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Saha A, Baca M, Popović D, Mohammadi Z, Olsson U, Roycroft E, Fostowicz-Frelik Ł. The first complete mitochondrial genome data of the Afghan pika Ochotona rufescens (Lagomorpha, Ochotonidae), near the type locality. Data Brief 2024; 53:110246. [PMID: 38533117 PMCID: PMC10964060 DOI: 10.1016/j.dib.2024.110246] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/03/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
The Afghan pika Ochotona rufescens (Gray, 1842) is widely distributed across the mountains of Afghanistan, Iran, Pakistan, and southwestern Turkmenistan, most often at elevations between 2,000 and 3,000 m. Here we present, for the first time, the complete mitochondrial genomes of two specimens of the nominotypical subspecies Ochotona rufescens rufescens, de novo assembled from Illumina short reads of fragmented probe-enriched DNA. The lengths of the circular mitogenomes are 16,408 bp and 16,407 bp, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), two ribosomal RNAs (16S rRNA and 12S rRNA), 22 transfer RNA genes, and a control region. The gene NAD6 and the tRNA (Gln), tRNA (Ala), tRNA (Asn), tRNA (Cys), tRNA (Tyr), tRNA (Ser), tRNA (Glu), and tRNA (Pro) are encoded on the light strand while the rest are encoded on the heavy strand. The overall nucleotide composition was ∼30% for A, 25% for T, 15% for G, and 29% for C. The mitogenome data are available in the GenBank under the accession numbers ON859136 and ON859137.
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Affiliation(s)
- Anwesha Saha
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00–818 Warsaw, Poland
- Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02–097 Warsaw, Poland
| | - Mateusz Baca
- Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02–097 Warsaw, Poland
| | - Danijela Popović
- Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02–097 Warsaw, Poland
| | | | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Emily Roycroft
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Acton, ACT 2601, Australia
| | - Łucja Fostowicz-Frelik
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00–818 Warsaw, Poland
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Baca M, Popović D, Agadzhanyan AK, Baca K, Conard NJ, Fewlass H, Filek T, Golubiński M, Horáček I, Knul MV, Krajcarz M, Krokhaleva M, Lebreton L, Lemanik A, Maul LC, Nagel D, Noiret P, Primault J, Rekovets L, Rhodes SE, Royer A, Serdyuk NV, Soressi M, Stewart JR, Strukova T, Talamo S, Wilczyński J, Nadachowski A. Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals. Proc Biol Sci 2023; 290:20222238. [PMID: 36787794 PMCID: PMC9928523 DOI: 10.1098/rspb.2022.2238] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.
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Affiliation(s)
- Mateusz Baca
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Katarzyna Baca
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology and.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thomas Filek
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | | | - Ivan Horáček
- Department of Zoology, Charles University, Prague, Czechia
| | - Monika V Knul
- Department of Archaeology, Anthropology and Geography, University of Winchester, Winchester, UK
| | - Magdalena Krajcarz
- Institute of Archaeology, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Maria Krokhaleva
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Loïc Lebreton
- Department of Human and Environment, (HNHP) UMR 7194MNHN-CNRS-UPVD, National Museum of Natural History, Paris, France.,Catalan Institute of Human Paleoecology and Social Evolution (IPHES-CERCA), Tarragona, Spain.,Department of History and Art History, Rovira i Virgili University, Tarragona, Spain
| | - Anna Lemanik
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Cracow, Poland
| | - Lutz C Maul
- Senckenberg Research Station of Quaternary Palaeontology, Weimar, Germany
| | - Doris Nagel
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Pierre Noiret
- Research Group Prehistory, University of Liège, Liège, Belgium
| | - Jérome Primault
- DRAC/SRA Poitou-Charentes, Ministry of Culture and Communications, Poitiers, France
| | - Leonid Rekovets
- Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Sara E Rhodes
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior, University of Algavre, Faro, Portugal
| | - Aurélien Royer
- Biogéosciences, UMR 6282 CNRS, University of Burgundy, Dijon, France
| | - Natalia V Serdyuk
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - John R Stewart
- Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Tatiana Strukova
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Cracow, Poland
| | - Adam Nadachowski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Cracow, Poland
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3
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Lord E, Marangoni A, Baca M, Popović D, Goropashnaya AV, Stewart JR, Knul MV, Noiret P, Germonpré M, Jimenez EL, Abramson NI, Vartanyan S, Prost S, Smirnov NG, Kuzmina EA, Olsen RA, Fedorov VB, Dalén L. Population dynamics and demographic history of Eurasian collared lemmings. BMC Ecol Evol 2022; 22:126. [PMID: 36329382 PMCID: PMC9632076 DOI: 10.1186/s12862-022-02081-y] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species. RESULTS Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene. CONCLUSIONS This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.
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Affiliation(s)
- Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 10691, Stockholm, Sweden. .,Department of Zoology, Stockholm University, 10691, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.
| | - Aurelio Marangoni
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 10691, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden
| | - Mateusz Baca
- Centre of New Technologies, University of Warsaw, S. Banacha 2C, 02-097, Warsaw, Poland
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, S. Banacha 2C, 02-097, Warsaw, Poland
| | - Anna V Goropashnaya
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775-7000, USA
| | - John R Stewart
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, BH12 5BB, Dorset, UK
| | - Monika V Knul
- Department of Archaeology, Anthropology and Geography, University of Winchester, Winchester, SO22 4NR, UK
| | - Pierre Noiret
- Service de Préhistoire, Université de Liège, Place du 20 Août 7, 4000, Liège, Belgium
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels, Belgium
| | - Elodie-Laure Jimenez
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels, Belgium.,School of Geosciences, University of Aberdeen, Aberdeen, Scotland
| | - Natalia I Abramson
- Department of Molecular Systematics, Zoological Institute RAS, St Petersburg, Russia
| | - Sergey Vartanyan
- Far East Branch, N.A. Shilo North-East Interdisciplinary Scientific Research Institute Russian Academy of Sciences (NEISRI FEB RAS), 685000, Magadan, Russia
| | - Stefan Prost
- Central Research Laboratories, Natural History Museum Vienna, 1010, Vienna, Austria.,Department of Cognitive Biology, University of Vienna, 1090, Vienna, Austria.,Konrad Lorenz Institute of Ethology, 1160, Vienna, Austria.,South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Nickolay G Smirnov
- Institute of Plant and Animal Ecology UB RAS, Russian Academy of Sciences, 202 8 Marta Street, 620144, Ekaterinburg, Russia
| | - Elena A Kuzmina
- Institute of Plant and Animal Ecology UB RAS, Russian Academy of Sciences, 202 8 Marta Street, 620144, Ekaterinburg, Russia
| | - Remi-André Olsen
- Science for Life Laboratory (SciLifeLab), Dept of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Vadim B Fedorov
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775-7000, USA
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 10691, Stockholm, Sweden. .,Department of Zoology, Stockholm University, 10691, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.
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4
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Baca M, Popović D, Lemanik A, Fewlass H, Talamo S, Zima J, Ridush B, Popov V, Nadachowski A. The Tien Shan vole ( Microtus ilaeus; Rodentia: Cricetidae) as a new species in the Late Pleistocene of Europe. Ecol Evol 2021; 11:16113-16125. [PMID: 34824815 PMCID: PMC8601874 DOI: 10.1002/ece3.8289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022] Open
Abstract
Grey voles (subgenus Microtus) represent a complex of at least seven closely related and partly cryptic species. The range of these species extends from the Atlantic to the Altai Mountains, but most of them occur east of the Black Sea. Using ancient DNA analyses of the Late Pleistocene specimens, we identified a new mtDNA lineage of grey voles in Europe. Phylogenetic analysis of mitochondrial DNA cytochrome b sequences from 23 voles from three caves, namely, Emine-Bair-Khosar (Crimea, Ukraine), Cave 16 (Bulgaria), and Bacho Kiro (Bulgaria), showed that 14 specimens form a previously unrecognized lineage, sister to the Tien Shan vole. The average sequence divergence of this lineage and the extant Tien Shan vole was 4.8%, which is similar to the divergence of grey vole forms, which are considered distinct species or being on the verge of speciation; M. arvalis and M. obscurus or M. mystacinus and M. rossiaemeridionalis. We estimated the time to the most recent common ancestor of the grey voles to be 0.66 Ma, which is over twice the recent estimates, while the divergence of the extant Tien Shan vole and the new lineage to be 0.29 Ma. Our discovery suggests that grey voles may have been more diversified in the past and that their ranges may have differed substantially from current ones. It also underlines the utility of ancient DNA to decipher the evolutionary history of voles.
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Affiliation(s)
- Mateusz Baca
- Centre of New TechnologiesUniversity of WarsawWarszawaPoland
| | | | - Anna Lemanik
- Institute of Systematics and Evolution of AnimalsPolish Academy of SciencesKrakówPoland
| | - Helen Fewlass
- Department of Human EvolutionMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Sahra Talamo
- Department of Human EvolutionMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
- Department of Chemistry G. CiamicianUniversity of BolognaBolognaItaly
| | - Jan Zima
- Institute of Vertebrate BiologyAcademy of Sciences of Czech RepublicBrnoCzech Republic
| | - Bogdan Ridush
- Department of Physical Geography, Geomorphology and PaleogeographyYuriy Fedkovych Chernivtsi National UniversityChernivtsiUkraine
| | - Vasil Popov
- Institute of Biodiversity and Ecosystem ResearchBulgarian Academy of SciencesSophiaBulgaria
| | - Adam Nadachowski
- Institute of Systematics and Evolution of AnimalsPolish Academy of SciencesKrakówPoland
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5
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Di Fusco S, Pignalberi C, Spinelli A, Baca M, Cappuccio C, Russo M, Pandozi C, Colivicchi F. Clinical characteristics, management, and outcomes of patients with electrical storm: single centre experience. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.0694] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Electrical storm (ES) is a life-threatening condition caused by recurrent malignant ventricular arrhythmia (≥3 episodes of ventricular tachycardia (VT) or ventricular fibrillation within 24 hours). ES patient management is challenging and can involve antiarrhythmic medication, sedation, and invasive procedures such as catheter ablation.
Purpose
The aim of this study is to report the clinical profile and management of ES patients who attended an arrhythmia reference centre.
Methods
Patients who presented with ES at our centre over a five-year period were consecutively enrolled. Patient data were retrospectively collected from hospital records. Patients with in-hospital death were excluded form data analysis.
Results
Seventy-six patients were included (84% male, mean age 73±10 years). 55% of patients had ischemic heart disease. The mean left ventricle ejection fraction (LVEF) was 33±4%, with 22% of patients having a severe reduction in systolic ventricular function (EF <35%). Baseline characteristics are reported in Table 1. During hospitalisation, 30% of patients underwent coronary angiography and 30% of these had percutaneous coronary revascularization. Patients were managed with pharmacological treatment, including continuous infusion of antiarrhythmic drugs (45% of patients received at least one antiarrhythmic), sedation (12%), and electrolytic solutions (38%). More details on ES management are reported in Table 2. All patients were evaluated for transcatheter ablation. After a mean of 6 days, 25% underwent transcatheter VT ablation during hospitalisation. In 7 patients (9%), catheter ablation was planned and performed during a subsequent hospitalisation.
At discharge, 93% of patients received beta blockers and 68% received amiodarone. Overall, 65% were discharged with at least two antiarrhythmic drugs. The mean length of hospitalisation was 10±9 days, with 6±4 days spent in the intensive care unit. Eighteen patients (23%) had at least one subsequent hospitalisation for ES. After a mean follow-up of 20 months, the cumulative mortality rate was 27%, without a significant difference in mortality rates between ablated and non-ablated patients (27% and 28%, respectively). Baseline mean creatinine levels were higher (1.73±1.1 vs. 1.27±0.1 mg/dl, p<0.05), and LVEF was lower (27±3% vs. 35±17%, p<0.05) in patients who died during follow-up as compared to survivors. A trend toward a longer QTc interval duration (482±47 vs. 467±28 ms) and longer QRS duration (139±36 vs. 131±7 ms) was also found among patients who died during follow-up.
Conclusion
In our centre, ischemic heart disease was the most common heart disease in patients presenting with ES. In more than one third of patients, VT transcatheter ablation was performed as a therapeutic strategy in addition to drug therapy. Among patients who died during the follow-up, baseline creatinine levels were higher and LVEF was lower compared with survivors.
Funding Acknowledgement
Type of funding sources: None. Table 1Table 2
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Affiliation(s)
| | | | | | - M Baca
- San Filippo Neri Hospital, Rome, Italy
| | | | - M Russo
- San Filippo Neri Hospital, Rome, Italy
| | - C Pandozi
- San Filippo Neri Hospital, Rome, Italy
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Popović D, Molak M, Ziółkowski M, Vranich A, Sobczyk M, Vidaurre DU, Agresti G, Skrzypczak M, Ginalski K, Lamnidis TC, Nakatsuka N, Mallick S, Baca M. Ancient genomes reveal long-range influence of the pre-Columbian culture and site of Tiwanaku. Sci Adv 2021; 7:eabg7261. [PMID: 34559567 PMCID: PMC8462900 DOI: 10.1126/sciadv.abg7261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 08/03/2021] [Indexed: 05/18/2023]
Abstract
Tiwanaku civilization flourished in the Lake Titicaca basin between 500 and 1000 CE and at its apogee influenced wide areas across the southern Andes. Despite a considerable amount of archaeological data, little is known about the Tiwanaku population. We analyzed 17 low-coverage genomes from individuals dated between 300 and 1500 CE and demonstrated genetic continuity in the Lake Titicaca basin throughout this period, which indicates that the substantial cultural and political changes in the region were not accompanied by large-scale population movements. Conversely, the ritual center of Tiwanaku revealed high diversity, including individuals with primarily local genetic ancestry and those with foreign admixture or provenance from as far as the Amazon. Nonetheless, most human offerings associated with the Akapana platform exhibited pure Titicaca basin ancestry and dated to ca. 950 CE—the onset of Tiwanaku’s decline as a sociopolitical center. Our results strengthen the view of Tiwanaku as a complex and far-reaching polity.
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Affiliation(s)
- Danijela Popović
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
- Corresponding author. (D.P.); (M.B.)
| | - Martyna Molak
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warsaw, Poland
| | - Mariusz Ziółkowski
- Centre for Andean Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927 Warsaw, Poland
| | - Alexei Vranich
- Department of Anthropology, University of Texas San Antonio College of Liberal and Fine Arts, One UTSA Circle, San Antonio, TX 78249-1644, USA
| | - Maciej Sobczyk
- Centre for Andean Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927 Warsaw, Poland
- Faculty of Archaeology University of Warsaw, Krakowskie Przedmieście 26/28, 00-927 Warsaw, Poland
| | - Delfor Ulloa Vidaurre
- Unit of Archeology and Museums, Vice Ministry of Interculturality, Tiahuanaco Street No. 93 at the corner of Federico Suazo, Box 4856, La Paz, Bolivia
| | - Guido Agresti
- Centre for Andean Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927 Warsaw, Poland
| | - Magdalena Skrzypczak
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Krzysztof Ginalski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Thiseas Christos Lamnidis
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Mateusz Baca
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
- Corresponding author. (D.P.); (M.B.)
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7
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Doan K, Niedziałkowska M, Stefaniak K, Sykut M, Jędrzejewska B, Ratajczak-Skrzatek U, Piotrowska N, Ridush B, Zachos FE, Popović D, Baca M, Mackiewicz P, Kosintsev P, Makowiecki D, Charniauski M, Boeskorov G, Bondarev AA, Danila G, Kusak J, Rannamäe E, Saarma U, Arakelyan M, Manaseryan N, Krasnodębski D, Titov V, Hulva P, Bălășescu A, Trantalidou K, Dimitrijević V, Shpansky A, Kovalchuk O, Klementiev AM, Foronova I, Malikov DG, Juras A, Nikolskiy P, Grigoriev SE, Cheprasov MY, Novgorodov GP, Sorokin AD, Wilczyński J, Protopopov AV, Lipecki G, Stanković A. Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b, including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum.
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Affiliation(s)
- Karolina Doan
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, S. Banacha 2C, 02-097 Warsaw, Poland
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warsaw, Poland
| | | | - Krzysztof Stefaniak
- Department of Palaeozoology, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Maciej Sykut
- Mammal Research Institute Polish Academy of Sciences, Stoczek 1c, 17-230 Białowieża, Poland
| | - Bogumiła Jędrzejewska
- Mammal Research Institute Polish Academy of Sciences, Stoczek 1c, 17-230 Białowieża, Poland
| | | | - Natalia Piotrowska
- Radiocarbon Laboratory Institute of Physics–Center for Science and Education, Silesian University of Technology, Konarskiego 22b,44-100 Gliwice, Poland
| | - Bogdan Ridush
- Department of Physical Geography, Geomorphology and Paleogeography, Yuriy Fedkovych Chernivtsi National University, Kotsubynskogo 2, Chernivtsi 58012, Ukraine
| | - Frank E Zachos
- Natural History Museum Vienna, 1010 Vienna, Austria
- Department of Genetics, University of the Free State, 9301 Bloemfontein, South Africa
- Department of Evolutionary Biology, University of Vienna, 1090 Vienna, Austria
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Mateusz Baca
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta 202, Yekaterinburg 620144, Russia
| | - Daniel Makowiecki
- Nicolaus Copernicus University, Institute of Archaeology, Department of Historical Sciences, Szosa Bydgoska 44/48, 87-100 Toruń, Poland
| | - Maxim Charniauski
- Institute of History of the National Academy of Sciences of Belarus, Academic 1, 220072 Minsk, Belarus
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of Russian Academy of Sciences, Yakutsk, Yakutia, Russian Federation
| | | | - Gabriel Danila
- Universitatea Stefan cel Mare Suceava, Facultatea de Silvicultura, Suceava, Romania
| | - Josip Kusak
- Veterinary Faculty, University of Zagreb, 10000 Zagreb, Croatia
| | - Eve Rannamäe
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Marine Arakelyan
- Yerevan State University, Faculty of Biology, Department of Zoology, Alex Manoogian 1, 0025 Yerevan, Republic of Armenia
| | - Ninna Manaseryan
- The Scientific Center of Zoology and Hydroecology of National Academy of Sciences of Armenia, P. Sevak 7, Yerevan 0014, Republic of Armenia
| | - Dariusz Krasnodębski
- Institute of Archaeology and Ethnology Polish Academy of Sciences, Al. Solidarności 105, 00-140 Warsaw, Poland
| | - Vadim Titov
- Southern Scientific Centre Russian Academy of Sciences, Chekhov 41, Rostov-on-Don 344006, Russian Federation
| | - Pavel Hulva
- Charles University in Prague, Department of Zoology, Viničná 1594/7, 128 00 Nové Město, Prague, Czech Republic
- University of Ostrava, Department of Biology and Ecology, Chittussiho 10, 710 00 Slezská Ostrava, Czech Republic
| | - Adrian Bălășescu
- ’Vasile Pârvan’ Institute of Archaeology, Romanian Academy, Henri Coandă 11, 010667 Bucharest, Romania
| | | | - Vesna Dimitrijević
- Laboratory for Bioarchaeology, Department of Archaeology, Faculty of Philosophy, University of Belgrade, Čika Ljubina 18-20, 11000 Belgrade, Serbia
| | - Andrey Shpansky
- Department of Palaeontology and Historical Geology, Tomsk State University, 634050 Tomsk, Russian Federation
| | - Oleksandr Kovalchuk
- Department of Paleontology, National Museum of Natural History National Academy of Sciences of Ukraine, 15 B. Khmelnytsky 15, Kyiv 01030Ukraine
| | - Alexey M Klementiev
- Institute of the Earth’s Crust, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russian Federation
| | - Irina Foronova
- V. S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Koptyuga pr. 3, Novosibirsk, Russian Federation
| | - Dmitriy G Malikov
- V. S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Koptyuga pr. 3, Novosibirsk, Russian Federation
| | - Anna Juras
- Institute of Human Biology & Evolution, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Pavel Nikolskiy
- Laboratory of Quaternary Stratigraphy, Geological Institute, Russian Academy of Sciences, 119017 Moscow, Russia
| | - Semyon Egorovich Grigoriev
- Laboratory of P. A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University named after M. K. Ammosov, Building of Faculties of Natural Sciences (KFEN), 48 Kulakovsky Str., 677000 Yakutsk, Republic of Sakha (Yakutia), Russian Federation
| | - Maksim Yurievich Cheprasov
- Laboratory of P. A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University named after M. K. Ammosov, Building of Faculties of Natural Sciences (KFEN), 48 Kulakovsky Str., 677000 Yakutsk, Republic of Sakha (Yakutia), Russian Federation
| | - Gavril Petrovich Novgorodov
- Laboratory of P. A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University named after M. K. Ammosov, Building of Faculties of Natural Sciences (KFEN), 48 Kulakovsky Str., 677000 Yakutsk, Republic of Sakha (Yakutia), Russian Federation
| | | | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Cracow, Poland
| | - Albert Vasilievich Protopopov
- Department of Study of Mammoth Fauna, Academy of Science of Sakha Republic (Yakutia), Lenin Avenue 33, Yakutsk, 677027, Republic of Sakha (Yakutia), Russian Federation
| | - Grzegorz Lipecki
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Cracow, Poland
| | - Ana Stanković
- Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
- The Antiquity of Southeastern Europe Research Centre, University of Warsaw, Krakowskie Przedmieście 32, 00-927 Warsaw, Poland
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8
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Martinón-Torres F, Halperin SA, Nolan T, Tapiero B, Perrett KP, de la Cueva IS, García-Sicilia J, Stranak Z, Vanderkooi OG, Kosina P, Virta M, Merino Arribas JM, Miranda-Valdivieso M, Arias Novas B, Bozensky J, Cilleruelo Ortega M, Ramos Amador JT, Baca M, Escribano PE, Zuccotti GV, Janota J, Marchisio PG, Kostanyan L, Meyer N, Ceregido MA, Cheuvart B, Kuriyakose SO, Mesaros N. Immunantwort auf die DTPa-HBV-IPV/Hib-Auffrischimpfung bei Kleinkindern von Müttern, die während der Schwangerschaft mit Tdap-Impfstoff geimpft worden waren: Folgestudie einer randomisierten, placebokontrollierten Studie. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1717189] [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: 10/23/2022] Open
Affiliation(s)
- F Martinón-Torres
- Hospital Clínico Universitario de Santiago, Pediatría Clínica, Infectológica y Traslacional
| | - SA Halperin
- Dalhousie University, Canadian Center for Vaccinology
| | - T Nolan
- University of Melbourne, Murdoch Children’s Research Institute and Melbourne School of Population and Global Health
| | - B Tapiero
- Université de Montréal, CHU Sainte Justine
| | - KP Perrett
- University of Melbourne, Murdoch Children’s Research Institute and Melbourne School of Population and Global Health
| | - IS de la Cueva
- Instituto Hispalense de Pediatría, Unidad de Investigación
| | - J García-Sicilia
- Hospital Universitario Madrid Sanchinarro, Servicio de Pediatría
| | - Z Stranak
- Institute for the Care of Mother and Child, Neonatology Department
| | - OG Vanderkooi
- Alberta Children’s Hospital, University of Calgary, Departments of Pediatrics, Microbiology, Immunology and Infectious DiseasesPathology and Laboratory Medicine and Community Health Sciences, Pathology and Laboratory Medicine and Community Health Sciences, Alberta Children’s Hospital Research Institut
| | - P Kosina
- University Hospital, Department of Infectious Diseases
| | - M Virta
- Tampere University, Tampere Vaccine Research Center
| | | | | | - B Arias Novas
- Hospital Universitario Sanitas La Zarzuela, Servicio de Pediatría
| | - J Bozensky
- Vitkovice Hospital, Pediatrics Department
| | | | | | - M Baca
- Hospital Quiron Malaga, Departamento de Pediatría y Neonatología
| | | | - GV Zuccotti
- University of Milan, Ospedale dei Bambini Vittore Buzzi
| | - J Janota
- Thomayer Hospital Prague, Department of Neonatology
| | - PG Marchisio
- University of Milan, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico
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9
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Arnaez J, Herranz-Rubia N, Garcia-Alix A, Diez-Delgado J, Benavente-Fernández I, Tofé I, Jerez A, Hurtado J, Ceballos J, Millán M, Esquivel M, Ruiz C, Baca M, Tapia E, Losada M, Torres E, Pavón A, Jiménez P, Jiménez F, Ventura M, Rite S, González T, Arias R, Balliu P, Lloreda-García J, Alcaráz J, Tapia C, de la Morena A, Centelles I, Güemes I, Estañ J, Alberola A, Aparici S, López R, Beceiro J, García B, Martínez L, González E, Arruza L, Blanco M, Moral M, Arias B, Mar F, Jiménez J, Romera G, Cuñarro A, Muñóz C, Cabañas F, Valverde E, Montero R, Tejedor J, Santana C, Reyes B, Romero S, Orizaola A, Baquero M, Hernández D, Pantoja A, Vega-del-Val C, Castañón L, Gutiérrez E, Benito M, Caserío S, Arca G, García M, López-Vílchez M, Castells L, Domingo M, Coroleu W, Boix H, Porta R, García-Alix A, Martínez-Nadal S, Jiménez E, Sole E, Albújar M, Fernández E, Barrio A, Piñán E, Avila-Alvarez A, Vázquez M, Balado N, Crespo P, Couce M, Concheiro-Guisán A, Esteban I, Lavilla A, Alzina V, Aguirre A, Loureiro B, Echániz I, Elorza M, Euba A. Atención integral del neonato con encefalopatía hipóxico-isquémica en España. An Pediatr (Barc) 2020; 92:286-296. [DOI: 10.1016/j.anpedi.2019.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 10/26/2022] Open
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10
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Baca M, Popović D, Panagiotopoulou H, Marciszak A, Krajcarz M, Krajcarz MT, Makowiecki D, Węgleński P, Nadachowski A. Human-mediated dispersal of cats in the Neolithic Central Europe. Heredity (Edinb) 2018; 121:557-563. [PMID: 29588507 PMCID: PMC6221894 DOI: 10.1038/s41437-018-0071-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 11/09/2022] Open
Abstract
Archeological and genetic evidence suggest that all domestic cats derived from the Near Eastern wildcat (Felis silvestris lybica) and were first domesticated in the Near East around 10,000 years ago. The spread of the domesticated form in Europe occurred much later, primarily mediated by Greek and Phoenician traders and afterward by Romans who introduced cats to Western and Central Europe around 2000 years ago. We investigated mtDNA of Holocene Felis remains and provide evidence of an unexpectedly early presence of cats bearing the Near Eastern wildcat mtDNA haplotypes in Central Europe, being ahead of Roman period by over 2000 years. The appearance of the Near Eastern wildcats in Central Europe coincides with the peak of Neolithic settlement density, moreover most of those cats belonged to the same mtDNA lineages as those domesticated in the Near East. Thus, although we cannot fully exclude that the Near Eastern wildcats appeared in Central Europe as a result of introgression with European wildcat, our findings support the hypothesis that the Near Eastern wildcats spread across Europe together with the first farmers, perhaps as commensal animals. We also found that cats dated to the Neolithic period belonged to different mtDNA lineages than those brought to Central Europe in Roman times, this supports the hypothesis that the gene pool of contemporary European domestic cats might have been established from two different source populations that contributed in different periods.
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Affiliation(s)
- Mateusz Baca
- Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-079, Warsaw, Poland.
| | - Danijela Popović
- Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-079, Warsaw, Poland
| | - Hanna Panagiotopoulou
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Adrian Marciszak
- Department of Paleozoology, Institute of Environmental Biology, University of Wroclaw, Sienkiewicza 21, 50-335, Wrocław, Poland
| | - Magdalena Krajcarz
- Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Szosa Bydgoska 44/48, 87-100, Torun, Poland
| | - Maciej T Krajcarz
- Institute of Geological Sciences, Polish Academy of Sciences, Research Centre in Warsaw, Twarda 51/55, 00-818, Warsaw, Poland
| | - Daniel Makowiecki
- Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Szosa Bydgoska 44/48, 87-100, Torun, Poland
| | - Piotr Węgleński
- Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-079, Warsaw, Poland
| | - Adam Nadachowski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Krakow, Poland
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11
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Arnaez J, Garcia-Alix A, Calvo S, Lubián-López S, Diez-Delgado J, Benavente I, Tofé I, Jerez A, Hurtado J, Ceballos J, Millán M, Esquivel M, Ruiz C, Baca M, Tapia E, Losada M, Torres E, Pavón A, Jiménez P, Jiménez F, Ventura M, Rite S, González T, Arias R, Balliu P, Lloreda-García J, Alcaráz J, Tapia C, de la Morena A, Centelles I, Güemes I, Estañ J, Alberola A, Aparici S, López R, Beceiro J, García B, Martínez L, González E, Arruza L, Blanco M, Moral M, Arias B, Mar F, Jiménez J, Romera G, Cuñarro A, Muñóz C, Cabañas F, Valverde E, Montero R, Tejedor J, Santana C, Reyes B, Romero S, Orizaola A, Baquero M, Hernández D, Pantoja A, Vega C, Castañón L, Gutiérrez E, Benito M, Caserío S, Arca G, García M, López-Vílchez M, Castells L, Domingo M, Coroleu W, Boix H, Porta R, García-Alix A, Martínez-Nadal S, Jiménez E, Sole E, Albújar M, Fernández E, Barrio A, Piñán E, Avila-Alvarez A, Vázquez M, Balado N, Crespo P, Couce M, Concheiro-Guisán A, Esteban I, Lavilla A, Alzina V, Aguirre A, Loureiro B, Echániz I, Euba MEA. Care of the newborn with perinatal asphyxia candidate for therapeutic hypothermia during the first six hours of life in Spain. Anales de Pediatría (English Edition) 2018. [DOI: 10.1016/j.anpede.2017.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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12
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Pengo V, Boschello M, Marzari A, Baca M, Schivazappa L, Volta SD. Adenosine Diphosphate (ADP)-Induced ⍺-Granules Release from Platelets of Native Whole Blood Is Reduced by Ticlopidine but Not by Aspirin or Dipyridamole. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1661629] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryA brief contact between native whole blood and ADP promotes a dose-dependent release of platelet a-granules without a fall in the platelet number. We assessed the “ex vivo” effect of three widely used antiplatelet drugs, aspirin dipyridamole and ticlopidine, on this system. Aspirin (a single 800 mg dose) and dipyridamole (300 mg/die for four days) had no effect, while ticlopidine (500 mg/die for four days) significantly reduced the a-granules release for an ADP stimulation of 0.4 (p <0.02), 1.2 (p <0.01) and 2 pM (p <0.01). No drug, however, completeley inhibits this early stage of platelet activation. The platelet release of α-granules may be related to platelet shape change of the light transmission aggregometer and may be important “in vivo” by enhancing platelet adhesiveness and by liberating the plateletderived growth factor.
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Affiliation(s)
- V Pengo
- The Department of Cardiology, Padua University, Padua, Italy
| | - M Boschello
- The Department of Cardiology, Padua University, Padua, Italy
| | - A Marzari
- The Department of Cardiology, Padua University, Padua, Italy
| | - M Baca
- The Department of Cardiology, Padua University, Padua, Italy
| | - L Schivazappa
- The Department of Cardiology, Padua University, Padua, Italy
| | - S Dalla Volta
- The Department of Cardiology, Padua University, Padua, Italy
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13
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Palkopoulou E, Baca M, Abramson NI, Sablin M, Socha P, Nadachowski A, Prost S, Germonpré M, Kosintsev P, Smirnov NG, Vartanyan S, Ponomarev D, Nyström J, Nikolskiy P, Jass CN, Litvinov YN, Kalthoff DC, Grigoriev S, Fadeeva T, Douka A, Higham TFG, Ersmark E, Pitulko V, Pavlova E, Stewart JR, Węgleński P, Stankovic A, Dalén L. Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings. Glob Chang Biol 2016; 22:1710-1721. [PMID: 26919067 DOI: 10.1111/gcb.13214] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 07/15/2015] [Revised: 10/08/2015] [Accepted: 12/07/2015] [Indexed: 06/05/2023]
Abstract
Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D. torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D. torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50 000 years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. All Holocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D. torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D. groenlandicus and D. richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D. groenlandicus had a more southern and D. richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom-up effects in the Late Pleistocene steppe-tundra ecosystem.
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Affiliation(s)
- Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
- Department of Zoology, Stockholm University, 10405 Stockholm, Sweden
| | - Mateusz Baca
- Center for Pre-Columbian Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927 Warsaw, Poland
| | - Natalia I Abramson
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Mikhail Sablin
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Paweł Socha
- Department of Palaeozoology, Institute of Environmental Biology, University of Wrocław, Sienkiewicza Str. 21, 50-335 Wrocław, Poland
| | - Adam Nadachowski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska Str. 17, 31-016 Kraków, Poland
| | - Stefan Prost
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
- Department of Anatomy and Structural Biology, Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin 9054, New Zealand
| | - Mietje Germonpré
- Operational Direction "Earth and History of Life", Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Russian Academy of Sciences, 202 8 Marta Street, 620144 Ekaterinburg, Russia
| | - Nickolay G Smirnov
- Institute of Plant and Animal Ecology, Russian Academy of Sciences, 202 8 Marta Street, 620144 Ekaterinburg, Russia
| | - Sergey Vartanyan
- Northeast Interdisciplinary Research Institute, Far East Branch, Russian Academy of Sciences, Magadan 685000, Russia
| | - Dmitry Ponomarev
- Laboratory of Paleontology, Institute of Geology of Komi Science Center, Russian Academy of Sciences, 54 Pervomayskaya Street, 167982 Syktyvkar, Russia
| | - Johanna Nyström
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - Pavel Nikolskiy
- Geological Institute of the Russian Academy of Sciences, Pyzhevsky pereulok 7, Moscow 119017, Russia
| | | | - Yuriy N Litvinov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Frunze Str. 11, Novosibirsk 630091, Russia
| | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - Semyon Grigoriev
- Mammoth Museum, Institute of Applied Ecology of the North, North-Eastern Federal University, 48 Kulakovskogo St., Yakutsk, 677000 Republic of Sakha, Russia
| | - Tatyana Fadeeva
- Mining Institute Russian Academy of Sciences, 78A Sibirskaya Street, 614007 Perm, Russia
| | - Aikaterini Douka
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Thomas F G Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
- Department of Zoology, Stockholm University, 10405 Stockholm, Sweden
| | - Vladimir Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, Dvortsovaya nab. 18, 191186 St Petersburg, Russia
| | - Elena Pavlova
- Arctic & Antarctic Research Institute, Bering St. 35, 199397 St Petersburg, Russia
| | - John R Stewart
- Faculty of Science and Technology, Bournemouth University, Dorset BH12 5BB, UK
| | - Piotr Węgleński
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Anna Stankovic
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
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14
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Abstract
Rheumatoid arthritis (RA) is a chronic debilitating autoimmune disorder characterized by synovitis that leads to cartilage and bone erosion by invading fibrovascular tissue. Mouse models of RA recapitulate many features of the human disease. Despite the availability of medicines that are highly effective in many patient populations, autoimmune diseases (including RA) remain an area of active biomedical research, and consequently mouse models of RA are still extensively used for mechanistic studies and validation of therapeutic targets. This review aims to integrate morphologic features with model biology and cover the key characteristics of the most commonly used induced and spontaneous mouse models of RA. Induced models emphasized in this review include collagen-induced arthritis and antibody-induced arthritis. Collagen-induced arthritis is an example of an active immunization strategy, whereas antibody- induced arthritis models, such as collagen antibody–induced arthritis and K/BxN antibody transfer arthritis, represent examples of passive immunization strategies. The coverage of spontaneous models in this review is focused on the TNFΔ ARE mouse, in which arthritis results from overexpression of TNF-α, a master proinflammatory cytokine that drives disease in many patients.
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Affiliation(s)
- P. Caplazi
- Departments of Research Pathology, Genentech Inc, South San Francisco, CA, USA
| | - M. Baca
- Departments of Research Pathology, Genentech Inc, South San Francisco, CA, USA
| | - K. Barck
- Biomedical Imaging, Genentech Inc, South San Francisco, CA, USA
| | - R. A. D. Carano
- Biomedical Imaging, Genentech Inc, South San Francisco, CA, USA
| | - J. DeVoss
- Translational Immunology, Genentech Inc, South San Francisco, CA, USA
| | - W. P. Lee
- Translational Immunology, Genentech Inc, South San Francisco, CA, USA
| | - B. Bolon
- Department of Veterinary Biosciences and the Comparative Pathology and Mouse Phenotyping Shared Resource, The Ohio State University, Columbus, OH, USA
| | - L. Diehl
- Departments of Research Pathology, Genentech Inc, South San Francisco, CA, USA
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15
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Popović D, Baca M, Panagiotopoulou H. Complete mitochondrial genome sequences of Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, Gulf sturgeon, A. o. desotoi and European sturgeon A. sturio (Acipenseriformes: Acipenseridae) obtained through next generation sequencing. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2549-51. [PMID: 26017050 DOI: 10.3109/19401736.2015.1038799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Complete mitochondrial genome sequences of European sturgeon and two subspecies of the North American, Atlantic and Gulf sturgeons were determined using MiSeq Illumina technology. All three genomes show typical vertebrate organization. They possess 22 tRNA genes, 13 protein-coding genes, 2 rRNA (ribosomal RNA) genes and a non-coding control region. Excluding ND6, all protein-coding genes are on the heavy strand. The whole mitogenome sequences have been deposited in GenBank under accession numbers KP997216-KP997218.
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Affiliation(s)
| | - Mateusz Baca
- b Center for Pre-Columbian Studies, University of Warsaw , Warsaw , Poland , and
| | - Hanna Panagiotopoulou
- c Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw , Poland
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16
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Gilbreth RN, Chacko BM, Grinberg L, Swers JS, Baca M. Stabilization of the third fibronectin type III domain of human tenascin-C through minimal mutation and rational design. Protein Eng Des Sel 2014; 27:411-8. [PMID: 24996411 DOI: 10.1093/protein/gzu024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Non-antibody scaffolds are increasingly used to generate novel binding proteins for both research and therapeutic applications. Our group has developed the tenth fibronectin type III domain of human tenascin-C (TNfn3) as one such scaffold. As a scaffold, TNfn3 must tolerate extensive mutation to introduce novel binding sites. However, TNfn3's marginal stability (T(m) ∼ 59°C, ΔG(unfolding) = 5.7 kcal/mol) stands as a potential obstacle to this process. To address this issue, we sought to engineer highly stable TNfn3 variants. We used two parallel strategies. Using insights gained from structural analysis of other FN3 family members, we (1) rationally designed stabilizing point mutations or (2) introduced novel stabilizing disulfide bonds. Both strategies yielded highly stable TNfn3 variants with T(m) values as high as 83°C and ΔG(unfolding) values as high as 9.4 kcal/mol. Notably, only three or four mutations were required to achieve this level of stability with either approach. These results validate our rational design strategies and illustrate that substantial stability increases can be achieved with minimal mutation. One TNfn3 variant reported here has now been successfully used as a scaffold to develop two promising therapeutic molecules. We anticipate that other variants described will exhibit similar utility.
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Affiliation(s)
- R N Gilbreth
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - B M Chacko
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - L Grinberg
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - J S Swers
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - M Baca
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
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Baca M, Molak M, Sobczyk M, Węgleński P, Stankovic A. Locals, resettlers, and pilgrims: a genetic portrait of three pre-Columbian Andean populations. Am J Phys Anthropol 2014; 154:402-12. [PMID: 24801631 DOI: 10.1002/ajpa.22524] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 04/18/2014] [Indexed: 01/15/2023]
Abstract
The common practice of resettlement and the development of administrative and ceremonial systems shaped the population landscape of the Andean region under the Inca rule. The area surrounding Coropuna and Solimana volcanoes, in the Arequipa region (Peru), carried a high-density, multiethnic population. We studied the genetic variation among three pre-Columbian populations from three functionally diverse archaeological sites excavated in this region. By analyzing the genetic composition of a large ceremonial center (Acchaymarca), an isolated pastoral settlement (Tompullo 2), and an agricultural settlement characterized by architectural features rare in the region (Puca), we investigated the patterns of population movements and the distribution of genetic diversity. We obtained mitochondrial DNA sequences for 25 individuals and autosomal microsatellite profiles for 20 individuals from Acchaymarca and Puca sites. These were compared with previously published genetic data for Tompullo 2 and other pre-Columbian populations. We found differences among the genetic portraits of the three populations, congruent with the archaeologically described functions and characteristics of the sites. The Acchaymarca population had the highest genetic diversity and possessed the lowest number of unique mtDNA haplotypes. The Tompullo 2 population exhibited the lowest level of genetic diversity. The Puca population was distinct from the other two populations owing to a high frequency of haplogroup A haplotypes, what potentially explains the non-local character of the burial architecture. Our analyses of microsatellite data suggest that gene flow between sites was mostly mediated by females, which is consistent with ethnohistorical knowledge of the social organization of the pre-Columbian communities.
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Affiliation(s)
- Mateusz Baca
- Centre for Pre-Columbian Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927, Warsaw, Poland
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Nagy V, Baca M, Boor A. Primary obstructed megaureter (POM) in children. ACTA ACUST UNITED AC 2013; 114:650-6. [PMID: 24236436 DOI: 10.4149/bll_2013_139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
UNLABELLED The aim of this study was to analyze the results of surgical and conservative treatment of non-refluxing POM. In the period 2000-2009, 45 children (52 ureters) were treated, the average age was 5.8 months (±10.33), 24 children (26 ureters) by surgery (I) and 21 children (26 ureters) by conservative means (II). The average follow-up period was 73.8 (±32.91) and 30.85 months (±23.1) resp. Urine examination, USG, DTPA99mTc, biochemical testing, micturating cystouretography in all patients were performed. Significant difference was present in the occurrence of hydronephrosis of 0th, 3rd and 4th grade, p10 mm, p<0.01; and in the occurrence of normal and prolonged time T ½, p<0.01. The health condition was adjusted in 13 (54.20 %), improved on DTPA99mTc in 5 (20.85 %), non-improved in 3 (12.50 %), deteriorated in 1 (4.15 %) and unknown in 2 (8.3 %) patients. In the IInd group a significant difference was in case of occurrence of hydronephrosis of 0th, 2nd and 3rd grade, (p<0.01, or p=0.037 and p=0.011) and in occurrence of normal ureter, with ureter 0-5 mm and dilated ureter 5-10 mm, p<0.01. The condition at the end of the follow-up period was assessed DTPA99mTc as adjusted in 11 (52.39 %) patients, improved in 6 (28.57 %), unimproved in 3 (14.28 %) and no patient was assessed as having deteriorated and unknown in 1 (4.76 %). CONCLUSION In patients with an impaired separate kidney function, early surgical treatment helps to minimize damage to the kidney function and prevents future complications (Tab. 6, Fig. 3, Ref. 32).
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Baca M, Doan K, Sobczyk M, Stankovic A, Węgleński P. Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community. BMC Genet 2012; 13:30. [PMID: 22524324 PMCID: PMC3470988 DOI: 10.1186/1471-2156-13-30] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 03/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A detailed genetic study of the pre-Columbian population inhabiting the Tompullo 2 archaeological site (department Arequipa, Peru) was undertaken to resolve the kin relationships between individuals buried in six different chullpas. Kin relationships were an important factor shaping the social organization in the pre-Columbian Andean communities, centering on the ayllu, a group of relatives that shared a common land and responsibilities. The aim of this study was to evaluate whether this Andean model of a social organization had an influence on mortuary practices, in particular to determine whether chullpas served as family graves. RESULTS The remains of forty-one individuals were analyzed with both uniparental (mtDNA, Y-chromosome) and biparental (autosomal microsatellites) markers. Reproducible HVRI sequences, autosomal and Y chromosomal STR profiles were obtained for 24, 16 and 11 individuals, respectively. Mitochondrial DNA diversity was comparable to that of ancient and contemporary Andean populations. The Tompullo 2 population exhibited the closest relationship with the modern population from the same region. A kinship analysis revealed complex pattern of relations within and between the graves. However mean relatedness coefficients regarding the pairs of individuals buried in the same grave were significantly higher than those regarding pairs buried in different graves. The Y chromosome profiles of 11 males suggest that only members of one male line were buried in the same grave. CONCLUSIONS Genetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site was organized into extended family groups that were buried in different graves. This finding is in congruence with known models of social organization of Andean communities.
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Affiliation(s)
- Mateusz Baca
- Center for Precolumbian Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927, Warsaw, Poland
| | - Karolina Doan
- Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Pawińskiego 5A, 02–106, Warsaw, Poland
| | - Maciej Sobczyk
- Center for Precolumbian Studies, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927, Warsaw, Poland
| | - Anna Stankovic
- Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Pawińskiego 5A, 02–106, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Piotr Węgleński
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5A, 02-106, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
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Dimitriadis E, Stoikos C, Baca M, Fairlie WD, McCoubrie JE, Salamonsen LA. Relaxin and prostaglandin E(2) regulate interleukin 11 during human endometrial stromal cell decidualization. J Clin Endocrinol Metab 2005; 90:3458-65. [PMID: 15784719 DOI: 10.1210/jc.2004-1014] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [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: 11/19/2022]
Abstract
Decidualization of endometrial stromal cells and IL-11 signaling are essential for embryo implantation in the mouse. We investigated the effects of relaxin (RLX) and prostaglandin E(2) (PGE(2)) on IL-11 secretion by human endometrial stromal cells (HESC) and during cAMP or medroxyprogesterone acetate (P)-induced decidualization. cAMP-decidualized HESC secreted high levels of IL-11. RLX, cAMP, or PGE(2) increased IL-11 mRNA and IL-11 secretion, with maximal response to RLX and cAMP. Addition of the cAMP/protein kinase A inhibitor Rp-adenosine-3,5-cyclic-monophosphorothioate to either RLX- or PGE(2)-treated cells decreased IL-11 secretion. Indomethacin treatment decreased IL-11 secretion, which was largely restored by cotreatment with PGE(2) or RLX. Cotreatment of HESC with RLX, PGE(2), or cAMP and estrogen plus P down-regulated IL-11 mRNA and IL-11 secretion at 24 h, before secretion of prolactin (decidualization marker). Addition of W147AIL-11 (IL-11 signaling inhibitor) reduced prolactin secretion stimulated by RLX or PGE(2) and estrogen plus P. This is the first demonstration that cAMP-decidualized HESC secrete IL-11 and that IL-11 mRNA and IL-11 secretion are regulated by RLX and PGE(2), partly via a cAMP/protein kinase A-dependent pathway. Blocking IL-11 signaling reduced RLX+P- or PGE(2)+P-induced decidualization, suggesting that RLX and PGE(2) act via IL-11. This is important in understanding implantation and regulation of fertility.
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Affiliation(s)
- E Dimitriadis
- Prince Henry's Institute of Medical Research, P.O. Box 5152, Clayton, VIC 3168, Australia.
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Baca M, Pigamo A, Dubois J, Millet J. Fourier transform infrared spectroscopic study of surface acidity by pyridine adsorption on the M1 active phase of the MoVTe(Sb)NbO catalysts used in propane oxidation. CATAL COMMUN 2005. [DOI: 10.1016/j.catcom.2004.12.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Aguilar E, Peterson TC, Obando PR, Frutos R, Retana JA, Solera M, Soley J, García IG, Araujo RM, Santos AR, Valle VE, Brunet M, Aguilar L, Álvarez L, Bautista M, Castañón C, Herrera L, Ruano E, Sinay JJ, Sánchez E, Oviedo GIH, Obed F, Salgado JE, Vázquez JL, Baca M, Gutiérrez M, Centella C, Espinosa J, Martínez D, Olmedo B, Espinoza CEO, Núñez R, Haylock M, Benavides H, Mayorga R. Changes in precipitation and temperature extremes in Central America and northern South America, 1961–2003. ACTA ACUST UNITED AC 2005. [DOI: 10.1029/2005jd006119] [Citation(s) in RCA: 371] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Dimitriadis E, Stoikos C, Baca M, Fairlie W, Uboldi AD, McCoubrie JE, Salamonsen LA. 227.An inhibitor of leukemia inhibitory factor signalling blocks embryo implantation in the mouse. Reprod Fertil Dev 2004. [DOI: 10.1071/srb04abs227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Embryo implantation is a critical step in the establishment of pregnancy. Endometrial leukemia inhibitory factor (LIF) is essential for embryo implantation in the mouse (1). Uterine LIF is expressed in the luminal epithelium on Day 3 of pregnancy (D3) (D0�=�day of plug detection) and signals via activation of signal transducer and activator of transcription (Stat) 3 (2). We examined the effect of a novel LIF signalling inhibitor on the phosphorylation (p) of Stat3 during early pregnancy and on embryo implantation in the mouse. We injected LIF inhibitor into one uterine horn and PBS into the other uterine horn of the mouse at D3 and examined the effect on pStat3 immunostaining in the luminal epithelium between 30 and 360�min later. We found no immunoreactive pStat3 in luminal epithelium following treatment with LIF inhibitor at 60 and 90�min but variable staining at other time points. The PBS-treated uterine horn showed intense immunostaining at all times. LIF inhibitor (1mg/kg body weight per day) or PBS was administered to mice (a) subcutaneously, (b) intraperitoneally, at 8-hourly intervals for 3�days from D2, or (c) continuously into the peritoneal cavity via Alzet pumps from D2. No effect was seen on implantation at D6. When LIF antagonist (3.5mg/kg/day) or PBS were administered by Alzet pumps from D2 together with ip injections, 4-hourly from D3 for 36�h, there were no implantation sites in the uteri of treated mice (n�=�5) while the control mice (n�=�4) had 3.6���0.5�sites (P�<�0.001). Histologically, the uteri of the treated mice resembled non-pregnant uterus, while the control uterus resembled post-implantation uterus. The results demonstrate that treatment of mice during early pregnancy with a novel LIF inhibitor blocks LIF action in vivo and embryo implantation. This knowledge is important for development of novel contraceptives.
(1) Stewart, C. L., Kaspar, P., Brunet, L. J., Bhatt, H., Gadi, I., Kontgen, F., Abbondanzo, S. J. (1992) Nature 359, 76–79. (2) Cheng, J. G., Chen, J. R., Hernandez, L., Alvord, W. G., Stewart, C. L. (2001) Proc. Natl Acad. Sci. USA 98, 8680–8685.
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Valanský L, Lachvác L, Baca M. [Long-term results of retropubic vesicopexy in the treatment of urinary stress incontinence in women]. Ceska Gynekol 2002; 67:106-10. [PMID: 11987568] [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: 02/24/2023]
Abstract
OBJECTIVE To evaluate long-term results of retropubic vesicopexy (e.g. direct suspension of the anterior and lateral walls of the bladder base) in the treatment of female stress urinary incontinence (SUI) caused by hypermobile urethra. DESIGN Retrospective clinical study. SETTING Department of Urology, Faculty of Medicine, University of P. J. Safarik, Kosice, Slovakia. METHODS From a total of 44 females operated on between 1985-1992, 41 (93%) were available for the study (mean age 50 years, 28 pure SUI, 13 mixed incontinence). 18 (44%) patients had failed previous incontinence surgery. Based on the data collected by a detailed questionnaire as a success cure and/or significant improvement (max. 1 pad/day) of SUI have been considered. RESULTS With a mean of 103 month follow-up period (48-160 months), 32 (78%) patients reported to have their SUI cured, another 5 (12%) significantly improved. Both persistent (8/13, 62%) and de novo urge incontinence (5/28, 18%) have shown to the main reasons for "partial" satisfaction only with the outcome of surgery. Perioperative bleeding requiring blood transfusion was the only serious complication met with this procedure (2 patients). CONCLUSION Long-term results of vesicopexy is comparable with the effect of standard retropubic procedures like Burch colposuspension or MMK urethropexy. Technical simplicity, no risk of osteitis pubis as well as persisting micturition problems may be considered the main advantages of the procedure. Because of lower cure rate the procedure is less suitable for SUI type IIB.
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Skelton NJ, Chen YM, Dubree N, Quan C, Jackson DY, Cochran A, Zobel K, Deshayes K, Baca M, Pisabarro MT, Lowman HB. Structure-function analysis of a phage display-derived peptide that binds to insulin-like growth factor binding protein 1. Biochemistry 2001; 40:8487-98. [PMID: 11456486 DOI: 10.1021/bi0103866] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Highly structured, peptide antagonists of the interaction between insulin-like growth factor 1 (IGF-I) and IGF binding protein 1 (IGFBP-1) have recently been discovered by phage display of naïve peptide libraries [Lowman, H. B., et al. (1998) Biochemistry 37, 8870--8878]. We now report a detailed analysis of the features of this turn-helix peptide motif that are necessary for IGFBP-1 binding and structural integrity. Further rounds of phage randomization indicate the importance of residues contributing to a hydrophobic patch on one face of the helix. Alanine-scanning substitutions confirm that the hydrophobic residues are necessary for binding. However, structural analysis by NMR spectroscopy indicates that some of these analogues are less well folded. Structured, high-affinity analogues that lack the disulfide bond were prepared by introducing a covalent constraint between side chains at positions i and i + 7 or i + 8 within the helix. Analogues based on this scaffold demonstrate that a helical conformation is present in the bound state, and that hydrophobic side chains in this helix, and residues immediately preceding it, interact with IGFBP-1. By comparison of alanine scanning data for IGF-I and the turn-helix peptide, we propose a model for common surface features of these molecules that recognize IGFBP-1.
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Affiliation(s)
- N J Skelton
- Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
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Nicola NA, Nicholson SE, Metcalf D, Zhang JG, Baca M, Farley A, Willson TA, Starr R, Alexander W, Hilton DJ. Negative regulation of cytokine signaling by the SOCS proteins. Cold Spring Harb Symp Quant Biol 2001; 64:397-404. [PMID: 11232314 DOI: 10.1101/sqb.1999.64.397] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- N A Nicola
- Walter and Eliza Hall Institute of Medical Research, Cooperative Research Centre for Cellular Growth Factors, P.O. Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
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29
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Kile BT, Viney EM, Willson TA, Brodnicki TC, Cancilla MR, Herlihy AS, Croker BA, Baca M, Nicola NA, Hilton DJ, Alexander WS. Cloning and characterization of the genes encoding the ankyrin repeat and SOCS box-containing proteins Asb-1, Asb-2, Asb-3 and Asb-4. Gene 2000; 258:31-41. [PMID: 11111040 DOI: 10.1016/s0378-1119(00)00402-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Members of the suppressor of cytokine signalling (SOCS) family of proteins have been shown to inhibit cytokine signalling via direct interactions with JAK kinases or activated cytokine receptors. In addition to their novel amino-terminal regions and SH2 domains that mediate these interactions, the SOCS proteins also contain carboxy-terminal regions of homology called the SOCS box. The SOCS box serves to couple SOCS proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. Several other families of proteins also contain SOCS boxes but differ from the SOCS proteins in the type of domain or motif they contain upstream of the SOCS box. We report here the cloning, characterization, mapping and expression analysis of four members of the ankyrin repeat and SOCS box-containing (Asb) protein family.
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MESH Headings
- Amino Acid Sequence
- Animals
- Ankyrin Repeat/genetics
- Base Sequence
- Blotting, Northern
- Carrier Proteins/genetics
- Chromosome Mapping
- Cloning, Molecular
- DNA/chemistry
- DNA/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Exons
- Gene Expression
- Genes/genetics
- Humans
- Introns
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred Strains
- Molecular Sequence Data
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tissue Distribution
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Affiliation(s)
- B T Kile
- The Walter and Eliza Hall Institute for Medical Research and The Cooperative Research Centre for Cellular Growth Factors, Post Office, Royal Melbourne Hospital, Melbourne, Victoria 3050, Australia.
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Coulson EJ, Reid K, Baca M, Shipham KA, Hulett SM, Kilpatrick TJ, Bartlett PF. Chopper, a new death domain of the p75 neurotrophin receptor that mediates rapid neuronal cell death. J Biol Chem 2000; 275:30537-45. [PMID: 10882742 DOI: 10.1074/jbc.m005214200] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The cytoplasmic juxtamembrane region of the p75 neurotrophin receptor (p75(NTR)) has been found to be necessary and sufficient to initiate neural cell death. The region was named "Chopper" to distinguish it from CD95-like death domains. A 29-amino acid peptide corresponding to the Chopper region induced caspase- and calpain-mediated death in a variety of neural and non-neural cell types and was not inhibited by signaling through Trk (unlike killing by full-length p75(NTR)). Chopper triggered cell death only when bound to the plasma membrane by a lipid anchor, whereas non-anchored Chopper acted in a dominant-negative manner, blocking p75(NTR)-mediated death both in vitro and in vivo. Removal of the ectodomain of p75(NTR) increased the potency of Chopper activity, suggesting that it regulates the association of Chopper with downstream signaling proteins.
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Affiliation(s)
- E J Coulson
- Walter and Eliza Hall Institute of Medical Research, Post Office, Royal Melbourne Hospital, Victoria 3050, Australia.
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31
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Nicholson SE, De Souza D, Fabri LJ, Corbin J, Willson TA, Zhang JG, Silva A, Asimakis M, Farley A, Nash AD, Metcalf D, Hilton DJ, Nicola NA, Baca M. Suppressor of cytokine signaling-3 preferentially binds to the SHP-2-binding site on the shared cytokine receptor subunit gp130. Proc Natl Acad Sci U S A 2000; 97:6493-8. [PMID: 10829066 PMCID: PMC18633 DOI: 10.1073/pnas.100135197] [Citation(s) in RCA: 356] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Suppressor of cytokine signaling-3 (SOCS-3) is one member of a family of intracellular inhibitors of signaling pathways initiated by cytokines that use, among others, the common receptor subunit gp130. The SH2 domain of SOCS-3 has been shown to be essential for this inhibitory activity, and we have used a quantitative binding analysis of SOCS-3 to synthetic phosphopeptides to map the potential sites of interaction of SOCS-3 with different components of the gp130 signaling pathway. The only high-affinity ligand found corresponded to the region of gp130 centered around phosphotyrosine-757 (pY757), previously shown to be a docking site for the tyrosine phosphatase SHP-2. By contrast, phosphopeptides corresponding to other regions within gp130, Janus kinase, or signal transducer and activator of transcription proteins bound to SOCS-3 with weak or undetectable affinity. The significance of pY757 in gp130 as a biologically relevant SOCS-3 docking site was investigated by using transfected 293T fibroblasts. Although SOCS-3 inhibited signaling in cells transfected with a chimeric receptor containing the wild-type gp130 intracellular domain, inhibition was considerably impaired for a receptor carrying a Y-->F point mutation at residue 757. Taken together, these data suggest that the mechanism by which SOCS-3 inhibits the gp130 signaling pathway depends on recruitment to the phosphorylated gp130 receptor, and that some of the negative regulatory roles previously attributed to the phosphatase SHP-2 might in fact be caused by the action of SOCS-3.
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Affiliation(s)
- S E Nicholson
- The Walter and Eliza Hall Institute of Medical Research and The Cooperative Research Centre for Cellular Growth Factors, Parkville, Victoria 3050, Australia
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Probe RA, Baca M, Adams R, Preece C. Night splint treatment for plantar fasciitis. A prospective randomized study. Clin Orthop Relat Res 1999:190-5. [PMID: 10613168] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A prospective randomized study of 116 patients with plantar fasciitis was performed to determine the effectiveness of adjuvant night splint therapy in relieving the acute symptoms of plantar fasciitis. Patients were randomized into one of two groups. Patients in Group 1 were treated with 1 month of oral antiinflammatory medication, Achilles stretching exercises, and shoe recommendations. Patients in Group 2 received identical treatment but also used a dorsiflexion night splint for 3 months. Blinded clinical review of patients was performed at 4, 6, and 12 weeks. Health status data Short Form 36 also was collected at these times and again at an average 19 months of followup. Overall, 68% of patients reported improvement with this nonoperative protocol for a 12-week period. No statistical difference was seen with the presence or absence of a night splint. In addition, no differences in improvement rates were observed with gender, duration of antecedent symptoms, the presence of bilateral symptoms, or the presence of a heel spur. Age older than 45 years did prove to be a statistically significant poor prognostic factor for improvement at the 12-week follow-up. Short Form 36 data obtained at baseline showed significantly lowered perception of health when compared with age matched controls. Patients in both treatment groups had significant improvement in Short Form 36 scores with 12 weeks of conservative care.
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Affiliation(s)
- R A Probe
- Department of Orthopedics, Scott & White Clinic, Temple, TX 76508, USA
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Alexander WS, Starr R, Metcalf D, Nicholson SE, Farley A, Elefanty AG, Brysha M, Kile BT, Richardson R, Baca M, Zhang JG, Willson TA, Viney EM, Sprigg NS, Rakar S, Corbin J, Mifsud S, DiRago L, Cary D, Nicola NA, Hilton DJ. Suppressors of cytokine signaling (SOCS): negative regulators of signal transduction. J Leukoc Biol 1999; 66:588-92. [PMID: 10534114 DOI: 10.1002/jlb.66.4.588] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
SOCS-1 was originally identified as an inhibitor of interleukin-6 signal transduction and is a member of a family of proteins (SOCS-1 to SOCS-7 and CIS) that contain an SH2 domain and a conserved carboxyl-terminal SOCS box motif. Mutation studies have established that critical contributions from both the amino-terminal and SH2 domains are essential for SOCS-1 and SOCS-3 to inhibit cytokine signaling. Inhibition of cytokine-dependent activation of STAT3 occurred in cells expressing either SOCS-1 or SOCS-3, but unlike SOCS-1, SOCS-3 did not directly interact with or inhibit the activity of JAK kinases. Although the conserved SOCS box motif appeared to be dispensable for SOCS-1 and SOCS-3 action when overexpressed, this domain interacts with elongin proteins and may be important in regulating protein turnover. In gene knockout studies, SOCS-1(-/-) mice were born but failed to thrive and died within 3 weeks of age with fatty degeneration of the liver and hemopoietic infiltration of several organs. The thymus in SOCS-1(-/-) mice was small, the animals were lymphopenic, and deficiencies in B lymphocytes were evident within hemopoietic organs. We propose that the absence of SOCS-1 in these mice prevents lymphocytes and liver cells from appropriately controlling signals from cytokines with cytotoxic side effects.
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Affiliation(s)
- W S Alexander
- The Walter and Eliza Hall Institute of Medical Research and the Cooperative Research Centre for Cellular Growth Factors, Royal Melbourne Hospital, Victoria, Australia.
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34
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Zhang JG, Farley A, Nicholson SE, Willson TA, Zugaro LM, Simpson RJ, Moritz RL, Cary D, Richardson R, Hausmann G, Kile BT, Kile BJ, Kent SB, Alexander WS, Metcalf D, Hilton DJ, Nicola NA, Baca M. The conserved SOCS box motif in suppressors of cytokine signaling binds to elongins B and C and may couple bound proteins to proteasomal degradation. Proc Natl Acad Sci U S A 1999; 96:2071-6. [PMID: 10051596 PMCID: PMC26738 DOI: 10.1073/pnas.96.5.2071] [Citation(s) in RCA: 522] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The suppressors of cytokine signaling (SOCS) family of proteins act as intracellular inhibitors of several cytokine signal transduction pathways. Their expression is induced by cytokine activation of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway and they act as a negative feedback loop by subsequently inhibiting the JAK/STAT pathway either by direct interaction with activated JAKs or with the receptors. These interactions are mediated at least in part by the SH2 domain of SOCS proteins but these proteins also contain a highly conserved C-terminal homology domain termed the SOCS box. Here we show that the SOCS box mediates interactions with elongins B and C, which in turn may couple SOCS proteins and their substrates to the proteasomal protein degradation pathway. Analogous to the family of F-box-containing proteins, it appears that the SOCS proteins may act as adaptor molecules that target activated cell signaling proteins to the protein degradation pathway.
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Affiliation(s)
- J G Zhang
- Walter and Eliza Hall Institute of Medical Research and the Cooperative Research Centre for Cellular Growth Factors, P.O. Royal Melbourne Hospital, Victoria 3050, Australia
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35
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Nicholson SE, Willson TA, Farley A, Starr R, Zhang JG, Baca M, Alexander WS, Metcalf D, Hilton DJ, Nicola NA. Mutational analyses of the SOCS proteins suggest a dual domain requirement but distinct mechanisms for inhibition of LIF and IL-6 signal transduction. EMBO J 1999; 18:375-85. [PMID: 9889194 PMCID: PMC1171132 DOI: 10.1093/emboj/18.2.375] [Citation(s) in RCA: 336] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
SOCS-1 (suppressor of cytokine signaling-1) is a representative of a family of negative regulators of cytokine signaling (SOCS-1 to SOCS-7 and CIS) characterized by a highly conserved C-terminal SOCS box preceded by an SH2 domain. This study comprehensively examined the ability of several SOCS family members to negatively regulate the gp130 signaling pathway. SOCS-1 and SOCS-3 inhibited both interleukin-6 (IL-6)- and leukemia inhibitory factor (LIF)-induced macrophage differentiation of murine monocytic leukemic M1 cells and LIF induction of a Stat3-responsive reporter construct in 293T fibroblasts. Deletion of amino acids 51-78 in the N-terminal region of SOCS-1 prevented inhibition of LIF signaling. The SOCS-1 and SOCS-3 N-terminal regions were functionally interchangeable, but this did not extend to other SOCS family members. Mutation of SH2 domains abrogated the ability of both SOCS-1 and SOCS-3 to inhibit LIF signal transduction. Unlike SOCS-1, SOCS-3 was unable to inhibit JAK kinase activity in vitro, suggesting that SOCS-1 and SOCS-3 act on the JAK-STAT pathway in different ways. Thus, although inhibition of signaling by SOCS-1 and SOCS-3 requires both the SH2 and N-terminal domains, their mechanisms of action appear to be biochemically different.
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Affiliation(s)
- S E Nicholson
- The Walter and Eliza Hall Institute of Medical Research and the Cooperative Research Center for Cellular Growth Factors, Parkville, Victoria 3050, Australia.
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36
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Abstract
A 16-year-old boy is presented with the problem of free micturition, having a palpable, painless tumour spreading from the symphysis to the umbilicus. Cystoscopy revealed an impression in the vertex of the urinary bladder covered by the inflamed mucous membrane with a bulbar oedema. Fistulography showed transitional urachus persistens communicating with the terminal loops of the ileum. During surgery, a solid, fan-like fibrous connective tissue was removed, together with the vertex of the urinary bladder and peritoneum. Adhering loops of the terminal ileum were sharply separated and sutured. Histopathological examination confirmed actinomycosis of the urachus persistens penetrating into the ileum.
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Affiliation(s)
- V Nagy
- Clinic of Urology, Safarik University School of Medicine, Kosice, Slovakia
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37
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Baca M, Scanlan TS, Stephenson RC, Wells JA. Phage display of a catalytic antibody to optimize affinity for transition-state analog binding. Proc Natl Acad Sci U S A 1997; 94:10063-8. [PMID: 9294163 PMCID: PMC23305 DOI: 10.1073/pnas.94.19.10063] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Catalytic antibodies have shown great promise for catalyzing a tremendously diverse set of natural and unnatural chemical transformations. However, few catalytic antibodies have efficiencies that approach those of natural enzymes. In principle, random mutagenesis procedures such as phage display could be used to improve the catalytic activities of existing antibodies; however, these studies have been hampered by difficulties in the recombinant expression of antibodies. Here, we have grafted the antigen binding loops from a murine-derived catalytic antibody, 17E8, onto a human antibody framework in an effort to overcome difficulties associated with recombinant expression and phage display of this antibody. "Humanized" 17E8 retained similar catalytic and hapten binding properties as the murine antibody while levels of functional Fab displayed on phage were 200-fold higher than for a murine variable region/human constant region chimeric Fab. This construct was used to prepare combinatorial libraries. Affinity panning of these resulted in the selection of variants with 2- to 8-fold improvements in binding affinity for a phosphonate transition-state analog. Surprisingly, none of the affinity-matured variants was more catalytically active than the parent antibody and some were significantly less active. By contrast, a weaker binding variant was identified with 2-fold greater catalytic activity and incorporation of a single substitution (Tyr-100aH --> Asn) from this variant into the parent antibody led to a 5-fold increase in catalytic efficiency. Thus, phage display methods can be readily used to optimize binding of catalytic antibodies to transition-state analogs, and when used in conjunction with limited screening for catalysis can identify variants with higher catalytic efficiencies.
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Affiliation(s)
- M Baca
- Department of Protein Engineering, Genentech, Inc., 460 Point San Bruno Boulevard, South San Francisco, CA 94080, USA
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38
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Abstract
Antibody humanization often requires the replacement of key residues in the framework regions with corresponding residues from the parent non-human antibody. These changes are in addition to grafting of the antigen-binding loops. Although guided by molecular modeling, assessment of which framework changes are beneficial to antigen binding usually requires the analysis of many different antibody mutants. Here we describe a phage display method for optimizing the framework of humanized antibodies by random mutagenesis of important framework residues. We have applied this method to humanization of the anti-vascular endothelial growth factor murine monoclonal antibody A4.6.1. Affinity panning of a library of humanized A4.6.1 antibody mutants led to the selection of one variant with greater than 125-fold enhanced affinity for antigen relative to the initial humanized antibody with no framework changes. A single additional mutation gave a further 6-fold improvement in binding. The affinity of this variant, 9.3 nM, was only 6-fold weaker than that of a murine/human chimera of A4.6.1. This method provides a general means of rapidly selecting framework mutations that improve the binding of humanized antibodies to their cognate antigens and may prove an attractive alternative to current methods of framework optimization based on cycles of site-directed mutagenesis.
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Affiliation(s)
- M Baca
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA
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39
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Wood SC, Fedde MR, Baca M, Pickard T. EFFECT OF RACING AND GENDER ON VISCOELASTIC PROPERTIES OF HORSE BLOOD 499. Med Sci Sports Exerc 1996. [DOI: 10.1097/00005768-199605001-00499] [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: 11/25/2022]
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40
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Sciutto E, Aluja A, Fragoso G, Rodarte LF, Hernández M, Villalobos MN, Padilla A, Keilbach N, Baca M, Govezensky T. Immunization of pigs against Taenia solium cysticercosis: factors related to effective protection. Vet Parasitol 1995; 60:53-67. [PMID: 8644459 DOI: 10.1016/0304-4017(94)00781-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fifty-six (56) pigs were immunized against Taenia solium cysticercosis with antigens from Taenia crassiceps metacestodes, in a variety of protocols, and then challenged orally with Taenia solium proglottids or eggs. Results of immunization (expressed as individual parasite loads) ranged from significant reduction of parasite loads (host protection) to clear increase (parasite facilitation) in apparent relation to the immunogen dose, adjuvant employed and genetic background of the pigs. In all trials, however, immunized pigs harboured more damaged cysticerci than controls, indicating that immunization does induce some restrictions to parasite these are eventually overwhelmed by other parasite-promoting factors. Western blots in immunized-protected pigs indicated antigens of 242, 234, 118, 77, 55 and 45 kDa as possibly being involved in immunological protection.
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Affiliation(s)
- E Sciutto
- Instituto de Investigaciones Biomédicas, Mexico
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41
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Abstract
The products of oxidation of the alpha-tocopherol model compound, 2,2,5,7,8-pentamethyl-6-chromanol (PH) by t-butyl hydroperoxide in chloroform varied with the amount of water present. In the presence of a trace of water, the main products were the spirodimer (PSD) and spirotrimer (PST). As the content of water increased, the main product became 2-(3-hydroxy-3-methylbutyl)-3,5,6-trimethyl-1,4-benzoquinone (PQ). Oxidation of PH in aqueous liposome suspension also produced PQ as the major product. These results suggested that, in aqueous solutions, the major oxidation product of PH would be PQ and of alpha-tocopherol (TH) would be alpha-tocopheryl quinone (TQ). The ease of reduction of PQ and TQ was studied in chemical and biological systems. PQ, TQ, and ubiquinone-10 (UQ) were rapidly reduced to their respective hydroquinones (PQH2, TQH2, and UQH2) at pH 7.3 by NADH plus FAD. Whole blood reduced PQ rapidly at 37 degrees C to PQH2 but did not reduce TQ to TQH2. Human peripheral blood mononuclear cells took up TQ from a bovine serum albumin complex and reduced it to TQH2. Ingestion of TQ (350 mg) by one of us (PSK) resulted in the formation of TQH2 during a 5 h period. These results demonstrate that several biological systems are able to reduce TQ to TQH2 and that it is a reaction that may occur normally in vivo.
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Affiliation(s)
- I Kohar
- Department of Organic Chemistry, University of New South Wales, Sydney, Australia
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42
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Sciutto E, Fragoso G, Baca M, De la Cruz V, Lemus L, Lamoyi E. Depressed T-cell proliferation associated with susceptibility to experimental Taenia crassiceps infection. Infect Immun 1995; 63:2277-81. [PMID: 7768609 PMCID: PMC173297 DOI: 10.1128/iai.63.6.2277-2281.1995] [Citation(s) in RCA: 50] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Peritoneal infection with Taenia crassiceps cysticerci of naturally resistant (C57BL/10J and C57BL/6J) and susceptible (BALB/cAnN) mice induces a cellular immune depression. T-cell proliferation in response to concanavalin A (ConA) or anti-CD3 was significantly depressed in infected mice of all strains tested. However, in resistant mice, the diminished response to ConA was transient and animals recovered normal responsiveness at day 40, whereas susceptible mice remained suppressed throughout the 40 days of the experiment. In contrast, the proliferative response to anti-CD3 was lower in infected mice than in noninfected controls regardless of differences in natural susceptibility of the strains. Intraperitoneal injection of mice with a parasite extract also induced a depression of the response to ConA, although not as strong as that produced by the parasite itself. This depression is not due to direct effects by parasite antigens over host lymphocytes, as proliferation is not affected by the presence of cysticercal antigens added in vitro. Diminished interleukin-2 production during the parasitosis accounts at least in part for the diminished responses to ConA. A primary infection favors parasite establishment after a second challenge, pointing to the relevance of the immunodepression in generating a host environment favorable to the parasite.
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Affiliation(s)
- E Sciutto
- Department of Immunology, Universidad Nacional Autónoma de México, México, D.F
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43
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Kent SB, Baca M, Elder J, Miller M, Milton R, Milton S, Rao JK, Schnölzer M. Breaking the shackles of the genetic code: engineering retroviral proteases through total chemical synthesis. Adv Exp Med Biol 1995; 362:425-38. [PMID: 8540353 DOI: 10.1007/978-1-4615-1871-6_55] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- S B Kent
- Scripps Research Institute, La Jolla, California 92037, USA
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44
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Baca M, Borgstahl GE, Boissinot M, Burke PM, Williams DR, Slater KA, Getzoff ED. Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry. Biochemistry 1994; 33:14369-77. [PMID: 7981196 DOI: 10.1021/bi00252a001] [Citation(s) in RCA: 233] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The unique ability of photoactive proteins to capture and use energy from a photon of light depends on the chromophore, its linkage to the protein, and the surrounding protein environment. To understand the molecular mechanisms by which a chromophore and protein interact to undergo a light cycle, we are studying photoactive yellow protein (PYP), a 14-kDa water-soluble photoreceptor from Ectothiorhodospira halophila with a photocycle similar to that of sensory rhodopsin. Here, we report the cloning and sequencing of the pyp gene and the chemical identification of both the chromophore and its covalent linkage to the protein. Elemental composition data from high-resolution mass spectrometry of a proteolytically derived chromopeptide, pH titrations and UV-visible spectroscopy of the protein-bound and chemically released chromophore, and fragmentation mass spectrometry of the liberated chromophore amide were combined with results from the 1.4-A-resolution protein crystal structure to identify the chromophore in PYP as a 4-hydroxycinnamyl group covalently bound to the sole cysteine residue via a thioester linkage. While 4-hydroxycinnamate is a metabolic product of the phenylpropanoid pathway and a key molecule in plant stress response, this is the first report of covalent modification of a protein by this group. In the dark (yellow) state of PYP, the protein stabilizes the chromophore as the deprotonated phenolate anion. By combining our biochemical characterization of the chromophore with other published observations, we propose a chemical basis for the photocycle: following the initial absorption of a photon, the photocycle of PYP involves protonation of the chromophore to a neutral phenol form corresponding to the observed photobleached intermediate.
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Affiliation(s)
- M Baca
- Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037
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45
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Valanský L, Kurcinová Z, Lachvác L, Nagy V, Baca M. [Urologic complications in sacrococcygeal agenesis]. Rozhl Chir 1994; 73:294-7. [PMID: 7716661] [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: 01/26/2023]
Abstract
In 11 children with partial sacrococcygeal agenesis without concurrent patent cystic myelomeningocele clinical symptoms were analyzed as well as the character of dysfunction of the bladder and therapeutic results. The cause of urinary incontinence, which was a constant symptom, was not diagnosed correctly in six children. Due to impaired innervation, mostly of the supranuclear type, the bladder dysfunction had more frequently the character of impaired evacuation (8 children) always with obstruction of the flow at the level of the external sphincter. Areflexia of the detrusor was found in three children. In this group changes of the upper urinary pathways were found in four children (three times unilateral reflux, twice dilated ureters, twice also pyelonephritis), always in conjunction with a bladder of low compliance. The impaired storage of urine found in three children was due to hyperreflexia of the bladder. After surgery (three children), conservative treatment (8 children) and their combination progression of changes of the upper urinary pathways was arrested and the degree of incontinence improved or was completed relieved during the 18-78-month follow-up of all patients. Extirpation of the associated subcutaneous lipomyelomeningocele and release of the attached spinal cord in three children aged 5, 10 and 12 years did not lead to improvement of the nervous lesion in any of the patients.
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46
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Abstract
An analogue of "HIV-1 protease" was designed in which the ability to donate important water-mediated hydrogen bonds to substrate was precisely and directly deleted. Chemical ligation of unprotected peptide segments was used to synthesize this "backbone-engineered" enzyme. The functionally relevant amide -CONH- linkage between residues Gly49-Ile50 in each flap of the enzyme was replaced by an isosteric thioester -COS- bond. The backbone-engineered enzyme had normal substrate specificity and affinity (Km). However, the catalytic activity (kcat) was reduced approximately 3000-fold compared to the native amide bond-containing enzyme. Inhibition by the reduced peptide bond substrate analogue MVT-101 was unaffected compared with native enzyme. By contrast, the normally tight-binding hydroxyethylamine inhibitor JG-365 bound to the backbone-engineered enzyme with an approximately 2500-fold reduction in affinity. The reduced catalytic activity of the -Gly49-psi(COS)-Ile50-backbone-engineered enzyme analogue provides direct experimental evidence to support the suggestion that backbone hydrogen bonds from the enzyme flaps to the substrate are important for the catalytic function of the HIV-1 protease.
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Affiliation(s)
- M Baca
- Scripps Research Institute, La Jolla, CA 92037
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47
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Abstract
An important goal in the de novo design of enzymes is the control of molecular geometry. To this end, an analog of the protease from human immunodeficiency virus 1 (HIV-1 protease) was prepared by total chemical synthesis, containing a constrained, nonpeptidic type II' beta-turn mimic of predetermined three-dimensional structure. The mimic beta-turn replaced residues Gly16,17 in each subunit of the homodimeric molecule. These residues constitute the central amino acids of two symmetry-related type I' beta-turns in the native, unliganded enzyme. The beta-turn mimic-containing enzyme analog was fully active, possessed the same substrate specificity as the Gly16,17-containing enzyme, and showed enhanced resistance to thermal inactivation. These results indicate that the precise geometry of the beta-turn at residues 15-18 in each subunit is not critical for activity, and that replacement of the native sequence with a rigid beta-turn mimic can lead to enhanced protein stability. Finally, the successful incorporation of a fixed element of secondary structure illustrates the potential of a "molecular kit set" approach to protein design and synthesis.
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Affiliation(s)
- M Baca
- Scripps Research Institute, La Jolla, California 92037
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48
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Affiliation(s)
- I Obando
- Department of Pediatrics, Hospital General Basico de la Axarquia, Velez-Malaga, Spain
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49
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Pengo V, Peruzzi P, Baca M, Marzari A, Zanon F, Schivapappa L, Dalla Volta S. The optimal therapeutic range for oral anticoagulant treatment as suggested by fibrinopeptide A (FpA) levels in patients with heart valve prostheses. Eur J Clin Invest 1989; 19:181-4. [PMID: 2499477 DOI: 10.1111/j.1365-2362.1989.tb00215.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [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: 01/01/2023]
Abstract
Fibrinopeptide A is a good marker of in vivo thrombin formation. The aim of oral anticoagulants (OA) is to lower in vivo thrombin formation. We therefore assessed FpA levels on several occasions in 38 patients receiving OA for artificial heart valve prostheses and in 20 patients receiving OA for biological heart valve prostheses. The mean FpA level, 1.82 ng ml-1 (SEM 0.14, n = 176), in patients with artificial valves was significantly higher than the mean, 1.02 ng ml-1 (SEM 0.4), obtained in 41 healthy subjects (P = 0.01). FpA mean value for biological valves was 1.41 ng ml-1 (SEM 0.14, n = 76), which was not significantly higher than controls (P = 0.08). A decrease in FpA levels, for both artificial and biological heart valve prostheses, was associated with a parallel increase in the intensity of anticoagulation. When considering FpA values obtained in the optimal therapeutic range for oral anticoagulant treatment, (International Normalized Ratio [INR] between 3 and 4.5), the mean level for artificial valves, 1.87 ng ml-1 (SEM 0.18, n = 102), was significantly higher than the mean value, 1.25 ng ml-1 (SEM 0.16, n = 55), obtained for biological valves. From a biological point of view, this indicates that artificial valves should be kept at a higher intensity of anticoagulation.
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Affiliation(s)
- V Pengo
- Department of Cardiology, Padua University, Padova, Italy
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50
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Pengo V, Boschello M, Marzari A, Baca M, Schivazappa L, Dalla Volta S. Adenosine diphosphate (ADP)-induced alpha-granules release from platelets of native whole blood is reduced by ticlopidine but not by aspirin or dipyridamole. Thromb Haemost 1986; 56:147-50. [PMID: 3810554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A brief contact between native whole blood and ADP promotes a dose-dependent release of platelet alpha-granules without a fall in the platelet number. We assessed the "ex vivo" effect of three widely used antiplatelet drugs, aspirin dipyridamole and ticlopidine, on this system. Aspirin (a single 800 mg dose) and dipyridamole (300 mg/die for four days) had no effect, while ticlopidine (500 mg/die for four days) significantly reduced the alpha-granules release for an ADP stimulation of 0.4 (p less than 0.02), 1.2 (p less than 0.01) and 2 microM (p less than 0.01). No drug, however, completely inhibits this early stage of platelet activation. The platelet release of alpha-granules may be related to platelet shape change of the light transmission aggregometer and may be important "in vivo" by enhancing platelet adhesiveness and by liberating the platelet-derived growth factor.
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