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Antony C, Somers P, Gray EM, Pimkin M, Paralkar VR. FISH-Flow to quantify nascent and mature ribosomal RNA in mouse and human cells. STAR Protoc 2023; 4:102463. [PMID: 37481729 PMCID: PMC10374870 DOI: 10.1016/j.xpro.2023.102463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/09/2023] [Accepted: 06/24/2023] [Indexed: 07/25/2023] Open
Abstract
FISH-Flow (fluorescence in situ hybridization-flow cytometry) involves hybridizing fluorescent oligos to RNA and quantifying fluorescence at a single-cell level using flow cytometry. Here, we present a FISH-Flow protocol to quantify nascent 47S and mature 18S and 28S rRNAs in mouse and human cells, including rRNA quantification across cell cycle stages using DNA staining. We describe steps for cell preparation, hybridization of fluorescent probes against rRNA, and DNA staining. We then detail procedures for flow cytometry and data analysis. For complete details on the use and execution of this protocol, please refer to Antony et al. (2022).1.
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Affiliation(s)
- Charles Antony
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Patrick Somers
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Erin M Gray
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Vikram R Paralkar
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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Gagnon DK, Kasl EA, Preisser WC, Belden LK, Detwiler JT. Morphological and molecular characterization of Quinqueserialis (Digenea: Notocotylidae) species diversity in North America. Parasitology 2021; 148:1083-1091. [PMID: 34027840 PMCID: PMC11010126 DOI: 10.1017/s0031182021000792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 11/07/2022]
Abstract
Estimates of trematode diversity are inaccurate due to unrecognized cryptic species and phenotypic plasticity within species. Integrative taxonomy (genetics, morphology and host use) increases the clarity of species delineation and improves knowledge of parasite biology. In this study, we used this approach to resolve taxonomic issues and test hypotheses of cryptic species in a genus of trematode, Quinqueserialis. Specimens from throughout North America were field collected from hosts and obtained from museums. We found three morphologically distinct groups and successfully sequenced specimens from two of these groups. DNA sequencing at the 28S and CO1 gene regions revealed that two of the three groups were genetically distinct. One genetic group included two morphological clusters demonstrating host-induced phenotypic plasticity within Quinqueserialis quinqueserialis. The other unique genetic group is a novel species, Quinqueserialis kinsellai n. sp., which is described herein. Our study illustrates the importance of integrating multiple sources of evidence when investigating trematode diversity to account for the influence of cryptic species or phenotypic plasticity. However, further sampling is needed to understand Quinqueserialis spp. diversity as some species have no genetic information associated with them.
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Affiliation(s)
- Demi K. Gagnon
- Department of Biological Sciences, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
| | - Emily A. Kasl
- Department of Biology, University of North Alabama, Florence, AL35632, USA
| | - Whitney C. Preisser
- School of Aquatic and Fishery Science, University of Washington, Seattle, WA98105, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA24061, USA
| | - Jillian T. Detwiler
- Department of Biological Sciences, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
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Hayashi K, Kitayama C, Saito T, Ohari Y, Hayashi K, Kondo S, Takashima Y, Kuroki T, Shibahara T, Itagaki T. Detection and molecular characteristics of Pyelosomum cochlear (Digenea: Pronocephalidae) in the urinary bladder of the green sea turtle (Chelonia mydas) in the Northwest Pacific Ocean. Infect Genet Evol 2021; 93:104962. [PMID: 34111570 DOI: 10.1016/j.meegid.2021.104962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/20/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022]
Abstract
The genus Pyelosomum consists of parasitic flukes occurring primarily in marine turtles; Pyelosomum cochlear Looss 1899 is the only species of this genus that parasitizes the urinary bladder. In this study, we detected flukes in the urinary bladders of 20 of 88 green sea turtles (Chelonia mydas) harvested in the Ogasawara Islands, in the Northwest Pacific Ocean. We identified the flukes as P. cochlear based on detailed morphological observations and comparisons of morphometric measurements of the species reported previously. Nucleotide sequences of nuclear ribosomal 18S and 28S regions and the mitochondrial cytochrome c oxidase subunit 1 (COI) region were determined for the flukes. The 18S and 28S phylogenetic trees revealed that the species of the superfamily Pronocephaloidea, including P. cochlear, constituted a single clade, but the species of the family Pronocephalidae did not constitute a single taxon. These findings suggest that Pronocephalidae is a paraphyletic group. The COI sequences of P. cochlear exhibited high genetic diversity, suggesting that they would be useful markers to understand the genetic structure of the parasite and its evolutionary relationship with the host turtle populations. This is the first study to provide the nucleotide sequences of Pyelosomum species; these data will be available for further molecular studies of this genus and its related taxa.
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Affiliation(s)
- Kei Hayashi
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoinooka, Imabari 794-8555, Japan
| | - Chiyo Kitayama
- Everlasting Nature of Asia (ELNA), Ogasawara Marine Center, Ogasawara, Tokyo 100-2101, Japan
| | - Taizo Saito
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yuma Ohari
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 9, Kita-ku Sapporo, Hokkaido 060-0818, Japan
| | - Kaoru Hayashi
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoinooka, Imabari 794-8555, Japan
| | - Satomi Kondo
- Everlasting Nature of Asia (ELNA), Ogasawara Marine Center, Ogasawara, Tokyo 100-2101, Japan
| | - Yasuhiro Takashima
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Department of Veterinary Parasitological Diseases, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Toshiro Kuroki
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoinooka, Imabari 794-8555, Japan
| | - Toshiyuki Shibahara
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoinooka, Imabari 794-8555, Japan
| | - Tadashi Itagaki
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka 020-8550, Japan.
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Biswas R, Oros M, Barčák D, Scholz T, Ash A. Crossing barriers of zoogeographical regions: Molecular evidence of vicariance of the only cestode parasite of loaches (Cobitidae) in the Indomalayan region, Paracaryophyllaeus lepidocephali (Cestoda: Caryophyllidea), and its redescription. Parasitol Int 2021; 83:102309. [PMID: 33640409 DOI: 10.1016/j.parint.2021.102309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/09/2021] [Accepted: 02/14/2021] [Indexed: 11/18/2022]
Abstract
Tapeworms of the genus Paracaryophyllaeus Kulakovskaya, 1961 (Cestoda: Caryophyllidea) are specific parasites of loaches (Cypriniformes: Cobitoidea) and occur almost exclusively in the Palaearctic region. The only exception and example of vicariance over the borders of two zoogeographical regions is Paracaryophyllaeus lepidocephali (Kundu, 1985), an insufficiently known species described from the Indomalayan region, with uncertain generic allocation. In the present paper, the species is redescribed based on new material collected from the type host, Lepidocephalichthys guntea, in West Bengal, India. Molecular data reveal this species as a member of Paracaryophyllaeus, within which it is the most closely related to P. cf. gotoi from Misgurnus anguillicaudatus in China and Japan on the basis of large subunit of ribosomal nuclear DNA (28S rDNA). Generic position of P. lepidocephali examined herein is also confirmed by morphology including cross sections, in particular, by a small, cylindrical body, medullary testes with testicular fields crossing the anterior margin of the cirrus sac, medullary vitelline follicles, with some follicles paramuscular, a shallow common genital atrium, short vagina and uterus not extending anteriorly beyond the cirrus sac. It differs from all Palaearctic congeners but Paracaryophyllaeus vladkae Scholz, Oros and Aydogdu, 2014 by the testicular field crossing the anterior margin of the cirrus sac. It differs from P. vladkae by more anterior position of the first vitelline follicles compared to the first testes. This species is a unique example of a fish tapeworm crossing the borders of the Palaearctic and Indomalayan zoogeographical regions.
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Affiliation(s)
- Roshmi Biswas
- Department of Zoology, University of Burdwan, Golapbag, Burdwan 713104, India
| | - Mikuláš Oros
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
| | - Daniel Barčák
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
| | - Tomáš Scholz
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic & Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Anirban Ash
- Department of Zoology, University of Burdwan, Golapbag, Burdwan 713104, India.
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Horn IR, Verleg PA, Ibrahim NZ, Soeleman K, van Kampen F, Ruesen MO, Reulen NM, Breij H, Bakker RJ, Gravendeel B. Mushroom DNA barcoding project: Sequencing a segment of the 28S rRNA gene. Biochem Mol Biol Educ 2020; 48:404-410. [PMID: 32585770 PMCID: PMC7497104 DOI: 10.1002/bmb.21388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/22/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
DNA barcoding is an important molecular methodology for species identification that was developed over the last two decades and it should be covered in the biology bachelor curriculum. Here, we present an example of DNA barcoding by sequencing a segment of the 28S nuclear ribosomal large subunit rRNA gene of wild mushrooms and framing the education in a project form for undergraduate students in biology. Students perform this project in 6-8 weeks, which also includes preparing a poster, writing a report and presenting a paper related to the work in a journal club format. First, fieldwork in the Netherlands was carried out, during which students collected mushrooms under supervision of a professional mycologist with the goal to (a) verify morphologically based identifications with a molecular method and (b) assess phylogenetic relationships of the different species collected. Next, DNA extractions and quantitation were performed, PCR amplification was done, and samples were sent out for Sanger sequencing. Students aligned and analyzed the sequences using BLAST and Geneious and subsequently created a phylogenetic tree. In case of collecting DNA barcodes of an earlier sequenced species, students could upload the data to a repository established for facilitation of future research projects. The method described is very robust, reagents and equipment are readily available, and costs are relatively low. In addition, the results can be compared to published fungal phylogenetic trees.
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Affiliation(s)
- Ivo R. Horn
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
- Naturalis Biodiversity Center, Endless Forms GroupLeidenThe Netherlands
- Leiden Centre for Applied BioscienceLeidenThe Netherlands
| | - Peter A. Verleg
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Nafiesa Z. Ibrahim
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Khadiedjah Soeleman
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Floris van Kampen
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Mia O. Ruesen
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Naïsha M. Reulen
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Henk Breij
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Roderick J. Bakker
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Barbara Gravendeel
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
- Naturalis Biodiversity Center, Endless Forms GroupLeidenThe Netherlands
- Institute of Biology Leiden, Leiden UniversityLeidenThe Netherlands
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Atopkin DM, Besprozvannykh VV, Ha DN, Nguyen VH, Nguyen VT. New species and new genus of Pseudohaploporinae (Digenea): Pseudohaploporus pusitestis sp. n. and Parahaploporus elegantus n. g., sp. n. (Digenea: Pseudohaploporinae) from Vietnamese mullet fish. Parasitol Int 2019; 75:102023. [PMID: 31715266 DOI: 10.1016/j.parint.2019.102023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 11/17/2022]
Abstract
Two new species of Pseudohaploporinae, Pseudohaploporus pusitestis sp. n. and Parahaploporus elegantus n. g., sp. n., are described from intestines of the Vietnamese mullet fish Moolgarda seheli and Osteomugil cunnesius, respectively. Pseudohaploporus pusitestis sp. n. differs from two known Pseudohaploporus species, P. vietnamensis and P. planiliza, by the absence of a diverticulate hermaphroditic duct and muscular sphincters at the proximal end of the hermaphroditic sac. Metrically, P. pusitestis sp. n. is close to P. vietnamensis and differs from this species and from P. planilizum by lower maximum sizes of most parameters. Parahaploporus elegantus n. g., sp. differs from representatives of Pseudohaploporus by the presence of a single testis and the armament of hermaphroditic duct and is morphologically close to trematodes of the genus Haploporus. However, P. elegantus n. g differs from all known Haploporus species from mugilids of the Indo-West Pacific by the structure of the armament of the hermaphroditic duct and also by size of body, organs and eggs. The validity of designating two new species and a new genus of trematodes is supported by ITS and 28S rDNA sequence data. Phylogenetic reconstructions showed that the new trematodes belong to the Pseudohaploporinae, which formed a well-supported cluster within the monophyletic Haploporidae.
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Affiliation(s)
- D M Atopkin
- Federal Scientific Center of East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia; Department of Cell Biology and Genetics, Far Eastern Federal University, 690051, Ajax-10 str, Vladivostok, Russia.
| | - V V Besprozvannykh
- Federal Scientific Center of East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - D N Ha
- Institute of Ecology and Biological Resources, Vietnamese Academy of Sciences and Technology, Hanoi, Viet Nam
| | - V H Nguyen
- Institute of Ecology and Biological Resources, Vietnamese Academy of Sciences and Technology, Hanoi, Viet Nam
| | - V T Nguyen
- Hai Duong Medical Technical University, Hanoi, Viet Nam
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Okabe T, Oyama H, Kashitani M, Ishimaru Y, Suo R, Sugita H, Itoi S. Toxic Flatworm Egg Plates Serve as a Possible Source of Tetrodotoxin for Pufferfish. Toxins (Basel) 2019; 11:E402. [PMID: 31373322 PMCID: PMC6669758 DOI: 10.3390/toxins11070402] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 11/26/2022] Open
Abstract
The pufferfish Takifugu niphobles (at present Takifugu alboplumbeus) possesses highly concentrated tetrodotoxin (TTX), an extremely potent neurotoxin that provides effective protection from predators, at least at the larval stages. However, the source of the toxin has remained unclear. Recently, DNA from the toxic flatworm Planocera multitentaculata was detected in the intestinal contents of juveniles and young of the pufferfish, suggesting that the flatworm contributes to its toxification at various stages of its life. In this study, we describe the behavior of the pufferfish in the intertidal zone that appears to contribute to its toxification before and during its spawning period: pufferfish were found to aggregate and ingest flatworm egg plates by scraping them off the surface of rocks. DNA analysis based on 28S rRNA and cytochrome c oxidase subunit I (COI) genes identified the egg plates as those of P. multitentaculata. Liquid chromatography with tandem mass spectrometry analysis revealed that the egg plates contain highly concentrated TTX. The feeding behavior of the pufferfish on the flatworm egg plates was also observed in the aquarium. These results suggest that pufferfish feed on the flatworm egg plate, which enables them to acquire toxicity themselves while providing their offspring with the protective shield of TTX.
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Affiliation(s)
- Taiki Okabe
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Hikaru Oyama
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Maho Kashitani
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Yuta Ishimaru
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Rei Suo
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Haruo Sugita
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Shiro Itoi
- Department of Marine Science and Resources, Nihon University, Fujisawa, Kanagawa 252-0880, Japan.
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Duarte ME, de Mendonça RS, Skoracka A, Silva ES, Navia D. Integrative taxonomy of Abacarus mites (Eriophyidae) associated with hybrid sugarcane plants, including description of a new species. Exp Appl Acarol 2019; 78:373-401. [PMID: 31278610 DOI: 10.1007/s10493-019-00388-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/30/2019] [Indexed: 06/09/2023]
Abstract
Phytophagous mites belonging to the Eriophyoidea are extremely diverse and highly host-specific. Their accurate morphological identification is hampered by their reduced size and simplified bodies and by the existence of cryptic species complexes. Previous studies have demonstrated the urgency of applying multisource methods to accurate taxonomic identification of eriophyoid mites, especially species belonging to the genus Abacarus. This genus comprises 65 species, of which 37 are associated with grasses and four with sugarcane Saccharum (Poaceae). Recently, Abacarus specimens very similar to Abacarus sacchari were collected from the sugarcane crop in Brazil; however, their taxonomic placement was uncertain. In this study, we used an integrative approach to determine whether A. aff. sacchari specimens belong to A. sacchari or constitute a cryptic species. Morphological data were combined with molecular phylogeny based on the nucleotide sequences of three markers, one mitochondrial (COI) and two nuclear (D2 region of 28S and ITS). Morphological differences were observed between A. aff. sacchari, A. sacchari and A. doctus. The phylogenetic relationships among these three taxa and the genetic distances separating them revealed an interspecific divergence. The results of the morphological and molecular methods were congruent and supported the existence of a new species: Abacarus neosacchari n. sp. Duarte and Navia, herein described. This species belongs to the Abacarus cryptic species complex associated with sugarcane in the Americas. The results of this study, presenting the occurrence of multiple Abacarus species associated with sugarcane, contribute to the knowledge on plants and mites diversity by adding up one more clue highlighting that plant hybridization can be an important mechanism contributing to the speciation of plant-feeding arthropods.
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Affiliation(s)
- Mércia Elias Duarte
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, Distrito Federal, 70770-900, Brazil
| | - Renata Santos de Mendonça
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, 70297-400, Brazil
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Edmilson Santos Silva
- Universidade Federal de Alagoas, Campus Arapiraca, Arapiraca, 57309-005, Brazil
- Universidade Federal de Alagoas, Centro de Ciências Agrárias (CECA), Alagoas, 57100-000, Brazil
| | - Denise Navia
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, Distrito Federal, 70770-900, Brazil.
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Leung PTY, Yan M, Lam VTT, Yiu SKF, Chen CY, Murray JS, Harwood DT, Rhodes LL, Lam PKS, Wai TC. Phylogeny, morphology and toxicity of benthic dinoflagellates of the genus Fukuyoa (Goniodomataceae, Dinophyceae) from a subtropical reef ecosystem in the South China Sea. Harmful Algae 2018; 74:78-97. [PMID: 29724345 DOI: 10.1016/j.hal.2018.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
Species of Fukuyoa, recently revised from the globular Gambierdiscus, are toxic benthic dinoflagellates associated with ciguatera. In this study, a total of ten strains of Fukuyoa collected from Hong Kong waters were characterized using morphological and phylogenetic analyses. Results from both analyses showed that one of the strains is a putative new species, namely Fukuyoa sp. HK Type 1 (plate formula Po, 3', 7″, 6c, 7s, 5‴, 1p and 2'‴ with a distinctive small and narrow cell shape, narrow Po plate, high Po pore density, large and broad Plate 1' but small and round Po pore size, small and narrow Plate 2', long and narrow Plates 2'‴ and 1p), and the others were F. ruetzleri. This is the first report of these two species of Fukuyoa in the South China Sea and Asia-Pacific region. Phylogenies on 18S, 28S D1/D3 and D8/D10 ribosomal DNA sequences strongly support that Fukuyoa sp. HK Type 1 is currently the most divergent species in the genus Fukuyoa. The diagrammatic plots on the p-distance matrices of 18S, 28S D1/D3 and D8/D10 and ITS regions resolved that the species of Fukuyoa were separated into three main groups, i.e., Fukuyoa sp. HK Type 1, F. paulensis and a group consisting of F. ruetzleri, F. yasumotoi and F. cf. yasumotoi, while Fukuyoa sp. HK Type 1 was always the most distant from the other two groups. Additionally, the pairwise p-distance values calculated based on the ITS region have always been the highest for pairs between Fukuyoa sp. HK Type 1 and other Fukuyoa species, ranging from 0.142 to 0.150. Our molecular results suggested that Fukuyoa sp. HK Type 1 is a putative new species. Both morphological and molecular data of more strains from different localities should be, however, collected to address its intraspecific variability and further evaluate its taxonomic status. A bioassay analysis demonstrated that algal lysates extracted from F. ruetzleri and Fukuyoa sp. HK Type 1 were lethal to brine shrimp larvae, indicating that both species were toxic. Bulk cultures were tested for Pacific ciguatoxins (P-CTXs) and maitotoxins (MTXs) by liquid chromatography-tandem mass spectrometry (LC-MS/MS). All isolates of Fukuyoa produced neither P-CTXs nor MTX-1, but isolates of F. ruetzleri produced a compound putatively assigned as MTX-3. This study has updated the current biodiversity and distribution of the toxic benthic dinoflagellates Fukuyoa, and thus contributes to the understanding of their emerging threats to the sub-tropical reef systems locally and regionally.
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Affiliation(s)
- Priscilla T Y Leung
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Meng Yan
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Veronica T T Lam
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Sam K F Yiu
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Chia-Yun Chen
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China
| | | | | | | | - Paul K S Lam
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China; Department of Chemistry, City University of Hong Kong, Hong Kong, China.
| | - Tak-Cheung Wai
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
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Heumüller-Klug S, Sticht C, Kaiser K, Wink E, Hagl C, Wessel L, Schäfer KH. Degradation of intestinal mRNA: A matter of treatment. World J Gastroenterol 2015; 21:3499-3508. [PMID: 25834314 PMCID: PMC4375571 DOI: 10.3748/wjg.v21.i12.3499] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 11/11/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To characterize the influence of location, species and treatment upon RNA degradation in tissue samples from the gastrointestinal tract.
METHODS: The intestinal samples were stored in different medium for different times under varying conditions: different species (human and rat), varying temperature (storage on crushed ice or room temperature), time point of dissection of the submucous-mucous layer from the smooth muscle (before or after storage), different rinsing methods (rinsing with Medium, PBS, RNALater or without rinsing at all) and different regions of the gut (proximal and distal small intestine, caecum, colon and rectum). The total RNA from different parts of the gut (rat: proximal and distal small intestine, caecum, colon and rectum, human: colon and rectum) and individual gut layers (muscle and submucosal/mucosal) was extracted. The quality of the RNA was assessed by micro capillary electrophoresis. The RNA quality was expressed by the RNA integrity number which is calculated from the relative height and area of the 18 S and 28 S RNA peaks. From rat distal small intestine qPCR was performed for neuronal and glial markers.
RESULTS: RNA obtained from smooth muscle tissue is much longer stable than those from submucosal/mucosal tissue. At RT muscle RNA degrades after one day, on ice it is stable at least three days. Cleaning and separation of gut layers before storage and use of RNALater, maintains the stability of muscle RNA at RT for much longer periods. Different parts of the gut show varying degradation periods. RNA obtained from the submucosal/mucosal layer always showed a much worse amplification rate than RNA from muscle tissue. In general RNA harvested from rat tissue, either smooth muscle layer or submucosal/mucosal layer is much longer stable than RNA from human gut tissue, and RNA obtained from smooth muscle tissue shows an increased stability compared to RNA from submucosal/mucosal tissue. At RT muscle RNA degrades after one day, while the stability on ice lasts at least three days. Cleaning and separation of gut layers before storage and use of RNALater, maintains the stability of muscle RNA at RT for much longer periods. Different parts of the gut show varying degradation periods. The RNA from muscle and submucosal/mucosal tissue of the proximal small intestine degrades much faster than the RNA of distal small intestine, caecum or colon with rectum. RNA obtained from the submucosal/mucosal layer always showed a much more reduced amplification rate than RNA from muscle tissue [β-Tubulin III for muscle quantification cycle (Cp): 22.07 ± 0.25, for β-Tubulin III submucosal/mucosal Cp: 27.42 ± 0.19].
CONCLUSION: Degradation of intestinal mRNA depends on preparation and storage conditions of the tissue. Cooling, rinsing and separating of intestinal tissue reduce the degradation of mRNA.
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MESH Headings
- Animals
- Animals, Newborn
- Child, Preschool
- Dissection
- Electrophoresis, Capillary
- Humans
- Infant
- Intestinal Mucosa/anatomy & histology
- Intestinal Mucosa/chemistry
- Intestines/anatomy & histology
- Intestines/chemistry
- Muscle, Smooth/anatomy & histology
- Muscle, Smooth/chemistry
- Neuroglia/chemistry
- Neurons/chemistry
- RNA Stability
- RNA, Messenger/analysis
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 28S/analysis
- Rats, Sprague-Dawley
- Species Specificity
- Specimen Handling/methods
- Temperature
- Time Factors
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11
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Spille JH, Kaminski TP, Scherer K, Rinne JS, Heckel A, Kubitscheck U. Direct observation of mobility state transitions in RNA trajectories by sensitive single molecule feedback tracking. Nucleic Acids Res 2015; 43:e14. [PMID: 25414330 PMCID: PMC4333372 DOI: 10.1093/nar/gku1194] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/01/2014] [Accepted: 11/03/2014] [Indexed: 11/12/2022] Open
Abstract
Observation and tracking of fluorescently labeled molecules and particles in living cells reveals detailed information about intracellular processes on the molecular level. Whereas light microscopic particle observation is usually limited to two-dimensional projections of short trajectory segments, we report here image-based real-time three-dimensional single particle tracking in an active feedback loop with single molecule sensitivity. We tracked particles carrying only 1-3 fluorophores deep inside living tissue with high spatio-temporal resolution. Using this approach, we succeeded to acquire trajectories containing several hundred localizations. We present statistical methods to find significant deviations from random Brownian motion in such trajectories. The analysis allowed us to directly observe transitions in the mobility of ribosomal (r)RNA and Balbiani ring (BR) messenger (m)RNA particles in living Chironomus tentans salivary gland cell nuclei. We found that BR mRNA particles displayed phases of reduced mobility, while rRNA particles showed distinct binding events in and near nucleoli.
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Affiliation(s)
- Jan-Hendrik Spille
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
| | - Tim P Kaminski
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
| | - Katharina Scherer
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
| | - Jennifer S Rinne
- Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
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12
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Yamamura S, Yatsushiro S, Yamaguchi Y, Abe K, Shinohara Y, Kataoka M. Detection of miRNA in cell cultures by using microchip electrophoresis with a fluorescence-labeled riboprobe. Sensors (Basel) 2012; 12:7576-86. [PMID: 22969361 PMCID: PMC3435990 DOI: 10.3390/s120607576] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/28/2012] [Accepted: 05/31/2012] [Indexed: 11/18/2022]
Abstract
The analysis of a microRNA (miRNA), miR-222 isolated from the PC12 cell line, was performed by use of the ribonuclease (RNase) protection assay, cyanine 5 (Cy5)-labeled miR-222 riboprobe, and a Hitachi SV1210 microchip electrophoresis system, which can be used to evaluate the integrity of total RNA. The fluorescence intensity corresponding to the protected RNA fragment increased in a dose-dependent manner with respect to the complementary-strand RNA. More highly sensitive detection of miRNA by microchip electrophoresis than by conventional method using fluorescence-labeled riboprobe could be obtained in 180 s. An obvious increase in miR-222 expression induced by nerve growth factor in PC12 cells could be observed. These results clearly indicate the potential of microchip electrophoresis for the analysis of miRNA using RNase protection assay with a fluorescence-labeled riboprobe.
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Affiliation(s)
- Shohei Yamamura
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; E-Mails: (S.Y.); (S.Y.); (Y.Y.); (K.A.)
| | - Shouki Yatsushiro
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; E-Mails: (S.Y.); (S.Y.); (Y.Y.); (K.A.)
| | - Yuka Yamaguchi
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; E-Mails: (S.Y.); (S.Y.); (Y.Y.); (K.A.)
| | - Kaori Abe
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; E-Mails: (S.Y.); (S.Y.); (Y.Y.); (K.A.)
| | - Yasuo Shinohara
- Division of Protein Expression, Institute for Genome Research, University of Tokushima, Kuramoto 3-18-15, Tokushima 770-8503, Japan; E-Mail:
| | - Masatoshi Kataoka
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; E-Mails: (S.Y.); (S.Y.); (Y.Y.); (K.A.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-87-869-3576; Fax: +81-87-869-3551
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13
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Brockman J, Gibbs PM, Polenakovik H, Gandhi D, Walusimbi M. Acute appendicitis due to Malassezia restricta. Mycoses 2011; 55:e13-4. [PMID: 21797936 DOI: 10.1111/j.1439-0507.2011.02070.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Hou Z, Fu J, Li S. A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences. Mol Phylogenet Evol 2007; 45:596-611. [PMID: 17686635 DOI: 10.1016/j.ympev.2007.06.006] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 05/10/2007] [Accepted: 06/11/2007] [Indexed: 10/23/2022]
Abstract
A phylogeny of the genus Gammarus Fabricius, 1775 was constructed using DNA sequence data from the mitochondrial genes COI and 16S, and the nuclear genes 18S and 28S. Both parsimony and Bayesian analyses were conducted on separate and combined data partitions. The Bayesian phylogeny from the combined analysis was selected as the preferred phylogenetic hypothesis. The hypothesis supports monophyly of the genus Gammarus, paraphyly of the European-North American Gammarus, and monophyly of the Asian Gammarus. The Asian clade was further split into a southeastern group and a northwestern group. The dramatic climate change following the uplift of the Tibetan Plateau was probably the most important factor in triggering the diversification of southeastern and northwestern groups. The genus Sinogammarus is invalid and should be part of the genus Gammarus.
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MESH Headings
- Amphipoda/classification
- Amphipoda/genetics
- Animals
- Cell Nucleus/genetics
- Electron Transport Complex IV/analysis
- Electron Transport Complex IV/genetics
- Europe
- Evolution, Molecular
- Genes, Mitochondrial
- Genetic Speciation
- North America
- Phylogeny
- Protein Subunits/analysis
- Protein Subunits/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 28S/analysis
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
- Time Factors
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Affiliation(s)
- Zhonge Hou
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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15
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Mejía O, Zúñiga G. Phylogeny of the three brown banded land snail genus Humboldtiana (Pulmonata: Humboldtianidae). Mol Phylogenet Evol 2007; 45:587-95. [PMID: 17728155 DOI: 10.1016/j.ympev.2007.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 05/16/2007] [Accepted: 07/09/2007] [Indexed: 11/19/2022]
Abstract
The three brown banded land snail genus Humboldtiana (Pulmonata: Humboldtianidae) comprises 50 species of insular distribution from southern Texas to central México; its low vagility and dispersal potential are reflected in high levels of endemism and highly restricted distributions. A current scheme of classification recognizes six subgenera: Polyomphala, Oreades, Gymnopallax, Clydonacme, Aglotrochus, and Humboldtiana (the latter containing three species groups). In the present work, mitochondrial 16S rDNA and partial ITS region and ribosomal large subunit (5.8S+ITS-2+28S) sequences from 26 recognized species and 2 populations of unknown identity were studied to assess phylogenetic relationships of Humboldtiana species using parsimony and Bayesian analysis, and AU test was used to compare the different phylogenetic hypotheses. The same four major clades were recovered by both methods (buffoniana, queretaroana, montezumae and fortis), although none of them support the current scheme of classification, with the only exception being the subgenus Gymnopallax included in the clade buffoniana. The results suggest that speciation patterns observed in the genus Humboldtiana could be explained as a morphostatic radiation.
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Affiliation(s)
- Omar Mejía
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas-IPN, Prolongación de Carpio y Plan de Ayala s/n, Delegación Miguel Hidalgo, C.P. 11340 México DF, Mexico.
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16
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Eklöf J, Pleijel F, Sundberg P. Phylogeny of benthic Phyllodocidae (Polychaeta) based on morphological and molecular data. Mol Phylogenet Evol 2007; 45:261-71. [PMID: 17560800 DOI: 10.1016/j.ympev.2007.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 03/14/2007] [Accepted: 04/17/2007] [Indexed: 10/23/2022]
Abstract
A combined molecular (18S rDNA, 28S rDNA, 16S rDNA and COI) and morphological analysis of the benthic phyllodocids is presented for the first time. Nineteen phyllodocids and two outgroup taxa are assessed using parsimony, maximum likelihood and Bayesian analyses. We demonstrate high degrees in homoplasy in the traditionally used morphological phyllodocid characters, and show that all the three current subfamilies Phyllodocinae, Eteoninae and Notophyllinae are non-monophyletic. The genera Eulalia, Eumida, Protomystides, Pseudomystides, Pterocirrus and Sige form a well-supported group, as does Mystides and Nereiphylla. Another clade with strong support includes Eteone and Paranaitis, although with Eteone nested within a paraphyletic Paranaitis. The relationship between these two taxa indicate that the unusual arrangement of modified cirri on the first segments in Eteone is due to a fusion of segment 1 and 2 where the cirri of segment 1 have been reduced. Eulalia is non-monophyletic and should be split, minimally into two groups. Our results are ambiguous regarding the ancestral phyllodocid condition of absence-presence of median antenna or nuchal papilla and uniramous or biramous parapodia, but shows that the absence of cirri on segment 3 (previously an apomorphy, for e.g., Mystides, Pseudomystides and Hesionura) is maximally homoplastic.
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MESH Headings
- Animals
- Electron Transport Complex IV/analysis
- Electron Transport Complex IV/genetics
- Phylogeny
- Polychaeta/anatomy & histology
- Polychaeta/classification
- Polychaeta/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 28S/analysis
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Jenny Eklöf
- Department of Zoology, University of Göteborg, P.O. Box 463, SE-405 30 Göteborg, Sweden.
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17
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Blanquer A, Uriz MJ. Cryptic speciation in marine sponges evidenced by mitochondrial and nuclear genes: A phylogenetic approach. Mol Phylogenet Evol 2007; 45:392-7. [PMID: 17434762 DOI: 10.1016/j.ympev.2007.03.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 02/13/2007] [Accepted: 03/02/2007] [Indexed: 10/23/2022]
Affiliation(s)
- Andrea Blanquer
- Centre d'Estudis Avançats de Blanes-CSIC, c/ Accés cala St Francesc, 14 17300 Blanes-Girona, Spain.
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18
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Monaghan MT, Inward DJG, Hunt T, Vogler AP. A molecular phylogenetic analysis of the Scarabaeinae (dung beetles). Mol Phylogenet Evol 2007; 45:674-92. [PMID: 17656114 DOI: 10.1016/j.ympev.2007.06.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 06/06/2007] [Accepted: 06/12/2007] [Indexed: 10/23/2022]
Abstract
The dung beetles (Scarabaeinae) include ca. 5000 species and exhibit a diverse array of morphologies and behaviors. This variation presumably reflects the adaptation to a diversity of food types and the different strategies used to avoid competition for vertebrate dung, which is the primary breeding environment for most species. The current classification gives great weight to the major behavioral types, separating the ball rollers and the tunnelers, but existing phylogenetic studies have been based on limited taxonomic or biogeographic sampling and have been contradictory. Here, we present a molecular phylogenetic analysis of 214 species of Scarabaeinae, representing all 12 traditionally recognized tribes and six biogeographical regions, using partial gene sequences from one nuclear (28S) and two mitochondrial (cox1, rrnL) genes. Length variation in 28S (588-621 bp) and rrnL (514-523 bp) was subjected to a thorough evaluation of alternative alignments, gap-coding methods, and tree searches using model-based (Bayesian and likelihood), maximum parsimony, and direct optimization analyses. The small-bodied, non-dung-feeding Sarophorus+Coptorhina were basal in all reconstructions. These were closely related to rolling Odontoloma+Dicranocara, suggesting an early acquisition of rolling behavior. Smaller tribes and most genera were monophyletic, while Canthonini and Dichotomiini each consisted of multiple paraphyletic lineages at hierarchical levels equivalent to the smaller tribes. Plasticity of rolling and tunneling was evidenced by a lack of monophyly (S-H test, p > 0.05) and several reversals within clades. The majority of previously unrecognized clades were geographical, including the well-supported Neotropical Phanaeini+Eucraniini, and a large Australian clade of rollers as well as tunneling Coptodactyla and Demarziella. Only three lineages, Gymnopleurini, Copris+Microcopris and Onthophagus, were widespread and therefore appear to be dispersive at a global scale. A reconstruction of biogeographical characters recovered 38-48 transitions between regions and an African origin for most lineages. Dispersal-vicariance analysis supported an African origin with links to all other regions and little back-migration. Our results provide a new synthesis of global-scale dung beetle evolution, demonstrating the great plasticity of behavioral and morphological traits and the importance of biogeographic distributions as the basis for a new classification.
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Affiliation(s)
- Michael T Monaghan
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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19
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Petersen FT, Meier R, Kutty SN, Wiegmann BM. The phylogeny and evolution of host choice in the Hippoboscoidea (Diptera) as reconstructed using four molecular markers. Mol Phylogenet Evol 2007; 45:111-22. [PMID: 17583536 DOI: 10.1016/j.ympev.2007.04.023] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 04/26/2007] [Accepted: 04/27/2007] [Indexed: 10/23/2022]
Abstract
Hippoboscoidea is a superfamily of Diptera that contains the Glossinidae or tsetse flies, the Hippoboscidae or louse flies, and two families of bat flies, the Streblidae and the Nycteribiidae. We reconstruct the phylogenetic relationships within Hippoboscoidea using maximum parsimony and Bayesian methods based on nucleotide sequences from fragments of four genes: nuclear 28S ribosomal DNA and the CPSase domain of CAD, and mitochondrial 16S rDNA and cytochrome oxidase I. We recover monophyly for most of the presently recognized groups within Hippoboscoidea including the superfamily as a whole, the Hippoboscidae, the Nycteribiidae, the bat flies, and the Pupipara (=Hippoboscidae+Nycteribiidae+Streblidae), as well as several subfamilies within the constituent families. Streblidae appear to be paraphyletic. Our phylogenetic hypothesis is well supported and decisive in that most competing topological hypotheses for the Hippoboscoidea require significantly longer trees. We confirm a single shift from a free-living fly to a blood-feeding ectoparasite of vertebrates and demonstrate that at least two host shifts from mammals to birds have occurred. Wings have been repeatedly lost, but never regained. The hippoboscoid ancestor also evolved adenotrophic viviparity and our cladogram is consistent with a gradual reduction in the motility of the deposited final instar larvae from active burrowing in the soil to true pupiparity where adult females glue the puparium within the confines of bat roosts.
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MESH Headings
- Animals
- Aspartate Carbamoyltransferase/analysis
- Aspartate Carbamoyltransferase/genetics
- Biomarkers/analysis
- Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/analysis
- Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/genetics
- Dihydroorotase/analysis
- Dihydroorotase/genetics
- Diptera/classification
- Diptera/genetics
- Electron Transport Complex IV/analysis
- Electron Transport Complex IV/genetics
- Evolution, Molecular
- Phylogeny
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 28S/analysis
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Frederik Torp Petersen
- Zoological Museum, University of Copenhagen, Universitetsparken 15, DK - 2100 Copenhagen Ø, Denmark
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20
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Amato A, Kooistra WHCF, Ghiron JHL, Mann DG, Pröschold T, Montresor M. Reproductive isolation among sympatric cryptic species in marine diatoms. Protist 2006; 158:193-207. [PMID: 17145201 DOI: 10.1016/j.protis.2006.10.001] [Citation(s) in RCA: 204] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Accepted: 10/01/2006] [Indexed: 11/22/2022]
Abstract
Pseudo-nitzschia is a marine cosmopolitan genus of chain-forming planktonic diatoms. As for the vast majority of phytoplankton organisms, species identification within this genus mostly relies upon morphological features. Taxa were initially identified based on cell shape and gross morphology of their composite silica cell wall, called the frustule. Yet, observations of the frustule in electron microscopy showed many additional characters for species identification and results of molecular studies have demonstrated that genetically distinct groups might exist within morpho-species. However, these studies have not addressed the biological meaning of these genetic differences. Here, we bridge that gap by comparing ultrastructural features and sequence data (three ribosomal and one plastid marker) of 95 strains with results of mating experiments among these strains. Experiments were performed on two morphologically distinct entities: P. delicatissima and P. pseudodelicatissima. Each of the two entities consisted of multiple genetically distinct and reproductively isolated taxa, all occurring in sympatry: P. delicatissima was composed of three phylogenetic and reproductively distinct groups, whereas P. pseudodelicatissima consisted of up to five. Once these taxa had been defined both genetically and biologically, subtle ultrastructural differences could be detected as well. Our findings not only show that cryptic genetic variants abound in sympatry, but also that they are reproductively isolated and, therefore, biologically distinct units.
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Affiliation(s)
- Alberto Amato
- Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Napoli, Italy.
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21
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Goldsmith JG, Ntuen EC, Goldsmith. EC. Direct quantification of gene expression using capillary electrophoresis with laser-induced fluorescence. Anal Biochem 2006; 360:23-9. [PMID: 17113023 PMCID: PMC1829314 DOI: 10.1016/j.ab.2006.10.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 10/03/2006] [Accepted: 10/12/2006] [Indexed: 10/24/2022]
Abstract
Quantification of gene expression provides valuable information regarding the response of cells or tissue to stimuli and often is accomplished by monitoring the level of messenger RNA (mRNA) being transcribed for a particular protein. Although numerous methods are commonly used to monitor gene expression, including Northern blotting, real-time polymerase chain reaction, and RNase protection assay, each method has its own drawbacks and limitations. Capillary electrophoresis with laser-induced fluorescence (CE-LIF) can reduce protocol time, eliminate the need for radioactivity, and provide superior sensitivity and dynamic range for quantification of RNA. In addition, CE-LIF can be used to directly determine the amount of an RNA species present, something that is difficult and not normally accomplished using current methods. Gene expression is detected using a fluorescently labeled riboprobe specific for a given RNA species. This direct approach was validated by analyzing levels of 28S RNA and also used to determine the amount of discoidin domain receptor 2 mRNA in cardiac tissue.
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Affiliation(s)
- Jack G. Goldsmith
- Department of Chemistry, University of South Carolina Aiken, Aiken, SC 29801
| | - Edidiong C. Ntuen
- Department of Cell and Developmental Biology & Anatomy, University of South Carolina, Columbia, SC 29209
| | - Edie C. Goldsmith.
- Department of Cell and Developmental Biology & Anatomy, University of South Carolina, Columbia, SC 29209
- Corresponding Author: Edie C. Goldsmith, Department of Cell and Developmental Biology & Anatomy, University of South Carolina, Columbia, SC 29209,
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22
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Singh R, Gupta V, Chakarborty A, Nijhawan R, Arora S, Gupta A. Fungal endophthalmitis complicating subconjunctival injection of triamcinolone acetonide in anterior scleritis. ACTA ACUST UNITED AC 2006; 38:253-6. [PMID: 17416964 DOI: 10.1007/s12009-006-0015-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 11/30/1999] [Accepted: 06/29/2006] [Indexed: 10/23/2022]
Abstract
Fungal endophthalmitis following subconjunctival triamcinolone acetonide in anterior scleritis is a rare complication. Two patients with anterior scleritis, who received subconjunctival injection of triamcinolone developed fungal endophthalmitis. Both patients were positive by smear and polymerase chain reaction for 28S ribosomal RNA gene for fungus. Colletotrichum dematium was identified in one patient. Both patients responded well to pars plana vitrectomy and antifungal therapy.
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Affiliation(s)
- Ramandeep Singh
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research Postgraduate Institute of Medical Education and Research, Chandigarh, India
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23
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Dohrmann M, Voigt O, Erpenbeck D, Wörheide G. Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA. Mol Phylogenet Evol 2006; 40:830-43. [PMID: 16762568 DOI: 10.1016/j.ympev.2006.04.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 03/21/2006] [Accepted: 04/04/2006] [Indexed: 10/24/2022]
Abstract
Calcareous sponges (Porifera, Calcarea) play an important role for our understanding of early metazoan evolution, since several molecular studies suggested their closer relationship to Eumetazoa than to the other two sponge 'classes,' Demospongiae and Hexactinellida. The division of Calcarea into the subtaxa Calcinea and Calcaronea is well established by now, but their internal relationships remain largely unresolved. Here, we estimate phylogenetic relationships within Calcarea in a Bayesian framework, using full-length 18S and partial 28S ribosomal DNA sequences. Both genes were analyzed separately and in combination and were further partitioned by stem and loop regions, the former being modelled to take non-independence of paired sites into account. By substantially increasing taxon sampling, we show that most of the traditionally recognized supraspecific taxa within Calcinea and Calcaronea are not monophyletic, challenging the existing classification system, while monophyly of Calcinea and Calcaronea is again highly supported.
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Affiliation(s)
- Martin Dohrmann
- Department of Geobiology, Geoscience Centre Göttingen, Goldschmidtstr. 3, D-37077 Göttingen, Germany
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24
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Mallatt J, Giribet G. Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. Mol Phylogenet Evol 2006; 40:772-94. [PMID: 16781168 DOI: 10.1016/j.ympev.2006.04.021] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 02/28/2006] [Accepted: 04/03/2006] [Indexed: 10/24/2022]
Abstract
This work expands on a study from 2004 by Mallatt, Garey, and Shultz [Mallatt, J.M., Garey, J.R., Shultz, J.W., 2004. Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 31, 178-191] that evaluated the phylogenetic relationships in Ecdysozoa (molting animals), especially arthropods. Here, the number of rRNA gene-sequences was effectively doubled for each major group of arthropods, and sequences from the phylum Kinorhyncha (mud dragons) were also included, bringing the number of ecdysozoan taxa to over 80. The methods emphasized maximum likelihood, Bayesian inference and statistical testing with parametric bootstrapping, but also included parsimony and minimum evolution. Prominent findings from our combined analysis of both genes are as follows. The fundamental subdivisions of Hexapoda (insects and relatives) are Insecta and Entognatha, with the latter consisting of collembolans (springtails) and a clade of proturans plus diplurans. Our rRNA-gene data provide the strongest evidence to date that the sister group of Hexapoda is Branchiopoda (fairy shrimps, tadpole shrimps, etc.), not Malacostraca. The large, Pancrustacea clade (hexapods within a paraphyletic Crustacea) divided into a few basic subclades: hexapods plus branchiopods; cirripedes (barnacles) plus malacostracans (lobsters, crabs, true shrimps, isopods, etc.); and the basally located clades of (a) ostracods (seed shrimps) and (b) branchiurans (fish lice) plus the bizarre pentastomids (tongue worms). These findings about Pancrustacea agree with a recent study by Regier, Shultz, and Kambic that used entirely different genes [Regier, J.C., Shultz, J.W., Kambic, R.E., 2005a. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc. R. Soc. B 272, 395-401]. In Malacostraca, the stomatopod (mantis shrimp) was not at the base of the eumalacostracans, as is widely claimed, but grouped instead with an euphausiacean (krill). Within centipedes, Craterostigmus was the sister to all other pleurostigmophorans, contrary to the consensus view. Our trees also united myriapods (millipedes and centipedes) with chelicerates (horseshoe crabs, spiders, scorpions, and relatives) and united pycnogonids (sea spiders) with chelicerates, but with much less support than in the previous rRNA-gene study. Finally, kinorhynchs joined priapulans (penis worms) at the base of Ecdysozoa.
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Affiliation(s)
- Jon Mallatt
- School of Biological Sciences, Washington State University, Pullman, 99164-4236, USA.
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25
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Fleige S, Walf V, Huch S, Prgomet C, Sehm J, Pfaffl MW. Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR. Biotechnol Lett 2006; 28:1601-13. [PMID: 16900335 DOI: 10.1007/s10529-006-9127-2] [Citation(s) in RCA: 430] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 06/06/2006] [Indexed: 01/08/2023]
Abstract
Relative quantification in quantitative real-time RT-PCR is increasingly used to quantify gene expression changes. In general, two different relative mRNA quantification models exist: the delta-delta Ct and the efficiency-corrected Ct model. Both models have their advantages and disadvantages in terms of simplification on the one hand and efficiency correction on the other. The particular problem of RNA integrity and its effect on relative quantification in qRT-PCR performance was tested in different bovine tissues and cell lines (n = 11). Therefore different artificial and standardized RNA degradation levels were used. Currently fully automated capillary electrophoresis systems have become the new standard in RNA quality assessment. RNA quality was rated according the RNA integrity number (RIN). Furthermore, the effect of different length of amplified products and RNA integrity on expression analyses was investigated. We found significant impact of RNA integrity on relative expression results, mainly on cycle threshold (Ct) values and a minor effect on PCR efficiency. To minimize the interference of RNA integrity on relative quantification models, we can recommend to normalize gene expression by an internal reference gene and to perform an efficiency correction. Results demonstrate that innovative new quantification methods and normalization models can improve future mRNA quantification.
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Affiliation(s)
- Simone Fleige
- Physiology Weihenstephan, Center of Life and Food Sciences (ZIEL), Technical University Munich, Germany
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26
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Abstract
The addition of poly(A)-tails to RNA is a process common to almost all organisms. In eukaryotes, stable poly(A)-tails, important for mRNA stability and translation initiation, are added to the 3′ ends of most nuclear-encoded mRNAs, but not to rRNAs. Contrarily, in prokaryotes and organelles, polyadenylation stimulates RNA degradation. Recently, polyadenylation of nuclear-encoded transcripts in yeast was reported to promote RNA degradation, demonstrating that polyadenylation can play a double-edged role for RNA of nuclear origin. Here we asked whether in human cells ribosomal RNA can undergo polyadenylation. Using both molecular and bioinformatic approaches, we detected non-abundant polyadenylated transcripts of the 18S and 28S rRNAs. Interestingly, many of the post-transcriptionally added tails were composed of heteropolymeric poly(A)-rich sequences containing the other nucleotides in addition to adenosine. These polyadenylated RNA fragments are most likely degradation intermediates, as primer extension (PE) analysis revealed the presence of distal fragmented molecules, some of which matched the polyadenylation sites of the proximal cleavage products revealed by oligo(dT) and circled RT–PCR. These results suggest the presence of a mechanism to degrade ribosomal RNAs in human cells, that possibly initiates with endonucleolytic cleavages and involves the addition of poly(A) or poly(A)-rich tails to truncated transcripts, similar to that which operates in prokaryotes and organelles.
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MESH Headings
- Cell Line, Tumor
- Expressed Sequence Tags
- Humans
- Oligonucleotide Probes
- Poly A/analysis
- Polyadenylation
- RNA Stability
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/analysis
- RNA, Ribosomal, 28S/chemistry
- RNA, Ribosomal, 28S/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
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Affiliation(s)
| | - David Laufer
- Department of Computer Science, Technion—Israel Institute of TechnologyHaifa 32000, Israel
| | - Dan Geiger
- Department of Computer Science, Technion—Israel Institute of TechnologyHaifa 32000, Israel
| | - Gadi Schuster
- To whom correspondence should be addressed. Tel: 972 4 8293171; Fax: 972 4 8295587;
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27
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Denz CR, Dube DK. The benefits of 28S rRNA for standardization of reverse transcription-polymerase chain reaction for studying gene expression. Anal Biochem 2005; 341:382-4. [PMID: 15907888 DOI: 10.1016/j.ab.2005.01.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Indexed: 11/25/2022]
Affiliation(s)
- Christopher R Denz
- Department of Medicine, Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
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28
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Campbell J, Volkmann-Kohlmeyer B, Gräfenhan T, Spatafora JW, Kohlmeyer J. A re-evaluation of Lulworthiales: relationships based on 18S and 28S rDNA. ACTA ACUST UNITED AC 2005; 109:556-68. [PMID: 16018310 DOI: 10.1017/s0953756205002716] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Lulworthiales consists of four genera: three that were removed from the Halosphaeriales, namely Lulworthia, Lindra, and Kohlmeyeriella; and Spathulospora, reassigned from the Spathulosporales. However, studies have shown that neither Lulworthia nor Lindra are monophyletic genera. This study was therefore undertaken to re-evaluate the genera of the Lulworthiales based on the SSU and LSU rDNA genes. Taxonomic revisions are proposed here for Lulworthia crassa, L. lignoarenaria, L. uniseptata and Lindra marinera: Lulworthia crassa is transferred into the genus Kohlmeyeriella; Lulwoidea gen. nov. is established for L. lignoarenaria; Lulwoana gen. nov. is established for L. uniseptata; and Lindra marinera is reduced to synonymy with L. thalassiae. Taxonomic descriptions are emended for the genus Lulworthia s. str., and for L. grandispora and Lindra thalassiae. A neotype is designated for Lulworthia grandispora.
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Affiliation(s)
- Jinx Campbell
- Department of Coastal Sciences, University of Southern Mississippi, 703 East Beach Drive, Ocean Springs, Mississippi 39564, USA.
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29
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Burbach GJ, Dehn D, Nagel B, Del Turco D, Deller T. Laser microdissection of immunolabeled astrocytes allows quantification of astrocytic gene expression. J Neurosci Methods 2004; 138:141-8. [PMID: 15325122 DOI: 10.1016/j.jneumeth.2004.03.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Revised: 03/29/2004] [Accepted: 03/30/2004] [Indexed: 10/26/2022]
Abstract
Astrocytes represent the major glial cell population within the central nervous system. In order to elucidate the function of astrocytes under physiological conditions and during the course of neurological disease, astrocytic gene expression profiling is necessary. However, since astrocytes form an intimately connected network with neurons and other cell types in the brain, gene expression analysis of astrocytes with a sufficient degree of cellular specificity is difficult. Here we are presenting a rapid and, thus, RNA preserving immunostaining protocol for the detection of astrocytes in rodent brain. This protocol can readily be combined with laser microdissection (Leica AS LMD platform) and quantitative RT-PCR (qPCR). Employing this method, we studied changes in glial fibrillary acidic protein (GFAP) expression in astrocytes of mouse entorhinal cortex following entorhinal cortex lesion. Using laser microdissection, astrocytes (n = 60) were collected in the tissue surrounding the lesion, the entorhinal cortex contralateral to the lesion, and in unlesioned control animals. Changes in GFAP mRNA were quantified using qPCR. GFAP mRNA levels were 82-fold higher in astrocytes of lesioned animals at the site of the lesion compared to GFAP mRNA levels in entorhinal cortex astrocytes of control mice. GFAP mRNA levels were only slightly elevated at the contralateral side (lesioned animals). This optimized protocol for immunolabeling and laser microdissection of astrocytes followed by qPCR allows quantification of astrocytic gene expression levels with a high degree of cellular specificity. It may similarly be employed in different settings where other cell types need to be identified and microdissected for gene expression profiling.
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Affiliation(s)
- Guido J Burbach
- Institute of Clinical Neuroanatomy, Johann Wolfgang Goethe-University, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
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30
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Duan Y, Kerdelhué C, Ye H, Lieutier F. Genetic study of the forest pest Tomicus piniperda (Col., Scolytinae) in Yunnan province (China) compared to Europe: new insights for the systematics and evolution of the genus Tomicus. Heredity (Edinb) 2004; 93:416-22. [PMID: 15280894 DOI: 10.1038/sj.hdy.6800518] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The pine shoot beetle Tomicus piniperda is present throughout Eurasia. In Europe, it is considered as a secondary pest that rarely causes tree mortality, while heavy damage is observed in Yunnan Province (China) where it exhibits a novel aggregative behaviour during shoot attack. To understand why the ecological characteristics of the European and Chinese populations differ so strongly, we conducted an analysis of population genetic structure on 12 populations in Yunnan and one in JiLin using mitochondrial (COI-COII) and nuclear (ITS2 and 28S rDNA) DNA sequences, and compared the results to those obtained in France. We showed that the Yunnan populations differed markedly from French and JiLin populations. For all three markers, the genetic distances measured between the Tomicus from Yunnan and those from France were similar to distances previously observed between species. Similar distances were found between Yunnan and JiLin populations. Conversely, the distances between French and JiLin individuals were substantially lower, falling in the intraspecific range. We concluded that the individuals sampled in Yunnan belong to a new, undescribed species (Tomicus sp. nov.). We also showed that some individuals belong to the species T. brevipilosus that had never been recorded from this region before. Evolution of the genus Tomicus is discussed in the light of these new results.
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MESH Headings
- Animals
- Cell Nucleus
- China
- Coleoptera/classification
- Coleoptera/genetics
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/genetics
- DNA, Ribosomal Spacer/analysis
- DNA, Ribosomal Spacer/genetics
- Europe
- Evolution, Molecular
- Genetic Variation/genetics
- Genetics, Population
- Host-Parasite Interactions/genetics
- Phylogeny
- RNA, Ribosomal, 28S/analysis
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
- Trees
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Affiliation(s)
- Y Duan
- INRA, Zoologie forestière, BP 20619 Ardon, F-45166 Olivet cedex, France
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31
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Kimura T, Kosaka J, Nomura T, Yamada T, Miki Y, Takagi K, Kogami T, Sasaki J. Quantification of in situ hybridization signals in rat testes. J Histochem Cytochem 2004; 52:813-20. [PMID: 15150290 DOI: 10.1369/jhc.4a6249.2004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We performed basic research into quantifying in situ hybridization (ISH) signals in rat testis, a suitable organ for the quantification because germ cells undergo synchronized development and show stage-specific gene expression. In this model experiment, rRNA was selected as the hybridizable RNA in paraffin sections. Specimens fixed with Bouin's fixative and hybridized with digoxygenin-labeled probes could easily be analyzed quantitatively through "posterization" of the images. The amount of rRNA hybridized with the probe was greatest in early primary spermatocytes, followed by pachytene primary spermatocytes, then diplotene spermatocytes, and finally by secondary spermatocytes and spermatids. The amounts reached low levels in metaphase, anaphase, and telophase of meiotic division and early step 1 spermatids, and then slightly increased during spermiogenesis. ISH rRNA staining was a useful parameter for evaluation of the quantitative analysis of mRNA and the levels of hybridizable RNA in tissue sections.
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Affiliation(s)
- Touji Kimura
- Department of Cytology and Histology, Okayama University Graduate School of Medicine and Dentistry, Okayama, Japan
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32
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Abstract
Development of methods based on determining expression of individual genes resulted in the need for large amounts of high quality RNA preparations. It is widely accepted that in intact rRNA the 28S and 18S band ratio must be 2:1. It is not quite clear what is the main cause of lower rRNA bands intensity ratio. It is difficult to isolate RNA with 2:1 28S/18S ratio from RNase-rich and some tumor tissues. At the same time this requirement may be excessive and RNA preparations with lower 28S/18S rRNA ratio may be quite adequate for most techniques of determining gene expression. As demonstrated in this study, the level of a particular RNA may be reliably determined by RT-PCR even in a total RNA that is usually considered as degraded (28S to 18S ratio as low as 0.4), provided that random primer is used in RT. In contrast, the use of the oligo(dT) primer in RT-PCR may lead to underestimation of specific mRNA level in the degraded RNA samples, depending on the distance of amplified fragment from the poly(A) end. A criterion based on average degradation level of a number of reference genes is suggested to discriminate specific RNA degradation from random and unspecific ones.
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Affiliation(s)
- Natalia A Skrypina
- Russian Cardiology Research and Development Center, 3rd Cherepkovskaya str, 15a, Moscow 121552, Russia.
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33
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Kim JJ, Lim YW, Wingfield MJ, Breuil C, Kim GH. Leptographium bistatum sp. nov., a new species with a Sporothrix synanamorph from Pinus radiata in Korea. ACTA ACUST UNITED AC 2004; 108:699-706. [PMID: 15323253 DOI: 10.1017/s0953756204000036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Radiata pine (Pinus radiata) lumber from Australia, Chile, and New Zealand is imported into Korea where it represents one of the most important sources of timber. Blue stain of this timber is a serious problem for which an integrated control strategy is being developed. One of the fungi that has been isolated from stained radiata pine sapwood in Korea is a Leptographium sp. that has a distinct Sporothrix synanamorph. The aim of this study was to classify this fungus. Morphological comparisons showed that this fungus is distinct from all other species of Leptographium and especially L. elegans and L. francke-grosmanniae that also have Sporothrix synanamorphs. Comparisons of sequence data for the ITS2 and part of the 28S rDNA genes as well as the beta-tubulin gene also confirmed that this fungus represents an undescribed taxon, described here as Leptographium bistatum sp. nov.
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Affiliation(s)
- Jae-Jin Kim
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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34
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de Chambrier A, Zehnder M, Vaucher C, Mariaux J. The evolution of the Proteocephalidea (Platyhelminthes, Eucestoda) based on an enlarged molecular phylogeny, with comments on their uterine development. Syst Parasitol 2004; 57:159-71. [PMID: 15010590 DOI: 10.1023/b:sypa.0000019083.26876.34] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We present a molecular phylogeny of the Proteocephalidea based on 28S rDNA sequence data that is a follow-up to the paper by Zehnder & Mariaux (1999). Twenty-three new sequences, including three outgroups are added in our new data-set. The Gangesiinae Mola, 1929 and the Acanthotaeniinae Freze, 1963 appear to be the most primitive clades. They are followed by a robust clade comprising the Palaearctic Proteocephalinae Mola, 1929 from freshwater fishes. The structure of the more derived clades, comprising most Neotropical and Nearctic species, is less resolved. At the nomenclatural level, we erect a new genus, Glanitaenia n. g. for G. osculata (Goeze, 1782) n. comb., previously Proteocephalus osculatus, and define an aggregate for the Palaearctic Proteocephalus Weinland, 1858. After a re-examination of all of the studied taxa, we identify two types of uterine development and show the importance of this character for the systematics of the order. Our phylogeny does not support the classical view of a Neotropical origin for the Proteocephalidea but rather favours an Old World origin of the group either in saurians or Palaearctic Siluriformes.
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Affiliation(s)
- Alain de Chambrier
- Département des Invertébrés, Muséum d'Histoire Naturelle, PO Box 6434, CH-1211 Geneva 6, Switzerland
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35
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Ninet B, Jan I, Bontems O, Léchenne B, Jousson O, Panizzon R, Lew D, Monod M. Identification of dermatophyte species by 28S ribosomal DNA sequencing with a commercial kit. J Clin Microbiol 2003; 41:826-30. [PMID: 12574293 PMCID: PMC149666 DOI: 10.1128/jcm.41.2.826-830.2003] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have shown that dermatophyte species can be easily identified on the basis of a DNA sequence encoding a part of the large-subunit (LSU) rRNA (28S rRNA) by using the MicroSeq D2 LSU rRNA Fungal Sequencing Kit. Two taxa causing distinct dermatophytoses were clearly distinguished among isolates of the Trichophyton mentagrophytes species complex.
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Affiliation(s)
- Béatrice Ninet
- Division des Maladies Infectieuses, Hôpital Cantonal Universitaire, 1211 Geneva
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36
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Kano R, Okayama T, Hamamoto M, Nagata T, Ohno K, Tsujimoto H, Nakayama H, Doi K, Fujiwara K, Hasegawa A. Isolation of Fusarium solani from a dog: identification by molecular analysis. Med Mycol 2002; 40:435-7. [PMID: 12230226 DOI: 10.1080/mmy.40.4.435.437] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A strain of Fusarium solani was isolated from a dog showing many cutaneous and submucosal nodules and pyogranulomatous kidney lesions. Clinical isolates from this systemic infection were identified using microscopic examination and confirmed by molecular analysis.
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Affiliation(s)
- R Kano
- Department of Pathology, Nihon University School of Veterinary Medicine, Fujisawa Kanagawa, Japan.
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37
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Abstract
When BALB/c mouse spleens were gently homogenized in saline, the resultant supernatant (without cells and tissue debris) contained significant amount of 28S and 18S ribosomal RNA, reaching up to 70% of the total spleen RNA. Haemoglobin assays indicated that less than 15% of the spleen cells were lysed during the homogenization process, indicating that the majority of the spleen 'supernatant RNA' was from the extracellular space of the organ rather than released by the splenocytes as a consequence of grinding. Quantitative RNA analysis showed that the ratio of spleen supernatant RNA/total RNA of BALB/c mice was inversely correlated with age (from approximately 70% at 3 weeks to 45% at 6 months), but that of BXSB mice (an animal model for systemic lupus erythematosus) remained at about 70% irrespective of age. Methyl Green-Pyronin Y staining of paraffin sections of mouse spleen revealed that extracellular RNA was distributed mainly in the sinuses of the organ. Culture supernatants of apoptotic splenocytes contained significant amounts of RNA, suggesting that the extracellular RNA in the spleen might have come from apoptotic lymphocytes. This is supported by the fact that 'thymus supernatant' also contained significant amount of RNA. A possible correlation between spleen extracellular RNA and autoimmune diseases is discussed.
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Affiliation(s)
- Wen-Pu Zhao
- Department of Immunology, Peking University Health Science Center, Peking University, Beijing 100083, China
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38
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Abstract
The locations of the 3' ends of RNAs in rat ribosome were studied by a fluorescence-labeling method combined with high hydrostatic pressure and agarose electrophoresis. Under physiological conditions, only the 3' ends of 28 S and 5.8 S RNA in 80 S ribosome could be labeled with a high sensitive fluorescent probe - fluorescein 5-thiosemicarbazide (FTSC), indicating that the 3' termini of 28 S and 5.8 S RNA were located on or near the surface of 80 S ribosome. The 3' terminus of 5 S RNA could be attacked by FTSC only in the case of the dissociation of the 80 S ribosome into two subunits induced by high salt concentration (1 M KCl) or at high hydrostatic pressure, showing that the 3' end of 5 S RNA was located on the interface of two subunits. However, no fluorescence-labeled 18 S RNA could be detected under all the conditions studied, suggesting that the 3' end of 18 S RNA was either located deeply inside ribosome or on the surface but protected by proteins. It was interesting to note that modifications of the 3' ends of ribosomal RNAs including oxidation with NaIO4, reduction with KBH4 and labeling with fluorescent probe did not destroy the translation activity of ribosome, indicating that the 3' ends of RNAs were not involved in the translation activity of ribosome.
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MESH Headings
- 3' Untranslated Regions/analysis
- Animals
- Cell-Free System/metabolism
- Electrophoresis, Agar Gel
- Fluorescent Dyes/chemistry
- Hydrostatic Pressure
- Kinetics
- Protein Biosynthesis
- RNA, Ribosomal/analysis
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 28S/analysis
- RNA, Ribosomal, 28S/chemistry
- RNA, Ribosomal, 5.8S/analysis
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5S/analysis
- Rats
- Rats, Inbred Strains
- Ribosomes/chemistry
- Ribosomes/metabolism
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Affiliation(s)
- X Gao
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences
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39
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Abstract
The performance of the computer program for phylogenetic analysis, POY, and its two implemented methods, "optimization alignment" and "fixed-states optimization," are explored for four data sets. Four gap costs are analyzed for every partition; some of the partitions (the 18S rRNA) are treated as a single fragment or in increasing fragments of 3, 10, and 30. Comparisons within and among methods are undertaken according to gap cost, number of fragments in which the sequences are divided, tree length, character congruence, topological congruence, primary homology statements, and computation time.
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Affiliation(s)
- G Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Black WC, Lanzaro GC. Distribution of genetic variation among chromosomal forms of Anopheles gambiae s.s: introgressive hybridization, adaptive inversions, or recent reproductive isolation? Insect Mol Biol 2001; 10:3-7. [PMID: 11240631 DOI: 10.1046/j.1365-2583.2001.00234.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A series of four papers in this issue explores the reproductive status of the five chromosomal forms of An. gambiae s.s. using molecular techniques to examine the variation among twelve different genes located throughout the An. gambiae s.s. genome. Results of these and previous studies are consistent with a hypothesis of at least partial barriers to gene flow between some chromosomal forms in the Ivory Coast and other West African countries to the north and west, but introgression between S and M types in Benin and countries to the east. Collectively, these studies indicate the need for a broader geographical sampling of An. gambiae s.s., increased research on mechanisms of prezygotic reproductive isolation and field-based studies of survival and fecundity in hybrids to test for postzygotic reproductive isolation.
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Affiliation(s)
- W C Black
- Department of Microbiology, Colorado State University, Fort Collins, CO 80523-1677, USA.
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Solanas M, Moral R, Escrich E. Unsuitability of using ribosomal RNA as loading control for Northern blot analyses related to the imbalance between messenger and ribosomal RNA content in rat mammary tumors. Anal Biochem 2001; 288:99-102. [PMID: 11141312 DOI: 10.1006/abio.2000.4889] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
MESH Headings
- Animals
- Blotting, Northern/methods
- Blotting, Northern/standards
- Gene Expression Regulation, Neoplastic
- Mammary Neoplasms, Experimental/genetics
- RNA, Messenger/analysis
- RNA, Ribosomal/analysis
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 28S/analysis
- Rats
- Reference Standards
- Reproducibility of Results
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Affiliation(s)
- M Solanas
- Department of Cellular Biology, Physiology and Immunology, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), 08193, Spain
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42
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Abstract
The ribosomal RNA (rRNA) genes are located in nucleolus during active transcription and are transcribed by RNA polymerase I. This group of genes is involved in transcription and translation processes which can modulate gene expression. The association between rRNA levels and aging has been reported. In the present study, we investigated the ratio of mature rRNA 28S and 18S in peripheral blood of 15 Alzheimer's disease (AD) patients, 15 elderly healthy controls and 15 healthy young controls. Our results showed a statistically significant decrease of the mature rRNA 28S/18S ratio in AD patients when compared with the elderly and young control groups. Thus we can suggest that there is a possible change in the transcriptional or maturation process or a preferential degradation of the 28S subunit in AD.
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Affiliation(s)
- A M da Silva
- Departamento de Morfologia, Disciplina de Genética, UNIFESP Escola Paulista de Medicina, Rua Botucatu, 740, Vila Clementino-CEP 04023-900, São Paulo, Brazil
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43
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Hui M, Ip M, Chan PK, Chin ML, Cheng AF. Rapid identification of medically important Candida to species level by polymerase chain reaction and single-strand conformational polymorphism. Diagn Microbiol Infect Dis 2000; 38:95-9. [PMID: 11035240 DOI: 10.1016/s0732-8893(00)00171-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Invasive fungal disease has taken a great toll on immunocompromised patients. With the emergence of fluconazole and amphotericin B resistance, the rapid identification of fungi to species level is of clinical relevance in guiding appropriate antifungal therapy. Among these opportunistic fungi, Candida species are the most commonly encountered. We had developed a molecular method utilizing single-strand conformational polymorphism (SSCP) to delineate different patterns on a 260-bp amplicon from the 28S rRNA gene from six medically important Candida species. The SSCP banding patterns obtained from a total of 52 isolates were sufficiently unique to allow distinction between the species, thus indicated a high level of specificity. This method of PCR-SSCP can provide a simple and specific method for the rapid identification of medically important Candida to species level.
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Affiliation(s)
- M Hui
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong, China.
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44
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Abstract
Several approaches are commonly used to normalize variations in RNA loading on Northern blots, including: ethidium bromide (EthBr) fluorescence of 18S or 28S rRNA or autoradiograms of radioactive probes hybridized with constitutively expressed RNAs such as elongation factor-1alpha (ELF), glyceraldehyde-3-phosphate dehydrogenase (G3PDH), actin, 18S or 28S rRNA, or others. However, in osteoarthritis (OA) the amount of total RNA changes significantly and none of these RNAs has been clearly demonstrated to be expressed at a constant level, so it is unclear if any of these approaches can be used reliably for normalizing RNA extracted from osteoarthritic cartilage. Total RNA was extracted from normal and osteoarthritic cartilage and assessed by EthBr fluorescence. RNA was then transferred to a nylon membrane hybridized with radioactive probes for ELF, G3PDH, Max, actin, and an oligo-dT probe. The autoradiographic signal across the six lanes of a gel was quantified by scanning densitometry. When compared on the basis of total RNA, the coefficient of variation was lowest for 28S ethidium bromide fluorescence and oligo-dT (approximately 7%), followed by 18S ethidium bromide fluorescence and G3PDH (approximately 13%). When these values were normalized to DNA concentration, the coefficient of variation exceeded 50% for all signals. Total RNA and the signals for 18S, 28S rRNA, and oligo-dT all correlated highly. These data indicate that osteoarthritic chondrocytes express similar ratios of mRNA to rRNA and mRNA to total RNA as do normal chondrocytes. Of all the "housekeeping" probes, G3PDH correlated best with the measurements of RNA. All of these "housekeeping" probes are expressed at greater levels by osteoarthritic chondrocytes when compared with normal chondrocytes. Thus, while G3PDH is satisfactory for evaluating the amount of RNA loaded, its level of expression is not the same in normal and osteoarthritic chondrocytes.
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Affiliation(s)
- J R Matyas
- Department of Anatomy and Pathology, McCaig Centre for Joint Injury and Arthritis Research, University af Calgary Health Sciences Centre, Alberta, Canada.
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45
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Mallon PW, Millar BC, Moore JE, Murphy PG, McClurg RB, Chew EW, Crowe MJ. Molecular identification of Acinetobacter sp. in a patient with culture-negative endocarditis. Clin Microbiol Infect 2000; 6:277-8. [PMID: 11168128 DOI: 10.1046/j.1469-0691.2000.00058-4.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- P W Mallon
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, Northern Ireland, UK
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46
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Affiliation(s)
- R L Eykholt
- Department of Pharmacology and Clinical Pharmacology, Faculty of Medical and Health Sciences, University of Auckland, New Zealand.
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47
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Bassy O, Jiménez-García LF, Echeverría OM, Vázquez-Nin GH, Díaz de la Espina SM. High resolution detection of rRNA and rDNA in plant nucleoli with different activities by in situ hybridization. Biol Cell 2000; 92:59-70. [PMID: 10761698 DOI: 10.1016/s0248-4900(00)88764-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the present work we perform in situ hybridization with probes to different stretches of rDNA and electron microscopy of nucleoli with different activities, to gain insight into the ultrastructural organization of transcription and processing in the plant nucleolus. The main ultrastructural nucleolar components: fibrillar centers (FC), dense fibrillar component (DFC), and granular component (GC), are arranged in different ways depending on nucleolar activity. Heterogeneous FCs containing RNP fibrils and nucleolar perichromatin granules are frequently seen in nucleoli in the process of activation. DNA-RNA in situ hybridization with biotinylated probes spanning different sequences of the rDNA unit followed by immunogold detection of biotin, demonstrated the localization of the ribosomal transcripts in DFC, mainly in the zones around the FCs, in GC, and in the periphery of pale FC. The internal region of the heterogeneous FCs is labeled only in cells in the process of activation of transcription after dormancy. The distribution of the U3 probe indicates that the processing of the rRNA takes place in the DFC and inside the heterogeneous FCs, in which transcription occurs. DNA-DNA hybridization demonstrates the presence of rDNA in the compact and extended chromatin located in the interior and at the periphery of FCs and in nucleolar associated chromatin. Our results support the view that the plant nucleolus has a highly dynamic morphological and functional organization composed of a bipartite domain formed by FCs surrounded by DFC, which is associated with rRNA transcription and processing, and the GC representing a store of preribosomal particles.
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Affiliation(s)
- O Bassy
- Dpto. Biología Vegetal, Centro Investigaciones Biológicas, C.S.I.C. Velázquez, Madrid, Spain
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Takahashi K, MacDonald D, Murayama Y, Kinane D. Cell synthesis, proliferation and apoptosis in human dental periapical lesions analysed by in situ hybridisation and immunohistochemistry. Oral Dis 1999; 5:313-20. [PMID: 10561720 DOI: 10.1111/j.1601-0825.1999.tb00096.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The role of structural and host defensive cells in periapical lesions has been assessed previously by morphometric and immunohistochemical studies. The aim of this study was to investigate the function of peri- apical cells by employing molecular techniques to estimate the cell synthetic activity, proliferation and apoptosis in these lesions. We specifically sought answers to the following questions. Which cells of the periapical lesions are quiescent or actively synthesising proteins? Do immune cells proliferate in this region in the same way as epithelial cells proliferate? Furthermore do cells in peri- apical lesions undergo apoptosis, and if so which cells exhibit this programmed cell death? MATERIALS Twenty-five periapical tissue samples (15 granulomas and 10 radicular cysts) were assessed. Poly-adenosine (poly (A)) RNA and ribosomal RNA (rRNA) bearing cells in formalin-fixed/paraffin-embedded peri- apical tissues were analysed by in situ hybridization (ISH) using digoxigenin-labelled oligo d (T) and 28S rRNA probes respectively in order to estimate cell synthetic activity. Furthermore, S-phase proliferating and cycling cells were examined by ISH using a histone probe and Ki-67 immunostaining so as to assess cellular proliferation. Mononuclear cells were further differentiated by immunohistochemistry (IHC) as T cells, B cells and macrophages. Apoptotic cells were determined by in situ end-labelling methodology for detecting fragmented DNA. RESULTS Poly (A) RNA (mostly messenger RNA) and 28S rRNA-expressing cells were detected in all samples. Plasma cells exhibited strongest staining for the two probes, with slight to moderate staining found in the epithelium, fibroblasts, macrophages, endothelial cells and lymphocytes, whereas almost all polymorphonuclear leucocytes (PMN) were negative for these probes. A few histone mRNA-expressing cells were detected in basal and suprabasal epithelial cells and mononuclear cells in 15/25 cases but their reactivity was weak. Ki-67 positive cells were found in all samples and their numbers were generally higher than histone mRNA positive cells. Apo- ptotic cells were detected in 23/25 cases and the majority of apoptotic cells were PMN which were engulfed by large cytophagocytic macrophages. CONCLUSION This study indicates that in dental periapical lesions, apoptosis occurs predominantly in PMN. It is evident that most cells apart from PMN are exhibiting synthetic activity but only epithelial cells undergo proliferation which implies that immune cells must proliferate at distant lymph nodes and travel to the periapical lesion rather than proliferating within the lesion. These results suggest considerable advantages in estimating gene expression within cells in addition to the immunohistochemical detection of cells to determine cell activity at inflamed sites. Clearly, functional cell synthetic activity, resolution and clearance systems operate in peri- apical cystic and granuloma lesions.
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Affiliation(s)
- K Takahashi
- Periodontology Unit, Glasgow Dental Hospital and School, Glasgow, Scotland, UK
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49
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Abstract
mRNA encoding histamine H1 and H2 receptors were detected in the human nasal mucosa using reverse transcriptase-polymerase chain reaction. The possibility of local release in connection with specific target receptors suggests a role for histamine in the regulation of vascular tone, glandular secretion and epithelial functions.
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MESH Headings
- Adult
- DNA Primers
- DNA, Complementary
- Electrophoresis, Agar Gel
- Epithelium/physiology
- Gene Expression Regulation
- Histamine/physiology
- Humans
- Nasal Mucosa/blood supply
- Nasal Mucosa/metabolism
- Polymerase Chain Reaction
- RNA, Messenger/analysis
- RNA, Ribosomal, 28S/analysis
- RNA-Directed DNA Polymerase
- Receptors, Histamine H1/analysis
- Receptors, Histamine H1/genetics
- Receptors, Histamine H2/analysis
- Receptors, Histamine H2/genetics
- Rhinitis/metabolism
- Rhinitis/pathology
- Sequence Analysis, DNA
- Vasomotor System/physiology
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Affiliation(s)
- R Uddman
- Department of Oto-rhino-laryngology, Malmö General Hospital, Sweden
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50
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Koulouri O, Lappin DF, Radvar M, Kinane DF. Cell division, synthetic capacity and apoptosis in periodontal lesions analysed by in situ hybridisation and immunohistochemistry. J Clin Periodontol 1999; 26:552-9. [PMID: 10450817 DOI: 10.1034/j.1600-051x.1999.260810.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this study, we investigated the synthetic and proliferative activity of infiltrating mononuclear cells in sections of granulation tissue from periodontitis lesions in both adult periodontitis (AP) and early onset periodontitis (EOP) patients. We also investigated the role of apoptosis in the remodelling of the inflamed tissue. We utilised a Ki-67 antigen specific antibody and a histone messenger RNA (mRNA) probe to detect cells undergoing cell division in the sections. Oligonucleotide probes for 28S ribosomal RNA and for the detection of poly A mRNA were utilised to detect cells with synthetic capacity. Apoptosis was determined using terminal transferase labelling of fragmented DNA with Biotin labelled dUTP. Biopsies of granulation tissue were obtained from 9 AP patients, from 10 EOP patients and for comparative purposes, biopsies of gingival tissue from 4 patients with AP. There were no differences regarding the relative proportions of cells with synthetic capacity or in the numbers of dividing cells in the periodontitis tissue sections. However, we observed an increase in the number of dividing cells in the AP granulation tissues compared to the AP gingival sections and that these cells were predominantly fibroblast like in appearance. Apoptotic cells consisted mainly of connective tissue cells; mainly fibroblasts with few if any leukocytes being apoptotic other than polymorphonuclear leukocytes. Only a few cyto-phagocytic macrophages were ever observed in the gingival and granulation tissues. We conclude that the turnover of infiltrating leukocytes in inflamed periodontal tissue is low, that they probably arrive at this site by recruitment from distant lymph nodes, and that neither cell division nor programmed cell death significantly alter the numbers of inflammatory cells. On the other hand, fibroblast apoptosis and cell division occur within the periodontium as these are typical processes in the normal turnover and remodelling of these tissues.
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Affiliation(s)
- O Koulouri
- Periodontology Unit, Glasgow Dental Hospital and School, Scotland, UK
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