The chinstrap (Pygoscelis antarcticus) and gentoo (P. papua) penguins are distributed throughout Antarctica and the sub-Antarctic islands. In this study, high-quality de novo assemblies of blood transcriptomes from these penguins were generated using the Illumina MiSeq platform. A total of 22.2 and 21.8 raw reads were obtained from chinstrap and gentoo penguins, respectively. These reads were assembled using the Oases assembly platform and resulted in 26,036 and 21,854 contigs with N50 values of 929 and 933 base pairs, respectively. Functional gene annotations through pathway analyses of the Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were performed for each blood transcriptome, resulting in a similar compositional order between the two transcriptomes. Ortholog comparisons with previously published transcriptomes from the Adélie (P. adeliae) and emperor (Aptenodytes forsteri) penguins revealed that a high proportion of the four penguins’ transcriptomes had significant sequence homology. Because blood and tissues of penguins have been used to monitor pollution in Antarctica, immune parameters in blood could be important indicators for understanding the health status of penguins and other Antarctic animals. In the blood transcriptomes, KEGG analyses detected many essential genes involved in the major innate immunity pathways, which are key metabolic pathways for maintaining homeostasis against exogenous infections or toxins. Blood transcriptome studies such as this may be useful for checking the immune and health status of penguins without sacrifice.
Animals ; Base Pairing ; Gene Ontology ; Genes, Essential ; Genome ; Homeostasis ; Immunity, Innate ; Islands ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Sequence Homology ; Spheniscidae ; Transcriptome

Avian malaria is one of the most important general blood parasites of poultry in Southeast Asia. Plasmodium (P.) juxtanucleare causes avian malaria in wild and domestic fowl. This study aimed to identify and characterize the Plasmodium species infecting in Thai native fowl. Blood samples were collected for microscopic examination, followed by detection of the Plasmodium cox I gene by using PCR. Five of the 10 sampled fowl had the desired 588 base pair amplicons. Sequence analysis of the five amplicons indicated that the nucleotide and amino acid sequences were homologous to each other and were closely related (100% identity) to a P. juxtanucleare strain isolated in Japan (AB250415). Furthermore, the phylogenetic tree of the cox I gene showed that the P. juxtanucleare in this study were grouped together and clustered with the Japan strain. The presence of P. juxtanucleare described in this study is the first report of P. juxtanucleare in the Thai native fowl of Thailand.
Amino Acid Sequence ; Animals ; Asia, Southeastern ; Asian Continental Ancestry Group ; Base Pairing ; Cytochromes c ; Cytochromes ; Electron Transport Complex IV ; Humans ; Japan ; Malaria, Avian ; Parasites ; Plasmodium ; Polymerase Chain Reaction ; Poultry ; Sequence Analysis ; Thailand ; Trees

McLeod syndrome is a rare X-linked multisystem disorder which forms the core of neuroacanthocytosis syndrome. Neurological symptoms characterized by chorea, seizure, cognitive impairment, and psychosis mostly develop around the 5-6th decades, accompanied by multisystem involvement comprising neuropathy, myopathy, acanthocytosis and hepatosplenomegaly. We hereby present a 60-year-old male who is the first genetically confirmed Korean McLeod syndrome patient. Genetic analysis of his XK gene revealed a previously reported 5 base pair deletion of exon 3 (c.856_860delCTCTA).
Abetalipoproteinemia ; Base Pairing ; Chorea ; Cognition Disorders ; Exons ; Humans ; Korea* ; Male ; Middle Aged ; Muscular Diseases ; Neuroacanthocytosis ; Psychotic Disorders ; Seizures

Animals ; Base Pairing ; Binding Sites ; CCCTC-Binding Factor ; metabolism ; Consensus Sequence ; Humans ; Mutation ; Nucleotide Motifs

The emergence of regenerative medicine has raised the hope of treating an extraordinary range of disease and serious injuries. Understanding the processes of cell proliferation, differentiation and pattern formation in regenerative organisms could help find ways to enhance the poor regenerative abilities shown by many other animals, including humans. Recently, planarians have emerged as an attractive model in which to study regeneration. These animals are considering as in vivo plate, during which we can study the behavior and characristics of stem cells in their own niche. A variety of characteristic such as: simplicity, easy to manipulate experimentally, the existence of more than 100 years of literature, makes these animals an extraordinary model for regenerative medicine researches. Among planarians free-living freshwater hermaphrodite Schmidtea mediterranea has emerged as a suitable model system because it displays robust regenerative properties and, unlike most other planarians, it is a stable diploid with a genome size of about 4.8x108 base pairs, nearly half that of other common planarians. Planarian regeneration involves two highly flexible systems: pluripotent neoblasts that can generate any new cell type and muscle cells that provide positional instructions for the regeneration of anybody region. neoblasts represent roughly 25~30 percent of all planarian cells and are scattered broadly through the parenchyma, being absent only from the animal head tips and the pharynx. Two models for neo-blast specification have been proposed; the naive model posits that all neoblasts are stem cells with the same potential and are a largely homogeneous population.
Animals ; Base Pairing ; Cell Proliferation ; Diploidy ; Fresh Water ; Genome Size ; Head ; Hope ; Humans ; Muscle Cells ; Pharynx ; Planarians* ; Regeneration ; Regenerative Medicine* ; Stem Cells

PURPOSE: Recently, mitochondrial DNA 4977bp deletion (mtDNA4977-mut), a somatic mutation related to oxidative stress, has been shown to be associated with atrial fibrillation (AF). We hypothesized that patient age, as well as electroanatomical characteristics of fibrillating left atrial (LA), vary depending on the presence of mtDNA4977-mut in peripheral blood among patients with non-valvular AF. MATERIALS AND METHODS: Analyzing clinical and electroanatomical characteristics, we investigated the presence of the mtDNA4977-mut in peripheral blood of 212 patients (51.1+/-13.2 years old, 83.5% male) undergoing catheter ablation for non-valvular AF, as well as 212 age-matched control subjects. RESULTS: The overall frequency of peripheral blood mtDNA4977-mut in patients with AF and controls was not significantly different (24.5% vs. 19.3%, p=0.197). When the AF patient group was stratified according to age, mtDNA4977-mut was more common (47.4% vs. 20.0%, p=0.019) in AF patients older than 65 years than their age-matched controls. Among AF patients, those with mtDNA4977-mut were older (58.1+/-11.9 years old vs. 48.8+/-11.9 years old, p<0.001). AF patients positive for the mtDNA mutation had greater LA dimension (p=0.014), higher mitral inflow peak velocity (E)/diastolic mitral annular velocity (Em) ratio (p<0.001), as well as lower endocardial voltage (p=0.035), and slower conduction velocity (p=0.048) in the posterior LA than those without the mutation. In multivariate analysis, E/Em ratio was found to be significantly associated with the presence of mtDNA4977-mut in peripheral blood. CONCLUSION: mtDNA4977-mut, an age-related somatic mutation detected in the peripheral blood, is associated with advanced age and electro-anatomical remodeling of the atrium in non-valvular AF.
Adult ; Aged ; Atrial Fibrillation/blood/*genetics/*physiopathology ; Atrial Remodeling/*genetics ; Base Pairing/*genetics ; Case-Control Studies ; DNA, Mitochondrial/*blood/*genetics ; Female ; Heart Atria/pathology/physiopathology ; Humans ; Kaplan-Meier Estimate ; Logistic Models ; Male ; Middle Aged ; Mutation Rate ; Phenotype ; Sequence Deletion/*genetics

Almost all pre-miRNAs in eukaryotic cytoplasm are recognized and processed into double-stranded microRNAs by the endonuclease Dicer protein comprising of multiple domains. As a key player in the small RNA induced gene silencing pathway, the major domains of Dicer are conserved among different species with the exception of the N-terminal components. Human Dicer's N-terminal domain has been shown to play an auto-inhibitory function of the protein's dicing activity. Such an auto-inhibition can be released when the human Dicer protein dimerizes with its partner protein, such as TRBP, PACT through the N-terminal DExH/D (ATPase-helicase) domain. The typical feature of a pre-miRNA contains a terminal loop and a stem duplex, which bind to human Dicer's DExH/D (ATPase-helicase) domain and PAZ domain respectively during the dicing reaction. Here, we show that pre-miRNA's terminal loop can regulate human Dicer's enzymatic activity by interacting with the DExH/D (ATPase-helicase) domain. We found that various editing products of pre-miR-151 by the ADAR1P110 protein, an A-to-I editing enzyme that modifies pre-miRNAs sequence, have different terminal loop structures and different activity regulatory effects on human Dicer. Single particle electron microscopy reconstruction revealed that pre-miRNAs with different terminal loop structures induce human Dicer's DExH/D (ATPase-helicase) domain into different conformational states, in correlation with their activity regulatory effects.
Base Pairing ; Base Sequence ; DEAD-box RNA Helicases ; chemistry ; genetics ; Humans ; MicroRNAs ; chemistry ; genetics ; Molecular Conformation ; Molecular Sequence Data ; Protein Structure, Tertiary ; RNA Editing ; genetics ; Ribonuclease III ; chemistry ; genetics

The aim of this study was to identify a new gene of Haemophilus parasuis that could be used to develop a polymerase chain reaction (PCR) test for this porcine pathogen. H. parasuis genomic DNA was cloned into a set of expression vectors, and transformants expressing His-tagged polypeptides were identified by colony blotting. An ABC transporter-like gene was isolated. The cloned DNA fragment is 1,105 base pair and shows 78% similarity at the nucleotide level with an ABC transporter gene of H. ducreyi. Based on this sequence, two PCR primers were designed to amplify the entire 1,105-bp fragment in the proposed diagnostic PCR test. PCR amplification was able to detect a minimum of 1 x 10(4) CFU/ml of H. parasuis organisms. Fifteen different H. parasuis serovars were positive using the PCR test. No amplification was observed when the test was done using DNA from 16 other bacterial species commonly isolated from swine.
Base Pairing ; Clone Cells ; Cloning, Organism ; DNA ; Haemophilus ; Haemophilus parasuis ; Peptides ; Polymerase Chain Reaction ; Swine

MicroRNAs (miRNAs, miRs) are about 21-25 nucleotides in length and regulate mRNA translation by base pairing to partially complementary sites, predominantly in the 3'-untranslated region (3'-UTR) of the target mRNA. In this study, the expression profile of miRNAs was compared and analyzed for the establishment of miRNA-related odontoblast differentiation using MDPC-23 cells derived from mouse dental papilla cells. To determine the expression profile of miRNAs during the differentiation of MDPC-23 cells, we employed miRNA microarray analysis, quantitative real-time PCR (qRT-PCR) and Alizaline red-S staining. In the miRNA microarray analysis, 11 miRNAs were found to be up- or down-regulated more than 3-fold between day 0 (control) and day 5 of MDPC-23 cell differentiation among the 1,769 miRNAs examined. In qRT-PCR analysis, the expression levels of two of these molecules, miR-194 and miR-126, were increased and decreased in the control MDPC-23 cells compared with the MDPC-23 cells at day 5 of differentiation, respectively. Importantly, the overexpression of miR-194 significantly accelerated mineralization compared with the control cultures during the differentiation of MDPC-23 cells. These results suggest that the miR-194 augments MDPC-23 cell differentiation, and potently accelerates the mineralization process. Moreover, these in vitro results show that different miRNAs are deregulated during the differentiation of MDPC-23 cells, suggesting the involvement of these genes in the differentiation and mineralization of odontoblasts.
Animals ; Base Pairing ; Cell Differentiation ; Dental Papilla ; Mice ; Microarray Analysis ; MicroRNAs ; Nucleotides ; Odontoblasts ; Protein Biosynthesis ; Real-Time Polymerase Chain Reaction ; RNA, Messenger

OBJECTIVES: In order to identify the possibility of slender bitterling (SB) (Acheilognathus yamatsutae) being used as a test species for estrogenic endocrine disrupting chemicals (EEDCs), we carried out the cloning and sequence characterization of the estrogen receptor (ER). METHODS: The ER from a slender bitterling was obtained by reverse transcriptase-polymerase chain reaction (RT-PCR), 5'- and 3'-rapid amplification of cDNA ends (5'-RACE and 3'-RACE) and T-vector cloning. The expression of ER mRNA was also analyzed in six tissues (brain, liver, kidney, gill, gonad, and intestines) by real-time PCR. RESULTS: We obtained an ER from the slender bitterling. The SB ER cDNA was 2189 base pairs (bp) in length and contained a 1707 bp open reading frame that encoded 568 amino acid residues. The SB ER amino acid sequence clustered in a monophyletic group with the ERalpha of other fish, and was more closely related to zebrafish ERalpha (88% identity) than to the ERalpha of other fish. The SB ER cDNA was divided into A/B, C, D, E and F domains. The SB ER has conserved important sequences for ER functions, such as the DNA binding domain (D domain), which are consistent with those of other teleosts. CONCLUSIONS: The ER of the slender bitterling could provide basic information in toxicological studies of EEDCs in the slender bitterling.
Amino Acid Sequence ; Animals ; Base Pairing ; Clone Cells ; Cloning, Molecular ; Cloning, Organism ; DNA ; DNA, Complementary ; Endocrine Disruptors ; Estrogen Receptor alpha ; Estrogens ; Gills ; Gonads ; Kidney ; Liver ; Open Reading Frames ; RNA, Messenger ; Zebrafish