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Fröhlich E. Animals in Respiratory Research. Int J Mol Sci 2024; 25:2903. [PMID: 38474149 DOI: 10.3390/ijms25052903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The respiratory barrier, a thin epithelial barrier that separates the interior of the human body from the environment, is easily damaged by toxicants, and chronic respiratory diseases are common. It also allows the permeation of drugs for topical treatment. Animal experimentation is used to train medical technicians, evaluate toxicants, and develop inhaled formulations. Species differences in the architecture of the respiratory tract explain why some species are better at predicting human toxicity than others. Some species are useful as disease models. This review describes the anatomical differences between the human and mammalian lungs and lists the characteristics of currently used mammalian models for the most relevant chronic respiratory diseases (asthma, chronic obstructive pulmonary disease, cystic fibrosis, pulmonary hypertension, pulmonary fibrosis, and tuberculosis). The generation of animal models is not easy because they do not develop these diseases spontaneously. Mouse models are common, but other species are more appropriate for some diseases. Zebrafish and fruit flies can help study immunological aspects. It is expected that combinations of in silico, in vitro, and in vivo (mammalian and invertebrate) models will be used in the future for drug development.
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Affiliation(s)
- Eleonore Fröhlich
- Center for Medical Research, Medical University of Graz, 8010 Graz, Austria
- Research Center Pharmaceutical Engineering GmbH, 8010 Graz, Austria
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2
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Wallace MN, Zobay O, Hardman E, Thompson Z, Dobbs P, Chakrabarti L, Palmer AR. The large numbers of minicolumns in the primary visual cortex of humans, chimpanzees and gorillas are related to high visual acuity. Front Neuroanat 2022; 16:1034264. [PMID: 36439196 PMCID: PMC9681811 DOI: 10.3389/fnana.2022.1034264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
Minicolumns are thought to be a fundamental neural unit in the neocortex and their replication may have formed the basis of the rapid cortical expansion that occurred during primate evolution. We sought evidence of minicolumns in the primary visual cortex (V-1) of three great apes, three rodents and representatives from three other mammalian orders: Eulipotyphla (European hedgehog), Artiodactyla (domestic pig) and Carnivora (ferret). Minicolumns, identified by the presence of a long bundle of radial, myelinated fibers stretching from layer III to the white matter of silver-stained sections, were found in the human, chimpanzee, gorilla and guinea pig V-1. Shorter bundles confined to one or two layers were found in the other species but represent modules rather than minicolumns. The inter-bundle distance, and hence density of minicolumns, varied systematically both within a local area that might represent a hypercolumn but also across the whole visual field. The distance between all bundles had a similar range for human, chimpanzee, gorilla, ferret and guinea pig: most bundles were 20-45 μm apart. By contrast, the space between bundles was greater for the hedgehog and pig (20-140 μm). The mean density of minicolumns was greater in tangential sections of the gorilla and chimpanzee (1,243-1,287 bundles/mm2) than in human (314-422 bundles/mm2) or guinea pig (643 bundles/mm2). The minicolumnar bundles did not form a hexagonal lattice but were arranged in thin curving and branched bands separated by thicker bands of neuropil/somata. Estimates of the total number of modules/minicolumns within V-1 were strongly correlated with visual acuity.
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Affiliation(s)
- Mark N. Wallace
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
- Hearing Sciences, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Oliver Zobay
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
- School of Medicine, University of Nottingham, Hearing Sciences—Scottish Section, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Eden Hardman
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
| | - Zoe Thompson
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
| | - Phillipa Dobbs
- Veterinary Department, Twycross Zoo, East Midland Zoological Society, Atherstone, United Kingdom
| | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Nottingham, United Kingdom
| | - Alan R. Palmer
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
- Hearing Sciences, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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3
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Lee H, Patel V, Onushko M, Fang X, Chemtob S, Olson D. A Leukocyte Migration Assay Assists Understanding of Interleukin-1β-Induced Leukocyte Migration Into Preterm Mouse Uterus. Front Pharmacol 2022; 13:898008. [PMID: 35694257 PMCID: PMC9174527 DOI: 10.3389/fphar.2022.898008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/18/2022] [Indexed: 11/24/2022] Open
Abstract
Neutrophils and other leukocytes invade the mouse uterus at term birth, which is normal for activating the uterus for labor. To better understand the regulation of this migration at term and interleukin (IL)-1β—induced preterm birth, we developed a mouse leukocyte migration assay (mLMA) and used it with rytvela, an IL-1 receptor allosteric antagonist. The mLMA uses term peripheral blood leukocytes that migrate in a Boyden chamber in response to a chemoattractant. We tested several mouse uterine tissues after homogenization and sedimentation of debris for chemoattractant activity. The most active chemoattractant homogenate came from the mouse lower uterus on gestational day (GD) 18.5. Using flow cytometry, we demonstrated that 99% of the cells that migrate are neutrophils. IL-1β administered on GD 16 stimulated neutrophil migration and invasion into the uterus and the fetal brain along with preterm birth on GD 17. Preterm birth and the increased leukocyte invasion of the maternal uterus and fetal brain were all blocked by the co-administration of rytvela. To test where the site of IL-1β action might be, we examined the potency of lower uterine chemoattractant and the activation of leukocytes following IL-1β +/- rytvela administration. IL-1β did not increase lower uterus homogenate chemoattractant activity, but it significantly (p < 0.05) increased leukocyte activation as defined by cytokine and chemokine expression. Rytvela blocked this activation of leukocytes by IL-1β. We conclude that IL-1β stimulates preterm birth in mice by increasing leukocyte activation leading to increased uterine and fetal brain leukocyte invasion.
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Affiliation(s)
- Han Lee
- Olson Laboratory, Department of Physiology, University of Alberta, Edmonton, AB, Canada
| | - Vaishvi Patel
- Olson Laboratory, Faculty of Science, University of Alberta, Edmonton, AB, Canada
| | - Meghan Onushko
- Olson Laboratory, Faculty of Science, University of Alberta, Edmonton, AB, Canada
| | - Xin Fang
- Olson Laboratory, Department of Obstetrics/Gynecology, University of Alberta, Edmonton, AB, Canada
| | - Sylvain Chemtob
- Chemtob Laboratory, Departments of Pediatrics and Ophthalmology/Pharmacology, University of Montreal, Montreal, QC, Canada
| | - David Olson
- Olson Laboratory, Department of Physiology, University of Alberta, Edmonton, AB, Canada
- Olson Laboratory, Department of Obstetrics/Gynecology, University of Alberta, Edmonton, AB, Canada
- Olson Laboratory, Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
- *Correspondence: David Olson,
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Ai JQ, Luo R, Tu T, Yang C, Jiang J, Zhang B, Bi R, Tu E, Yao YG, Yan XX. Doublecortin-Expressing Neurons in Chinese Tree Shrew Forebrain Exhibit Mixed Rodent and Primate-Like Topographic Characteristics. Front Neuroanat 2021; 15:727883. [PMID: 34602987 PMCID: PMC8481370 DOI: 10.3389/fnana.2021.727883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
Doublecortin (DCX) is transiently expressed in new-born neurons in the subventricular zone (SVZ) and subgranular zone (SGZ) related to adult neurogenesis in the olfactory bulb (OB) and hippocampal formation. DCX immunoreactive (DCX+) immature neurons also occur in the cerebral cortex primarily over layer II and the amygdala around the paralaminar nucleus (PLN) in various mammals, with interspecies differences pointing to phylogenic variation. The tree shrews (Tupaia belangeri) are phylogenetically closer to primates than to rodents. Little is known about DCX+ neurons in the brain of this species. In the present study, we characterized DCX immunoreactivity (IR) in the forebrain of Chinese tree shrews aged from 2 months- to 6 years-old (n = 18). DCX+ cells were present in the OB, SVZ, SGZ, the piriform cortex over layer II, and the amygdala around the PLN. The numerical densities of DCX+ neurons were reduced in all above neuroanatomical regions with age, particularly dramatic in the DG in the 5–6 years-old animals. Thus, DCX+ neurons are present in the two established neurogenic sites (SVZ and SGZ) in the Chinese tree shrew as seen in other mammals. DCX+ cortical neurons in this animal exhibit a topographic pattern comparable to that in mice and rats, while these immature neurons are also present in the amygdala, concentrating around the PLN as seen in primates and some nonprimate mammals.
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Affiliation(s)
- Jia-Qi Ai
- Department of Anatomy and Neurobiology, Central South University Xiangya School of Medicine, Changsha, China
| | - Rongcan Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Tian Tu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Chen Yang
- Department of Anatomy and Neurobiology, Central South University Xiangya School of Medicine, Changsha, China
| | - Juan Jiang
- Department of Anatomy and Neurobiology, Central South University Xiangya School of Medicine, Changsha, China
| | - Bo Zhang
- Department of Neurology, Brain Hospital of Hunan Province, Changsha, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ewen Tu
- Department of Neurology, Brain Hospital of Hunan Province, Changsha, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,CSA Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Xin Yan
- Department of Anatomy and Neurobiology, Central South University Xiangya School of Medicine, Changsha, China
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Felter SP, Zhang X, Thompson C. Butylated hydroxyanisole: Carcinogenic food additive to be avoided or harmless antioxidant important to protect food supply? Regul Toxicol Pharmacol 2021; 121:104887. [DOI: 10.1016/j.yrtph.2021.104887] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/19/2021] [Accepted: 02/01/2021] [Indexed: 01/31/2023]
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Phillips MJ, Shazwani Zakaria S. Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals. Mol Phylogenet Evol 2021; 158:107082. [PMID: 33482383 DOI: 10.1016/j.ympev.2021.107082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.
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Affiliation(s)
- Matthew J Phillips
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia.
| | - Sarah Shazwani Zakaria
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia; School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM) Caw. Negeri Sembilan, Kuala Pilah 72000, Malaysia
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7
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Use of Fourier-Transform Infrared Spectroscopy (FT-IR) for Monitoring Experimental Helicobacter pylori Infection and Related Inflammatory Response in Guinea Pig Model. Int J Mol Sci 2020; 22:ijms22010281. [PMID: 33396581 PMCID: PMC7795336 DOI: 10.3390/ijms22010281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/25/2020] [Accepted: 12/26/2020] [Indexed: 12/17/2022] Open
Abstract
Infections due to Gram-negative bacteria Helicobacter pylori may result in humans having gastritis, gastric or duodenal ulcer, and even gastric cancer. Investigation of quantitative changes of soluble biomarkers, correlating with H. pylori infection, is a promising tool for monitoring the course of infection and inflammatory response. The aim of this study was to determine, using an experimental model of H. pylori infection in guinea pigs, the specific characteristics of infrared spectra (IR) of sera from H. pylori infected (40) vs. uninfected (20) guinea pigs. The H. pylori status was confirmed by histological, molecular, and serological examination. The IR spectra were measured using a Fourier-transform (FT)-IR spectrometer Spectrum 400 (PerkinElmer) within the range of wavenumbers 3000–750 cm−1 and converted to first derivative spectra. Ten wavenumbers correlated with H. pylori infection, based on the chi-square test, were selected for a K-nearest neighbors (k-NN) algorithm. The wavenumbers correlating with infection were identified in the W2 and W3 windows associated mainly with proteins and in the W4 window related to nucleic acids and hydrocarbons. The k-NN for detection of H. pylori infection has been developed based on chemometric data. Using this model, animals were classified as infected with H. pylori with 100% specificity and 97% sensitivity. To summarize, the IR spectroscopy and k-NN algorithm are useful for monitoring experimental H. pylori infection and related inflammatory response in guinea pig model and may be considered for application in humans.
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8
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Springer MS, Molloy EK, Sloan DB, Simmons MP, Gatesy J. ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets. J Hered 2019; 111:147-168. [DOI: 10.1093/jhered/esz076] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022] Open
Abstract
Abstract
DNA sequence alignments have provided the majority of data for inferring phylogenetic relationships with both concatenation and coalescent methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroelement insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroelement insertions satisfy the “no intralocus-recombination” assumption of summary coalescent methods because they are singular events and better approximate neutrality relative to DNA loci commonly sampled in phylogenomic studies. Retroelements have traditionally been analyzed with parsimony, distance, and network methods. Here, we analyze retroelement data sets for vertebrate clades (Placentalia, Laurasiatheria, Balaenopteroidea, Palaeognathae) with 2 ILS-aware methods that operate by extracting, weighting, and then assembling unrooted quartets into a species tree. The first approach constructs a species tree from retroelement bipartitions with ASTRAL, and the second method is based on split-decomposition with parsimony. We also develop a Quartet-Asymmetry test to detect hybridization using retroelements. Both ILS-aware methods recovered the same species-tree topology for each data set. The ASTRAL species trees for Laurasiatheria have consecutive short branch lengths in the anomaly zone whereas Palaeognathae is outside of this zone. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both ILS-aware methods resolved balaeonopterids as paraphyletic. Application of the Quartet-Asymmetry test to this data set detected 19 different quartets of species for which historical introgression may be inferred. Evidence for introgression was not detected in the other data sets.
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Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA
| | - Erin K Molloy
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO
| | - John Gatesy
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
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Springer MS, Foley NM, Brady PL, Gatesy J, Murphy WJ. Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary. Front Genet 2019; 10:1241. [PMID: 31850081 PMCID: PMC6896846 DOI: 10.3389/fgene.2019.01241] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/08/2019] [Indexed: 01/29/2023] Open
Abstract
Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.
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Affiliation(s)
- Mark S. Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - Nicole M. Foley
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Peggy L. Brady
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
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Lavoie JC, Chessex P. Parenteral nutrition and oxidant stress in the newborn: A narrative review. Free Radic Biol Med 2019; 142:155-167. [PMID: 30807828 DOI: 10.1016/j.freeradbiomed.2019.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/06/2019] [Accepted: 02/18/2019] [Indexed: 01/27/2023]
Abstract
There is strong evidence that oxidant molecules from various sources contaminate solutions of parenteral nutrition following interactions between the mixture of nutrients and some of the environmental conditions encountered in clinical practice. The continuous infusion of these organic and nonorganic peroxides provided us with a unique opportunity to study in cells, in vascular and animal models, the mechanisms involved in the deleterious reactions of oxidation in premature infants. Potential clinical impacts of peroxides infused with TPN include: a redox imbalance, vasoactive responses, thrombosis of intravenous catheters, TPN-related hepatobiliary complications, bronchopulmonary dysplasia and mortality. This is a narrative review of published data.
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Affiliation(s)
- Jean-Claude Lavoie
- Centre de Recherche Hôpital Ste-Justine, Department of Nutrition, University of Montreal, Montreal, QC, Canada
| | - Philippe Chessex
- Division of Neonatology, Department of Pediatrics, Children's and Women's Health Center of British Columbia, University of British Columbia, Vancouver, BC, Canada.
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D’Elía G, Fabre PH, Lessa EP. Rodent systematics in an age of discovery: recent advances and prospects. J Mammal 2019. [DOI: 10.1093/jmammal/gyy179] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pierre-Henri Fabre
- Institut des Sciences de l’Evolution (ISEM, UMR 5554 CNRS-UM2-IRD), Université Montpellier, Montpellier Cedex 5, France
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Pregnancy Promotes Maternal Hippocampal Neurogenesis in Guinea Pigs. Neural Plast 2019; 2019:5765284. [PMID: 31097956 PMCID: PMC6487096 DOI: 10.1155/2019/5765284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/08/2019] [Accepted: 02/21/2019] [Indexed: 11/26/2022] Open
Abstract
Adult neurogenesis in the hippocampal dentate gyrus (DG) modulates cognition and behavior in mammals, while motherhood is associated with cognitive and behavioral changes essential for the care of the young. In mice and rats, hippocampal neurogenesis is reported to be reduced or unchanged during pregnancy, with few data available from other species. In guinea pigs, pregnancy lasts ~9 weeks; we set to explore if hippocampal neurogenesis is altered in these animals, relative to gestational stages. Time-pregnant primigravidas (3-5 months old) and age-matched nonpregnant females were examined, with neurogenic potential evaluated via immunolabeling of Ki67, Sp8, doublecortin (DCX), and neuron-specific nuclear antigen (NeuN) combined with bromodeoxyuridine (BrdU) birth-dating. Relative to control, subgranular Ki67, Sp8, and DCX-immunoreactive (+) cells tended to increase from early gestation to postpartum and peaked at the late gestational stage. In BrdU pulse-chasing experiments in nonpregnant females surviving for different time points (2-120 days), BrdU+ cells in the DG colocalized with DCX partially from 2 to 42 days (most frequently at 14-30 days) and with NeuN increasingly from 14 to 120 days. In pregnant females that received BrdU at early, middle, and late gestational stages and survived for 42 days, the density of BrdU+ cells in the DG was mostly high in the late gestational group. The rates of BrdU/DCX and BrdU/NeuN colocalization were similar among these groups and comparable to those among the corresponding control group. Together, the findings suggest that pregnancy promotes maternal hippocampal neurogenesis in guinea pigs, at least among primigravidas.
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Matsuzawa S, Isobe M, Kurosawa N. Guinea pig immunoglobulin VH and VL naïve repertoire analysis. PLoS One 2018; 13:e0208977. [PMID: 30543679 PMCID: PMC6292586 DOI: 10.1371/journal.pone.0208977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
The guinea pig has been used as a model to study various human infectious diseases because of its similarity to humans regarding symptoms and immune response, but little is known about the humoral immune response. To better understand the mechanism underlying the generation of the antibody repertoire in guinea pigs, we performed deep sequencing of full-length immunoglobulin variable chains from naïve B and plasma cells. We gathered and analyzed nearly 16,000 full-length VH, Vκ and Vλ genes and analyzed V and J gene segment usage profiles and mutation statuses by annotating recently reported genome data of guinea pig immunoglobulin genes. We found that approximately 70% of heavy, 73% of kappa and 81% of lambda functional germline V gene segments are integrated into the actual V(D)J recombination events. We also found preferential use of a particular V gene segment and accumulated mutation in CDRs 1 and 2 in antigen-specific plasma cells. Our study represents the first attempt to characterize sequence diversity in the expressed guinea pig antibody repertoire and provides significant insight into antibody repertoire generation and Ig-based immunity of guinea pigs.
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Affiliation(s)
- Shun Matsuzawa
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Research, University of Toyama, Toyama-shi, Toyama, Japan
- Medical & Biological Laboratories Co., Ltd., Ina-shi, Nagano, Japan
| | - Masaharu Isobe
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Research, University of Toyama, Toyama-shi, Toyama, Japan
| | - Nobuyuki Kurosawa
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Research, University of Toyama, Toyama-shi, Toyama, Japan
- * E-mail:
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Myers EA, Burgoon JL, Ray JM, Martínez-Gómez JE, Matías-Ferrer N, Mulcahy DG, Burbrink FT. Coalescent Species Tree Inference of Coluber and Masticophis. COPEIA 2017. [DOI: 10.1643/ch-16-552] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Gajos-Draus A, Duda M, Beręsewicz A. Cardiac and renal upregulation of Nox2 and NF- κB and repression of Nox4 and Nrf2 in season- and diabetes-mediated models of vascular oxidative stress in guinea-pig and rat. Physiol Rep 2017; 5:e13474. [PMID: 29084841 PMCID: PMC5661235 DOI: 10.14814/phy2.13474] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/11/2017] [Accepted: 09/19/2017] [Indexed: 12/31/2022] Open
Abstract
The superoxide-forming NADPH oxidase homologues, Nox1, Nox2, and Nox5, seem to mediate the pro-atherosclerotic vascular phenotype. The hydrogen peroxide-forming Nox4 afforded vascular protection, likely via NF-E2-related factor-2 (Nrf2) activation and/or Nox2 downregulation in transgenic mice. We hypothesized that oxidative stress in the intact vasculature involves, aside from the upregulation of the superoxide-forming Noxs, the downregulation of the Nox4/Nrf2 pathway. Guinea-pigs and rats were studied either in winter or in summer, and the streptozotocin diabetic rats in winter. Plasma nitrite, and superoxide production by isolated hearts were measured, while frozen tissues served in biochemical analyses. Summer in both species and diabetes in rats downregulated myocardial Nox4 while reciprocally upregulating Nox2 and Nox5 in guinea-pigs, and Nox2 in rats. Simultaneously, myocardial Nrf2 activity and the expression of the Nrf2-directed heme oxygenase-1 and endothelial NO synthase were reduced while activity of the nuclear factor κB (NF-κB) and the expression of NF-κB-directed inducible NO synthase and the vascular cell adhesion molecule-1 were increased. Cardiac superoxide production was increased while plasma nitrite was decreased reciprocally. Analogous disregulation of Noxs, Nrf2, and NF-κB, occurred in diabetic rat kidneys. Given the diversity of the experimental settings and the uniform pattern of the responses, we speculate that: (1) chronic vascular oxidative stress is a nonspecific (model-, species-, organ-independent) response involving the induction of Nox2 (and Nox5 in guinea-pigs) and the NF-κB pathway, and the repression of Nox4 and the Nrf2 pathway; and (2) the systems Nox2-NF-κB and Nox4-Nrf2 regulate each other negatively.
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Affiliation(s)
- Anna Gajos-Draus
- Department of Clinical Physiology, Postgraduate Medical School, Warsaw, Poland
| | - Monika Duda
- Department of Clinical Physiology, Postgraduate Medical School, Warsaw, Poland
| | - Andrzej Beręsewicz
- Department of Clinical Physiology, Postgraduate Medical School, Warsaw, Poland
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Ma L, Yang J, Yang L, Shi J, Xue J, Li Y, Liu X. Developmental expression of Toll‑like receptors in the guinea pig lung. Mol Med Rep 2017; 15:1243-1251. [PMID: 28098883 PMCID: PMC5367368 DOI: 10.3892/mmr.2017.6129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 11/21/2016] [Indexed: 12/27/2022] Open
Abstract
The guinea pig is a useful model for investigating infectious and non‑infectious lung diseases due to the sensitivity of its respiratory system and susceptibility to infectious agents. Toll‑like receptors (TLRs) are important components of the innate immune response and are critical for lung immune function. In the present study, the differentiation of epithelial cells in the guinea pig lung was examined during gestation by studying anatomic morphology and the major epithelial cell types using cell type‑specific markers. The developmental expression of all 9 TLRs and the TLR signaling adaptors myeloid differentiation factor 88 (MyD88) and tumor necrosis factor receptor associated factor 6 (TRAF‑6) were investigated by reverse transcription‑quantitative polymerase chain reaction and western blotting analysis. The formation of lung lobes in guinea pigs was observed at 45 days of gestation (dGA), along with the expression of the basal cell marker keratin 14 and the alveolar type II cell marker pro‑surfactant protein. However, the cube cell marker secretoglobin family1A member 1 and ciliated cell marker b‑tubulin IV were only detected in the lungs from 52 dGA onward. The expression levels of all TLRs, MyD88 and TRAF‑6 were determined in lung tissues harvested from embryos, newborn, postnatal and adult animals. The expression levels of all TLR signaling components displayed similar dynamic expression patterns with gestation age and postnatal maturation time, except for TLR‑4 and TLR‑7. mRNA expression levels of TLR components were significantly increased in the lungs at 45 and 52 dGA, compared with later developmental stages. These results suggest that TLR expression in the guinea pig lung is developmentally regulated, enhancing the understanding of lung biology in guinea pig models.
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Affiliation(s)
- Lingjie Ma
- Key Laboratory of The Ministry of Education for The Conservation and Utilization of Special Biological Resources of Western China, Ningxia University, Yinchuan, Ningxia 750021, P.R. China
| | - Jiali Yang
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Li Yang
- The Center of Experimental Animals, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Juan Shi
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Jing Xue
- Key Laboratory of The Ministry of Education for The Conservation and Utilization of Special Biological Resources of Western China, Ningxia University, Yinchuan, Ningxia 750021, P.R. China
| | - Yong Li
- Key Laboratory of The Ministry of Education for The Conservation and Utilization of Special Biological Resources of Western China, Ningxia University, Yinchuan, Ningxia 750021, P.R. China
| | - Xiaoming Liu
- Key Laboratory of The Ministry of Education for The Conservation and Utilization of Special Biological Resources of Western China, Ningxia University, Yinchuan, Ningxia 750021, P.R. China
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Wise MJ. dCITE: Measuring Necessary Cladistic Information Can Help You Reduce Polytomy Artefacts in Trees. PLoS One 2016; 11:e0166991. [PMID: 27898695 PMCID: PMC5127522 DOI: 10.1371/journal.pone.0166991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/07/2016] [Indexed: 11/19/2022] Open
Abstract
Biologists regularly create phylogenetic trees to better understand the evolutionary origins of their species of interest, and often use genomes as their data source. However, as more and more incomplete genomes are published, in many cases it may not be possible to compute genome-based phylogenetic trees due to large gaps in the assembled sequences. In addition, comparison of complete genomes may not even be desirable due to the presence of horizontally acquired and homologous genes. A decision must therefore be made about which gene, or gene combinations, should be used to compute a tree. Deflated Cladistic Information based on Total Entropy (dCITE) is proposed as an easily computed metric for measuring the cladistic information in multiple sequence alignments representing a range of taxa, without the need to first compute the corresponding trees. dCITE scores can be used to rank candidate genes or decide whether input sequences provide insufficient cladistic information, making artefactual polytomies more likely. The dCITE method can be applied to protein, nucleotide or encoded phenotypic data, so can be used to select which data-type is most appropriate, given the choice. In a series of experiments the dCITE method was compared with related measures. Then, as a practical demonstration, the ideas developed in the paper were applied to a dataset representing species from the order Campylobacterales; trees based on sequence combinations, selected on the basis of their dCITE scores, were compared with a tree constructed to mimic Multi-Locus Sequence Typing (MLST) combinations of fragments. We see that the greater the dCITE score the more likely it is that the computed phylogenetic tree will be free of artefactual polytomies. Secondly, cladistic information saturates, beyond which little additional cladistic information can be obtained by adding additional sequences. Finally, sequences with high cladistic information produce more consistent trees for the same taxa.
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Affiliation(s)
- Michael J. Wise
- Computer Science and Software Engineering, The University of Western Australia, Perth, Australia
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Perth, Australia
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Abstract
Abstract
Background
Intrathecal infusion of opioids in dogs, sheep, and humans produces local space-occupying masses. To develop a small-animal model, the authors examined effects of intrathecal catheterization and morphine infusion in guinea pigs.
Methods
Under isoflurane, polyethylene or polyurethane catheters were advanced from the cisterna magna to the lumbar enlargement. Drugs were delivered as a bolus through the externalized catheter or continuously by subcutaneous minipumps. Hind paw withdrawal to a thermal stimulus was assessed. Spinal histopathology was systematically assessed in a blinded fashion. To assist in determining catheter placement, ex vivo images were obtained using magnetic resonance imaging in several animals. Canine spinal tissue from previous intrathecal morphine studies was analyzed in parallel.
Results
(1) Polyethylene (n = 30) and polyurethane (n = 25) catheters were implanted in the lumbar intrathecal space. (2) Bolus intrathecal morphine produced a dose-dependent (20 to 40 μg/10 μl) increase in thermal escape latencies. (3) Absent infusion, a catheter-associated distortion of the spinal cord and a fibrotic investment were noted along the catheter tract (polyethylene > polyurethane). (4) Intrathecal morphine infusion (25 mg/ml/0.5 μl/h for 14 days) resulted in intrathecal masses (fibroblasts, interspersed collagen, lymphocytes, and macrophages) arising from meninges proximal to the catheter tip in both polyethylene- and polyurethane-catheterized animals. This closely resembles mass histopathology from intrathecal morphine canine studies.
Conclusions
Continuous intrathecal infusion of morphine leads to pericatheter masses that morphologically resemble those observed in dogs and humans. This small-animal model may be useful for studying spinal drug toxicology in general and the biology of intrathecal granuloma formation in particular.
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Rivera-Rivera CJ, Montoya-Burgos JI. LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa. Mol Biol Evol 2016; 33:1625-34. [PMID: 26912812 PMCID: PMC4868118 DOI: 10.1093/molbev/msw043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them. The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long-branch attraction (LBA) artifact. Here, we define an objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate (homogeneous model) and a model in which different lineage rates are allowed (heterogeneous model). We implement this criterion in the algorithm Locus Specific Sequence Subsampling (LS³), aimed at reducing the effects of LBA in multi-gene datasets. For each gene, LS³ sequentially removes the fastest-evolving taxon of the ingroup and tests for lineage rate homogeneity until all lineages have uniform evolutionary rates. The sequences excluded from the homogeneously evolving taxon subset are flagged as potentially problematic. The software implementation provides the user with the possibility to remove the flagged sequences for generating a new concatenated alignment. We tested LS³ with simulations and two real datasets containing LBA artifacts: a nucleotide dataset regarding the position of Glires within mammals and an amino-acid dataset concerning the position of nematodes within bilaterians. The initially incorrect phylogenies were corrected in all cases upon removing data flagged by LS³.
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Affiliation(s)
- Carlos J Rivera-Rivera
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
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20
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Springer MS, Gatesy J. The gene tree delusion. Mol Phylogenet Evol 2016; 94:1-33. [DOI: 10.1016/j.ympev.2015.07.018] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/04/2015] [Accepted: 07/22/2015] [Indexed: 10/23/2022]
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21
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Ostrin LA, Wildsoet CF. Optic nerve head and intraocular pressure in the guinea pig eye. Exp Eye Res 2015; 146:7-16. [PMID: 26698659 DOI: 10.1016/j.exer.2015.12.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/02/2015] [Accepted: 12/11/2015] [Indexed: 10/22/2022]
Abstract
The guinea pig is becoming an increasingly popular model for studying human myopia, which carries an increased risk of glaucoma. As a step towards understanding this association, this study sought to characterize the normal, developmental intraocular pressure (IOP) profiles, as well as the anatomy of the optic nerve head (ONH) and adjacent sclera of young guinea pigs. IOP was tracked in pigmented guinea pigs up to 3 months of age. One guinea pig was imaged in vivo with OCT and one with a fundus camera. The eyes of pigmented and albino guinea pigs (ages 2 months) were enucleated and sections from the posterior segment, including the ONH and surrounding sclera, processed for histological analyses - either hematoxylin and eosin (H&E) staining of paraffin embedded, sectioned tissue (n = 1), or cryostat sectioned tissue, processed for immunohistochemistry (n = 3), using primary antibodies against collagen types I-V, elastin, fibronectin and glial fibrillary acidic protein (GFAP). Transmission and scanning electron microscopy (TEM, SEM) studies of ONHs were also undertaken (n = 2 & 5 respectively). Mean IOPs ranged from 17.33 to 22.7 mmHg, increasing slightly across the age range studied, and the IOPs of individual animals also exhibited diurnal variations, peaking in the early morning (mean of 25.8, mmHg, ∼9 am), and decreasing across the day. H&E-stained sections showed retinal ganglion cell axons organized into fascicles in the prelaminar and laminar region of the ONHs, with immunostained sections revealing collagen types I, III, IV and V, as well as elastin, GFAP and fibronectin in the ONHs. SEM revealed a well-defined lamina cribrosa (LC), with radially-oriented collagen beams. TEM revealed collagen fibrils surrounding non-myelinated nerve fiber bundles in the LC region, with myelination and decreased collagen posterior to the LC. The adjacent sclera comprised mainly crimped collagen fibers in a crisscross arrangement. Both the sclera and LC were qualitatively similar in structure in pigmented and albino guinea pigs. The well-organized, collagen-based LC of the guinea pig ONH is similar to that described for tree shrews and more similar to the human LC than that of other rodents that lack collagen. Based on these latter structural similarities the guinea pig would seem a promising model for investigating the relationship between myopia and glaucoma.
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Affiliation(s)
- Lisa A Ostrin
- College of Optometry University of Houston, 4901 Calhoun, Houston, TX 77004, USA.
| | - Christine F Wildsoet
- School of Optometry University of California Berkeley, 588 Minor Hall, Berkeley, CA 94720, USA.
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Deckmann K, Krasteva-Christ G, Rafiq A, Herden C, Wichmann J, Knauf S, Nassenstein C, Grevelding CG, Dorresteijn A, Chubanov V, Gudermann T, Bschleipfer T, Kummer W. Cholinergic urethral brush cells are widespread throughout placental mammals. Int Immunopharmacol 2015; 29:51-6. [DOI: 10.1016/j.intimp.2015.05.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 12/23/2022]
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Abstract
Cavia aperea which is a Brazilian guinea pig is found in the South America. Recently the genome sequencing of C. aperea was done, but no more information of its mitochondrial had been reported. Herein, we assembled the complete mitochondrial genome sequence of C. aperea. It is a 16 835 bp long sequence with most mitogenome's characteristic structure; 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, 1 D-loop region, 1 repeat region and 3 STS regions. The GC-content of our fresh sequence is 39%. It can verify the accuracy and utility of newly determined mitogenome sequences by the phylogenetic analysis, based on whole mitogenome alignment with C. porcellus, which is the closest relative to C. aperea. We expect that using the full mitogenome we can address the taxonomic issues and study the related the evolution events.
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Affiliation(s)
- Wei Cao
- a School of Biomedical Engineering, Med-X Research Institute, Shanghai Jiao Tong University , Shanghai , China and
| | - Yan Xia
- b BGI Education Center University of Chinese Academy of Sciences , Shenzhen , China
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24
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Zhou X, Sun F, Xu S, Yang G, Li M. The position of tree shrews in the mammalian tree: Comparing multi-gene analyses with phylogenomic results leaves monophyly of Euarchonta doubtful. Integr Zool 2015; 10:186-98. [PMID: 25311886 DOI: 10.1111/1749-4877.12116] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The well-accepted Euarchonta grandorder is a pruned version of Archonta nested within the Euarchontoglires (or Supraprimates) clade. At present, it includes tree shrews (Scandentia), flying lemurs (Dermoptera) and primates (Primates). Here, a phylogenomic dataset containing 1912 exons from 22 representative mammals was compiled to investigate the phylogenetic relationships within this group. Phylogenetic analyses and hypothesis testing suggested that tree shrews can be classified as a sister group to Primates or to Glires or even as a basal clade within Euarchontoglires. Further analyses of both modified and original previously published datasets found that the phylogenetic position of tree shrews is unstable. We also found that two of three exonic indels reported as synapomorphies of Euarchonta in a previous study do not unambiguously support the monophyly of such a clade. Therefore, the monophyly of both Euarchonta and Sundatheria (Dermoptera + Scandentia) are suspect. Molecular dating and divergence rate analyses suggested that the ancestor of Euarchontoglires experienced a rapid divergence, which may cause the unresolved position of tree shrews even using the whole genomic data.
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Affiliation(s)
- Xuming Zhou
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
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25
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Hussein OA, Elgamal DA, Elgayar SAM. Structure of the secretory cells of male and female adult guinea pigs Harderian gland. Tissue Cell 2015; 47:323-35. [PMID: 25960413 DOI: 10.1016/j.tice.2015.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/28/2015] [Accepted: 04/09/2015] [Indexed: 11/26/2022]
Abstract
The main objective of this study was to investigate the structure of the Harderian gland (HG) in male and female guinea pigs. A total number of sixteen animals of 4 months age were divided according to sex into two groups; eight animals each. Unfixed glands were weighed and their length and width were measured. Specimens from fixed glands were processed and examined using light, transmission electron microscopy and immunohistochemistry for the detection of the presence of chromogranin A (CgA). The gland consisted of a well-developed duct system which included both intra and extra parenchymal ducts and secretory end pieces lined by many types of cells of variable morphological features and modes of secretion. However, the holocrine mode of secretion was rare as mitotic figures were occasionally present. The interstitial cells included fibroblasts and immune cells (mast cells, lymphocyte, plasma cells and macrophages). The secretion produced by the gland included lipid, protein, neutral mucin and CgA which may be a newly identified constituent of biologically potent proteins stored in the cells of the guinea pig HG. Neutral mucin and CgA may function in photoprotection. The gland revealed sexual dimorphism in mast cells and blood capillaries number and chromogranin secretory activity.
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Affiliation(s)
- Ola A Hussein
- Histology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Dalia A Elgamal
- Histology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Sanaa A M Elgayar
- Histology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt.
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26
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A species-level phylogeny of all extant and late Quaternary extinct mammals using a novel heuristic-hierarchical Bayesian approach. Mol Phylogenet Evol 2014; 84:14-26. [PMID: 25542649 DOI: 10.1016/j.ympev.2014.11.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 10/30/2014] [Accepted: 11/02/2014] [Indexed: 11/20/2022]
Abstract
Across large clades, two problems are generally encountered in the estimation of species-level phylogenies: (a) the number of taxa involved is generally so high that computation-intensive approaches cannot readily be utilized and (b) even for clades that have received intense study (e.g., mammals), attention has been centered on relatively few selected species, and most taxa must therefore be positioned on the basis of very limited genetic data. Here, we describe a new heuristic-hierarchical Bayesian approach and use it to construct a species-level phylogeny for all extant and late Quaternary extinct mammals. In this approach, species with large quantities of genetic data are placed nearly freely in the mammalian phylogeny according to these data, whereas the placement of species with lower quantities of data is performed with steadily stricter restrictions for decreasing data quantities. The advantages of the proposed method include (a) an improved ability to incorporate phylogenetic uncertainty in downstream analyses based on the resulting phylogeny, (b) a reduced potential for long-branch attraction or other types of errors that place low-data taxa far from their true position, while maintaining minimal restrictions for better-studied taxa, and (c) likely improved placement of low-data taxa due to the use of closer outgroups.
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27
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Persistent structural adaptation in the lungs of guinea pigs raised at high altitude. Respir Physiol Neurobiol 2014; 208:37-44. [PMID: 25534146 DOI: 10.1016/j.resp.2014.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/18/2014] [Accepted: 12/15/2014] [Indexed: 11/20/2022]
Abstract
Laboratory guinea pigs raised at high altitude (HA, 3800 m) for up to 6 mo exhibit enhanced alveolar growth and remodeling (Hsia et al., 2005. Resp. Physiol. Neurobiol. 147, 105-115). To determine whether initial HA-induced structural enhancement persists following return to intermediate altitude (IA), we raised weanling guinea pigs at (a) HA for 11-12 mo, (b) IA (1200 m) for 11-12 mo, and (c) HA for 4 mo followed by IA for 7-8 mo (HA-to-IA). Morphometric analysis was performed under light and electron microscopy. Body weight and lung volume were similar among groups. Prolonged HA residence increased alveolar epithelium and interstitium volumes while reducing alveolar-capillary blood volume. The HA-induced gains in type-1 epithelium volume and alveolar surface area were no longer present following return to IA whereas volume increases in type-2 epithelium and interstitium and the reduction in alveolar duct volume persisted. Results demonstrate persistent augmentation of some but not all aspects of lung structure throughout prolonged HA residence, with partial reversibility following re-acclimatization to IA.
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28
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Averianov AO, Lopatin AV. High-level systematics of placental mammals: Current status of the problem. BIOL BULL+ 2014. [DOI: 10.1134/s1062359014090039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Tchitchek N, Safronetz D, Rasmussen AL, Martens C, Virtaneva K, Porcella SF, Feldmann H, Ebihara H, Katze MG. Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome. PLoS One 2014; 9:e112617. [PMID: 25398096 PMCID: PMC4232415 DOI: 10.1371/journal.pone.0112617] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 10/06/2014] [Indexed: 11/18/2022] Open
Abstract
Background The Syrian hamster (golden hamster, Mesocricetus auratus) is gaining importance as a new experimental animal model for multiple pathogens, including emerging zoonotic diseases such as Ebola. Nevertheless there are currently no publicly available transcriptome reference sequences or genome for this species. Results A cDNA library derived from mRNA and snRNA isolated and pooled from the brains, lungs, spleens, kidneys, livers, and hearts of three adult female Syrian hamsters was sequenced. Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons). This combined contig/singleton dataset, designated as the Syrian hamster transcriptome, represents a total of 60,117,204 nucleotides. Our Mesocricetus auratus Syrian hamster transcriptome mapped to 11,648 mouse transcripts representing 9,562 distinct genes, and mapped to a similar number of transcripts and genes in the rat. We identified 214 quasi-complete transcripts based on mouse annotations. Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library. The Syrian hamster transcriptome was aligned to the current release of the Chinese hamster ovary (CHO) cell transcriptome and genome to improve the genomic annotation of this species. Finally, our Syrian hamster transcriptome was aligned against 14 other rodents, primate and laurasiatheria species to gain insights about the genetic relatedness and placement of this species. Conclusions This Syrian hamster transcriptome dataset significantly improves our knowledge of the Syrian hamster's transcriptome, especially towards its future use in infectious disease research. Moreover, this library is an important resource for the wider scientific community to help improve genome annotation of the Syrian hamster and other closely related species. Furthermore, these data provide the basis for development of expression microarrays that can be used in functional genomics studies.
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Affiliation(s)
- Nicolas Tchitchek
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - David Safronetz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Angela L Rasmussen
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Craig Martens
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Kimmo Virtaneva
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Hideki Ebihara
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Michael G Katze
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America; Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
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30
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Book Reviews. COPEIA 2014. [DOI: 10.1643/ot-13-166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Pozzi L, Hodgson JA, Burrell AS, Sterner KN, Raaum RL, Disotell TR. Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2014; 75:165-83. [PMID: 24583291 PMCID: PMC4059600 DOI: 10.1016/j.ympev.2014.02.023] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 01/23/2023]
Abstract
The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany.
| | - Jason A Hodgson
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Andrew S Burrell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States.
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, OR, United States.
| | - Ryan L Raaum
- New York Consortium in Evolutionary Primatology, United States; Department of Anthropology, Lehman College & The Graduate Center, City University of New York, Bronx, NY, United States.
| | - Todd R Disotell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States.
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Mehrabani D, Mahboobi R, Dianatpour M, Zare S, Tamadon A, Hosseini SE. Establishment, culture, and characterization of Guinea pig fetal fibroblast cell. Vet Med Int 2014; 2014:510328. [PMID: 24790770 PMCID: PMC3984808 DOI: 10.1155/2014/510328] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/01/2014] [Accepted: 03/01/2014] [Indexed: 01/02/2023] Open
Abstract
Establishment of Guinea pig fetal fibroblast cells and their biological evaluation before and after cryopreservation were the main purposes of this study. After determination of the proper age of pregnancy by ultrasonography, 30 days old fetuses of Guinea pigs were recovered. Their skins were cut into small pieces (1 mm(2)) and were cultured. When reaching 80-90% confluence, the cells were passaged. Cells of the second and eighth passages were cultured in 24-well plates (4 × 10(4) cells/well) for 6 days and three wells per day were counted. The average cell counts at each time point were then plotted against time and the population doubling time (PDT) was determined. Then, vials of cells (2 × 10(6) cells/mL) were cryopreserved for 1 month and after thawing, the cell viability was evaluated. The PDT of the second passage was about 23 h and for the eighth passage was about 30 h. The viability of the cultures was 95% in the second passage and 74.5% in the eighth passage. It was shown that the Guinea pig fetal fibroblast cell culture can be established using the adherent culture method while, after freezing, the viability indices of these cells were favorable.
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Affiliation(s)
- Davood Mehrabani
- Stem Cell and Transgenic Technology Research Center, Shiraz University of Medical Sciences, 71348 Shiraz, Iran
| | - Reza Mahboobi
- Stem Cell and Transgenic Technology Research Center, Shiraz University of Medical Sciences, 71348 Shiraz, Iran
| | - Mehdi Dianatpour
- Stem Cell and Transgenic Technology Research Center, Shiraz University of Medical Sciences, 71348 Shiraz, Iran
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, 71348 Shiraz, Iran
| | - Shahrokh Zare
- Stem Cell and Transgenic Technology Research Center, Shiraz University of Medical Sciences, 71348 Shiraz, Iran
| | - Amin Tamadon
- Stem Cell and Transgenic Technology Research Center, Shiraz University of Medical Sciences, 71348 Shiraz, Iran
| | - Seyed Ebrahim Hosseini
- Department of Physiology, Islamic Azad University, Marvdasht Branch, 73985 Marvdasht, Iran
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Brown JM. Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit. Syst Biol 2014; 63:334-48. [PMID: 24415681 DOI: 10.1093/sysbio/syu002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Systematic phylogenetic error caused by the simplifying assumptions made in models of molecular evolution may be impossible to avoid entirely when attempting to model evolution across massive, diverse data sets. However, not all deficiencies of inference models result in unreliable phylogenetic estimates. The field of phylogenetics lacks a direct method to identify cases where model specification adversely affects inferences. Posterior predictive simulation is a flexible and intuitive approach for assessing goodness-of-fit of the assumed model and priors in a Bayesian phylogenetic analysis. Here, I propose new test statistics for use in posterior predictive assessment of model fit. These test statistics compare phylogenetic inferences from posterior predictive data sets to inferences from the original data. A simulation study demonstrates the utility of these new statistics. The new tests reject the plausibility of inferred tree lengths or topologies more often when data/model combinations produce biased inferences. I also apply this approach to exemplar empirical data sets, highlighting the value of the novel assessments.
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Affiliation(s)
- Jeremy M Brown
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Fabre PH, Jønsson KA, Douzery EJP. Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach. Gene 2013; 531:388-97. [PMID: 23973722 DOI: 10.1016/j.gene.2013.07.059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/10/2013] [Accepted: 07/16/2013] [Indexed: 10/26/2022]
Abstract
An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes+Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.
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Affiliation(s)
- Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 UM2-CNRS-IRD), Université Montpellier II, Place Eugène Bataillon - CC 064 - 34095 Montpellier Cedex 5, France; Center for Macroecology Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, 15, DK-2100 Copenhagen Ø, Denmark
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Ekdale EG. Comparative Anatomy of the Bony Labyrinth (Inner Ear) of Placental Mammals. PLoS One 2013; 8:e66624. [PMID: 23805251 PMCID: PMC3689836 DOI: 10.1371/journal.pone.0066624] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 05/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Variation is a naturally occurring phenomenon that is observable at all levels of morphology, from anatomical variations of DNA molecules to gross variations between whole organisms. The structure of the otic region is no exception. The present paper documents the broad morphological diversity exhibited by the inner ear region of placental mammals using digital endocasts constructed from high-resolution X-ray computed tomography (CT). Descriptions cover the major placental clades, and linear, angular, and volumetric dimensions are reported. PRINCIPAL FINDINGS The size of the labyrinth is correlated to the overall body mass of individuals, such that large bodied mammals have absolutely larger labyrinths. The ratio between the average arc radius of curvature of the three semicircular canals and body mass of aquatic species is substantially lower than the ratios of related terrestrial taxa, and the volume percentage of the vestibular apparatus of aquatic mammals tends to be less than that calculated for terrestrial species. Aspects of the bony labyrinth are phylogenetically informative, including vestibular reduction in Cetacea, a tall cochlear spiral in caviomorph rodents, a low position of the plane of the lateral semicircular canal compared to the posterior canal in Cetacea and Carnivora, and a low cochlear aspect ratio in Primatomorpha. SIGNIFICANCE The morphological descriptions that are presented add a broad baseline of anatomy of the inner ear across many placental mammal clades, for many of which the structure of the bony labyrinth is largely unknown. The data included here complement the growing body of literature on the physiological and phylogenetic significance of bony labyrinth structures in mammals, and they serve as a source of data for future studies on the evolution and function of the vertebrate ear.
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Affiliation(s)
- Eric G. Ekdale
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Department of Paleontology, San Diego Natural History Museum, San Diego, California, United States of America
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Voloch CM, Vilela JF, Loss-Oliveira L, Schrago CG. Phylogeny and chronology of the major lineages of New World hystricognath rodents: insights on the biogeography of the Eocene/Oligocene arrival of mammals in South America. BMC Res Notes 2013; 6:160. [PMID: 23607317 PMCID: PMC3644239 DOI: 10.1186/1756-0500-6-160] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 04/11/2013] [Indexed: 11/30/2022] Open
Abstract
Background The hystricognath rodents of the New World, the Caviomorpha, are a diverse lineage with a long evolutionary history, and their representation in South American fossil record begins with their occurrence in Eocene deposits from Peru. Debates regarding the origin and diversification of this group represent longstanding issues in mammalian evolution because early hystricognaths, as well as Platyrrhini primates, appeared when South American was an isolated landmass, which raised the possibility of a synchronous arrival of these mammalian groups. Thus, an immediate biogeographic problem is posed by the study of caviomorph origins. This problem has motivated the analysis of hystricognath evolution with molecular dating techniques that relied essentially on nuclear data. However, questions remain about the phylogeny and chronology of the major caviomorph lineages. To enhance the understanding of the evolution of the Hystricognathi in the New World, we sequenced new mitochondrial genomes of caviomorphs and performed a combined analysis with nuclear genes. Results Our analysis supports the existence of two major caviomorph lineages: the (Chinchilloidea + Octodontoidea) and the (Cavioidea + Erethizontoidea), which diverged in the late Eocene. The Caviomorpha/phiomorph divergence also occurred at approximately 43 Ma. We inferred that all family-level divergences of New World hystricognaths occurred in the early Miocene. Conclusion The molecular estimates presented in this study, inferred from the combined analysis of mitochondrial genomes and nuclear data, are in complete agreement with the recently proposed paleontological scenario of Caviomorpha evolution. A comparison with recent studies on New World primate diversification indicate that although the hypothesis that both lineages arrived synchronously in the Neotropics cannot be discarded, the times elapsed since the most recent common ancestor of the extant representatives of both groups are different.
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Wise MJ. Mean protein evolutionary distance: a method for comparative protein evolution and its application. PLoS One 2013; 8:e61276. [PMID: 23613826 PMCID: PMC3626687 DOI: 10.1371/journal.pone.0061276] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 03/08/2013] [Indexed: 12/26/2022] Open
Abstract
Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED), measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins’ roles. Different species’ proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV), dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza), and viroporins agnoprotein (polyomavirus), p7 (hepatitis C) and VPU (HIV) emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles), PB1/PB2 (influenza) and VP1 (rotavirus), and internal serine proteases such as NS3 (dengue and hepatitis C virus) emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz.
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Affiliation(s)
- Michael J Wise
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia.
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Abstract
A recent paper by a science journalist in Nature shows major errors in understanding phylogenies, in this case of placental mammals. The underlying unrooted tree is probably correct, but the placement of the root just reflects a well-known error from the acceleration in the rate of evolution among some myomorph rodents.
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Affiliation(s)
- David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
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39
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Seeding and Cross-seeding in Amyloid Diseases. PROTEOPATHIC SEEDS AND NEURODEGENERATIVE DISEASES 2013. [DOI: 10.1007/978-3-642-35491-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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40
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Complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Sciuromorpha, Sciuridae) and revision of rodent phylogeny. Mol Biol Rep 2012; 40:1917-26. [PMID: 23114915 DOI: 10.1007/s11033-012-2248-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
Abstract
In this study, the complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Rodentia, Sciuromorpha, Sciuridae) was sequenced and characterized in detail. The entire mitochondrial genome of P. volans consisted of 16,513 bp and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Its gene arrangement pattern was consistent with the mammalian ground pattern. The overall base composition and AT contents were similar to those of other rodent mitochondrial genomes. The light-strand origin generally identified between tRNA ( Asn ) and tRNA ( Cys ) consisted of a secondary structure with an 11-bp stem and an 11-bp loop. The large control region was constructed of three characteristic domains, ETAS, CD, and CSB without any repeat sequences. Each domain contained ETAS1, subsequences A, B, and C, and CSB1, respectively. In order to examine phylogenetic contentious issues of the monophyly of rodents and phylogenetic relationships among five rodent suborders, here, phylogenetic analyses based on nucleotide sequence data of the 35 rodent and 3 lagomorph mitochondrial genomes were performed using the Bayesian inference and maximum likelihood method. The result strongly supported the rodent monophyly with high node confidence values (BP 100 % in ML and BPP 1.00 in BI) and also monophylies of four rodent suborders (BP 85-100 % in ML and BPP 1.00 in BI), except for Anomalumorpha in which only one species was examined here. Also, phylogenetic relationships among the five rodent suborders were suggested and discussed in detail.
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Lambret-Frotté J, Perini FA, de Moraes Russo CA. Efficiency of nuclear and mitochondrial markers recovering and supporting known amniote groups. Evol Bioinform Online 2012; 8:463-73. [PMID: 23032608 PMCID: PMC3422098 DOI: 10.4137/ebo.s9656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We have analysed the efficiency of all mitochondrial protein coding genes and six nuclear markers (Adora3, Adrb2, Bdnf, Irbp, Rag2 and Vwf) in reconstructing and statistically supporting known amniote groups (murines, rodents, primates, eutherians, metatherians, therians). The efficiencies of maximum likelihood, Bayesian inference, maximum parsimony, neighbor-joining and UPGMA were also evaluated, by assessing the number of correct and incorrect recovered groupings. In addition, we have compared support values using the conservative bootstrap test and the Bayesian posterior probabilities. First, no correlation was observed between gene size and marker efficiency in recovering or supporting correct nodes. As expected, tree-building methods performed similarly, even UPGMA that, in some cases, outperformed other most extensively used methods. Bayesian posterior probabilities tend to show much higher support values than the conservative bootstrap test, for correct and incorrect nodes. Our results also suggest that nuclear markers do not necessarily show a better performance than mitochondrial genes. The so-called dependency among mitochondrial markers was not observed comparing genome performances. Finally, the amniote groups with lowest recovery rates were therians and rodents, despite the morphological support for their monophyletic status. We suggest that, regardless of the tree-building method, a few carefully selected genes are able to unfold a detailed and robust scenario of phylogenetic hypotheses, particularly if taxon sampling is increased.
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Affiliation(s)
- Julia Lambret-Frotté
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro
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Guo Y, Bao Y, Meng Q, Hu X, Meng Q, Ren L, Li N, Zhao Y. Immunoglobulin genomics in the guinea pig (Cavia porcellus). PLoS One 2012; 7:e39298. [PMID: 22761756 PMCID: PMC3382241 DOI: 10.1371/journal.pone.0039298] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 05/17/2012] [Indexed: 01/06/2023] Open
Abstract
In science, the guinea pig is known as one of the gold standards for modeling human disease. It is especially important as a molecular and cellular biology model for studying the human immune system, as its immunological genes are more similar to human genes than are those of mice. The utility of the guinea pig as a model organism can be further enhanced by further characterization of the genes encoding components of the immune system. Here, we report the genomic organization of the guinea pig immunoglobulin (Ig) heavy and light chain genes. The guinea pig IgH locus is located in genomic scaffolds 54 and 75, and spans approximately 6,480 kb. 507 V(H) segments (94 potentially functional genes and 413 pseudogenes), 41 D(H) segments, six J(H) segments, four constant region genes (μ, γ, ε, and α), and one reverse δ remnant fragment were identified within the two scaffolds. Many V(H) pseudogenes were found within the guinea pig, and likely constituted a potential donor pool for gene conversion during evolution. The Igκ locus mapped to a 4,029 kb region of scaffold 37 and 24 is composed of 349 V(κ) (111 potentially functional genes and 238 pseudogenes), three J(κ) and one C(κ) genes. The Igλ locus spans 1,642 kb in scaffold 4 and consists of 142 V(λ) (58 potentially functional genes and 84 pseudogenes) and 11 J(λ) -C(λ) clusters. Phylogenetic analysis suggested the guinea pig's large germline V(H) gene segments appear to form limited gene families. Therefore, this species may generate antibody diversity via a gene conversion-like mechanism associated with its pseudogene reserves.
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Affiliation(s)
- Yongchen Guo
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Yonghua Bao
- Department of Basic Immunology, Xinxiang Medical University, Xinxiang, People's Republic of China
| | - Qingwen Meng
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Xiaoxiang Hu
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Qingyong Meng
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Liming Ren
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Ning Li
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, People's Republic of China
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Mariadassou M, Bar-Hen A, Kishino H. Taxon influence index: assessing taxon-induced incongruities in phylogenetic inference. Syst Biol 2012; 61:337-45. [PMID: 22228800 DOI: 10.1093/sysbio/syr129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the evolutionary history of species is at the core of molecular evolution and is done using several inference methods. The critical issue is to quantify the uncertainty of the inference. The posterior probabilities in Bayesian phylogenetic inference and the bootstrap values in frequentist approaches measure the variability of the estimates due to the sampling of sites from genes and the sampling of genes from genomes. However, they do not measure the uncertainty due to taxon sampling. Taxa that experienced molecular homoplasy, recent selection, a spur of evolution, and so forth may disrupt the inference and cause incongruences in the estimated phylogeny. We define a taxon influence index to assess the influence of each taxon on the phylogeny. We found that although most taxa have a weak influence on the phylogeny, a small fraction of influential taxa strongly alter it even in clades only loosely related to them. We conclude that highly influential taxa should be given special attention and sampling them more thoroughly can lead to more dependable phylogenies.
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Affiliation(s)
- Mahendra Mariadassou
- Department of Mathematics and Informatics, MAP5, Université Paris Descartes, 45 rue des Saints Pères, 75270 Paris Cedex 06, France.
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Can sensitivity analysis help to detect long-branch attraction? Mol Phylogenet Evol 2011; 61:899-903. [DOI: 10.1016/j.ympev.2011.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 08/01/2011] [Accepted: 08/04/2011] [Indexed: 11/19/2022]
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Finckbeiner S, Ko PJ, Carrington B, Sood R, Gross K, Dolnick B, Sufrin J, Liu P. Transient knockdown and overexpression reveal a developmental role for the zebrafish enosf1b gene. Cell Biosci 2011; 1:32. [PMID: 21943404 PMCID: PMC3197473 DOI: 10.1186/2045-3701-1-32] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 09/26/2011] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Despite detailed in vivo knowledge of glycolytic enolases and many bacterial non-enolase members of the superfamily, little is known about the in vivo function of vertebrate non-enolase enolase superfamily members (ENOSF1s). Results of previous studies suggest involvement of the β splice form of ENOSF1 in breast and colon cancers. This study used the zebrafish (Danio rerio) as a vertebrate model of ENOSF1β function. RESULTS Whole mount in situ hybridization (WISH) showed that zebrafish ENOSF1β (enosf1b) is zygotic and expressed ubiquitously through the first 24 hours post fertilization (hpf). After 24 hpf, enosf1b expression is restricted to the notochord. Embryos injected with enosf1b-EGFP mRNA grew slower than EGFP mRNA-injected embryos but caught up to the EGFP-injected embryos by 48 hpf. Embryos injected with ATG or exon 10 enosf1b mRNA-targeting morpholinos had kinked notochords, shortened anterior-posterior axes, and circulatory edema. WISH for ntl or pax2a expression showed that embryos injected with either morpholino have deformed notochord and pronephros. TUNEL staining revealed increased apoptosis in the peri-notochord region. CONCLUSIONS This study is the first report of ENOSF1 function in a vertebrate and shows that ENOSF1 is required for embryonic development. Increased apoptosis following enosf1b knockdown suggests a potential survival advantage for increased ENOSF1β expression in human cancers.
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Affiliation(s)
- Steve Finckbeiner
- Oncogenesis and Development Section, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
- Program of Molecular Pharmacology and Cancer Therapeutics, Roswell Park Graduate Division, State University of New York at Buffalo, Elm and Carlton Streets, Buffalo NY, 14263, USA
| | - Pin-Joe Ko
- Oncogenesis and Development Section, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
| | - Blake Carrington
- Zebrafish Core, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
| | - Raman Sood
- Oncogenesis and Development Section, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
- Zebrafish Core, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
| | - Kenneth Gross
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo NY, 14263, USA
| | - Bruce Dolnick
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo NY, 14263, USA
| | - Janice Sufrin
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo NY, 14263, USA
| | - Paul Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
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Kitazawa T, Nakamura T, Saeki A, Teraoka H, Hiraga T, Kaiya H. Molecular identification of ghrelin receptor (GHS-R1a) and its functional role in the gastrointestinal tract of the guinea-pig. Peptides 2011; 32:1876-86. [PMID: 21843569 DOI: 10.1016/j.peptides.2011.07.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 11/20/2022]
Abstract
Ghrelin stimulates gastric motility in vivo in the guinea-pig through activation of growth hormone secretagogue receptor (GHS-R). In this study, we identified GHS-R1a in the guinea-pig, and examined its distribution and cellular function and compared them with those in the rat. Effects of ghrelin in different regions of gastrointestinal tract were also examined. GHS-R1a was identified in guinea-pig brain cDNA. Amino acid identities of guinea-pig GHS-R1a were 93% to horses and 85% to dogs. Expression levels of GHS-R1a mRNA were high in the pituitary and hypothalamus, moderate in the thalamus, cerebral cortex, pons, medulla oblongata and olfactory bulb, and low in the cerebellum and peripheral tissues including gastrointestinal tract. Comparison of GHS-R1a expression patterns showed that those in the brain were similar but the expression level in the gastrointestinal tract was higher in rats than in guinea-pigs. Guinea-pig GHS-R1a expressed in HEK 293 cells responded to rat ghrelin and GHS-R agonists. Rat ghrelin was ineffective in inducing mechanical changes in the stomach and colon but caused a slight contraction in the small intestine. 1,1-Dimethyl-4-phenylpiperazinium and electrical field stimulation (EFS) caused cholinergic contraction in the intestine, and these contractions were not affected by ghrelin. Ghrelin did not change spontaneous and EFS-evoked [(3)H]-efflux from [(3)H]-choline-loaded ileal strips. In summary, guinea-pig GHS-R1a was identified and its functions in isolated gastrointestinal strips were characterized. The distribution of GHS-R1a in peripheral tissues was different from that in rats, suggesting that the functional role of ghrelin in the guinea-pig is different from that in other animal species.
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Affiliation(s)
- Takio Kitazawa
- Department of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan.
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Li Y, Wang J, He HY, Ma LJ, Zeng J, Deng GC, Liu X, Engelhardt JF, Wang Y. Immunohistochemical demonstration of airway epithelial cell markers of guinea pig. Tissue Cell 2011; 43:283-90. [PMID: 21705035 DOI: 10.1016/j.tice.2011.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 05/15/2011] [Accepted: 05/24/2011] [Indexed: 11/25/2022]
Abstract
The guinea pig (Cavea porcellus) is a mammalian non-rodent species in the Caviidae family. The sensitivity of the respiratory system and the susceptibility to infectious diseases allows the guinea pig to be a useful model for both infectious and non-infectious lung diseases such as asthma and tuberculosis. In this report, we demonstrated for the first time, the major cell types and composition in the guinea pig airway epithelium, using cell type-specific markers by immunohistochemical staining using the commercial available immunological reagents that cross-react with guinea pig. Our results revealed the availability of antibodies cross-reacting with airway epithelial cell types of basal, non-ciliated columnar, ciliated, Clara, goblet and alveolar type II cells, as well as those cells expressing Mucin 5AC, Mucin 2, Aquaporin 4 and Calcitonin Gene Related Peptide. The distribution of these various cell types were quantified in the guinea pig airway by immunohistochemical staining and were comparable with morphometric studies using an electron microscopy assay. Moreover, this study also demonstrated that goblet cells are the main secretory cell type in the guinea pig's airway, distinguishing this species from rats and mice. These results provide useful information for the understanding of airway epithelial cell biology and mechanisms of epithelial-immune integration in guinea pig models.
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Affiliation(s)
- Yong Li
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources of Western China, Yinchuan, Ningxia 750021, China
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Tardif S, Cormier N. Role of zonadhesin during sperm-egg interaction: a species-specific acrosomal molecule with multiple functions. Mol Hum Reprod 2011; 17:661-8. [PMID: 21602212 DOI: 10.1093/molehr/gar039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Sperm-zona adhesion is an essential event in mammalian fertilization, failure of which causes sterility. However, the molecular mechanisms involved in this process are still poorly understood. It has been suggested by few laboratories studying gamete interaction that acrosomal molecules are implicated in sperm-zona pellucida adhesion prior to the acrosome reaction (AR). Zonadhesin, a sperm-specific protein located in the acrosome is critically involved in zona binding. Here we describe the cellular and molecular interaction of zonadhesin during fertilization and also discuss its role in species-specific gamete interaction--an intriguing question in biology. We propose a model in which sperm could transiently expose acrosomal molecules that adhere to the zona independently of the AR in a 'kiss and run' mechanism. This could be a valuable framework for further investigations and a detailed understanding of the molecular events during gamete adhesion is likely to provide new approaches for the design of more effective male contraceptives and better diagnostic methods for sperm dysfunction.
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Affiliation(s)
- Steve Tardif
- Reproductive and Developmental Biology Group, Maternal and Child Health Sciences Laboratories, Centre for Oncology and Molecular Medicine, Division of Medical Sciences, Ninewells Hospital, University of Dundee, DD1 9SY, Dundee, UK.
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Goremykin VV, Nikiforova SV, Bininda-Emonds ORP. Automated Removal of Noisy Data in Phylogenomic Analyses. J Mol Evol 2010; 71:319-31. [DOI: 10.1007/s00239-010-9398-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 10/06/2010] [Indexed: 10/18/2022]
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Identification of novel cyclic nucleotide phosphodiesterase gene cDNAs in the brain of guinea pig. Neurosci Bull 2010; 26:365-70. [PMID: 20882062 DOI: 10.1007/s12264-010-0517-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVE Cyclic nucleotide phosphodiesterase (PDE) is a critical component of the nitric oxide (NO) signaling pathway and plays critical roles in cognition and learning, Parkinson's disease, attention deficit hyperactivity disorder, psychosis and depression. The PDEs in the brain of guinea pig have not yet been reported. The present study aimed to detect the unknown Pde cDNAs in the brain of guinea pig. METHODS Reverse transcription polymerase chain reaction (RT-PCR) and sequence comparison analysis were performed to detect the expression of Pde cDNAs and to assess the identity rates of cDNA and amino acid sequences between guinea pig and human or mouse, respectvely. The RT-PCR primers were located on the conserved region of human PDE and mouse Pde cDNAs. RESULTS Eleven novel Pde cDNAs were detected in the brain of guinea pig (Cavia porcellus), including CpPde1a, CpPde1b, CpPde2a, CpPde4a, CpPde4d, CpPde5a, CpPde6c, CpPde7b, CpPde8a, CpPde9a, and CpPde10a. The identity rates of the Pde cDNA sequences between guinea pig and human ranged from 83.8% to 94.3%, and those of the amino acid sequences ranged from 91.9% to 100%. The identity rates of Pde cDNA sequences between guinea pig and mouse ranged from 84.6% to 92.1%, and those of amino acid sequences ranged from 91.2% to 99.2%. The average identity rate of the 11 Pde cDNA sequences between guinea pig and human was significantly higher (P < 0.01) than that between guinea pig and mouse. The putative partial amino acid sequences of guinea pig contained at least one of the conserved domains of human and mouse PDE proteins. CONCLUSION These results indicate that the brain-expressed Pde genes are identified in guinea pig, which lays the foundation for further investigating the physiological roles of PDE proteins in the brain.
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