Dermatophytes are fungi that can be contagious and cause infections in the keratinized skin of mammals, including humans. The etiological diagnosis of dermatophytosis relies on a combination of in vitro-culture and microscopic methods. Effective molecular tools could overcome the limitations of conventional methods of identification. In the present study, following ... More
Diazotrophic bacteria associated with Hawaiian Montipora corals: Diversity and abundance in correlation with symbiotic dinoflagellates
AuthorsOlson, ND; Ainsworth, TD; Gates, RD; Takabayashi, M
JournalJOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY
PubMed ID
The primary productivity of coral-dinoflagellate symbiosis is classically viewed as nitrogen (N)-limited. However, the recent discovery of N-fixing bacteria residing within coral tissues challenges this view. This study investigated the diversity and abundance of N-fixing bacteria associated with Hawaiian corals of the genus Montipora. Phylogenetic analysis of a partial sequence ... More
A set of nuclear DNA markers diagnostic for marble trout, Salmo marmoratus
AuthorsSusnik, S; Sivka, U; Snoj, A
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PubMed ID
'Single nucleotide polymorphisms (SNPs) have become popular markers for population genetics and conservation applications. The use of SNPs is increasing in studies on salmonid fishes, particularly in Salmo salar and several Oncorhynchus species, but they are used only occasionally in S. trutta and not at all in marble trout (Salmo ... More
Seasonal variation of microbial populations and biomass in Tatachia grassland soils of Taiwan
AuthorsCho, ST; Tsai, SH; Ravindran, A; Selvam, A; Yang, SS
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PubMed ID
'To investigate the seasonal variations of microbial ecology in grassland of Tatachia forest, soil properties, microbial populations, microbial biomass, and 16S rDNA clone library analysis were determined. The soil had temperatures 6.6-18.4¿C, pH 3.6-5.1, total organic carbon 1.11-10.68%, total nitrogen 0.18-0.78%, and C/N ratios 3.46-20.55. Each gram of dry soil ... More
Molecular Diversity of the Rumen Microbiome of Norwegian Reindeer on Natural Summer Pasture
AuthorsSundset, M; Edwards, J; Cheng, Y; Senosiain, R; Fraile, M; Northwood, K; Praaesteng, KE; Glad, T; Mathiesen, S; Wright, AD
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PubMed ID
'The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer (Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00A° N, 25.30A° E). Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, ... More
Transmission efficiency of Grapevine leafroll-associated virus 3 (GLRaV-3) by the mealybugs Planococcus ficus and Pseudococcus longispinus (Hemiptera: Pseudococcidae)
AuthorsDouglas, N; Krueger, K
Journal
PubMed ID
'Grapevine leafroll-associated virus 3 (GLRaV-3) is transmitted from grapevine to grapevine through grafting infected material, as well as mealybug and soft scale insect vectors. We determined the transmission efficiency of GLRaV-3 by two mealybug vectors, Planococcus ficus and Pseudococcus longispinus, by examining the relationship between the number of nymphs per ... More
High-resolution HLA matching in double-umbilical-cord-blood reduced-intensity transplantation in adults
'Double-cord-blood transplantation (DCBT) offers an option for patients receiving reduced-intensity transplants. These unique transplants have two donors, both of whom are usually HLA mismatched at one to two loci. Fifty-three patients were recipients of a reduced-intensity DCBT. Cords were at least 4/6 allele-level HLA-A, -B, and -DR match with the ... More
Inhibition of subgenomic hepatitis C virus RNA transcription by chinese herbal extracts
'Hepatitis C virus (HCV) causes chronic hepatitis, cirrhosis and hepatocellular carcinoma. Some patients are resistant to interferon-α (IFN-α) treatment, and thus there is urgent need to improve anti-HCV therapies and discover novel therapeutic approaches in the form of new antiviral agents. Using real-time PCR (RT-PCR) and the MTS assay, we ... More
Use of a dual priming oligonucleotide system to detect multiple sexually transmitted pathogens in clinical specimens
AuthorsHorii, T; Ohtsuka, H; Osaki, M; Ohkuni, H
Journal
PubMed ID
'Aims: To evaluate a new dual priming oligonucleotide (DPO)-based multiplex polymerase chain reaction (PCR) assay for detection of six sexually transmitted pathogens, including Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum and Trichomonas vaginalis. Methods and Results: Using 130 clinical specimens, the results obtained by the multiplex ... More
Detection of unknown deletions in β-globin gene cluster using relative quantitative PCR methods
AuthorsBabashah, S; Jamali, S; Mahdian, R; Nosaeid, MH; Karimipoor, M; Alimohammadi, R; Raeisi, M; Maryami, F; Masoudifar, M; Zeinali, S
Journal
PubMed ID
'β-Thalassemia is mainly caused by mutations involving single base substitution and small deletions. However, a considerable number of carriers are suspected to have large deletions in β-globin gene cluster. Common strategy for identifying deletions with definite breakpoints is based on Gap PCR. There are, however, some cases with indefinite breakpoints ... More
Analysis of genetic variation in Globocephaloides populations from macropodid marsupials using a mutation scanning-based approach
'Three species of Globocephaloides, parasitic nematodes occurring in macropodid marsupials in different areas of Australia, were characterized by the sequences of the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA. Samples were subjected to PCR-coupled SSCP analysis and targeted sequencing, in order to assess genetic ... More
International Collaborative Study of the Endogenous Reference Gene, Sucrose Phosphate Synthase (SPS), Used for Qualitative and Quantitative Analysis of Genetically Modified Rice
AuthorsJiang, LX; Yang, LT; Zhang, HB; Guo, JC; Mazzara, M; Van den Eede, G; Zhang, DB
Journal
PubMed ID
'One rice (Oryza sativa) gene, sucrose phosphate synthase (SPS), has been proven to be a suitable endogenous reference gene for genetically modified (GM) rice detection in a previous study. Herein are the reported results of an international collaborative ring trial for validation of the SPS gene as an endogenous reference ... More
Satellite panicum mosaic virus coat protein enhances the performance of plant virus gene vectors
AuthorsEverett, AL; Scholthof, HB; Scholthof, KBG
Journal
PubMed ID
'The coat protein of satellite panicum mosaic virus (SPCP) is known to effectively protect its cognate RNA from deleterious events, and here, we tested its stabilizing potential for heterologous virus-based gene vectors in planta. In support of this, a Potato virus X (PVX) vector carrying the SPMV capsid protein (PVX-SPCP) ... More
Quantitative Correlation Between mRNA Secondary Structure Around the Region Downstream of the Initiation Codon and Translational Efficiency in Escherichia coli
AuthorsSeo, SW; Yang, J; Jung, GY
Journal
PubMed ID
'Translational efficiency in Escherichia coli is known to be strongly influenced by the secondary structure around the ribosome-binding site and the initiation codon in the translational-initiation region of the mRNA. Several quantitative studies have reported that translational efficiency is attributable to effects on ribosome accessibility predominantly caused by the secondary ... More
The Prevalence of Erythromycin Resistance in Group B Streptococcal Isolates at a University Hospital in Taiwan
'Due to reduced antibiotic consumption in Taiwan, erythromycin resistance rate had decreased in Streptococcus pyogenes, but it increased in Streptococcus pneumoniae. The objectives of the present study were (1) to determine the erythromycin and clindamycin resistance rate and minimum inhibitory concentration (MIC) of the group B streptococcus (GBS) clinical isolates, ... More
Molecular signature detection of circulating tumor cells using a panel of selected genes
'Circulating tumor cell (CTC) detection in peripheral blood of colon and other epithelial cancer patients is becoming a scientifically recognised indicator for the presence of primary tumors and/or metastasis. The resulting need to further develop CTC detection-based systems for improved diagnosis, prognosis and assessment of therapy efficacy in tumour patients ... More
Influence of Long Time Storage in Mineral Water on RNA Stability of Pseudomonas aeruginosa and Escherichia coli after Heat Inactivation
AuthorsCenciarini, C; Courtois, S; Raoult, D; La Scola, B
Journal
PubMed ID
'Background: Research of RNA viability markers was previously studied for many bacterial species. Few and different targets of each species have been checked and motley results can be found in literature. No research has been done about Pseudomonas aeruginosa in this way. Methodology/Principal Findings: Disappearance of 48 transcripts was ... More
Authentication of meat from game and domestic species by SNaPshot minisequencing analysis
AuthorsLa Neve, F; Civera, T; Mucci, N; Bottero, MT
Journal
PubMed ID
'The aim of the present study is to develop an assay for the specific identification of meat from Capreolus capreolus, Cervus elaphus, Capra ibex, Rupicapra rupicapra, targeting sequences of the cytochrome b (cyt b) gene of mitochondrial DNA. The assay is also intended to enable differentiation between meat from these ... More
Effect of manganese exposure on intracellular Ca(2+) homeostasis and expression of NMDA receptor subunits in primary cultured neurons
Authors
Journal
PubMed ID
'Overexposure to manganese (Mn) has been known to induce neuronal damage. However, the mechanisms of Mn-induced neuronal cell death are incompletely understood. The objective of this study is to explore mechanisms that contribute to Mn-induced neuronal apoptosis focusing on the alteration of intracellular Ca(2+) homeostasis and expression of NMDA receptor ... More
An intronic polymorphism in the corticotropin-releasing hormone receptor 2 gene increases susceptibility to HBV-related hepatocellular carcinoma in Chinese population
'Corticotropin-releasing hormone receptor 2 (CRHR2) plays a role in both the central nervous system (CNS) and the peripheral nervous system. CRHR2 together with its ligands, urocortins (Ucns) and corticotropin-releasing hormone (CRH), functions as a mediator of inflammatory response and inhibitor of angiogenesis. Recently, it has been reported to be expressed ... More
Effect of Variation for Major Growth Habit Genes on Maturity and Yield in Five Spring Wheat Populations
AuthorsBlake, NK; Lanning, SP; Martin, JM; Doyle, M; Sherman, JD; Naruoka, Y; Talbert, LE
Journal
PubMed ID
'Segregation at major genes controlling plant height, photoperiod response, and vernalization response in wheat (Triticum aestivum L. em. Thell.) may have pleiotropic effects on several traits. Allelic variation at these loci can be monitored using polymerase chain reaction (PCR) markers. The effect of segregation at these loci on maturity and ... More
A new single-step quantitative pathogen detection system: Template-tagging followed by multiplex asymmetric PCR using common primers and CE-SSCP
'Rapid diagnosis of bacterial infection is important for patient management and appropriate therapy during the early phase of bacteria-induced disease. Among the existing techniques for identifying microbial, CE-SSCP combined with 16S ribosomal RNA gene-specific PCR has the benefits of excellent sensitivity, resolution, and reproducibility. However, even though CE-SSCP can separate ... More
Anticoagulant resistance: a relevant issue in sewer rat (Rattus norvegicus) control?
AuthorsHeiberg, AC
Journal
PubMed ID
'BACKGROUND: The majority of rat problems in cities are thought to be related to defective sewers, and the use of anticoagulant rodenticides in such places is often implemented as part of regular urban rodent control. Knowledge pertaining to the resistance status of sewer rat populations is non-existent, which may be ... More
Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda)
AuthorsJex, AR; Hu, M; Littlewood, DTJ; Waeschenbach, A; Gasser, RB
Journal
PubMed ID
'Background: Mitochondrial (mt) genomes represent a rich source of molecular markers for a range of applications, including population genetics, systematics, epidemiology and ecology. In the present study, we used 454 technology (or the GS20, massively parallel picolitre reactor platform) to determine the complete mt genome of Haemonchus contortus (Nematoda: Trichostrongylidae), ... More
A common JAK2 haplotype confers susceptibility to myeloproliferative neoplasms
'Genome-wide association studies have identified a number of new disease susceptibility loci that represent haplotypes defined by numerous SNPs. SNPs within a disease-associated haplotype are thought to influence either the expression of genes or the sequence of the proteins they encode. In a series of investigations of the JAK2 gene ... More
Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family
'Background: Restriction-modification systems are a diverse class of enzymes. They are classified into four major types: I, II, III and IV. We have previously proposed the existence of a Thermus sp. enzyme family, which belongs to type II restriction endonucleases (REases), however, it features also some characteristics of types I ... More
Intron polymorphism pattern in AOX1b of wild St John's wort (Hypericum perforatum) allows discrimination between individual plants
AuthorsFerreira, AO; Cardoso, HG; Macedo, ES; Breviario, D; Arnholdt-Schmitt, B
Journal
PubMed ID
'The present paper deals with the analysis of natural polymorphism in a selected alternative oxidase (AOX) gene of the medicinal plant, St John''s wort. Four partial AOX gene sequences were isolated from the genomic DNA of a wild plant of Hypericum perforatum L. Three genes belong to the subfamily AOX1 ... More
Fine-scale genetic structure of Atlantic salmon (Salmo salar) using microsatellite markers: effects of restocking and natural recolonization
AuthorsGrandjean, F; Verne, S; Cherbonnel, C; Richard, A
Journal
PubMed ID
'1. An important goal of conservation biology is to preserve the evolutionary potential of a species by maintaining natural levels of genetic diversity. Here, we assess the population differentiation in the Atlantic salmon, Salmo salar, listed in Annex II of the European Habitats Directive, to provide valuable information for its ... More
Genetic identification of edible birds' nest based on mitochondrial DNA sequences
'Edible bird''s nest (EBN) is a functional food constructed with swiftlets'' salivary glue. Counterfeit EBN products have been found in the market due to limited supply and high price of genuine EBN. In this article, a method for genetic identification of EBN was developed. The technique is based on sequence ... More
Characterization of age-related changes in natural killer cells during primary influenza infection in mice
AuthorsNogusa, S; Ritz, BW; Kassim, SH; Jennings, SR; Gardner, EM
Journal
PubMed ID
'The current investigation examined the importance of natural killer (NK) cells during the innate immune response to primary influenza infection in young and aged mice. Young (6-8 weeks) and aged (22 months) C57BL/6 mice were infected intranasally with influenza A virus, and NK cell-mediated cytotoxicity was determined in lung and ... More
Sediment microbial community analysis: Establishing impacts of aquaculture on a tropical mangrove ecosystem
AuthorsCastine, SA; Bourne, DG; Trott, LA; McKinnon, DA
Journal
PubMed ID
'The impact of organic loading from a tropical finfish cage farm was investigated by comparing the microbial community in surface sediments (0-8.5 cm) at sites under fish cages and on a gradient away from the farm lease area. Both total bacteria and Vibrio sp., enumerated by epifluorescence microscopy and TCBS ... More
Combination of Chromogenic Differential Medium and estA-Specific PCR for Isolation and Detection of Phytopathogenic Xanthomonas spp.
AuthorsLee, YA; Sung, AN; Liu, TF; Lee, YS
Journal
PubMed ID
'A xanthomonad differential medium (designated Xan-D medium) was developed, on which streaks and colonies of xanthomonads, including 13 species of the genus Xanthomonas, turned wet-shining yellow-green and were surrounded with a smaller milky zone and a bigger clear zone in 3 to 4 days. The characteristics could easily be differentiated ... More
Assessment of dietary ratios of red clover and grass silages on milk production and milk quality in dairy cows
'Twenty-four multiparous Holstein-Friesian dairy cows were used in a replicated 4 x 4 Latin square changeover design experiment to test the effects of changing from ryegrass (Lolium perenne) silage to red clover (Trifolium pratense) silage in graded proportions on feed intakes, milk production, milk organoleptic qualities, and whole-body nitrogen partitioning. ... More
Effectiveness of the postponed isolation (post-frozen isolation) method for PCR-quality Sarcoptes mite gDNA
'The aim of the present study was to assess whether individual Sarcoptes mites collected from frozen skin (''postponed isolation'' method) are suitable sources of PCR-quality genomic DNA, and to test the effectiveness of this method in comparison with the ''direct isolation'' method, often used through force of habit. Hundreds of ... More
Promoter variants of KIR2DL5 add to diversity and may impact gene expression
'Sequencing of polymerase chain reaction (PCR)-amplified genomic DNA encompassing the putative proximal promoter and the coding region was used to identify KIR2DL5 alleles from 77 unrelated Caucasian individuals. PCR and sequencing were used to link each new allele to its neighboring KIR locus to identify 2DL5A or 2DL5B loci. Allele ... More
Serotonin transporter promoter region polymorphisms do not influence treatment response to escitalopram in patients with major depression
'Several studies and meta-analyses have implicated a polymorphism in the promoter region of the serotonin transporter (5-HTT) gene, 5-HTTLPR in treatment outcomes of selective serotonin re-uptake inhibitors in patients with major depression. In this study we investigated the impact of 5-HTTLPR and a functional SNP rs25531 on the treatment outcomes ... More
Overall Alteration of Circadian Clock Gene Expression in the Chestnut Cold Response
'Cold acclimation in woody plants may have special features compared to similar processes in herbaceous plants. Recent studies have shown that circadian clock behavior in the chestnut tree (Castanea sativa) is disrupted by cold temperatures and that the primary oscillator feedback loop is not functional at 4°C or in winter. ... More
Expression of pig7 gene in acute leukemia and its potential to modulate the chemosensitivity of leukemic cells
'We analyzed expression of p53-induced gene 7 (pig7), at the transcript level, in bone marrow samples from patients with de novo acute leukemia (AL) and normal controls by quantitative reverse transcription PCR (RT-PCR), and revealed a markedly decreased pig 7 expression in the patient group, as well as in the ... More
Comparative analysis of DNA methylation between primary and metastatic gastric carcinoma
AuthorsKim, JH; Jung, EJ; Lee, HS; Kim, MA; Kim, WH
Journal
PubMed ID
'Metastasis is a multi-step process involving many biomolecular changes and DNA methylation is one such molecular change. Although differences in DNA methylation have been reported in matched primary and metastatic mammary carcinoma, no such differences have been reported in gastric carcinoma. Accordingly, to investigate whether DNA methylation profiles in metastatic ... More
Mixed infections of Helicobacter pylori: tissue tropism and histological significance
'Mixed infections with Helicobacter pylori facilitate interstrain gene transfer and the maintenance of genetic diversity for adaptation to the gastric environment, but whether mixed infections with histological significance and tissue tropism occur in the human stomach is still unclear. Helicobacter pylori was isolated from the antrum and the corpus of ... More
Identification of novel Bach2 transcripts and protein isoforms through tagging analysis of retroviral integrations in B-cell lymphomas
'Background: The Bach2 gene functions as a transcriptional repressor in B-cells, showing high expression level only before the plasma cell stage. Several lines of evidence indicate that Bach2 is a B-cell specific tumor suppressor. We here address patterns of insertional mutagenesis and expression of Bach2 is a murine retroviral model ... More
An environmental sensor, TRPV4 is a novel regulator of intracellular Ca(2+) in human synoviocytes
'Itoh Y, Hatano N, Hayashi H, Onozaki K, Miyazawa K, Muraki K. An environmental sensor, TRPV4 is a novel regulator of intracellular Ca(2+) in human synoviocytes. Am J Physiol Cell Physiol 297: C1082-C1090, 2009. First published September 16, 2009; doi:10.1152/ajpcell.00204.2009.-The activation of a vanilloid type 4 transient receptor potential channel ... More
Disposable Magnetic DNA Sensors for the Determination at the Attomolar Level of a Specific Enterobacteriaceae Family Gene
AuthorsLoaiza, OA; Campuzano, S; Pedrero, M; Pividori, MI; Garcia, P; Pingarron, JM
Journal
PubMed ID
'Disposable magnetic DNA sensors using an enzyme-amplified strategy for the specific detection of a gene related to the Enterobacteriaceae bacterial family, based on the coupling of streptavidin-peroxidase to biotinylated lacZ gene target sequences, has been developed. A biotinylated 25-mer capture probe was attached to streptavidin-modified magnetic beads and hybridization with ... More
Plant-rhizobia mutualism influences aphid abundance on soybean
AuthorsDean, JM; Mescher, MC; De Moraes, CM
Journal
PubMed ID
'The mutualism between legumes and nitrogen-fixing soil bacteria (rhizobia) is a key feature of many ecological and agricultural systems, yet little is known about how this relationship affects aboveground interactions between plants and herbivores. We investigated the effects of the rhizobia mutualism on the abundance of a specialized legume herbivore ... More
Rumen protozoa are rich in polyunsaturated fatty acids due to the ingestion of chloroplasts
'Within this study, we investigated whether the polyunsaturated fatty acids (PUFA)-rich nature of rumen protozoa is a consequence of ingestion of PUFA-rich chloroplasts. Four Hereford x Friesian steers were offered hay [low 18:3 (n-3) and low chlorophyll concentration] followed by freshly cut perennial ryegrass [high 18:3 (n-3) and high chlorophyll ... More
Isolation and characterisation of 11 tetranucleotide microsatellite loci in the common genet (Genetta genetta)
AuthorsFernandes, CA; Rodrigues, M; Hajji, GM; Vercammen, P; Bruford, MW; Santos-Reis, M
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PubMed ID
'We report the isolation and characterization of 11 polymorphic tetranucleotide microsatellite loci in the common genet (Genetta genetta) from genomic libraries enriched for (AAAG) (n) and (AGAT) (n) repeat sequences. We chose to develop tetranucleotide repeats because they can be scored less ambiguously. In a sample of 25 individuals, we ... More
A multiplex PCR for rapid and simultaneous detection of porcine circovirus type 2, porcine parvovirus, porcine pseudorabies virus, and porcine reproductive and respiratory syndrome virus in clinical specimens
AuthorsYue, FX; Cui, SJ; Zhang, CF; Yoon, KJ
Journal
PubMed ID
'A multiplex PCR (mPCR) assay was developed and evaluated for its ability to simultaneously detect multiple viral infections of swine. Specific primers were designed for each of the following four DNA or RNA viruses: porcine circovirus type 2 (PCV2), porcine parvovirus (PPV), pseudorabies virus (PRV), and porcine reproductive and respiratory ... More
Simple, Sensitive, and Swift Sequencing of Complete H5N1 Avian Influenza Virus Genomes
AuthorsHoeper, D; Hoffmann, B; Beer, M
Journal
PubMed ID
'The spread of highly pathogenic avian influenza A virus (HPAIV) of subtype H5N1 demands fast and reliable methods for in-depth, full-length sequence analysis. For this purpose, we designed a simple and sensitive method for the preparation of sequencing libraries from H5N1 HPAIV diagnostic RNA samples for sequencing with the Genome ... More
International collaborative study of the endogenous reference gene LAT52 used for qualitative and quantitative analyses of genetically modified tomato
AuthorsYang, LT; Zhang, HB; Guo, JC; Pan, LW; Zhang, DB
Journal
PubMed ID
'One tomato (Lycopersicon esculentum) gene, LAT52, has been proved to be a suitable endogenous reference gene for genetically modified (GM) tomato detection in a previous study. Herein are reported the results of a collaborative ring trial for international validation of the LAT52 gene as endogenous reference gene and its analytical ... More
Enhanced recognition of non-complementary hybridization by single-LNA-modified oligonucleotide probes
AuthorsPiao, XY; Yan, Y; Yan, J; Guan, YF
Journal
PubMed ID
'Locked nucleic acid (LNA) is a deoxyribonucleotide analogue with an unusual ''locked'' furanose conformation. LNA-modified oligonucleotide probes have demonstrated an enhanced binding affinity towards their complementary strands; however, their potential to discriminate non-complementary hybridization of mismatches has not been explored. In this study, we investigated the effect of the chemical ... More
Development and validation of reverse transcription loop-mediated isothermal amplification for detection of PRRSV
'To establish a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) method for rapid detection of porcine reproductive and respiratory syndrome virus (PRRSV), four primers specific to six regions of the N gene were designed. After amplification in an isothermal water bath for 1 h, samples containing PRRSV generated the expected ladder-like products ... More
Twenty-three novel microsatellite markers developed from Atlantic cod Gadus morhua L. expressed sequence tags
AuthorsDelghandi, M; Wesmajervi, MS; Tafese, T; Nilsen, F
Journal
PubMed ID
'Twenty-three novel polymorphic microsatellite markers were developed from c. 2000 expressed sequence tags of Atlantic cod Gadus morhua L. Gene identity was determined at 12 loci, confirming the associated microsatellites as type I markers. These microsatellite markers provide useful tools for studies of population genetics and reproductive ecology and for ... More
Ultrasensitive detection of coliforms by means of direct asymmetric PCR combined with disposable magnetic amperometric genosensors
AuthorsLoaiza, OA; Campuzano, S; Pedrero, M; Garcia, P; Pingarron, JM
Journal
PubMed ID
'An extremely sensitive procedure for the isolation and detection of DNA from bacterial cell cultures is described. Direct asymmetric PCR amplified products from E. coli cultures are specifically detected, at a concentration level as low as 0.01 cfu mL(-1) (cfu, colony forming unit), using disposable magnetic DNA hybridization amperometric sensors ... More
Deployable laboratory response to emergence of melioidosis in central Sri Lanka
'A portable molecular diagnostic laboratory was used to provide molecular confirmation of suspected melioidosis cases seen at Peradeniya Hospital, central Sri Lanka. Soil supernatants from rice field and rubber plantation samples also produced PCR-positive results. These procedures could be used for melioidosis field work in other remote locations.' ... More
Identification, by RT-PCR, of four novel T-1-superfamily conotoxins from the vermivorous snail Conus spurius from the Gulf of Mexico
AuthorsZamora-Bustillos, R; Aguilar, MB; Falcon, A; de la Cotera, EPH
Journal
PubMed ID
'cDNA was prepared from the venom duct of a single Conus spurius specimen collected near the coast of Campeche, Mexico. From it, PCR products were generated, sequenced, and predicted to encode eight distinct precursors of T-1-conotoxins. These precursors contain five different mature toxins, of which four are novel and one ... More
The Oligopeptide Transport System Is Essential for the Development of Natural Competence in Streptococcus thermophilus Strain LMD-9
AuthorsGardan, R; Besset, C; Guillot, A; Gitton, C; Monnet, V
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PubMed ID
'In gram-positive bacteria, oligopeptide transport systems, called Opp or Ami, play a role in nutrition but are also involved in the internalization of signaling peptides that take part in the functioning of quorum-sensing pathways. Our objective was to reveal functions that are controlled by Ami via quorum-sensing mechanisms in Streptococcus ... More
Genetic and virulence characterization of Flavobacterium columnare from channel catfish (Ictalurus punctatus)
AuthorsSoto, E; Mauel, MJ; Karsi, A; Lawrence, ML
Journal
PubMed ID
'Aim: To develop a method for conducting pulsed-field gel electrophoresis (PFGE) on Flavobacterium columnare, to use PFGE to characterize F. columnare channel catfish isolates, and to determine whether variation in pathogenic potential exists in F. columnare isolates from channel catfish. Methods and Results: On the basis of PFGE-derived profiles, similarity ... More
Cloning, bacterial expression, and unique structure of adenosylhomocysteine hydrolase-like protein 1, or inositol 1,4,5-triphosphate receptor-binding protein from mouse kidney
AuthorsGomi, T; Takusagawa, F; Nishizawa, M; Agussalim, B; Usui, I; Sugiyama, E; Taki, H; Shinoda, K; Hounoki, H; Miwa, T; Tobe, K; Kobayashi, M; Ishimoto, T; Ogawa, H; Mori, H
Journal
PubMed ID
'Adenosylhomocysteine hydrolase (SAHase)-like protein 1 (SAH-L), also called inositol 1,4,5-triphosphate receptor-binding protein (IRBIT) is a novel protein involved in fish embryo development and calcium release in mammalian cells through protein-protein interactions. To better understand its reaction mechanism, purified protein is indispensable. Here we describe a simple purification procedure and the ... More
Atorvastatin and fenofibrate increase apolipoprotein AV and decrease triglycerides by up-regulating peroxisome proliferator-activated receptor-α
'Background and purpose: Combining statin and fibrate in clinical practice provides a greater reduction of triglycerides than either drug given alone, but the mechanism for this effect is poorly understood. Apolipoprotein AV (apoAV) has been implicated in triglyceride metabolism. This study was designed to investigate the effect of the ... More
Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen
'Anaerobic fungi (Neocallimastigales) are active degraders of fibrous plant material in the rumen. However, only limited information is available relating to how quickly they colonize ingested feed particles. The aim of this study was to determine the dynamics of initial colonization of forage by anaerobic fungi in the rumen and ... More
Combined inhibition of complement and CD14 abolish E. coli-induced cytokine-, chemokine- and growth factor-synthesis in human whole blood
AuthorsBrekke, OL; Christiansen, D; Fure, H; Pharo, A; Fung, M; Riesenfeld, J; Mollnes, TE
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PubMed ID
'The relative role of complement and CD14 in E. coli-induced cytokine synthesis in an in vitro human whole blood model of sepsis was examined, Fresh lepiruclin-anticoagulated whole blood was incubated with E. coli for 2 h. Monoclonal antibodies or a C5a receptor antagonist were used to block complement. Inflammatory mediators ... More
Genetic Identification of the Bacteriocins Produced by Enterococcus faecium IT62 and Evidence that Bacteriocin 32 Is Identical to Enterocin IT
AuthorsIzquierdo, E; Cai, YM; Marchioni, E; Ennahar, S
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PubMed ID
'Enterococcus faecium IT62, a strain isolated from ryegrass in Japan, produces three bacteriocins (enterocins L50A, L50B, and IT) that have been previously purified and the primary structures of which have been determined by amino acid sequencing (E. Izquierdo, A. Bednarczyk, C. Schaeffer, Y. Cai, E. Marchioni, A. Van Dorsselaer, and ... More
Sequential CaCl(2), polyethylene glycol precipitation for RNase-free plasmid DNA isolation
AuthorsSauer, ML; Kollars, B; Geraets, R; Sutton, F
Journal
PubMed ID
'Functional genomics is facilitated by the ability to express genes in heterologous systems. In some cases function can be assayed by generation of in vitro transcripts of the unknown genes and expressing those transcripts in various expression systems. Plasmids bearing phage promoters are used to generate in vitro transcripts. Therefore, ... More
Molecular cloning and tissue distribution of reduced folate carrier and effect of dietary folate supplementation on the expression of reduced folate carrier in laying hens
AuthorsJing, M; Tactacan, GB; Rodriguez-Lecompte, JC; Kroeker, A; House, JD
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PubMed ID
'The reduced folate carrier (RFC) has been postulated to be a major entity for folate transport activity in humans and other mammals. However, there are limited reports of the importance of RFC in an avian system. In the current study, therefore, the molecular cloning and tissue distribution of RFC, as ... More
Tumour necrosis factor alpha gene (TNF-α) -376 polymorphism in Hungarian patients with primary progressive multiple sclerosis
'Tumour necrosis factor alpha (TNF-α) is associated with clinical activity in relapsing-remitting multiple sclerosis (RRMS) and the development of progressive disease. Our aim was to investigate the TNF-α-376 polymorphism in primary progressive MS (PPMS) patients. Polymerase chain reaction and restriction fragment length polymorphism were carried out on 45 PPMS patients, ... More
Multiple Didymella teleomorphs are linked to the Phoma clematidina morphotype
'The fungal pathogen Phoma clematidina is used as a biological agent to control the invasive plant species Clematis vitalba in New Zealand. Research conducted on P. clematidina as a potential biocontrol agent against C. vitalba, led to the discovery of two perithecial-forming strains. To assess the diversity of P clematidina ... More
Detection and hazard assessment of pathogenic microorganisms in medical wastes
AuthorsPark, H; Lee, K; Kim, M; Lee, J; Seong, SY; Ko, G
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'This study was undertaken to investigate the types and concentrations of microbial agents in various medical wastes as well as to characterize their survivals in these wastes at different temperatures for microbial risk assessment. Medical wastes collected from 5 major hospitals in South Korea were classified and stored at three ... More
Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20
'Background: Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequencing, mapping tools such as radiation hybrid DNA panels remain useful aids ... More
Development of taxon-specific sequence characterized amplified region (SCAR) markers based on actin sequences and DNA amplification fingerprinting (DAF): a case study in the Phoma exigua species complex
'Phoma exigua is considered to be an assemblage of at least nine varieties that are mainly distinguished on the basis of host specificity and pathogenicity. However, these varieties are also reported to be weak pathogens and secondary invaders on non-host tissue. In practice, it is difficult to distinguish P. exigua ... More
Molecular phylogeny of Phoma and allied anamorph genera: Towards a reclassification of the Phoma complex
'The present generic concept of Phoma is broadly defined, with nine sections being recognised based on morphological characters. Teleomorph states of Phoma have been described in the genera Didymella, Leptosphaeria, Pleospora and Mycosphaerella, indicating that Phoma anamorphs represent a polyphyletic group. In an attempt to delineate generic boundaries, representative strains ... More
Application of SNaPshot Multiplex Assays for Simultaneous Multigene Mutation Screening in Patients With Idiopathic Sensorineural Hearing Impairment
'Objectives/Hypothesis: To develop a cost-effective and robust genetic diagnostic tool for patients with idiopathic nonsyndromic sensorineural hearing impairment. Study Design: Development of a diagnostic tool and validation in a prospective cohort. Methods: Twenty common sequence variants in GJB2, SLC26A4, and the mitochondrial 12S rRNA gene were selected based ... More
Bone marrow mesenchymal stromal cells of patients with myeloproliferative disorders do not carry the JAK2-V617F mutation
AuthorsMercier, F; Monczak, Y; Francois, M; Prchal, J; Galipeau, J
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'Myeloproliferative disorders (MPDs) are often associated with the presence of the JAK2-V617F mutation in hematopoietic cells. It is currently not known if this mutation is carried as well by bone marrow mesenchymal stromal cells (MSCs) in these patients. To test this hypothesis, we recruited seven patients with JAK2-V617F(+) MPD, isolated ... More
Retinoid X receptor beta polymorphisms do not explain functional differences in vitamins D and A response in Antineutrophil cytoplasmic antibody associated vasculitis patients
'It has been suggested that the retinoid X receptor beta (RXRB) gene is a risk factor for Wegener''s granulomatosis. We addressed if there is a functional difference in the response to retinoic acid (RA) and vitamin D in Antineutrophil cytoplasmic antibody (ANCA) associated systemic vasculitis (AASV) patients and if this ... More
Mutations in STK11 gene in Czech Peutz-Jeghers patients
AuthorsVasovcak, P; Puchmajerova, A; Roubalik, J; Krepelova, A
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'Background: Peutz-Jeghers syndrome (PJS) is an autosomal dominant hereditary disease characterized by mucocutaneous pigmentation and gastrointestinal hamartomatous polyposis. The germline mutations in the serine/threonine kinase 11 (STK11) gene have been shown to be associated with the disease. Individuals with PJS are at increased risk for development of various neoplasms. The ... More
Hypermethylation of the 5′CpG island of the FHIT gene in clear cell renal carcinomas
'FHIT is a tumour suppressor gene which is frequently inactivated in different types of cancer. Both genetic (mutations, deletions, chromosomal rearrangements) and epigenetic (aberrant methylation of the 5''CpG island) alterations of the FHIT gene have been reported in various malignancies. Yet little is known about the mechanism of FHIT inactivation ... More
Newly developed polymorphic microsatellite markers for frogs of the genus Ascaphus
AuthorsSpear, SF; Baumsteiger, J; Storfer, A
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'Thirteen polymorphic microsatellite loci were identified and developed for the coastal tailed frog, Ascaphus truei, from sites within the Olympic Peninsula of Washington, USA. These tetranucleotide repeat loci were highly variable, averaging 19 alleles per locus and expected heterozygosity of 0.91. In addition, these loci cross-amplify in the sister species, ... More
Genetic characterization of two low pathogenic avian influenza virus H5N1 isolates from Ontario, Canada
AuthorsPei, YL; Swinton, J; Ojkic, D; Sharif, S
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'Genomes of two low pathogenic H5N1 avian influenza (LPAI) viruses, A/Turkey/ON/84/1983 and A/Mallard/ON/499/2005 from Ontario, Canada were cloned and genetically characterized. Phylogenetic analysis showed that the Canadian isolates cluster with other North American AIVs and are distinct from the Euro-Asian H5N1 isolates. Individual gene comparisons demonstrated that the Ontario isolates ... More
SNP deserts of Asian cultivated rice: genomic regions under domestication
'When performing a genome-wide comparison between indica (93-11) and japonica (Nipponbare), we find 8% of the genome, which have an extremely low SNP rate (< 1 SNP/kb). Inside these ''SNP deserts'', experimentally confirmed genes show increased K(a)/K(s) that indicate adaptive selection. To further elucidate this connection, we survey the level ... More
'Background and Objective: Octamer-4 (Oct4), a transcription factor involved in regulating human embryonic stern cells (ESCs), may play a role in tumorigenesis. Since little is known about the efficacy of Oct4 its a potential biomarker for gastric cancer (GC), we investigated its expression in GC tissues and its relationship to ... More
Separation of plant viral satellite double-stranded RNA using high-performance liquid chromatography
AuthorsLikic, S; Rusak, G; Krajacic, M
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'High-performance liquid chromatography was developed for further separation of double-stranded (ds) RNAs obtained by CF-11 cellulose chromatography from plants infected with satellite associated cucumber mosaic virus. Fractions separated by monolithic polymer column, especially applicable for nucleic acid analyses, were identified electrophoretically and confirmed with a polymerase chain reaction test. Once ... More
Multiplex primer-extension assay for identification of six pathogenic vibrios
AuthorsDalmasso, A; Civera, T; Bottero, MT
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'A multiplex Primer-Extension Reaction (PER) assay, was specifically designed for the identification, of the major human pathogenic Vibrio species (V cholerae, V. parahaemolyticus, V. vulnificus, V. mimicus, V. alginolyticus and V. fluvialis) in fishery products. The assay, directed towards the rpoA gene, was tested on a total of 287 samples ... More
Methods for sampling free-living Symbiodinium (zooxanthellae) and their distribution and abundance at Lizard Island (Great Barrier Reef)
AuthorsLittman, RA; van Oppen, MJH; Willis, BL
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'The abundance and distribution of free-living dinoflagellates in the genus Symbiodinium have important implications for the ecology of coral reefs, determining both the symbionts available to newly recruited corals and symbiont types available for uptake by adult corals during environmental stress. However, little is known about where symbiotic dinoflagellates reside ... More
Evaluating the potential impact of mismatches outside the antigen recognition site in unrelated hematopoietic stem cell transplantation: HLA-DRB1*1454 and DRB1*140101
AuthorsXiao, Y; Lazaro, AM; Masaberg, C; Haagenson, M; Vierra-Green, C; Spellman, S; Dakshanamurthy, S; Ng, J; Hurley, CK
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'DNA sequencing of 268 individuals drawn from four US populations carrying two unresolved DRB1*14 alleles differing only outside the antigen recognition site identified DRB1*1454 in the majority. A database of 4222 human leukocyte antigen (HLA)-matched hematopoietic stem cell transplantation donor-recipient pairs was queried to determine the number likely mismatched for ... More
Do circum-Antarctic species exist in peracarid Amphipoda? A case study in the genus Epimeria Costa, 1851 (Crustacea, Peracarida, Epimeriidae)
AuthorsLoerz, AN; Maas, EW; Linse, K; Coleman, CO
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'The amphipod genus Epimeria is species rich in the Southern Ocean and at present eight of its 19 species are reported with circum-Antarctic distributions. For the first time, specimens of epimeriid species from the Antarctic Peninsula, the Weddell Sea and the Ross Sea were analysed using partial COI genes sequences ... More
Isolation and characterization of eleven microsatellite loci in small abalone, Haliotis diversicolor Reeve
'Eleven novel microsatellite markers were isolated from small abalone, Haliotis diversicolor Reeve. These loci were tested on 22 individuals from two different geographic populations. We identified a total of 162 alleles from the 11 microsatellite loci. All of the loci were highly polymorphic. Polymorphism information content (PIC) is ranging from ... More
Enterocin 96, a Novel Class II Bacteriocin Produced by Enterococcus faecalis WHE 96, Isolated from Munster Cheese
AuthorsIzquierdo, E; Wagner, C; Marchioni, E; Aoude-Werner, D; Ennahar, S
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'Enterococcus faecalis WHE 96, a strain isolated from soft cheese based on its anti-Listeria activity, produced a 5,494-Da bacteriocin that was purified to homogeneity by ultrafiltration and cation-exchange and reversed-phase chromatographies. The amino acid sequence of this bacteriocin, named enterocin 96, was determined by Edman degradation, and its structural gene ... More
Complement Factor H Variant Y402H is Not a Risk Factor for Preeclampsia in the Finnish Population
AuthorsKaare, M; Seitsonen, S; Jaervelae, I; Meri, S; Laivuori, H
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'Objective: Variations in complement factor H, which down-regulates the activity of the alternative complement pathway, have been associated with different vascular disorders. Here we examine whether factor H variation is involved in the etiology of preeclampsia. Methods: We studied 110 women with preeclampsia and 99 controls for complement factor H ... More
Cymadothea trifolii, an obligate biotrophic leaf parasite of Trifolium, belongs to Mycosphaerellaceae as shown by nuclear ribosomal DNA analyses
AuthorsSimon, UK; Groenewald, JZ; Crous, PW
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'The ascomycete Cymadothea trifolii, a member of the Dothideomycetes, is unique among obligate biotrophic fungi in its capability to only partially degrade the host cell wall and in forming an astonishingly intricate interaction apparatus (IA) in its own hyphae, while the attacked host plant cell is triggered to produce a ... More
No involvement of non-synonymous TLR2 polymorphisms in Japanese leprosy patients
AuthorsMikita, N; Kanazawa, N; Ozaki, M; Kosaka, M; Ishii, N; Nishimura, H; Furukawa, F
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Characterization of polymorphic microsatellite loci in the marine isopod Sphaeroma terebrans (Crustacea, Isopoda)
AuthorsBaratti, M; Filippelli, M; Messana, G; Papetti, C; Patarnello, T; Zane, L
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Nine polymorphic microsatellites were characterized in the marine isopod Sphaeroma terebrans (Isopoda, Sphaeromatidae) for phylogeographic and parentage analyses. The number of alleles ranged from 3 to 10. Observed heterozygosity ranged from 0.428 to 0.950, while expected heterozygosity ranged from 0.532 to 0.889. Heterozygote deficiency was detected for one locus, possibly ... More
Isolation of eight microsatellite markers from Moina macrocopa for assessing cryptic genetic structure in the wild
AuthorsTatsuta, H; Yao, I; Tanaka, Y
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We isolated eight polymorphic microsatellite loci from the zooplankton Moina macrocopa (Straus), which is sensitive to pollutants such as insecticides and heavy metals. The isolated loci were polymorphic, with three to seven alleles among 23 individuals. Expected heterozygosities ranged from 0.167 to 0.787. These loci can be used to examine ... More
Isolation and characterization of 11 tetranucleotide microsatellite loci in the Egyptian mongoose (Herpestes ichneumon)
AuthorsRodrigues, M; Fernandes, CA; Palomares, F; Amorim, IR; Bruford, MW; Santos-Reis, M
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We report the isolation of 11 polymorphic tetranucleotide microsatellite loci in the Egyptian mongoose (Herpestes ichneumon). In a sample of 27 individuals, we observed between 4 and 7 alleles per locus and their observed and expected heterozygosities ranged from 0.37 to 0.85 and from 0.44 to 0.79, respectively. All genotypic ... More
Polymorphic microsatellite loci for the ant-garden ant, Crematogaster levior (Forel)
AuthorsBooth, W; Youngsteadt, E; Schal, C; Vargo, EL
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Throughout Amazonia, the ant Crematogaster levior is known for its participation in a complex ant-garden mutualism with the ant Camponotus femoratus and several species of epiphytic plants for which it plays an important role in seed viability. We isolated nine polymorphic microsatellite loci for C. levior from a genomic library ... More
Prevalence and Genotypes of Helicobacter pylori in Gastric Biopsy Specimens from Patients with Gastroduodenal Pathologies in the Cukurova Region of Turkey
AuthorsNagiyev, T; Yula, E; Abayli, B; Koksal, F
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The effects of Helicobacter pylori genotypes on clinical prognosis in the Cukurova region of Turkey were investigated by PCR. The prevalence of type I strains carrying the s1c allele, unlike in neighboring regions and countries, was found to be significantly higher in patients with gastritis and/or gastric ulcers (P = ... More
Characterization of polymorphic microsatellite markers for the green turtle (Chelonia mydas)
AuthorsDutton, PH; Frey, A
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We describe primers and polymerase chain reaction conditions to amplify 12 microsatellite loci from the green turtle (Chelonia mydas), including one dinucleotide, four trinucleotide and seven tetranucleotide loci. The primers were tested on 78 individuals from a Pacific population nesting in the Hawaiian Islands. The primer pairs developed in this ... More
Polymorphic tetranucleotide microsatellites for Cope's giant salamander (Dicamptodon copei) and Pacific giant salamander (Dicamptodon tenebrosus)
AuthorsSteele, CA; Baumsteiger, J; Storfer, A
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Vie present primers and amplification conditions for 15 microsatellite loci developed for the Cope's giant salamander (Dicamptodon copei), 14 of which are tetranucleotide repeats. Cross-species amplification revealed 10 of these loci to also be polymorphic in the Pacific giant salamander (Dicamptodon tenebrosus). Several loci produced nonoverlapping allelic ranges between the ... More
Identification and characterization of 15 polymorphic microsatellite loci in the western drywood termite, Incisitermes minor (Hagen)
AuthorsBooth, W; Lewis, VR; Taylor, RL; Schal, C; Vargo, EL
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Despite recognition of the western drywood termite, Incisitermes minor (Hagen), as one of the most economically important and destructive termite species in the USA, both its population and colony breeding structure genetically remain unclear. Here, we present primer sequences and initial characterization for 15 polymorphic microsatellite loci. In a sample ... More
Isolation and characterization of microsatellite markers from reed parrotbill, Paradoxornis heudei (Aves: Timaliidae)
AuthorsChang, Q; Shen, FF; Xie, WL; Zhang, BW; Zhou, KY
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Eleven microsatellite markers were obtained from reed parrotbill, Paradoxornis heudei, using the fast isolation by AFLP of sequences containing repeats (FIASCO) method as part of an effort to compare levels of genetic diversity in different populations of China. Polymorphism levels ranged form 5 to 11 alleles (mean = 9.27) using ... More
Characterization of 8 polymorphic microsatellite loci in the neotropical ant-garden ant, Camponotus femoratus (Fabricius)
AuthorsBooth, W; Youngsteadt, E; Schal, C; Vargo, EL
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Camponotus femoratus is an abundant and behaviorally dominant ant in lowland Amazonian rainforests, where this species participates in a complex and obligate seed-dispersal mutualism. C. femoratus typically cohabits with another ant species Crematogaster levior in an apparently amiable but poorly understood interaction. Despite these outstanding characteristics, the population genetics and ... More
Ten polymorphic microsatellite loci for Allobates femoralis, an Amazonian dendrobatoid frog
AuthorsJehle, R; Gasser, H; Pfunder, M; Amezquita, A; Lima, AP; Hoedl, W
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Within the anuran amphibians, dendrobatoids (poison-arrow frogs) are renowned for their parental care, but the lack of highly variable DNA markers so far precluded precise and comprehensive measurements of their genetic mating system. Here we present 10 polymorphic microsatellites for Allobates femoralis, a widespread dendrobatoid from the Amazon basin. In ... More