118 results match your criteria 28s construct

Exploring the relationship of and (Blattodea, Blattidae, Blattinae) from a morphological and molecular perspective, including a description of four new species.

PeerJ 2021 13;9:e10618. Epub 2021 Jan 13.

College of Plant Protection, Southwest University, Chongqing, Beibei, China.

This study utilized six genes (, , , , and ) from a total of 40 samples to construct maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees in order to infer the relationships between the morphologically similar genera Stål, 1874 and Bey-Bienko, 1957. The phylogenetic analysis showed the two genera have a close relationship and were recovered as sister groups based on ML and BI analyses. Four new species are described among these samples, i. Read More

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January 2021

Phylogenetic Assignment of the Fungicolous (Ascomycota, Xylariales) and Investigation of its Secondary Metabolites.

Microorganisms 2020 Sep 11;8(9). Epub 2020 Sep 11.

Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany.

The ascomycete was described in 2014 as a fungicolous species growing on a member of its own genus, , which is considered a rare lifestyle in the Hypoxylaceae. This renders an interesting target in our efforts to find new bioactive secondary metabolites from members of the Xylariales. So far, only volatile organic compounds have been reported from , but no investigation of non-volatile compounds had been conducted. Read More

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September 2020

The human ribosomal protein eL29 binds in vivo to the cognate mRNA by interacting with its coding sequence, as revealed from in-cell cross-linking data.

Biochimie 2020 Oct 13;177:68-77. Epub 2020 Aug 13.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. Electronic address:

The balance of ribosomal proteins is important for the assembly of ribosomal subunits and cell viability. The synthesis of ribosomal proteins in a eukaryotic cell is controlled by various mechanisms, including autoregulation, which so far has been revealed for only a few of these proteins. We applied the photoactivatable 4-thiouridine-enhanced cross-linking and immunoprecipitation assay to HEK293T cells overproducing FLAG-labeled human ribosomal protein eL29 (eL29) to determine which RNAs other than rRNA interact with eL29. Read More

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October 2020

Characterization and phylogenomics of the complete mitochondrial genome of the polyzoic cestode (Platyhelminthes: Onchoproteocephalidea).

J Helminthol 2019 Jul 5;94:e58. Epub 2019 Jul 5.

Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.

The order Onchoproteocephalidea (Eucestoda) was recently erected to accommodate the hook-bearing tetraphyllideans and the proteocephalideans, which are characterized by internal proglottization and a tetra-acetabulate scolex. The recognized subfamilies in the Proteocephalidae appeared to be non-monophyletic based on 28S recombinant DNA (rDNA) sequence data. Other molecular markers with higher phylogenetic resolution, such as large mitochondrial DNA fragments and multiple genes, are obviously needed. Read More

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Structural basis for neutralization of cytotoxic abrin by monoclonal antibody D6F10.

FEBS J 2019 03 8;286(5):1003-1029. Epub 2019 Jan 8.

Department of Physics, Indian Institute of Science, Bengaluru, India.

Abrin, an extremely cytotoxic Type II ribosome-inactivating protein (RIP), is a potential bio-warfare agent. Abrin A-chain (ABA) depurinates an adenosine of sarcin-ricin loop (SRL) from eukaryotic 28S rRNA, thereby arresting protein synthesis and leading to cell death. Monoclonal antibody (mAb) D6F10 is the only known antibody that neutralizes ABA's activity in cell-free systems as well as abrin's toxicity in vitro and in vivo. Read More

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Molecular Characterization and Phylogeny of from in the Prairie Provinces of Canada.

J Nematol 2018 Sep 3;50(2):163-182. Epub 2018 Sep 3.

Department of Soil Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.

Ditylenchus weischeri that parasitizes the weed Cirsium arvense (L.) Scop., 1772, (creeping thistle) was described in 2011 from Russia based on their morphology, ITS-RFLP analysis, and Hsp 90 gene sequence of a few individuals and one field collection of the plant. Read More

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September 2018

Construction and characterization of the recombinant immunotoxin RTA-4D5-KDEL targeting HER2/neu-positive cancer cells and locating the endoplasmic reticulum.

Appl Microbiol Biotechnol 2018 Nov 24;102(22):9585-9594. Epub 2018 Aug 24.

State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.

The specific targeting of immunotoxins enables their wide application in cancer therapy. The A-chain of the ricin protein (RTA) is an N-glycosidase that catalyzes the removal of adenine from the 28S rRNA, preventing protein translation and leading to cell death. Ricin is highly toxic but can only exert its toxic effects from within the cytoplasm. Read More

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November 2018

Scytalidium candidum 3C is a new name for the Geotrichum candidum Link 3C strain.

J Basic Microbiol 2018 Oct 1;58(10):883-891. Epub 2018 Aug 1.

National Research Center «Kurchatov Institute», B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad Region, Russia.

In the 1970s, the strain Geotrichum candidum Link 3C was isolated from rotting rope and since then has been extensively studied as a source of cellulose and xylan-degrading enzymes. The original identification of the strain was based only on morphological characters of the fungal mycelium in culture. Recent comparison of the internal transcribed spacer (ITS) fragments derived from the draft genome published in 2015 did not show its similarity to G. Read More

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October 2018

Lost and found: the Bermudan Donadinia seaveri found in North America, with comments on its juniper associates.

Mycologia 2018 Jan-Feb;110(1):215-221

a Farlow Reference Library and Herbarium and the Department of Organismic and Evolutionary Biology , Harvard University , 22 Divinity Ave., Cambridge , Massachusetts 02138.

Collections of a species referred to Sarcosomataceae (Pezizomycetes) from eastern North America were studied both morphologically and using nuc rDNA internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2 = ITS) and approximately 800 bp from the 5' region of the nuc 28S rDNA (28S) to construct a phylogeny. The analyses indicate that these collections are Donadinia seaveri, a species previously known only from Bermuda. Read More

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December 2018

Flow Perfusion Maintaining Long-term Viability of the Rat Groin Fat Flap: A Novel Model for Research on Large-scale Engineered Tissues.

Chin Med J (Engl) 2018 Jan;131(2):213-217

Department of Plastic Surgery, Peking University Third Hospital, Beijing 100191, China.

Background: Large-scale muscle tissue engineering remains a major challenge. An axial vascular pedicle and perfusion bioreactor are necessary for the development and maintenance of large-scale engineered muscle to ensure circulation within the construct. We aimed to develop a novel experimental model of a large-scale engineered muscle flap from an existing rat groin fat flap. Read More

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January 2018

Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina.

R Soc Open Sci 2017 Oct 25;4(10):171095. Epub 2017 Oct 25.

Department of Invertebrate Zoology and Geology, California Academy of Sciences, 55 Music Concourse Dr Golden Gate Park, San Francisco, CA 94118, USA.

Molecular estimates of phylogenetic relationships rely heavily on multiple sequence alignment construction. There has been little consensus, however, on how to properly address issues pertaining to the alignment of variable regions. Here, we construct alignments from four commonly sequenced molecular markers (16S, 18S, 28S and cytochrome c oxidase subunit I) for the Nudibranchia using three different methodologies: (i) strict mathematical algorithm; (ii) exclusion of variable or divergent regions and (iii) manually curated, and examine how different alignment construction methods can affect phylogenetic signal and phylogenetic estimates for the suborder Doridina. Read More

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October 2017

The taxonomic and phylogenetic status of digeneans from the genus Timoniella (Digenea: Cryptogonimidae) in the Black and Baltic seas.

J Helminthol 2018 Sep 4;92(5):596-603. Epub 2017 Oct 4.

Institut für Biowissenschaften/Zoologie,Universität Rostock, Universitätsplatz 2,18055 Rostock,Germany.

Timoniella spp. are cryptogonimid flukes (Digenea: Cryptogonimidae) that parasitize the guts of fish in brackish waters. Timoniella imbutiforme, a species from the Mediterranean Sea, is recorded in the Black Sea, while T. Read More

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September 2018

Breeding system, shell size and age at sexual maturity affect sperm length in stylommatophoran gastropods.

BMC Evol Biol 2016 Apr 29;16:89. Epub 2016 Apr 29.

Department of Environmental Sciences, Section of Conservation Biology, University of Basel, St. Johanns-Vorstadt 10, 4056, Basel, Switzerland.

Background: Sperm size and quality are key factors for fertilization success. There is increasing empirical evidence demonstrating that sperm form and function are influenced by selective pressures. Theoretical models predict that sperm competition could favour the evolution of longer sperm. Read More

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Both the Exact Target Site Sequence and a Long Poly(A) Tail Are Required for Precise Insertion of the 18S Ribosomal DNA-Specific Non-Long Terminal Repeat Retrotransposon R7Ag.

Mol Cell Biol 2016 05 2;36(10):1494-508. Epub 2016 May 2.

Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan

Ribosomal elements (R elements) are site-specific non-long terminal repeat (LTR) retrotransposons that target ribosomal DNA (rDNA). To elucidate how R elements specifically access their target sites, we isolated and characterized the 18S rDNA-specific R element R7Ag from Anopheles gambiae Using an in vivo and ex vivo recombinant baculovirus retrotransposition system, we found that the exact host 18S rDNA sequence at the target site is essential for the precise insertion of R7Ag. In addition, a long poly(A) tail is necessary for the accurate initiation of R7Ag reverse transcription, a novel mechanism found in non-LTR elements. Read More

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The RNA recognition motif of NIFK is required for rRNA maturation during cell cycle progression.

RNA Biol 2015 ;12(3):255-67

a Institute of Biological Chemistry; Academia Sinica ; Taipei , Taiwan.

Ribosome biogenesis governs protein synthesis. NIFK is transactivated by c-Myc, the key regulator of ribosome biogenesis. The biological function of human NIFK is not well established, except that it has been shown to interact with Ki67 and NPM1. Read More

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December 2015

Genetic characterization and phylogenetic analysis of echinostomes.

Southeast Asian J Trop Med Public Health 2014 Sep;45(5):1003-10

We conducted this study to identify species and determine the phylogenetic relationships using ribosomal DNA (rDNA) sequences [partial sequences of 28S rDNA and second internal transcribed spacer (IT52)] of echinostomes collected from free-grazing ducks in Phitsanulok Province, Thailand. Four adult echinostomes were morphologically identified as Echinostoma revolutum, 4 as Hypoderaeulm conoideurn and 2 unidentified. Sequences of other species/isolates of echinostomes retrieved from the GenBank database were employed to compare and construct the phylogenetic tree. Read More

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September 2014

Genetics and shell morphometrics of assimineids (Mollusca, Caenogastropoda, Truncatelloidea) in the St Lucia Estuary, South Africa.

Zookeys 2014 23(419):73-86. Epub 2014 Jun 23.

DST/NRF Research Chair in Shallow Water Ecosystems, c/o Department of Zoology, Nelson Mandela Metropolitan University, P O Box 77000, Port Elizabeth, 6031, South Africa ; School of Life Sciences, University of KwaZulu-Natal, Westville, Private Bag X5401, Durban, 4000, South Africa.

The Assimineidae are a family of amphibious microgastropods that can be mostly found in estuaries and mangroves in South Africa. These snails often occur in great numbers and are ecologically important to the St Lucia Estuary, which forms a crucial part of the iSimangaliso Wetland Park, a UNESCO World Heritage Site. Genetic and shell morphometric analyses were conducted on individuals collected from nine localities distributed from the northern lake regions to the southern lake and the mouth of the St Lucia estuarine lake. Read More

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Lentiviral protein transduction with genome-modifying HIV-1 integrase-I-PpoI fusion proteins: studies on specificity and cytotoxicity.

Biomed Res Int 2014 22;2014:379340. Epub 2014 Apr 22.

Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland ; Department of Medicine, University of Eastern Finland, 70120 Kuopio, Finland ; Gene Therapy Unit, Kuopio University Hospital, 70120 Kuopio, Finland.

Rare-cutting endonucleases, such as the I-PpoI, can be used for the induction of double strand breaks (DSBs) in genome editing and targeted integration based on homologous recombination. For therapeutic approaches, the specificity and the pattern of off-target effects are of high importance in these techniques. For its applications, the endonuclease needs to be transported into the target cell nucleus, where the mechanism of transport may affect its function. Read More

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January 2015

Identification of novel fusion genes with 28S ribosomal DNA in hematologic malignancies.

Int J Oncol 2014 Apr 5;44(4):1193-8. Epub 2014 Feb 5.

Department of Molecular Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan.

Fusion genes are frequently observed in hematologic malignancies and soft tissue sarcomas, and are usually associated with chromosome abnormalities. Many of these fusion genes create in-frame fusion transcripts that result in the production of fusion proteins, and some of which aid tumorigenesis. These fusion proteins are often associated with disease phenotype and clinical outcome, and act as markers for minimal residual disease and indicators of therapeutic targets. Read More

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A novel multigene expression construct for modification of glycerol metabolism in Yarrowia lipolytica.

Microb Cell Fact 2013 Nov 4;12:102. Epub 2013 Nov 4.

Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, Poznań 60-627, Poland.

Background: High supply of raw, residual glycerol from biodiesel production plants promote the search for novel biotechnological methods of its utilization. In this study we attempted modification of glycerol catabolism in a nonconventional yeast species Yarrowia lipolytica through genetic engineering approach.

Results: To address this, we developed a novel genetic construct which allows transferring three heterologous genes, encoding glycerol dehydratase, its reactivator and a wide-spectrum alcohol oxidoreductase under the control of glycerol-induced promoter. Read More

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November 2013

Relationship between two androgenetic clam species, Corbicula leana and Corbicula fluminea, inferred from mitochondrial cytochrome b and nuclear 28S rRNA markers.

Zoolog Sci 2013 May;30(5):360-5

Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Mie 514-8507, Japan.

Two shell color types, yellow (type I) and brown (type II), of hermaphrodite Corbicula fluminea clams from Ritto, Shiga Prefecture, Japan, are sympatric with both male and hermaphrodite Corbicula leana. In the present study, the mitochondrial DNA (mtDNA) cytochrome b and nuclear 28S rRNA genes of C. fluminea were sequenced to construct a haplotype network in order to investigate the genetic relationship with C. Read More

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Evolution of a transposon in Daphnia hybrid genomes.

Mob DNA 2013 Feb 6;4(1). Epub 2013 Feb 6.

Department of Integrative Biology, University of Guelph, Science complex, N1G 2 W1, Guelph, ON, Canada.


Background: Transposable elements play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes, and may have dramatic consequences on genome structure. Hybrid and polyploid clones have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Read More

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February 2013

Global phylogeny and new classification of the Rapaninae (Gastropoda: Muricidae), dominant molluscan predators on tropical rocky seashores.

Mol Phylogenet Evol 2013 Jan 28;66(1):91-102. Epub 2012 Sep 28.

Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK.

The monophyly of the muricid subfamily Rapaninae has recently been confirmed with molecular techniques, but its composition and the relationships among its constituent genera remain unclear. We use four genes (28S rRNA, 12S rRNA, 16S rRNA and cytochrome c oxidase subunit I, COI) to construct a Bayesian phylogeny of 80 rapanine species (73% of the approximately 109 currently accepted), representing 27 of the 31 nominal genera. This is the most complete phylogeny of this taxonomically confusing subfamily yet produced. Read More

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January 2013

AAV vectors containing rDNA homology display increased chromosomal integration and transgene persistence.

Mol Ther 2012 Oct 18;20(10):1902-11. Epub 2012 Sep 18.

Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, Oregon 97239-3098, USA.

Although recombinant adeno-associated viral (rAAV) vectors are promising tools for gene therapy of genetic disorders, they remain mostly episomal and hence are lost during cell replication. For this reason, rAAV vectors capable of chromosomal integration would be desirable. Ribosomal DNA (rDNA) repeat sequences are overrepresented during random integration of rAAV. Read More

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October 2012

Human C4orf14 interacts with the mitochondrial nucleoid and is involved in the biogenesis of the small mitochondrial ribosomal subunit.

Nucleic Acids Res 2012 Jul 24;40(13):6097-108. Epub 2012 Mar 24.

MRC-Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Hills Road Cambridge, CB2 0XY, UK.

The bacterial homologue of C4orf14, YqeH, has been linked to assembly of the small ribosomal subunit. Here, recombinant C4orf14 isolated from human cells, co-purified with the small, 28S subunit of the mitochondrial ribosome and the endogenous protein co-fractionated with the 28S subunit in sucrose gradients. Gene silencing of C4orf14 specifically affected components of the small subunit, leading to decreased protein synthesis in the organelle. Read More

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Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage.

BMC Evol Biol 2011 Nov 25;11:343. Epub 2011 Nov 25.

Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, Provo, UT 84602, USA.

Background: Understanding how freshwater assemblages have been formed and maintained is a fundamental goal in evolutionary and ecological disciplines. Here we use a historical approach to test the hypothesis of codivergence in three clades of the Chilean freshwater species assemblage. Molecular studies of freshwater crabs (Aegla: Aeglidae: Anomura) and catfish (Trichomycterus arealatus: Trichomycteridae: Teleostei) exhibited similar levels of genetic divergences of mitochondrial lineages between species of crabs and phylogroups of the catfish, suggesting a shared evolutionary history among the three clades in this species assemblage. Read More

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November 2011

Phytoseiid mite species composition in Japanese peach orchards estimated using quantitative sequencing.

Exp Appl Acarol 2012 Jan 10;56(1):9-22. Epub 2011 Sep 10.

Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan.

We attempted a population survey of spider mites and phytoseiid mites in Japanese peach orchards with different pesticide practices; however, we had difficulty discriminating phytoseiid mites. To estimate phytoseiid mite species composition, ribosomal gene fragments were amplified from genomic DNA of five phytoseiid mite species using PCR. Cloning and nucleotide sequencing of amplified fragments identified species-specific polymorphic sites. Read More

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January 2012

The phylogenetic position of the 'living fossils' Neoglyphea and Laurentaeglyphea (Decapoda: Glypheidea).

C R Biol 2010 Oct 29;333(10):755-9. Epub 2010 Sep 29.

UMR 7138, systématique, évolution, adaptation, Muséum national d'histoire naturelle, 43, rue Cuvier, 75005 Paris, France.

The Glypheidea is a group of lobster-like decapods that appeared in the Triassic and that was thought to be extinct until 1975, when a specimen of the species Neoglyphea inopinata was caught off the Philippines. More recently, in 2005, a specimen of another glypheid species, Laurentaeglyphea neocaledonica, was discovered near New Caledonia. Here, we construct a decapod molecular data set including the two extant glypheid species sequenced from eight nuclear and mitochondrial genes. Read More

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October 2010

Evolutionary history and taxonomy of a short-horned grasshopper subfamily: the Melanoplinae (Orthoptera: Acrididae).

Mol Phylogenet Evol 2011 Jan 17;58(1):22-32. Epub 2010 Jul 17.

Laboratoire d'Ecologie Alpine, Université Joseph Fourier UMR CNRS 5553, Grenoble Cedex 09, France.

The Melanoplinae is one of the largest subfamilies of the Acrididae grasshoppers, with a Holarctic-Neotropical distribution. To investigate its controversial taxonomy and evolutionary history, we studied 19 species representative of its main tribes, and 7 Acridoidea outgroup species. More than 1650 base pairs of three regions of nuclear rDNA (18S, ITS1, 28S) and one mitochondrial rDNA (12S) were combined and used to construct parsimony, maximum likelihood and Bayesian phylogenies. Read More

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January 2011

Preferential selection of the 5'-terminal start codon on leaderless mRNAs by mammalian mitochondrial ribosomes.

J Biol Chem 2010 Sep 7;285(36):28379-86. Epub 2010 Jul 7.

Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA.

Mammalian mitochondrial mRNAs are basically leaderless, having few or no untranslated nucleotides prior to the 5'-start codon. We demonstrate here that mammalian mitochondrial 55 S ribosomes preferentially form initiation complexes at a 5'-terminal AUG codon over an internal AUG. The preferential use of the 5'-start codon is also seen on mitochondrial 28 S small subunits, which suggests that mitochondrial translation initiation on leaderless mRNAs does not require the large ribosomal subunit. Read More

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September 2010