the Na+/Ca2+ and Na+/H+ exchangers which remove intracellular Na+ ions. Pre-exposure of the cells to 0.5 mM dibutyryl cAMP was found to greatly enhance the kainate-induced 22Na+ ion influx. We propose that the Bergmann glia kainate receptors modulate the efficacy of the glutamatergic synapses between the parallel fibers and Purkinje cell spines and form part of a glial machinery responsible for plastic changes in synaptic transmission.
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Vilaseca J, González A, Cid MC, Lopez-Vivancos J, Ortega A. Clinical usefulness of temporal artery biopsy. Ann Rheum Dis 1987; 46:282-5. [PMID: 3592783 PMCID: PMC1002120 DOI: 10.1136/ard.46.4.282] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
To assess the diagnostic usefulness of temporal artery biopsy in temporal arteritis (TA) and establish clinical features capable of predicting its positivity we have retrospectively studied the biopsy specimens and the clinical features of 103 patients who had undergone temporal artery biopsy. Temporal artery biopsy reached a positive predictive value of 90.2% with respect to the final diagnosis based on the criteria proposed by Ellis and Ralston and the clinical course. The simultaneous presence of recent onset headache, jaw claudication, and abnormalities of the temporal arteries on physical examination had a specificity of 94.8% with respect to the histological diagnosis and of 100% with respect to final diagnosis. The presence of any of these clinical features, though of little specificity (34.4%), had a sensitivity of 100% with respect to histological diagnosis, selecting a group of patients in whom temporal artery biopsy has more discriminative value.
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research-article |
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Leichman L, Lenz HJ, Leichman CG, Groshen S, Danenberg K, Baranda J, Spears CP, Boswell W, Silberman H, Ortega A. Quantitation of intratumoral thymidylate synthase expression predicts for resistance to protracted infusion of 5-fluorouracil and weekly leucovorin in disseminated colorectal cancers: preliminary report from an ongoing trial. Eur J Cancer 1995; 31A:1306-10. [PMID: 7577041 DOI: 10.1016/0959-8049(95)00326-e] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A clinical trial for patients with measurable, disseminated colorectal cancer is being conducted to determine: (1) if intratumoral expression of thymidylate synthase (TS) affects response to protracted-infusion 5-fluorouracil (5FU); and (2) whether intratumoral expression of TS increases when clinical resistance is found after response to 5-FU. Polymerase chain reaction technology is employed to determine TS expression. Using beta-actin as an internal standard, TS expressions for 26 patients range from 0.5 x 10(-3) to 22.6 x 10(-3). Currently, 22 patients are evaluable for response and TS quantitation of their measurable tumour. 8 patients (36%) have had partial responses; 3 responding patients had been previously treated with 5-FU. A strong statistical association between TS expression and resistance to therapy has been found (P = 0.004). No patient with TS expression of 4.0 x 10(-3) or greater has responded. On average, patients previously treated with 5-FU have slightly higher levels of TS expression in their measurable tumours (P = 0.4). Whether responding patients will develop increased expressions of TS upon clinical progression of their cancer remains to be determined. Confirmation of these results in a larger cohort could lead to a scientific rationale for deciding upon specific therapy for patients with disseminated colorectal cancers.
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Clinical Trial |
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73 |
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Fernandes MX, Ortega A, López Martínez MC, García de la Torre J. Calculation of hydrodynamic properties of small nucleic acids from their atomic structure. Nucleic Acids Res 2002; 30:1782-8. [PMID: 11937632 PMCID: PMC113193 DOI: 10.1093/nar/30.8.1782] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2001] [Revised: 02/14/2002] [Accepted: 02/14/2002] [Indexed: 11/13/2022] Open
Abstract
Hydrodynamic properties (translational diffusion, sedimentation coefficients and correlation times) of short B-DNA oligonucleotides are calculated from the atomic-level structure using a bead modeling procedure in which each non-hydrogen atom is represented by a bead. Using available experimental data of hydrodynamic properties for several oligonucleotides, the best fit for the hydrodynamic radius of the atoms is found to be approximately 2.8 A. Using this value, the predictions for the properties corresponding to translational motion and end-over-end rotation are accurate to within a few percent error. Analysis of NMR correlation times requires accounting for the internal flexibility of the double helix, and allows an estimation of approximately 0.85 for the Lipari-Szabo generalized order parameter. Also, the degree of hydration can be determined from hydrodynamics, with a result of approximately 0.3 g (water)/g (DNA). These numerical results are quite similar to those found for globular proteins. If the hydrodynamic model for the short DNA is simply a cylindrical rod, the predictions for overall translation and rotation are slightly worse, but the NMR correlation times and the degree of hydration, which depend more on the cross-sectional structure, are more severely affected.
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research-article |
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Pasantes-Morales H, Franco R, Torres-Marquez ME, Hernández-Fonseca K, Ortega A. Amino acid osmolytes in regulatory volume decrease and isovolumetric regulation in brain cells: contribution and mechanisms. Cell Physiol Biochem 2001; 10:361-70. [PMID: 11125217 DOI: 10.1159/000016369] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Brain adaptation to hyposmolarity is accomplished by loss of both electrolytes and organic osmolytes, including amino acids, polyalcohols and methylamines. In brain in vivo, the organic osmolytes account for about 35% of the total solute loss. This review focus on the role of amino acids in cell volume regulation, in conditions of sudden hyposmosis, when cells respond by active regulatory volume decrease (RVD) or after gradual exposure to hyposmotic solutions, a condition where cell volume remains unchanged, named isovolumetric regulation (IVR). The amino acid efflux pathway during RVD is passive and is similar in many respects to the volume-activated anion pathway. The molecular identity of this pathway is still unknown, but the anion exchanger and the phospholemman are good candidates in certain cells. The activation trigger of the osmosensitive amino acid pathway is unclear, but intracellular ionic strength seems to be critically involved. Tyrosine protein kinases markedly influence amino acid efflux during RVD and may play an important role in the transduction signaling cascades for osmosensitive amino acid fluxes. During IVR, amino acids, particularly taurine are promptly released with an efflux threshold markedly lower than that of K(+), emphasizing their contribution (possibly as well as of other organic osmolytes) vs inorganic ions, in the osmolarity range corresponding to physiopathological conditions. Amino acid efflux also occurs in response to isosmotic swelling as that associated with ischemia or trauma. Characterization of the pathway involved in this type of swelling is hampered by the fact that most osmolyte amino acids are also neuroactive amino acids and may be released in response to stimuli concurrent with swelling, such as depolarization or intracellular Ca(++) elevation.
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Review |
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70 |
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Chaves F, Dronda F, Cave MD, Alonso-Sanz M, Gonzalez-Lopez A, Eisenach KD, Ortega A, Lopez-Cubero L, Fernandez-Martin I, Catalan S, Bates JH. A longitudinal study of transmission of tuberculosis in a large prison population. Am J Respir Crit Care Med 1997; 155:719-25. [PMID: 9032218 DOI: 10.1164/ajrccm.155.2.9032218] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The purpose of this study was to determine the extent of transmission of tuberculosis in a large prison population over an 18-mo period. Restriction-fragment-length polymorphism (RFLP) analysis of isolates of Mycobacterium tuberculosis was performed, using the insertion sequence IS6110 and the plasmid pTBN12. Patients infected with strains having the same fingerprint were grouped in clusters. Medical records were reviewed and movement of inmates among prisons was examined for selected patients. Tuberculosis was diagnosed in 216 inmates (case rate = 2,283 per 100,000 per year). Isolates from 210 (97%) patients were fingerprinted, 155 (74%) were grouped in 25 clusters, and 55 (26%) showed a unique fingerprint. Recent infection was inferred in 62% of these patients. Eighty-four percent (161 of 192) of patients tested were human immunodeficiency virus (HIV)-positive, of whom 121 were in clusters and 40 were not (p = 0.74). Patients in clusters were less adherent with tuberculosis treatment than those not in clusters (p < 0.05), and prison transmission of resistant strains was observed. It is crucial that infection control guidelines be fully implemented in the prison setting to prevent tuberculosis transmission.
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Criado J, Ortega A. Non-isothermal crystallization kinetics of metal glasses: simultaneous determination of both the activation energy and the exponent n of the JMA kinetic law. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0001-6160(87)90117-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38 |
69 |
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Ortega A, García de la Torre J. Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility. Biomacromolecules 2007; 8:2464-75. [PMID: 17645309 DOI: 10.1021/bm700473f] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The equivalent radius for any solution property is the radius of a spherical particle having the same value of solution property as that of the macromolecule under consideration. Equivalent radii for different properties present a dependence on size and shape that are more similar than the values of the properties themselves. Furthermore, the ratios of equivalent radii of two properties depend on the conformation (shape or flexibility), but not on the absolute sizes. We define equivalent radii and their ratios, and describe their evaluation for some common models of rigid and flexible macromolecules. Using radii and ratios, we have devised procedures to fit macromolecular models to experimental properties, allowing the determination of the model parameters. Using these quantities, we can construct target functions for an equilibrated, unbiased optimization. The procedures, which have been implemented in public-domain computer programs, are illustrated for rigid, globular proteins, and the rodlike tobacco mosaic virus, and for semiflexible, wormlike heparin molecules.
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Research Support, Non-U.S. Gov't |
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65 |
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Ramiro-Ibáñez F, Ortega A, Brun A, Escribano JM, Alonso C. Apoptosis: a mechanism of cell killing and lymphoid organ impairment during acute African swine fever virus infection. J Gen Virol 1996; 77 ( Pt 9):2209-19. [PMID: 8811021 DOI: 10.1099/0022-1317-77-9-2209] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Induction of programmed cell death has been described during infection with many different viruses. We have investigated the influence of African swine fever virus (ASFV) on apoptosis of different cell populations during in vitro and in vivo infection. We observed apoptosis in ASFV-infected monocyte/macrophage and peripheral blood mononuclear cell cultures. Apoptosis was demonstrated in these cells by DNA fragmentation, DNA staining and DNA-associated histone fraction detection assays. Flow cytometry analysis of infected cultures also showed morphological and functional alterations, including changes in the cell cycle and percentage of cell fractions stained with propidium iodide. After in vivo infection with three different virulent strains of ASFV, apoptosis of infected cells from the mononuclear phagocytic system and closely related elements from different tissues was observed. Additionally, infected pigs showed an intense degree of apoptosis of lymphocytes, which are not infected by the virus. In lymph nodes and other lymphoid organs, broad bands of apoptotic cells presented typical nuclear changes under light microscopy. The occurrence of DNA fragmentation was confirmed in these tissues using terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling. These findings, together with the pathological observations in infected pigs of a depletion in cell populations in lymphoid organs, suggest that virus interference with programmed cell death plays a central role in pathogenesis of this disease, being responsible for lymphoid organ impairment in acute ASFV infection.
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Rullán JV, Herrera D, Cano R, Moreno V, Godoy P, Peiró EF, Castell J, Ibañez C, Ortega A, Agudo LS, Pozo F. Nosocomial transmission of multidrug-resistant Mycobacterium tuberculosis in Spain. Emerg Infect Dis 1996; 2:125-9. [PMID: 8903213 PMCID: PMC2639835 DOI: 10.3201/eid0202.960208] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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research-article |
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Aguirre A, López T, López-Bayghen E, Ortega A. Glutamate regulates kainate-binding protein expression in cultured chick Bergmann glia through an activator protein-1 binding site. J Biol Chem 2000; 275:39246-53. [PMID: 10993879 DOI: 10.1074/jbc.m002847200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The expression of the chick kainate-binding protein, a member of the ionotropic glutamate receptor family, is restricted to the cerebellum, specifically to Bergmann glia. Glutamate induces a membrane to nuclei signaling involved in gene expression regulation. Exposure of cultured chick Bergmann glia cells to glutamate leads to an increase in kainate binding protein and mRNA levels, suggesting a transcriptional level of regulation. The 5' proximal region of the chick kainate binding gene was cloned and transfected 4into Bergmann glia cells. Three main regulatory regions could be defined, a minimal promoter region, a negative regulatory region, and interestingly, a glutamate-responsive element. Deletion of this element abolishes the agonist effect. Moreover, electrophoretic mobility shift assays, cotransfection experiments, and site-directed mutagenesis clearly suggest that the glutamate effect is mediated through an AP-1 site by a Fos/Jun heterodimer. The present results favor the notion of a functional role of kainate-binding protein in glutamatergic cerebellar neurotransmission.
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MESH Headings
- Animals
- Base Sequence
- Binding Sites
- Blotting, Northern
- Blotting, Western
- Cell Nucleus/metabolism
- Cells, Cultured
- Cerebellum/metabolism
- Chick Embryo
- Chloramphenicol O-Acetyltransferase/metabolism
- Cloning, Molecular
- Dose-Response Relationship, Drug
- Electrophoresis, Polyacrylamide Gel
- Gene Expression Regulation
- Glutamic Acid/physiology
- Models, Biological
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Neuroglia/metabolism
- Plasmids/metabolism
- Promoter Regions, Genetic
- Proto-Oncogene Proteins c-fos/metabolism
- Proto-Oncogene Proteins c-jun/metabolism
- RNA, Messenger/metabolism
- Receptors, Glutamate/biosynthesis
- Receptors, Glutamate/genetics
- Receptors, Kainic Acid/biosynthesis
- Receptors, Kainic Acid/genetics
- Response Elements
- Reverse Transcriptase Polymerase Chain Reaction
- Time Factors
- Transcription Factor AP-1/chemistry
- Transcription Factor AP-1/metabolism
- Transcription, Genetic
- Transfection
- Up-Regulation
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57 |
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Gregor P, Eshhar N, Ortega A, Teichberg VI. Isolation, immunochemical characterization and localization of the kainate sub-class of glutamate receptor from chick cerebellum. EMBO J 1988; 7:2673-9. [PMID: 2846279 PMCID: PMC457055 DOI: 10.1002/j.1460-2075.1988.tb03120.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The low-affinity kainate binding sites, present at high density in chick cerebellar membranes, were solubilized with Triton X-100 and purified 41-fold. The purified kainate binding sites, therein referred to as the kainate receptor, displayed the expected pharmacological specificity: domoate = kainate much greater than L-glutamate much greater than D-glutamate, quisqualate, N-methyl-D-aspartate. Analysed by SDS-PAGE under reducing conditions, a single polypeptide with a Mr = 49,000 was observed. Western blots of membranes prepared from different brain areas and animal species were analysed using a monoclonal antibody, named mAb IX-50, raised against the purified kainate receptor. The mAb IX-50 stained the 49,000 polypeptide in chick, goldfish and mammalian brain tissues indicating its conservation during evolution. The staining intensity correlated with the density of kainate binding sites. The mAb IX-50 stained also a 93,000 polypeptide but the latter did not copurify with the 49,000 polypeptide. The kainate binding activity was selectively immunoadsorbed on mAb IX-50 coupled to Sepharose which, upon elution, released a 49,000 polypeptide. The immunohistochemical localization of mAb IX-50 binding sites in the chick cerebellar molecular layer coincided with that of the kainate receptor. We conclude that the 49,000 polypeptide is part of the kainate receptor and carries the kainate recognition site.
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MESH Headings
- Animals
- Antibodies, Monoclonal
- Blotting, Western
- Centrifugation, Density Gradient
- Cerebellum/analysis
- Cerebellum/metabolism
- Chick Embryo
- Chickens
- Chromatography, Gel
- Detergents/metabolism
- Electrophoresis, Polyacrylamide Gel
- Glutamates/metabolism
- Immunohistochemistry
- Kainic Acid/metabolism
- Ligands
- Mice
- Molecular Weight
- Radioimmunoassay
- Receptors, Glutamate
- Receptors, Kainic Acid
- Receptors, Neurotransmitter/analysis
- Receptors, Neurotransmitter/immunology
- Receptors, Neurotransmitter/metabolism
- Solubility
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Skinner AR, Blackwell BAB, Martin S, Ortega A, Blickstein JIB, Golovanova LV, Doronichev VB. ESR dating at Mezmaiskaya Cave, Russia. Appl Radiat Isot 2005; 62:219-24. [PMID: 15607452 DOI: 10.1016/j.apradiso.2004.08.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mezmaiskaya Cave has yielded more than 10,000 artifacts, thousands of very well preserved faunal remains, and hominin remains, found in seven Middle Paleolithic (Mousterian) and three Upper Paleolithic levels. A complete Neanderthal infant skeleton was preserved in anatomical juxtaposition lying on a large limestone block, overlain by the earliest Mousterian layer, Layer 3. Twenty-four skull fragments from a 1-2 year-old Neanderthal infant, showing post-mortem deformation, occurred in a pit originating in the Mousterian Layer 2 and penetrating into underlying layers 2A and 2B(1). Bone from Layer 2A was dated by AMS 14C at 35.8-36.3+/-0.5 kyr BP. Direct dating of Neanderthal bone from Layer 3 gave an age of 29 kyr, but that is now considered to be due to contamination by modern carbon. Fourteen large mammal teeth from Layers 2 through 3 have been dated by standard electron spin resonance (ESR). Low U concentrations in both the enamel and dentine ensure that ESR ages do not depend significantly on the U uptake model, but do depend strongly on the sedimentary dose rates. Assuming a sedimentary water concentration equal to 20 wt%, ESR ages for the Mousterian layers range from 36.2 to 73.0+/-5.0 ka.
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